# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 13:58:31 2022
#   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  36  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  OP    -1  -0.755  -0.2050   3.5672  -0.4200
 OVE  P     P  P      0   1.170   0.1825   2.3680   0.3750
 OVE  S2P   S  S2     0  -0.499   1.7027   3.0689   1.7256
 OVE  O3P   O  O      0  -0.739  -0.7615   1.5118   1.1499
 OVE  O2'   O  O2     0  -0.604   1.0664   1.4359  -0.6585
 OVE  C2'   C  CR15   0  -0.011   1.5066   0.1803  -0.2478
 OVE  C3'   C  CR15   0  -0.020   2.9476  -0.1298  -0.6263
 OVE  O3'   O  OH1    0  -0.666   3.1575   0.3150  -1.9391
 OVE  C1'   C  CR15   0   0.212   0.7540  -0.9583  -0.9444
 OVE  O4'   O  O      0  -0.496   1.6139  -2.0586  -0.9074
 OVE  C4'   C  CR15   0  -0.051   2.9329  -1.6570  -0.5179
 OVE  C5'   C  CH2    0  -0.156   3.2596  -2.1401   0.8824
 OVE  O5'   O  OH1    0  -0.667   3.0919  -3.5342   0.9265
 OVE  N9    N  NR5    0  -0.531  -0.4874  -1.2998  -0.2951
 OVE  C8    C  CR15   0   0.100  -0.6451  -2.0006   0.8684
 OVE  N7    N  N      0  -0.457  -1.8758  -2.0342   1.2870
 OVE  C5    C  CR56   0  -0.003  -2.5688  -1.2983   0.3613
 OVE  C6    C  CR6    0   0.447  -3.9224  -0.9407   0.2445
 OVE  N6    N  NH2    0  -0.820  -4.8525  -1.3351   1.1195
 OVE  C4    C  CR56   0   0.524  -1.7209  -0.8264  -0.6277
 OVE  N3    N  N      0  -0.461  -2.0656  -0.0817  -1.6749
 OVE  C2    C  CR16   0   0.037  -3.3575   0.1907  -1.6767
 OVE  N1    N  N      0  -0.477  -4.2842  -0.1832  -0.7967
 OVE  H2P   H  HSH1   0   0.221   1.6287   2.0783   2.6218
 OVE  H2'   H  HCR5   0   0.245   1.4091   0.0501   0.8370
 OVE  H3'   H  HCR5   0   0.253   3.6607   0.3203   0.0759
 OVE  H1'   H  HCR5   0   0.262   0.5012  -0.6730  -1.9714
 OVE  HA    H  HOH1   0   0.459   4.0645   0.1119  -2.1891
 OVE  H4'   H  HCR5   0   0.262   3.6402  -2.1098  -1.2199
 OVE  H5'1  H  HCH2   0   0.220   4.2929  -1.8415   1.1018
 OVE  H5'2  H  HCH2   0   0.195   2.6218  -1.6350   1.6211
 OVE  H5'   H  HOH1   0   0.459   3.3176  -3.8345   1.8114
 OVE  H2    H  HCR6   0   0.247  -3.7179   0.7975  -2.5009
 OVE  H8    H  HCR5   0   0.294   0.1844  -2.4979   1.3484
 OVE  H61N  H  HNH2   0   0.408  -4.5960  -1.8307   1.9551
 OVE  H62N  H  HNH2   0   0.400  -5.7914  -0.9830   1.0486

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     deloc     1.490  0.020  1.490
 OVE  P    S2P   single    2.151  0.020  2.151
 OVE  P    O3P   deloc     1.492  0.020  1.492
 OVE  P    O2'   single    1.649  0.020  1.649
 OVE  O2'  C2'   single    1.393  0.020  1.393
 OVE  C2'  C3'   single    1.522  0.020  1.522
 OVE  C2'  C1'   single    1.532  0.020  1.532
 OVE  C3'  O3'   single    1.402  0.020  1.402
 OVE  C3'  C4'   single    1.531  0.020  1.531
 OVE  C1'  O4'   single    1.397  0.020  1.397
 OVE  C1'  N9    single    1.442  0.020  1.442
 OVE  O4'  C4'   single    1.433  0.020  1.433
 OVE  C4'  C5'   single    1.517  0.020  1.517
 OVE  C5'  O5'   single    1.405  0.020  1.405
 OVE  N9   C8    aromatic  1.367  0.020  1.367
 OVE  N9   C4    aromatic  1.362  0.020  1.362
 OVE  C8   N7    aromatic  1.300  0.020  1.300
 OVE  N7   C5    aromatic  1.371  0.020  1.371
 OVE  C5   C6    aromatic  1.405  0.020  1.405
 OVE  C5   C4    aromatic  1.386  0.020  1.386
 OVE  C6   N6    single    1.337  0.020  1.337
 OVE  C6   N1    aromatic  1.337  0.020  1.337
 OVE  C4   N3    aromatic  1.330  0.020  1.330
 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  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  O2'   P    O3P   109.90  3.000
 OVE  O2'   P    S2P   101.48  3.000
 OVE  O3P   P    S2P   107.94  3.000
 OVE  O2'   P    O1P   105.07  3.000
 OVE  O3P   P    O1P   125.07  3.000
 OVE  S2P   P    O1P   104.87  3.000
 OVE  H2P   S2P  P      98.06  3.000
 OVE  C2'   O2'  P     119.63  3.000
 OVE  H2'   C2'  C1'   108.53  3.000
 OVE  H2'   C2'  C3'   107.81  3.000
 OVE  C1'   C2'  C3'   101.57  3.000
 OVE  H2'   C2'  O2'   111.75  3.000
 OVE  C1'   C2'  O2'   112.37  3.000
 OVE  C3'   C2'  O2'   114.19  3.000
 OVE  H3'   C3'  C4'   111.72  3.000
 OVE  H3'   C3'  O3'   111.83  3.000
 OVE  C4'   C3'  O3'   112.59  3.000
 OVE  H3'   C3'  C2'   111.88  3.000
 OVE  C4'   C3'  C2'   100.16  3.000
 OVE  O3'   C3'  C2'   108.06  3.000
 OVE  HA    O3'  C3'   108.50  3.000
 OVE  H1'   C1'  N9    106.57  3.000
 OVE  H1'   C1'  O4'   111.84  3.000
 OVE  N9    C1'  O4'   109.36  3.000
 OVE  H1'   C1'  C2'   110.25  3.000
 OVE  N9    C1'  C2'   113.21  3.000
 OVE  O4'   C1'  C2'   105.72  3.000
 OVE  C4'   O4'  C1'   110.68  3.000
 OVE  H4'   C4'  C5'   108.73  3.000
 OVE  H4'   C4'  O4'   107.73  3.000
 OVE  C5'   C4'  O4'   111.10  3.000
 OVE  H4'   C4'  C3'   111.16  3.000
 OVE  C5'   C4'  C3'   112.40  3.000
 OVE  O4'   C4'  C3'   105.62  3.000
 OVE  H5'2  C5'  H5'1  106.67  3.000
 OVE  H5'2  C5'  O5'   111.45  3.000
 OVE  H5'1  C5'  O5'   112.09  3.000
 OVE  H5'2  C5'  C4'   110.43  3.000
 OVE  H5'1  C5'  C4'   107.50  3.000
 OVE  O5'   C5'  C4'   108.63  3.000
 OVE  H5'   O5'  C5'   108.11  3.000
 OVE  C4    N9   C8    106.34  3.000
 OVE  C4    N9   C1'   125.95  3.000
 OVE  C8    N9   C1'   127.15  3.000
 OVE  H8    C8   N7    124.90  3.000
 OVE  H8    C8   N9    121.71  3.000
 OVE  N7    C8   N9    113.35  3.000
 OVE  C5    N7   C8    104.32  3.000
 OVE  C4    C5   C6    116.33  3.000
 OVE  C4    C5   N7    110.82  3.000
 OVE  C6    C5   N7    132.84  3.000
 OVE  N1    C6   N6    119.25  3.000
 OVE  N1    C6   C5    118.00  3.000
 OVE  N6    C6   C5    122.75  3.000
 OVE  H62N  N6   H61N  118.03  3.000
 OVE  H62N  N6   C6    120.03  3.000
 OVE  H61N  N6   C6    120.82  3.000
 OVE  N3    C4   C5    126.44  3.000
 OVE  N3    C4   N9    128.41  3.000
 OVE  C5    C4   N9    105.15  3.000
 OVE  C2    N3   C4    111.72  3.000
 OVE  H2    C2   N1    115.34  3.000
 OVE  N1    C2   N3    128.47  3.000
 OVE  H2    C2   N3    116.19  3.000
 OVE  C2    N1   C6    119.03  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     0.00  0.0  0
 OVE  CONST_27  H62N  N6  C6  C5   180.00  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

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

