# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 09:49:32 2021
#   Inital geometry file: a 92 line input string
#   Ligand name: ~{N}-[3-(5-carbamimidoylthiophen-3-yl)phenyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1cccc(c1)c2csc(c2)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
 KM8  KM8  ~{N}-[3-(5-carbamimidoylthiophen-3-yl)phenyl]propanamide  ligand  34  19  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KM8
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
 KM8  C1   C  CH2   0  -0.585  -19.9737  -26.6780   -6.2710
 KM8  C2   C  C     0   0.551  -19.9103  -25.1787   -6.4768
 KM8  C3   C  CR6   0   0.401  -19.9917  -23.5326   -8.3515
 KM8  C7   C  CR6   0   0.124  -19.8141  -21.1189   -8.2776
 KM8  C8   C  CR16  0  -0.397  -19.8414  -22.3528   -7.6252
 KM8  C9   C  CR5   0   0.189  -19.6382  -19.8852   -7.4969
 KM8  C10  C  CR15  0  -0.240  -20.1939  -18.6234   -7.8543
 KM8  C11  C  CR5   0  -0.208  -19.9045  -17.6347   -6.9620
 KM8  C12  C  CR15  0  -0.560  -18.9217  -19.8038   -6.3322
 KM8  C13  C  C     0   0.337  -20.3406  -16.2284   -7.0254
 KM8  O    O  O     0  -0.467  -19.7421  -24.3951   -5.5605
 KM8  C    C  CH3   0  -0.658  -20.2576  -27.0740   -4.8328
 KM8  N    N  NH1   0  -0.750  -20.0411  -24.8050   -7.7784
 KM8  C6   C  CR16  0  -0.341  -19.9509  -21.0644   -9.6626
 KM8  C5   C  CR16  0  -0.226  -20.1041  -22.2398  -10.3832
 KM8  C4   C  CR16  0  -0.359  -20.1235  -23.4643   -9.7416
 KM8  S    S  S2    0   0.263  -18.9219  -18.2294   -5.6777
 KM8  N2   N  N     0  -0.642  -20.6276  -15.7371   -8.1677
 KM8  N1   N  NH2   0  -0.827  -20.3361  -15.5721   -5.8246
 KM8  H1   H  HCH2  0   0.262  -20.7239  -27.1074   -6.9396
 KM8  H2   H  HCH2  0   0.279  -19.0146  -27.0959   -6.5944
 KM8  H3   H  HCR6  0   0.275  -19.7675  -22.3862   -6.5506
 KM8  H4   H  HCR5  0   0.266  -20.8175  -18.4566   -8.7211
 KM8  H5   H  HCR5  0   0.298  -18.3661  -20.5881   -5.8403
 KM8  H6   H  HCH3  0   0.237  -20.2666  -28.1594   -4.7413
 KM8  H7   H  HCH3  0   0.231  -19.4997  -26.6902   -4.1518
 KM8  H8   H  HCH3  0   0.230  -21.2275  -26.7052   -4.4999
 KM8  H9   H  HNH1  0   0.416  -20.1776  -25.5575   -8.4368
 KM8  H10  H  HCR6  0   0.254  -19.9220  -20.1156  -10.1824
 KM8  H11  H  HCR6  0   0.262  -20.2045  -22.2025  -11.4598
 KM8  H12  H  HCR6  0   0.271  -20.2466  -24.3735  -10.3184
 KM8  H13  H  H     0   0.329  -20.9657  -14.7825   -8.0797
 KM8  H14  H  HNH2  0   0.395  -20.5618  -16.0986   -4.9951
 KM8  H15  H  HNH2  0   0.395  -20.7283  -14.6433   -5.8158

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
 KM8  C5   C4   aromatic  1.383  0.020  1.383
 KM8  C5   C6   aromatic  1.387  0.020  1.387
 KM8  C4   C3   aromatic  1.398  0.020  1.398
 KM8  C6   C7   aromatic  1.393  0.020  1.393
 KM8  C3   N    single    1.396  0.020  1.396
 KM8  C3   C8   aromatic  1.394  0.020  1.394
 KM8  C7   C8   aromatic  1.396  0.020  1.396
 KM8  C7   C9   single    1.471  0.020  1.471
 KM8  N2   C13  double    1.276  0.020  1.276
 KM8  N    C2   single    1.361  0.020  1.361
 KM8  C10  C9   aromatic  1.424  0.020  1.424
 KM8  C10  C11  aromatic  1.363  0.020  1.363
 KM8  C9   C12  aromatic  1.370  0.020  1.370
 KM8  C13  C11  single    1.474  0.020  1.474
 KM8  C13  N1   single    1.368  0.020  1.368
 KM8  C11  S    aromatic  1.723  0.020  1.723
 KM8  C2   C1   single    1.515  0.020  1.515
 KM8  C2   O    double    1.217  0.020  1.217
 KM8  C1   C    single    1.518  0.020  1.518
 KM8  C12  S    aromatic  1.705  0.020  1.705
 KM8  C1   H1   single    0.970  0.020  1.090
 KM8  C1   H2   single    0.970  0.020  1.090
 KM8  C8   H3   single    0.930  0.020  1.080
 KM8  C10  H4   single    0.930  0.020  1.080
 KM8  C12  H5   single    0.930  0.020  1.080
 KM8  C    H6   single    0.970  0.020  1.090
 KM8  C    H7   single    0.970  0.020  1.090
 KM8  C    H8   single    0.970  0.020  1.090
 KM8  N    H9   single    0.860  0.020  1.020
 KM8  C6   H10  single    0.930  0.020  1.080
 KM8  C5   H11  single    0.930  0.020  1.080
 KM8  C4   H12  single    0.930  0.020  1.080
 KM8  N2   H13  single    0.890  0.020  1.040
 KM8  N1   H14  single    0.890  0.020  1.040
 KM8  N1   H15  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
 KM8  H2   C1   H1   105.70  3.000
 KM8  H2   C1   C    110.12  3.000
 KM8  H1   C1   C    110.41  3.000
 KM8  H2   C1   C2   107.52  3.000
 KM8  H1   C1   C2   109.54  3.000
 KM8  C    C1   C2   113.24  3.000
 KM8  N    C2   O    123.82  3.000
 KM8  O    C2   C1   122.73  3.000
 KM8  N    C2   C1   113.44  3.000
 KM8  C4   C3   N    116.69  3.000
 KM8  N    C3   C8   124.15  3.000
 KM8  C4   C3   C8   119.15  3.000
 KM8  C6   C7   C9   120.46  3.000
 KM8  C9   C7   C8   119.72  3.000
 KM8  C6   C7   C8   119.83  3.000
 KM8  H3   C8   C7   119.47  3.000
 KM8  H3   C8   C3   120.06  3.000
 KM8  C7   C8   C3   120.45  3.000
 KM8  C12  C9   C10  111.39  3.000
 KM8  C12  C9   C7   124.32  3.000
 KM8  C10  C9   C7   124.29  3.000
 KM8  H4   C10  C11  122.39  3.000
 KM8  H4   C10  C9   124.27  3.000
 KM8  C11  C10  C9   113.30  3.000
 KM8  S    C11  C13  122.02  3.000
 KM8  S    C11  C10  111.02  3.000
 KM8  C13  C11  C10  126.96  3.000
 KM8  H5   C12  S    119.73  3.000
 KM8  H5   C12  C9   127.83  3.000
 KM8  S    C12  C9   112.41  3.000
 KM8  N1   C13  N2   126.98  3.000
 KM8  N1   C13  C11  114.77  3.000
 KM8  N2   C13  C11  118.19  3.000
 KM8  H8   C    H7   108.01  3.000
 KM8  H8   C    H6   107.71  3.000
 KM8  H7   C    H6   107.73  3.000
 KM8  H8   C    C1   111.56  3.000
 KM8  H7   C    C1   111.73  3.000
 KM8  H6   C    C1   109.94  3.000
 KM8  H9   N    C3   114.62  3.000
 KM8  H9   N    C2   115.62  3.000
 KM8  C3   N    C2   129.75  3.000
 KM8  H10  C6   C5   119.75  3.000
 KM8  H10  C6   C7   120.62  3.000
 KM8  C5   C6   C7   119.62  3.000
 KM8  H11  C5   C4   119.40  3.000
 KM8  H11  C5   C6   119.87  3.000
 KM8  C4   C5   C6   120.73  3.000
 KM8  H12  C4   C5   119.84  3.000
 KM8  H12  C4   C3   119.94  3.000
 KM8  C5   C4   C3   120.22  3.000
 KM8  C12  S    C11   91.87  3.000
 KM8  H13  N2   C13  111.03  3.000
 KM8  H15  N1   H14  112.76  3.000
 KM8  H15  N1   C13  116.63  3.000
 KM8  H14  N1   C13  118.08  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
 KM8  CONST_01  C6   C5   C4   C3      0.00   0.0  0
 KM8  CONST_02  C6   C7   C8   C3      0.00   0.0  0
 KM8  CONST_03  C9   C7   C8   C3    180.00   0.0  0
 KM8  CONST_04  C4   C5   C6   C7      0.00   0.0  0
 KM8  CONST_05  C4   C3   C8   C7      0.00   0.0  0
 KM8  CONST_06  C11  C10  C9   C7    180.00   0.0  0
 KM8  CONST_07  S    C12  C9   C7    180.00   0.0  0
 KM8  CONST_08  C5   C4   C3   C8      0.00   0.0  0
 KM8  CONST_09  C5   C6   C7   C8      0.00   0.0  0
 KM8  CONST_12  C5   C6   C7   C9    180.00   0.0  0
 KM8  CONST_13  S    C11  C10  C9      0.00   0.0  0
 KM8  CONST_14  C11  S    C12  C9      0.00   0.0  0
 KM8  CONST_16  S    C12  C9   C10     0.00   0.0  0
 KM8  CONST_17  C12  S    C11  C10     0.00   0.0  0
 KM8  CONST_18  C12  C9   C10  C11     0.00   0.0  0
 KM8  CONST_20  N    C3   C8   C7    180.00   0.0  0
 KM8  CONST_21  C13  C11  C10  C9    180.00   0.0  0
 KM8  CONST_22  C13  C11  S    C12   180.00   0.0  0
 KM8  CONST_23  C5   C4   C3   N     180.00   0.0  0
 KM8  CONST_24  H11  C5   C4   C3    180.00   0.0  0
 KM8  CONST_25  H4   C10  C9   C7      0.00   0.0  0
 KM8  CONST_26  H5   C12  C9   C7      0.00   0.0  0
 KM8  CONST_27  H12  C4   C3   C8    180.00   0.0  0
 KM8  CONST_28  H10  C6   C7   C8    180.00   0.0  0
 KM8  CONST_29  H3   C8   C7   C9      0.00   0.0  0
 KM8  CONST_30  C4   C3   N    C2    180.00   0.0  0
 KM8  CONST_31  C8   C3   N    C2      0.00   0.0  0
 KM8  CONST_32  H9   N    C3   C8    180.00   0.0  0
 KM8  CONST_33  C3   N    C2   C1    180.00   0.0  0
 KM8  CONST_34  O    C2   N    C3      0.00   0.0  0
 KM8  CONST_35  H13  N2   C13  C11   180.00   0.0  0
 KM8  CONST_37  H15  N1   C13  C11   180.00   0.0  0
 KM8  Var_01    N2   C13  C11  C10   -24.95  30.0  2
 KM8  Var_02    C    C1   C2   O      18.60  30.0  3
 KM8  Var_03    H6   C    C1   C2   -178.58  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
 KM8  plan-1  C7   0.020
 KM8  plan-1  C9   0.020
 KM8  plan-1  C10  0.020
 KM8  plan-1  C11  0.020
 KM8  plan-1  C12  0.020
 KM8  plan-1  C13  0.020
 KM8  plan-1  S    0.020
 KM8  plan-1  H4   0.020
 KM8  plan-1  H5   0.020
 KM8  plan-2  C3   0.020
 KM8  plan-2  C7   0.020
 KM8  plan-2  C8   0.020
 KM8  plan-2  C9   0.020
 KM8  plan-2  N    0.020
 KM8  plan-2  C6   0.020
 KM8  plan-2  C5   0.020
 KM8  plan-2  C4   0.020
 KM8  plan-2  H3   0.020
 KM8  plan-2  H10  0.020
 KM8  plan-2  H11  0.020
 KM8  plan-2  H12  0.020
 KM8  plan-3  C1   0.020
 KM8  plan-3  C2   0.020
 KM8  plan-3  C3   0.020
 KM8  plan-3  O    0.020
 KM8  plan-3  N    0.020
 KM8  plan-3  H9   0.020
 KM8  plan-4  C11  0.020
 KM8  plan-4  C13  0.020
 KM8  plan-4  N2   0.020
 KM8  plan-4  N1   0.020
 KM8  plan-4  H13  0.020
 KM8  plan-4  H14  0.020
 KM8  plan-4  H15  0.020

