# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 02:51:25 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  40  24  .  2022-03-23  2022-11-17
;
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   0.555   3.4088  -1.5990   0.6528
 OD4  C2   C  CR5   0  -0.322   1.9562  -1.8818   0.6114
 OD4  C3   C  CR5   0  -0.249  -0.5023  -1.9402   0.2598
 OD4  C4   C  CR15  0  -0.193  -0.0490  -2.9538   1.0604
 OD4  C5   C  CR15  0  -0.170   1.3484  -2.9203   1.2590
 OD4  C6   C  CR6   0   0.112  -1.8740  -1.7160  -0.1965
 OD4  C10  C  CR56  0  -0.228  -3.8078  -0.3076  -0.6322
 OD4  C11  C  CR56  0   0.225  -2.4875  -0.4441  -0.1601
 OD4  C12  C  CR5   0  -0.312  -2.8723   1.8107   0.2088
 OD4  C13  C  CR15  0  -0.256  -1.9793   0.7967   0.3299
 OD4  C14  C  C     0   0.529  -2.6398   3.1968   0.6324
 OD4  C15  C  CH2   0  -0.243   5.2012  -0.0076   0.1667
 OD4  C16  C  CH2   0  -0.481   5.4052   1.2059  -0.7244
 OD4  C17  C  CH2   0  -0.272   6.8467   1.6903  -0.6879
 OD4  N1   N  NH1   0  -0.668   3.8108  -0.4168   0.1621
 OD4  O1   O  O     0  -0.485   4.1820  -2.4278   1.1150
 OD4  S1   S  S2    0   0.247   0.8049  -0.9501  -0.2683
 OD4  C7   C  CR16  0  -0.312  -2.6129  -2.7867  -0.6711
 OD4  C8   C  CR16  0  -0.247  -3.9275  -2.6271  -1.1223
 OD4  C9   C  CR16  0  -0.283  -4.5369  -1.3903  -1.1183
 OD4  S2   S  S2    0   0.284  -4.3771   1.3175  -0.4952
 OD4  O2   O  O     0  -0.425  -1.6092   3.5833   1.1249
 OD4  O3   O  OH1   0  -0.597  -3.6992   3.9584   0.4049
 OD4  N2   N  NH2   0  -0.799   7.0240   2.8390  -1.5631
 OD4  H3   H  HCR5  0   0.274  -0.7047  -3.6882   1.5062
 OD4  H5   H  HCR5  0   0.276   1.8875  -3.6305   1.8689
 OD4  H8   H  HCR5  0   0.281  -1.0021   0.9325   0.7703
 OD4  H10  H  HCH2  0   0.241   5.8161  -0.8369  -0.1876
 OD4  H11  H  HCH2  0   0.234   5.5267   0.2176   1.1878
 OD4  H12  H  HCH2  0   0.236   5.1280   0.9631  -1.7535
 OD4  H13  H  HCH2  0   0.230   4.7448   2.0167  -0.3967
 OD4  H14  H  HCH2  0   0.194   7.1298   1.8850   0.3567
 OD4  H15  H  HCH2  0   0.218   7.5022   0.8883  -1.0382
 OD4  H16  H  HNH1  0   0.403   3.1300   0.2866  -0.0780
 OD4  H17  H  HCR6  0   0.267  -2.1563  -3.7668  -0.7161
 OD4  H18  H  HCR6  0   0.274  -4.4673  -3.4891  -1.4904
 OD4  H19  H  HCR6  0   0.280  -5.5496  -1.2655  -1.4774
 OD4  H20  H  HOH1  0   0.496  -3.5311   4.8713   0.6841
 OD4  H21  H  HNH2  0   0.339   6.5055   3.6253  -1.1903
 OD4  H22  H  HNH2  0   0.348   7.9946   3.1247  -1.5492

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  1.399  0.020  1.399
 OD4  C8   C9   aromatic  1.379  0.020  1.379
 OD4  C7   C6   aromatic  1.385  0.020  1.385
 OD4  C9   C10  aromatic  1.393  0.020  1.393
 OD4  S1   C3   aromatic  1.723  0.020  1.723
 OD4  S1   C2   aromatic  1.723  0.020  1.723
 OD4  O1   C1   double    1.224  0.020  1.224
 OD4  C6   C3   single    1.463  0.020  1.463
 OD4  C6   C11  aromatic  1.413  0.020  1.413
 OD4  N2   C17  single    1.455  0.020  1.455
 OD4  C10  C11  aromatic  1.409  0.020  1.409
 OD4  C10  S2   aromatic  1.727  0.020  1.727
 OD4  C3   C4   aromatic  1.369  0.020  1.369
 OD4  C1   C2   single    1.480  0.020  1.480
 OD4  C1   N1   single    1.342  0.020  1.342
 OD4  C2   C5   aromatic  1.366  0.020  1.366
 OD4  C11  C13  aromatic  1.428  0.020  1.428
 OD4  C17  C16  single    1.521  0.020  1.521
 OD4  C15  N1   single    1.449  0.020  1.449
 OD4  C15  C16  single    1.519  0.020  1.519
 OD4  S2   C12  aromatic  1.733  0.020  1.733
 OD4  C4   C5   aromatic  1.412  0.020  1.412
 OD4  C13  C12  aromatic  1.357  0.020  1.357
 OD4  C12  C14  single    1.468  0.020  1.468
 OD4  C14  O2   double    1.206  0.020  1.206
 OD4  C14  O3   single    1.324  0.020  1.324
 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  O3   H20  single    0.850  0.020  0.980
 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   123.06  3.000
 OD4  N1   C1   C2   116.88  3.000
 OD4  O1   C1   C2   120.07  3.000
 OD4  S1   C2   C5   110.84  3.000
 OD4  C5   C2   C1   124.64  3.000
 OD4  S1   C2   C1   124.52  3.000
 OD4  S1   C3   C6   121.85  3.000
 OD4  C6   C3   C4   127.33  3.000
 OD4  S1   C3   C4   110.70  3.000
 OD4  H3   C4   C5   123.96  3.000
 OD4  H3   C4   C3   122.92  3.000
 OD4  C5   C4   C3   113.11  3.000
 OD4  H5   C5   C4   123.90  3.000
 OD4  H5   C5   C2   123.04  3.000
 OD4  C4   C5   C2   113.05  3.000
 OD4  C7   C6   C11  118.25  3.000
 OD4  C11  C6   C3   122.49  3.000
 OD4  C7   C6   C3   119.25  3.000
 OD4  S2   C10  C9   125.90  3.000
 OD4  S2   C10  C11  111.93  3.000
 OD4  C9   C10  C11  122.16  3.000
 OD4  C13  C11  C10  111.38  3.000
 OD4  C13  C11  C6   129.55  3.000
 OD4  C10  C11  C6   119.05  3.000
 OD4  S2   C12  C14  121.57  3.000
 OD4  C14  C12  C13  125.15  3.000
 OD4  S2   C12  C13  113.27  3.000
 OD4  H8   C13  C12  122.54  3.000
 OD4  H8   C13  C11  124.83  3.000
 OD4  C12  C13  C11  112.62  3.000
 OD4  O3   C14  O2   124.71  3.000
 OD4  O3   C14  C12  111.52  3.000
 OD4  O2   C14  C12  123.77  3.000
 OD4  H11  C15  H10  106.94  3.000
 OD4  H11  C15  N1   110.25  3.000
 OD4  H10  C15  N1   108.96  3.000
 OD4  H11  C15  C16  110.04  3.000
 OD4  H10  C15  C16  109.93  3.000
 OD4  N1   C15  C16  110.64  3.000
 OD4  H13  C16  H12  107.04  3.000
 OD4  H13  C16  C17  109.17  3.000
 OD4  H12  C16  C17  109.49  3.000
 OD4  H13  C16  C15  109.55  3.000
 OD4  H12  C16  C15  109.91  3.000
 OD4  C17  C16  C15  111.56  3.000
 OD4  H15  C17  H14  106.25  3.000
 OD4  H15  C17  N2   108.26  3.000
 OD4  H14  C17  N2   113.59  3.000
 OD4  H15  C17  C16  109.08  3.000
 OD4  H14  C17  C16  108.85  3.000
 OD4  N2   C17  C16  110.63  3.000
 OD4  H16  N1   C15  116.85  3.000
 OD4  H16  N1   C1   119.98  3.000
 OD4  C15  N1   C1   122.35  3.000
 OD4  C3   S1   C2    92.28  3.000
 OD4  H17  C7   C8   119.10  3.000
 OD4  H17  C7   C6   119.31  3.000
 OD4  C8   C7   C6   121.58  3.000
 OD4  H18  C8   C9   119.69  3.000
 OD4  H18  C8   C7   119.20  3.000
 OD4  C9   C8   C7   121.11  3.000
 OD4  H19  C9   C8   121.09  3.000
 OD4  H19  C9   C10  121.08  3.000
 OD4  C8   C9   C10  117.83  3.000
 OD4  C12  S2   C10   90.79  3.000
 OD4  H20  O3   C14  110.70  3.000
 OD4  H22  N2   H21  105.48  3.000
 OD4  H22  N2   C17  109.36  3.000
 OD4  H21  N2   C17  109.21  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  H20  O3   C14  C12  180.00   0.0  0
 OD4  CONST_45  O1   C1   N1   C15    0.00   0.0  0
 OD4  Var_01    O1   C1   C2   C5    11.70  30.0  2
 OD4  Var_02    O2   C14  C12  C13    0.89  30.0  2
 OD4  Var_03    C16  C15  N1   C1   166.89  30.0  1
 OD4  Var_04    N2   C17  C16  C15  179.12  30.0  2
 OD4  Var_05    N1   C15  C16  C17  177.53  30.0  2
 OD4  Var_06    H21  N2   C17  C16   67.02  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
 OD4  plan-4  H20  0.020

