# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 07:15:42 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 1-(5-bromo-1-benzothiophen-3-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1csc2ccc(Br)cc12
#
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
 513  513  1-(5-bromo-1-benzothiophen-3-yl)methanamine  ligand  20  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_513
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
 513  C4    C   CR15  0  -0.542   3.4024  -0.0564   0.2569
 513  N7    N   NH2   0  -0.794   2.0969  -3.0162  -0.7977
 513  S3    S   S2    0   0.219   3.0500   1.6202   0.0200
 513  C2    C   CR56  0  -0.216   1.3524   1.2880  -0.0283
 513  C1    C   CR56  0   0.190   1.0985  -0.0835   0.1383
 513  C5    C   CR5   0   0.209   2.3079  -0.8499   0.3021
 513  C8    C   CR16  0  -0.265   0.3200   2.2059  -0.1944
 513  C9    C   CR16  0  -0.247  -0.9824   1.7481  -0.1942
 513  C6    C   CH2   0  -0.394   2.3349  -2.3382   0.4731
 513  C10   C   CR6   0  -0.105  -1.2385   0.3824  -0.0245
 513  C11   C   CR16  0  -0.317  -0.2256  -0.5377   0.1406
 513  BR1   BR  BR    0  -0.045  -3.0327  -0.2101  -0.0235
 513  H8    H   HCR6  0   0.280   0.5227   3.2612  -0.3205
 513  H9    H   HCR6  0   0.283  -1.7946   2.4503  -0.3221
 513  H11   H   HCR6  0   0.278  -0.4412  -1.5902   0.2750
 513  H4    H   HCR5  0   0.300   4.4316  -0.3698   0.3551
 513  H61C  H   HCH2  0   0.217   1.6213  -2.6154   1.2611
 513  H62C  H   HCH2  0   0.250   3.3204  -2.6330   0.8364
 513  H71N  H   HNH2  0   0.355   2.1403  -4.0163  -0.6437
 513  H72N  H   HNH2  0   0.345   1.1517  -2.8351  -1.1137

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
 513  C8   C9    aromatic  1.380  0.020  1.380
 513  C8   C2    aromatic  1.391  0.020  1.391
 513  C9   C10   aromatic  1.400  0.020  1.400
 513  C11  C1    aromatic  1.400  0.020  1.400
 513  C11  C10   aromatic  1.378  0.020  1.378
 513  C4   C5    aromatic  1.353  0.020  1.353
 513  C4   S3    aromatic  1.730  0.020  1.730
 513  C1   C5    aromatic  1.441  0.020  1.441
 513  C1   C2    aromatic  1.405  0.020  1.405
 513  C5   C6    single    1.498  0.020  1.498
 513  C2   S3    aromatic  1.730  0.020  1.730
 513  C10  BR1   single    1.889  0.020  1.889
 513  C6   N7    single    1.460  0.020  1.460
 513  C8   H8    single    0.930  0.020  1.080
 513  C9   H9    single    0.930  0.020  1.080
 513  C11  H11   single    0.930  0.020  1.080
 513  C4   H4    single    0.930  0.020  1.080
 513  C6   H61C  single    0.970  0.020  1.090
 513  C6   H62C  single    0.970  0.020  1.090
 513  N7   H71N  single    0.890  0.020  1.040
 513  N7   H72N  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
 513  H4    C4   C5    126.70  3.000
 513  H4    C4   S3    119.19  3.000
 513  C5    C4   S3    114.11  3.000
 513  H72N  N7   H71N  105.30  3.000
 513  H72N  N7   C6    109.92  3.000
 513  H71N  N7   C6    108.62  3.000
 513  C2    S3   C4     91.01  3.000
 513  C8    C2   C1    121.61  3.000
 513  C1    C2   S3    111.19  3.000
 513  C8    C2   S3    127.20  3.000
 513  C11   C1   C5    128.40  3.000
 513  C5    C1   C2    112.39  3.000
 513  C11   C1   C2    119.21  3.000
 513  C6    C5   C1    123.80  3.000
 513  C6    C5   C4    124.89  3.000
 513  C1    C5   C4    111.30  3.000
 513  H8    C8   C9    120.02  3.000
 513  H8    C8   C2    121.22  3.000
 513  C9    C8   C2    118.76  3.000
 513  H9    C9   C10   120.70  3.000
 513  H9    C9   C8    119.55  3.000
 513  C10   C9   C8    119.75  3.000
 513  H62C  C6   H61C  106.24  3.000
 513  H62C  C6   C5    108.83  3.000
 513  H61C  C6   C5    108.71  3.000
 513  H62C  C6   N7    108.16  3.000
 513  H61C  C6   N7    113.66  3.000
 513  C5    C6   N7    111.05  3.000
 513  BR1   C10  C11   119.23  3.000
 513  BR1   C10  C9    118.67  3.000
 513  C11   C10  C9    122.10  3.000
 513  H11   C11  C10   121.17  3.000
 513  H11   C11  C1    120.26  3.000
 513  C10   C11  C1    118.58  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
 513  CONST_01  C11   C1   C5   C4   180.00   0.0  0
 513  CONST_02  C2    C1   C5   C4     0.00   0.0  0
 513  CONST_03  C8    C2   S3   C4   180.00   0.0  0
 513  CONST_04  C1    C2   S3   C4     0.00   0.0  0
 513  CONST_05  C1    C5   C4   S3     0.00   0.0  0
 513  CONST_06  C9    C8   C2   S3   180.00   0.0  0
 513  CONST_07  C11   C1   C2   S3   180.00   0.0  0
 513  CONST_08  C5    C1   C2   S3     0.00   0.0  0
 513  CONST_09  C10   C9   C8   C2     0.00   0.0  0
 513  CONST_10  C10   C11  C1   C2     0.00   0.0  0
 513  CONST_11  C5    C4   S3   C2     0.00   0.0  0
 513  CONST_12  C9    C10  C11  C1     0.00   0.0  0
 513  CONST_13  C9    C8   C2   C1     0.00   0.0  0
 513  CONST_14  C10   C11  C1   C5   180.00   0.0  0
 513  CONST_15  C8    C2   C1   C5   180.00   0.0  0
 513  CONST_16  C11   C10  C9   C8     0.00   0.0  0
 513  CONST_17  C11   C1   C2   C8     0.00   0.0  0
 513  CONST_18  C6    C5   C4   S3   180.00   0.0  0
 513  CONST_19  C6    C5   C1   C2   180.00   0.0  0
 513  CONST_20  BR1   C10  C11  C1   180.00   0.0  0
 513  CONST_21  BR1   C10  C9   C8   180.00   0.0  0
 513  CONST_22  C11   C1   C5   C6     0.00   0.0  0
 513  CONST_23  H8    C8   C2   S3     0.00   0.0  0
 513  CONST_24  H9    C9   C8   C2   180.00   0.0  0
 513  CONST_25  H11   C11  C1   C2   180.00   0.0  0
 513  CONST_26  H4    C4   S3   C2   180.00   0.0  0
 513  Var_01    N7    C6   C5   C4  -102.82  30.0  2
 513  Var_02    H71N  N7   C6   C5   178.94  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
 513  plan-1  C4   0.020
 513  plan-1  S3   0.020
 513  plan-1  C2   0.020
 513  plan-1  C1   0.020
 513  plan-1  C5   0.020
 513  plan-1  C8   0.020
 513  plan-1  C9   0.020
 513  plan-1  C6   0.020
 513  plan-1  C10  0.020
 513  plan-1  C11  0.020
 513  plan-1  BR1  0.020
 513  plan-1  H8   0.020
 513  plan-1  H9   0.020
 513  plan-1  H11  0.020
 513  plan-1  H4   0.020

