# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 22:44:27 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: (2~{S})-2-[5-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]furan-2-yl]-2,3,5,6,7,8-hexahydro-1~{H}-[1]benzothiolo[2,3-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [OH-][N+](=O)c1oc(cc1)[C@H]2NC(=O)c3c(N2)sc4CCCCc34
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 OTQ  OTQ  (2~{S})-2-[5-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]furan-2-yl]-2,3,5,6,7,8-hexahydro-1~{H}-[1]benzothiolo[2,3-d]pyrimidin-4-one  ligand  36  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OTQ
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
 OTQ  C1   C  CR5    0  -0.127  40.2033  19.8346  -4.1493
 OTQ  C2   C  CR5    0   0.199  39.8722  21.1581  -4.6047
 OTQ  C3   C  CR5    0  -0.283  40.2358  21.3636  -5.8946
 OTQ  C4   C  CH2    0  -0.473  40.0428  22.6177  -6.6836
 OTQ  C5   C  CH2    0  -0.445  39.7024  23.7676  -5.7365
 OTQ  C6   C  CH2    0  -0.447  38.6587  23.3396  -4.7123
 OTQ  C7   C  CH2    0  -0.491  39.1851  22.2272  -3.8075
 OTQ  N1   N  NH1    0  -0.666  41.2313  17.7970  -4.9291
 OTQ  N2   N  N      1   0.149  40.7347  12.4440  -3.1959
 OTQ  C8   C  C      0   0.535  40.1317  19.2936  -2.7962
 OTQ  C10  C  CR5    0   0.349  41.2088  15.8289  -3.5520
 OTQ  N    N  NH1    0  -0.678  40.5139  17.9819  -2.7107
 OTQ  C    C  CR5    0   0.072  40.7967  19.0753  -5.1287
 OTQ  O    O  O      0  -0.467  39.8383  19.9422  -1.8025
 OTQ  C11  C  CR15   0  -0.339  42.4975  15.5377  -3.2426
 OTQ  C12  C  CR15   0  -0.327  42.5652  14.1367  -3.0354
 OTQ  C13  C  CR5    0   0.524  41.2864  13.6922  -3.2389
 OTQ  C9   C  CH1    0   0.033  40.5172  17.1081  -3.8691
 OTQ  O1   O  O      0  -0.423  40.4600  14.6961  -3.5488
 OTQ  O2   O  O     -1  -0.535  41.5911  11.4899  -2.7355
 OTQ  O3   O  O      0  -0.414  39.5472  12.1769  -3.4090
 OTQ  S    S  S2     0   0.217  40.9773  19.9479  -6.5965
 OTQ  H1   H  HCH2   0   0.244  39.2392  22.4851  -7.4156
 OTQ  H2   H  HCH2   0   0.251  40.9419  22.8565  -7.2573
 OTQ  H3   H  HCH2   0   0.225  40.6087  24.0920  -5.2169
 OTQ  H4   H  HCH2   0   0.239  39.3460  24.6217  -6.3146
 OTQ  H5   H  HCH2   0   0.236  38.3536  24.1912  -4.1015
 OTQ  H6   H  HCH2   0   0.223  37.7618  22.9937  -5.2353
 OTQ  H7   H  HCH2   0   0.237  39.8838  22.6418  -3.0745
 OTQ  H8   H  HCH2   0   0.243  38.3678  21.7947  -3.2283
 OTQ  H9   H  HNH1   0   0.407  41.4027  17.2358  -5.7512
 OTQ  H10  H  HNH1   0   0.403  40.3923  17.5391  -1.8112
 OTQ  H11  H  HCR5   0   0.282  43.3099  16.2429  -3.1727
 OTQ  H12  H  HCR5   0   0.291  43.4291  13.5487  -2.7780
 OTQ  H13  H  HCH1   0   0.268  39.4843  16.8869  -4.1844
 OTQ  H14  H  H      0   0.488  41.7184  10.8577  -3.4620

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
 OTQ  C4   C5   single    1.528  0.020  1.528
 OTQ  C4   C3   single    1.494  0.020  1.494
 OTQ  S    C3   aromatic  1.746  0.020  1.746
 OTQ  S    C    aromatic  1.717  0.020  1.717
 OTQ  C5   C6   single    1.524  0.020  1.524
 OTQ  C3   C2   aromatic  1.356  0.020  1.356
 OTQ  O3   N2   double    1.236  0.020  1.236
 OTQ  C    N1   single    1.365  0.020  1.365
 OTQ  C    C1   aromatic  1.374  0.020  1.374
 OTQ  C6   C7   single    1.527  0.020  1.527
 OTQ  C2   C1   aromatic  1.438  0.020  1.438
 OTQ  C2   C7   single    1.500  0.020  1.500
 OTQ  N1   C9   single    1.452  0.020  1.452
 OTQ  N2   O2   single    1.362  0.020  1.362
 OTQ  N2   C13  single    1.365  0.020  1.365
 OTQ  O1   C13  aromatic  1.337  0.020  1.337
 OTQ  O1   C10  aromatic  1.358  0.020  1.358
 OTQ  C1   C8   single    1.459  0.020  1.459
 OTQ  C13  C12  aromatic  1.369  0.020  1.369
 OTQ  C9   C10  single    1.488  0.020  1.488
 OTQ  C9   N    single    1.451  0.020  1.451
 OTQ  C10  C11  aromatic  1.357  0.020  1.357
 OTQ  C8   N    single    1.369  0.020  1.369
 OTQ  C8   O    double    1.222  0.020  1.222
 OTQ  C12  C11  aromatic  1.418  0.020  1.418
 OTQ  C4   H1   single    0.970  0.020  1.090
 OTQ  C4   H2   single    0.970  0.020  1.090
 OTQ  C5   H3   single    0.970  0.020  1.090
 OTQ  C5   H4   single    0.970  0.020  1.090
 OTQ  C6   H5   single    0.970  0.020  1.090
 OTQ  C6   H6   single    0.970  0.020  1.090
 OTQ  C7   H7   single    0.970  0.020  1.090
 OTQ  C7   H8   single    0.970  0.020  1.090
 OTQ  N1   H9   single    0.890  0.020  1.040
 OTQ  N    H10  single    0.890  0.020  1.040
 OTQ  C11  H11  single    0.930  0.020  1.080
 OTQ  C12  H12  single    0.930  0.020  1.080
 OTQ  C9   H13  single    0.970  0.020  1.090
 OTQ  O2   H14  single    0.850  0.020  0.980

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
 OTQ  C    C1   C8   118.51  3.000
 OTQ  C8   C1   C2   128.58  3.000
 OTQ  C    C1   C2   112.47  3.000
 OTQ  C7   C2   C3   121.35  3.000
 OTQ  C7   C2   C1   126.37  3.000
 OTQ  C3   C2   C1   112.27  3.000
 OTQ  S    C3   C4   121.55  3.000
 OTQ  S    C3   C2   111.93  3.000
 OTQ  C4   C3   C2   126.51  3.000
 OTQ  H2   C4   H1   106.22  3.000
 OTQ  H2   C4   C5   110.13  3.000
 OTQ  H1   C4   C5   110.00  3.000
 OTQ  H2   C4   C3   110.75  3.000
 OTQ  H1   C4   C3   110.25  3.000
 OTQ  C5   C4   C3   109.46  3.000
 OTQ  H4   C5   H3   106.87  3.000
 OTQ  H4   C5   C6   110.63  3.000
 OTQ  H3   C5   C6   109.36  3.000
 OTQ  H4   C5   C4   109.47  3.000
 OTQ  H3   C5   C4   109.45  3.000
 OTQ  C6   C5   C4   110.97  3.000
 OTQ  H6   C6   H5   106.56  3.000
 OTQ  H6   C6   C7   109.59  3.000
 OTQ  H5   C6   C7   109.46  3.000
 OTQ  H6   C6   C5   109.20  3.000
 OTQ  H5   C6   C5   110.39  3.000
 OTQ  C7   C6   C5   111.51  3.000
 OTQ  H8   C7   H7   105.84  3.000
 OTQ  H8   C7   C6   110.18  3.000
 OTQ  H7   C7   C6   109.93  3.000
 OTQ  H8   C7   C2   110.04  3.000
 OTQ  H7   C7   C2   109.48  3.000
 OTQ  C6   C7   C2   111.23  3.000
 OTQ  H9   N1   C9   114.46  3.000
 OTQ  H9   N1   C    117.08  3.000
 OTQ  C9   N1   C    113.24  3.000
 OTQ  O3   N2   O2   120.73  3.000
 OTQ  O2   N2   C13  113.38  3.000
 OTQ  O3   N2   C13  125.49  3.000
 OTQ  O    C8   N    121.65  3.000
 OTQ  O    C8   C1   124.67  3.000
 OTQ  N    C8   C1   113.55  3.000
 OTQ  O1   C10  C9   117.47  3.000
 OTQ  C9   C10  C11  132.41  3.000
 OTQ  O1   C10  C11  110.13  3.000
 OTQ  H10  N    C9   116.57  3.000
 OTQ  H10  N    C8   116.24  3.000
 OTQ  C9   N    C8   121.85  3.000
 OTQ  S    C    N1   124.58  3.000
 OTQ  N1   C    C1   123.42  3.000
 OTQ  S    C    C1   111.95  3.000
 OTQ  H11  C11  C12  126.93  3.000
 OTQ  H11  C11  C10  126.17  3.000
 OTQ  C12  C11  C10  106.90  3.000
 OTQ  H12  C12  C13  127.44  3.000
 OTQ  H12  C12  C11  127.81  3.000
 OTQ  C13  C12  C11  104.75  3.000
 OTQ  O1   C13  C12  111.60  3.000
 OTQ  C12  C13  N2   132.03  3.000
 OTQ  O1   C13  N2   116.37  3.000
 OTQ  H13  C9   N    110.30  3.000
 OTQ  H13  C9   C10  108.90  3.000
 OTQ  N    C9   C10  110.40  3.000
 OTQ  H13  C9   N1   110.33  3.000
 OTQ  N    C9   N1   107.35  3.000
 OTQ  C10  C9   N1   109.56  3.000
 OTQ  C13  O1   C10  106.63  3.000
 OTQ  H14  O2   N2   106.58  3.000
 OTQ  C    S    C3    91.36  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
 OTQ  CONST_01  C3   S    C    C1      0.00   0.0  0
 OTQ  CONST_02  S    C3   C2   C1      0.00   0.0  0
 OTQ  CONST_03  C    S    C3   C2      0.00   0.0  0
 OTQ  CONST_04  S    C    C1   C2      0.00   0.0  0
 OTQ  CONST_05  C    C1   C2   C3      0.00   0.0  0
 OTQ  CONST_06  C12  C13  O1   C10     0.00   0.0  0
 OTQ  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 OTQ  CONST_08  C13  O1   C10  C11     0.00   0.0  0
 OTQ  CONST_09  O1   C13  C12  C11     0.00   0.0  0
 OTQ  CONST_10  O1   C10  C11  C12     0.00   0.0  0
 OTQ  CONST_11  C9   C10  C11  C12   180.00   0.0  0
 OTQ  CONST_12  C9   C10  O1   C13   180.00   0.0  0
 OTQ  CONST_14  C10  O1   C13  N2    180.00   0.0  0
 OTQ  CONST_15  C11  C12  C13  N2    180.00   0.0  0
 OTQ  CONST_17  H12  C12  C11  C10   180.00   0.0  0
 OTQ  CONST_18  H11  C11  C12  C13   180.00   0.0  0
 OTQ  CONST_19  H10  N    C8   C1    180.00   0.0  0
 OTQ  CONST_20  O3   N2   C13  C12   180.00   0.0  0
 OTQ  CONST_21  O2   N2   C13  C12     0.00   0.0  0
 OTQ  CONST_22  O3   N2   C13  O1      0.00   0.0  0
 OTQ  CONST_23  O2   N2   C13  O1    180.00   0.0  0
 OTQ  Var_01    C9   N1   C    C1     26.23  30.0  1
 OTQ  Var_02    C6   C7   C2   C1   -164.22  30.0  1
 OTQ  Var_03    C5   C4   C3   C2     14.57  30.0  1
 OTQ  Var_04    N    C8   C1   C2    179.54  30.0  1
 OTQ  Var_05    C5   C6   C7   C2    -45.90  30.0  1
 OTQ  Var_06    C6   C5   C4   C3    -45.10  30.0  1
 OTQ  Var_07    C7   C6   C5   C4     63.41  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
 OTQ  chir_01  C9  N1  C10  N  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
 OTQ  plan-1  N2   0.020
 OTQ  plan-1  C10  0.020
 OTQ  plan-1  C11  0.020
 OTQ  plan-1  C12  0.020
 OTQ  plan-1  C13  0.020
 OTQ  plan-1  C9   0.020
 OTQ  plan-1  O1   0.020
 OTQ  plan-1  H11  0.020
 OTQ  plan-1  H12  0.020
 OTQ  plan-2  C1   0.020
 OTQ  plan-2  C2   0.020
 OTQ  plan-2  C3   0.020
 OTQ  plan-2  C4   0.020
 OTQ  plan-2  C7   0.020
 OTQ  plan-2  N1   0.020
 OTQ  plan-2  C8   0.020
 OTQ  plan-2  C    0.020
 OTQ  plan-2  S    0.020
 OTQ  plan-3  N2   0.020
 OTQ  plan-3  C13  0.020
 OTQ  plan-3  O2   0.020
 OTQ  plan-3  O3   0.020
 OTQ  plan-4  C1   0.020
 OTQ  plan-4  C8   0.020
 OTQ  plan-4  N    0.020
 OTQ  plan-4  O    0.020
 OTQ  plan-4  C9   0.020
 OTQ  plan-4  H10  0.020

