# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 20:33:47 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: N~1~-[(4-fluorophenyl)methyl]-N~1~-methyl-N~4~-(4-methyl-1,3-thiazol-2-yl)piperidine-1,4-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1ccc(F)cc1)C(=O)N2CCC(CC2)C(=O)Nc3scc(C)n3
#
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
 Q5A  Q5A  N~1~-[(4-fluorophenyl)methyl]-N~1~-methyl-N~4~-(4-methyl-1,3-thiazol-2-yl)piperidine-1,4-dicarboxamide  ligand  50  27  .  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_Q5A
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
 Q5A  C18  C  CH3   0  -0.724  -8.6399   1.6058   0.3674
 Q5A  C17  C  CR5   0   0.324  -7.4097   0.8117   0.6466
 Q5A  N4   N  N     0  -0.439  -6.3234   0.9412  -0.1821
 Q5A  C19  C  CR15  0  -0.564  -7.2381  -0.0587   1.6722
 Q5A  S1   S  S2    0   0.217  -5.6613  -0.7575   1.6228
 Q5A  C16  C  CR5   0   0.288  -5.3491   0.1861   0.2078
 Q5A  N3   N  NH1   0  -0.696  -4.1551   0.1475  -0.4699
 Q5A  C15  C  C     0   0.596  -3.0755  -0.6016  -0.1085
 Q5A  O2   O  O     0  -0.450  -3.1190  -1.3358   0.8608
 Q5A  C12  C  CH1   0  -0.423  -1.8556  -0.4036  -0.9756
 Q5A  C13  C  CH2   0  -0.418  -1.1115   0.8670  -0.5356
 Q5A  C14  C  CH2   0  -0.343   0.1632   1.0627  -1.3496
 Q5A  C11  C  CH2   0  -0.419  -0.9180  -1.6057  -0.9337
 Q5A  C10  C  CH2   0  -0.325   0.3431  -1.3123  -1.7364
 Q5A  N2   N  NT    0  -0.485   1.0263  -0.1105  -1.2835
 Q5A  C9   C  C     0   0.730   1.9465  -0.2545  -0.2674
 Q5A  O1   O  O     0  -0.525   2.0605  -1.3006   0.3642
 Q5A  N1   N  NT    0  -0.468   2.7454   0.8239  -0.0223
 Q5A  C1   C  CH3   0  -0.553   3.1009   1.8202  -1.0101
 Q5A  C2   C  CH2   0  -0.387   3.4935   0.8904   1.2186
 Q5A  C3   C  CR6   0   0.101   4.9516   0.5234   1.0790
 Q5A  C4   C  CR16  0  -0.279   5.3380  -0.7697   0.7272
 Q5A  C5   C  CR16  0  -0.397   6.6766  -1.1066   0.6009
 Q5A  C6   C  CR6   0   0.514   7.6303  -0.1320   0.8318
 Q5A  F1   F  F     0  -0.317   8.9296  -0.4534   0.7103
 Q5A  C7   C  CR16  0  -0.399   7.2894   1.1577   1.1826
 Q5A  C8   C  CR16  0  -0.291   5.9414   1.4743   1.3016
 Q5A  H1   H  HCH3  0   0.248  -9.0448   1.3675  -0.6173
 Q5A  H2   H  HCH3  0   0.246  -9.4112   1.4071   1.1088
 Q5A  H3   H  HCH3  0   0.247  -8.4245   2.6753   0.3791
 Q5A  H4   H  HCR5  0   0.295  -7.9438  -0.3235   2.4439
 Q5A  H5   H  HNH1  0   0.427  -4.1001   0.7410  -1.2861
 Q5A  H6   H  HCH1  0   0.272  -2.1951  -0.2554  -2.0083
 Q5A  H7   H  HCH2  0   0.257  -1.7450   1.7488  -0.6570
 Q5A  H8   H  HCH2  0   0.243  -0.8585   0.7971   0.5266
 Q5A  H9   H  HCH2  0   0.248  -0.0896   1.2477  -2.3974
 Q5A  H10  H  HCH2  0   0.281   0.6782   1.9489  -0.9904
 Q5A  H11  H  HCH2  0   0.239  -0.6445  -1.8370   0.0970
 Q5A  H12  H  HCH2  0   0.248  -1.4123  -2.4877  -1.3467
 Q5A  H13  H  HCH2  0   0.260   1.0259  -2.1581  -1.6995
 Q5A  H14  H  HCH2  0   0.242   0.0837  -1.1614  -2.7890
 Q5A  H15  H  HCH3  0   0.239   2.7112   2.8086  -0.7550
 Q5A  H16  H  HCH3  0   0.256   4.1880   1.8973  -1.0756
 Q5A  H17  H  HCH3  0   0.264   2.7351   1.5417  -1.9940
 Q5A  H18  H  HCH2  0   0.261   3.4197   1.9130   1.5988
 Q5A  H19  H  HCH2  0   0.272   3.0129   0.2480   1.9545
 Q5A  H20  H  HCR6  0   0.267   4.5837  -1.5263   0.5559
 Q5A  H21  H  HCR6  0   0.277   6.9746  -2.1114   0.3313
 Q5A  H22  H  HCR6  0   0.278   8.0550   1.9024   1.3565
 Q5A  H23  H  HCR6  0   0.265   5.6613   2.4847   1.5747

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
 Q5A  C18  C17  single    1.491  0.020  1.491
 Q5A  C17  N4   aromatic  1.372  0.020  1.372
 Q5A  C17  C19  aromatic  1.356  0.020  1.356
 Q5A  N4   C16  aromatic  1.293  0.020  1.293
 Q5A  C19  S1   aromatic  1.725  0.020  1.725
 Q5A  C16  S1   aromatic  1.729  0.020  1.729
 Q5A  C16  N3   single    1.374  0.020  1.374
 Q5A  N3   C15  single    1.363  0.020  1.363
 Q5A  C15  C12  single    1.510  0.020  1.510
 Q5A  C15  O2   double    1.217  0.020  1.217
 Q5A  C13  C12  single    1.537  0.020  1.537
 Q5A  C13  C14  single    1.525  0.020  1.525
 Q5A  C12  C11  single    1.525  0.020  1.525
 Q5A  C14  N2   single    1.458  0.020  1.458
 Q5A  C11  C10  single    1.523  0.020  1.523
 Q5A  N2   C10  single    1.455  0.020  1.455
 Q5A  N2   C9   single    1.378  0.020  1.378
 Q5A  O1   C9   double    1.227  0.020  1.227
 Q5A  C9   N1   single    1.364  0.020  1.364
 Q5A  N1   C1   single    1.447  0.020  1.447
 Q5A  N1   C2   single    1.450  0.020  1.450
 Q5A  C2   C3   single    1.510  0.020  1.510
 Q5A  C3   C8   aromatic  1.391  0.020  1.391
 Q5A  C3   C4   aromatic  1.395  0.020  1.395
 Q5A  C8   C7   aromatic  1.390  0.020  1.390
 Q5A  C4   C5   aromatic  1.386  0.020  1.386
 Q5A  C7   C6   aromatic  1.379  0.020  1.379
 Q5A  C5   C6   aromatic  1.383  0.020  1.383
 Q5A  C6   F1   single    1.344  0.020  1.344
 Q5A  C18  H1   single    0.970  0.020  1.090
 Q5A  C18  H2   single    0.970  0.020  1.090
 Q5A  C18  H3   single    0.970  0.020  1.090
 Q5A  C19  H4   single    0.930  0.020  1.080
 Q5A  N3   H5   single    0.860  0.020  1.020
 Q5A  C12  H6   single    0.970  0.020  1.090
 Q5A  C13  H7   single    0.970  0.020  1.090
 Q5A  C13  H8   single    0.970  0.020  1.090
 Q5A  C14  H9   single    0.970  0.020  1.090
 Q5A  C14  H10  single    0.970  0.020  1.090
 Q5A  C11  H11  single    0.970  0.020  1.090
 Q5A  C11  H12  single    0.970  0.020  1.090
 Q5A  C10  H13  single    0.970  0.020  1.090
 Q5A  C10  H14  single    0.970  0.020  1.090
 Q5A  C1   H15  single    0.970  0.020  1.090
 Q5A  C1   H16  single    0.970  0.020  1.090
 Q5A  C1   H17  single    0.970  0.020  1.090
 Q5A  C2   H18  single    0.970  0.020  1.090
 Q5A  C2   H19  single    0.970  0.020  1.090
 Q5A  C4   H20  single    0.930  0.020  1.080
 Q5A  C5   H21  single    0.930  0.020  1.080
 Q5A  C7   H22  single    0.930  0.020  1.080
 Q5A  C8   H23  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
 Q5A  H3   C18  H2   108.16  3.000
 Q5A  H3   C18  H1   107.28  3.000
 Q5A  H2   C18  H1   108.19  3.000
 Q5A  H3   C18  C17  110.93  3.000
 Q5A  H2   C18  C17  111.10  3.000
 Q5A  H1   C18  C17  111.04  3.000
 Q5A  C19  C17  N4   114.65  3.000
 Q5A  C19  C17  C18  126.02  3.000
 Q5A  N4   C17  C18  119.33  3.000
 Q5A  C16  N4   C17  111.05  3.000
 Q5A  H4   C19  S1   121.26  3.000
 Q5A  H4   C19  C17  128.01  3.000
 Q5A  S1   C19  C17  110.73  3.000
 Q5A  C16  S1   C19   88.13  3.000
 Q5A  N3   C16  S1   123.05  3.000
 Q5A  N3   C16  N4   121.52  3.000
 Q5A  S1   C16  N4   115.44  3.000
 Q5A  H5   N3   C15  119.60  3.000
 Q5A  H5   N3   C16  115.42  3.000
 Q5A  C15  N3   C16  124.98  3.000
 Q5A  C12  C15  O2   124.44  3.000
 Q5A  O2   C15  N3   120.97  3.000
 Q5A  C12  C15  N3   114.56  3.000
 Q5A  H6   C12  C11  108.82  3.000
 Q5A  H6   C12  C13  107.92  3.000
 Q5A  C11  C12  C13  110.25  3.000
 Q5A  H6   C12  C15  107.96  3.000
 Q5A  C11  C12  C15  112.18  3.000
 Q5A  C13  C12  C15  109.59  3.000
 Q5A  H8   C13  H7   107.07  3.000
 Q5A  H8   C13  C14  109.45  3.000
 Q5A  H7   C13  C14  108.77  3.000
 Q5A  H8   C13  C12  109.70  3.000
 Q5A  H7   C13  C12  110.78  3.000
 Q5A  C14  C13  C12  110.98  3.000
 Q5A  H10  C14  H9   106.76  3.000
 Q5A  H10  C14  N2   111.15  3.000
 Q5A  H9   C14  N2   108.45  3.000
 Q5A  H10  C14  C13  108.93  3.000
 Q5A  H9   C14  C13  109.87  3.000
 Q5A  N2   C14  C13  111.55  3.000
 Q5A  H12  C11  H11  107.43  3.000
 Q5A  H12  C11  C10  109.32  3.000
 Q5A  H11  C11  C10  109.33  3.000
 Q5A  H12  C11  C12  110.36  3.000
 Q5A  H11  C11  C12  110.32  3.000
 Q5A  C10  C11  C12  110.04  3.000
 Q5A  H14  C10  H13  106.78  3.000
 Q5A  H14  C10  N2   107.26  3.000
 Q5A  H13  C10  N2   109.70  3.000
 Q5A  H14  C10  C11  109.70  3.000
 Q5A  H13  C10  C11  110.61  3.000
 Q5A  N2   C10  C11  112.57  3.000
 Q5A  C9   N2   C10  117.18  3.000
 Q5A  C9   N2   C14  120.84  3.000
 Q5A  C10  N2   C14  111.88  3.000
 Q5A  N1   C9   O1   121.80  3.000
 Q5A  N1   C9   N2   116.15  3.000
 Q5A  O1   C9   N2   122.03  3.000
 Q5A  C2   N1   C1   115.19  3.000
 Q5A  C2   N1   C9   119.47  3.000
 Q5A  C1   N1   C9   124.42  3.000
 Q5A  H17  C1   H16  107.41  3.000
 Q5A  H17  C1   H15  108.86  3.000
 Q5A  H16  C1   H15  107.77  3.000
 Q5A  H17  C1   N1   111.05  3.000
 Q5A  H16  C1   N1   109.52  3.000
 Q5A  H15  C1   N1   112.07  3.000
 Q5A  H19  C2   H18  106.68  3.000
 Q5A  H19  C2   C3   110.20  3.000
 Q5A  H18  C2   C3   108.94  3.000
 Q5A  H19  C2   N1   108.88  3.000
 Q5A  H18  C2   N1   107.79  3.000
 Q5A  C3   C2   N1   114.07  3.000
 Q5A  C8   C3   C4   118.50  3.000
 Q5A  C4   C3   C2   121.08  3.000
 Q5A  C8   C3   C2   120.42  3.000
 Q5A  H20  C4   C5   119.27  3.000
 Q5A  H20  C4   C3   119.67  3.000
 Q5A  C5   C4   C3   121.05  3.000
 Q5A  H21  C5   C6   120.40  3.000
 Q5A  H21  C5   C4   120.94  3.000
 Q5A  C6   C5   C4   118.65  3.000
 Q5A  C7   C6   F1   119.05  3.000
 Q5A  F1   C6   C5   118.88  3.000
 Q5A  C7   C6   C5   122.07  3.000
 Q5A  H22  C7   C8   121.04  3.000
 Q5A  H22  C7   C6   120.63  3.000
 Q5A  C8   C7   C6   118.33  3.000
 Q5A  H23  C8   C7   119.00  3.000
 Q5A  H23  C8   C3   119.61  3.000
 Q5A  C7   C8   C3   121.39  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
 Q5A  CONST_01  S1   C16  N4   C17    0.00   0.0  0
 Q5A  CONST_02  C16  S1   C19  C17    0.00   0.0  0
 Q5A  CONST_03  S1   C19  C17  N4     0.00   0.0  0
 Q5A  CONST_04  C19  S1   C16  N4     0.00   0.0  0
 Q5A  CONST_05  C16  N4   C17  C19    0.00   0.0  0
 Q5A  CONST_06  C6   C7   C8   C3     0.00   0.0  0
 Q5A  CONST_07  C6   C5   C4   C3     0.00   0.0  0
 Q5A  CONST_08  C7   C8   C3   C4     0.00   0.0  0
 Q5A  CONST_09  C7   C6   C5   C4     0.00   0.0  0
 Q5A  CONST_10  C8   C3   C4   C5     0.00   0.0  0
 Q5A  CONST_11  C8   C7   C6   C5     0.00   0.0  0
 Q5A  CONST_12  C16  N4   C17  C18  180.00   0.0  0
 Q5A  CONST_13  S1   C19  C17  C18  180.00   0.0  0
 Q5A  CONST_14  N3   C16  N4   C17  180.00   0.0  0
 Q5A  CONST_15  N3   C16  S1   C19  180.00   0.0  0
 Q5A  CONST_16  C7   C8   C3   C2   180.00   0.0  0
 Q5A  CONST_17  C5   C4   C3   C2   180.00   0.0  0
 Q5A  CONST_18  F1   C6   C5   C4   180.00   0.0  0
 Q5A  CONST_19  C8   C7   C6   F1   180.00   0.0  0
 Q5A  CONST_20  H4   C19  C17  N4   180.00   0.0  0
 Q5A  CONST_21  H22  C7   C8   C3   180.00   0.0  0
 Q5A  CONST_22  H21  C5   C4   C3   180.00   0.0  0
 Q5A  CONST_23  H23  C8   C3   C4   180.00   0.0  0
 Q5A  CONST_24  H20  C4   C5   C6   180.00   0.0  0
 Q5A  CONST_25  C12  C15  N3   C16  180.00   0.0  0
 Q5A  CONST_27  O1   C9   N2   C10    0.00   0.0  0
 Q5A  CONST_28  C15  N3   C16  N4   180.00   0.0  0
 Q5A  CONST_29  C15  N3   C16  S1     0.00   0.0  0
 Q5A  CONST_31  N1   C9   N2   C10  180.00   0.0  0
 Q5A  CONST_32  H5   N3   C16  N4     0.00   0.0  0
 Q5A  CONST_33  O2   C15  N3   C16    0.00   0.0  0
 Q5A  Var_01    N2   C14  C13  C12  -55.07  30.0  1
 Q5A  Var_02    N2   C10  C11  C12   55.97  30.0  1
 Q5A  Var_03    C10  N2   C14  C13   57.06  30.0  1
 Q5A  Var_04    C11  C10  N2   C14  -57.99  30.0  1
 Q5A  Var_05    C8   C3   C2   N1   114.69  30.0  2
 Q5A  Var_06    H1   C18  C17  N4    60.02  30.0  2
 Q5A  Var_07    C3   C2   N1   C9   101.32  30.0  3
 Q5A  Var_08    H15  C1   N1   C9   116.05  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
 Q5A  chir_01  C12  C15  C13  C11  negativ

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
 Q5A  plan-1  C18  0.020
 Q5A  plan-1  C17  0.020
 Q5A  plan-1  N4   0.020
 Q5A  plan-1  C19  0.020
 Q5A  plan-1  S1   0.020
 Q5A  plan-1  C16  0.020
 Q5A  plan-1  N3   0.020
 Q5A  plan-1  H4   0.020
 Q5A  plan-2  C2   0.020
 Q5A  plan-2  C3   0.020
 Q5A  plan-2  C4   0.020
 Q5A  plan-2  C5   0.020
 Q5A  plan-2  C6   0.020
 Q5A  plan-2  F1   0.020
 Q5A  plan-2  C7   0.020
 Q5A  plan-2  C8   0.020
 Q5A  plan-2  H20  0.020
 Q5A  plan-2  H21  0.020
 Q5A  plan-2  H22  0.020
 Q5A  plan-2  H23  0.020
 Q5A  plan-3  C14  0.020
 Q5A  plan-3  C10  0.020
 Q5A  plan-3  N2   0.020
 Q5A  plan-3  C9   0.020
 Q5A  plan-3  O1   0.020
 Q5A  plan-3  N1   0.020
 Q5A  plan-3  C1   0.020
 Q5A  plan-3  C2   0.020
 Q5A  plan-4  C16  0.020
 Q5A  plan-4  N3   0.020
 Q5A  plan-4  C15  0.020
 Q5A  plan-4  O2   0.020
 Q5A  plan-4  C12  0.020
 Q5A  plan-4  H5   0.020

