# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 16:28:39 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 1-(3-amino-2-methylbenzyl)-4-[2-(thiophen-2-yl)ethoxy]pyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(N)cccc1CN2C=CC(=CC2=O)OCCc3sccc3
#
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
 PT6  PT6  1-(3-amino-2-methylbenzyl)-4-[2-(thiophen-2-yl)ethoxy]pyridin-2(1H)-one  ligand  44  24  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PT6
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
 PT6  O1    O  O     0  -0.516   1.4199  -0.1159   2.0296
 PT6  C18   C  CR6   0   0.561   0.9766   0.5380   1.0886
 PT6  N1    N  NR6   0  -0.528   1.8411   1.3011   0.3037
 PT6  C7    C  CH2   0  -0.377   3.2614   1.2578   0.6018
 PT6  C6    C  CR6   0   0.065   3.9721   0.0604   0.0074
 PT6  C5    C  CR16  0  -0.327   3.3087  -0.8048  -0.8580
 PT6  C4    C  CR16  0  -0.254   3.9802  -1.8921  -1.3981
 PT6  C3    C  CR16  0  -0.332   5.3031  -2.1299  -1.0784
 PT6  C2    C  CR6   0   0.269   5.9839  -1.2672  -0.2142
 PT6  N     N  NH2   0  -0.859   7.3227  -1.4783   0.0588
 PT6  C1    C  CR6   0   0.013   5.3170  -0.1516   0.3254
 PT6  C     C  CH3   0  -0.769   6.0925   0.7739   1.2216
 PT6  C17   C  CR16  0  -0.583  -0.4037   0.5828   0.7096
 PT6  C10   C  CR6   0   0.504  -0.8311   1.3154  -0.3646
 PT6  C9    C  CR16  0  -0.464   0.1044   2.0704  -1.1232
 PT6  C8    C  CR16  0   0.056   1.4038   2.0268  -0.7548
 PT6  O     O  O2    0  -0.460  -2.0921   1.3890  -0.7858
 PT6  C11   C  CH2   0  -0.169  -3.0921   0.6400  -0.1080
 PT6  C12   C  CH2   0  -0.531  -4.4082   0.8706  -0.8340
 PT6  C13   C  CR5   0  -0.165  -5.5192   0.1098  -0.1866
 PT6  S     S  S2    0   0.204  -5.6814  -1.5950  -0.4008
 PT6  C16   C  CR15  0  -0.470  -7.0477  -1.6670   0.6324
 PT6  C15   C  CR15  0  -0.182  -7.3649  -0.4374   1.1198
 PT6  C14   C  CR15  0  -0.232  -6.4866   0.5791   0.6514
 PT6  H17   H  HCR6  0   0.287  -1.0796  -0.0045   1.3145
 PT6  H71C  H  HCH2  0   0.281   3.7025   2.1821   0.2248
 PT6  H72C  H  HCH2  0   0.282   3.3803   1.2752   1.6838
 PT6  H8    H  HCR6  0   0.312   2.1604   2.5778  -1.2956
 PT6  H5    H  HCR6  0   0.233   2.2714  -0.6454  -1.1197
 PT6  H4    H  HCR6  0   0.249   3.4619  -2.5651  -2.0692
 PT6  H3    H  HCR6  0   0.251   5.8200  -2.9869  -1.4945
 PT6  HN1   H  HNH2  0   0.378   7.6551  -2.4076  -0.1454
 PT6  HN2   H  HNH2  0   0.382   7.6477  -1.1723   0.9619
 PT6  HC1   H  HCH3  0   0.249   6.3406   0.3017   2.1766
 PT6  HC2   H  HCH3  0   0.249   7.0373   1.0632   0.7568
 PT6  HC3   H  HCH3  0   0.264   5.5615   1.6932   1.4539
 PT6  H9    H  HCR6  0   0.283  -0.2057   2.6603  -1.9728
 PT6  H111  H  HCH2  0   0.236  -2.8306  -0.4233  -0.1103
 PT6  H112  H  HCH2  0   0.244  -3.1730   0.9653   0.9338
 PT6  H121  H  HCH2  0   0.272  -4.6570   1.9333  -0.8137
 PT6  H122  H  HCH2  0   0.268  -4.3009   0.5837  -1.8828
 PT6  H14   H  HCR5  0   0.263  -6.5696   1.6223   0.9249
 PT6  H16   H  HCR5  0   0.295  -7.5441  -2.6070   0.8176
 PT6  H15   H  HCR5  0   0.266  -8.1965  -0.2583   1.7863

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
 PT6  O1   C18   double    1.229  0.020  1.229
 PT6  C18  N1    single    1.395  0.020  1.395
 PT6  C18  C17   single    1.432  0.020  1.432
 PT6  N1   C7    single    1.452  0.020  1.452
 PT6  N1   C8    single    1.356  0.020  1.356
 PT6  C7   C6    single    1.514  0.020  1.514
 PT6  C6   C5    aromatic  1.392  0.020  1.392
 PT6  C6   C1    aromatic  1.398  0.020  1.398
 PT6  C5   C4    aromatic  1.387  0.020  1.387
 PT6  C4   C3    aromatic  1.382  0.020  1.382
 PT6  C3   C2    aromatic  1.398  0.020  1.398
 PT6  C2   N     single    1.383  0.020  1.383
 PT6  C2   C1    aromatic  1.407  0.020  1.407
 PT6  C1   C     single    1.504  0.020  1.504
 PT6  C17  C10   double    1.369  0.020  1.369
 PT6  C10  C9    single    1.422  0.020  1.422
 PT6  C10  O     single    1.332  0.020  1.332
 PT6  C9   C8    double    1.351  0.020  1.351
 PT6  O    C11   single    1.421  0.020  1.421
 PT6  C11  C12   single    1.521  0.020  1.521
 PT6  C12  C13   single    1.494  0.020  1.494
 PT6  C13  S     aromatic  1.726  0.020  1.726
 PT6  C13  C14   aromatic  1.363  0.020  1.363
 PT6  S    C16   aromatic  1.714  0.020  1.714
 PT6  C16  C15   aromatic  1.360  0.020  1.360
 PT6  C15  C14   aromatic  1.423  0.020  1.423
 PT6  C17  H17   single    0.930  0.020  1.080
 PT6  C7   H71C  single    0.970  0.020  1.090
 PT6  C7   H72C  single    0.970  0.020  1.090
 PT6  C8   H8    single    0.930  0.020  1.080
 PT6  C5   H5    single    0.930  0.020  1.080
 PT6  C4   H4    single    0.930  0.020  1.080
 PT6  C3   H3    single    0.930  0.020  1.080
 PT6  N    HN1   single    0.890  0.020  1.040
 PT6  N    HN2   single    0.890  0.020  1.040
 PT6  C    HC1   single    0.970  0.020  1.090
 PT6  C    HC2   single    0.970  0.020  1.090
 PT6  C    HC3   single    0.970  0.020  1.090
 PT6  C9   H9    single    0.930  0.020  1.080
 PT6  C11  H111  single    0.970  0.020  1.090
 PT6  C11  H112  single    0.970  0.020  1.090
 PT6  C12  H121  single    0.970  0.020  1.090
 PT6  C12  H122  single    0.970  0.020  1.090
 PT6  C14  H14   single    0.930  0.020  1.080
 PT6  C16  H16   single    0.930  0.020  1.080
 PT6  C15  H15   single    0.930  0.020  1.080

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
 PT6  C17   C18  N1    115.55  3.000
 PT6  C17   C18  O1    124.55  3.000
 PT6  N1    C18  O1    119.90  3.000
 PT6  C8    N1   C7    119.46  3.000
 PT6  C8    N1   C18   122.16  3.000
 PT6  C7    N1   C18   118.32  3.000
 PT6  H72C  C7   H71C  106.60  3.000
 PT6  H72C  C7   C6    110.59  3.000
 PT6  H71C  C7   C6    110.15  3.000
 PT6  H72C  C7   N1    108.09  3.000
 PT6  H71C  C7   N1    107.41  3.000
 PT6  C6    C7   N1    113.71  3.000
 PT6  C1    C6   C5    120.37  3.000
 PT6  C1    C6   C7    118.83  3.000
 PT6  C5    C6   C7    120.80  3.000
 PT6  H5    C5   C4    119.04  3.000
 PT6  H5    C5   C6    121.05  3.000
 PT6  C4    C5   C6    119.90  3.000
 PT6  H4    C4   C3    119.66  3.000
 PT6  H4    C4   C5    119.79  3.000
 PT6  C3    C4   C5    120.55  3.000
 PT6  H3    C3   C2    119.54  3.000
 PT6  H3    C3   C4    120.26  3.000
 PT6  C2    C3   C4    120.20  3.000
 PT6  C1    C2   N     120.28  3.000
 PT6  C1    C2   C3    119.70  3.000
 PT6  N     C2   C3    119.96  3.000
 PT6  HN2   N    HN1   110.81  3.000
 PT6  HN2   N    C2    116.30  3.000
 PT6  HN1   N    C2    114.84  3.000
 PT6  C     C1   C2    118.17  3.000
 PT6  C     C1   C6    122.56  3.000
 PT6  C2    C1   C6    119.26  3.000
 PT6  HC3   C    HC2   106.84  3.000
 PT6  HC3   C    HC1   106.83  3.000
 PT6  HC2   C    HC1   106.84  3.000
 PT6  HC3   C    C1    113.34  3.000
 PT6  HC2   C    C1    110.83  3.000
 PT6  HC1   C    C1    111.81  3.000
 PT6  H17   C17  C10   122.34  3.000
 PT6  H17   C17  C18   115.96  3.000
 PT6  C10   C17  C18   121.70  3.000
 PT6  O     C10  C9    115.16  3.000
 PT6  O     C10  C17   125.00  3.000
 PT6  C9    C10  C17   119.84  3.000
 PT6  H9    C9   C8    120.55  3.000
 PT6  H9    C9   C10   121.40  3.000
 PT6  C8    C9   C10   118.05  3.000
 PT6  H8    C8   C9    121.35  3.000
 PT6  H8    C8   N1    115.95  3.000
 PT6  C9    C8   N1    122.70  3.000
 PT6  C11   O    C10   119.10  3.000
 PT6  H112  C11  H111  107.95  3.000
 PT6  H112  C11  C12   110.21  3.000
 PT6  H111  C11  C12   110.67  3.000
 PT6  H112  C11  O     110.45  3.000
 PT6  H111  C11  O     110.04  3.000
 PT6  C12   C11  O     107.54  3.000
 PT6  H122  C12  H121  107.21  3.000
 PT6  H122  C12  C13   110.81  3.000
 PT6  H121  C12  C13   108.55  3.000
 PT6  H122  C12  C11   109.48  3.000
 PT6  H121  C12  C11   109.63  3.000
 PT6  C13   C12  C11   111.07  3.000
 PT6  C14   C13  S     110.47  3.000
 PT6  C14   C13  C12   128.23  3.000
 PT6  S     C13  C12   121.27  3.000
 PT6  C16   S    C13    92.38  3.000
 PT6  H16   C16  C15   128.22  3.000
 PT6  H16   C16  S     120.44  3.000
 PT6  C15   C16  S     111.34  3.000
 PT6  H15   C15  C14   124.04  3.000
 PT6  H15   C15  C16   123.39  3.000
 PT6  C14   C15  C16   112.58  3.000
 PT6  H14   C14  C15   123.95  3.000
 PT6  H14   C14  C13   122.82  3.000
 PT6  C15   C14  C13   113.23  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
 PT6  CONST_01  C3   C4   C5   C6      0.00   0.0  0
 PT6  CONST_02  C3   C2   C1   C6      0.00   0.0  0
 PT6  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 PT6  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 PT6  CONST_05  C1   C6   C5   C4      0.00   0.0  0
 PT6  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 PT6  CONST_07  C15  C16  S    C13     0.00   0.0  0
 PT6  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 PT6  CONST_09  C15  C14  C13  S       0.00   0.0  0
 PT6  CONST_10  C14  C15  C16  S       0.00   0.0  0
 PT6  CONST_11  C14  C13  S    C16     0.00   0.0  0
 PT6  CONST_12  C8   N1   C18  C17     0.00   0.0  0
 PT6  CONST_13  C4   C5   C6   C7    180.00   0.0  0
 PT6  CONST_14  C2   C1   C6   C7    180.00   0.0  0
 PT6  CONST_15  N    C2   C1   C6    180.00   0.0  0
 PT6  CONST_16  C    C1   C6   C5    180.00   0.0  0
 PT6  CONST_17  N    C2   C3   C4    180.00   0.0  0
 PT6  CONST_18  C    C1   C2   C3    180.00   0.0  0
 PT6  CONST_19  C16  S    C13  C12   180.00   0.0  0
 PT6  CONST_20  C15  C14  C13  C12   180.00   0.0  0
 PT6  CONST_21  C8   N1   C18  O1    180.00   0.0  0
 PT6  CONST_22  C17  C18  N1   C7    180.00   0.0  0
 PT6  CONST_23  H4   C4   C5   C6    180.00   0.0  0
 PT6  CONST_24  H3   C3   C4   C5    180.00   0.0  0
 PT6  CONST_25  H5   C5   C4   C3    180.00   0.0  0
 PT6  CONST_26  H16  C16  S    C13   180.00   0.0  0
 PT6  CONST_27  H15  C15  C14  C13   180.00   0.0  0
 PT6  CONST_28  H14  C14  C13  S     180.00   0.0  0
 PT6  CONST_29  C7   N1   C18  O1      0.00   0.0  0
 PT6  Var_01    C6   C7   N1   C18    82.04  30.0  3
 PT6  Var_02    C5   C6   C7   N1      6.62  30.0  2
 PT6  Var_03    S    C13  C12  C11   -75.79  30.0  2
 PT6  Var_04    HC1  C    C1   C6    111.15  30.0  2
 PT6  Var_05    C12  C11  O    C10  -177.72  30.0  3
 PT6  Var_06    C13  C12  C11  O     179.74  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
 PT6  plan-1  C12  0.020
 PT6  plan-1  C13  0.020
 PT6  plan-1  S    0.020
 PT6  plan-1  C16  0.020
 PT6  plan-1  C15  0.020
 PT6  plan-1  C14  0.020
 PT6  plan-1  H14  0.020
 PT6  plan-1  H16  0.020
 PT6  plan-1  H15  0.020
 PT6  plan-2  O1   0.020
 PT6  plan-2  C18  0.020
 PT6  plan-2  N1   0.020
 PT6  plan-2  C7   0.020
 PT6  plan-2  C17  0.020
 PT6  plan-2  C10  0.020
 PT6  plan-2  C9   0.020
 PT6  plan-2  C8   0.020
 PT6  plan-2  O    0.020
 PT6  plan-2  H17  0.020
 PT6  plan-2  H8   0.020
 PT6  plan-2  H9   0.020
 PT6  plan-3  C7   0.020
 PT6  plan-3  C6   0.020
 PT6  plan-3  C5   0.020
 PT6  plan-3  C4   0.020
 PT6  plan-3  C3   0.020
 PT6  plan-3  C2   0.020
 PT6  plan-3  N    0.020
 PT6  plan-3  C1   0.020
 PT6  plan-3  C    0.020
 PT6  plan-3  H5   0.020
 PT6  plan-3  H4   0.020
 PT6  plan-3  H3   0.020
 PT6  plan-4  C2   0.020
 PT6  plan-4  N    0.020
 PT6  plan-4  HN1  0.020
 PT6  plan-4  HN2  0.020

