# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:49:53 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: 5-(4,4-dimethyl-2-thioxo-1,4-dihydro-2H-3,1-benzoxazin-6-yl)-1-methyl-1H-pyrrole-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c(ccc1c2ccc3NC(=S)OC(C)(C)c3c2)C#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
 T98  T98  5-(4,4-dimethyl-2-thioxo-1,4-dihydro-2H-3,1-benzoxazin-6-yl)-1-methyl-1H-pyrrole-2-carbonitrile  ligand  36  21  .  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_T98
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
 T98  C1    C  CH3   0  -0.670  -2.0646  -2.4604   1.2133
 T98  C2    C  CT    0   0.115  -2.3817  -1.4013   0.1755
 T98  C3    C  CR6   0   0.115  -1.2524  -0.4353  -0.0670
 T98  C4    C  CR16  0  -0.385   0.0861  -0.7772  -0.0123
 T98  C5    C  CR6   0   0.054   1.0807   0.1434  -0.3487
 T98  C6    C  CR16  0  -0.299   0.6987   1.4254  -0.7482
 T98  C7    C  CR16  0  -0.302  -0.6351   1.7897  -0.7810
 T98  C8    C  CR6   0   0.351  -1.6044   0.8579  -0.4366
 T98  N1    N  NH1   0  -0.686  -2.9547   1.1927  -0.4356
 T98  C9    C  C     0   0.378  -3.8832   0.4982   0.2395
 T98  S1    S  S1    0  -0.352  -5.4192   1.0608   0.4912
 T98  O1    O  O2    0  -0.429  -3.5101  -0.6619   0.7370
 T98  C10   C  CR5   0   0.348   2.4792  -0.2836  -0.3291
 T98  C11   C  CR15  0  -0.382   3.0065  -1.4762  -0.8035
 T98  C12   C  CR15  0  -0.301   4.3892  -1.4404  -0.6040
 T98  C13   C  CR5   0   0.280   4.6693  -0.2267  -0.0050
 T98  N2    N  NR5   0  -0.507   3.4984   0.4677   0.1622
 T98  C14   C  CH3   0  -0.555   3.3985   1.7567   0.8178
 T98  C15   C  CSP   0  -0.007   5.9154   0.2845   0.4005
 T98  N3    N  NS    0  -0.253   6.9474   0.6885   0.7262
 T98  C16   C  CH3   0  -0.645  -2.8304  -2.0278  -1.1402
 T98  H11A  H  HCH3  0   0.261  -2.9415  -3.0808   1.3990
 T98  H12A  H  HCH3  0   0.246  -1.2731  -3.1163   0.8551
 T98  H13   H  HCH3  0   0.256  -1.7420  -2.0149   2.1540
 T98  H4    H  HCR6  0   0.262   0.3745  -1.7738   0.2964
 T98  H6    H  HCR6  0   0.272   1.4420   2.1498  -1.0534
 T98  H7    H  HCR6  0   0.284  -0.9206   2.7899  -1.0802
 T98  HN1   H  HNH1  0   0.429  -3.2328   2.0967  -0.7888
 T98  H11   H  HCR5  0   0.267   2.4414  -2.2673  -1.2697
 T98  H12   H  HCR5  0   0.274   5.1147  -2.1939  -0.8648
 T98  H141  H  HCH3  0   0.269   3.5117   2.5733   0.1064
 T98  H142  H  HCH3  0   0.280   2.4354   1.8439   1.3121
 T98  H143  H  HCH3  0   0.280   4.1732   1.8416   1.5757
 T98  H161  H  HCH3  0   0.248  -3.1132  -1.2749  -1.8769
 T98  H162  H  HCH3  0   0.252  -2.0102  -2.6075  -1.5629
 T98  H163  H  HCH3  0   0.254  -3.6755  -2.6983  -0.9813

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
 T98  C1   C2    single    1.516  0.020  1.516
 T98  C1   H11A  single    0.970  0.020  1.090
 T98  C1   H12A  single    0.970  0.020  1.090
 T98  C1   H13   single    0.970  0.020  1.090
 T98  C2   C3    single    1.506  0.020  1.506
 T98  C2   O1    single    1.461  0.020  1.461
 T98  C2   C16   single    1.525  0.020  1.525
 T98  C3   C4    aromatic  1.383  0.020  1.383
 T98  C3   C8    aromatic  1.390  0.020  1.390
 T98  C4   C5    aromatic  1.396  0.020  1.396
 T98  C4   H4    single    0.930  0.020  1.080
 T98  C5   C6    aromatic  1.396  0.020  1.396
 T98  C5   C10   single    1.462  0.020  1.462
 T98  C6   C7    aromatic  1.383  0.020  1.383
 T98  C6   H6    single    0.930  0.020  1.080
 T98  C7   C8    aromatic  1.388  0.020  1.388
 T98  C7   H7    single    0.930  0.020  1.080
 T98  C8   N1    single    1.391  0.020  1.391
 T98  N1   C9    single    1.342  0.020  1.342
 T98  N1   HN1   single    0.860  0.020  1.020
 T98  C9   S1    double    1.655  0.020  1.655
 T98  C9   O1    single    1.316  0.020  1.316
 T98  C10  C11   aromatic  1.388  0.020  1.388
 T98  C10  N2    aromatic  1.358  0.020  1.358
 T98  C11  C12   aromatic  1.398  0.020  1.398
 T98  C11  H11   single    0.930  0.020  1.080
 T98  C12  C13   aromatic  1.382  0.020  1.382
 T98  C12  H12   single    0.930  0.020  1.080
 T98  C13  N2    aromatic  1.372  0.020  1.372
 T98  C13  C15   single    1.407  0.020  1.407
 T98  N2   C14   single    1.450  0.020  1.450
 T98  C14  H141  single    0.970  0.020  1.090
 T98  C14  H142  single    0.970  0.020  1.090
 T98  C14  H143  single    0.970  0.020  1.090
 T98  C15  N3    triple    1.155  0.020  1.155
 T98  C16  H161  single    0.970  0.020  1.090
 T98  C16  H162  single    0.970  0.020  1.090
 T98  C16  H163  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
 T98  H13   C1   H12A  108.37  3.000
 T98  H13   C1   H11A  108.89  3.000
 T98  H12A  C1   H11A  107.34  3.000
 T98  H13   C1   C2    111.55  3.000
 T98  H12A  C1   C2    110.35  3.000
 T98  H11A  C1   C2    110.23  3.000
 T98  C16   C2   O1    108.19  3.000
 T98  C16   C2   C3    110.20  3.000
 T98  O1    C2   C3    108.45  3.000
 T98  C16   C2   C1    111.42  3.000
 T98  O1    C2   C1    104.59  3.000
 T98  C3    C2   C1    113.67  3.000
 T98  C8    C3   C4    119.05  3.000
 T98  C8    C3   C2    116.73  3.000
 T98  C4    C3   C2    124.13  3.000
 T98  H4    C4   C5    119.08  3.000
 T98  H4    C4   C3    119.79  3.000
 T98  C5    C4   C3    121.13  3.000
 T98  C10   C5   C6    122.25  3.000
 T98  C10   C5   C4    119.04  3.000
 T98  C6    C5   C4    118.65  3.000
 T98  H6    C6   C7    118.65  3.000
 T98  H6    C6   C5    120.51  3.000
 T98  C7    C6   C5    120.84  3.000
 T98  H7    C7   C8    120.32  3.000
 T98  H7    C7   C6    120.29  3.000
 T98  C8    C7   C6    119.39  3.000
 T98  N1    C8   C7    121.09  3.000
 T98  N1    C8   C3    118.00  3.000
 T98  C7    C8   C3    120.91  3.000
 T98  HN1   N1   C9    116.67  3.000
 T98  HN1   N1   C8    118.86  3.000
 T98  C9    N1   C8    123.19  3.000
 T98  O1    C9   S1    120.34  3.000
 T98  O1    C9   N1    116.76  3.000
 T98  S1    C9   N1    122.88  3.000
 T98  C9    O1   C2    121.31  3.000
 T98  N2    C10  C11   108.30  3.000
 T98  N2    C10  C5    124.12  3.000
 T98  C11   C10  C5    127.58  3.000
 T98  H11   C11  C12   126.80  3.000
 T98  H11   C11  C10   125.40  3.000
 T98  C12   C11  C10   107.77  3.000
 T98  H12   C12  C13   125.61  3.000
 T98  H12   C12  C11   127.84  3.000
 T98  C13   C12  C11   106.55  3.000
 T98  C15   C13  N2    122.49  3.000
 T98  C15   C13  C12   128.58  3.000
 T98  N2    C13  C12   108.93  3.000
 T98  C14   N2   C13   124.34  3.000
 T98  C14   N2   C10   127.14  3.000
 T98  C13   N2   C10   108.45  3.000
 T98  H143  C14  H142  107.96  3.000
 T98  H143  C14  H141  108.83  3.000
 T98  H142  C14  H141  109.23  3.000
 T98  H143  C14  N2    109.61  3.000
 T98  H142  C14  N2    109.77  3.000
 T98  H141  C14  N2    111.36  3.000
 T98  N3    C15  C13   180.00  3.000
 T98  H163  C16  H162  108.22  3.000
 T98  H163  C16  H161  108.78  3.000
 T98  H162  C16  H161  107.48  3.000
 T98  H163  C16  C2    110.79  3.000
 T98  H162  C16  C2    109.38  3.000
 T98  H161  C16  C2    112.06  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
 T98  CONST_01  C6    C5   C4   C3     0.00   0.0  0
 T98  CONST_02  C10   C5   C4   C3   180.00   0.0  0
 T98  CONST_03  C6    C7   C8   C3     0.00   0.0  0
 T98  CONST_04  C7    C8   C3   C4     0.00   0.0  0
 T98  CONST_05  C7    C6   C5   C4     0.00   0.0  0
 T98  CONST_08  C8    C3   C4   C5     0.00   0.0  0
 T98  CONST_09  C8    C7   C6   C5     0.00   0.0  0
 T98  CONST_10  C12   C11  C10  C5   180.00   0.0  0
 T98  CONST_11  C13   N2   C10  C5   180.00   0.0  0
 T98  CONST_14  C10   C5   C6   C7   180.00   0.0  0
 T98  CONST_15  C13   C12  C11  C10    0.00   0.0  0
 T98  CONST_16  C12   C13  N2   C10    0.00   0.0  0
 T98  CONST_17  C13   N2   C10  C11    0.00   0.0  0
 T98  CONST_18  N2    C13  C12  C11    0.00   0.0  0
 T98  CONST_19  N2    C10  C11  C12    0.00   0.0  0
 T98  CONST_20  C14   N2   C10  C5     0.00   0.0  0
 T98  CONST_21  C15   C13  N2   C10  180.00   0.0  0
 T98  CONST_22  C14   N2   C10  C11  180.00   0.0  0
 T98  CONST_23  C15   C13  C12  C11  180.00   0.0  0
 T98  CONST_24  C14   N2   C13  C12  180.00   0.0  0
 T98  CONST_25  H4    C4   C3   C2     0.00   0.0  0
 T98  CONST_26  H7    C7   C8   C3   180.00   0.0  0
 T98  CONST_27  H6    C6   C5   C4   180.00   0.0  0
 T98  CONST_28  H11   C11  C10  C5     0.00   0.0  0
 T98  CONST_29  H12   C12  C11  C10  180.00   0.0  0
 T98  Var_01    N1    C9   O1   C2   -23.47  30.0  1
 T98  Var_02    C9    N1   C8   C3    19.39  30.0  1
 T98  Var_03    O1    C2   C3   C4   150.00  30.0  1
 T98  Var_04    O1    C9   N1   C8   -11.01  30.0  1
 T98  Var_05    H11A  C1   C2   C3   175.76  30.0  3
 T98  Var_06    H161  C16  C2   C3   -55.96  30.0  3
 T98  Var_07    H141  C14  N2   C10  -92.83  30.0  2

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
 T98  plan-1  C5   0.020
 T98  plan-1  C10  0.020
 T98  plan-1  C11  0.020
 T98  plan-1  C12  0.020
 T98  plan-1  C13  0.020
 T98  plan-1  N2   0.020
 T98  plan-1  C14  0.020
 T98  plan-1  C15  0.020
 T98  plan-1  N3   0.020
 T98  plan-1  H11  0.020
 T98  plan-1  H12  0.020
 T98  plan-2  C2   0.020
 T98  plan-2  C3   0.020
 T98  plan-2  C4   0.020
 T98  plan-2  C5   0.020
 T98  plan-2  C6   0.020
 T98  plan-2  C7   0.020
 T98  plan-2  C8   0.020
 T98  plan-2  N1   0.020
 T98  plan-2  C10  0.020
 T98  plan-2  H4   0.020
 T98  plan-2  H6   0.020
 T98  plan-2  H7   0.020
 T98  plan-3  C8   0.020
 T98  plan-3  N1   0.020
 T98  plan-3  C9   0.020
 T98  plan-3  HN1  0.020
 T98  plan-4  N1   0.020
 T98  plan-4  C9   0.020
 T98  plan-4  S1   0.020
 T98  plan-4  O1   0.020

