# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 09:36:32 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: 1-(3-methylthiophen-2-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccsc1CN
#
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
 02T  02T  1-(3-methylthiophen-2-yl)methanamine  ligand  17  8  .  2021-07-27  2021-07-27  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_02T
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
 02T  C4    C  CR15  0  -0.475   1.9428  -0.0891  -0.5163
 02T  C5    C  CR15  0  -0.212   1.5324   1.1806  -0.2599
 02T  C6    C  CR5   0   0.134   0.1441   1.2699   0.0686
 02T  C7    C  CH3   0  -0.732  -0.5331   2.5628   0.4050
 02T  S3    S  S2    0   0.193   0.6500  -1.2067  -0.3728
 02T  C1    C  CR5   0  -0.218  -0.4612   0.0452   0.0494
 02T  C2    C  CH2   0  -0.339  -1.8711  -0.3305   0.3746
 02T  N29   N  NH2   0  -0.796  -2.2480  -1.5482  -0.3218
 02T  H4    H  HCR5  0   0.285   2.9290  -0.4220  -0.8010
 02T  H5    H  HCR5  0   0.257   2.1878   2.0402  -0.3077
 02T  H7    H  HCH3  0   0.244  -0.1360   3.3793  -0.1984
 02T  H7A   H  HCH3  0   0.239  -1.6090   2.5185   0.2379
 02T  H7B   H  HCH3  0   0.245  -0.3804   2.8323   1.4521
 02T  H2    H  HCH2  0   0.248  -1.9563  -0.5204   1.4485
 02T  H2A   H  HCH2  0   0.221  -2.5243   0.5277   0.1697
 02T  HN29  H  HNH2  0   0.359  -3.1327  -1.8824   0.0368
 02T  H1    H  HNH2  0   0.348  -2.3960  -1.3506  -1.3033

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
 02T  C5   C4    aromatic  1.359  0.020  1.359
 02T  C4   S3    aromatic  1.715  0.020  1.715
 02T  C4   H4    single    0.930  0.020  1.080
 02T  C6   C5    aromatic  1.429  0.020  1.429
 02T  C5   H5    single    0.930  0.020  1.080
 02T  C7   C6    single    1.498  0.020  1.498
 02T  C6   C1    aromatic  1.366  0.020  1.366
 02T  C7   H7    single    0.970  0.020  1.090
 02T  C7   H7A   single    0.970  0.020  1.090
 02T  C7   H7B   single    0.970  0.020  1.090
 02T  C1   S3    aromatic  1.726  0.020  1.726
 02T  C2   C1    single    1.495  0.020  1.495
 02T  C2   N29   single    1.453  0.020  1.453
 02T  C2   H2    single    0.970  0.020  1.090
 02T  C2   H2A   single    0.970  0.020  1.090
 02T  N29  HN29  single    0.890  0.020  1.040
 02T  N29  H1    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
 02T  H4    C4   S3    120.66  3.000
 02T  H4    C4   C5    127.89  3.000
 02T  S3    C4   C5    111.44  3.000
 02T  H5    C5   C6    123.28  3.000
 02T  H5    C5   C4    123.44  3.000
 02T  C6    C5   C4    113.27  3.000
 02T  C1    C6   C7    125.21  3.000
 02T  C1    C6   C5    111.78  3.000
 02T  C7    C6   C5    123.01  3.000
 02T  H7B   C7   H7A   107.17  3.000
 02T  H7B   C7   H7    107.16  3.000
 02T  H7A   C7   H7    107.77  3.000
 02T  H7B   C7   C6    111.42  3.000
 02T  H7A   C7   C6    112.14  3.000
 02T  H7    C7   C6    110.95  3.000
 02T  C1    S3   C4     91.89  3.000
 02T  C2    C1   S3    118.56  3.000
 02T  C2    C1   C6    129.79  3.000
 02T  S3    C1   C6    111.61  3.000
 02T  H2A   C2   H2    105.82  3.000
 02T  H2A   C2   N29   114.30  3.000
 02T  H2    C2   N29   107.75  3.000
 02T  H2A   C2   C1    108.91  3.000
 02T  H2    C2   C1    109.31  3.000
 02T  N29   C2   C1    110.55  3.000
 02T  H1    N29  HN29  106.28  3.000
 02T  H1    N29  C2    109.83  3.000
 02T  HN29  N29  C2    109.51  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
 02T  CONST_01  C1    C6   C5  C4    0.00   0.0  0
 02T  CONST_02  C6    C1   S3  C4    0.00   0.0  0
 02T  CONST_03  C1    S3   C4  C5    0.00   0.0  0
 02T  CONST_04  S3    C1   C6  C5    0.00   0.0  0
 02T  CONST_05  S3    C4   C5  C6    0.00   0.0  0
 02T  CONST_06  C7    C6   C5  C4  180.00   0.0  0
 02T  CONST_07  C2    C1   S3  C4  180.00   0.0  0
 02T  CONST_08  C2    C1   C6  C5  180.00   0.0  0
 02T  CONST_09  S3    C1   C6  C7  180.00   0.0  0
 02T  CONST_10  H4    C4   C5  C6  180.00   0.0  0
 02T  CONST_11  H5    C5   C4  S3  180.00   0.0  0
 02T  Var_01    N29   C2   C1  C6  154.34  30.0  1
 02T  Var_02    H7    C7   C6  C5   36.58  30.0  2
 02T  Var_03    HN29  N29  C2  C1  169.53  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
 02T  plan-1  C4  0.020
 02T  plan-1  C5  0.020
 02T  plan-1  C6  0.020
 02T  plan-1  C7  0.020
 02T  plan-1  S3  0.020
 02T  plan-1  C1  0.020
 02T  plan-1  C2  0.020
 02T  plan-1  H4  0.020
 02T  plan-1  H5  0.020

