# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 11:33:11 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: ~{N}-methyl-1-(3-thiophen-2-ylphenyl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1cccc(c1)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
 60L  60L  ~{N}-methyl-1-(3-thiophen-2-ylphenyl)methanamine  ligand  27  14  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_60L
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
 60L  S8   S  S2    0   0.211  -2.0172  -1.3520   0.4863
 60L  C14  C  CH3   0  -0.519   4.4366  -2.1392  -0.3885
 60L  N13  N  NH1   0  -0.587   3.2945  -1.2577  -0.5197
 60L  C2   C  CR6   0   0.107   2.0481   0.6455   0.3817
 60L  C3   C  CR16  0  -0.325   2.1488   2.0297   0.4615
 60L  C4   C  CR16  0  -0.221   1.0105   2.8225   0.3768
 60L  C5   C  CR16  0  -0.335  -0.2357   2.2439   0.2123
 60L  C6   C  CR6   0   0.170  -0.3588   0.8541   0.1181
 60L  C1   C  CR16  0  -0.366   0.7930   0.0721   0.2002
 60L  C7   C  CR5   0  -0.216  -1.6781   0.2497  -0.0676
 60L  C11  C  CR15  0  -0.244  -2.7894   0.7957  -0.6504
 60L  C10  C  CR15  0  -0.173  -3.9069  -0.0788  -0.6531
 60L  C9   C  CR15  0  -0.469  -3.6343  -1.2792  -0.0714
 60L  H1   H  HCH3  0   0.195   5.4062  -1.6222  -0.3767
 60L  H2   H  HCH3  0   0.223   4.3614  -2.7094   0.5396
 60L  H3   H  HCH3  0   0.234   4.4471  -2.8513  -1.2131
 60L  H4   H  HNH1  0   0.346   3.3180  -0.8181  -1.4315
 60L  H6   H  HCH2  0   0.239   3.2671  -0.7193   1.4744
 60L  H7   H  HCH2  0   0.214   4.1702   0.4108   0.4858
 60L  H8   H  HCR6  0   0.251   3.1199   2.4922   0.5918
 60L  H9   H  HCR6  0   0.258   1.0968   3.8992   0.4439
 60L  H10  H  HCR6  0   0.254  -1.1163   2.8718   0.1711
 60L  H11  H  HCR6  0   0.244   0.7270  -1.0055   0.1033
 60L  H12  H  HCR5  0   0.263  -2.8058   1.7865  -1.0833
 60L  H13  H  HCR5  0   0.268  -4.8684   0.1738  -1.0765
 60L  H14  H  HCR5  0   0.297  -4.2959  -2.1214   0.0603
 60L  C12  C  CH2   0  -0.319   3.2716  -0.2255   0.4962

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
 60L  C4   C3   aromatic  1.390  0.020  1.390
 60L  C4   C5   aromatic  1.384  0.020  1.384
 60L  C3   C2   aromatic  1.390  0.020  1.390
 60L  C14  N13  single    1.449  0.020  1.449
 60L  N13  C12  single    1.448  0.020  1.448
 60L  C5   C6   aromatic  1.398  0.020  1.398
 60L  C2   C12  single    1.506  0.020  1.506
 60L  C2   C1   aromatic  1.392  0.020  1.392
 60L  C6   C1   aromatic  1.395  0.020  1.395
 60L  C6   C7   single    1.463  0.020  1.463
 60L  C7   C11  aromatic  1.369  0.020  1.369
 60L  C7   S8   aromatic  1.728  0.020  1.728
 60L  C11  C10  aromatic  1.419  0.020  1.419
 60L  C10  C9   aromatic  1.362  0.020  1.362
 60L  S8   C9   aromatic  1.712  0.020  1.712
 60L  C14  H1   single    0.970  0.020  1.090
 60L  C14  H2   single    0.970  0.020  1.090
 60L  C14  H3   single    0.970  0.020  1.090
 60L  N13  H4   single    0.890  0.020  1.040
 60L  C12  H6   single    0.970  0.020  1.090
 60L  C12  H7   single    0.970  0.020  1.090
 60L  C3   H8   single    0.930  0.020  1.080
 60L  C4   H9   single    0.930  0.020  1.080
 60L  C5   H10  single    0.930  0.020  1.080
 60L  C1   H11  single    0.930  0.020  1.080
 60L  C11  H12  single    0.930  0.020  1.080
 60L  C10  H13  single    0.930  0.020  1.080
 60L  C9   H14  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
 60L  C9   S8   C7    92.38  3.000
 60L  H3   C14  H2   107.62  3.000
 60L  H3   C14  H1   107.89  3.000
 60L  H2   C14  H1   107.30  3.000
 60L  H3   C14  N13  109.68  3.000
 60L  H2   C14  N13  109.90  3.000
 60L  H1   C14  N13  114.23  3.000
 60L  H4   N13  C12  108.81  3.000
 60L  H4   N13  C14  109.11  3.000
 60L  C12  N13  C14  112.49  3.000
 60L  C1   C2   C3   118.88  3.000
 60L  C1   C2   C12  120.28  3.000
 60L  C3   C2   C12  120.84  3.000
 60L  H8   C3   C4   119.86  3.000
 60L  H8   C3   C2   119.79  3.000
 60L  C4   C3   C2   120.35  3.000
 60L  H9   C4   C5   119.68  3.000
 60L  H9   C4   C3   119.90  3.000
 60L  C5   C4   C3   120.42  3.000
 60L  H10  C5   C6   120.16  3.000
 60L  H10  C5   C4   119.65  3.000
 60L  C6   C5   C4   120.19  3.000
 60L  C7   C6   C1   121.37  3.000
 60L  C7   C6   C5   119.90  3.000
 60L  C1   C6   C5   118.73  3.000
 60L  H11  C1   C6   120.12  3.000
 60L  H11  C1   C2   118.43  3.000
 60L  C6   C1   C2   121.43  3.000
 60L  C11  C7   C6   128.43  3.000
 60L  C11  C7   S8   110.30  3.000
 60L  C6   C7   S8   121.27  3.000
 60L  H12  C11  C10  123.50  3.000
 60L  H12  C11  C7   123.25  3.000
 60L  C10  C11  C7   113.23  3.000
 60L  H13  C10  C9   123.48  3.000
 60L  H13  C10  C11  123.88  3.000
 60L  C9   C10  C11  112.64  3.000
 60L  H14  C9   C10  128.14  3.000
 60L  H14  C9   S8   120.41  3.000
 60L  C10  C9   S8   111.45  3.000
 60L  H7   C12  H6   105.80  3.000
 60L  H7   C12  C2   109.15  3.000
 60L  H6   C12  C2   108.97  3.000
 60L  H7   C12  N13  113.10  3.000
 60L  H6   C12  N13  107.76  3.000
 60L  C2   C12  N13  111.81  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
 60L  CONST_03  C10  C11  C7   S8      0.00   0.0  0
 60L  CONST_04  C11  C10  C9   S8      0.00   0.0  0
 60L  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 60L  CONST_06  C5   C6   C1   C2      0.00   0.0  0
 60L  CONST_07  C7   C6   C1   C2    180.00   0.0  0
 60L  CONST_08  C6   C5   C4   C3      0.00   0.0  0
 60L  CONST_09  C6   C1   C2   C3      0.00   0.0  0
 60L  CONST_10  C1   C2   C3   C4      0.00   0.0  0
 60L  CONST_11  C1   C6   C5   C4      0.00   0.0  0
 60L  CONST_12  C7   C6   C5   C4    180.00   0.0  0
 60L  CONST_14  C10  C11  C7   C6    180.00   0.0  0
 60L  CONST_15  C9   S8   C7   C6    180.00   0.0  0
 60L  CONST_17  C9   C10  C11  C7      0.00   0.0  0
 60L  CONST_18  C10  C9   S8   C7      0.00   0.0  0
 60L  CONST_19  C9   S8   C7   C11     0.00   0.0  0
 60L  CONST_20  C4   C3   C2   C12   180.00   0.0  0
 60L  CONST_21  C6   C1   C2   C12   180.00   0.0  0
 60L  CONST_22  H12  C11  C7   S8    180.00   0.0  0
 60L  CONST_23  H13  C10  C9   S8    180.00   0.0  0
 60L  CONST_24  H9   C4   C3   C2    180.00   0.0  0
 60L  CONST_25  H10  C5   C4   C3    180.00   0.0  0
 60L  CONST_26  H11  C1   C2   C3    180.00   0.0  0
 60L  CONST_27  H8   C3   C4   C5    180.00   0.0  0
 60L  CONST_28  H14  C9   S8   C7    180.00   0.0  0
 60L  Var_01    C3   C2   C12  N13  -134.45  30.0  2
 60L  Var_02    C2   C12  N13  C14  -177.56  30.0  3
 60L  Var_03    H1   C14  N13  C12   -54.78  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
 60L  plan-1  S8   0.020
 60L  plan-1  C6   0.020
 60L  plan-1  C7   0.020
 60L  plan-1  C11  0.020
 60L  plan-1  C10  0.020
 60L  plan-1  C9   0.020
 60L  plan-1  H12  0.020
 60L  plan-1  H13  0.020
 60L  plan-1  H14  0.020
 60L  plan-2  C2   0.020
 60L  plan-2  C3   0.020
 60L  plan-2  C4   0.020
 60L  plan-2  C5   0.020
 60L  plan-2  C6   0.020
 60L  plan-2  C1   0.020
 60L  plan-2  C7   0.020
 60L  plan-2  H8   0.020
 60L  plan-2  H9   0.020
 60L  plan-2  H10  0.020
 60L  plan-2  H11  0.020
 60L  plan-2  C12  0.020

