# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 17:41:48 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 1-(1-benzothiophen-3-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1csc2ccccc12
#
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
 K9S  K9S  1-(1-benzothiophen-3-yl)methanamine  ligand  20  11  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_K9S
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
 K9S  C1    C  CR15  0  -0.551   1.3434  -1.4374  -0.2568
 K9S  N1    N  NH2   0  -0.787   2.6722   1.6766   0.6742
 K9S  S2    S  S2    0   0.194  -0.2033  -2.1898  -0.0578
 K9S  C3    C  CR56  0  -0.218  -0.9839  -0.6416  -0.0059
 K9S  C4    C  CR56  0   0.179  -0.0517   0.4022  -0.1321
 K9S  C5    C  CR5   0   0.203   1.2970  -0.0862  -0.2860
 K9S  C6    C  CR16  0  -0.276  -2.3486  -0.3974   0.1301
 K9S  C7    C  CR16  0  -0.271  -2.7791   0.9154   0.1368
 K9S  C10   C  CH2   0  -0.377   2.4935   0.7950  -0.4697
 K9S  C8    C  CR16  0  -0.253  -1.8653   1.9704   0.0150
 K9S  C9    C  CR16  0  -0.324  -0.5133   1.7239  -0.1147
 K9S  H1    H  HCR5  0   0.294   2.2234  -2.0577  -0.3481
 K9S  H11N  H  HNH2  0   0.342   2.9632   1.1329   1.4769
 K9S  H12N  H  HNH2  0   0.352   3.4295   2.3202   0.4837
 K9S  H101  H  HCH2  0   0.236   2.3378   1.4213  -1.3528
 K9S  H102  H  HCH2  0   0.223   3.3648   0.1648  -0.6901
 K9S  H6    H  HCR6  0   0.267  -3.0540  -1.2126   0.2246
 K9S  H9    H  HCR6  0   0.252   0.1925   2.5405  -0.1862
 K9S  H7    H  HCR6  0   0.259  -3.8352   1.1284   0.2389
 K9S  H8    H  HCR6  0   0.255  -2.2258   2.9909   0.0283

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
 K9S  C1   S2    aromatic  1.731  0.020  1.731
 K9S  C1   C5    aromatic  1.352  0.020  1.352
 K9S  N1   C10   single    1.455  0.020  1.455
 K9S  S2   C3    aromatic  1.735  0.020  1.735
 K9S  C3   C4    aromatic  1.405  0.020  1.405
 K9S  C3   C6    aromatic  1.393  0.020  1.393
 K9S  C4   C5    aromatic  1.443  0.020  1.443
 K9S  C4   C9    aromatic  1.400  0.020  1.400
 K9S  C5   C10   single    1.497  0.020  1.497
 K9S  C6   C7    aromatic  1.382  0.020  1.382
 K9S  C7   C8    aromatic  1.401  0.020  1.401
 K9S  C8   C9    aromatic  1.380  0.020  1.380
 K9S  C1   H1    single    0.930  0.020  1.080
 K9S  N1   H11N  single    0.890  0.020  1.040
 K9S  N1   H12N  single    0.890  0.020  1.040
 K9S  C10  H101  single    0.970  0.020  1.090
 K9S  C10  H102  single    0.970  0.020  1.090
 K9S  C6   H6    single    0.930  0.020  1.080
 K9S  C9   H9    single    0.930  0.020  1.080
 K9S  C7   H7    single    0.930  0.020  1.080
 K9S  C8   H8    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
 K9S  H1    C1   C5    126.85  3.000
 K9S  H1    C1   S2    119.20  3.000
 K9S  C5    C1   S2    113.95  3.000
 K9S  H12N  N1   H11N  106.01  3.000
 K9S  H12N  N1   C10   109.23  3.000
 K9S  H11N  N1   C10   109.47  3.000
 K9S  C3    S2   C1     91.01  3.000
 K9S  C6    C3   C4    121.90  3.000
 K9S  C6    C3   S2    126.89  3.000
 K9S  C4    C3   S2    111.21  3.000
 K9S  C9    C4   C5    128.99  3.000
 K9S  C9    C4   C3    118.78  3.000
 K9S  C5    C4   C3    112.23  3.000
 K9S  C10   C5   C4    124.12  3.000
 K9S  C10   C5   C1    124.28  3.000
 K9S  C4    C5   C1    111.59  3.000
 K9S  H6    C6   C7    120.81  3.000
 K9S  H6    C6   C3    121.00  3.000
 K9S  C7    C6   C3    118.19  3.000
 K9S  H7    C7   C8    119.77  3.000
 K9S  H7    C7   C6    119.44  3.000
 K9S  C8    C7   C6    120.79  3.000
 K9S  H102  C10  H101  106.23  3.000
 K9S  H102  C10  C5    108.73  3.000
 K9S  H101  C10  C5    108.80  3.000
 K9S  H102  C10  N1    114.09  3.000
 K9S  H101  C10  N1    107.78  3.000
 K9S  C5    C10  N1    110.99  3.000
 K9S  H8    C8   C9    119.72  3.000
 K9S  H8    C8   C7    119.45  3.000
 K9S  C9    C8   C7    120.83  3.000
 K9S  H9    C9   C8    120.69  3.000
 K9S  H9    C9   C4    119.78  3.000
 K9S  C8    C9   C4    119.52  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
 K9S  CONST_01  C4    C3   S2   C1      0.00   0.0  0
 K9S  CONST_02  C6    C3   S2   C1    180.00   0.0  0
 K9S  CONST_03  C3    C4   C5   C1      0.00   0.0  0
 K9S  CONST_04  C9    C4   C5   C1    180.00   0.0  0
 K9S  CONST_05  C4    C5   C1   S2      0.00   0.0  0
 K9S  CONST_06  C5    C4   C3   S2      0.00   0.0  0
 K9S  CONST_07  C9    C4   C3   S2    180.00   0.0  0
 K9S  CONST_08  C7    C6   C3   S2    180.00   0.0  0
 K9S  CONST_09  C5    C1   S2   C3      0.00   0.0  0
 K9S  CONST_10  C8    C9   C4   C3      0.00   0.0  0
 K9S  CONST_11  C8    C7   C6   C3      0.00   0.0  0
 K9S  CONST_12  C7    C6   C3   C4      0.00   0.0  0
 K9S  CONST_13  C7    C8   C9   C4      0.00   0.0  0
 K9S  CONST_14  C6    C3   C4   C5    180.00   0.0  0
 K9S  CONST_15  C8    C9   C4   C5    180.00   0.0  0
 K9S  CONST_16  C9    C4   C3   C6      0.00   0.0  0
 K9S  CONST_17  C9    C8   C7   C6      0.00   0.0  0
 K9S  CONST_18  C10   C5   C1   S2    180.00   0.0  0
 K9S  CONST_19  C10   C5   C4   C3    180.00   0.0  0
 K9S  CONST_20  C9    C4   C5   C10     0.00   0.0  0
 K9S  CONST_21  H6    C6   C3   S2      0.00   0.0  0
 K9S  CONST_22  H1    C1   S2   C3    180.00   0.0  0
 K9S  CONST_23  H9    C9   C4   C3    180.00   0.0  0
 K9S  CONST_24  H7    C7   C6   C3    180.00   0.0  0
 K9S  CONST_25  H8    C8   C9   C4    180.00   0.0  0
 K9S  Var_01    N1    C10  C5   C1   -119.71  30.0  2
 K9S  Var_02    H11N  N1   C10  C5     69.86  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
 K9S  plan-1  C1   0.020
 K9S  plan-1  S2   0.020
 K9S  plan-1  C3   0.020
 K9S  plan-1  C4   0.020
 K9S  plan-1  C5   0.020
 K9S  plan-1  C6   0.020
 K9S  plan-1  C7   0.020
 K9S  plan-1  C10  0.020
 K9S  plan-1  C8   0.020
 K9S  plan-1  C9   0.020
 K9S  plan-1  H1   0.020
 K9S  plan-1  H6   0.020
 K9S  plan-1  H9   0.020
 K9S  plan-1  H7   0.020
 K9S  plan-1  H8   0.020

