# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 15:30:34 2021
#   Inital geometry file: a 88 line input string
#   Ligand name: 2'-O-(sulfidophosphinato)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O[P](O)(S)=O
#
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
 OVE  OVE  2'-O-(sulfidophosphinato)adenosine  ligand  37  23  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OVE
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
 OVE  O1P   O  OH1   0  -0.733  36.7828  3.6062  71.6710
 OVE  P     P  P     0   1.240  38.1906  3.3713  70.9597
 OVE  S2P   S  S2    0  -0.364  38.7815  1.5695  71.8239
 OVE  O3P   O  O     0  -0.661  38.2630  3.4115  69.4886
 OVE  O2'   O  O2    0  -0.568  39.0758  4.5302  71.6038
 OVE  C2'   C  CH1   0  -0.046  39.1951  4.7670  72.9917
 OVE  C3'   C  CH1   0  -0.037  38.2501  5.8308  73.5376
 OVE  O3'   O  OH1   0  -0.667  38.0996  6.8125  72.5458
 OVE  C1'   C  CH1   0   0.234  40.5519  5.4074  73.2691
 OVE  O4'   O  O2    0  -0.494  40.4134  5.9707  74.5376
 OVE  C4'   C  CH1   0  -0.000  39.0458  6.3379  74.7586
 OVE  C5'   C  CH2   0  -0.179  38.5615  5.7960  76.0824
 OVE  O5'   O  OH1   0  -0.656  38.4564  4.3982  76.0120
 OVE  N9    N  NR5   0  -0.557  41.6681  4.5083  73.2372
 OVE  C8    C  CR15  0   0.116  42.8382  4.7538  72.5674
 OVE  N7    N  N     0  -0.452  43.7163  3.8073  72.6858
 OVE  C5    C  CR56  0  -0.004  43.1015  2.8765  73.4847
 OVE  C6    C  CR6   0   0.456  43.5192  1.6267  73.9787
 OVE  N6    N  NH2   0  -0.817  44.7263  1.1171  73.7235
 OVE  C4    C  CR56  0   0.490  41.8282  3.2897  73.8456
 OVE  N3    N  N     0  -0.430  40.9729  2.6176  74.6097
 OVE  C2    C  CR16  0   0.038  41.4707  1.4619  75.0079
 OVE  N1    N  N     0  -0.473  42.6661  0.9392  74.7438
 OVE  H1P   H  HOH1  0   0.508  36.0587  3.0497  71.3518
 OVE  H2P   H  HSH1  0   0.267  39.8526  1.3954  71.0382
 OVE  H2'   H  HCH1  0   0.311  39.0977  3.8477  73.5764
 OVE  H3'   H  HCH1  0   0.259  37.2849  5.4125  73.8396
 OVE  H1'   H  HCH1  0   0.258  40.7600  6.1676  72.5049
 OVE  HA    H  HOH1  0   0.460  37.5241  7.5040  72.8875
 OVE  H4'   H  HCH1  0   0.256  38.9753  7.4304  74.8096
 OVE  H5'1  H  HCH2  0   0.218  39.2512  6.1211  76.8724
 OVE  H5'2  H  HCH2  0   0.206  37.5951  6.2738  76.2907
 OVE  H5'   H  HOH1  0   0.459  38.1428  4.0716  76.8597
 OVE  H2    H  HCR6  0   0.249  40.8251  0.8544  75.6333
 OVE  H8    H  HCR5  0   0.302  42.9708  5.6642  72.0011
 OVE  H61N  H  HNH2  0   0.403  44.9563  0.1899  74.0368
 OVE  H62N  H  HNH2  0   0.410  45.3561  1.5716  73.0860

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
 OVE  O1P  P     single    1.595  0.020  1.595
 OVE  P    S2P   single    2.084  0.020  2.084
 OVE  P    O3P   double    1.474  0.020  1.474
 OVE  P    O2'   single    1.594  0.020  1.594
 OVE  O2'  C2'   single    1.413  0.020  1.413
 OVE  C2'  C3'   single    1.524  0.020  1.524
 OVE  C2'  C1'   single    1.526  0.020  1.526
 OVE  C3'  O3'   single    1.404  0.020  1.404
 OVE  C3'  C4'   single    1.543  0.020  1.543
 OVE  C1'  O4'   single    1.395  0.020  1.395
 OVE  C1'  N9    single    1.434  0.020  1.434
 OVE  O4'  C4'   single    1.433  0.020  1.433
 OVE  C4'  C5'   single    1.510  0.020  1.510
 OVE  C5'  O5'   single    1.404  0.020  1.404
 OVE  N9   C8    aromatic  1.370  0.020  1.370
 OVE  N9   C4    aromatic  1.371  0.020  1.371
 OVE  C8   N7    aromatic  1.297  0.020  1.297
 OVE  N7   C5    aromatic  1.372  0.020  1.372
 OVE  C5   C6    aromatic  1.407  0.020  1.407
 OVE  C5   C4    aromatic  1.386  0.020  1.386
 OVE  C6   N6    single    1.335  0.020  1.335
 OVE  C6   N1    aromatic  1.336  0.020  1.336
 OVE  C4   N3    aromatic  1.329  0.020  1.329
 OVE  N3   C2    aromatic  1.320  0.020  1.320
 OVE  H2   C2    single    0.930  0.020  1.080
 OVE  N1   C2    aromatic  1.331  0.020  1.331
 OVE  O1P  H1P   single    0.850  0.020  0.980
 OVE  S2P  H2P   single    1.200  0.020  1.300
 OVE  C2'  H2'   single    0.970  0.020  1.090
 OVE  C3'  H3'   single    0.970  0.020  1.090
 OVE  C1'  H1'   single    0.970  0.020  1.090
 OVE  O3'  HA    single    0.850  0.020  0.980
 OVE  C4'  H4'   single    0.970  0.020  1.090
 OVE  C5'  H5'1  single    0.970  0.020  1.090
 OVE  C5'  H5'2  single    0.970  0.020  1.090
 OVE  O5'  H5'   single    0.850  0.020  0.980
 OVE  C8   H8    single    0.930  0.020  1.080
 OVE  N6   H61N  single    0.860  0.020  1.020
 OVE  N6   H62N  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
 OVE  H1P   O1P  P     115.40  3.000
 OVE  O2'   P    O3P   110.87  3.000
 OVE  O2'   P    S2P   107.67  3.000
 OVE  O3P   P    S2P   115.07  3.000
 OVE  O2'   P    O1P   101.71  3.000
 OVE  O3P   P    O1P   118.99  3.000
 OVE  S2P   P    O1P   101.11  3.000
 OVE  H2P   S2P  P      95.50  3.000
 OVE  C2'   O2'  P     124.44  3.000
 OVE  H2'   C2'  C1'   109.55  3.000
 OVE  H2'   C2'  C3'   109.88  3.000
 OVE  C1'   C2'  C3'   101.14  3.000
 OVE  H2'   C2'  O2'   112.13  3.000
 OVE  C1'   C2'  O2'   108.91  3.000
 OVE  C3'   C2'  O2'   114.61  3.000
 OVE  H3'   C3'  C4'   111.22  3.000
 OVE  H3'   C3'  O3'   111.58  3.000
 OVE  C4'   C3'  O3'   112.62  3.000
 OVE  H3'   C3'  C2'   112.26  3.000
 OVE  C4'   C3'  C2'   101.13  3.000
 OVE  O3'   C3'  C2'   107.55  3.000
 OVE  HA    O3'  C3'   108.41  3.000
 OVE  H1'   C1'  N9    105.73  3.000
 OVE  H1'   C1'  O4'   111.85  3.000
 OVE  N9    C1'  O4'   110.54  3.000
 OVE  H1'   C1'  C2'   109.43  3.000
 OVE  N9    C1'  C2'   115.16  3.000
 OVE  O4'   C1'  C2'   104.28  3.000
 OVE  C4'   O4'  C1'   109.78  3.000
 OVE  H4'   C4'  C5'   107.23  3.000
 OVE  H4'   C4'  O4'   108.91  3.000
 OVE  C5'   C4'  O4'   110.44  3.000
 OVE  H4'   C4'  C3'   109.34  3.000
 OVE  C5'   C4'  C3'   114.23  3.000
 OVE  O4'   C4'  C3'   106.61  3.000
 OVE  H5'2  C5'  H5'1  106.71  3.000
 OVE  H5'2  C5'  O5'   112.15  3.000
 OVE  H5'1  C5'  O5'   112.22  3.000
 OVE  H5'2  C5'  C4'   107.00  3.000
 OVE  H5'1  C5'  C4'   108.85  3.000
 OVE  O5'   C5'  C4'   109.72  3.000
 OVE  H5'   O5'  C5'   108.58  3.000
 OVE  C4    N9   C8    106.04  3.000
 OVE  C4    N9   C1'   129.66  3.000
 OVE  C8    N9   C1'   124.28  3.000
 OVE  H8    C8   N7    125.45  3.000
 OVE  H8    C8   N9    120.80  3.000
 OVE  N7    C8   N9    113.75  3.000
 OVE  C5    N7   C8    104.18  3.000
 OVE  C4    C5   C6    116.48  3.000
 OVE  C4    C5   N7    111.16  3.000
 OVE  C6    C5   N7    132.36  3.000
 OVE  N1    C6   N6    119.36  3.000
 OVE  N1    C6   C5    117.93  3.000
 OVE  N6    C6   C5    122.71  3.000
 OVE  H62N  N6   H61N  118.13  3.000
 OVE  H62N  N6   C6    121.02  3.000
 OVE  H61N  N6   C6    119.96  3.000
 OVE  N3    C4   C5    126.15  3.000
 OVE  N3    C4   N9    128.98  3.000
 OVE  C5    C4   N9    104.86  3.000
 OVE  C2    N3   C4    111.93  3.000
 OVE  H2    C2   N1    115.40  3.000
 OVE  N1    C2   N3    128.51  3.000
 OVE  H2    C2   N3    116.10  3.000
 OVE  C2    N1   C6    119.00  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
 OVE  CONST_01  C5    N7  C8  N9     0.00  0.0  0
 OVE  CONST_02  N7    C5  C4  N9     0.00  0.0  0
 OVE  CONST_03  C6    C5  C4  N9   180.00  0.0  0
 OVE  CONST_04  C2    N3  C4  N9   180.00  0.0  0
 OVE  CONST_05  C5    C4  N9  C8     0.00  0.0  0
 OVE  CONST_06  N3    C4  N9  C8   180.00  0.0  0
 OVE  CONST_07  C6    C5  N7  C8   180.00  0.0  0
 OVE  CONST_08  C4    C5  N7  C8     0.00  0.0  0
 OVE  CONST_09  C4    N9  C8  N7     0.00  0.0  0
 OVE  CONST_10  N1    C6  C5  N7   180.00  0.0  0
 OVE  CONST_11  N3    C4  C5  N7   180.00  0.0  0
 OVE  CONST_12  C2    N1  C6  C5     0.00  0.0  0
 OVE  CONST_13  C2    N3  C4  C5     0.00  0.0  0
 OVE  CONST_14  N3    C4  C5  C6     0.00  0.0  0
 OVE  CONST_15  N3    C2  N1  C6     0.00  0.0  0
 OVE  CONST_16  N1    C6  C5  C4     0.00  0.0  0
 OVE  CONST_17  N1    C2  N3  C4     0.00  0.0  0
 OVE  CONST_18  N7    C8  N9  C1'  180.00  0.0  0
 OVE  CONST_19  C5    C4  N9  C1'  180.00  0.0  0
 OVE  CONST_20  N3    C4  N9  C1'    0.00  0.0  0
 OVE  CONST_21  N6    C6  C5  N7     0.00  0.0  0
 OVE  CONST_22  C4    C5  C6  N6   180.00  0.0  0
 OVE  CONST_23  C2    N1  C6  N6   180.00  0.0  0
 OVE  CONST_24  H8    C8  N9  C1'    0.00  0.0  0
 OVE  CONST_25  H2    C2  N1  C6   180.00  0.0  0
 OVE  CONST_26  H61N  N6  C6  C5   180.00  0.0  0
 OVE  CONST_27  H62N  N6  C6  C5     0.00  0.0  0

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
 OVE  chir_02  C2'  O2'  C3'  C1'  positiv
 OVE  chir_03  C3'  O3'  C4'  C2'  positiv
 OVE  chir_04  C1'  O4'  N9   C2'  negativ
 OVE  chir_05  C4'  O4'  C3'  C5'  negativ
 OVE  chir_06  P    S2P  O3P  O2'  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
 OVE  plan-1  C1'   0.020
 OVE  plan-1  N9    0.020
 OVE  plan-1  C8    0.020
 OVE  plan-1  N7    0.020
 OVE  plan-1  C5    0.020
 OVE  plan-1  C6    0.020
 OVE  plan-1  N6    0.020
 OVE  plan-1  C4    0.020
 OVE  plan-1  N3    0.020
 OVE  plan-1  C2    0.020
 OVE  plan-1  N1    0.020
 OVE  plan-1  H2    0.020
 OVE  plan-1  H8    0.020
 OVE  plan-2  C6    0.020
 OVE  plan-2  N6    0.020
 OVE  plan-2  H61N  0.020
 OVE  plan-2  H62N  0.020

