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Valence and Ideal Geometry for Nucleic Acids

1996 Standards

The data provided below are based on the following references.

  • Gelbin A, Schneider B, Clowney L, Hsieh S-H, Olson WK, Berman HM (1996) Geometric Parameters in Nucleic Acids: Sugar Phosphate Constituents. J. Am. Chem. Soc. 118, 519-529. doi
  • Clowney L, Jain SC, Srinivasan AR, Westbrook J, Olson WK, Berman HM (1996) Geometric Parameters in Nucleic Acids: Nitrogenous Bases. J. Am. Chem. Soc. 118, 519-529.doi
  • Parkinson G, Vojtechovsky J, Clowney L, Brunger A, Berman HM (1996) New Parameters for the Refinement of Nucleic Acid Containing Structures. Acta Cryst. D 52, 57-64. doi
Valence Geometry: Sugar and Phosphate Constituents
Furanose Rings Bond Lengths

Bond Lengths in Furanose Rings

-----------------------------------------------------
                    ribose           deoxyribose   
-----------------------------------------------------
bond           mean   esd    N     mean   esd    N
               value               value
-----------------------------------------------------
C1'-C2'        1.528 (0.010, 80)   1.521 (0.014, 47) 
C2'-C3'        1.525 (0.011, 80)   1.518 (0.010, 47) 
C3'-C4'        1.524 (0.011, 80)   1.528 (0.010, 47) 
C4'-O4'        1.453 (0.012, 80)   1.446 (0.011, 47) 
O4'-C1'        1.414 (0.012, 80)   1.420 (0.013, 47) 
C3'-O3'        1.423 (0.014, 80)   1.431 (0.013, 47) 
C5'-C4'        1.510 (0.013, 80)   1.511 (0.008, 47)
C2'-O2'        1.413 (0.013, 80)    na              
C1'-N1/N9      1.471 (0.017, 80)   1.474 (0.020, 47)
(H)O5'-C5'     1.423 (0.014, 61)   1.420 (0.021, 37)
-----------------------------------------------------


-----------------------------------------------------------------------------------------------------
              C2'-endo ribose     C2'-endo deoxyribose      C3'-endo ribose      C3'-endo deoxyribose
-----------------------------------------------------------------------------------------------------
bond           mean   esd    N     mean   esd    N           mean   esd    N      mean   esd    N 
               value               value                     value                value
-----------------------------------------------------------------------------------------------------
C1'-C2'       1.526 (0.008, 49)    1.518 (0.010, 29)         1.529 (0.011, 24)    1.519 (0.010, 7)  
C2'-C3'       1.525 (0.011, 49)    1.516 (0.008, 29)         1.523 (0.011, 24)    1.518 (0.012, 7)  
C3'-C4'       1.527 (0.011, 49)    1.529 (0.010, 29)         1.521 (0.010, 24)    1.521 (0.010, 7)  
C4'-O4'       1.454 (0.010, 49)    1.446 (0.010, 29)         1.451 (0.013, 24)    1.449 (0.009, 7)  
O4'-C1'       1.415 (0.012, 49)    1.420 (0.011, 29)         1.412 (0.013, 24)    1.418 (0.012, 7)  
C3'-O3'       1.427 (0.012, 49)    1.435 (0.013, 29)         1.417 (0.014, 24)    1.419 (0.006, 7)  
C5'-C4'       1.509 (0.012, 49)    1.512 (0.007, 29)         1.508 (0.007, 24)    1.509 (0.011, 7)  
C2'-O2'       1.412 (0.013, 49)     na                       1.420 (0.010, 24)     na
C1'-N1/N9     1.464 (0.014, 49)    1.468 (0.014, 29)         1.483 (0.015, 24)    1.488 (0.013, 7) 
(H)O5'-C5'    1.424 (0.016, 31)    1.418 (0.025, 25)         1.420 (0.009, 20)    1.423 (0.011, 7) 
-----------------------------------------------------------------------------------------------------

Bond angles in Furanose Rings

-----------------------------------------------------
                    ribose           deoxyribose 
-----------------------------------------------------
angle          mean   esd    N     mean   esd    N
               value               value
-----------------------------------------------------
C1'-C2'-C3'    101.5  (0.9, 80)   102.7  (1.4, 47)
C2'-C3'-C4'    102.7  (1.0, 80)   103.2  (1.0, 47)
C3'-C4'-O4'    105.5  (1.4, 80)   105.6  (1.0, 47)
C4'-O4'-C1'    109.6  (0.9, 80)   109.7  (1.4, 47)
O4'-C1'-C2'    106.4  (1.4, 80)   106.1  (1.0, 47)
C1'-C2'-O2'    110.6  (3.0, 80)    na             
C3'-C2'-O2'    113.3  (2.9, 80)    na 
C2'-C3'-O3'    111.0  (2.8, 80)   110.6  (2.7, 47)
C4'-C3'-O3'    110.6  (2.6, 80)   110.3  (2.2, 47)
C5'-C4'-C3'    115.5  (1.5, 80)   114.7  (1.5, 47)
C5'-C4'-O4'    109.2  (1.4, 80)   109.4  (1.6, 47)
O4'-C1'-N1/N9  108.2  (1.0, 80)   107.8  (0.8, 47)
C2'-C1'-N1/N9  113.4  (1.6, 80)   114.2  (1.6, 47)
(H)O5'-C5'-C4' 111.6  (1.7, 61)   110.9  (2.0, 37)
C1'-N9-C4      127.1  (1.8, 46)   125.9  (1.4, 13)
C1'-N1-C2      117.9  (1.3, 34)   117.8  (1.4, 34)
--------------------------------------------------------

-----------------------------------------------------------------------------------------------------
              C2'-endo ribose     C2'-endo deoxyribose     C3'-endo ribose      C3'-endo deoxyribose 
-----------------------------------------------------------------------------------------------------
angle          mean    esd  N      mean    esd  N           mean    esd  N       mean    esd  N 
               value               value                    value                value
-----------------------------------------------------------------------------------------------------
C1'-C2'-C3'    101.5  (0.8, 49)    102.5  (1.2, 29)         101.3  (0.7, 24)     102.4  (0.8, 7)
C2'-C3'-C4'    102.6  (1.0, 49)    103.1  (0.9, 29)         102.6  (1.0, 24)     102.2  (0.7, 7)
C3'-C4'-O4'    106.1  (0.8, 49)    106.0  (0.6, 29)         104.0  (1.0, 24)     104.5  (0.4, 7)
C4'-O4'-C1'    109.7  (0.7, 49)    110.1  (1.0, 29)         109.9  (0.8, 24)     110.3  (0.7, 7)
O4'-C1'-C2'    105.8  (1.0, 49)    105.9  (0.8, 29)         107.6  (0.9, 24)     106.8  (0.5, 7)
C1'-C2'-O2'    111.8  (2.6, 49)     na                      108.4  (2.4, 24)      na            
C3'-C2'-O2'    114.6  (2.2, 49)     na                      110.7  (2.1, 24)      na            
C2'-C3'-O3'    109.5  (2.2, 49)    109.4  (2.5, 29)         113.7  (1.6, 24)     112.6  (3.3, 7)
C4'-C3'-O3'    109.4  (2.1, 49)    109.7  (2.5, 29)         113.0  (2.0, 24)     112.3  (2.0, 7)
C5'-C4'-C3'    115.2  (1.4, 49)    114.1  (1.8, 29)         116.0  (1.6, 24)     115.7  (1.2, 7)
C5'-C4'-O4'    109.1  (1.2, 49)    109.3  (1.9, 29)         109.8  (0.9, 24)     109.8  (1.1, 7)
O4'-C1'-N1/N9  108.2  (0.8, 49)    108.0  (0.7, 29)         108.5  (0.7, 24)     108.3  (0.3, 7)
C2'-C1'-N1/N9  114.0  (1.3, 49)    114.3  (1.4, 29)         112.0  (1.1, 24)     112.6  (1.9, 7)
(H)O5'-C5'-C4' 111.7  (1.9, 61)    110.9  (1.7, 25)         111.5  (1.6, 20)     111.0  (2.5, 7)
C1'-N9-C4      127.4  (1.2, 28)    126.3  (1.2,  7)         126.3  (2.8, 12)     123.9  (1.0, 2)
C1'-N1-C2      118.5  (1.1, 21)    117.8  (1.8, 22)         116.7  (0.6, 12)     117.5  (1.4, 5)
----------------------------------------------------------------------------------------------------

Torsion Angles in Furanose Rings

-----------------------------------------------------------------------------------------------------------
                      C2'-endo ribose     C2'-endo deoxyribose    C3'-endo ribose      C3'-endo deoxyribose 
-----------------------------------------------------------------------------------------------------------
torsion angle          mean   esd  N       mean   esd  N           mean    esd  N       mean    esd  N 
                       value               value                   value                value
-----------------------------------------------------------------------------------------------------------
C4'-O4'-C1'-C2'        339.2 (5.2, 49)     340.7 (6.3, 27)           2.8 (6.1, 24)        6.6 (3.1, 5)   
O4'-C1'-C2'-C3'         35.2 (3.4, 49)      32.8 (4.9, 27)         335.4 (4.9, 24)      333.3 (2.1, 5)   
C1'-C2'-C3'-C4'        324.6 (2.8, 49)     326.9 (3.6, 27)          35.9 (2.8, 24)       35.6 (1.3, 5)   
C2'-C3'-C4'-O4'         24.2 (4.4, 49)      22.6 (4.5, 27)         324.7 (3.0, 24)      327.7 (2.3, 5)   
C3'-C4'-O4'-C1'        357.7 (5.7, 49)     357.7 (6.1, 27)          20.4 (5.1, 24)       16.4 (3.2, 5)   
C5'-C4'-C3'-C2'        263.4 (4.1, 49)     262.0 (4.1, 27)         204.0 (3.1, 24)      207.0 (2.2, 5)   
C5'-C4'-C3'-O3'        147.3 (4.9, 49)     145.2 (4.0, 27)          81.0 (4.4, 24)       84.8 (4.5, 5)   
O4'-C4'-C3'-O3'        268.1 (5.3, 49)     265.8 (4.3, 27)         201.8 (4.2, 24)      205.4 (4.8, 5)   
C4'-O4'-C1'-N1/9       216.6 (5.4, 49)     217.7 (6.7, 27)         241.4 (6.5, 24)      245.6 (2.5, 5)   
O3'-C3'-C2'-O2'        319.7 (4.2, 49)      na                      44.3 (4.5, 24)       na              
----------------------------------------------------------------------------------------------------------

                      C2'-endo ribose/deoxyribose                 C3'-endo ribose/deoxyribose
----------------------------------------------------------------------------------------------------------
                       mean   esd  N                               mean   esd  N 
                       value                                       value   
----------------------------------------------------------------------------------------------------------
O4'-C1'-N1-C2 (anti)   229.8 (18.4, 38)                            195.7 (6.6, 16) 
O4'-C1'-N1-C2 (syn)     63.4 (10.2,  2)                             na
O4'-C1'-N9-C4 (anti)   237.0 (24.3, 18)                            193.3(14.0, 12)
O4'-C1'-N9-C4 (syn)     58.6 (12.0, 15)                             35.6 (0.0,  2)
----------------------------------------------------------------------------------------------------------
                       mean   esd  N    
                       value            
----------------------------------------------------------------------------------------------------------
O5'-C5'-C4'-C3 (-sc)   292.9(12.3, 12)         
O5'-C5'-C4'-C3 (ap)    179.4 (6.4, 22)         
O5'-C5'-C4'-C3 (+sc)    52.5 (5.7, 93)
----------------------------------------------------------------------------------------------------------

Bond Lengths and Angles in the Phosphodiester Linkage in Dinucleoside Monophosphates and Trinucleoside Diphosphates

------------------------------------------
bond                    mean   esd    N 
                        value            
------------------------------------------
P-O1P/O2P               1.485 (0.017, 30)  
P-O3'                   1.607 (0.012, 13)  
P-O5'                   1.593 (0.010, 15)  
(P)O5'-C5'              1.440 (0.016, 14)  
(P)O3'-C3'              1.433 (0.019, 13)
------------------------------------------


------------------------------------------
angle                   mean   esd    N 
                        value            
------------------------------------------
O1P-P-O2P               119.6  (1.5, 15)      
O5'-P-O1P/O2P large*    110.7  (1.2, 16)      
O5'-P-O1P/O2P small**   105.7  (0.9, 16)      
O3'-P-O5'               104.0  (1.9, 13)      
P-O5'-C5'               120.9  (1.6, 15)      
C3'-O3'-P               119.7  (1.2, 13)      
O3'-P-O1P/O2P large*    110.5  (1.1, 13)      
O3'-P-O1P/O2P small**   105.2  (2.2, 13)      
(P)O5'-C5'-C4'          109.4  (0.8, 14)
(P)O3'-C3'-C4'          109.3  (1.5, 13)
-----------------------------------------
*Geometries for the subset with large Ox-P-O1P/O2P angles,
where x = 3' or 5'.

**Geometries for the subset with small Ox-P-O1P/O2P angles, 
where x = 3' or5'.

Torsion Angles in the Phosphodiester Linkage in Dinucleoside Monophosphates and Trinucleoside Diphosphates

-----------------------------------------
torsion angle          mean   esd    N  
                       value          
-----------------------------------------
O3'-P-O5'-C5' (-sc)    285.3  (9.8,  8)          
O3'-P-O5'-C5' (+sc)     81.0 (12.1,  5)
P-O5'-C5'-C4'          183.5 (13.0, 15)
P-O5'-C5'-C4'*         163.8 (23.0, 24) 
C4'-C3'-O3'-P          214.0  (8.6, 13)
C3'-O3'-P-O5' (-sc)    289.2  (4.8,  6)
C3'-O3'-P-O5' (ap)     163.1  (0.6,  2) 
C3'-O3'-P-O5' (+sc)     80.7 (14.3,  5) 
-----------------------------------------
*Parameter found for mononucleotides.
Valence Geometry: Nitrogenous Bases
Cytosine

Bond Lengths and Angles in Cytosine

----------------------------------------------------
Bond or Angle   Mean  (esd,    N)
                Value
----------------------------------------------------
N1-C2           1.397 (0.010, 28)
C2-N3           1.353 (0.008, 28)
N3-C4           1.335 (0.007, 28)
C4-C5           1.425 (0.008, 28)
C5-C6           1.339 (0.008, 28)
C6-N1           1.367 (0.006, 28)
C2-O2           1.240 (0.009, 28)
C4-N4           1.335 (0.009, 28)
N1-C1'          1.470 (0.012, 28)
C6-N1-C2	120.3 (0.4,   28)
N1-C2-N3	119.2 (0.7,   28)
C2-N3-C4	119.9 (0.5,   28)
N3-C4-C5	121.9 (0.4,   28)
C4-C5-C6	117.4 (0.5,   28)
C5-C6-N1	121.0 (0.5,   28)
N1-C2-O2	118.9 (0.6,   28)
N3-C2-O2	121.9 (0.7,   28)
N3-C4-N4	118.0 (0.7,   28)
C5-C4-N4	120.2 (0.7,   28)
C6-N1-C1'	120.8 (1.2,   28)
C2-N1-C1'	118.8 (1.1,   28)

Bond Lengths and Angles in Protonated Cytosine

----------------------------------------------------
Bond or Angle   Mean  (esd,    N)
                Value
----------------------------------------------------
N1-C2           1.381 (0.007, 17)
C2-N3           1.384 (0.007, 17)
N3-C4           1.353 (0.006, 17)
C4-C5           1.413 (0.005, 17)
C5-C6           1.346 (0.006, 17)
C6-N1           1.365 (0.007, 17)
C2-O2           1.212 (0.006, 17)
C4-N4           1.315 (0.007, 17)
N1-C1'          1.483 (0.015, 17)
C6-N1-C2	121.7 (0.5,   17)
N1-C2-N3	114.7 (0.7,   17)
C2-N3-C4	125.3 (0.7,   17)
N3-C4-C5	117.6 (0.5,   17)
C4-C5-C6	118.4 (0.5,   17)
C5-C6-N1	122.2 (0.5,   17)
N1-C2-O2	123.4 (0.7,   17)
N3-C2-O2	121.9 (0.5,   17)
N3-C4-N4	119.5 (0.7,   17)
C5-C4-N4	123.0 (0.8,   17)
C6-N1-C1'	121.2 (0.9,   17)
C2-N1-C1'	116.9 (1.0,   17)

Bond Lengths and Angles in Thymine

----------------------------------------------------
Bond or Angle   Mean  (esd,    N)
                Value
----------------------------------------------------
N1-C2           1.376 (0.008, 50)
C2-N3           1.373 (0.008, 50)
N3-C4           1.382 (0.008, 50)
C4-C5           1.445 (0.009, 50)
C5-C6           1.339 (0.007, 50)
C6-N1           1.378 (0.007, 50)
C2-O2           1.220 (0.008, 50)
C4-O4           1.228 (0.009, 50)
C5-M5           1.496 (0.006, 50)
N1-C1'          1.473 (0.014, 50)
C6-N1-C2	121.3 (0.5,   50)
N1-C2-N3	114.6 (0.6,   50)
C2-N3-C4	127.2 (0.6,   50)
N3-C4-C5	115.2 (0.6,   50)
C4-C5-C6	118.0 (0.6,   50)
C5-C6-N1	123.7 (0.6,   50)
N1-C2-O2	123.1 (0.8,   50)
N3-C2-O2	122.3 (0.6,   50)
N3-C4-O4	119.9 (0.6,   50)
C5-C4-O4	124.9 (0.7,   50)
C4-C5-M5	119.0 (0.6,   50)
C6-C5-M5	122.9 (0.6,   50)
C6-N1-C1'	120.4 (1.5,   50)
C2-N1-C1'	118.2 (1.6,   50)

Bond Lengths and Angles in Uracil

----------------------------------------------------
Bond or Angle   Mean  (esd,    N)
                Value
----------------------------------------------------
N1-C2           1.381 (0.009, 46)
C2-N3           1.373 (0.007, 46)
N3-C4           1.380 (0.009, 46)
C4-C5           1.431 (0.009, 46)
C5-C6           1.337 (0.009, 46)
C6-N1           1.375 (0.009, 46)
C2-O2           1.219 (0.009, 46)
C4-O4           1.232 (0.008, 46)
N1-C1'          1.469 (0.014, 46)
C6-N1-C2	121.0 (0.6,   46)
N1-C2-N3	114.9 (0.6,   46)
C2-N3-C4	127.0 (0.6,   46)
N3-C4-C5	114.6 (0.6,   46)
C4-C5-C6	119.7 (0.6,   46)
C5-C6-N1	122.7 (0.5,   46)
N1-C2-O2	122.8 (0.7,   46)
N3-C2-O2	122.2 (0.7,   46)
N3-C4-O4	119.4 (0.7,   46)
C5-C4-O4	125.9 (0.6,   46)
C6-N1-C1'	121.2 (1.4,   46)
C2-N1-C1'	117.7 (1.2,   46)

Bond Lengths and Angles in Adenine

----------------------------------------------------
Bond or Angle   Mean  (esd,    N)
                Value
----------------------------------------------------
N1-C2           1.339 (0.009, 48)
C2-N3           1.331 (0.009, 48)
N3-C4           1.344 (0.006, 48)
C4-C5           1.383 (0.007, 48)
C5-C6           1.406 (0.009, 48)
C6-N1           1.351 (0.007, 48)
C5-N7           1.388 (0.006, 48)
N7-C8           1.311 (0.007, 48)
C8-N9           1.373 (0.008, 48)
N9-C4           1.374 (0.006, 48)
C6-N6           1.335 (0.008, 48)
N9-C1'          1.462 (0.010, 48)
C6-N1-C2	118.6 (0.6,   48)
N1-C2-N3	129.3 (0.5,   48)
C2-N3-C4	110.6 (0.5,   48)
N3-C4-C5	126.8 (0.7,   48)
C4-C5-C6	117.0 (0.5,   48)
C5-C6-N1	117.7 (0.5,   48)
C4-C5-N7	110.7 (0.5,   48)
C5-N7-C8	103.9 (0.5,   48)
N7-C8-N9	113.8 (0.5,   48)
C8-N9-C4	105.8 (0.4,   48)
N9-C4-C5	105.8 (0.4,   48)
N3-C4-N9	127.4 (0.8,   48)
C6-C5-N7	132.3 (0.7,   48)
N1-C6-N6	118.6 (0.6,   48)
C5-C6-N6	123.7 (0.8,   48)
C8-N9-C1'	127.7 (1.8,   48)
C4-N9-C1'	126.3 (1.8,   48)

Bond Lengths and Angles in Protonated Adenine

----------------------------------------------------
Bond or Angle   Mean  (esd,    N)
                Value
----------------------------------------------------
N1-C2           1.357 (0.009, 15)
C2-N3           1.305 (0.008, 15)
N3-C4           1.356 (0.006, 15)
C4-C5           1.378 (0.008, 15)
C5-C6           1.403 (0.007, 15)
C6-N1           1.359 (0.007, 15)
C5-N7           1.379 (0.005, 15)
N7-C8           1.312 (0.008, 15)
C8-N9           1.373 (0.009, 15)
N9-C4           1.365 (0.007, 15)
C6-N6           1.320 (0.008, 15)
N9-C1'          1.466 (0.009, 15)
C6-N1-C2	123.3 (0.6,   15)
N1-C2-N3	125.7 (0.6,   15)
C2-N3-C4	111.6 (0.4,   15)
N3-C4-C5	127.4 (0.6,   15)
C4-C5-C6	117.9 (0.5,   15)
C5-C6-N1	114.0 (0.4,   15)
C4-C5-N7	111.0 (0.3,   15)
C5-N7-C8	103.7 (0.4,   15)
N7-C8-N9	113.5 (0.6,   15)
C8-N9-C4	105.9 (0.4,   15)
N9-C4-C5	105.8 (0.5,   15)
N3-C4-N9	126.7 (0.8,   15)
C6-C5-N7	131.0 (0.5,   15)
N1-C6-N6	120.2 (0.7,   15)
C5-C6-N6	125.8 (0.8,   15)
C8-N9-C1'	127.2 (1.6,   15)
C4-N9-C1'	126.8 (1.8,   15)

Bond Lengths and Angles in Guanine

----------------------------------------------------
Bond or Angle   Mean  (esd,    N)
                Value
----------------------------------------------------
N1-C2           1.373 (0.008, 21)
C2-N3           1.323 (0.008, 21)
N3-C4           1.350 (0.007, 21)
C4-C5           1.379 (0.007, 21)
C5-C6           1.419 (0.010, 21)
C6-N1           1.391 (0.007, 21)
C5-N7           1.388 (0.006, 21)
N7-C8           1.305 (0.006, 21)
C8-N9           1.374 (0.007, 21)
N9-C4           1.375 (0.008, 21)
C2-N2           1.341 (0.010, 21)
C6-O6           1.237 (0.009, 21)
N9-C1'          1.459 (0.009, 21)
C6-N1-C2        125.1 (0.6,   21)
N1-C2-N3        123.9 (0.6,   21)
C2-N3-C4        111.9 (0.5,   21)
N3-C4-C5        128.6 (0.5,   21)
C4-C5-C6        118.8 (0.6,   21)
C5-C6-N1        111.5 (0.5,   21)
C4-C5-N7        110.8 (0.4,   21)
C5-N7-C8        104.3 (0.5,   21)
N7-C8-N9        113.1 (0.5,   21)
C8-N9-C4        106.4 (0.4,   21)
N9-C4-C5        105.4 (0.4,   21)
N3-C4-N9        126.0 (0.6,   21)
C6-C5-N7        130.4 (0.6,   21)
N1-C2-N2        116.2 (0.9,   21)
N3-C2-N2        119.9 (0.7,   21)
N1-C6-O6        119.9 (0.6,   21)
C5-C6-O6        128.6 (0.6,   21)
C8-N9-C1'       127.0 (1.3,   21)
C4-N9-C1'       126.5 (1.3,   21)
Ideal Geometry: DNA/RNA Bases
Adenine
Adenine 

REMARK 1 ADENINE, v.1.0
REMARK 2 top_ndbx.dna
REMARK 3 G.PARKINSON, J.VOJTECHOVSKY, L.CLOWNEY, A.T.BRUNGER, 
REMARK 3 H.M.BERMAN
REMARK 3 NEW PARAMETERS FOR THE REFINEMENT OF NUCLEIC ACID CONTAINING 
REMARK 3 STRUCTURES
REMARK 3 ACTA CRYST.D	(1996)	 v. 52	 57-64
ATOM      1  N9  A       1       0.213   0.660   1.287
ATOM      2  C4  A       1       0.250   2.016   1.509
ATOM      3  N3  A       1       0.016   2.995   0.619
ATOM      4  C2  A       1       0.142   4.189   1.194
ATOM      5  N1  A       1       0.451   4.493   2.459
ATOM      6  C6  A       1       0.681   3.485   3.329
ATOM      7  N6  A       1       0.990   3.787   4.592
ATOM      8  C5  A       1       0.579   2.170   2.844
ATOM      9  N7  A       1       0.747   0.934   3.454
ATOM     10  C8  A       1       0.520   0.074   2.491
END
Cytosine 

REMARK 1 CYTOSINE, v.1.0
REMARK 2 top_ndbx.dna
REMARK 3 G.PARKINSON, J.VOJTECHOVSKY, L.CLOWNEY, A.T.BRUNGER, 
REMARK 3 H.M.BERMAN
REMARK 3 NEW PARAMETERS FOR THE REFINEMENT OF NUCLEIC ACID CONTAINING 
REMARK 3 STRUCTURES
REMARK 3 ACTA CRYST.D	(1996)	 v. 52	 57-64
ATOM      1  N1  C       1       0.212   0.668   1.294
ATOM      2  C6  C       1       0.193  -0.043   2.462
ATOM      3  C2  C       1       0.374   2.055   1.315
ATOM      4  O2  C       1       0.388   2.673   0.240
ATOM      5  N3  C       1       0.511   2.687   2.504
ATOM      6  C4  C       1       0.491   1.984   3.638
ATOM      7  N4  C       1       0.631   2.649   4.788
ATOM      8  C5  C       1       0.328   0.569   3.645
END
Guanine 

REMARK 1 GUANINE, v.1.0
REMARK 2 top_ndbx.dna
REMARK 3 G.PARKINSON, J.VOJTECHOVSKY, L.CLOWNEY, A.T.BRUNGER, 
REMARK 3 H.M.BERMAN
REMARK 3 NEW PARAMETERS FOR THE REFINEMENT OF NUCLEIC ACID CONTAINING 
REMARK 3 STRUCTURES
REMARK 3 ACTA CRYST.D	(1996)	 v. 52	 57-64
ATOM      1  N9  G       1       0.214   0.659   1.283
ATOM      2  C4  G       1       0.254   2.014   1.509
ATOM      3  N3  G       1       0.034   2.979   0.591
ATOM      4  C2  G       1       0.142   4.190   1.110
ATOM      5  N2  G       1      -0.047   5.269   0.336
ATOM      6  N1  G       1       0.444   4.437   2.427
ATOM      7  C6  G       1       0.676   3.459   3.389
ATOM      8  O6  G       1       0.941   3.789   4.552
ATOM      9  C5  G       1       0.562   2.154   2.846
ATOM     10  N7  G       1       0.712   0.912   3.448
ATOM     11  C8  G       1       0.498   0.057   2.485
END
Thymine 

REMARK 1 THYMINE, v.1.0
REMARK 2 top_ndbx.dna
REMARK 3 G.PARKINSON, J.VOJTECHOVSKY, L.CLOWNEY, A.T.BRUNGER, 
REMARK 3 H.M.BERMAN
REMARK 3 NEW PARAMETERS FOR THE REFINEMENT OF NUCLEIC ACID CONTAINING 
REMARK 3 STRUCTURES
REMARK 3 ACTA CRYST.D	(1996)	 v. 52	 57-64
ATOM      1  N1  T       1       0.214   0.668   1.296
ATOM      2  C6  T       1       0.171  -0.052   2.470
ATOM      3  C2  T       1       0.374   2.035   1.303
ATOM      4  O2  T       1       0.416   2.705   0.284
ATOM      5  N3  T       1       0.483   2.592   2.553
ATOM      6  C4  T       1       0.449   1.933   3.767
ATOM      7  O4  T       1       0.560   2.568   4.812
ATOM      8  C5  T       1       0.279   0.500   3.685
ATOM      9  C5A T       1       0.231  -0.299   4.949
END
Uracil 

REMARK 1 URACIL, v.1.0
REMARK 2 top_ndbx.dna
REMARK 3 G.PARKINSON, J.VOJTECHOVSKY, L.CLOWNEY, A.T.BRUNGER, 
REMARK 3 H.M.BERMAN
REMARK 3 NEW PARAMETERS FOR THE REFINEMENT OF NUCLEIC ACID CONTAINING 
REMARK 3 STRUCTURES
REMARK 3 ACTA CRYST.D	(1996)	 v. 52	 57-64
ATOM      5  N1  U       1       0.212   0.676   1.281  
ATOM      6  C6  U       1       0.195  -0.023   2.466  
ATOM      7  C2  U       1       0.370   2.048   1.265  
ATOM      8  O2  U       1       0.390   2.698   0.235  
ATOM      9  N3  U       1       0.505   2.629   2.502  
ATOM     11  C4  U       1       0.497   1.990   3.725  
ATOM     12  O4  U       1       0.629   2.653   4.755  
ATOM     13  C5  U       1       0.329   0.571   3.657  
END
Ideal Geometry: Sugar/Phosphate Backbone
DNA Sugar Phosphate
DNA Sugar Phosphate 

REMARK 1 DNA SUGAR PHOSPHATE, C2'-endo, v.1.0
REMARK 2 top_ndbx.dna
REMARK 3 G.PARKINSON, J.VOJTECHOVSKY, L.CLOWNEY, A.T.BRUNGER, 
REMARK 3 H.M.BERMAN
REMARK 3 NEW PARAMETERS FOR THE REFINEMENT OF NUCLEIC ACID CONTAINING 
REMARK 3 STRUCTURES
REMARK 3 ACTA CRYST.D	(1996)	 v. 52	 57-64
ATOM      1  P                   0.224  -4.365   2.383
ATOM      2  O1P                 1.336  -3.982   3.290
ATOM      3  O2P                 0.278  -5.664   1.666
ATOM      4  O5'                 0.042  -3.205   1.307
ATOM      5  C2'                 1.149  -0.891  -0.438
ATOM      6  C5'                -1.014  -3.256   0.347
ATOM      7  C4'                -0.913  -2.083  -0.600
ATOM      8  O4'                -1.127  -0.853   0.133
ATOM      9  C1'                 0.000   0.000   0.000
ATOM     10  C3'                 0.445  -1.932  -1.287
ATOM     11  O3'                 0.272  -1.450  -2.624
END
RNA Sugar Phosphate 

REMARK 1 RNA SUGAR PHOSPHATE, C3'-endo, v.1.1
REMARK 2 top_ndbx.dna
REMARK 3 G.PARKINSON, J.VOJTECHOVSKY, L.CLOWNEY, A.T.BRUNGER, 
REMARK 3 H.M.BERMAN
REMARK 3 NEW PARAMETERS FOR THE REFINEMENT OF NUCLEIC ACID CONTAINING 
REMARK 3 STRUCTURES
REMARK 3 ACTA CRYST.D   (1996)   v. 52   57-64
ATOM      1  P		         4.691   0.327  -2.444
ATOM      2  O1P		 5.034   1.678  -1.932
ATOM      3  O2P		 4.718   0.068  -3.906
ATOM      4  O5'		 3.246  -0.057  -1.895
ATOM      5  C5'		 2.957  -1.393  -1.443
ATOM      6  C4'		 1.509  -1.478  -1.022
ATOM      7  O4'		 1.286  -0.587   0.103
ATOM      8  C1'		 0.000   0.000   0.000
ATOM      9  C2'		-0.694  -0.627  -1.210
ATOM     10  O2'		-1.474  -1.731  -0.795
ATOM     11  C3'		 0.499  -1.031  -2.067
ATOM     12  O3'		 0.178  -2.084  -2.981
END
Xplor Refinement Parameters

The DNA/RNA topology and parameter files for X-PLOR are linked below. These were tested with DNA structures and with protein-DNA complexes. For refinement of high resolution structures (< 1.7 Angstroms) the second parameter file with distinct bond distances and bond angles for both C2'-endo and C3'-endo conformations should be considered.

Valence Geometry Working Group

A 2020 IUCr newsletter Special Report describes an initiative to establish the Nucleic Acid Valence Geometry Working Group. The group is meeting regularly to define and implement an updated, uniform dictionary for nucleic acid valence geometry parameters for use in modeling, refinement and validation systems.