# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 13:40:02 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 5-[3-(benzylamino)phenyl]-4-bromo-3-(carboxymethoxy)thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COc1c(Br)c(sc1C(O)=O)c2cccc(NCc3ccccc3)c2
#
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
 910  910  '5-[3-(benzylamino)phenyl]-4-bromo-3-(carboxymethoxy)thiophene-2-carboxylic acid'  ligand  42  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_910
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
 910  S1    S   S2     0   0.238   0.7499   1.5532   0.9674
 910  C2    C   CR5    0  -0.441   2.4087   1.6015   0.5201
 910  C3    C   CR5    0   0.435   2.8585   0.3544   0.1775
 910  C4    C   CR5    0  -0.144   1.8260  -0.6295   0.2725
 910  C5    C   CR5    0  -0.205   0.6213  -0.1429   0.6932
 910  C6    C   C      0   0.425   3.0885   2.9412   0.6114
 910  O7    O   OC    -1  -0.598   2.3425   3.8642   0.9951
 910  O8    O   O      0  -0.569   4.2911   3.0020   0.3106
 910  C9    C   CR6    0   0.104  -0.6582  -0.8219   0.9192
 910  C10   C   CR16   0  -0.407  -1.8220  -0.2742   0.3937
 910  C11   C   CR6    0   0.394  -3.0744  -0.8638   0.6195
 910  C12   C   CR16   0  -0.357  -3.1264  -2.0289   1.3944
 910  C13   C   CR16   0  -0.231  -1.9591  -2.5724   1.9129
 910  C14   C   CR16   0  -0.331  -0.7252  -1.9853   1.6909
 910  BR19  BR  BR     0  -0.034   2.1547  -2.4069  -0.2170
 910  O20   O   O2     0  -0.460   4.1043   0.0234  -0.1969
 910  C21   C   CH2    0  -0.291   4.4247   0.3450  -1.5484
 910  C22   C   C      0   0.368   5.8614  -0.0685  -1.8877
 910  O25   O   OC    -1  -0.627   6.1946   0.2024  -3.0593
 910  O26   O   O      0  -0.596   6.5442  -0.6144  -1.0087
 910  N29   N   NH1    0  -0.686  -4.1930  -0.3031   0.0508
 910  C30   C   CH2    0  -0.340  -5.5237  -0.6661   0.4901
 910  C31   C   CR6    0   0.079  -6.5508   0.1232  -0.2740
 910  C34   C   CR16   0  -0.282  -6.7517  -0.1127  -1.6330
 910  C35   C   CR16   0  -0.242  -7.6882   0.6218  -2.3450
 910  C36   C   CR16   0  -0.266  -8.4347   1.6065  -1.7070
 910  C37   C   CR16   0  -0.240  -8.2375   1.8513  -0.3558
 910  C38   C   CR16   0  -0.305  -7.2975   1.1131   0.3546
 910  H10   H   HCR6   0   0.257  -1.7641   0.6192  -0.2186
 910  H12   H   HCR6   0   0.268  -4.0701  -2.5149   1.6014
 910  H13   H   HCR6   0   0.255  -2.0223  -3.4675   2.5186
 910  H14   H   HCR6   0   0.247   0.1668  -2.4042   2.1351
 910  H211  H   HCH2   0   0.228   4.3085   1.4194  -1.7119
 910  H212  H   HCH2   0   0.214   3.7352  -0.1691  -2.2291
 910  HN29  H   HNH1   0   0.381  -4.0915   0.6672  -0.2042
 910  H301  H   HCH2   0   0.248  -5.6811  -1.7329   0.3094
 910  H302  H   HCH2   0   0.238  -5.6589  -0.5056   1.5677
 910  H34   H   HCR6   0   0.252  -6.1751  -0.8808  -2.1350
 910  H35   H   HCR6   0   0.256  -7.8393   0.4249  -3.3986
 910  H36   H   HCR6   0   0.256  -9.1669   2.1772  -2.2634
 910  H37   H   HCR6   0   0.256  -8.8124   2.6170   0.1489
 910  H38   H   HCR6   0   0.253  -7.1444   1.3094   1.4092

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
 910  S1   C2    aromatic  1.719  0.020  1.719
 910  S1   C5    aromatic  1.723  0.020  1.723
 910  C2   C3    aromatic  1.369  0.020  1.369
 910  C2   C6    single    1.505  0.020  1.505
 910  C3   C4    aromatic  1.429  0.020  1.429
 910  C3   O20   single    1.342  0.020  1.342
 910  C4   C5    aromatic  1.366  0.020  1.366
 910  C4   BR19  single    1.873  0.020  1.873
 910  C5   C9    single    1.466  0.020  1.466
 910  C6   O7    deloc     1.247  0.020  1.247
 910  C6   O8    deloc     1.241  0.020  1.241
 910  C9   C10   aromatic  1.389  0.020  1.389
 910  C9   C14   aromatic  1.398  0.020  1.398
 910  C10  C11   aromatic  1.402  0.020  1.402
 910  C10  H10   single    0.930  0.020  1.080
 910  C11  C12   aromatic  1.400  0.020  1.400
 910  C11  N29   single    1.374  0.020  1.374
 910  C12  C13   aromatic  1.388  0.020  1.388
 910  C12  H12   single    0.930  0.020  1.080
 910  C13  C14   aromatic  1.384  0.020  1.384
 910  C13  H13   single    0.930  0.020  1.080
 910  C14  H14   single    0.930  0.020  1.080
 910  O20  C21   single    1.426  0.020  1.426
 910  C21  C22   single    1.533  0.020  1.533
 910  C21  H211  single    0.970  0.020  1.090
 910  C21  H212  single    0.970  0.020  1.090
 910  C22  O25   deloc     1.248  0.020  1.248
 910  C22  O26   deloc     1.240  0.020  1.240
 910  N29  C30   single    1.448  0.020  1.448
 910  N29  HN29  single    0.890  0.020  1.040
 910  C30  C31   single    1.504  0.020  1.504
 910  C30  H301  single    0.970  0.020  1.090
 910  C30  H302  single    0.970  0.020  1.090
 910  C31  C34   aromatic  1.394  0.020  1.394
 910  C31  C38   aromatic  1.390  0.020  1.390
 910  C34  C35   aromatic  1.387  0.020  1.387
 910  C34  H34   single    0.930  0.020  1.080
 910  C35  C36   aromatic  1.391  0.020  1.391
 910  C35  H35   single    0.930  0.020  1.080
 910  C36  C37   aromatic  1.387  0.020  1.387
 910  C36  H36   single    0.930  0.020  1.080
 910  C37  C38   aromatic  1.390  0.020  1.390
 910  C37  H37   single    0.930  0.020  1.080
 910  C38  H38   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
 910  C5    S1   C2     93.34  3.000
 910  C6    C2   C3    132.65  3.000
 910  C6    C2   S1    116.43  3.000
 910  C3    C2   S1    110.89  3.000
 910  O20   C3   C4    121.28  3.000
 910  O20   C3   C2    126.81  3.000
 910  C4    C3   C2    111.90  3.000
 910  BR19  C4   C5    125.00  3.000
 910  BR19  C4   C3    120.60  3.000
 910  C5    C4   C3    114.36  3.000
 910  C9    C5   C4    130.72  3.000
 910  C9    C5   S1    119.77  3.000
 910  C4    C5   S1    109.51  3.000
 910  O8    C6   O7    128.17  3.000
 910  O8    C6   C2    117.81  3.000
 910  O7    C6   C2    114.03  3.000
 910  C14   C9   C10   119.79  3.000
 910  C14   C9   C5    120.83  3.000
 910  C10   C9   C5    119.35  3.000
 910  H10   C10  C11   119.00  3.000
 910  H10   C10  C9    119.57  3.000
 910  C11   C10  C9    121.42  3.000
 910  N29   C11  C12   122.56  3.000
 910  N29   C11  C10   119.25  3.000
 910  C12   C11  C10   118.17  3.000
 910  H12   C12  C13   119.09  3.000
 910  H12   C12  C11   120.82  3.000
 910  C13   C12  C11   120.09  3.000
 910  H13   C13  C14   119.50  3.000
 910  H13   C13  C12   118.93  3.000
 910  C14   C13  C12   121.57  3.000
 910  H14   C14  C13   120.34  3.000
 910  H14   C14  C9    120.66  3.000
 910  C13   C14  C9    118.97  3.000
 910  C21   O20  C3    114.67  3.000
 910  H212  C21  H211  107.52  3.000
 910  H212  C21  C22   108.99  3.000
 910  H211  C21  C22   109.37  3.000
 910  H212  C21  O20   109.96  3.000
 910  H211  C21  O20   109.86  3.000
 910  C22   C21  O20   111.08  3.000
 910  O26   C22  O25   127.90  3.000
 910  O26   C22  C21   118.55  3.000
 910  O25   C22  C21   113.55  3.000
 910  HN29  N29  C30   114.24  3.000
 910  HN29  N29  C11   114.53  3.000
 910  C30   N29  C11   121.35  3.000
 910  H302  C30  H301  106.69  3.000
 910  H302  C30  C31   109.75  3.000
 910  H301  C30  C31   109.25  3.000
 910  H302  C30  N29   111.99  3.000
 910  H301  C30  N29   109.08  3.000
 910  C31   C30  N29   110.00  3.000
 910  C38   C31  C34   118.94  3.000
 910  C38   C31  C30   120.72  3.000
 910  C34   C31  C30   120.33  3.000
 910  H34   C34  C35   119.79  3.000
 910  H34   C34  C31   119.66  3.000
 910  C35   C34  C31   120.54  3.000
 910  H35   C35  C36   120.03  3.000
 910  H35   C35  C34   119.84  3.000
 910  C36   C35  C34   120.13  3.000
 910  H36   C36  C37   120.25  3.000
 910  H36   C36  C35   120.04  3.000
 910  C37   C36  C35   119.70  3.000
 910  H37   C37  C38   119.77  3.000
 910  H37   C37  C36   120.23  3.000
 910  C38   C37  C36   120.00  3.000
 910  H38   C38  C37   119.78  3.000
 910  H38   C38  C31   119.54  3.000
 910  C37   C38  C31   120.68  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
 910  CONST_01  C4    C3   C2   S1      0.00   0.0  0
 910  CONST_02  C3    C4   C5   S1      0.00   0.0  0
 910  CONST_05  C4    C5   S1   C2      0.00   0.0  0
 910  CONST_06  C9    C5   S1   C2    180.00   0.0  0
 910  CONST_07  C5    C4   C3   C2      0.00   0.0  0
 910  CONST_08  C5    S1   C2   C3      0.00   0.0  0
 910  CONST_09  C9    C5   C4   C3    180.00   0.0  0
 910  CONST_12  C11   C10  C9   C5    180.00   0.0  0
 910  CONST_13  C13   C14  C9   C5    180.00   0.0  0
 910  CONST_14  C12   C11  C10  C9      0.00   0.0  0
 910  CONST_15  C12   C13  C14  C9      0.00   0.0  0
 910  CONST_16  C13   C14  C9   C10     0.00   0.0  0
 910  CONST_17  C13   C12  C11  C10     0.00   0.0  0
 910  CONST_18  C14   C9   C10  C11     0.00   0.0  0
 910  CONST_19  C14   C13  C12  C11     0.00   0.0  0
 910  CONST_20  C36   C35  C34  C31     0.00   0.0  0
 910  CONST_21  C36   C37  C38  C31     0.00   0.0  0
 910  CONST_22  C37   C38  C31  C34     0.00   0.0  0
 910  CONST_23  C37   C36  C35  C34     0.00   0.0  0
 910  CONST_24  C38   C31  C34  C35     0.00   0.0  0
 910  CONST_25  C38   C37  C36  C35     0.00   0.0  0
 910  CONST_26  O20   C3   C2   S1    180.00   0.0  0
 910  CONST_27  BR19  C4   C5   S1    180.00   0.0  0
 910  CONST_28  BR19  C4   C3   C2    180.00   0.0  0
 910  CONST_29  C6    C2   C3   C4    180.00   0.0  0
 910  CONST_30  C6    C2   S1   C5    180.00   0.0  0
 910  CONST_31  O20   C3   C4   C5    180.00   0.0  0
 910  CONST_32  BR19  C4   C5   C9      0.00   0.0  0
 910  CONST_33  N29   C11  C10  C9    180.00   0.0  0
 910  CONST_34  N29   C11  C12  C13   180.00   0.0  0
 910  CONST_35  C35   C34  C31  C30   180.00   0.0  0
 910  CONST_36  C37   C38  C31  C30   180.00   0.0  0
 910  CONST_37  H10   C10  C9   C5      0.00   0.0  0
 910  CONST_38  H14   C14  C9   C5      0.00   0.0  0
 910  CONST_39  H13   C13  C14  C9    180.00   0.0  0
 910  CONST_40  H12   C12  C11  C10   180.00   0.0  0
 910  CONST_41  H35   C35  C34  C31   180.00   0.0  0
 910  CONST_42  H37   C37  C38  C31   180.00   0.0  0
 910  CONST_43  H38   C38  C31  C34   180.00   0.0  0
 910  CONST_44  H36   C36  C35  C34   180.00   0.0  0
 910  CONST_45  H34   C34  C35  C36   180.00   0.0  0
 910  CONST_46  C30   N29  C11  C10   180.00   0.0  0
 910  Var_01    O7    C6   C2   S1     -0.66  30.0  2
 910  Var_02    C31   C30  N29  C11   178.47  30.0  3
 910  Var_03    C34   C31  C30  N29    68.78  30.0  2
 910  Var_04    C22   C21  O20  C3   -179.94  30.0  3
 910  Var_05    O25   C22  C21  O20  -179.45  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
 910  plan-1  S1    0.020
 910  plan-1  C2    0.020
 910  plan-1  C3    0.020
 910  plan-1  C4    0.020
 910  plan-1  C5    0.020
 910  plan-1  C6    0.020
 910  plan-1  C9    0.020
 910  plan-1  BR19  0.020
 910  plan-1  O20   0.020
 910  plan-2  C5    0.020
 910  plan-2  C9    0.020
 910  plan-2  C10   0.020
 910  plan-2  C11   0.020
 910  plan-2  C12   0.020
 910  plan-2  C13   0.020
 910  plan-2  C14   0.020
 910  plan-2  N29   0.020
 910  plan-2  H10   0.020
 910  plan-2  H12   0.020
 910  plan-2  H13   0.020
 910  plan-2  H14   0.020
 910  plan-3  C30   0.020
 910  plan-3  C31   0.020
 910  plan-3  C34   0.020
 910  plan-3  C35   0.020
 910  plan-3  C36   0.020
 910  plan-3  C37   0.020
 910  plan-3  C38   0.020
 910  plan-3  H34   0.020
 910  plan-3  H35   0.020
 910  plan-3  H36   0.020
 910  plan-3  H37   0.020
 910  plan-3  H38   0.020
 910  plan-4  C11   0.020
 910  plan-4  N29   0.020
 910  plan-4  C30   0.020
 910  plan-4  HN29  0.020
 910  plan-5  C2    0.020
 910  plan-5  C6    0.020
 910  plan-5  O7    0.020
 910  plan-5  O8    0.020
 910  plan-6  C21   0.020
 910  plan-6  C22   0.020
 910  plan-6  O25   0.020
 910  plan-6  O26   0.020

