# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 11:30:14 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 5-chloro-N-[(1R,2S)-2-({[4-(2-oxopyridin-1(2H)-yl)phenyl]carbonyl}amino)cyclopentyl]thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1sc(cc1)C(=O)N[C@@H]2CCC[C@@H]2NC(=O)c3ccc(cc3)N4C=CC=CC4=O
#
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
 ME5  ME5  5-chloro-N-[(1R,2S)-2-({[4-(2-oxopyridin-1(2H)-yl)phenyl]carbonyl}amino)cyclopentyl]thiophene-2-carboxamide  ligand  50  30  .  2021-08-14  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ME5
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
 ME5  C1    C   C     0   0.559   2.8545   -4.5128  -1.0681
 ME5  C2    C   CR15  0  -0.179   5.0712   -5.6288  -1.5497
 ME5  C3    C   CR5   0  -0.316   4.3304   -4.5477  -1.1693
 ME5  C7    C   CR6   0  -0.019   1.7221   -5.9712   2.5041
 ME5  C8    C   CH2   0  -0.473   0.4203   -1.7412  -1.4033
 ME5  C10   C   CH2   0  -0.460   0.8605   -0.6728  -0.3820
 ME5  C12   C   CH2   0  -0.480   1.0954   -1.4262   0.9422
 ME5  C13   C   CH1   0  -0.035   0.6158   -2.8577   0.6867
 ME5  C14   C   CR16  0  -0.240   3.9089   -6.7477   3.1672
 ME5  C15   C   CR16  0   0.049   4.1961   -9.9639   4.1852
 ME5  C16   C   CR6   0   0.286   3.3168   -7.7477   3.9228
 ME5  C19   C   CH1   0  -0.126   0.8772   -3.0715  -0.8176
 ME5  C21   C   CR6   0   0.552   4.7918   -8.2300   5.7819
 ME5  C22   C   CR16  0  -0.277   1.1445   -6.9938   3.2494
 ME5  C24   C   CR16  0  -0.453   5.5709   -9.2384   6.4494
 ME5  C44   C   CR16  0  -0.289   3.1109   -5.8631   2.4616
 ME5  N2    N   NR6   0  -0.612   4.1296   -8.6796   4.6355
 ME5  C18   C   CR16  0  -0.248   1.9370   -7.8723   3.9704
 ME5  C23   C   CR16  0  -0.399   4.9295  -10.9030   4.8276
 ME5  C26   C   CR16  0  -0.118   5.6345  -10.5153   5.9923
 ME5  N4    N   NH1   0  -0.663   1.2721   -3.8101   1.5439
 ME5  N1    N   NH1   0  -0.663   2.2901   -3.2897  -1.0614
 ME5  O3    O   O     0  -0.469   2.2239   -5.5554  -0.9866
 ME5  C4    C   CR15  0  -0.123   6.4657   -5.3917  -1.5207
 ME5  S1    S   S2    0   0.293   5.3432   -3.2175  -0.7361
 ME5  C5    C   CR5   0  -0.242   6.7500   -4.1293  -1.0988
 ME5  CL1   CL  CL    0  -0.061   8.2945   -3.4373  -0.9029
 ME5  H2    H   HCR5  0   0.283   4.6305   -6.5675  -1.8523
 ME5  H81   H   HCH2  0   0.257  -0.6675   -1.7610  -1.4836
 ME5  H82   H   HCH2  0   0.257   0.8093   -1.5681  -2.4073
 ME5  H101  H   HCH2  0   0.248   0.1004    0.1000  -0.2767
 ME5  H102  H   HCH2  0   0.243   1.7718   -0.1682  -0.7054
 ME5  H121  H   HCH2  0   0.235   2.1588   -1.4300   1.1972
 ME5  H122  H   HCH2  0   0.260   0.5731   -0.9743   1.7846
 ME5  H13   H   HCH1  0   0.265  -0.4641   -2.9193   0.8455
 ME5  H14   H   HCR6  0   0.276   4.9864   -6.6697   3.1126
 ME5  H15   H   HCR6  0   0.315   3.6390  -10.1766   3.2839
 ME5  H19   H   HCH1  0   0.275   0.3172   -3.9181  -1.2125
 ME5  H22   H   HCR6  0   0.269   0.0686   -7.1007   3.2799
 ME5  H24   H   HCR6  0   0.276   6.1020   -8.9353   7.3415
 ME5  H44   H   HCR6  0   0.246   3.5952   -5.1056   1.8587
 ME5  H18   H   HCR6  0   0.278   1.4818   -8.6539   4.5650
 ME5  H23   H   HCR6  0   0.280   4.9694  -11.9119   4.4473
 ME5  H26   H   HCR6  0   0.281   6.2322  -11.2454   6.5225
 ME5  HN4   H   HNH1  0   0.402   2.1230   -3.5209   1.9979
 ME5  HN1   H   HNH1  0   0.402   2.8480   -2.4894  -1.3174
 ME5  H4    H   HCR5  0   0.295   7.2171   -6.1176  -1.7936
 ME5  C17   C   C     0   0.543   0.8227   -5.0631   1.7265
 ME5  O1    O   O     0  -0.502   4.6774   -7.0656   6.1442
 ME5  O2    O   O     0  -0.481  -0.2565   -5.4534   1.3074

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
 ME5  C1   O3    double    1.221  0.020  1.221
 ME5  C1   N1    single    1.347  0.020  1.347
 ME5  C1   C3    single    1.480  0.020  1.480
 ME5  C2   C3    double    1.365  0.020  1.365
 ME5  C2   C4    single    1.415  0.020  1.415
 ME5  C2   H2    single    0.930  0.020  1.080
 ME5  C3   S1    single    1.727  0.020  1.727
 ME5  C7   C44   aromatic  1.394  0.020  1.394
 ME5  C7   C22   aromatic  1.391  0.020  1.391
 ME5  C7   C17   single    1.496  0.020  1.496
 ME5  C8   C19   single    1.524  0.020  1.524
 ME5  C8   C10   single    1.542  0.020  1.542
 ME5  C8   H81   single    0.970  0.020  1.090
 ME5  C8   H82   single    0.970  0.020  1.090
 ME5  C10  C12   single    1.542  0.020  1.542
 ME5  C10  H101  single    0.970  0.020  1.090
 ME5  C10  H102  single    0.970  0.020  1.090
 ME5  C12  C13   single    1.531  0.020  1.531
 ME5  C12  H121  single    0.970  0.020  1.090
 ME5  C12  H122  single    0.970  0.020  1.090
 ME5  C13  N4    single    1.440  0.020  1.440
 ME5  C13  C19   single    1.542  0.020  1.542
 ME5  C13  H13   single    0.970  0.020  1.090
 ME5  C14  C16   aromatic  1.386  0.020  1.386
 ME5  C14  C44   aromatic  1.385  0.020  1.385
 ME5  C14  H14   single    0.930  0.020  1.080
 ME5  C15  C23   double    1.354  0.020  1.354
 ME5  C15  N2    single    1.363  0.020  1.363
 ME5  C15  H15   single    0.930  0.020  1.080
 ME5  C16  N2    single    1.427  0.020  1.427
 ME5  C16  C18   aromatic  1.386  0.020  1.386
 ME5  C19  N1    single    1.450  0.020  1.450
 ME5  C19  H19   single    0.970  0.020  1.090
 ME5  C21  C24   single    1.439  0.020  1.439
 ME5  C21  O1    double    1.225  0.020  1.225
 ME5  C21  N2    single    1.398  0.020  1.398
 ME5  C22  C18   aromatic  1.386  0.020  1.386
 ME5  C22  H22   single    0.930  0.020  1.080
 ME5  C24  C26   double    1.358  0.020  1.358
 ME5  C24  H24   single    0.930  0.020  1.080
 ME5  C17  O2    double    1.222  0.020  1.222
 ME5  C17  N4    single    1.344  0.020  1.344
 ME5  C44  H44   single    0.930  0.020  1.080
 ME5  C18  H18   single    0.930  0.020  1.080
 ME5  C23  C26   single    1.416  0.020  1.416
 ME5  C23  H23   single    0.930  0.020  1.080
 ME5  C26  H26   single    0.930  0.020  1.080
 ME5  N4   HN4   single    0.860  0.020  1.020
 ME5  N1   HN1   single    0.860  0.020  1.020
 ME5  C4   C5    double    1.361  0.020  1.361
 ME5  C4   H4    single    0.930  0.020  1.080
 ME5  S1   C5    single    1.715  0.020  1.715
 ME5  C5   CL1   single    1.704  0.020  1.704

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
 ME5  O3    C1   N1    123.95  3.000
 ME5  N1    C1   C3    116.08  3.000
 ME5  O3    C1   C3    119.96  3.000
 ME5  H2    C2   C4    123.60  3.000
 ME5  H2    C2   C3    123.03  3.000
 ME5  C4    C2   C3    113.36  3.000
 ME5  S1    C3   C2    111.21  3.000
 ME5  S1    C3   C1    123.34  3.000
 ME5  C2    C3   C1    125.39  3.000
 ME5  C44   C7   C17   122.42  3.000
 ME5  C17   C7   C22   118.36  3.000
 ME5  C44   C7   C22   119.16  3.000
 ME5  H82   C8   H81   106.90  3.000
 ME5  H82   C8   C19   112.68  3.000
 ME5  H81   C8   C19   108.15  3.000
 ME5  H82   C8   C10   113.45  3.000
 ME5  H81   C8   C10   110.24  3.000
 ME5  C19   C8   C10   105.35  3.000
 ME5  H102  C10  H101  106.46  3.000
 ME5  H102  C10  C12   110.70  3.000
 ME5  H101  C10  C12   111.72  3.000
 ME5  H102  C10  C8    111.26  3.000
 ME5  H101  C10  C8    110.88  3.000
 ME5  C12   C10  C8    105.89  3.000
 ME5  H122  C12  H121  106.70  3.000
 ME5  H122  C12  C13   111.52  3.000
 ME5  H121  C12  C13   109.89  3.000
 ME5  H122  C12  C10   112.86  3.000
 ME5  H121  C12  C10   110.49  3.000
 ME5  C13   C12  C10   105.42  3.000
 ME5  H13   C13  N4    109.06  3.000
 ME5  H13   C13  C19   107.54  3.000
 ME5  N4    C13  C19   114.32  3.000
 ME5  H13   C13  C12   109.75  3.000
 ME5  C19   C13  C12   103.85  3.000
 ME5  N4    C13  C12   112.11  3.000
 ME5  H14   C14  C44   120.15  3.000
 ME5  H14   C14  C16   120.34  3.000
 ME5  C44   C14  C16   119.50  3.000
 ME5  H15   C15  C23   122.58  3.000
 ME5  H15   C15  N2    115.85  3.000
 ME5  C23   C15  N2    121.57  3.000
 ME5  C18   C16  N2    119.41  3.000
 ME5  C18   C16  C14   120.58  3.000
 ME5  N2    C16  C14   119.99  3.000
 ME5  H19   C19  N1    108.84  3.000
 ME5  H19   C19  C13   111.98  3.000
 ME5  N1    C19  C13   110.49  3.000
 ME5  H19   C19  C8    112.65  3.000
 ME5  N1    C19  C8    111.04  3.000
 ME5  C13   C19  C8    101.72  3.000
 ME5  O1    C21  N2    120.26  3.000
 ME5  N2    C21  C24   114.30  3.000
 ME5  O1    C21  C24   125.43  3.000
 ME5  H22   C22  C18   119.45  3.000
 ME5  H22   C22  C7    120.06  3.000
 ME5  C18   C22  C7    120.49  3.000
 ME5  H24   C24  C26   121.21  3.000
 ME5  H24   C24  C21   116.89  3.000
 ME5  C26   C24  C21   121.90  3.000
 ME5  H44   C44  C14   118.24  3.000
 ME5  H44   C44  C7    121.14  3.000
 ME5  C14   C44  C7    120.61  3.000
 ME5  C21   N2   C16   117.99  3.000
 ME5  C21   N2   C15   123.43  3.000
 ME5  C16   N2   C15   118.56  3.000
 ME5  H18   C18  C22   120.21  3.000
 ME5  H18   C18  C16   120.16  3.000
 ME5  C22   C18  C16   119.64  3.000
 ME5  H23   C23  C26   121.85  3.000
 ME5  H23   C23  C15   120.10  3.000
 ME5  C26   C23  C15   118.05  3.000
 ME5  H26   C26  C23   119.56  3.000
 ME5  H26   C26  C24   119.69  3.000
 ME5  C23   C26  C24   120.75  3.000
 ME5  HN4   N4   C17   119.29  3.000
 ME5  HN4   N4   C13   117.63  3.000
 ME5  C17   N4   C13   123.05  3.000
 ME5  HN1   N1   C19   117.53  3.000
 ME5  HN1   N1   C1    119.17  3.000
 ME5  C19   N1   C1    123.07  3.000
 ME5  H4    C4   C5    123.81  3.000
 ME5  H4    C4   C2    124.62  3.000
 ME5  C5    C4   C2    111.57  3.000
 ME5  C5    S1   C3     91.06  3.000
 ME5  CL1   C5   S1    120.22  3.000
 ME5  CL1   C5   C4    126.99  3.000
 ME5  S1    C5   C4    112.79  3.000
 ME5  O2    C17  N4    123.14  3.000
 ME5  N4    C17  C7    115.83  3.000
 ME5  O2    C17  C7    121.03  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
 ME5  CONST_01  C16  C14  C44  C7      0.00   0.0  0
 ME5  CONST_02  C16  C18  C22  C7      0.00   0.0  0
 ME5  CONST_03  C22  C18  C16  C14     0.00   0.0  0
 ME5  CONST_04  C22  C7   C44  C14     0.00   0.0  0
 ME5  CONST_05  C18  C22  C7   C44     0.00   0.0  0
 ME5  CONST_06  C18  C16  C14  C44     0.00   0.0  0
 ME5  CONST_07  N2   C16  C18  C22   180.00   0.0  0
 ME5  CONST_08  N2   C16  C14  C44   180.00   0.0  0
 ME5  CONST_09  C24  C21  N2   C15     0.00   0.0  0
 ME5  CONST_10  C24  C21  N2   C16   180.00   0.0  0
 ME5  CONST_11  C17  C7   C44  C14   180.00   0.0  0
 ME5  CONST_12  C18  C22  C7   C17   180.00   0.0  0
 ME5  CONST_13  O1   C21  N2   C15   180.00   0.0  0
 ME5  CONST_14  O1   C21  N2   C16     0.00   0.0  0
 ME5  CONST_15  H14  C14  C44  C7    180.00   0.0  0
 ME5  CONST_16  H18  C18  C22  C7    180.00   0.0  0
 ME5  CONST_17  H44  C44  C14  C16   180.00   0.0  0
 ME5  CONST_18  H22  C22  C18  C16   180.00   0.0  0
 ME5  CONST_19  C19  N1   C1   C3    180.00   0.0  0
 ME5  CONST_20  C13  N4   C17  C7    180.00   0.0  0
 ME5  CONST_21  O2   C17  N4   C13     0.00   0.0  0
 ME5  CONST_22  O3   C1   N1   C19     0.00   0.0  0
 ME5  CONST_23  HN1  N1   C1   C3      0.00   0.0  0
 ME5  CONST_24  HN4  N4   C17  C7      0.00   0.0  0
 ME5  Var_01    C13  C12  C10  C8     -6.94  30.0  1
 ME5  Var_02    C19  C8   C10  C12   -19.35  30.0  1
 ME5  Var_03    C15  N2   C16  C14  -108.38  30.0  2
 ME5  Var_04    O3   C1   C3   C2     19.26  30.0  2
 ME5  Var_05    O2   C17  C7   C22   -28.49  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
 ME5  chir_01  C13  C12  N4  C19  positiv
 ME5  chir_02  C19  N1   C8  C13  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
 ME5  plan-1  C1   0.020
 ME5  plan-1  C2   0.020
 ME5  plan-1  C3   0.020
 ME5  plan-1  C4   0.020
 ME5  plan-1  S1   0.020
 ME5  plan-1  C5   0.020
 ME5  plan-1  CL1  0.020
 ME5  plan-1  H2   0.020
 ME5  plan-1  H4   0.020
 ME5  plan-2  C7   0.020
 ME5  plan-2  C14  0.020
 ME5  plan-2  C16  0.020
 ME5  plan-2  C22  0.020
 ME5  plan-2  C44  0.020
 ME5  plan-2  N2   0.020
 ME5  plan-2  C18  0.020
 ME5  plan-2  H14  0.020
 ME5  plan-2  H22  0.020
 ME5  plan-2  H44  0.020
 ME5  plan-2  H18  0.020
 ME5  plan-2  C17  0.020
 ME5  plan-3  C15  0.020
 ME5  plan-3  C16  0.020
 ME5  plan-3  C21  0.020
 ME5  plan-3  C24  0.020
 ME5  plan-3  N2   0.020
 ME5  plan-3  C23  0.020
 ME5  plan-3  C26  0.020
 ME5  plan-3  H15  0.020
 ME5  plan-3  H24  0.020
 ME5  plan-3  H23  0.020
 ME5  plan-3  H26  0.020
 ME5  plan-3  O1   0.020
 ME5  plan-4  C7   0.020
 ME5  plan-4  C13  0.020
 ME5  plan-4  N4   0.020
 ME5  plan-4  HN4  0.020
 ME5  plan-4  C17  0.020
 ME5  plan-4  O2   0.020
 ME5  plan-5  C1   0.020
 ME5  plan-5  C3   0.020
 ME5  plan-5  C19  0.020
 ME5  plan-5  N1   0.020
 ME5  plan-5  O3   0.020
 ME5  plan-5  HN1  0.020

