# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:49:25 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 4-{5-[(3-aminopropyl)carbamoyl]thiophen-2-yl}-1-benzothiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCNC(=O)c1sc(cc1)c2cccc3sc(cc23)C(O)=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
 OD4  OD4  '4-{5-[(3-aminopropyl)carbamoyl]thiophen-2-yl}-1-benzothiophene-2-carboxylic acid'  ligand  39  24  .  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_OD4
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
 OD4  C1   C  C      0   0.557   3.3631  -1.4607   0.8409
 OD4  C2   C  CR5    0  -0.326   1.9245  -1.7849   0.7159
 OD4  C3   C  CR5    0  -0.243  -0.5200  -1.8916   0.2674
 OD4  C4   C  CR15   0  -0.198  -0.0615  -2.9417   1.0178
 OD4  C5   C  CR15   0  -0.170   1.3247  -2.8774   1.2765
 OD4  C6   C  CR6    0   0.098  -1.8831  -1.6795  -0.2213
 OD4  C10  C  CR56   0  -0.231  -3.8434  -0.3146  -0.6586
 OD4  C11  C  CR56   0   0.214  -2.5309  -0.4271  -0.1547
 OD4  C12  C  CR5    0  -0.314  -2.9887   1.8111   0.2842
 OD4  C13  C  CR15   0  -0.298  -2.0746   0.8178   0.3897
 OD4  C14  C  C      0   0.405  -2.8970   3.2456   0.7373
 OD4  C15  C  CH2    0  -0.238   5.2150  -0.0270   0.1425
 OD4  C16  C  CH2    0  -0.488   5.4294   1.1959  -0.7331
 OD4  C17  C  CH2    0  -0.271   6.8736   1.6709  -0.6897
 OD4  N1   N  NH1    0  -0.670   3.8267  -0.4418   0.1028
 OD4  O1   O  O      0  -0.488   4.0759  -2.1108   1.5952
 OD4  S1   S  S2     0   0.240   0.7727  -0.8260  -0.1353
 OD4  C7   C  CR16   0  -0.317  -2.5751  -2.7561  -0.7577
 OD4  C8   C  CR16   0  -0.258  -3.8790  -2.6211  -1.2401
 OD4  C9   C  CR16   0  -0.291  -4.5230  -1.4004  -1.2036
 OD4  S2   S  S2     0   0.217  -4.4573   1.2936  -0.4739
 OD4  O2   O  O      0  -0.578  -1.8333   3.5903   1.2774
 OD4  O3   O  OC    -1  -0.592  -3.9140   3.9286   0.5152
 OD4  N2   N  NH2    0  -0.799   7.0568   2.8310  -1.5485
 OD4  H3   H  HCR5   0   0.271  -0.7080  -3.7245   1.3884
 OD4  H5   H  HCR5   0   0.274   1.8628  -3.6101   1.8601
 OD4  H8   H  HCR5   0   0.257  -1.1138   0.9705   0.8592
 OD4  H10  H  HCH2   0   0.235   5.8606  -0.8442  -0.1937
 OD4  H11  H  HCH2   0   0.236   5.4981   0.1977   1.1740
 OD4  H12  H  HCH2   0   0.234   5.1567   0.9682  -1.7678
 OD4  H13  H  HCH2   0   0.233   4.7703   2.0036  -0.3973
 OD4  H14  H  HCH2   0   0.194   7.1584   1.8485   0.3575
 OD4  H15  H  HCH2   0   0.218   7.5241   0.8704  -1.0524
 OD4  H16  H  HNH1   0   0.405   3.2297   0.0111  -0.5707
 OD4  H17  H  HCR6   0   0.260  -2.0854  -3.7192  -0.8242
 OD4  H18  H  HCR6   0   0.264  -4.3822  -3.4833  -1.6569
 OD4  H19  H  HCR6   0   0.270  -5.5297  -1.2915  -1.5857
 OD4  H21  H  HNH2   0   0.339   6.5387   3.6133  -1.1670
 OD4  H22  H  HNH2   0   0.348   8.0280   3.1140  -1.5275

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
 OD4  C8   C7   aromatic  1.397  0.020  1.397
 OD4  C8   C9   aromatic  1.381  0.020  1.381
 OD4  C7   C6   aromatic  1.388  0.020  1.388
 OD4  C9   C10  aromatic  1.392  0.020  1.392
 OD4  S1   C3   aromatic  1.723  0.020  1.723
 OD4  S1   C2   aromatic  1.724  0.020  1.724
 OD4  O1   C1   double    1.225  0.020  1.225
 OD4  C6   C3   single    1.463  0.020  1.463
 OD4  C6   C11  aromatic  1.412  0.020  1.412
 OD4  N2   C17  single    1.455  0.020  1.455
 OD4  C10  C11  aromatic  1.410  0.020  1.410
 OD4  C10  S2   aromatic  1.731  0.020  1.731
 OD4  C3   C4   aromatic  1.370  0.020  1.370
 OD4  C1   C2   single    1.480  0.020  1.480
 OD4  C1   N1   single    1.341  0.020  1.341
 OD4  C2   C5   aromatic  1.367  0.020  1.367
 OD4  C11  C13  aromatic  1.433  0.020  1.433
 OD4  C17  C16  single    1.521  0.020  1.521
 OD4  C15  N1   single    1.450  0.020  1.450
 OD4  C15  C16  single    1.519  0.020  1.519
 OD4  S2   C12  aromatic  1.732  0.020  1.732
 OD4  C4   C5   aromatic  1.412  0.020  1.412
 OD4  C13  C12  aromatic  1.354  0.020  1.354
 OD4  C12  C14  single    1.507  0.020  1.507
 OD4  C14  O2   deloc     1.242  0.020  1.242
 OD4  C14  O3   deloc     1.245  0.020  1.245
 OD4  C4   H3   single    0.930  0.020  1.080
 OD4  C5   H5   single    0.930  0.020  1.080
 OD4  C13  H8   single    0.930  0.020  1.080
 OD4  C15  H10  single    0.970  0.020  1.090
 OD4  C15  H11  single    0.970  0.020  1.090
 OD4  C16  H12  single    0.970  0.020  1.090
 OD4  C16  H13  single    0.970  0.020  1.090
 OD4  C17  H14  single    0.970  0.020  1.090
 OD4  C17  H15  single    0.970  0.020  1.090
 OD4  N1   H16  single    0.860  0.020  1.020
 OD4  C7   H17  single    0.930  0.020  1.080
 OD4  C8   H18  single    0.930  0.020  1.080
 OD4  C9   H19  single    0.930  0.020  1.080
 OD4  N2   H21  single    0.890  0.020  1.040
 OD4  N2   H22  single    0.890  0.020  1.040

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
 OD4  O1   C1   N1   122.76  3.000
 OD4  N1   C1   C2   117.13  3.000
 OD4  O1   C1   C2   120.10  3.000
 OD4  S1   C2   C5   110.74  3.000
 OD4  C5   C2   C1   124.55  3.000
 OD4  S1   C2   C1   124.71  3.000
 OD4  S1   C3   C6   122.08  3.000
 OD4  C6   C3   C4   127.29  3.000
 OD4  S1   C3   C4   110.55  3.000
 OD4  H3   C4   C5   123.89  3.000
 OD4  H3   C4   C3   122.88  3.000
 OD4  C5   C4   C3   113.22  3.000
 OD4  H5   C5   C4   123.87  3.000
 OD4  H5   C5   C2   123.04  3.000
 OD4  C4   C5   C2   113.09  3.000
 OD4  C7   C6   C11  118.54  3.000
 OD4  C11  C6   C3   122.70  3.000
 OD4  C7   C6   C3   118.76  3.000
 OD4  S2   C10  C9   126.38  3.000
 OD4  S2   C10  C11  111.47  3.000
 OD4  C9   C10  C11  122.14  3.000
 OD4  C13  C11  C10  111.26  3.000
 OD4  C13  C11  C6   129.97  3.000
 OD4  C10  C11  C6   118.75  3.000
 OD4  S2   C12  C14  117.88  3.000
 OD4  C14  C12  C13  129.33  3.000
 OD4  S2   C12  C13  112.79  3.000
 OD4  H8   C13  C12  122.05  3.000
 OD4  H8   C13  C11  124.82  3.000
 OD4  C12  C13  C11  113.12  3.000
 OD4  O3   C14  O2   128.68  3.000
 OD4  O3   C14  C12  114.76  3.000
 OD4  O2   C14  C12  116.56  3.000
 OD4  H11  C15  H10  106.90  3.000
 OD4  H11  C15  N1   109.43  3.000
 OD4  H10  C15  N1   110.06  3.000
 OD4  H11  C15  C16  109.99  3.000
 OD4  H10  C15  C16  109.92  3.000
 OD4  N1   C15  C16  110.47  3.000
 OD4  H13  C16  H12  107.06  3.000
 OD4  H13  C16  C17  109.41  3.000
 OD4  H12  C16  C17  109.19  3.000
 OD4  H13  C16  C15  109.39  3.000
 OD4  H12  C16  C15  110.03  3.000
 OD4  C17  C16  C15  111.65  3.000
 OD4  H15  C17  H14  106.27  3.000
 OD4  H15  C17  N2   108.24  3.000
 OD4  H14  C17  N2   113.62  3.000
 OD4  H15  C17  C16  109.07  3.000
 OD4  H14  C17  C16  108.88  3.000
 OD4  N2   C17  C16  110.59  3.000
 OD4  H16  N1   C15  117.21  3.000
 OD4  H16  N1   C1   120.31  3.000
 OD4  C15  N1   C1   122.25  3.000
 OD4  C3   S1   C2    92.40  3.000
 OD4  H17  C7   C8   119.14  3.000
 OD4  H17  C7   C6   119.24  3.000
 OD4  C8   C7   C6   121.61  3.000
 OD4  H18  C8   C9   119.86  3.000
 OD4  H18  C8   C7   119.36  3.000
 OD4  C9   C8   C7   120.78  3.000
 OD4  H19  C9   C8   120.90  3.000
 OD4  H19  C9   C10  120.92  3.000
 OD4  C8   C9   C10  118.18  3.000
 OD4  C12  S2   C10   91.35  3.000
 OD4  H22  N2   H21  105.49  3.000
 OD4  H22  N2   C17  109.37  3.000
 OD4  H21  N2   C17  109.22  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
 OD4  CONST_01  C6   C3   S1   C2    180.00   0.0  0
 OD4  CONST_02  C4   C3   S1   C2      0.00   0.0  0
 OD4  CONST_03  C3   C4   C5   C2      0.00   0.0  0
 OD4  CONST_04  C5   C2   S1   C3      0.00   0.0  0
 OD4  CONST_05  C8   C7   C6   C3    180.00   0.0  0
 OD4  CONST_06  C10  C11  C6   C3    180.00   0.0  0
 OD4  CONST_07  C13  C11  C6   C3      0.00   0.0  0
 OD4  CONST_10  S1   C2   C5   C4      0.00   0.0  0
 OD4  CONST_11  S1   C3   C4   C5      0.00   0.0  0
 OD4  CONST_12  C6   C3   C4   C5    180.00   0.0  0
 OD4  CONST_13  C9   C8   C7   C6      0.00   0.0  0
 OD4  CONST_14  C9   C10  C11  C6      0.00   0.0  0
 OD4  CONST_15  S2   C10  C11  C6    180.00   0.0  0
 OD4  CONST_16  C12  C13  C11  C6    180.00   0.0  0
 OD4  CONST_17  C7   C8   C9   C10     0.00   0.0  0
 OD4  CONST_18  C7   C6   C11  C10     0.00   0.0  0
 OD4  CONST_19  C12  C13  C11  C10     0.00   0.0  0
 OD4  CONST_20  C13  C12  S2   C10     0.00   0.0  0
 OD4  CONST_21  C8   C7   C6   C11     0.00   0.0  0
 OD4  CONST_23  C8   C9   C10  C11     0.00   0.0  0
 OD4  CONST_24  C12  S2   C10  C11     0.00   0.0  0
 OD4  CONST_25  S2   C12  C13  C11     0.00   0.0  0
 OD4  CONST_26  C9   C10  S2   C12   180.00   0.0  0
 OD4  CONST_27  C7   C6   C11  C13   180.00   0.0  0
 OD4  CONST_28  C9   C10  C11  C13   180.00   0.0  0
 OD4  CONST_29  S2   C10  C11  C13     0.00   0.0  0
 OD4  CONST_31  S2   C10  C9   C8    180.00   0.0  0
 OD4  CONST_32  C3   S1   C2   C1    180.00   0.0  0
 OD4  CONST_33  C4   C5   C2   C1    180.00   0.0  0
 OD4  CONST_34  C14  C12  S2   C10   180.00   0.0  0
 OD4  CONST_35  C14  C12  C13  C11   180.00   0.0  0
 OD4  CONST_36  H3   C4   C5   C2    180.00   0.0  0
 OD4  CONST_37  H17  C7   C6   C3      0.00   0.0  0
 OD4  CONST_38  H5   C5   C4   C3    180.00   0.0  0
 OD4  CONST_39  H18  C8   C7   C6    180.00   0.0  0
 OD4  CONST_40  H8   C13  C11  C6      0.00   0.0  0
 OD4  CONST_41  H19  C9   C10  C11   180.00   0.0  0
 OD4  CONST_42  C15  N1   C1   C2    180.00   0.0  0
 OD4  CONST_43  H16  N1   C1   C2      0.00   0.0  0
 OD4  CONST_44  O1   C1   N1   C15     0.00   0.0  0
 OD4  Var_01    O1   C1   C2   C5     -7.78  30.0  2
 OD4  Var_02    O2   C14  C12  C13     0.71  30.0  2
 OD4  Var_03    C16  C15  N1   C1   -176.79  30.0  1
 OD4  Var_04    N2   C17  C16  C15   179.27  30.0  1
 OD4  Var_05    N1   C15  C16  C17   178.89  30.0  1
 OD4  Var_06    H21  N2   C17  C16    66.71  30.0  3

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
 OD4  plan-1  C1   0.020
 OD4  plan-1  C2   0.020
 OD4  plan-1  C3   0.020
 OD4  plan-1  C4   0.020
 OD4  plan-1  C5   0.020
 OD4  plan-1  C6   0.020
 OD4  plan-1  S1   0.020
 OD4  plan-1  H3   0.020
 OD4  plan-1  H5   0.020
 OD4  plan-2  C3   0.020
 OD4  plan-2  C6   0.020
 OD4  plan-2  C10  0.020
 OD4  plan-2  C11  0.020
 OD4  plan-2  C12  0.020
 OD4  plan-2  C13  0.020
 OD4  plan-2  C14  0.020
 OD4  plan-2  C7   0.020
 OD4  plan-2  C8   0.020
 OD4  plan-2  C9   0.020
 OD4  plan-2  S2   0.020
 OD4  plan-2  H8   0.020
 OD4  plan-2  H17  0.020
 OD4  plan-2  H18  0.020
 OD4  plan-2  H19  0.020
 OD4  plan-3  C1   0.020
 OD4  plan-3  C2   0.020
 OD4  plan-3  C15  0.020
 OD4  plan-3  N1   0.020
 OD4  plan-3  O1   0.020
 OD4  plan-3  H16  0.020
 OD4  plan-4  C12  0.020
 OD4  plan-4  C14  0.020
 OD4  plan-4  O2   0.020
 OD4  plan-4  O3   0.020

