# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 18:02:56 2021
#   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  51  30  .  2022-03-15  2022-11-17
;
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  -0.559  20.9911  60.5756  26.8560
 C2G  C2    C  CR6   0   0.598  19.8745  61.3521  27.2204
 C2G  N3    N  N     0  -0.542  20.0983  62.5319  27.8337
 C2G  C4    C  CR6   0   0.518  21.3215  62.9491  28.0917
 C2G  C5    C  CR16  0  -0.477  22.4761  62.1775  27.7505
 C2G  C6    C  CR16  0   0.099  22.2488  61.0016  27.1380
 C2G  O2    O  OC    0  -0.516  18.7476  60.9455  26.9736
 C2G  N4    N  NH2   0  -0.807  21.4743  64.1254  28.6955
 C2G  C1'   C  CR15  0   0.186  20.8035  59.3116  26.1750
 C2G  C2'   C  CR15  0  -0.001  21.3899  59.2692  24.7666
 C2G  O2'   O  OH1   0  -0.650  20.5314  59.9042  23.8741
 C2G  C3'   C  CR15  0  -0.063  21.5810  57.7660  24.5681
 C2G  C4'   C  CR15  0  -0.007  21.9706  57.3108  25.9852
 C2G  O4'   O  O     0  -0.496  21.4776  58.3016  26.8825
 C2G  O3'   O  OH1   0  -0.663  20.3544  57.2251  24.1538
 C2G  C5'   C  CH2   0  -0.216  23.4484  57.0934  26.2013
 C2G  O5'   O  O2    0  -0.589  24.1634  58.2937  25.8677
 C2G  PA    P  P     0   1.515  25.6892  58.2289  25.4347
 C2G  O1A   O  O     0  -0.668  26.5771  57.3631  26.2211
 C2G  O2A   O  OH1   0  -0.725  25.9913  59.7802  25.3458
 C2G  O3A   O  O2    0  -0.692  25.6365  57.7132  23.8964
 C2G  PB    P  P     0   1.487  25.3194  58.4822  22.5107
 C2G  O1B   O  O     0  -0.669  26.5190  58.9371  21.7925
 C2G  O2B   O  OH1   0  -0.738  24.2490  59.6041  22.8706
 C2G  O3B   O  O2    0  -0.578  24.4361  57.3441  21.8521
 C2G  C1G   C  CH2   0  -0.158  21.8586  56.2282  21.1629
 C2G  C2G   C  CH1   0  -0.021  23.0105  56.3531  20.1834
 C2G  O2G   O  OH1   0  -0.663  23.7058  55.1312  20.1591
 C2G  C3G   C  CH2   0  -0.218  23.9147  57.5228  20.5225
 C2G  HC5   H  HCR6  0   0.290  23.4786  62.5104  27.9723
 C2G  HC6   H  HCR6  0   0.312  23.0631  60.3485  26.8576
 C2G  HN41  H  HNH2  0   0.415  22.3845  64.5042  28.8893
 C2G  HN42  H  HNH2  0   0.404  20.6701  64.6843  28.9255
 C2G  HC1   H  HCR5  0   0.272  19.7280  59.1294  26.1421
 C2G  HC2   H  HCR5  0   0.245  22.3797  59.7369  24.7754
 C2G  HO2   H  HOH1  0   0.458  21.0121  60.0973  23.0639
 C2G  HC3   H  HCR5  0   0.236  22.3739  57.5466  23.8432
 C2G  HC4   H  HCR5  0   0.272  21.4937  56.3492  26.2100
 C2G  HO3   H  HOH1  0   0.458  20.4413  56.2678  24.1086
 C2G  HC51  H  HCH2  0   0.279  23.6489  56.8389  27.2429
 C2G  HC52  H  HCH2  0   0.258  23.7678  56.2523  25.5801
 C2G  H2A   H  HOH1  0   0.515  26.9171  60.0197  25.4951
 C2G  H2B   H  HOH1  0   0.507  24.5864  60.5105  22.8592
 C2G  H1G   H  HOH1  0   0.455  20.2049  55.2264  21.2708
 C2G  H1G2  H  HCH2  0   0.199  22.2422  55.8919  22.1350
 C2G  H2G   H  HCH1  0   0.234  22.5886  56.5964  19.1971
 C2G  HOG   H  HOH1  0   0.456  24.2938  55.1272  19.3976
 C2G  H3G1  H  HCH2  0   0.250  23.3471  58.4549  20.4599
 C2G  H3G2  H  HCH2  0   0.267  24.7406  57.5796  19.8093
 C2G  H1G1  H  HCH2  0   0.200  21.4198  57.2239  21.3114
 C2G  O1G   O  OH1   0  -0.667  20.9211  55.3215  20.6371

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  1.408  0.020  1.408
 C2G  N1   C6    aromatic  1.357  0.020  1.357
 C2G  N1   C1'   single    1.448  0.020  1.448
 C2G  C2   N3    aromatic  1.348  0.020  1.348
 C2G  C2   O2    double    1.223  0.020  1.223
 C2G  N3   C4    aromatic  1.318  0.020  1.318
 C2G  C4   C5    aromatic  1.430  0.020  1.430
 C2G  C4   N4    single    1.331  0.020  1.331
 C2G  C5   C6    aromatic  1.345  0.020  1.345
 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    1.526  0.020  1.526
 C2G  C1'  O4'   single    1.405  0.020  1.405
 C2G  C1'  HC1   single    0.970  0.020  1.090
 C2G  C2'  O2'   single    1.392  0.020  1.392
 C2G  C2'  C3'   single    1.528  0.020  1.528
 C2G  C2'  HC2   single    0.970  0.020  1.090
 C2G  O2'  HO2   single    0.850  0.020  0.980
 C2G  C3'  C4'   single    1.539  0.020  1.539
 C2G  C3'  O3'   single    1.403  0.020  1.403
 C2G  C3'  HC3   single    0.970  0.020  1.090
 C2G  C4'  O4'   single    1.425  0.020  1.425
 C2G  C4'  C5'   single    1.509  0.020  1.509
 C2G  C4'  HC4   single    0.970  0.020  1.090
 C2G  O3'  HO3   single    0.850  0.020  0.980
 C2G  C5'  O5'   single    1.436  0.020  1.436
 C2G  C5'  HC51  single    0.970  0.020  1.090
 C2G  C5'  HC52  single    0.970  0.020  1.090
 C2G  O5'  PA    single    1.587  0.020  1.587
 C2G  PA   O1A   double    1.468  0.020  1.468
 C2G  PA   O2A   single    1.583  0.020  1.583
 C2G  PA   O3A   single    1.623  0.020  1.623
 C2G  O2A  H2A   single    0.850  0.020  0.980
 C2G  O3A  PB    single    1.616  0.020  1.616
 C2G  PB   O1B   double    1.470  0.020  1.470
 C2G  PB   O2B   single    1.592  0.020  1.592
 C2G  PB   O3B   single    1.584  0.020  1.584
 C2G  O2B  H2B   single    0.850  0.020  0.980
 C2G  O3B  C3G   single    1.439  0.020  1.439
 C2G  O1G  C1G   single    1.406  0.020  1.406
 C2G  O1G  H1G   single    0.850  0.020  0.980
 C2G  C1G  C2G   single    1.517  0.020  1.517
 C2G  C1G  H1G1  single    0.970  0.020  1.090
 C2G  C1G  H1G2  single    0.970  0.020  1.090
 C2G  C2G  O2G   single    1.406  0.020  1.406
 C2G  C2G  C3G   single    1.517  0.020  1.517
 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    119.45  3.000
 C2G  C1'   N1   C2    120.03  3.000
 C2G  C6    N1   C2    120.52  3.000
 C2G  O2    C2   N3    122.38  3.000
 C2G  O2    C2   N1    119.67  3.000
 C2G  N3    C2   N1    117.94  3.000
 C2G  C4    N3   C2    121.34  3.000
 C2G  N4    C4   C5    119.50  3.000
 C2G  N4    C4   N3    118.37  3.000
 C2G  C5    C4   N3    122.13  3.000
 C2G  HC5   C5   C6    121.34  3.000
 C2G  HC5   C5   C4    122.31  3.000
 C2G  C6    C5   C4    116.35  3.000
 C2G  HC6   C6   C5    121.26  3.000
 C2G  HC6   C6   N1    117.04  3.000
 C2G  C5    C6   N1    121.70  3.000
 C2G  HN42  N4   HN41  118.07  3.000
 C2G  HN42  N4   C4    120.20  3.000
 C2G  HN41  N4   C4    121.65  3.000
 C2G  HC1   C1'  O4'   111.59  3.000
 C2G  HC1   C1'  C2'   110.25  3.000
 C2G  O4'   C1'  C2'   105.09  3.000
 C2G  HC1   C1'  N1    106.72  3.000
 C2G  O4'   C1'  N1    109.17  3.000
 C2G  C2'   C1'  N1    114.11  3.000
 C2G  HC2   C2'  C3'   107.96  3.000
 C2G  HC2   C2'  O2'   111.59  3.000
 C2G  C3'   C2'  O2'   116.27  3.000
 C2G  HC2   C2'  C1'   109.15  3.000
 C2G  C3'   C2'  C1'   101.26  3.000
 C2G  O2'   C2'  C1'   110.00  3.000
 C2G  HO2   O2'  C2'   108.87  3.000
 C2G  HC3   C3'  O3'   111.08  3.000
 C2G  HC3   C3'  C4'   111.50  3.000
 C2G  O3'   C3'  C4'   112.29  3.000
 C2G  HC3   C3'  C2'   111.91  3.000
 C2G  O3'   C3'  C2'   107.95  3.000
 C2G  C4'   C3'  C2'   101.72  3.000
 C2G  HC4   C4'  C5'   105.68  3.000
 C2G  HC4   C4'  O4'   109.28  3.000
 C2G  C5'   C4'  O4'   110.41  3.000
 C2G  HC4   C4'  C3'   109.76  3.000
 C2G  C5'   C4'  C3'   114.99  3.000
 C2G  O4'   C4'  C3'   106.66  3.000
 C2G  C4'   O4'  C1'   110.41  3.000
 C2G  HO3   O3'  C3'   108.57  3.000
 C2G  HC52  C5'  HC51  108.02  3.000
 C2G  HC52  C5'  O5'   111.44  3.000
 C2G  HC51  C5'  O5'   108.98  3.000
 C2G  HC52  C5'  C4'   108.39  3.000
 C2G  HC51  C5'  C4'   110.50  3.000
 C2G  O5'   C5'  C4'   109.50  3.000
 C2G  PA    O5'  C5'   120.51  3.000
 C2G  O3A   PA   O2A   105.32  3.000
 C2G  O3A   PA   O1A   109.86  3.000
 C2G  O2A   PA   O1A   119.50  3.000
 C2G  O3A   PA   O5'   103.90  3.000
 C2G  O2A   PA   O5'    99.13  3.000
 C2G  O1A   PA   O5'   117.34  3.000
 C2G  H2A   O2A  PA    114.61  3.000
 C2G  PB    O3A  PA    131.89  3.000
 C2G  O3B   PB   O2B   103.03  3.000
 C2G  O3B   PB   O1B   118.30  3.000
 C2G  O2B   PB   O1B   116.16  3.000
 C2G  O3B   PB   O3A    97.13  3.000
 C2G  O2B   PB   O3A   105.87  3.000
 C2G  O1B   PB   O3A   113.95  3.000
 C2G  H2B   O2B  PB    115.04  3.000
 C2G  C3G   O3B  PB    119.79  3.000
 C2G  H1G2  C1G  H1G1  107.32  3.000
 C2G  H1G2  C1G  C2G   109.36  3.000
 C2G  H1G1  C1G  C2G   108.42  3.000
 C2G  H1G2  C1G  O1G   111.50  3.000
 C2G  H1G1  C1G  O1G   111.64  3.000
 C2G  C2G   C1G  O1G   108.53  3.000
 C2G  H2G   C2G  C3G   104.99  3.000
 C2G  H2G   C2G  O2G   111.49  3.000
 C2G  C3G   C2G  O2G   112.29  3.000
 C2G  H2G   C2G  C1G   107.81  3.000
 C2G  C3G   C2G  C1G   111.82  3.000
 C2G  O2G   C2G  C1G   108.37  3.000
 C2G  HOG   O2G  C2G   108.63  3.000
 C2G  H3G2  C3G  H3G1  108.11  3.000
 C2G  H3G2  C3G  C2G   110.16  3.000
 C2G  H3G1  C3G  C2G   109.59  3.000
 C2G  H3G2  C3G  O3B   109.61  3.000
 C2G  H3G1  C3G  O3B   110.30  3.000
 C2G  C2G   C3G  O3B   109.07  3.000
 C2G  H1G   O1G  C1G   108.31  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    180.00   0.0  0
 C2G  CONST_17  HN42  N4   C4   N3      0.00   0.0  0
 C2G  Var_01    O1A   PA   O5'  C5'   -44.14  30.0  3
 C2G  Var_02    O1B   PB   O3A  PA     95.66  30.0  3
 C2G  Var_03    C2G   C3G  O3B  PB   -174.99  30.0  3
 C2G  Var_04    HC51  C5'  O5'  PA     83.60  30.0  2

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
 C2G  chir_08  PA   O1A  O2A  O3A  both
 C2G  chir_09  PB   O1B  O2B  O3B  both

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

