# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 13:05:24 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: 5'-O-[(S)-{[(R)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@@H](O)CO)[C@@H](O)[C@H]2O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 C2G  C2G  5'-O-[(S)-{[(R)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine  ligand  49  30  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C2G
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 C2G  N1    N  NR6    0  -0.557   0.8249   0.7928  -4.2884
 C2G  C2    C  CR6    0   0.602   1.2536  -0.5300  -4.4891
 C2G  N3    N  N      0  -0.541   2.5267  -0.7358  -4.8805
 C2G  C4    C  CR6    0   0.515   3.3517   0.2736  -5.0796
 C2G  C5    C  CR16   0  -0.477   2.9505   1.6315  -4.8867
 C2G  C6    C  CR16   0   0.101   1.6810   1.8260  -4.4823
 C2G  O2    O  OC     0  -0.508   0.4631  -1.4459  -4.3109
 C2G  N4    N  NH2    0  -0.808   4.5966   0.0042  -5.4680
 C2G  C1'   C  CR15   0   0.209  -0.5191   1.0724  -3.8144
 C2G  C2'   C  CR15   0  -0.046  -1.6757   0.5259  -4.6721
 C2G  O2'   O  OH1    0  -0.677  -2.5548   1.5887  -4.9412
 C2G  C3'   C  CR15   0  -0.034  -2.3467  -0.5080  -3.7490
 C2G  C4'   C  CR15   0   0.019  -1.9375  -0.0340  -2.3562
 C2G  O4'   O  O      0  -0.491  -0.6674   0.5697  -2.5158
 C2G  O3'   O  OH1    0  -0.664  -3.7490  -0.5051  -3.8586
 C2G  C5'   C  CH2    0  -0.157  -1.8536  -1.1600  -1.3571
 C2G  O5'   O  O2     0  -0.620  -1.5169  -0.6426  -0.0879
 C2G  PA    P  P      0   1.340  -2.0108  -1.5024   1.2282
 C2G  O1A   O  O      0  -0.795  -1.4473  -2.8865   1.1509
 C2G  O2A   O  OP    -1  -0.798  -3.4765  -1.2913   1.4424
 C2G  O3A   O  O2     0  -0.736  -1.1412  -0.5838   2.2743
 C2G  PB    P  P      0   1.342  -1.5071  -0.4443   3.8689
 C2G  O1B   O  O      0  -0.800  -2.0036  -1.7510   4.4031
 C2G  O2B   O  OP    -1  -0.795  -2.2751   0.8166   4.1108
 C2G  O3B   O  O2     0  -0.615   0.0611  -0.2215   4.3179
 C2G  C1G   C  CH2    0  -0.163   2.0424   0.3226   7.4219
 C2G  C2G   C  CH1    0  -0.045   1.7900   0.0478   5.9477
 C2G  O2G   O  OH1    0  -0.659   2.5316   0.9017   5.1084
 C2G  C3G   C  CH2    0  -0.157   0.2972   0.1174   5.6671
 C2G  HC5   H  HCR6   0   0.289   3.6231   2.4615  -5.0397
 C2G  HC6   H  HCR6   0   0.320   1.2890   2.8165  -4.2977
 C2G  HN41  H  HNH2   0   0.403   4.8873  -0.9481  -5.6094
 C2G  HN42  H  HNH2   0   0.414   5.2615   0.7342  -5.6538
 C2G  HC1   H  HCR5   0   0.251  -0.5988   2.1641  -3.8121
 C2G  HC2   H  HCR5   0   0.245  -1.3168   0.0767  -5.6037
 C2G  HO2   H  HOH1   0   0.447  -3.4515   1.2433  -4.8290
 C2G  HC3   H  HCR5   0   0.258  -1.9354  -1.4980  -3.9496
 C2G  HC4   H  HCR5   0   0.229  -2.6664   0.7103  -2.0022
 C2G  HO3   H  HOH1   0   0.469  -4.0094  -1.1549  -4.5188
 C2G  HC51  H  HCH2   0   0.213  -2.8282  -1.6636  -1.3510
 C2G  HC52  H  HCH2   0   0.215  -1.1087  -1.8906  -1.6923
 C2G  H1G   H  HOH1   0   0.455   3.5541   0.3308   8.6273
 C2G  H2G   H  HCH1   0   0.229   2.1379  -0.9660   5.7212
 C2G  HOG   H  HOH1   0   0.442   2.2684   1.8111   5.2874
 C2G  H3G1  H  HCH2   0   0.206  -0.0727   1.1283   5.8854
 C2G  H3G2  H  HCH2   0   0.207  -0.2220  -0.5697   6.3466
 C2G  H1G1  H  HCH2   0   0.193   1.7017   1.3407   7.6619
 C2G  O1G   O  OH1    0  -0.669   3.4131   0.1566   7.6926
 C2G  H1G2  H  HCH2   0   0.200   1.4254  -0.3639   8.0157

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 C2G  N1   C2    aromatic  1.405  0.020  1.405
 C2G  N1   C6    aromatic  1.356  0.020  1.356
 C2G  N1   C1'   single    1.452  0.020  1.452
 C2G  C2   N3    aromatic  1.348  0.020  1.348
 C2G  C2   O2    double    1.223  0.020  1.223
 C2G  N3   C4    aromatic  1.319  0.020  1.319
 C2G  C4   C5    aromatic  1.429  0.020  1.429
 C2G  C4   N4    single    1.332  0.020  1.332
 C2G  C5   C6    aromatic  1.346  0.020  1.346
 C2G  C5   HC5   single    0.930  0.020  1.080
 C2G  C6   HC6   single    0.930  0.020  1.080
 C2G  N4   HN41  single    0.860  0.020  1.020
 C2G  N4   HN42  single    0.860  0.020  1.020
 C2G  C1'  C2'   single    1.540  0.020  1.540
 C2G  C1'  O4'   single    1.400  0.020  1.400
 C2G  C1'  HC1   single    0.970  0.020  1.090
 C2G  C2'  O2'   single    1.405  0.020  1.405
 C2G  C2'  C3'   single    1.540  0.020  1.540
 C2G  C2'  HC2   single    0.970  0.020  1.090
 C2G  O2'  HO2   single    0.850  0.020  0.980
 C2G  C3'  C4'   single    1.527  0.020  1.527
 C2G  C3'  O3'   single    1.407  0.020  1.407
 C2G  C3'  HC3   single    0.970  0.020  1.090
 C2G  C4'  O4'   single    1.415  0.020  1.415
 C2G  C4'  C5'   single    1.508  0.020  1.508
 C2G  C4'  HC4   single    0.970  0.020  1.090
 C2G  O3'  HO3   single    0.850  0.020  0.980
 C2G  C5'  O5'   single    1.411  0.020  1.411
 C2G  C5'  HC51  single    0.970  0.020  1.090
 C2G  C5'  HC52  single    0.970  0.020  1.090
 C2G  O5'  PA    single    1.648  0.020  1.648
 C2G  PA   O1A   deloc     1.496  0.020  1.496
 C2G  PA   O2A   deloc     1.496  0.020  1.496
 C2G  PA   O3A   single    1.641  0.020  1.641
 C2G  O3A  PB    single    1.642  0.020  1.642
 C2G  PB   O1B   deloc     1.496  0.020  1.496
 C2G  PB   O2B   deloc     1.496  0.020  1.496
 C2G  PB   O3B   single    1.646  0.020  1.646
 C2G  O3B  C3G   single    1.411  0.020  1.411
 C2G  O1G  C1G   single    1.407  0.020  1.407
 C2G  O1G  H1G   single    0.850  0.020  0.980
 C2G  C1G  C2G   single    1.521  0.020  1.521
 C2G  C1G  H1G1  single    0.970  0.020  1.090
 C2G  C1G  H1G2  single    0.970  0.020  1.090
 C2G  C2G  O2G   single    1.408  0.020  1.408
 C2G  C2G  C3G   single    1.521  0.020  1.521
 C2G  C2G  H2G   single    0.970  0.020  1.090
 C2G  O2G  HOG   single    0.850  0.020  0.980
 C2G  C3G  H3G1  single    0.970  0.020  1.090
 C2G  C3G  H3G2  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 C2G  C1'   N1   C6    118.97  3.000
 C2G  C1'   N1   C2    120.68  3.000
 C2G  C6    N1   C2    120.29  3.000
 C2G  O2    C2   N3    122.59  3.000
 C2G  O2    C2   N1    119.15  3.000
 C2G  N3    C2   N1    118.26  3.000
 C2G  C4    N3   C2    121.19  3.000
 C2G  N4    C4   C5    119.61  3.000
 C2G  N4    C4   N3    118.29  3.000
 C2G  C5    C4   N3    122.10  3.000
 C2G  HC5   C5   C6    121.27  3.000
 C2G  HC5   C5   C4    122.46  3.000
 C2G  C6    C5   C4    116.26  3.000
 C2G  HC6   C6   C5    121.70  3.000
 C2G  HC6   C6   N1    116.41  3.000
 C2G  C5    C6   N1    121.89  3.000
 C2G  HN42  N4   HN41  118.09  3.000
 C2G  HN42  N4   C4    121.70  3.000
 C2G  HN41  N4   C4    120.18  3.000
 C2G  HC1   C1'  O4'   110.39  3.000
 C2G  HC1   C1'  C2'   107.48  3.000
 C2G  O4'   C1'  C2'   108.03  3.000
 C2G  HC1   C1'  N1    105.07  3.000
 C2G  O4'   C1'  N1    109.37  3.000
 C2G  C2'   C1'  N1    116.42  3.000
 C2G  HC2   C2'  C3'   112.17  3.000
 C2G  HC2   C2'  O2'   110.64  3.000
 C2G  C3'   C2'  O2'   110.48  3.000
 C2G  HC2   C2'  C1'   111.92  3.000
 C2G  C3'   C2'  C1'   103.39  3.000
 C2G  O2'   C2'  C1'   107.95  3.000
 C2G  HO2   O2'  C2'   106.71  3.000
 C2G  HC3   C3'  O3'   111.32  3.000
 C2G  HC3   C3'  C4'   110.39  3.000
 C2G  O3'   C3'  C4'   109.73  3.000
 C2G  HC3   C3'  C2'   109.56  3.000
 C2G  O3'   C3'  C2'   112.73  3.000
 C2G  C4'   C3'  C2'   102.80  3.000
 C2G  HC4   C4'  C5'   109.20  3.000
 C2G  HC4   C4'  O4'   110.02  3.000
 C2G  C5'   C4'  O4'   110.08  3.000
 C2G  HC4   C4'  C3'   109.02  3.000
 C2G  C5'   C4'  C3'   112.80  3.000
 C2G  O4'   C4'  C3'   105.67  3.000
 C2G  C4'   O4'  C1'   110.66  3.000
 C2G  HO3   O3'  C3'   108.77  3.000
 C2G  HC52  C5'  HC51  107.43  3.000
 C2G  HC52  C5'  O5'   110.94  3.000
 C2G  HC51  C5'  O5'   112.03  3.000
 C2G  HC52  C5'  C4'   109.45  3.000
 C2G  HC51  C5'  C4'   107.28  3.000
 C2G  O5'   C5'  C4'   109.60  3.000
 C2G  PA    O5'  C5'   117.09  3.000
 C2G  O3A   PA   O2A   110.41  3.000
 C2G  O3A   PA   O1A   110.55  3.000
 C2G  O2A   PA   O1A   120.45  3.000
 C2G  O3A   PA   O5'    93.34  3.000
 C2G  O2A   PA   O5'   109.53  3.000
 C2G  O1A   PA   O5'   109.18  3.000
 C2G  PB    O3A  PA    123.26  3.000
 C2G  O3B   PB   O2B   109.32  3.000
 C2G  O3B   PB   O1B   109.69  3.000
 C2G  O2B   PB   O1B   120.52  3.000
 C2G  O3B   PB   O3A    93.67  3.000
 C2G  O2B   PB   O3A   110.06  3.000
 C2G  O1B   PB   O3A   110.27  3.000
 C2G  C3G   O3B  PB    116.91  3.000
 C2G  H1G2  C1G  H1G1  106.66  3.000
 C2G  H1G2  C1G  C2G   108.55  3.000
 C2G  H1G1  C1G  C2G   109.11  3.000
 C2G  H1G2  C1G  O1G   111.70  3.000
 C2G  H1G1  C1G  O1G   111.65  3.000
 C2G  C2G   C1G  O1G   109.08  3.000
 C2G  H2G   C2G  C3G   108.42  3.000
 C2G  H2G   C2G  O2G   105.70  3.000
 C2G  C3G   C2G  O2G   112.29  3.000
 C2G  H2G   C2G  C1G   108.36  3.000
 C2G  C3G   C2G  C1G   109.49  3.000
 C2G  O2G   C2G  C1G   112.38  3.000
 C2G  HOG   O2G  C2G   108.52  3.000
 C2G  H3G2  C3G  H3G1  107.09  3.000
 C2G  H3G2  C3G  C2G   108.76  3.000
 C2G  H3G1  C3G  C2G   109.64  3.000
 C2G  H3G2  C3G  O3B   111.26  3.000
 C2G  H3G1  C3G  O3B   110.78  3.000
 C2G  C2G   C3G  O3B   109.25  3.000
 C2G  H1G   O1G  C1G   107.97  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 C2G  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 C2G  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 C2G  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 C2G  CONST_04  C5    C4   N3   C2     0.00   0.0  0
 C2G  CONST_05  C6    N1   C2   N3     0.00   0.0  0
 C2G  CONST_06  C6    C5   C4   N3     0.00   0.0  0
 C2G  CONST_07  C1'   N1   C2   N3   180.00   0.0  0
 C2G  CONST_08  C1'   N1   C6   C5   180.00   0.0  0
 C2G  CONST_09  N4    C4   N3   C2   180.00   0.0  0
 C2G  CONST_10  O2    C2   N3   C4   180.00   0.0  0
 C2G  CONST_11  O2    C2   N1   C6   180.00   0.0  0
 C2G  CONST_12  N4    C4   C5   C6   180.00   0.0  0
 C2G  CONST_13  C1'   N1   C2   O2     0.00   0.0  0
 C2G  CONST_14  HC5   C5   C6   N1   180.00   0.0  0
 C2G  CONST_15  HC6   C6   N1   C2   180.00   0.0  0
 C2G  CONST_16  HN41  N4   C4   N3     0.00   0.0  0
 C2G  CONST_17  HN42  N4   C4   N3   180.00   0.0  0
 C2G  Var_01    O1A   PA   O5'  C5'   58.02  30.0  3
 C2G  Var_02    O1B   PB   O3A  PA    36.94  30.0  3
 C2G  Var_03    C2G   C3G  O3B  PB   170.40  30.0  3
 C2G  Var_04    HC51  C5'  O5'  PA    34.37  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 C2G  chir_01  C1'  N1   C2'  O4'  negativ
 C2G  chir_02  C2'  O2'  C3'  C1'  positiv
 C2G  chir_03  C3'  O3'  C2'  C4'  negativ
 C2G  chir_04  C4'  O4'  C3'  C5'  negativ
 C2G  chir_07  C2G  C1G  O2G  C3G  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 C2G  plan-1  N1    0.020
 C2G  plan-1  C2    0.020
 C2G  plan-1  N3    0.020
 C2G  plan-1  C4    0.020
 C2G  plan-1  C5    0.020
 C2G  plan-1  C6    0.020
 C2G  plan-1  O2    0.020
 C2G  plan-1  N4    0.020
 C2G  plan-1  C1'   0.020
 C2G  plan-1  HC5   0.020
 C2G  plan-1  HC6   0.020
 C2G  plan-2  C4    0.020
 C2G  plan-2  N4    0.020
 C2G  plan-2  HN41  0.020
 C2G  plan-2  HN42  0.020

