# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:10:02 2021
#   Inital geometry file: a 68 line input string
#   Ligand name: 1-(pyridin-4-yl)-N-[(thiophen-2-yl)methyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C(NCc1ccncc1)c2sccc2
#
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
 WLS  WLS  1-(pyridin-4-yl)-N-[(thiophen-2-yl)methyl]methanamine  ligand  26  14  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_WLS
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
 WLS  C10  C  CR5   0  -0.173  -35.0802  22.3335  -1.6377
 WLS  C13  C  CR15  0  -0.475  -34.5700  22.1914  -4.0563
 WLS  C01  C  CH2   0  -0.301  -35.7424  22.2180  -0.3050
 WLS  C03  C  CH2   0  -0.300  -37.8873  22.2809   0.8102
 WLS  C04  C  CR6   0   0.162  -39.3720  22.4135   0.6132
 WLS  C05  C  CR16  0  -0.365  -39.9840  22.1086  -0.5980
 WLS  C06  C  CR16  0  -0.059  -41.3624  22.2158  -0.7010
 WLS  C08  C  CR16  0  -0.063  -41.5646  22.8930   1.4521
 WLS  C09  C  CR16  0  -0.371  -40.1958  22.8203   1.6571
 WLS  C11  C  CR15  0  -0.239  -33.8230  22.7612  -1.9405
 WLS  C12  C  CR15  0  -0.185  -33.5269  22.6773  -3.3307
 WLS  N02  N  NH1   0  -0.601  -37.1568  22.5060  -0.4164
 WLS  N07  N  N     0  -0.412  -42.1515  22.5986   0.2972
 WLS  S14  S  S2    0   0.206  -35.9204  21.8342  -3.0582
 WLS  H1   H  HCR5  0   0.290  -34.6244  22.0436  -5.1240
 WLS  H2   H  HCH2  0   0.252  -35.6395  21.1932   0.0672
 WLS  H3   H  HCH2  0   0.227  -35.2101  22.8593   0.4119
 WLS  H4   H  HCH2  0   0.258  -37.6801  21.2585   1.1447
 WLS  H5   H  HCH2  0   0.227  -37.5722  22.9345   1.6366
 WLS  H6   H  HCR6  0   0.264  -39.3977  21.7963  -1.4514
 WLS  H7   H  HCR6  0   0.260  -41.8515  21.9786  -1.6399
 WLS  H8   H  HCR6  0   0.261  -42.2151  23.2092   2.2606
 WLS  H9   H  HCR6  0   0.264  -39.7815  23.0857   2.6218
 WLS  H10  H  HCR5  0   0.258  -33.1286  23.1253  -1.1952
 WLS  H11  H  HCR5  0   0.263  -32.5841  22.9767  -3.7659
 WLS  H12  H  HNH1  0   0.354  -37.2839  23.4658  -0.7157

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
 WLS  C13  S14  aromatic  1.717  0.020  1.717
 WLS  C13  C12  aromatic  1.360  0.020  1.360
 WLS  S14  C10  aromatic  1.724  0.020  1.724
 WLS  C12  C11  aromatic  1.424  0.020  1.424
 WLS  C10  C11  aromatic  1.362  0.020  1.362
 WLS  C10  C01  single    1.493  0.020  1.493
 WLS  C01  N02  single    1.448  0.020  1.448
 WLS  N02  C03  single    1.445  0.020  1.445
 WLS  C05  C06  aromatic  1.386  0.020  1.386
 WLS  C05  C04  aromatic  1.391  0.020  1.391
 WLS  C06  N07  aromatic  1.329  0.020  1.329
 WLS  N07  C08  aromatic  1.329  0.020  1.329
 WLS  C04  C03  single    1.504  0.020  1.504
 WLS  C04  C09  aromatic  1.391  0.020  1.391
 WLS  C08  C09  aromatic  1.386  0.020  1.386
 WLS  C13  H1   single    0.930  0.020  1.080
 WLS  C01  H2   single    0.970  0.020  1.090
 WLS  C01  H3   single    0.970  0.020  1.090
 WLS  C03  H4   single    0.970  0.020  1.090
 WLS  C03  H5   single    0.970  0.020  1.090
 WLS  C05  H6   single    0.930  0.020  1.080
 WLS  C06  H7   single    0.930  0.020  1.080
 WLS  C08  H8   single    0.930  0.020  1.080
 WLS  C09  H9   single    0.930  0.020  1.080
 WLS  C11  H10  single    0.930  0.020  1.080
 WLS  C12  H11  single    0.930  0.020  1.080
 WLS  N02  H12  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
 WLS  S14  C10  C11  110.95  3.000
 WLS  C11  C10  C01  129.21  3.000
 WLS  S14  C10  C01  119.80  3.000
 WLS  H1   C13  S14  120.46  3.000
 WLS  H1   C13  C12  127.97  3.000
 WLS  S14  C13  C12  111.55  3.000
 WLS  H3   C01  H2   106.19  3.000
 WLS  H3   C01  N02  114.03  3.000
 WLS  H2   C01  N02  107.70  3.000
 WLS  H3   C01  C10  108.81  3.000
 WLS  H2   C01  C10  109.52  3.000
 WLS  N02  C01  C10  110.44  3.000
 WLS  H5   C03  H4   105.73  3.000
 WLS  H5   C03  N02  113.60  3.000
 WLS  H4   C03  N02  107.99  3.000
 WLS  H5   C03  C04  109.21  3.000
 WLS  H4   C03  C04  108.00  3.000
 WLS  N02  C03  C04  111.97  3.000
 WLS  C09  C04  C05  117.20  3.000
 WLS  C09  C04  C03  120.82  3.000
 WLS  C05  C04  C03  121.96  3.000
 WLS  H6   C05  C06  120.18  3.000
 WLS  H6   C05  C04  120.79  3.000
 WLS  C06  C05  C04  119.03  3.000
 WLS  H7   C06  N07  116.45  3.000
 WLS  H7   C06  C05  119.71  3.000
 WLS  N07  C06  C05  123.84  3.000
 WLS  H8   C08  N07  116.59  3.000
 WLS  H8   C08  C09  119.82  3.000
 WLS  N07  C08  C09  123.59  3.000
 WLS  H9   C09  C08  119.78  3.000
 WLS  H9   C09  C04  120.92  3.000
 WLS  C08  C09  C04  119.30  3.000
 WLS  H10  C11  C12  123.99  3.000
 WLS  H10  C11  C10  123.03  3.000
 WLS  C12  C11  C10  112.98  3.000
 WLS  H11  C12  C11  123.94  3.000
 WLS  H11  C12  C13  123.58  3.000
 WLS  C11  C12  C13  112.48  3.000
 WLS  H12  N02  C03  109.56  3.000
 WLS  H12  N02  C01  109.49  3.000
 WLS  C03  N02  C01  113.42  3.000
 WLS  C08  N07  C06  117.04  3.000
 WLS  C13  S14  C10   92.03  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
 WLS  CONST_01  C12  C13  S14  C10     0.00   0.0  0
 WLS  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 WLS  CONST_03  C11  C10  S14  C13     0.00   0.0  0
 WLS  CONST_04  N07  C06  C05  C04     0.00   0.0  0
 WLS  CONST_05  N07  C08  C09  C04     0.00   0.0  0
 WLS  CONST_06  C08  N07  C06  C05     0.00   0.0  0
 WLS  CONST_07  C08  C09  C04  C05     0.00   0.0  0
 WLS  CONST_08  C09  C04  C05  C06     0.00   0.0  0
 WLS  CONST_09  C09  C08  N07  C06     0.00   0.0  0
 WLS  CONST_10  S14  C13  C12  C11     0.00   0.0  0
 WLS  CONST_11  S14  C10  C11  C12     0.00   0.0  0
 WLS  CONST_12  C01  C10  S14  C13   180.00   0.0  0
 WLS  CONST_13  C12  C11  C10  C01   180.00   0.0  0
 WLS  CONST_14  C06  C05  C04  C03   180.00   0.0  0
 WLS  CONST_15  C08  C09  C04  C03   180.00   0.0  0
 WLS  CONST_16  H1   C13  S14  C10   180.00   0.0  0
 WLS  CONST_17  H11  C12  C11  C10   180.00   0.0  0
 WLS  CONST_18  H10  C11  C12  C13   180.00   0.0  0
 WLS  CONST_19  H7   C06  C05  C04   180.00   0.0  0
 WLS  CONST_20  H8   C08  C09  C04   180.00   0.0  0
 WLS  CONST_21  H9   C09  C04  C05   180.00   0.0  0
 WLS  CONST_22  H6   C05  C04  C09   180.00   0.0  0
 WLS  Var_01    N02  C03  C04  C05    30.13  30.0  2
 WLS  Var_02    N02  C01  C10  C11   145.93  30.0  2
 WLS  Var_03    C03  N02  C01  C10   174.07  30.0  3
 WLS  Var_04    C04  C03  N02  C01  -172.47  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
 WLS  plan-1  C10  0.020
 WLS  plan-1  C13  0.020
 WLS  plan-1  C01  0.020
 WLS  plan-1  C11  0.020
 WLS  plan-1  C12  0.020
 WLS  plan-1  S14  0.020
 WLS  plan-1  H1   0.020
 WLS  plan-1  H10  0.020
 WLS  plan-1  H11  0.020
 WLS  plan-2  C03  0.020
 WLS  plan-2  C04  0.020
 WLS  plan-2  C05  0.020
 WLS  plan-2  C06  0.020
 WLS  plan-2  C08  0.020
 WLS  plan-2  C09  0.020
 WLS  plan-2  N07  0.020
 WLS  plan-2  H6   0.020
 WLS  plan-2  H7   0.020
 WLS  plan-2  H8   0.020
 WLS  plan-2  H9   0.020

