# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 04:38:26 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 3-(carbamoylamino)-5-(3-fluorophenyl)-N-[(3S)-piperidin-3-yl]thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)Nc1cc(sc1C(=O)N[C@H]2CCCNC2)c3cccc(F)c3
#
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
 YDJ  YDJ  3-(carbamoylamino)-5-(3-fluorophenyl)-N-[(3S)-piperidin-3-yl]thiophene-2-carboxamide  ligand  44  25  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YDJ
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
 YDJ  C1    C  CR16  0  -0.220   4.2267  -3.2891  -0.0309
 YDJ  C2    C  CR16  0  -0.336   3.0653  -2.5350  -0.0813
 YDJ  C3    C  CR6   0   0.190   3.1201  -1.1402  -0.0345
 YDJ  C4    C  CR16  0  -0.514   4.3682  -0.5201   0.0648
 YDJ  C5    C  CR6   0   0.575   5.5048  -1.2981   0.1141
 YDJ  C6    C  CR16  0  -0.423   5.4684  -2.6787   0.0683
 YDJ  F1    F  F     0  -0.313   6.6939  -0.6849   0.2100
 YDJ  C7    C  CR5   0  -0.171   1.9055  -0.3262  -0.0862
 YDJ  C8    C  CR15  0  -0.289   1.8099   1.0361  -0.0250
 YDJ  C9    C  CR5   0   0.503   0.4712   1.5083  -0.1155
 YDJ  C10   C  CR5   0  -0.472  -0.4402   0.4712  -0.2334
 YDJ  S1    S  S2    0   0.224   0.3611  -1.0579  -0.2573
 YDJ  C11   C  C     0   0.621  -1.8952   0.6168  -0.3297
 YDJ  O1    O  O     0  -0.518  -2.4024   1.7328  -0.4778
 YDJ  N1    N  NH1   0  -0.672  -2.6361  -0.5017  -0.2607
 YDJ  C12   C  CH1   0  -0.072  -4.0867  -0.4996  -0.3151
 YDJ  C13   C  CH2   0  -0.458  -4.5864  -1.8620  -0.7834
 YDJ  C14   C  CH2   0  -0.449  -6.1106  -1.9081  -0.7655
 YDJ  C15   C  CH2   0  -0.313  -6.6501  -1.4954   0.6011
 YDJ  N2    N  NH1   0  -0.578  -6.1492  -0.2115   1.0649
 YDJ  C16   C  CH2   0  -0.303  -4.7013  -0.1477   1.0475
 YDJ  N3    N  NH1   0  -0.782   0.0660   2.8209  -0.0924
 YDJ  C17   C  C     0   0.677   0.8554   3.9350   0.0870
 YDJ  O2    O  O     0  -0.513   2.0685   3.8876   0.2288
 YDJ  N4    N  NH2   0  -0.846   0.1571   5.0875   0.0932
 YDJ  H1    H  HCR6  0   0.278   4.1644  -4.3679  -0.0678
 YDJ  H2    H  HCR6  0   0.263   2.1165  -3.0517  -0.1569
 YDJ  H6    H  HCR6  0   0.286   6.3797  -3.2599   0.1097
 YDJ  H4    H  HCR6  0   0.278   4.4656   0.5568   0.1020
 YDJ  H8    H  HCR5  0   0.290   2.6587   1.6898   0.0741
 YDJ  H3    H  HNH1  0   0.419  -0.9367   2.9295  -0.2126
 YDJ  HA    H  HNH1  0   0.401  -2.2002  -1.3724   0.0041
 YDJ  H12   H  HCH1  0   0.243  -4.3937   0.2572  -1.0427
 YDJ  H131  H  HCH2  0   0.248  -4.2049  -2.0766  -1.7843
 YDJ  H132  H  HCH2  0   0.223  -4.1915  -2.6408  -0.1196
 YDJ  H161  H  HCH2  0   0.216  -4.3094  -0.8458   1.7965
 YDJ  H162  H  HCH2  0   0.243  -4.3867   0.8531   1.3490
 YDJ  H141  H  HCH2  0   0.220  -6.5092  -1.2358  -1.5324
 YDJ  H142  H  HCH2  0   0.234  -6.4572  -2.9126  -1.0194
 YDJ  H151  H  HCH2  0   0.237  -7.7410  -1.4572   0.5838
 YDJ  H152  H  HCH2  0   0.215  -6.3765  -2.2548   1.3422
 YDJ  HB    H  HNH1  0   0.342  -6.5238   0.5266   0.4801
 YDJ  H41N  H  HNH2  0   0.407  -0.8392   5.1331  -0.0321
 YDJ  H42N  H  HNH2  0   0.409   0.6510   5.9570   0.1920

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
 YDJ  C1   C2    aromatic  1.386  0.020  1.386
 YDJ  C1   C6    aromatic  1.387  0.020  1.387
 YDJ  C2   C3    aromatic  1.397  0.020  1.397
 YDJ  C3   C4    aromatic  1.397  0.020  1.397
 YDJ  C3   C7    single    1.463  0.020  1.463
 YDJ  C4   C5    aromatic  1.378  0.020  1.378
 YDJ  C5   C6    aromatic  1.382  0.020  1.382
 YDJ  C5   F1    single    1.341  0.020  1.341
 YDJ  C7   C8    aromatic  1.367  0.020  1.367
 YDJ  C7   S1    aromatic  1.717  0.020  1.717
 YDJ  C8   C9    aromatic  1.422  0.020  1.422
 YDJ  C9   C10   aromatic  1.386  0.020  1.386
 YDJ  C9   N3    single    1.374  0.020  1.374
 YDJ  C10  S1    aromatic  1.727  0.020  1.727
 YDJ  C10  C11   single    1.465  0.020  1.465
 YDJ  C11  O1    double    1.235  0.020  1.235
 YDJ  C11  N1    single    1.343  0.020  1.343
 YDJ  N1   C12   single    1.452  0.020  1.452
 YDJ  C12  C13   single    1.525  0.020  1.525
 YDJ  C12  C16   single    1.536  0.020  1.536
 YDJ  C13  C14   single    1.525  0.020  1.525
 YDJ  C14  C15   single    1.526  0.020  1.526
 YDJ  C15  N2    single    1.454  0.020  1.454
 YDJ  N2   C16   single    1.449  0.020  1.449
 YDJ  N3   C17   single    1.377  0.020  1.377
 YDJ  C17  O2    double    1.222  0.020  1.222
 YDJ  C17  N4    single    1.348  0.020  1.348
 YDJ  C1   H1    single    0.930  0.020  1.080
 YDJ  C2   H2    single    0.930  0.020  1.080
 YDJ  C6   H6    single    0.930  0.020  1.080
 YDJ  C4   H4    single    0.930  0.020  1.080
 YDJ  C8   H8    single    0.930  0.020  1.080
 YDJ  N3   H3    single    0.860  0.020  1.020
 YDJ  N1   HA    single    0.860  0.020  1.020
 YDJ  C12  H12   single    0.970  0.020  1.090
 YDJ  C13  H131  single    0.970  0.020  1.090
 YDJ  C13  H132  single    0.970  0.020  1.090
 YDJ  C16  H161  single    0.970  0.020  1.090
 YDJ  C16  H162  single    0.970  0.020  1.090
 YDJ  C14  H141  single    0.970  0.020  1.090
 YDJ  C14  H142  single    0.970  0.020  1.090
 YDJ  C15  H151  single    0.970  0.020  1.090
 YDJ  C15  H152  single    0.970  0.020  1.090
 YDJ  N2   HB    single    0.890  0.020  1.040
 YDJ  N4   H41N  single    0.860  0.020  1.020
 YDJ  N4   H42N  single    0.860  0.020  1.020

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
 YDJ  H1    C1   C6    119.54  3.000
 YDJ  H1    C1   C2    119.57  3.000
 YDJ  C6    C1   C2    120.89  3.000
 YDJ  H2    C2   C3    120.87  3.000
 YDJ  H2    C2   C1    118.50  3.000
 YDJ  C3    C2   C1    120.62  3.000
 YDJ  C7    C3   C4    119.81  3.000
 YDJ  C7    C3   C2    121.46  3.000
 YDJ  C4    C3   C2    118.73  3.000
 YDJ  H4    C4   C5    119.10  3.000
 YDJ  H4    C4   C3    121.64  3.000
 YDJ  C5    C4   C3    119.26  3.000
 YDJ  F1    C5   C6    118.85  3.000
 YDJ  F1    C5   C4    118.40  3.000
 YDJ  C6    C5   C4    122.75  3.000
 YDJ  H6    C6   C5    120.89  3.000
 YDJ  H6    C6   C1    121.36  3.000
 YDJ  C5    C6   C1    117.75  3.000
 YDJ  S1    C7   C8    111.48  3.000
 YDJ  S1    C7   C3    120.86  3.000
 YDJ  C8    C7   C3    127.65  3.000
 YDJ  H8    C8   C9    123.13  3.000
 YDJ  H8    C8   C7    123.67  3.000
 YDJ  C9    C8   C7    113.19  3.000
 YDJ  N3    C9   C10   121.50  3.000
 YDJ  N3    C9   C8    126.42  3.000
 YDJ  C10   C9   C8    112.08  3.000
 YDJ  C11   C10  S1    123.22  3.000
 YDJ  C11   C10  C9    125.75  3.000
 YDJ  S1    C10  C9    111.02  3.000
 YDJ  C10   S1   C7     92.22  3.000
 YDJ  N1    C11  O1    122.15  3.000
 YDJ  N1    C11  C10   117.48  3.000
 YDJ  O1    C11  C10   120.37  3.000
 YDJ  HA    N1   C12   116.27  3.000
 YDJ  HA    N1   C11   119.59  3.000
 YDJ  C12   N1   C11   123.23  3.000
 YDJ  H12   C12  C16   108.62  3.000
 YDJ  H12   C12  C13   108.79  3.000
 YDJ  C16   C12  C13   110.25  3.000
 YDJ  H12   C12  N1    107.84  3.000
 YDJ  C16   C12  N1    111.52  3.000
 YDJ  C13   C12  N1    109.74  3.000
 YDJ  H132  C13  H131  106.82  3.000
 YDJ  H132  C13  C14   109.34  3.000
 YDJ  H131  C13  C14   110.72  3.000
 YDJ  H132  C13  C12   109.30  3.000
 YDJ  H131  C13  C12   110.03  3.000
 YDJ  C14   C13  C12   110.54  3.000
 YDJ  H142  C14  H141  106.63  3.000
 YDJ  H142  C14  C15   110.16  3.000
 YDJ  H141  C14  C15   109.41  3.000
 YDJ  H142  C14  C13   110.00  3.000
 YDJ  H141  C14  C13   109.70  3.000
 YDJ  C15   C14  C13   110.84  3.000
 YDJ  H152  C15  H151  106.53  3.000
 YDJ  H152  C15  N2    108.07  3.000
 YDJ  H151  C15  N2    108.57  3.000
 YDJ  H152  C15  C14   109.27  3.000
 YDJ  H151  C15  C14   110.40  3.000
 YDJ  N2    C15  C14   113.74  3.000
 YDJ  HB    N2   C16   109.28  3.000
 YDJ  HB    N2   C15   109.37  3.000
 YDJ  C16   N2   C15   112.28  3.000
 YDJ  H162  C16  H161  106.99  3.000
 YDJ  H162  C16  N2    108.97  3.000
 YDJ  H161  C16  N2    108.71  3.000
 YDJ  H162  C16  C12   109.87  3.000
 YDJ  H161  C16  C12   108.49  3.000
 YDJ  N2    C16  C12   113.59  3.000
 YDJ  H3    N3   C17   119.66  3.000
 YDJ  H3    N3   C9    113.04  3.000
 YDJ  C17   N3   C9    127.30  3.000
 YDJ  N4    C17  O2    123.16  3.000
 YDJ  N4    C17  N3    113.29  3.000
 YDJ  O2    C17  N3    123.55  3.000
 YDJ  H42N  N4   H41N  117.40  3.000
 YDJ  H42N  N4   C17   119.06  3.000
 YDJ  H41N  N4   C17   123.50  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
 YDJ  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 YDJ  CONST_02  C7    C3   C2   C1   180.00   0.0  0
 YDJ  CONST_03  C4    C5   C6   C1     0.00   0.0  0
 YDJ  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 YDJ  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 YDJ  CONST_06  C8    C7   C3   C2   180.00   0.0  0
 YDJ  CONST_07  S1    C7   C3   C2     0.00   0.0  0
 YDJ  CONST_08  C6    C1   C2   C3     0.00   0.0  0
 YDJ  CONST_09  C6    C5   C4   C3     0.00   0.0  0
 YDJ  CONST_10  C9    C8   C7   C3   180.00   0.0  0
 YDJ  CONST_11  C10   S1   C7   C3   180.00   0.0  0
 YDJ  CONST_12  C8    C7   C3   C4     0.00   0.0  0
 YDJ  CONST_13  S1    C7   C3   C4   180.00   0.0  0
 YDJ  CONST_14  C7    C3   C4   C5   180.00   0.0  0
 YDJ  CONST_15  C10   C9   C8   C7     0.00   0.0  0
 YDJ  CONST_16  C9    C10  S1   C7     0.00   0.0  0
 YDJ  CONST_17  C10   S1   C7   C8     0.00   0.0  0
 YDJ  CONST_18  S1    C10  C9   C8     0.00   0.0  0
 YDJ  CONST_19  S1    C7   C8   C9     0.00   0.0  0
 YDJ  CONST_20  F1    C5   C6   C1   180.00   0.0  0
 YDJ  CONST_21  F1    C5   C4   C3   180.00   0.0  0
 YDJ  CONST_22  N3    C9   C8   C7   180.00   0.0  0
 YDJ  CONST_23  C11   C10  S1   C7   180.00   0.0  0
 YDJ  CONST_24  C11   C10  C9   C8   180.00   0.0  0
 YDJ  CONST_25  N3    C9   C10  S1   180.00   0.0  0
 YDJ  CONST_26  H6    C6   C1   C2   180.00   0.0  0
 YDJ  CONST_27  H4    C4   C3   C2   180.00   0.0  0
 YDJ  CONST_28  H1    C1   C2   C3   180.00   0.0  0
 YDJ  CONST_29  H8    C8   C7   C3     0.00   0.0  0
 YDJ  CONST_30  H2    C2   C3   C4   180.00   0.0  0
 YDJ  CONST_31  C12   N1   C11  C10  180.00   0.0  0
 YDJ  CONST_32  C17   N3   C9   C8     0.00   0.0  0
 YDJ  CONST_33  C17   N3   C9   C10  180.00   0.0  0
 YDJ  CONST_34  H3    N3   C9   C8   180.00   0.0  0
 YDJ  CONST_35  O2    C17  N3   C9     0.00   0.0  0
 YDJ  CONST_36  C12   N1   C11  O1     0.00   0.0  0
 YDJ  CONST_37  N4    C17  N3   C9   180.00   0.0  0
 YDJ  CONST_38  HA    N1   C11  C10    0.00   0.0  0
 YDJ  CONST_39  H41N  N4   C17  O2   180.00   0.0  0
 YDJ  CONST_40  H42N  N4   C17  O2     0.00   0.0  0
 YDJ  Var_01    C15   C14  C13  C12  -53.09  30.0  1
 YDJ  Var_02    C15   N2   C16  C12   53.93  30.0  1
 YDJ  Var_03    N2    C15  C14  C13   53.37  30.0  1
 YDJ  Var_04    C16   N2   C15  C14  -53.43  30.0  1
 YDJ  Var_05    O1    C11  C10  C9     9.08  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
 YDJ  chir_01  C12  N1  C13  C16  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
 YDJ  plan-1  C3    0.020
 YDJ  plan-1  C7    0.020
 YDJ  plan-1  C8    0.020
 YDJ  plan-1  C9    0.020
 YDJ  plan-1  C10   0.020
 YDJ  plan-1  S1    0.020
 YDJ  plan-1  C11   0.020
 YDJ  plan-1  N3    0.020
 YDJ  plan-1  H8    0.020
 YDJ  plan-2  C1    0.020
 YDJ  plan-2  C2    0.020
 YDJ  plan-2  C3    0.020
 YDJ  plan-2  C4    0.020
 YDJ  plan-2  C5    0.020
 YDJ  plan-2  C6    0.020
 YDJ  plan-2  F1    0.020
 YDJ  plan-2  C7    0.020
 YDJ  plan-2  H1    0.020
 YDJ  plan-2  H2    0.020
 YDJ  plan-2  H6    0.020
 YDJ  plan-2  H4    0.020
 YDJ  plan-3  C10   0.020
 YDJ  plan-3  C11   0.020
 YDJ  plan-3  O1    0.020
 YDJ  plan-3  N1    0.020
 YDJ  plan-3  C12   0.020
 YDJ  plan-3  HA    0.020
 YDJ  plan-4  C9    0.020
 YDJ  plan-4  N3    0.020
 YDJ  plan-4  C17   0.020
 YDJ  plan-4  O2    0.020
 YDJ  plan-4  N4    0.020
 YDJ  plan-4  H3    0.020
 YDJ  plan-4  H41N  0.020
 YDJ  plan-4  H42N  0.020

