# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 00:01:32 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 2-(3-fluorophenyl)-4-[[(3~{S})-piperidin-3-yl]amino]thieno[3,2-c]pyridine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cnc(N[C@H]2CCCNC2)c3cc(sc13)c4cccc(F)c4
#
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
 D4Q  D4Q  2-(3-fluorophenyl)-4-[[(3~{S})-piperidin-3-yl]amino]thieno[3,2-c]pyridine-7-carboxamide  ligand  45  26  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_D4Q
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
 D4Q  C1   C  CR16  0  -0.340   4.4963   0.1087   0.0886
 D4Q  C2   C  CR6   0   0.189   3.3070  -0.6218   0.0235
 D4Q  C3   C  CR16  0  -0.521   3.3833  -2.0177  -0.0117
 D4Q  C7   C  CR15  0  -0.295   0.7751  -0.5361  -0.0765
 D4Q  C8   C  CR56  0   0.109  -0.2827   0.4175  -0.1021
 D4Q  C9   C  CR56  0  -0.126   0.1771   1.7310  -0.0560
 D4Q  C10  C  CR6   0  -0.208  -0.7166   2.8175  -0.0797
 D4Q  C11  C  CR16  0  -0.089  -2.0553   2.4729  -0.1522
 D4Q  C12  C  CR6   0   0.513  -1.6899   0.2062  -0.1751
 D4Q  C13  C  CH1   0  -0.063  -3.6053  -1.3494  -0.3151
 D4Q  C14  C  CH2   0  -0.462  -3.7893  -2.7329  -0.9282
 D4Q  C15  C  CH2   0  -0.447  -5.2670  -3.1098  -0.9517
 D4Q  C16  C  CH2   0  -0.313  -5.8829  -2.9722   0.4377
 D4Q  O    O  O     0  -0.491   1.0358   4.3600   0.0167
 D4Q  C18  C  C     0   0.505  -0.1809   4.1907  -0.0330
 D4Q  N3   N  NH2   0  -0.831  -1.0447   5.2157  -0.0509
 D4Q  S    S  S2    0   0.251   1.8962   1.7861   0.0198
 D4Q  C6   C  CR5   0  -0.205   2.0042   0.0416  -0.0116
 D4Q  C4   C  CR6   0   0.574   4.6180  -2.6280   0.0180
 D4Q  F    F  F     0  -0.315   4.6689  -3.9686  -0.0199
 D4Q  C5   C  CR16  0  -0.427   5.8031  -1.9194   0.0831
 D4Q  C    C  CR16  0  -0.219   5.7236  -0.5356   0.1182
 D4Q  N    N  N     0  -0.481  -2.5340   1.2348  -0.1968
 D4Q  C17  C  CH2   0  -0.306  -4.2788  -1.2828   1.0629
 D4Q  N2   N  NH1   0  -0.579  -5.6781  -1.6653   1.0436
 D4Q  H1   H  HCR6  0   0.260   4.4809   1.1907   0.1168
 D4Q  H2   H  HCR6  0   0.278   2.4951  -2.6330  -0.0641
 D4Q  H3   H  HCR5  0   0.270   0.6272  -1.6066  -0.1044
 D4Q  H4   H  HCR6  0   0.254  -2.8197   3.2422  -0.1748
 D4Q  H5   H  HCH1  0   0.239  -4.0814  -0.6106  -0.9667
 D4Q  H6   H  HCH2  0   0.247  -3.3697  -2.7553  -1.9365
 D4Q  H7   H  HCH2  0   0.223  -3.2367  -3.4702  -0.3335
 D4Q  H8   H  HCH2  0   0.220  -5.8004  -2.4594  -1.6525
 D4Q  H9   H  HCH2  0   0.233  -5.3893  -4.1322  -1.3172
 D4Q  H10  H  HCH2  0   0.237  -6.9550  -3.1754   0.4019
 D4Q  H11  H  HCH2  0   0.215  -5.4429  -3.7246   1.1019
 D4Q  H12  H  HNH2  0   0.413  -2.0422   5.1041  -0.0736
 D4Q  H13  H  HNH2  0   0.407  -0.6945   6.1588  -0.0158
 D4Q  H14  H  HCR6  0   0.284   6.7557  -2.4317   0.1046
 D4Q  H15  H  HCR6  0   0.275   6.6314   0.0503   0.1687
 D4Q  H16  H  HNH1  0   0.406  -1.5536  -1.8093  -0.1759
 D4Q  H17  H  HCH2  0   0.215  -3.7418  -1.9502   1.7466
 D4Q  H18  H  HCH2  0   0.242  -4.1891  -0.2721   1.4654
 D4Q  H19  H  HNH1  0   0.342  -6.2070  -0.9708   0.5285
 D4Q  N1   N  NH1   0  -0.680  -2.1927  -1.0342  -0.2391

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
 D4Q  C    C5   aromatic  1.387  0.020  1.387
 D4Q  C    C1   aromatic  1.386  0.020  1.386
 D4Q  C16  N2   single    1.455  0.020  1.455
 D4Q  C16  C15  single    1.526  0.020  1.526
 D4Q  C5   C4   aromatic  1.382  0.020  1.382
 D4Q  C1   C2   aromatic  1.397  0.020  1.397
 D4Q  N2   C17  single    1.451  0.020  1.451
 D4Q  C15  C14  single    1.525  0.020  1.525
 D4Q  C17  C13  single    1.535  0.020  1.535
 D4Q  C14  C13  single    1.524  0.020  1.524
 D4Q  C4   F    single    1.342  0.020  1.342
 D4Q  C4   C3   aromatic  1.378  0.020  1.378
 D4Q  C2   C3   aromatic  1.398  0.020  1.398
 D4Q  C2   C6   single    1.462  0.020  1.462
 D4Q  C13  N1   single    1.449  0.020  1.449
 D4Q  C7   C6   aromatic  1.360  0.020  1.360
 D4Q  C7   C8   aromatic  1.424  0.020  1.424
 D4Q  N1   C12  single    1.340  0.020  1.340
 D4Q  C6   S    aromatic  1.748  0.020  1.748
 D4Q  C8   C12  aromatic  1.425  0.020  1.425
 D4Q  C8   C9   aromatic  1.392  0.020  1.392
 D4Q  C12  N    aromatic  1.331  0.020  1.331
 D4Q  S    C9   aromatic  1.722  0.020  1.722
 D4Q  C9   C10  aromatic  1.407  0.020  1.407
 D4Q  N    C11  aromatic  1.328  0.020  1.328
 D4Q  C11  C10  aromatic  1.384  0.020  1.384
 D4Q  C10  C18  single    1.475  0.020  1.475
 D4Q  C18  O    double    1.229  0.020  1.229
 D4Q  C18  N3   single    1.341  0.020  1.341
 D4Q  C1   H1   single    0.930  0.020  1.080
 D4Q  C3   H2   single    0.930  0.020  1.080
 D4Q  C7   H3   single    0.930  0.020  1.080
 D4Q  C11  H4   single    0.930  0.020  1.080
 D4Q  C13  H5   single    0.970  0.020  1.090
 D4Q  C14  H6   single    0.970  0.020  1.090
 D4Q  C14  H7   single    0.970  0.020  1.090
 D4Q  C15  H8   single    0.970  0.020  1.090
 D4Q  C15  H9   single    0.970  0.020  1.090
 D4Q  C16  H10  single    0.970  0.020  1.090
 D4Q  C16  H11  single    0.970  0.020  1.090
 D4Q  N3   H12  single    0.860  0.020  1.020
 D4Q  N3   H13  single    0.860  0.020  1.020
 D4Q  C5   H14  single    0.930  0.020  1.080
 D4Q  C    H15  single    0.930  0.020  1.080
 D4Q  N1   H16  single    0.860  0.020  1.020
 D4Q  C17  H17  single    0.970  0.020  1.090
 D4Q  C17  H18  single    0.970  0.020  1.090
 D4Q  N2   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
 D4Q  H1   C1   C    118.46  3.000
 D4Q  H1   C1   C2   120.77  3.000
 D4Q  C    C1   C2   120.77  3.000
 D4Q  C6   C2   C3   120.05  3.000
 D4Q  C6   C2   C1   121.48  3.000
 D4Q  C3   C2   C1   118.46  3.000
 D4Q  H2   C3   C4   119.00  3.000
 D4Q  H2   C3   C2   121.62  3.000
 D4Q  C4   C3   C2   119.38  3.000
 D4Q  H3   C7   C6   123.07  3.000
 D4Q  H3   C7   C8   124.11  3.000
 D4Q  C6   C7   C8   112.82  3.000
 D4Q  C12  C8   C9   117.88  3.000
 D4Q  C9   C8   C7   112.69  3.000
 D4Q  C12  C8   C7   129.43  3.000
 D4Q  S    C9   C10  127.61  3.000
 D4Q  C10  C9   C8   121.20  3.000
 D4Q  S    C9   C8   111.18  3.000
 D4Q  C18  C10  C11  125.78  3.000
 D4Q  C18  C10  C9   119.19  3.000
 D4Q  C11  C10  C9   115.02  3.000
 D4Q  H4   C11  N    113.98  3.000
 D4Q  H4   C11  C10  120.41  3.000
 D4Q  N    C11  C10  125.62  3.000
 D4Q  N1   C12  N    118.47  3.000
 D4Q  N    C12  C8   120.84  3.000
 D4Q  N1   C12  C8   120.68  3.000
 D4Q  H5   C13  C17  108.32  3.000
 D4Q  H5   C13  N1   107.97  3.000
 D4Q  C17  C13  N1   111.78  3.000
 D4Q  H5   C13  C14  108.71  3.000
 D4Q  N1   C13  C14  109.64  3.000
 D4Q  C17  C13  C14  110.33  3.000
 D4Q  H7   C14  H6   107.05  3.000
 D4Q  H7   C14  C15  109.30  3.000
 D4Q  H6   C14  C15  110.66  3.000
 D4Q  H7   C14  C13  109.34  3.000
 D4Q  H6   C14  C13  110.09  3.000
 D4Q  C15  C14  C13  110.33  3.000
 D4Q  H9   C15  H8   106.69  3.000
 D4Q  H9   C15  C16  110.11  3.000
 D4Q  H8   C15  C16  109.42  3.000
 D4Q  H9   C15  C14  110.17  3.000
 D4Q  H8   C15  C14  109.58  3.000
 D4Q  C16  C15  C14  110.78  3.000
 D4Q  H11  C16  H10  106.63  3.000
 D4Q  H11  C16  N2   107.93  3.000
 D4Q  H10  C16  N2   108.61  3.000
 D4Q  H11  C16  C15  109.14  3.000
 D4Q  H10  C16  C15  110.47  3.000
 D4Q  N2   C16  C15  113.79  3.000
 D4Q  N3   C18  O    122.21  3.000
 D4Q  N3   C18  C10  118.52  3.000
 D4Q  O    C18  C10  119.27  3.000
 D4Q  H13  N3   H12  116.78  3.000
 D4Q  H13  N3   C18  119.46  3.000
 D4Q  H12  N3   C18  123.74  3.000
 D4Q  C6   S    C9    91.66  3.000
 D4Q  S    C6   C7   111.65  3.000
 D4Q  S    C6   C2   120.49  3.000
 D4Q  C7   C6   C2   127.86  3.000
 D4Q  C5   C4   F    118.74  3.000
 D4Q  F    C4   C3   118.42  3.000
 D4Q  C5   C4   C3   122.84  3.000
 D4Q  H14  C5   C    121.51  3.000
 D4Q  H14  C5   C4   120.87  3.000
 D4Q  C    C5   C4   117.62  3.000
 D4Q  H15  C    C5   119.58  3.000
 D4Q  H15  C    C1   119.49  3.000
 D4Q  C5   C    C1   120.93  3.000
 D4Q  C12  N    C11  119.43  3.000
 D4Q  H18  C17  H17  107.07  3.000
 D4Q  H18  C17  N2   109.16  3.000
 D4Q  H17  C17  N2   108.68  3.000
 D4Q  H18  C17  C13  109.58  3.000
 D4Q  H17  C17  C13  108.58  3.000
 D4Q  N2   C17  C13  113.56  3.000
 D4Q  H19  N2   C17  109.23  3.000
 D4Q  H19  N2   C16  109.30  3.000
 D4Q  C17  N2   C16  112.21  3.000
 D4Q  H16  N1   C13  117.04  3.000
 D4Q  H16  N1   C12  118.13  3.000
 D4Q  C13  N1   C12  124.72  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
 D4Q  CONST_01  C4   C5   C    C1     0.00   0.0  0
 D4Q  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 D4Q  CONST_03  C7   C6   C2   C1   180.00   0.0  0
 D4Q  CONST_04  S    C6   C2   C1     0.00   0.0  0
 D4Q  CONST_05  C5   C    C1   C2     0.00   0.0  0
 D4Q  CONST_06  C5   C4   C3   C2     0.00   0.0  0
 D4Q  CONST_07  C8   C7   C6   C2   180.00   0.0  0
 D4Q  CONST_08  C9   S    C6   C2   180.00   0.0  0
 D4Q  CONST_09  C    C5   C4   C3     0.00   0.0  0
 D4Q  CONST_10  C    C1   C2   C3     0.00   0.0  0
 D4Q  CONST_11  C7   C6   C2   C3     0.00   0.0  0
 D4Q  CONST_12  S    C6   C2   C3   180.00   0.0  0
 D4Q  CONST_13  C9   S    C6   C7     0.00   0.0  0
 D4Q  CONST_14  N    C12  C8   C7   180.00   0.0  0
 D4Q  CONST_15  S    C9   C8   C7     0.00   0.0  0
 D4Q  CONST_16  C10  C9   C8   C7   180.00   0.0  0
 D4Q  CONST_17  S    C6   C7   C8     0.00   0.0  0
 D4Q  CONST_18  C11  N    C12  C8     0.00   0.0  0
 D4Q  CONST_19  C6   S    C9   C8     0.00   0.0  0
 D4Q  CONST_20  C11  C10  C9   C8     0.00   0.0  0
 D4Q  CONST_21  C6   C7   C8   C9     0.00   0.0  0
 D4Q  CONST_22  N    C12  C8   C9     0.00   0.0  0
 D4Q  CONST_23  N    C11  C10  C9     0.00   0.0  0
 D4Q  CONST_24  C12  C8   C9   C10    0.00   0.0  0
 D4Q  CONST_25  C6   S    C9   C10  180.00   0.0  0
 D4Q  CONST_26  C12  N    C11  C10    0.00   0.0  0
 D4Q  CONST_27  S    C9   C10  C11  180.00   0.0  0
 D4Q  CONST_28  C6   C7   C8   C12  180.00   0.0  0
 D4Q  CONST_29  S    C9   C8   C12  180.00   0.0  0
 D4Q  CONST_30  C    C1   C2   C6   180.00   0.0  0
 D4Q  CONST_31  C4   C3   C2   C6   180.00   0.0  0
 D4Q  CONST_32  F    C4   C3   C2   180.00   0.0  0
 D4Q  CONST_33  N1   C12  C8   C7     0.00   0.0  0
 D4Q  CONST_34  C18  C10  C9   C8   180.00   0.0  0
 D4Q  CONST_35  N1   C12  C8   C9   180.00   0.0  0
 D4Q  CONST_36  N1   C12  N    C11  180.00   0.0  0
 D4Q  CONST_37  S    C9   C10  C18    0.00   0.0  0
 D4Q  CONST_38  N    C11  C10  C18  180.00   0.0  0
 D4Q  CONST_39  C    C5   C4   F    180.00   0.0  0
 D4Q  CONST_40  C13  N1   C12  C8   180.00   0.0  0
 D4Q  CONST_41  N    C12  N1   C13    0.00   0.0  0
 D4Q  CONST_42  H14  C5   C    C1   180.00   0.0  0
 D4Q  CONST_43  H2   C3   C2   C1   180.00   0.0  0
 D4Q  CONST_44  H15  C    C1   C2   180.00   0.0  0
 D4Q  CONST_45  H3   C7   C6   C2     0.00   0.0  0
 D4Q  CONST_46  H1   C1   C2   C3   180.00   0.0  0
 D4Q  CONST_47  H4   C11  C10  C9   180.00   0.0  0
 D4Q  CONST_48  H16  N1   C12  C8     0.00   0.0  0
 D4Q  CONST_49  H12  N3   C18  C10    0.00   0.0  0
 D4Q  CONST_50  H13  N3   C18  C10  180.00   0.0  0
 D4Q  Var_01    C16  N2   C17  C13   53.72  30.0  1
 D4Q  Var_02    C16  C15  C14  C13  -53.41  30.0  1
 D4Q  Var_03    N2   C16  C15  C14   53.59  30.0  1
 D4Q  Var_04    C17  N2   C16  C15  -53.33  30.0  1
 D4Q  Var_05    O    C18  C10  C9     0.48  30.0  2

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
 D4Q  chir_01  C13  C17  C14  N1  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
 D4Q  plan-1  C1   0.020
 D4Q  plan-1  C2   0.020
 D4Q  plan-1  C3   0.020
 D4Q  plan-1  C6   0.020
 D4Q  plan-1  C4   0.020
 D4Q  plan-1  F    0.020
 D4Q  plan-1  C5   0.020
 D4Q  plan-1  C    0.020
 D4Q  plan-1  H1   0.020
 D4Q  plan-1  H2   0.020
 D4Q  plan-1  H14  0.020
 D4Q  plan-1  H15  0.020
 D4Q  plan-2  C2   0.020
 D4Q  plan-2  C7   0.020
 D4Q  plan-2  C8   0.020
 D4Q  plan-2  C9   0.020
 D4Q  plan-2  C10  0.020
 D4Q  plan-2  C11  0.020
 D4Q  plan-2  C12  0.020
 D4Q  plan-2  C18  0.020
 D4Q  plan-2  S    0.020
 D4Q  plan-2  C6   0.020
 D4Q  plan-2  N    0.020
 D4Q  plan-2  H3   0.020
 D4Q  plan-2  H4   0.020
 D4Q  plan-2  N1   0.020
 D4Q  plan-3  C12  0.020
 D4Q  plan-3  C13  0.020
 D4Q  plan-3  H16  0.020
 D4Q  plan-3  N1   0.020
 D4Q  plan-4  C10  0.020
 D4Q  plan-4  O    0.020
 D4Q  plan-4  C18  0.020
 D4Q  plan-4  N3   0.020
 D4Q  plan-4  H12  0.020
 D4Q  plan-4  H13  0.020

