# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 11:19:44 2020
#   Inital geometry file: a 160 line input string
#   Ligand name: 3-chloro-N-[(1R,2S)-2-({[4-(2-oxopyridin-1(2H)-yl)phenyl]carbonyl}amino)cyclohexyl]-1H-indole-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1c[nH]c2cc(ccc12)C(=O)N[C@@H]3CCCC[C@@H]3NC(=O)c4ccc(cc4)N5C=CC=CC5=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
 ME4  ME4  3-chloro-N-[(1R,2S)-2-({[4-(2-oxopyridin-1(2H)-yl)phenyl]carbonyl}amino)cyclohexyl]-1H-indole-6-carboxamide  ligand  60  35  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ME4
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
 ME4  C1    C   CH1   0  -0.107  -1.3401  -0.2170   2.2809
 ME4  C2    C   CH2   0  -0.447  -1.8089  -0.4486   0.8459
 ME4  C3    C   CH2   0  -0.457  -0.7057  -0.9973  -0.0543
 ME4  C10   C   CR6   0  -0.059  -0.2602  -0.9122   6.5700
 ME4  C11   C   CR16  0  -0.352   1.0944  -1.1435   6.7500
 ME4  C12   C   CR56  0   0.373   1.6553  -0.8059   7.9772
 ME4  C13   C   CR56  0   0.172   0.8863  -0.2476   9.0204
 ME4  C14   C   CR5   0  -0.231   1.7886  -0.0432  10.0990
 ME4  C15   C   CR15  0   0.022   3.0252  -0.4649   9.7017
 ME4  C19   C   CR16  0  -0.284  -1.0379  -0.3681   7.6129
 ME4  C24   C   CR16  0  -0.274   0.3913   4.1077   3.8031
 ME4  C27   C   CR16  0  -0.240   2.8664   3.6180   2.6432
 ME4  N29   N   NR6   0  -0.611   3.5776   5.8820   3.1952
 ME4  C30   C   CR16  0   0.050   4.2021   6.1782   4.3693
 ME4  C31   C   CR16  0  -0.398   5.1391   7.1522   4.4465
 ME4  C32   C   CR16  0  -0.118   5.4558   7.8659   3.2655
 ME4  C33   C   CR16  0  -0.453   4.8352   7.5785   2.0924
 ME4  C34   C   CR6   0   0.553   3.8356   6.5486   1.9946
 ME4  C4    C   CH2   0  -0.435  -0.1064  -2.2676   0.5369
 ME4  C5    C   CH2   0  -0.462   0.3974  -2.0358   1.9574
 ME4  C6    C   CH1   0  -0.045  -0.7102  -1.4993   2.8583
 ME4  N7    N   NH1   0  -0.657  -0.1879  -1.2796   4.1887
 ME4  O9    O   O     0  -0.492  -2.1558  -1.4967   5.2708
 ME4  N16   N   NR15  0  -0.690   2.9385  -0.9265   8.4238
 ME4  CL17  CL  CL    0  -0.154   1.3796   0.6151  11.6284
 ME4  C18   C   CR16  0  -0.324  -0.4810  -0.0294   8.8246
 ME4  N20   N   NH1   0  -0.656  -0.4025   0.8888   2.3461
 ME4  O22   O   O     0  -0.472  -1.2183   1.8218   4.2422
 ME4  C23   C   CR6   0  -0.020   0.6534   2.8629   3.2392
 ME4  C25   C   CR16  0  -0.245   1.3463   5.1102   3.7666
 ME4  C26   C   CR6   0   0.284   2.5820   4.8587   3.1909
 ME4  C28   C   CR16  0  -0.301   1.9008   2.6248   2.6661
 ME4  O35   O   O     0  -0.502   3.2259   6.2435   0.9768
 ME4  H1    H   HCH1  0   0.273  -2.2007   0.0537   2.8927
 ME4  H21   H   HCH2  0   0.250  -2.2192   0.4804   0.4440
 ME4  H22   H   HCH2  0   0.240  -2.6344  -1.1660   0.8759
 ME4  H31A  H   HCH2  0   0.216   0.0836  -0.2496  -0.1968
 ME4  H32A  H   HCH2  0   0.247  -1.1101  -1.1936  -1.0492
 ME4  H11   H   HCR6  0   0.269   1.7086  -1.5975   5.9820
 ME4  H15   H   HCR5  0   0.306   3.9600  -0.4669  10.2377
 ME4  H19   H   HCR6  0   0.253  -2.0942  -0.2060   7.4489
 ME4  H24   H   HCR6  0   0.269  -0.5677   4.3024   4.2635
 ME4  H27   H   HCR6  0   0.277   3.8408   3.4184   2.2180
 ME4  H30   H   HCR6  0   0.314   3.9064   5.5838   5.2222
 ME4  H31   H   HCR6  0   0.280   5.6241   7.3630   5.3871
 ME4  H32   H   HCR6  0   0.282   6.2010   8.6500   3.2997
 ME4  H33   H   HCR6  0   0.276   5.0669   8.1237   1.1873
 ME4  H41   H   HCH2  0   0.221  -0.8673  -3.0550   0.5473
 ME4  H42   H   HCH2  0   0.240   0.7105  -2.6328  -0.0887
 ME4  H51   H   HCH2  0   0.253   0.7859  -2.9646   2.3807
 ME4  H52   H   HCH2  0   0.221   1.2356  -1.3279   1.9371
 ME4  H6    H   HCH1  0   0.252  -1.5018  -2.2508   2.9247
 ME4  HN7   H   HNH1  0   0.394   0.7534  -0.9276   4.2499
 ME4  HN16  H   HNR5  0   0.421   3.7161  -1.2821   7.8920
 ME4  H18   H   HCR6  0   0.252  -1.0902   0.3973   9.6112
 ME4  HN20  H   HNH1  0   0.403   0.2072   1.0337   1.5571
 ME4  H25   H   HCR6  0   0.278   1.1307   6.0841   4.1867
 ME4  H28   H   HCR6  0   0.263   2.1521   1.6543   2.2573
 ME4  C8    C   C     0   0.552  -0.9570  -1.2512   5.2930
 ME4  C21   C   C     0   0.531  -0.4083   1.8107   3.3275

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
 ME4  C1   C2    single    1.527  0.020  1.527
 ME4  C1   N20   single    1.451  0.020  1.451
 ME4  C1   C6    single    1.541  0.020  1.541
 ME4  C1   H1    single    0.970  0.020  1.090
 ME4  C2   C3    single    1.526  0.020  1.526
 ME4  C2   H21   single    0.970  0.020  1.090
 ME4  C2   H22   single    0.970  0.020  1.090
 ME4  C3   C4    single    1.524  0.020  1.524
 ME4  C3   H31A  single    0.970  0.020  1.090
 ME4  C3   H32A  single    0.970  0.020  1.090
 ME4  C8   O9    double    1.224  0.020  1.224
 ME4  C8   N7    single    1.346  0.020  1.346
 ME4  C8   C10   single    1.494  0.020  1.494
 ME4  C10  C19   aromatic  1.410  0.020  1.410
 ME4  C10  C11   aromatic  1.386  0.020  1.386
 ME4  C11  C12   aromatic  1.391  0.020  1.391
 ME4  C11  H11   single    0.930  0.020  1.080
 ME4  C12  C13   aromatic  1.411  0.020  1.411
 ME4  C12  N16   single    1.364  0.020  1.364
 ME4  C13  C18   aromatic  1.398  0.020  1.398
 ME4  C13  C14   single    1.421  0.020  1.421
 ME4  C14  CL17  single    1.715  0.020  1.715
 ME4  C14  C15   double    1.366  0.020  1.366
 ME4  C15  N16   single    1.362  0.020  1.362
 ME4  C15  H15   single    0.930  0.020  1.080
 ME4  C19  C18   aromatic  1.376  0.020  1.376
 ME4  C19  H19   single    0.930  0.020  1.080
 ME4  C21  C23   single    1.497  0.020  1.497
 ME4  C21  N20   single    1.346  0.020  1.346
 ME4  C21  O22   double    1.222  0.020  1.222
 ME4  C24  C25   aromatic  1.385  0.020  1.385
 ME4  C24  C23   aromatic  1.391  0.020  1.391
 ME4  C24  H24   single    0.930  0.020  1.080
 ME4  C27  C26   aromatic  1.386  0.020  1.386
 ME4  C27  C28   aromatic  1.385  0.020  1.385
 ME4  C27  H27   single    0.930  0.020  1.080
 ME4  N29  C34   single    1.397  0.020  1.397
 ME4  N29  C30   single    1.362  0.020  1.362
 ME4  N29  C26   single    1.428  0.020  1.428
 ME4  C30  C31   double    1.354  0.020  1.354
 ME4  C30  H30   single    0.930  0.020  1.080
 ME4  C31  C32   single    1.416  0.020  1.416
 ME4  C31  H31   single    0.930  0.020  1.080
 ME4  C32  C33   double    1.358  0.020  1.358
 ME4  C32  H32   single    0.930  0.020  1.080
 ME4  C33  C34   single    1.439  0.020  1.439
 ME4  C33  H33   single    0.930  0.020  1.080
 ME4  C34  O35   double    1.225  0.020  1.225
 ME4  C4   C5    single    1.525  0.020  1.525
 ME4  C4   H41   single    0.970  0.020  1.090
 ME4  C4   H42   single    0.970  0.020  1.090
 ME4  C5   C6    single    1.525  0.020  1.525
 ME4  C5   H51   single    0.970  0.020  1.090
 ME4  C5   H52   single    0.970  0.020  1.090
 ME4  C6   N7    single    1.446  0.020  1.446
 ME4  C6   H6    single    0.970  0.020  1.090
 ME4  N7   HN7   single    0.860  0.020  1.020
 ME4  N16  HN16  single    0.860  0.020  1.020
 ME4  C18  H18   single    0.930  0.020  1.080
 ME4  N20  HN20  single    0.860  0.020  1.020
 ME4  C23  C28   aromatic  1.393  0.020  1.393
 ME4  C25  C26   aromatic  1.386  0.020  1.386
 ME4  C25  H25   single    0.930  0.020  1.080
 ME4  C28  H28   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
 ME4  H1    C1   N20   107.19  3.000
 ME4  H1    C1   C6    108.61  3.000
 ME4  N20   C1   C6    110.68  3.000
 ME4  H1    C1   C2    108.82  3.000
 ME4  C6    C1   C2    110.57  3.000
 ME4  N20   C1   C2    110.86  3.000
 ME4  H22   C2   H21   106.53  3.000
 ME4  H22   C2   C3    109.02  3.000
 ME4  H21   C2   C3    111.12  3.000
 ME4  H22   C2   C1    107.78  3.000
 ME4  H21   C2   C1    109.40  3.000
 ME4  C3    C2   C1    112.76  3.000
 ME4  H32A  C3   H31A  105.72  3.000
 ME4  H32A  C3   C4    110.45  3.000
 ME4  H31A  C3   C4    109.62  3.000
 ME4  H32A  C3   C2    109.54  3.000
 ME4  H31A  C3   C2    110.60  3.000
 ME4  C4    C3   C2    110.80  3.000
 ME4  C19   C10  C11   120.49  3.000
 ME4  C11   C10  C8    121.94  3.000
 ME4  C19   C10  C8    117.55  3.000
 ME4  H11   C11  C12   119.92  3.000
 ME4  H11   C11  C10   122.15  3.000
 ME4  C12   C11  C10   117.91  3.000
 ME4  N16   C12  C13   107.79  3.000
 ME4  N16   C12  C11   130.30  3.000
 ME4  C13   C12  C11   121.91  3.000
 ME4  C18   C13  C14   134.80  3.000
 ME4  C14   C13  C12   105.79  3.000
 ME4  C18   C13  C12   119.41  3.000
 ME4  CL17  C14  C15   126.45  3.000
 ME4  C15   C14  C13   108.04  3.000
 ME4  CL17  C14  C13   125.51  3.000
 ME4  H15   C15  N16   121.44  3.000
 ME4  H15   C15  C14   129.90  3.000
 ME4  N16   C15  C14   108.67  3.000
 ME4  H19   C19  C18   119.48  3.000
 ME4  H19   C19  C10   118.98  3.000
 ME4  C18   C19  C10   121.54  3.000
 ME4  H24   C24  C25   119.49  3.000
 ME4  H24   C24  C23   120.04  3.000
 ME4  C25   C24  C23   120.47  3.000
 ME4  H27   C27  C28   120.14  3.000
 ME4  H27   C27  C26   120.36  3.000
 ME4  C28   C27  C26   119.49  3.000
 ME4  C26   N29  C34   117.91  3.000
 ME4  C26   N29  C30   118.56  3.000
 ME4  C34   N29  C30   123.51  3.000
 ME4  H30   C30  C31   122.69  3.000
 ME4  H30   C30  N29   115.79  3.000
 ME4  C31   C30  N29   121.52  3.000
 ME4  H31   C31  C32   121.88  3.000
 ME4  H31   C31  C30   120.09  3.000
 ME4  C32   C31  C30   118.03  3.000
 ME4  H32   C32  C33   119.69  3.000
 ME4  H32   C32  C31   119.53  3.000
 ME4  C33   C32  C31   120.78  3.000
 ME4  H33   C33  C34   116.93  3.000
 ME4  H33   C33  C32   121.22  3.000
 ME4  C34   C33  C32   121.85  3.000
 ME4  O35   C34  C33   125.49  3.000
 ME4  O35   C34  N29   120.21  3.000
 ME4  C33   C34  N29   114.30  3.000
 ME4  H42   C4   H41   106.55  3.000
 ME4  H42   C4   C5    109.72  3.000
 ME4  H41   C4   C5    109.27  3.000
 ME4  H42   C4   C3    110.53  3.000
 ME4  H41   C4   C3    109.26  3.000
 ME4  C5    C4   C3    111.38  3.000
 ME4  H52   C5   H51   106.50  3.000
 ME4  H52   C5   C6    109.79  3.000
 ME4  H51   C5   C6    109.18  3.000
 ME4  H52   C5   C4    109.47  3.000
 ME4  H51   C5   C4    110.45  3.000
 ME4  C6    C5   C4    111.33  3.000
 ME4  H6    C6   N7    108.06  3.000
 ME4  H6    C6   C5    108.65  3.000
 ME4  N7    C6   C5    109.55  3.000
 ME4  H6    C6   C1    107.38  3.000
 ME4  N7    C6   C1    111.47  3.000
 ME4  C5    C6   C1    111.61  3.000
 ME4  HN7   N7   C6    116.53  3.000
 ME4  HN7   N7   C8    118.49  3.000
 ME4  C6    N7   C8    123.48  3.000
 ME4  HN16  N16  C15   124.49  3.000
 ME4  HN16  N16  C12   125.79  3.000
 ME4  C15   N16  C12   109.71  3.000
 ME4  H18   C18  C19   120.61  3.000
 ME4  H18   C18  C13   120.67  3.000
 ME4  C19   C18  C13   118.73  3.000
 ME4  HN20  N20  C21   118.36  3.000
 ME4  HN20  N20  C1    117.73  3.000
 ME4  C21   N20  C1    123.48  3.000
 ME4  C28   C23  C24   119.22  3.000
 ME4  C28   C23  C21   122.62  3.000
 ME4  C24   C23  C21   118.11  3.000
 ME4  H25   C25  C26   120.14  3.000
 ME4  H25   C25  C24   120.25  3.000
 ME4  C26   C25  C24   119.62  3.000
 ME4  C25   C26  N29   119.36  3.000
 ME4  C25   C26  C27   120.64  3.000
 ME4  N29   C26  C27   119.98  3.000
 ME4  H28   C28  C23   121.08  3.000
 ME4  H28   C28  C27   118.34  3.000
 ME4  C23   C28  C27   120.55  3.000
 ME4  O9    C8   N7    122.72  3.000
 ME4  N7    C8   C10   116.08  3.000
 ME4  O9    C8   C10   121.20  3.000
 ME4  C23   C21  O22   120.52  3.000
 ME4  O22   C21  N20   123.69  3.000
 ME4  C23   C21  N20   115.79  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
 ME4  CONST_01  C13   C18  C19  C10    0.00   0.0  0
 ME4  CONST_02  C13   C12  C11  C10    0.00   0.0  0
 ME4  CONST_03  C18   C19  C10  C11    0.00   0.0  0
 ME4  CONST_04  C18   C13  C12  C11    0.00   0.0  0
 ME4  CONST_05  C19   C10  C11  C12    0.00   0.0  0
 ME4  CONST_06  C19   C18  C13  C12    0.00   0.0  0
 ME4  CONST_07  C27   C26  C25  C24    0.00   0.0  0
 ME4  CONST_08  C27   C28  C23  C24    0.00   0.0  0
 ME4  CONST_09  C26   C25  C24  C23    0.00   0.0  0
 ME4  CONST_10  C26   C27  C28  C23    0.00   0.0  0
 ME4  CONST_11  C28   C23  C24  C25    0.00   0.0  0
 ME4  CONST_12  C28   C27  C26  C25    0.00   0.0  0
 ME4  CONST_13  N29   C26  C25  C24  180.00   0.0  0
 ME4  CONST_14  C28   C27  C26  N29  180.00   0.0  0
 ME4  CONST_15  C33   C34  N29  C30    0.00   0.0  0
 ME4  CONST_16  C26   N29  C34  C33  180.00   0.0  0
 ME4  CONST_17  C18   C19  C10  C8   180.00   0.0  0
 ME4  CONST_18  C12   C11  C10  C8   180.00   0.0  0
 ME4  CONST_19  C25   C24  C23  C21  180.00   0.0  0
 ME4  CONST_20  C27   C28  C23  C21  180.00   0.0  0
 ME4  CONST_21  O35   C34  N29  C30  180.00   0.0  0
 ME4  CONST_22  O35   C34  N29  C26    0.00   0.0  0
 ME4  CONST_23  H18   C18  C19  C10  180.00   0.0  0
 ME4  CONST_24  H19   C19  C10  C11  180.00   0.0  0
 ME4  CONST_25  H11   C11  C12  C13  180.00   0.0  0
 ME4  CONST_26  H28   C28  C23  C24  180.00   0.0  0
 ME4  CONST_27  H25   C25  C26  C27  180.00   0.0  0
 ME4  CONST_28  H27   C27  C26  N29    0.00   0.0  0
 ME4  CONST_29  H24   C24  C25  C26  180.00   0.0  0
 ME4  CONST_30  C23   C21  N20  C1   180.00   0.0  0
 ME4  CONST_31  C6    N7   C8   C10  180.00   0.0  0
 ME4  CONST_32  O22   C21  N20  C1     0.00   0.0  0
 ME4  CONST_33  O9    C8   N7   C6     0.00   0.0  0
 ME4  CONST_34  HN7   N7   C8   C10    0.00   0.0  0
 ME4  CONST_35  HN20  N20  C21  C23    0.00   0.0  0
 ME4  Var_01    C4    C3   C2   C1    54.85  30.0  1
 ME4  Var_02    C5    C4   C3   C2   -55.36  30.0  1
 ME4  Var_03    C6    C5   C4   C3    56.22  30.0  1
 ME4  Var_04    C34   N29  C26  C27   76.07  30.0  3
 ME4  Var_05    O9    C8   C10  C11  153.96  30.0  2
 ME4  Var_06    N20   C21  C23  C24  152.38  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
 ME4  chir_01  C1  C2  N20  C6  positiv
 ME4  chir_02  C6  N7  C5   C1  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
 ME4  plan-1  C24   0.020
 ME4  plan-1  C27   0.020
 ME4  plan-1  N29   0.020
 ME4  plan-1  C23   0.020
 ME4  plan-1  C25   0.020
 ME4  plan-1  C26   0.020
 ME4  plan-1  C28   0.020
 ME4  plan-1  H24   0.020
 ME4  plan-1  H27   0.020
 ME4  plan-1  H25   0.020
 ME4  plan-1  H28   0.020
 ME4  plan-1  C21   0.020
 ME4  plan-2  N29   0.020
 ME4  plan-2  C30   0.020
 ME4  plan-2  C31   0.020
 ME4  plan-2  C32   0.020
 ME4  plan-2  C33   0.020
 ME4  plan-2  C34   0.020
 ME4  plan-2  C26   0.020
 ME4  plan-2  O35   0.020
 ME4  plan-2  H30   0.020
 ME4  plan-2  H31   0.020
 ME4  plan-2  H32   0.020
 ME4  plan-2  H33   0.020
 ME4  plan-3  C10   0.020
 ME4  plan-3  C11   0.020
 ME4  plan-3  C12   0.020
 ME4  plan-3  C13   0.020
 ME4  plan-3  C14   0.020
 ME4  plan-3  C15   0.020
 ME4  plan-3  C19   0.020
 ME4  plan-3  N16   0.020
 ME4  plan-3  CL17  0.020
 ME4  plan-3  C18   0.020
 ME4  plan-3  H11   0.020
 ME4  plan-3  H15   0.020
 ME4  plan-3  H19   0.020
 ME4  plan-3  HN16  0.020
 ME4  plan-3  H18   0.020
 ME4  plan-3  C8    0.020
 ME4  plan-4  C1    0.020
 ME4  plan-4  N20   0.020
 ME4  plan-4  O22   0.020
 ME4  plan-4  C23   0.020
 ME4  plan-4  HN20  0.020
 ME4  plan-4  C21   0.020
 ME4  plan-5  C10   0.020
 ME4  plan-5  C6    0.020
 ME4  plan-5  N7    0.020
 ME4  plan-5  O9    0.020
 ME4  plan-5  HN7   0.020
 ME4  plan-5  C8    0.020

