# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 18:35:31 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: 4,5-dihydrobenzo[g][1]benzothiole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1sc2c(CCc3ccccc23)c1
#
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
 U4T  U4T  "4H,5H-naphtho[1,2-b]thiophene-2-carboxylic acid"  ligand  25  16  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U4T
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
 U4T  C13  C  CR16   0  -0.332   0.8341  -4.8844  4.4437
 U4T  C15  C  CR16   0  -0.258  -1.0746  -6.2625  4.9186
 U4T  C01  C  CR6    0   0.045   0.9895  -6.6128  6.1302
 U4T  C02  C  CH2    0  -0.518   1.7823  -7.2924  7.2164
 U4T  C03  C  CH2    0  -0.503   3.2583  -7.4468  6.8593
 U4T  C04  C  CR5    0   0.162   3.8014  -6.1447  6.3555
 U4T  C05  C  CR15   0  -0.251   5.1307  -5.6631  6.4481
 U4T  C06  C  CR5    0  -0.324   5.3065  -4.4507  5.8454
 U4T  C07  C  C      0   0.393   6.5406  -3.5970  5.7242
 U4T  C11  C  CR5    0  -0.295   2.9810  -5.2810  5.6747
 U4T  C12  C  CR6    0   0.167   1.5833  -5.5697  5.3992
 U4T  C14  C  CR16   0  -0.255  -0.4895  -5.2238  4.2078
 U4T  C16  C  CR16   0  -0.310  -0.3324  -6.9483  5.8732
 U4T  O08  O  O      0  -0.594   6.3838  -2.5299  5.1001
 U4T  O09  O  OC    -1  -0.578   7.5741  -4.0424  6.2522
 U4T  S10  S  S2     0   0.204   3.8367  -3.8801  5.1531
 U4T  H1   H  HCR6   0   0.245   1.2887  -4.0846  3.8703
 U4T  H2   H  HCR6   0   0.251  -2.1043  -6.5392  4.7330
 U4T  H3   H  HCH2   0   0.249   1.7069  -6.6869  8.1269
 U4T  H4   H  HCH2   0   0.254   1.3424  -8.2625  7.4519
 U4T  H5   H  HCH2   0   0.246   3.3819  -8.2188  6.0916
 U4T  H6   H  HCH2   0   0.254   3.8191  -7.7869  7.7312
 U4T  H7   H  HCR5   0   0.247   5.9302  -6.1944  6.9467
 U4T  H8   H  HCR6   0   0.253  -1.0592  -4.6832  3.4632
 U4T  H9   H  HCR6   0   0.247  -0.7904  -7.7565  6.4318

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
 U4T  C14  C13  aromatic  1.387  0.020  1.387
 U4T  C14  C15  aromatic  1.388  0.020  1.388
 U4T  C13  C12  aromatic  1.394  0.020  1.394
 U4T  C15  C16  aromatic  1.390  0.020  1.390
 U4T  S10  C11  aromatic  1.722  0.020  1.722
 U4T  S10  C06  aromatic  1.722  0.020  1.722
 U4T  O08  C07  deloc     1.246  0.020  1.246
 U4T  C12  C11  aromatic  1.454  0.020  1.454
 U4T  C12  C01  aromatic  1.405  0.020  1.405
 U4T  C11  C04  aromatic  1.372  0.020  1.372
 U4T  C07  C06  single    1.505  0.020  1.505
 U4T  C07  O09  deloc     1.243  0.020  1.243
 U4T  C06  C05  aromatic  1.365  0.020  1.365
 U4T  C16  C01  aromatic  1.388  0.020  1.388
 U4T  C01  C02  single    1.507  0.020  1.507
 U4T  C04  C05  aromatic  1.417  0.020  1.417
 U4T  C04  C03  single    1.498  0.020  1.498
 U4T  C03  C02  single    1.526  0.020  1.526
 U4T  C13  H1   single    0.930  0.020  1.080
 U4T  C15  H2   single    0.930  0.020  1.080
 U4T  C02  H3   single    0.970  0.020  1.090
 U4T  C02  H4   single    0.970  0.020  1.090
 U4T  C03  H5   single    0.970  0.020  1.090
 U4T  C03  H6   single    0.970  0.020  1.090
 U4T  C05  H7   single    0.930  0.020  1.080
 U4T  C14  H8   single    0.930  0.020  1.080
 U4T  C16  H9   single    0.930  0.020  1.080

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
 U4T  H1   C13  C14  119.40  3.000
 U4T  H1   C13  C12  119.99  3.000
 U4T  C14  C13  C12  120.61  3.000
 U4T  H2   C15  C16  119.97  3.000
 U4T  H2   C15  C14  120.30  3.000
 U4T  C16  C15  C14  119.73  3.000
 U4T  C16  C01  C12  119.05  3.000
 U4T  C16  C01  C02  121.71  3.000
 U4T  C12  C01  C02  119.17  3.000
 U4T  H4   C02  H3   106.51  3.000
 U4T  H4   C02  C03  110.52  3.000
 U4T  H3   C02  C03  108.47  3.000
 U4T  H4   C02  C01  110.16  3.000
 U4T  H3   C02  C01  108.27  3.000
 U4T  C03  C02  C01  112.69  3.000
 U4T  H6   C03  H5   106.40  3.000
 U4T  H6   C03  C04  110.70  3.000
 U4T  H5   C03  C04  109.62  3.000
 U4T  H6   C03  C02  109.97  3.000
 U4T  H5   C03  C02  110.14  3.000
 U4T  C04  C03  C02  109.96  3.000
 U4T  C11  C04  C05  112.30  3.000
 U4T  C05  C04  C03  127.85  3.000
 U4T  C11  C04  C03  119.82  3.000
 U4T  H7   C05  C06  122.99  3.000
 U4T  H7   C05  C04  123.82  3.000
 U4T  C06  C05  C04  113.19  3.000
 U4T  S10  C06  C07  118.65  3.000
 U4T  C07  C06  C05  130.14  3.000
 U4T  S10  C06  C05  111.21  3.000
 U4T  O09  C07  O08  128.62  3.000
 U4T  O09  C07  C06  116.37  3.000
 U4T  O08  C07  C06  115.01  3.000
 U4T  S10  C11  C12  125.58  3.000
 U4T  C12  C11  C04  122.95  3.000
 U4T  S10  C11  C04  111.42  3.000
 U4T  C11  C12  C01  117.07  3.000
 U4T  C01  C12  C13  119.62  3.000
 U4T  C11  C12  C13  123.29  3.000
 U4T  H8   C14  C15  120.28  3.000
 U4T  H8   C14  C13  119.82  3.000
 U4T  C15  C14  C13  119.90  3.000
 U4T  H9   C16  C01  119.16  3.000
 U4T  H9   C16  C15  119.74  3.000
 U4T  C01  C16  C15  121.09  3.000
 U4T  C11  S10  C06   91.88  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
 U4T  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 U4T  CONST_02  S10  C11  C12  C13     0.00   0.0  0
 U4T  CONST_04  C16  C01  C12  C13     0.00   0.0  0
 U4T  CONST_05  C12  C13  C14  C15     0.00   0.0  0
 U4T  CONST_06  C12  C01  C16  C15     0.00   0.0  0
 U4T  CONST_07  C14  C13  C12  C01     0.00   0.0  0
 U4T  CONST_08  S10  C11  C12  C01   180.00   0.0  0
 U4T  CONST_10  C14  C15  C16  C01     0.00   0.0  0
 U4T  CONST_12  C06  S10  C11  C04     0.00   0.0  0
 U4T  CONST_13  S10  C06  C05  C04     0.00   0.0  0
 U4T  CONST_14  C11  S10  C06  C05     0.00   0.0  0
 U4T  CONST_15  S10  C11  C04  C05     0.00   0.0  0
 U4T  CONST_16  C12  C11  C04  C05   180.00   0.0  0
 U4T  CONST_17  C12  C11  S10  C06   180.00   0.0  0
 U4T  CONST_18  C11  C04  C05  C06     0.00   0.0  0
 U4T  CONST_19  C14  C13  C12  C11   180.00   0.0  0
 U4T  CONST_20  C16  C01  C12  C11   180.00   0.0  0
 U4T  CONST_21  C07  C06  C05  C04   180.00   0.0  0
 U4T  CONST_22  C11  S10  C06  C07   180.00   0.0  0
 U4T  CONST_23  H2   C15  C14  C13   180.00   0.0  0
 U4T  CONST_24  H1   C13  C14  C15   180.00   0.0  0
 U4T  CONST_25  H1   C13  C12  C01   180.00   0.0  0
 U4T  CONST_26  H2   C15  C16  C01   180.00   0.0  0
 U4T  CONST_27  H9   C16  C01  C02     0.00   0.0  0
 U4T  CONST_28  H7   C05  C04  C03     0.00   0.0  0
 U4T  CONST_29  H1   C13  C12  C11     0.00   0.0  0
 U4T  CONST_30  H7   C05  C04  C11   180.00   0.0  0
 U4T  CONST_31  H8   C14  C13  C12   180.00   0.0  0
 U4T  CONST_32  H9   C16  C01  C12   180.00   0.0  0
 U4T  CONST_33  H9   C16  C15  C14   180.00   0.0  0
 U4T  CONST_34  H8   C14  C15  C16   180.00   0.0  0
 U4T  CONST_35  H7   C05  C06  S10   180.00   0.0  0
 U4T  Var_01    C11  C04  C03  C02   -31.48  30.0  1
 U4T  Var_02    C05  C04  C03  C02   150.83  30.0  1
 U4T  Var_03    C12  C01  C02  C03   -37.02  30.0  1
 U4T  Var_04    C16  C01  C02  C03   145.98  30.0  1
 U4T  Var_05    H5   C03  C02  C01   -72.48  30.0  1
 U4T  Var_06    H6   C03  C02  C01   170.57  30.0  1
 U4T  Var_07    H3   C02  C03  C04   -71.42  30.0  1
 U4T  Var_08    H4   C02  C03  C04   172.16  30.0  1
 U4T  Var_09    H5   C03  C04  C05   -87.95  30.0  1
 U4T  Var_10    H6   C03  C04  C05    29.12  30.0  1
 U4T  Var_11    H5   C03  C04  C11    89.74  30.0  1
 U4T  Var_12    H6   C03  C04  C11  -153.19  30.0  1
 U4T  Var_13    H3   C02  C01  C12    82.96  30.0  1
 U4T  Var_14    H4   C02  C01  C12  -160.94  30.0  1
 U4T  Var_15    H3   C02  C01  C16   -94.05  30.0  1
 U4T  Var_16    H4   C02  C01  C16    22.05  30.0  1
 U4T  Var_17    O08  C07  C06  C05   179.63  30.0  2
 U4T  Var_18    O09  C07  C06  C05    -0.30  30.0  2
 U4T  Var_19    S10  C06  C07  O08    -0.86  30.0  2
 U4T  Var_20    S10  C06  C07  O09   179.21  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
 U4T  plan-1  C06  0.020
 U4T  plan-1  C07  0.020
 U4T  plan-1  O08  0.020
 U4T  plan-1  O09  0.020
 U4T  plan-2  C03  0.020
 U4T  plan-2  C04  0.020
 U4T  plan-2  C05  0.020
 U4T  plan-2  C06  0.020
 U4T  plan-2  C07  0.020
 U4T  plan-2  C11  0.020
 U4T  plan-2  C12  0.020
 U4T  plan-2  S10  0.020
 U4T  plan-2  H7   0.020
 U4T  plan-3  C13  0.020
 U4T  plan-3  C15  0.020
 U4T  plan-3  C01  0.020
 U4T  plan-3  C02  0.020
 U4T  plan-3  C11  0.020
 U4T  plan-3  C12  0.020
 U4T  plan-3  C14  0.020
 U4T  plan-3  C16  0.020
 U4T  plan-3  H1   0.020
 U4T  plan-3  H2   0.020
 U4T  plan-3  H8   0.020
 U4T  plan-3  H9   0.020

