# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 09:59:58 2021
#   Inital geometry file: a 75 line input string
#   Ligand name: 4-methyl-5-phenyl-thiophene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(sc1c2ccccc2)C(N)=N
#
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
 L1T  L1T  4-methyl-5-phenyl-thiophene-2-carboximidamide  ligand  27  15  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L1T
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
 L1T  N1    N  NH2   0  -0.828  -20.2073  -15.6558   -5.9284
 L1T  C4    C  CR5   0  -0.189  -20.3012  -17.8488   -6.8932
 L1T  C5    C  C     0   0.343  -20.7070  -16.4371   -6.9291
 L1T  C6    C  CR5   0  -0.281  -20.0052  -20.2392   -7.4661
 L1T  C7    C  CR6   0   0.092  -20.0466  -21.5322   -8.1541
 L1T  C8    C  CR16  0  -0.312  -19.8582  -21.6110   -9.5368
 L1T  C10   C  CR16  0  -0.263  -20.1340  -24.0010   -9.4708
 L1T  C11   C  CR16  0  -0.237  -20.3261  -23.9343   -8.0972
 L1T  C12   C  CR16  0  -0.309  -20.2878  -22.7110   -7.4443
 L1T  C2    C  CR5   0   0.185  -19.4064  -19.9135   -6.2730
 L1T  C3    C  CR15  0  -0.247  -19.5870  -18.5390   -5.9578
 L1T  C9    C  CR16  0  -0.238  -19.9045  -22.8341  -10.1882
 L1T  N2    N  N     0  -0.659  -21.5210  -16.0805   -7.8481
 L1T  S1    S  S2    0   0.252  -20.7818  -18.8736   -8.1828
 L1T  H15   H  HNH2  0   0.397  -19.3232  -15.9075   -5.5180
 L1T  H81   H  HCR6  0   0.255  -19.6589  -20.7115  -10.1067
 L1T  H101  H  HCR6  0   0.260  -20.1655  -24.9557   -9.9795
 L1T  H12   H  HCH3  0   0.254  -17.8231  -20.3107   -4.8912
 L1T  H13   H  HCH3  0   0.252  -19.2574  -21.2893   -4.6241
 L1T  H11   H  HCH3  0   0.249  -18.1832  -21.6609   -5.9652
 L1T  H111  H  HCR6  0   0.260  -20.5172  -24.8363   -7.5307
 L1T  H121  H  HCR6  0   0.262  -20.4678  -22.6706   -6.3782
 L1T  H31   H  HCR5  0   0.264  -19.1864  -18.0963   -5.0551
 L1T  H91   H  HCR6  0   0.261  -19.7547  -22.8758  -11.2592
 L1T  H1    H  H     0   0.331  -21.7269  -15.0867   -7.8012
 L1T  H14   H  HNH2  0   0.395  -20.3346  -14.6602   -6.0188
 L1T  C1    C  CH3   0  -0.750  -18.6272  -20.8447   -5.3971

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
 L1T  C9   C10   aromatic  1.389  0.020  1.389
 L1T  C9   C8    aromatic  1.387  0.020  1.387
 L1T  C10  C11   aromatic  1.389  0.020  1.389
 L1T  C8   C7    aromatic  1.398  0.020  1.398
 L1T  C11  C12   aromatic  1.387  0.020  1.387
 L1T  C7   C12   aromatic  1.397  0.020  1.397
 L1T  C7   C6    single    1.465  0.020  1.465
 L1T  S1   C6    aromatic  1.727  0.020  1.727
 L1T  S1   C4    aromatic  1.716  0.020  1.716
 L1T  N2   C5    double    1.278  0.020  1.278
 L1T  C6   C2    aromatic  1.374  0.020  1.374
 L1T  C5   C4    single    1.469  0.020  1.469
 L1T  C5   N1    single    1.364  0.020  1.364
 L1T  C4   C3    aromatic  1.364  0.020  1.364
 L1T  C2   C3    aromatic  1.422  0.020  1.422
 L1T  C2   C1    single    1.497  0.020  1.497
 L1T  N1   H15   single    0.890  0.020  1.040
 L1T  C8   H81   single    0.930  0.020  1.080
 L1T  C10  H101  single    0.930  0.020  1.080
 L1T  C1   H12   single    0.970  0.020  1.090
 L1T  C1   H13   single    0.970  0.020  1.090
 L1T  C1   H11   single    0.970  0.020  1.090
 L1T  C11  H111  single    0.930  0.020  1.080
 L1T  C12  H121  single    0.930  0.020  1.080
 L1T  C3   H31   single    0.930  0.020  1.080
 L1T  C9   H91   single    0.930  0.020  1.080
 L1T  N2   H1    single    0.890  0.020  1.040
 L1T  N1   H14   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
 L1T  H14   N1   H15  113.24  3.000
 L1T  H14   N1   C5   116.99  3.000
 L1T  H15   N1   C5   118.52  3.000
 L1T  S1    C4   C3   111.09  3.000
 L1T  C3    C4   C5   130.34  3.000
 L1T  S1    C4   C5   118.56  3.000
 L1T  N2    C5   C4   117.48  3.000
 L1T  C4    C5   N1   115.54  3.000
 L1T  N2    C5   N1   126.92  3.000
 L1T  S1    C6   C2   111.65  3.000
 L1T  C2    C6   C7   128.99  3.000
 L1T  S1    C6   C7   119.36  3.000
 L1T  C12   C7   C8   118.57  3.000
 L1T  C12   C7   C6   120.73  3.000
 L1T  C8    C7   C6   120.70  3.000
 L1T  H81   C8   C9   119.43  3.000
 L1T  H81   C8   C7   119.89  3.000
 L1T  C9    C8   C7   120.67  3.000
 L1T  H101  C10  C9   120.21  3.000
 L1T  H101  C10  C11  120.22  3.000
 L1T  C9    C10  C11  119.57  3.000
 L1T  H111  C11  C12  119.58  3.000
 L1T  H111  C11  C10  120.15  3.000
 L1T  C12   C11  C10  120.27  3.000
 L1T  H121  C12  C11  119.48  3.000
 L1T  H121  C12  C7   119.86  3.000
 L1T  C11   C12  C7   120.65  3.000
 L1T  C3    C2   C1   122.53  3.000
 L1T  C1    C2   C6   125.97  3.000
 L1T  C3    C2   C6   111.49  3.000
 L1T  H31   C3   C2   122.24  3.000
 L1T  H31   C3   C4   123.96  3.000
 L1T  C2    C3   C4   113.80  3.000
 L1T  H91   C9   C10  120.11  3.000
 L1T  H91   C9   C8   119.62  3.000
 L1T  C10   C9   C8   120.26  3.000
 L1T  H1    N2   C5   111.63  3.000
 L1T  C6    S1   C4    91.97  3.000
 L1T  H11   C1   H13  107.42  3.000
 L1T  H11   C1   H12  107.97  3.000
 L1T  H13   C1   H12  107.26  3.000
 L1T  H11   C1   C2   111.91  3.000
 L1T  H13   C1   C2   111.54  3.000
 L1T  H12   C1   C2   110.54  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
 L1T  CONST_01  C7    C6   S1   C4    180.00   0.0  0
 L1T  CONST_02  C2    C6   S1   C4      0.00   0.0  0
 L1T  CONST_03  C6    C2   C3   C4      0.00   0.0  0
 L1T  CONST_04  C9    C8   C7   C6    180.00   0.0  0
 L1T  CONST_05  C11   C12  C7   C6    180.00   0.0  0
 L1T  CONST_06  C3    C4   S1   C6      0.00   0.0  0
 L1T  CONST_07  C10   C9   C8   C7      0.00   0.0  0
 L1T  CONST_08  C10   C11  C12  C7      0.00   0.0  0
 L1T  CONST_09  C3    C2   C6   C7    180.00   0.0  0
 L1T  CONST_10  C11   C10  C9   C8      0.00   0.0  0
 L1T  CONST_11  C11   C12  C7   C8      0.00   0.0  0
 L1T  CONST_14  C9    C10  C11  C12     0.00   0.0  0
 L1T  CONST_15  C9    C8   C7   C12     0.00   0.0  0
 L1T  CONST_18  S1    C4   C3   C2      0.00   0.0  0
 L1T  CONST_19  S1    C6   C2   C3      0.00   0.0  0
 L1T  CONST_20  C1    C2   C3   C4    180.00   0.0  0
 L1T  CONST_21  C6    S1   C4   C5    180.00   0.0  0
 L1T  CONST_22  C2    C3   C4   C5    180.00   0.0  0
 L1T  CONST_23  C1    C2   C6   C7      0.00   0.0  0
 L1T  CONST_24  S1    C6   C2   C1    180.00   0.0  0
 L1T  CONST_25  H81   C8   C7   C6      0.00   0.0  0
 L1T  CONST_26  H121  C12  C7   C6      0.00   0.0  0
 L1T  CONST_27  H31   C3   C2   C6    180.00   0.0  0
 L1T  CONST_28  H91   C9   C8   C7    180.00   0.0  0
 L1T  CONST_29  H111  C11  C12  C7    180.00   0.0  0
 L1T  CONST_30  H101  C10  C9   C8    180.00   0.0  0
 L1T  CONST_31  H1    N2   C5   C4    180.00   0.0  0
 L1T  CONST_33  H14   N1   C5   C4    180.00   0.0  0
 L1T  Var_01    S1    C4   C5   N1   -175.19  30.0  2
 L1T  Var_02    H12   C1   C2   C6    146.87  30.0  2

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
 L1T  plan-1  C4    0.020
 L1T  plan-1  C5    0.020
 L1T  plan-1  C6    0.020
 L1T  plan-1  C7    0.020
 L1T  plan-1  C2    0.020
 L1T  plan-1  C3    0.020
 L1T  plan-1  S1    0.020
 L1T  plan-1  H31   0.020
 L1T  plan-1  C1    0.020
 L1T  plan-2  C6    0.020
 L1T  plan-2  C7    0.020
 L1T  plan-2  C8    0.020
 L1T  plan-2  C10   0.020
 L1T  plan-2  C11   0.020
 L1T  plan-2  C12   0.020
 L1T  plan-2  C9    0.020
 L1T  plan-2  H81   0.020
 L1T  plan-2  H101  0.020
 L1T  plan-2  H111  0.020
 L1T  plan-2  H121  0.020
 L1T  plan-2  H91   0.020
 L1T  plan-3  N1    0.020
 L1T  plan-3  C4    0.020
 L1T  plan-3  C5    0.020
 L1T  plan-3  N2    0.020
 L1T  plan-3  H15   0.020
 L1T  plan-3  H1    0.020
 L1T  plan-3  H14   0.020

