# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 14:36:24 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 5'-O-[(S)-{[(R)-(2-aminoethyl)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC[P@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)N
#
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
 0RC  0RC  5'-O-[(S)-{[(R)-(2-aminoethyl)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine  ligand  45  27  .  2021-08-03  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0RC
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
 0RC  O3B   O  O      0  -0.807  -3.7776  -2.0206  -1.1963
 0RC  PB    P  P      0   1.283  -4.2817  -0.8333  -0.4213
 0RC  O2B   O  OP    -1  -0.814  -5.2345   0.1352  -1.0690
 0RC  C1B   C  CH2    0  -0.720  -4.9589  -1.4012   1.1782
 0RC  C14   C  CH2    0  -0.279  -6.1663  -2.3084   0.9819
 0RC  N15   N  NH2    0  -0.799  -6.6885  -2.7662   2.2636
 0RC  O3A   O  O2     0  -0.750  -2.9719   0.0104   0.1696
 0RC  PA    P  P      0   1.336  -2.2489   1.2480  -0.6134
 0RC  O1A   O  O      0  -0.807  -2.1336   0.9771  -2.0820
 0RC  O2A   O  OP    -1  -0.797  -2.7956   2.5569  -0.1330
 0RC  O5'   O  O2     0  -0.624  -0.7807   0.9924   0.1021
 0RC  C5'   C  CH2    0  -0.156   0.3236   1.6731  -0.4501
 0RC  C4'   C  CH1    0   0.018   1.4364   1.7478   0.5657
 0RC  C3'   C  CH1    0  -0.033   2.6570   2.5016   0.0398
 0RC  O3'   O  OH1    0  -0.665   2.5379   3.8705   0.3404
 0RC  C2'   C  CH1    0  -0.045   3.8244   1.8293   0.7849
 0RC  O2'   O  OH1    0  -0.678   4.1001   2.5134   1.9819
 0RC  O4'   O  O2     0  -0.491   1.8921   0.4451   0.8831
 0RC  C1'   C  CH1    0   0.207   3.2647   0.4449   1.1578
 0RC  N1    N  NR6    0  -0.556   3.8856  -0.7026   0.5171
 0RC  C6    C  CR16   0   0.102   4.3702  -1.7038   1.2925
 0RC  C5    C  CR16   0  -0.478   4.9126  -2.8160   0.7617
 0RC  C4    C  CR6    0   0.515   4.9307  -2.8916  -0.6651
 0RC  N4    N  NH2    0  -0.808   5.4419  -3.9677  -1.2599
 0RC  N3    N  N      0  -0.541   4.4522  -1.9253  -1.4241
 0RC  C2    C  CR6    0   0.603   3.9228  -0.8104  -0.8828
 0RC  O2    O  O      0  -0.508   3.4821   0.1058  -1.5625
 0RC  H1B1  H  HCH2   0   0.234  -4.1907  -1.9370   1.7422
 0RC  H1B2  H  HCH2   0   0.231  -5.2468  -0.5314   1.7774
 0RC  H141  H  HCH2   0   0.191  -6.9130  -1.7807   0.3730
 0RC  H142  H  HCH2   0   0.214  -5.8626  -3.1849   0.4047
 0RC  H151  H  HNH2   0   0.335  -7.0354  -1.9678   2.7821
 0RC  H152  H  HNH2   0   0.343  -7.4978  -3.3526   2.1020
 0RC  H5'1  H  HCH2   0   0.212   0.6875   1.1641  -1.3497
 0RC  H5'2  H  HCH2   0   0.208   0.0714   2.7033  -0.7325
 0RC  H4'   H  HCH1   0   0.229   1.0706   2.2504   1.4733
 0RC  H3'   H  HCH1   0   0.259   2.7680   2.3417  -1.0332
 0RC  HO3'  H  HOH1   0   0.469   3.0245   4.3769  -0.3174
 0RC  H2'   H  HCH1   0   0.245   4.7239   1.7563   0.1647
 0RC  HO2'  H  HOH1   0   0.447   3.8133   3.4278   1.8517
 0RC  H1'   H  HCH1   0   0.251   3.4390   0.2988   2.2285
 0RC  H6    H  HCR6   0   0.319   4.3002  -1.5606   2.3620
 0RC  H5    H  HCR6   0   0.289   5.2996  -3.6059   1.3873
 0RC  HN41  H  HNH2   0   0.414   5.8188  -4.7332  -0.7302
 0RC  HN42  H  HNH2   0   0.403   5.4492  -4.0366  -2.2633

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
 0RC  O2   C2    double  1.223  0.020  1.223
 0RC  N3   C2    single  1.348  0.020  1.348
 0RC  N3   C4    double  1.319  0.020  1.319
 0RC  C2   N1    single  1.405  0.020  1.405
 0RC  N15  C14   single  1.458  0.020  1.458
 0RC  O4'  C1'   single  1.400  0.020  1.400
 0RC  O4'  C4'   single  1.416  0.020  1.416
 0RC  N4   C4    single  1.332  0.020  1.332
 0RC  C4   C5    single  1.429  0.020  1.429
 0RC  N1   C1'   single  1.454  0.020  1.454
 0RC  N1   C6    single  1.356  0.020  1.356
 0RC  C1'  C2'   single  1.539  0.020  1.539
 0RC  C4'  C5'   single  1.509  0.020  1.509
 0RC  C4'  C3'   single  1.528  0.020  1.528
 0RC  C14  C1B   single  1.523  0.020  1.523
 0RC  C5   C6    double  1.346  0.020  1.346
 0RC  C5'  O5'   single  1.410  0.020  1.410
 0RC  O3'  C3'   single  1.407  0.020  1.407
 0RC  C1B  PB    single  1.827  0.020  1.827
 0RC  C3'  C2'   single  1.540  0.020  1.540
 0RC  C2'  O2'   single  1.406  0.020  1.406
 0RC  O5'  PA    single  1.653  0.020  1.653
 0RC  O3A  PB    single  1.666  0.020  1.666
 0RC  O3A  PA    single  1.633  0.020  1.633
 0RC  PB   O3B   deloc   1.505  0.020  1.505
 0RC  PB   O2B   deloc   1.505  0.020  1.505
 0RC  PA   O1A   deloc   1.498  0.020  1.498
 0RC  PA   O2A   deloc   1.498  0.020  1.498
 0RC  C1B  H1B1  single  0.970  0.020  1.090
 0RC  C1B  H1B2  single  0.970  0.020  1.090
 0RC  C14  H141  single  0.970  0.020  1.090
 0RC  C14  H142  single  0.970  0.020  1.090
 0RC  N15  H151  single  0.890  0.020  1.040
 0RC  N15  H152  single  0.890  0.020  1.040
 0RC  C5'  H5'1  single  0.970  0.020  1.090
 0RC  C5'  H5'2  single  0.970  0.020  1.090
 0RC  C4'  H4'   single  0.970  0.020  1.090
 0RC  C3'  H3'   single  0.970  0.020  1.090
 0RC  O3'  HO3'  single  0.850  0.020  0.980
 0RC  C2'  H2'   single  0.970  0.020  1.090
 0RC  O2'  HO2'  single  0.850  0.020  0.980
 0RC  C1'  H1'   single  0.970  0.020  1.090
 0RC  C6   H6    single  0.930  0.020  1.080
 0RC  C5   H5    single  0.930  0.020  1.080
 0RC  N4   HN41  single  0.860  0.020  1.020
 0RC  N4   HN42  single  0.860  0.020  1.020

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
 0RC  O3A   PB   C1B    97.95  3.000
 0RC  O3A   PB   O2B   108.93  3.000
 0RC  C1B   PB   O2B   110.00  3.000
 0RC  O2B   PB   O3B   119.88  3.000
 0RC  O3A   PB   O3B   108.59  3.000
 0RC  C1B   PB   O3B   109.25  3.000
 0RC  H1B2  C1B  H1B1  106.97  3.000
 0RC  H1B2  C1B  C14   109.59  3.000
 0RC  H1B1  C1B  C14   109.36  3.000
 0RC  H1B2  C1B  PB    109.25  3.000
 0RC  H1B1  C1B  PB    110.09  3.000
 0RC  C14   C1B  PB    111.47  3.000
 0RC  H142  C14  H141  106.35  3.000
 0RC  H142  C14  N15   108.19  3.000
 0RC  H141  C14  N15   113.25  3.000
 0RC  H142  C14  C1B   109.00  3.000
 0RC  H141  C14  C1B   108.92  3.000
 0RC  N15   C14  C1B   110.96  3.000
 0RC  H152  N15  H151  105.33  3.000
 0RC  H152  N15  C14   109.14  3.000
 0RC  H151  N15  C14   108.98  3.000
 0RC  PA    O3A  PB    124.17  3.000
 0RC  O5'   PA   O2A   108.70  3.000
 0RC  O2A   PA   O1A   120.04  3.000
 0RC  O5'   PA   O1A   109.15  3.000
 0RC  O2A   PA   O3A   110.30  3.000
 0RC  O1A   PA   O3A   111.54  3.000
 0RC  O5'   PA   O3A    93.93  3.000
 0RC  C5'   O5'  PA    116.84  3.000
 0RC  H5'2  C5'  H5'1  107.52  3.000
 0RC  H5'2  C5'  C4'   107.24  3.000
 0RC  H5'1  C5'  C4'   109.32  3.000
 0RC  H5'2  C5'  O5'   111.96  3.000
 0RC  H5'1  C5'  O5'   110.94  3.000
 0RC  C4'   C5'  O5'   109.75  3.000
 0RC  H4'   C4'  O4'   110.03  3.000
 0RC  H4'   C4'  C3'   108.92  3.000
 0RC  O4'   C4'  C3'   105.90  3.000
 0RC  H4'   C4'  C5'   109.44  3.000
 0RC  C3'   C4'  C5'   112.45  3.000
 0RC  O4'   C4'  C5'   110.05  3.000
 0RC  H3'   C3'  C2'   109.58  3.000
 0RC  H3'   C3'  O3'   111.20  3.000
 0RC  C2'   C3'  O3'   112.69  3.000
 0RC  H3'   C3'  C4'   110.34  3.000
 0RC  C2'   C3'  C4'   102.93  3.000
 0RC  O3'   C3'  C4'   109.81  3.000
 0RC  HO3'  O3'  C3'   108.86  3.000
 0RC  H2'   C2'  C1'   112.09  3.000
 0RC  H2'   C2'  O2'   110.71  3.000
 0RC  C1'   C2'  O2'   107.62  3.000
 0RC  H2'   C2'  C3'   112.20  3.000
 0RC  O2'   C2'  C3'   110.38  3.000
 0RC  C1'   C2'  C3'   103.55  3.000
 0RC  HO2'  O2'  C2'   106.69  3.000
 0RC  C1'   O4'  C4'   111.08  3.000
 0RC  H1'   C1'  N1    104.93  3.000
 0RC  H1'   C1'  O4'   110.37  3.000
 0RC  N1    C1'  O4'   109.42  3.000
 0RC  H1'   C1'  C2'   107.40  3.000
 0RC  N1    C1'  C2'   116.62  3.000
 0RC  O4'   C1'  C2'   108.00  3.000
 0RC  C2    N1   C6    120.26  3.000
 0RC  C6    N1   C1'   118.92  3.000
 0RC  C2    N1   C1'   120.74  3.000
 0RC  H6    C6   C5    121.69  3.000
 0RC  H6    C6   N1    116.40  3.000
 0RC  C5    C6   N1    121.90  3.000
 0RC  H5    C5   C4    122.38  3.000
 0RC  H5    C5   C6    121.36  3.000
 0RC  C4    C5   C6    116.26  3.000
 0RC  N3    C4   N4    118.32  3.000
 0RC  N4    C4   C5    119.58  3.000
 0RC  N3    C4   C5    122.10  3.000
 0RC  HN42  N4   HN41  118.12  3.000
 0RC  HN42  N4   C4    120.25  3.000
 0RC  HN41  N4   C4    121.63  3.000
 0RC  C2    N3   C4    121.17  3.000
 0RC  O2    C2   N3    122.55  3.000
 0RC  N3    C2   N1    118.31  3.000
 0RC  O2    C2   N1    119.14  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
 0RC  CONST_01  N3    C2   N1   C1'   180.00   0.0  0
 0RC  CONST_02  C4    N3   C2   N1      0.00   0.0  0
 0RC  CONST_03  N3    C2   N1   C6      0.00   0.0  0
 0RC  CONST_04  C2    N3   C4   C5      0.00   0.0  0
 0RC  CONST_05  O2    C2   N1   C1'     0.00   0.0  0
 0RC  CONST_06  O2    C2   N1   C6    180.00   0.0  0
 0RC  CONST_07  O2    C2   N3   C4    180.00   0.0  0
 0RC  CONST_08  C2    N3   C4   N4    180.00   0.0  0
 0RC  CONST_09  HN41  N4   C4   C5      0.00   0.0  0
 0RC  CONST_10  HN42  N4   C4   C5    180.00   0.0  0
 0RC  Var_01    C4'   C5'  O5'  PA    159.45  30.0  2
 0RC  Var_02    C14   C1B  PB   O3B   -63.53  30.0  2
 0RC  Var_03    N15   C14  C1B  PB    179.39  30.0  2
 0RC  Var_04    O5'   PA   O3A  PB   -152.90  30.0  3
 0RC  Var_05    H151  N15  C14  C1B    64.50  30.0  3

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
 0RC  chir_03  C4'  O4'  C5'  C3'  positiv
 0RC  chir_04  C3'  O3'  C4'  C2'  positiv
 0RC  chir_05  C2'  O2'  C3'  C1'  positiv
 0RC  chir_06  C1'  O4'  N1   C2'  negativ

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
 0RC  plan-1  C1'   0.020
 0RC  plan-1  N1    0.020
 0RC  plan-1  C6    0.020
 0RC  plan-1  C5    0.020
 0RC  plan-1  C4    0.020
 0RC  plan-1  N4    0.020
 0RC  plan-1  N3    0.020
 0RC  plan-1  C2    0.020
 0RC  plan-1  O2    0.020
 0RC  plan-1  H6    0.020
 0RC  plan-1  H5    0.020
 0RC  plan-1  HN41  0.020
 0RC  plan-1  HN42  0.020

