# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 16:52:32 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(cc1C(=O)N[C@@H](CN)c2ccccc2)c3ccccc3Cl
#
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
 94K  94K  ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide  ligand  44  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_94K
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
 94K  C16  C   CR16  0  -0.270  -5.1393   2.3959  -1.3013
 94K  C21  C   CR16  0  -0.227   5.6127   0.5332   1.3856
 94K  C15  C   CR16  0  -0.241  -5.7469   1.1491  -1.2361
 94K  C17  C   CR16  0  -0.240  -3.9214   2.5981  -0.6645
 94K  C22  C   CR16  0  -0.272   5.5607   1.9190   1.4270
 94K  C20  C   CR16  0  -0.325   4.5330  -0.1813   0.8960
 94K  C14  C   CR16  0  -0.310  -5.1378   0.1143  -0.5387
 94K  C18  C   CR16  0  -0.307  -3.3158   1.5605   0.0314
 94K  C23  C   CR16  0  -0.189   4.4319   2.5806   0.9701
 94K  C5   C   CR15  0  -0.232   0.9392  -0.2786   0.1837
 94K  C19  C   CR6   0   0.201   3.3801   0.4575   0.4291
 94K  C6   C   CR5   0   0.056   0.1666  -1.2611  -0.5006
 94K  C13  C   CR6   0   0.155  -3.9183   0.3076   0.1016
 94K  C24  C   CR6   0  -0.129   3.3591   1.8546   0.4742
 94K  C4   C   CR5   0  -0.225   2.2710  -0.3465  -0.0894
 94K  C2   C   CR5   0  -0.217   0.9312  -2.0755  -1.3009
 94K  C1   C   CH3   0  -0.704   0.5304  -3.2097  -2.1836
 94K  C11  C   CH2   0  -0.296  -3.6103  -0.6520   2.3892
 94K  C10  C   CH1   0  -0.149  -3.3010  -0.8173   0.9021
 94K  N9   N   NH1   0  -0.671  -1.8660  -0.8967   0.7186
 94K  N12  N   NH2   0  -0.795  -3.2267  -1.8330   3.1417
 94K  O8   O   O     0  -0.478  -1.9731  -1.9053  -1.2924
 94K  S3   S   S2    0   0.264   2.5824  -1.6343  -1.1962
 94K  CL1  CL  CL    0  -0.124   1.9993   2.7435  -0.1288
 94K  H1   H   HCR6  0   0.255  -5.6081   3.2031  -1.8488
 94K  H3   H   HCR6  0   0.255  -6.6926   0.9784  -1.7344
 94K  H4   H   HCR6  0   0.255  -3.4404   3.5669  -0.7090
 94K  H5   H   HCR6  0   0.272   6.3958   2.4892   1.8108
 94K  H6   H   HCR6  0   0.267   4.5719  -1.2635   0.8863
 94K  H7   H   HCR6  0   0.249  -5.6135  -0.8590  -0.4982
 94K  H8   H   HCR6  0   0.237  -2.3622   1.7360   0.5152
 94K  H9   H   HCR6  0   0.284   4.3870   3.6609   0.9913
 94K  H10  H   HCR5  0   0.263   0.5257   0.4621   0.8533
 94K  H11  H   HCH3  0   0.262   0.0188  -2.8495  -3.0756
 94K  H12  H   HCH3  0   0.247   1.3981  -3.7839  -2.5048
 94K  H13  H   HCH3  0   0.259  -0.1486  -3.8857  -1.6672
 94K  H14  H   HCH2  0   0.208  -3.1472   0.2824   2.7422
 94K  H15  H   HCH2  0   0.248  -4.6885  -0.5155   2.4866
 94K  H16  H   HCH1  0   0.260  -3.7434  -1.7623   0.5768
 94K  H17  H   HNH1  0   0.407  -1.2751  -0.4974   1.4301
 94K  H18  H   HNH2  0   0.343  -2.2187  -1.8995   3.2017
 94K  H19  H   HNH2  0   0.356  -3.5486  -1.7367   4.0960
 94K  C7   C   C     0   0.528  -1.3084  -1.3880  -0.4060
 94K  H2   H   HCR6  0   0.269   6.4880   0.0076   1.7422

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
 94K  C16  C15  aromatic  1.389  0.020  1.389
 94K  C16  C17  aromatic  1.389  0.020  1.389
 94K  C15  C14  aromatic  1.389  0.020  1.389
 94K  C17  C18  aromatic  1.388  0.020  1.388
 94K  C14  C13  aromatic  1.391  0.020  1.391
 94K  C18  C13  aromatic  1.392  0.020  1.392
 94K  C13  C10  single    1.512  0.020  1.512
 94K  C11  C10  single    1.528  0.020  1.528
 94K  C11  N12  single    1.452  0.020  1.452
 94K  C10  N9   single    1.449  0.020  1.449
 94K  N9   C7   single    1.348  0.020  1.348
 94K  O8   C7   double    1.223  0.020  1.223
 94K  C7   C6   single    1.484  0.020  1.484
 94K  C1   C2   single    1.492  0.020  1.492
 94K  C6   C2   aromatic  1.374  0.020  1.374
 94K  C6   C5   aromatic  1.425  0.020  1.425
 94K  C2   S3   aromatic  1.712  0.020  1.712
 94K  C5   C4   aromatic  1.361  0.020  1.361
 94K  CL1  C24  single    1.733  0.020  1.733
 94K  S3   C4   aromatic  1.726  0.020  1.726
 94K  C4   C19  single    1.465  0.020  1.465
 94K  C24  C19  aromatic  1.398  0.020  1.398
 94K  C24  C23  aromatic  1.387  0.020  1.387
 94K  C19  C20  aromatic  1.398  0.020  1.398
 94K  C23  C22  aromatic  1.386  0.020  1.386
 94K  C20  C21  aromatic  1.384  0.020  1.384
 94K  C22  C21  aromatic  1.387  0.020  1.387
 94K  C16  H1   single    0.930  0.020  1.080
 94K  C21  H2   single    0.930  0.020  1.080
 94K  C15  H3   single    0.930  0.020  1.080
 94K  C17  H4   single    0.930  0.020  1.080
 94K  C22  H5   single    0.930  0.020  1.080
 94K  C20  H6   single    0.930  0.020  1.080
 94K  C14  H7   single    0.930  0.020  1.080
 94K  C18  H8   single    0.930  0.020  1.080
 94K  C23  H9   single    0.930  0.020  1.080
 94K  C5   H10  single    0.930  0.020  1.080
 94K  C1   H11  single    0.970  0.020  1.090
 94K  C1   H12  single    0.970  0.020  1.090
 94K  C1   H13  single    0.970  0.020  1.090
 94K  C11  H14  single    0.970  0.020  1.090
 94K  C11  H15  single    0.970  0.020  1.090
 94K  C10  H16  single    0.970  0.020  1.090
 94K  N9   H17  single    0.860  0.020  1.020
 94K  N12  H18  single    0.890  0.020  1.040
 94K  N12  H19  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
 94K  H1   C16  C17  120.21  3.000
 94K  H1   C16  C15  120.26  3.000
 94K  C17  C16  C15  119.53  3.000
 94K  H2   C21  C20  119.80  3.000
 94K  H2   C21  C22  120.40  3.000
 94K  C20  C21  C22  119.79  3.000
 94K  H3   C15  C14  119.79  3.000
 94K  H3   C15  C16  120.16  3.000
 94K  C14  C15  C16  120.05  3.000
 94K  H4   C17  C18  119.71  3.000
 94K  H4   C17  C16  120.06  3.000
 94K  C18  C17  C16  120.22  3.000
 94K  H5   C22  C23  119.62  3.000
 94K  H5   C22  C21  120.54  3.000
 94K  C23  C22  C21  119.84  3.000
 94K  H6   C20  C19  118.89  3.000
 94K  H6   C20  C21  119.41  3.000
 94K  C19  C20  C21  121.70  3.000
 94K  H7   C14  C13  119.50  3.000
 94K  H7   C14  C15  119.69  3.000
 94K  C13  C14  C15  120.81  3.000
 94K  H8   C18  C13  120.27  3.000
 94K  H8   C18  C17  119.11  3.000
 94K  C13  C18  C17  120.61  3.000
 94K  H9   C23  C24  119.85  3.000
 94K  H9   C23  C22  120.28  3.000
 94K  C24  C23  C22  119.87  3.000
 94K  H10  C5   C4   122.20  3.000
 94K  H10  C5   C6   124.24  3.000
 94K  C4   C5   C6   113.56  3.000
 94K  C4   C19  C24  123.27  3.000
 94K  C24  C19  C20  117.27  3.000
 94K  C4   C19  C20  119.46  3.000
 94K  C7   C6   C2   122.67  3.000
 94K  C2   C6   C5   112.75  3.000
 94K  C7   C6   C5   124.57  3.000
 94K  C10  C13  C18  121.30  3.000
 94K  C10  C13  C14  119.88  3.000
 94K  C18  C13  C14  118.77  3.000
 94K  CL1  C24  C19  120.88  3.000
 94K  C19  C24  C23  121.53  3.000
 94K  CL1  C24  C23  117.57  3.000
 94K  S3   C4   C19  119.99  3.000
 94K  C19  C4   C5   129.97  3.000
 94K  S3   C4   C5   110.02  3.000
 94K  S3   C2   C1   119.41  3.000
 94K  S3   C2   C6   110.38  3.000
 94K  C1   C2   C6   130.21  3.000
 94K  H13  C1   H12  108.03  3.000
 94K  H13  C1   H11  107.51  3.000
 94K  H12  C1   H11  107.88  3.000
 94K  H13  C1   C2   111.04  3.000
 94K  H12  C1   C2   111.18  3.000
 94K  H11  C1   C2   111.05  3.000
 94K  H15  C11  H14  106.31  3.000
 94K  H15  C11  N12  108.45  3.000
 94K  H14  C11  N12  114.39  3.000
 94K  H15  C11  C10  107.49  3.000
 94K  H14  C11  C10  108.59  3.000
 94K  N12  C11  C10  111.28  3.000
 94K  H16  C10  N9   108.41  3.000
 94K  H16  C10  C11  107.53  3.000
 94K  N9   C10  C11  109.25  3.000
 94K  H16  C10  C13  108.68  3.000
 94K  N9   C10  C13  112.21  3.000
 94K  C11  C10  C13  110.61  3.000
 94K  H17  N9   C10  118.03  3.000
 94K  H17  N9   C7   119.41  3.000
 94K  C10  N9   C7   122.36  3.000
 94K  H19  N12  H18  105.50  3.000
 94K  H19  N12  C11  109.11  3.000
 94K  H18  N12  C11  110.32  3.000
 94K  C2   S3   C4    93.30  3.000
 94K  O8   C7   N9   122.29  3.000
 94K  O8   C7   C6   122.03  3.000
 94K  N9   C7   C6   115.68  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
 94K  CONST_01  C13  C14  C15  C16    0.00   0.0  0
 94K  CONST_02  C13  C18  C17  C16    0.00   0.0  0
 94K  CONST_03  C4   C19  C20  C21  180.00   0.0  0
 94K  CONST_04  C24  C19  C20  C21    0.00   0.0  0
 94K  CONST_05  C24  C23  C22  C21    0.00   0.0  0
 94K  CONST_06  C18  C17  C16  C15    0.00   0.0  0
 94K  CONST_07  C18  C13  C14  C15    0.00   0.0  0
 94K  CONST_08  C14  C15  C16  C17    0.00   0.0  0
 94K  CONST_09  C14  C13  C18  C17    0.00   0.0  0
 94K  CONST_10  C19  C24  C23  C22    0.00   0.0  0
 94K  CONST_11  C19  C20  C21  C22    0.00   0.0  0
 94K  CONST_14  C23  C24  C19  C20    0.00   0.0  0
 94K  CONST_15  C23  C22  C21  C20    0.00   0.0  0
 94K  CONST_16  C4   C19  C24  C23  180.00   0.0  0
 94K  CONST_17  S3   C2   C6   C5     0.00   0.0  0
 94K  CONST_18  C2   S3   C4   C5     0.00   0.0  0
 94K  CONST_20  C6   C5   C4   C19  180.00   0.0  0
 94K  CONST_21  C2   S3   C4   C19  180.00   0.0  0
 94K  CONST_22  C4   S3   C2   C6     0.00   0.0  0
 94K  CONST_23  S3   C4   C5   C6     0.00   0.0  0
 94K  CONST_25  C2   C6   C5   C4     0.00   0.0  0
 94K  CONST_26  C10  C13  C14  C15  180.00   0.0  0
 94K  CONST_27  C10  C13  C18  C17  180.00   0.0  0
 94K  CONST_28  CL1  C24  C23  C22  180.00   0.0  0
 94K  CONST_29  CL1  C24  C19  C20  180.00   0.0  0
 94K  CONST_30  C1   C2   C6   C5   180.00   0.0  0
 94K  CONST_31  C7   C6   C5   C4   180.00   0.0  0
 94K  CONST_32  C1   C2   S3   C4   180.00   0.0  0
 94K  CONST_33  CL1  C24  C19  C4     0.00   0.0  0
 94K  CONST_34  S3   C2   C6   C7   180.00   0.0  0
 94K  CONST_35  H7   C14  C15  C16  180.00   0.0  0
 94K  CONST_36  H8   C18  C17  C16  180.00   0.0  0
 94K  CONST_37  H9   C23  C22  C21  180.00   0.0  0
 94K  CONST_38  H4   C17  C16  C15  180.00   0.0  0
 94K  CONST_39  H3   C15  C16  C17  180.00   0.0  0
 94K  CONST_40  H6   C20  C21  C22  180.00   0.0  0
 94K  CONST_41  H5   C22  C21  C20  180.00   0.0  0
 94K  CONST_42  H1   C16  C15  C14  180.00   0.0  0
 94K  CONST_43  H2   C21  C22  C23  180.00   0.0  0
 94K  CONST_44  H10  C5   C4   C19    0.00   0.0  0
 94K  CONST_45  C10  N9   C7   C6   180.00   0.0  0
 94K  CONST_46  H17  N9   C7   C6     0.00   0.0  0
 94K  CONST_47  O8   C7   N9   C10    0.00   0.0  0
 94K  Var_01    N9   C7   C6   C5   -24.82  30.0  2
 94K  Var_02    H11  C1   C2   C6    72.68  30.0  2
 94K  Var_03    H18  N12  C11  C10   71.51  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 94K  chir_01  C10  C13  C11  N9  positiv

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
 94K  plan-1  C5   0.020
 94K  plan-1  C19  0.020
 94K  plan-1  C6   0.020
 94K  plan-1  C4   0.020
 94K  plan-1  C2   0.020
 94K  plan-1  C1   0.020
 94K  plan-1  S3   0.020
 94K  plan-1  H10  0.020
 94K  plan-1  C7   0.020
 94K  plan-2  C16  0.020
 94K  plan-2  C15  0.020
 94K  plan-2  C17  0.020
 94K  plan-2  C14  0.020
 94K  plan-2  C18  0.020
 94K  plan-2  C13  0.020
 94K  plan-2  C10  0.020
 94K  plan-2  H1   0.020
 94K  plan-2  H3   0.020
 94K  plan-2  H4   0.020
 94K  plan-2  H7   0.020
 94K  plan-2  H8   0.020
 94K  plan-3  C21  0.020
 94K  plan-3  C22  0.020
 94K  plan-3  C20  0.020
 94K  plan-3  C23  0.020
 94K  plan-3  C19  0.020
 94K  plan-3  C24  0.020
 94K  plan-3  C4   0.020
 94K  plan-3  CL1  0.020
 94K  plan-3  H5   0.020
 94K  plan-3  H6   0.020
 94K  plan-3  H9   0.020
 94K  plan-3  H2   0.020
 94K  plan-4  C6   0.020
 94K  plan-4  C10  0.020
 94K  plan-4  N9   0.020
 94K  plan-4  O8   0.020
 94K  plan-4  H17  0.020
 94K  plan-4  C7   0.020

