# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 10:42:13 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 1-(4-thiophen-2-ylphenyl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(cc1)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
 80G  80G  1-(4-thiophen-2-ylphenyl)methanamine  ligand  24  13  .  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_80G
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
 80G  C1    C  CR6   0   0.128   0.1403   0.1193   0.0585
 80G  C2    C  CR16  0  -0.306  -0.7019   1.1929  -0.2470
 80G  C3    C  CR16  0  -0.264  -2.0772   1.0662  -0.1595
 80G  C4    C  CR6   0   0.086  -2.6646  -0.1359   0.2322
 80G  C5    C  CR16  0  -0.293  -1.8271  -1.2075   0.5226
 80G  C6    C  CR16  0  -0.305  -0.4478  -1.0851   0.4449
 80G  C7    C  CR5   0  -0.213   1.5923   0.2710  -0.0247
 80G  C9    C  CR15  0  -0.471   4.0297  -0.1194  -0.2919
 80G  C10   C  CR15  0  -0.173   3.7363   1.1762   0.0062
 80G  C11   C  CR15  0  -0.245   2.3431   1.4004   0.1578
 80G  C12   C  CH2   0  -0.346  -4.1598  -0.2686   0.3594
 80G  N13   N  NH2   0  -0.792  -4.8528   0.3404  -0.7636
 80G  S8    S  S2    0   0.210   2.6122  -1.0745  -0.3946
 80G  H2    H  HCR6  0   0.251  -0.2776   2.1334  -0.5753
 80G  H3    H  HCR6  0   0.249  -2.7061   1.9102  -0.4124
 80G  H5    H  HCR6  0   0.252  -2.2551  -2.1565   0.8238
 80G  H6    H  HCR6  0   0.251   0.1699  -1.9375   0.7024
 80G  H9    H  HCR5  0   0.296   4.9994  -0.5616  -0.4601
 80G  H10   H  HCR5  0   0.268   4.4868   1.9446   0.1217
 80G  H11   H  HCR5  0   0.263   1.9167   2.3595   0.4167
 80G  H12   H  HCH2  0   0.216  -4.4052  -1.3275   0.5160
 80G  H12A  H  HCH2  0   0.240  -4.4804   0.2492   1.2683
 80G  HN13  H  HNH2  0   0.344  -4.7126  -0.2239  -1.5922
 80G  HN1A  H  HNH2  0   0.353  -5.8486   0.3325  -0.5846

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
 80G  C2   C1    aromatic  1.398  0.020  1.398
 80G  C1   C6    aromatic  1.395  0.020  1.395
 80G  C1   C7    single    1.462  0.020  1.462
 80G  C3   C2    aromatic  1.384  0.020  1.384
 80G  C2   H2    single    0.930  0.020  1.080
 80G  C3   C4    aromatic  1.394  0.020  1.394
 80G  C3   H3    single    0.930  0.020  1.080
 80G  C12  C4    single    1.506  0.020  1.506
 80G  C4   C5    aromatic  1.391  0.020  1.391
 80G  C5   C6    aromatic  1.387  0.020  1.387
 80G  C5   H5    single    0.930  0.020  1.080
 80G  C6   H6    single    0.930  0.020  1.080
 80G  C7   S8    aromatic  1.728  0.020  1.728
 80G  C7   C11   aromatic  1.368  0.020  1.368
 80G  S8   C9    aromatic  1.712  0.020  1.712
 80G  C9   C10   aromatic  1.361  0.020  1.361
 80G  C9   H9    single    0.930  0.020  1.080
 80G  C11  C10   aromatic  1.419  0.020  1.419
 80G  C10  H10   single    0.930  0.020  1.080
 80G  C11  H11   single    0.930  0.020  1.080
 80G  C12  N13   single    1.453  0.020  1.453
 80G  C12  H12   single    0.970  0.020  1.090
 80G  C12  H12A  single    0.970  0.020  1.090
 80G  N13  HN13  single    0.890  0.020  1.040
 80G  N13  HN1A  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
 80G  C7    C1   C6    121.60  3.000
 80G  C7    C1   C2    120.40  3.000
 80G  C6    C1   C2    118.00  3.000
 80G  H2    C2   C3    119.22  3.000
 80G  H2    C2   C1    119.81  3.000
 80G  C3    C2   C1    120.96  3.000
 80G  H3    C3   C4    119.55  3.000
 80G  H3    C3   C2    119.42  3.000
 80G  C4    C3   C2    121.03  3.000
 80G  C12   C4   C5    120.81  3.000
 80G  C5    C4   C3    117.99  3.000
 80G  C12   C4   C3    121.19  3.000
 80G  H5    C5   C6    119.05  3.000
 80G  H5    C5   C4    119.67  3.000
 80G  C6    C5   C4    121.28  3.000
 80G  H6    C6   C5    118.95  3.000
 80G  H6    C6   C1    120.31  3.000
 80G  C5    C6   C1    120.73  3.000
 80G  S8    C7   C11   110.32  3.000
 80G  C11   C7   C1    128.52  3.000
 80G  S8    C7   C1    121.16  3.000
 80G  H9    C9   S8    120.40  3.000
 80G  H9    C9   C10   128.16  3.000
 80G  S8    C9   C10   111.44  3.000
 80G  H10   C10  C11   123.93  3.000
 80G  H10   C10  C9    123.40  3.000
 80G  C11   C10  C9    112.66  3.000
 80G  H11   C11  C10   123.57  3.000
 80G  H11   C11  C7    123.21  3.000
 80G  C10   C11  C7    113.20  3.000
 80G  H12A  C12  H12   105.81  3.000
 80G  H12A  C12  N13   107.69  3.000
 80G  H12   C12  N13   114.06  3.000
 80G  H12A  C12  C4    108.62  3.000
 80G  H12   C12  C4    108.59  3.000
 80G  N13   C12  C4    111.78  3.000
 80G  HN1A  N13  HN13  106.07  3.000
 80G  HN1A  N13  C12   109.23  3.000
 80G  HN13  N13  C12   109.45  3.000
 80G  C9    S8   C7     92.38  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
 80G  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 80G  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 80G  CONST_03  C9    S8   C7   C1   180.00   0.0  0
 80G  CONST_04  C10   C11  C7   C1   180.00   0.0  0
 80G  CONST_05  C5    C6   C1   C2     0.00   0.0  0
 80G  CONST_08  C5    C4   C3   C2     0.00   0.0  0
 80G  CONST_09  C6    C1   C2   C3     0.00   0.0  0
 80G  CONST_10  C7    C1   C2   C3   180.00   0.0  0
 80G  CONST_11  C6    C5   C4   C3     0.00   0.0  0
 80G  CONST_12  C7    C1   C6   C5   180.00   0.0  0
 80G  CONST_15  C10   C9   S8   C7     0.00   0.0  0
 80G  CONST_16  C9    C10  C11  C7     0.00   0.0  0
 80G  CONST_17  C11   C7   S8   C9     0.00   0.0  0
 80G  CONST_18  S8    C7   C11  C10    0.00   0.0  0
 80G  CONST_19  S8    C9   C10  C11    0.00   0.0  0
 80G  CONST_20  C12   C4   C3   C2   180.00   0.0  0
 80G  CONST_21  C12   C4   C5   C6   180.00   0.0  0
 80G  CONST_22  H3    C3   C2   C1   180.00   0.0  0
 80G  CONST_23  H5    C5   C6   C1   180.00   0.0  0
 80G  CONST_24  H11   C11  C7   C1     0.00   0.0  0
 80G  CONST_25  H6    C6   C1   C2   180.00   0.0  0
 80G  CONST_26  H2    C2   C3   C4   180.00   0.0  0
 80G  CONST_27  H9    C9   S8   C7   180.00   0.0  0
 80G  CONST_28  H10   C10  C11  C7   180.00   0.0  0
 80G  Var_01    N13   C12  C4   C3    44.18  30.0  3
 80G  Var_02    HN13  N13  C12  C4    71.28  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
 80G  plan-1  C1   0.020
 80G  plan-1  C7   0.020
 80G  plan-1  C9   0.020
 80G  plan-1  C10  0.020
 80G  plan-1  C11  0.020
 80G  plan-1  S8   0.020
 80G  plan-1  H9   0.020
 80G  plan-1  H10  0.020
 80G  plan-1  H11  0.020
 80G  plan-2  C1   0.020
 80G  plan-2  C2   0.020
 80G  plan-2  C3   0.020
 80G  plan-2  C4   0.020
 80G  plan-2  C5   0.020
 80G  plan-2  C6   0.020
 80G  plan-2  C7   0.020
 80G  plan-2  C12  0.020
 80G  plan-2  H2   0.020
 80G  plan-2  H3   0.020
 80G  plan-2  H5   0.020
 80G  plan-2  H6   0.020

