# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu May 21 01:07:17 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: (2'S,3R,4'S,5'R)-N-(2-aminoethyl)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)C[C@@H]1N[C@H]([C@H](c2cccc(Cl)c2F)[C@]13C(=O)Nc4cc(Cl)ccc34)C(=O)NCCN
#
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
 1MT  1MT  (2'S,3R,4'S,5'R)-N-(2-aminoethyl)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide  ligand  63  34  .  2022-07-22  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_1MT
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
 1MT  CL1  CL  CL    0  -0.093  -1.2715  -4.6053  -1.3002
 1MT  C1   C   CR6   0  -0.227  -1.5506  -3.3596  -0.1425
 1MT  C2   C   CR6   0   0.620  -1.1106  -2.0746  -0.4146
 1MT  C3   C   CR16  0  -0.224  -2.2078  -3.6268   1.0462
 1MT  C4   C   CR16  0  -0.257  -2.4137  -2.5918   1.9443
 1MT  C5   C   CR16  0  -0.302  -1.9671  -1.3106   1.6593
 1MT  C6   C   CR6   0  -0.044  -1.2994  -1.0204   0.4703
 1MT  C7   C   CH1   0  -0.350  -0.7747   0.3453   0.1191
 1MT  C8   C   CH1   0  -0.187  -1.6056   1.5677   0.6189
 1MT  C9   C   CH1   0  -0.056   0.6373   2.2168   0.4605
 1MT  C10  C   CH2   0  -0.433   1.8176   2.9298   1.0968
 1MT  C11  C   CT    0  -0.073   1.9862   4.4304   0.7775
 1MT  C12  C   CH3   0  -0.641   3.3820   4.8422   1.2538
 1MT  C13  C   CH3   0  -0.663   1.8762   4.6835  -0.7265
 1MT  C14  C   CH3   0  -0.648   0.9522   5.2812   1.5172
 1MT  C15  C   C     0   0.553  -2.5337   1.9793  -0.5170
 1MT  O1   O   O     0  -0.483  -2.1975   2.7831  -1.3723
 1MT  N1   N   NH1   0  -0.637  -3.7016   1.3212  -0.5385
 1MT  C17  C   CH2   0  -0.251  -4.6806   1.4617  -1.5949
 1MT  C18  C   CR5   0  -0.295   0.6563   0.6648   0.6021
 1MT  C19  C   CR56  0   0.149   1.7589  -0.0260  -0.1312
 1MT  C20  C   CR16  0  -0.355   2.1023  -0.0370  -1.4654
 1MT  C21  C   CR16  0  -0.221   3.2196  -0.7589  -1.8802
 1MT  C22  C   CR6   0  -0.052   3.9632  -1.4559  -0.9406
 1MT  CL2  CL  CL    0  -0.125   5.3495  -2.3562  -1.4638
 1MT  C23  C   CR16  0  -0.268   3.6434  -1.4631   0.4133
 1MT  C24  C   CR56  0   0.375   2.5324  -0.7334   0.7868
 1MT  N2   N   NR15  0  -0.741   2.0036  -0.5633   2.0564
 1MT  C25  C   CR5   0   0.581   0.9022   0.2359   2.0486
 1MT  O2   O   O     0  -0.439   0.2511   0.5482   3.0241
 1MT  F1   F   F     0  -0.287  -0.4913  -1.8584  -1.5781
 1MT  C16  C   CH2   0  -0.318  -5.6514   0.2911  -1.5735
 1MT  N3   N   NH2   0  -0.799  -6.6161   0.4346  -2.6489
 1MT  N4   N   NH1   0  -0.566  -0.6625   2.6142   0.9576
 1MT  H1   H   HCR6  0   0.291  -2.5531  -4.6285   1.2614
 1MT  H2   H   HCR6  0   0.274  -2.9303  -2.7874   2.8737
 1MT  H3   H   HCR6  0   0.275  -2.1436  -0.5285   2.3837
 1MT  H4   H   HCH1  0   0.289  -0.7202   0.4129  -0.9711
 1MT  H5   H   HCH1  0   0.285  -2.1953   1.3169   1.5012
 1MT  H6   H   HCH1  0   0.252   0.6622   2.3990  -0.6197
 1MT  H7   H   HCH2  0   0.231   1.7875   2.8060   2.1857
 1MT  H8   H   HCH2  0   0.236   2.7223   2.4148   0.7540
 1MT  H9   H   HCH3  0   0.221   4.1642   4.2970   0.7208
 1MT  H10  H   HCH3  0   0.224   3.5490   5.9090   1.0917
 1MT  H11  H   HCH3  0   0.222   3.5085   4.6455   2.3210
 1MT  H12  H   HCH3  0   0.232   0.8645   4.5046  -1.0959
 1MT  H13  H   HCH3  0   0.228   2.1287   5.7197  -0.9597
 1MT  H14  H   HCH3  0   0.220   2.5589   4.0423  -1.2896
 1MT  H15  H   HCH3  0   0.216   1.0171   5.1255   2.5969
 1MT  H16  H   HCH3  0   0.218   1.1227   6.3438   1.3284
 1MT  H17  H   HCH3  0   0.237  -0.0625   5.0415   1.2032
 1MT  H18  H   HNH1  0   0.397  -3.9393   0.7351   0.2467
 1MT  H19  H   HCH2  0   0.234  -5.2367   2.3983  -1.4953
 1MT  H20  H   HCH2  0   0.236  -4.1626   1.4949  -2.5559
 1MT  H21  H   HCR6  0   0.262   1.5186   0.5048  -2.1990
 1MT  H22  H   HCR6  0   0.278   3.5007  -0.7774  -2.9237
 1MT  H23  H   HCR6  0   0.291   4.2367  -2.0122   1.1314
 1MT  H24  H   HNR5  0   0.415   2.3840  -0.9746   2.8959
 1MT  H25  H   HCH2  0   0.204  -5.0783  -0.6462  -1.6057
 1MT  H26  H   HCH2  0   0.231  -6.1944   0.2933  -0.6245
 1MT  H27  H   HNH2  0   0.344  -6.1685   0.2392  -3.5356
 1MT  H28  H   HNH2  0   0.354  -7.3408  -0.2631  -2.5468
 1MT  H30  H   HNH1  0   0.359  -0.6237   2.7078   1.9642

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
 1MT  C12  C11  single    1.531  0.020  1.531
 1MT  N2   C25  single    1.361  0.020  1.361
 1MT  N2   C24  single    1.386  0.020  1.386
 1MT  O2   C25  double    1.214  0.020  1.214
 1MT  C10  C11  single    1.543  0.020  1.543
 1MT  C10  C9   single    1.519  0.020  1.519
 1MT  C11  C14  single    1.530  0.020  1.530
 1MT  C11  C13  single    1.529  0.020  1.529
 1MT  C25  C18  single    1.529  0.020  1.529
 1MT  C23  C24  aromatic  1.381  0.020  1.381
 1MT  C23  C22  aromatic  1.391  0.020  1.391
 1MT  C24  C19  aromatic  1.393  0.020  1.393
 1MT  CL2  C22  single    1.734  0.020  1.734
 1MT  C22  C21  aromatic  1.386  0.020  1.386
 1MT  C9   C18  single    1.559  0.020  1.559
 1MT  C9   N4   single    1.447  0.020  1.447
 1MT  C18  C19  single    1.494  0.020  1.494
 1MT  C18  C7   single    1.544  0.020  1.544
 1MT  C19  C20  aromatic  1.378  0.020  1.378
 1MT  N4   C8   single    1.449  0.020  1.449
 1MT  C21  C20  aromatic  1.393  0.020  1.393
 1MT  C5   C4   aromatic  1.386  0.020  1.386
 1MT  C5   C6   aromatic  1.394  0.020  1.394
 1MT  C4   C3   aromatic  1.386  0.020  1.386
 1MT  C8   C7   single    1.560  0.020  1.560
 1MT  C8   C15  single    1.523  0.020  1.523
 1MT  C7   C6   single    1.505  0.020  1.505
 1MT  C6   C2   aromatic  1.389  0.020  1.389
 1MT  C3   C1   aromatic  1.384  0.020  1.384
 1MT  C2   C1   aromatic  1.385  0.020  1.385
 1MT  C2   F1   single    1.336  0.020  1.336
 1MT  C1   CL1  single    1.723  0.020  1.723
 1MT  C15  N1   single    1.341  0.020  1.341
 1MT  C15  O1   double    1.221  0.020  1.221
 1MT  N1   C17  single    1.447  0.020  1.447
 1MT  C16  N3   single    1.452  0.020  1.452
 1MT  C16  C17  single    1.521  0.020  1.521
 1MT  C3   H1   single    0.930  0.020  1.080
 1MT  C4   H2   single    0.930  0.020  1.080
 1MT  C5   H3   single    0.930  0.020  1.080
 1MT  C7   H4   single    0.970  0.020  1.090
 1MT  C8   H5   single    0.970  0.020  1.090
 1MT  C9   H6   single    0.970  0.020  1.090
 1MT  C10  H7   single    0.970  0.020  1.090
 1MT  C10  H8   single    0.970  0.020  1.090
 1MT  C12  H9   single    0.970  0.020  1.090
 1MT  C12  H10  single    0.970  0.020  1.090
 1MT  C12  H11  single    0.970  0.020  1.090
 1MT  C13  H12  single    0.970  0.020  1.090
 1MT  C13  H13  single    0.970  0.020  1.090
 1MT  C13  H14  single    0.970  0.020  1.090
 1MT  C14  H15  single    0.970  0.020  1.090
 1MT  C14  H16  single    0.970  0.020  1.090
 1MT  C14  H17  single    0.970  0.020  1.090
 1MT  N1   H18  single    0.860  0.020  1.020
 1MT  C17  H19  single    0.970  0.020  1.090
 1MT  C17  H20  single    0.970  0.020  1.090
 1MT  C20  H21  single    0.930  0.020  1.080
 1MT  C21  H22  single    0.930  0.020  1.080
 1MT  C23  H23  single    0.930  0.020  1.080
 1MT  N2   H24  single    0.860  0.020  1.020
 1MT  C16  H25  single    0.970  0.020  1.090
 1MT  C16  H26  single    0.970  0.020  1.090
 1MT  N3   H27  single    0.890  0.020  1.040
 1MT  N3   H28  single    0.890  0.020  1.040
 1MT  N4   H30  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
 1MT  C3   C1   C2   119.90  3.000
 1MT  C2   C1   CL1  119.15  3.000
 1MT  C3   C1   CL1  120.95  3.000
 1MT  F1   C2   C6   119.68  3.000
 1MT  F1   C2   C1   117.94  3.000
 1MT  C6   C2   C1   122.38  3.000
 1MT  H1   C3   C4   121.04  3.000
 1MT  H1   C3   C1   120.08  3.000
 1MT  C4   C3   C1   118.88  3.000
 1MT  H2   C4   C5   119.85  3.000
 1MT  H2   C4   C3   119.54  3.000
 1MT  C5   C4   C3   120.60  3.000
 1MT  H3   C5   C6   119.95  3.000
 1MT  H3   C5   C4   118.59  3.000
 1MT  C6   C5   C4   121.46  3.000
 1MT  C7   C6   C5   123.72  3.000
 1MT  C7   C6   C2   119.51  3.000
 1MT  C5   C6   C2   116.77  3.000
 1MT  H4   C7   C18  104.65  3.000
 1MT  H4   C7   C8   107.30  3.000
 1MT  C18  C7   C8   103.37  3.000
 1MT  H4   C7   C6   107.83  3.000
 1MT  C8   C7   C6   116.78  3.000
 1MT  C18  C7   C6   115.98  3.000
 1MT  H5   C8   N4   109.21  3.000
 1MT  H5   C8   C15  109.63  3.000
 1MT  N4   C8   C15  112.07  3.000
 1MT  H5   C8   C7   111.53  3.000
 1MT  C15  C8   C7   107.29  3.000
 1MT  N4   C8   C7   107.11  3.000
 1MT  H6   C9   N4   108.26  3.000
 1MT  H6   C9   C18  104.77  3.000
 1MT  N4   C9   C18  104.66  3.000
 1MT  H6   C9   C10  108.50  3.000
 1MT  N4   C9   C10  115.16  3.000
 1MT  C18  C9   C10  114.84  3.000
 1MT  H8   C10  H7   106.27  3.000
 1MT  H8   C10  C11  107.57  3.000
 1MT  H7   C10  C11  108.56  3.000
 1MT  H8   C10  C9   106.85  3.000
 1MT  H7   C10  C9   109.98  3.000
 1MT  C11  C10  C9   117.05  3.000
 1MT  C14  C11  C13  109.56  3.000
 1MT  C13  C11  C12  109.09  3.000
 1MT  C14  C11  C12  108.43  3.000
 1MT  C13  C11  C10  110.89  3.000
 1MT  C14  C11  C10  111.52  3.000
 1MT  C12  C11  C10  107.26  3.000
 1MT  H11  C12  H10  107.65  3.000
 1MT  H11  C12  H9   107.69  3.000
 1MT  H10  C12  H9   107.80  3.000
 1MT  H11  C12  C11  111.16  3.000
 1MT  H10  C12  C11  110.85  3.000
 1MT  H9   C12  C11  111.51  3.000
 1MT  H14  C13  H13  107.60  3.000
 1MT  H14  C13  H12  107.96  3.000
 1MT  H13  C13  H12  107.31  3.000
 1MT  H14  C13  C11  111.39  3.000
 1MT  H13  C13  C11  110.52  3.000
 1MT  H12  C13  C11  111.86  3.000
 1MT  H17  C14  H16  108.05  3.000
 1MT  H17  C14  H15  107.99  3.000
 1MT  H16  C14  H15  107.46  3.000
 1MT  H17  C14  C11  111.59  3.000
 1MT  H16  C14  C11  110.60  3.000
 1MT  H15  C14  C11  111.00  3.000
 1MT  N1   C15  O1   123.49  3.000
 1MT  O1   C15  C8   122.17  3.000
 1MT  N1   C15  C8   114.21  3.000
 1MT  H18  N1   C17  117.74  3.000
 1MT  H18  N1   C15  118.57  3.000
 1MT  C17  N1   C15  123.60  3.000
 1MT  H20  C17  H19  107.17  3.000
 1MT  H20  C17  C16  109.79  3.000
 1MT  H19  C17  C16  109.47  3.000
 1MT  H20  C17  N1   108.92  3.000
 1MT  H19  C17  N1   111.14  3.000
 1MT  C16  C17  N1   110.29  3.000
 1MT  C25  C18  C19  102.48  3.000
 1MT  C19  C18  C9   115.15  3.000
 1MT  C25  C18  C9   111.55  3.000
 1MT  C19  C18  C7   115.78  3.000
 1MT  C9   C18  C7    99.58  3.000
 1MT  C25  C18  C7   112.78  3.000
 1MT  C24  C19  C20  119.72  3.000
 1MT  C20  C19  C18  131.54  3.000
 1MT  C24  C19  C18  108.73  3.000
 1MT  H21  C20  C21  119.33  3.000
 1MT  H21  C20  C19  121.18  3.000
 1MT  C21  C20  C19  119.49  3.000
 1MT  H22  C21  C22  120.42  3.000
 1MT  H22  C21  C20  120.32  3.000
 1MT  C22  C21  C20  119.26  3.000
 1MT  C23  C22  CL2  118.35  3.000
 1MT  CL2  C22  C21  119.04  3.000
 1MT  C23  C22  C21  122.61  3.000
 1MT  H23  C23  C24  122.02  3.000
 1MT  H23  C23  C22  121.52  3.000
 1MT  C24  C23  C22  116.46  3.000
 1MT  N2   C24  C23  128.30  3.000
 1MT  C23  C24  C19  122.46  3.000
 1MT  N2   C24  C19  109.24  3.000
 1MT  H24  N2   C25  123.31  3.000
 1MT  H24  N2   C24  124.63  3.000
 1MT  C25  N2   C24  112.06  3.000
 1MT  O2   C25  N2   125.50  3.000
 1MT  O2   C25  C18  127.01  3.000
 1MT  N2   C25  C18  107.48  3.000
 1MT  H26  C16  H25  106.62  3.000
 1MT  H26  C16  N3   108.22  3.000
 1MT  H25  C16  N3   114.15  3.000
 1MT  H26  C16  C17  109.13  3.000
 1MT  H25  C16  C17  108.85  3.000
 1MT  N3   C16  C17  109.74  3.000
 1MT  H28  N3   H27  105.80  3.000
 1MT  H28  N3   C16  109.47  3.000
 1MT  H27  N3   C16  109.63  3.000
 1MT  H30  N4   C9   109.43  3.000
 1MT  H30  N4   C8   108.93  3.000
 1MT  C9   N4   C8   107.82  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
 1MT  CONST_01  C5   C4   C3   C1      0.00   0.0  0
 1MT  CONST_02  C5   C6   C2   C1      0.00   0.0  0
 1MT  CONST_03  C4   C5   C6   C2      0.00   0.0  0
 1MT  CONST_04  C4   C3   C1   C2      0.00   0.0  0
 1MT  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 1MT  CONST_06  C6   C2   C1   C3      0.00   0.0  0
 1MT  CONST_07  C22  C23  C24  C19     0.00   0.0  0
 1MT  CONST_08  C22  C21  C20  C19     0.00   0.0  0
 1MT  CONST_09  C23  C24  C19  C20     0.00   0.0  0
 1MT  CONST_10  C23  C22  C21  C20     0.00   0.0  0
 1MT  CONST_11  C24  C23  C22  C21     0.00   0.0  0
 1MT  CONST_12  C24  C19  C20  C21     0.00   0.0  0
 1MT  CONST_13  C7   C6   C2   C1    180.00   0.0  0
 1MT  CONST_14  C7   C6   C5   C4    180.00   0.0  0
 1MT  CONST_15  N2   C24  C19  C18     0.00   0.0  0
 1MT  CONST_16  C23  C24  C19  C18   180.00   0.0  0
 1MT  CONST_17  C21  C20  C19  C18   180.00   0.0  0
 1MT  CONST_18  C24  N2   C25  C18     0.00   0.0  0
 1MT  CONST_19  C4   C3   C1   CL1   180.00   0.0  0
 1MT  CONST_20  C6   C2   C1   CL1   180.00   0.0  0
 1MT  CONST_21  F1   C2   C1   C3    180.00   0.0  0
 1MT  CONST_22  F1   C2   C6   C5    180.00   0.0  0
 1MT  CONST_23  F1   C2   C6   C7      0.00   0.0  0
 1MT  CONST_24  CL2  C22  C21  C20   180.00   0.0  0
 1MT  CONST_25  C24  C23  C22  CL2   180.00   0.0  0
 1MT  CONST_26  O2   C25  N2   C24   180.00   0.0  0
 1MT  CONST_27  H2   C4   C3   C1    180.00   0.0  0
 1MT  CONST_28  H3   C5   C6   C2    180.00   0.0  0
 1MT  CONST_29  H1   C3   C1   C2    180.00   0.0  0
 1MT  CONST_30  H21  C20  C19  C18     0.00   0.0  0
 1MT  CONST_31  H23  C23  C24  C19   180.00   0.0  0
 1MT  CONST_32  H22  C21  C20  C19   180.00   0.0  0
 1MT  CONST_33  H24  N2   C25  C18   180.00   0.0  0
 1MT  CONST_34  C17  N1   C15  C8    180.00   0.0  0
 1MT  CONST_35  H18  N1   C15  C8      0.00   0.0  0
 1MT  CONST_36  C17  N1   C15  O1      0.00   0.0  0
 1MT  Var_01    C12  C11  C10  C9   -167.42  30.0  3
 1MT  Var_02    C16  C17  N1   C15   161.69  30.0  3
 1MT  Var_03    N3   C16  C17  N1   -179.21  30.0  1
 1MT  Var_04    H9   C12  C11  C10    62.16  30.0  3
 1MT  Var_05    H15  C14  C11  C10    57.40  30.0  3
 1MT  Var_06    H12  C13  C11  C10    68.11  30.0  3
 1MT  Var_07    H27  N3   C16  C17    72.98  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
 1MT  chir_01  C7   C18  C8   C6   positiv
 1MT  chir_02  C8   N4   C7   C15  positiv
 1MT  chir_03  C9   N4   C18  C10  positiv
 1MT  chir_04  C18  C9   C19  C7   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
 1MT  plan-1  CL1  0.020
 1MT  plan-1  C1   0.020
 1MT  plan-1  C2   0.020
 1MT  plan-1  C3   0.020
 1MT  plan-1  C4   0.020
 1MT  plan-1  C5   0.020
 1MT  plan-1  C6   0.020
 1MT  plan-1  C7   0.020
 1MT  plan-1  F1   0.020
 1MT  plan-1  H1   0.020
 1MT  plan-1  H2   0.020
 1MT  plan-1  H3   0.020
 1MT  plan-2  C8   0.020
 1MT  plan-2  C15  0.020
 1MT  plan-2  O1   0.020
 1MT  plan-2  N1   0.020
 1MT  plan-2  C17  0.020
 1MT  plan-2  H18  0.020
 1MT  plan-3  C18  0.020
 1MT  plan-3  C19  0.020
 1MT  plan-3  C20  0.020
 1MT  plan-3  C21  0.020
 1MT  plan-3  C22  0.020
 1MT  plan-3  CL2  0.020
 1MT  plan-3  C23  0.020
 1MT  plan-3  C24  0.020
 1MT  plan-3  N2   0.020
 1MT  plan-3  C25  0.020
 1MT  plan-3  O2   0.020
 1MT  plan-3  H21  0.020
 1MT  plan-3  H22  0.020
 1MT  plan-3  H23  0.020
 1MT  plan-3  H24  0.020

