# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 19:36:12 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: N-[2-(aminomethyl)-5-chlorobenzyl]-1-{[(5R)-5-hydroxy-2-oxido-5H-indeno[1,2-c]pyridin-5-yl]carbonyl}-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(Cl)cc1CNC(=O)[C@@H]2CCCN2C(=O)[C@@]3(O)c4ccccc4c5c[n+]([O-])ccc35
#
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
 062  062  N-[2-(aminomethyl)-5-chlorobenzyl]-1-{[(5R)-5-hydroxy-2-oxido-5H-indeno[1,2-c]pyridin-5-yl]carbonyl}-L-prolinamide  ligand  60  35  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_062
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
 062  N1    N   NR6    1  -0.026  -4.7090  -0.3625   3.5086
 062  C2    C   CR16   0  -0.070  -4.9591  -1.2000   2.4700
 062  C3    C   CR56   0  -0.038  -4.4443  -0.9203   1.2270
 062  C4    C   CR56   0   0.262  -3.6631   0.2102   1.0171
 062  C5    C   CR16   0  -0.408  -3.4161   1.0536   2.0764
 062  C6    C   CR16   0  -0.013  -3.9528   0.7463   3.3110
 062  C10   C   CR56   0   0.121  -4.5778  -1.6422  -0.0370
 062  C11   C   CR56   0   0.112  -3.8924  -0.9286  -1.0219
 062  C12   C   CR5    0  -0.097  -3.2416   0.3152  -0.4371
 062  C13   C   CR16   0  -0.339  -5.2451  -2.8161  -0.3439
 062  C14   C   CR16   0  -0.250  -5.2191  -3.2664  -1.6592
 062  C15   C   CR16   0  -0.248  -4.5409  -2.5531  -2.6410
 062  C16   C   CR16   0  -0.303  -3.8676  -1.3746  -2.3277
 062  O21   O   OH1    0  -0.623  -3.7674   1.4456  -1.0671
 062  C22   C   C      0   0.561  -1.7120   0.1417  -0.5166
 062  N23   N   NT     0  -0.485  -0.9993   0.7334  -1.4835
 062  C24   C   CH1    0  -0.171   0.4471   0.5636  -1.4404
 062  C25   C   CH2    0  -0.484   0.9526   1.3969  -2.6247
 062  C26   C   CH2    0  -0.472  -0.2280   1.3905  -3.5844
 062  C27   C   CH2    0  -0.278  -1.4240   1.5095  -2.6526
 062  C34   C   C      0   0.565   1.0191   1.0879  -0.1296
 062  N36   N   NH1    0  -0.630   2.0965   0.4196   0.3074
 062  C37   C   CH2    0  -0.381   2.8744   0.8012   1.4655
 062  C38   C   CR6    0   0.070   4.3521   0.6748   1.1994
 062  C41   C   CR16   0  -0.259   5.0715  -0.2774   1.9115
 062  C42   C   CR6    0  -0.041   6.4318  -0.4272   1.6964
 062  C43   C   CR16   0  -0.210   7.0923   0.3598   0.7719
 062  C44   C   CR16   0  -0.300   6.3685   1.3086   0.0630
 062  C45   C   CR6    0   0.059   5.0031   1.4852   0.2576
 062  CL1   CL  CL     0  -0.136   7.3116  -1.6187   2.6004
 062  C53   C   CH2    0  -0.344   4.2446   2.5192  -0.5403
 062  N54   N   NH2    0  -0.794   5.1157   3.5280  -1.1130
 062  O60   O   O     -1  -0.578  -5.1811  -0.6176   4.6606
 062  O63   O   O      0  -0.474  -1.1776  -0.5702   0.3233
 062  O64   O   O      0  -0.486   0.5669   2.0861   0.4064
 062  H2    H   HCR6   0   0.306  -5.5663  -2.0628   2.7027
 062  H5    H   HCR6   0   0.288  -2.8083   1.9450   1.9904
 062  H6    H   HCR6   0   0.317  -3.8014   1.3598   4.1860
 062  H13   H   HCR6   0   0.259  -5.7786  -3.3741   0.4149
 062  H14   H   HCR6   0   0.269  -5.7328  -4.1817  -1.9214
 062  H15   H   HCR6   0   0.268  -4.5340  -2.9171  -3.6597
 062  H16   H   HCR6   0   0.264  -3.3395  -0.8338  -3.1023
 062  H21   H   HOH1   0   0.465  -3.4320   2.2446  -0.6441
 062  H24   H   HCH1   0   0.282   0.7047  -0.4909  -1.5807
 062  H251  H   HCH2   0   0.251   1.1663   2.4198  -2.3064
 062  H252  H   HCH2   0   0.269   1.8640   0.9787  -3.0485
 062  H261  H   HCH2   0   0.261  -0.1933   2.2052  -4.3060
 062  H262  H   HCH2   0   0.246  -0.2698   0.4502  -4.1379
 062  H271  H   HCH2   0   0.249  -1.5985   2.5539  -2.3836
 062  H272  H   HCH2   0   0.264  -2.3325   1.1172  -3.1000
 062  H36   H   HNH1   0   0.403   2.3453  -0.4449  -0.1478
 062  H371  H   HCH2   0   0.273   2.6023   0.1823   2.3243
 062  H372  H   HCH2   0   0.273   2.6172   1.8289   1.7244
 062  H41   H   HCR6   0   0.275   4.5653  -0.9011   2.6380
 062  H43   H   HCR6   0   0.276   8.1539   0.2418   0.6012
 062  H44   H   HCR6   0   0.263   6.8819   1.9319  -0.6563
 062  H531  H   HCH2   0   0.219   3.4467   2.9413   0.0853
 062  H532  H   HCH2   0   0.249   3.7351   2.0099  -1.3641
 062  H541  H   HNH2   0   0.358   4.5757   4.1099  -1.7398
 062  H542  H   HNH2   0   0.347   5.4502   4.1429  -0.3815

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
 062  N1   C2    aromatic  1.357  0.020  1.357
 062  N1   C6    aromatic  1.357  0.020  1.357
 062  N1   O60   single    1.271  0.020  1.271
 062  C2   C3    aromatic  1.374  0.020  1.374
 062  C2   H2    single    0.930  0.020  1.080
 062  C3   C4    aromatic  1.390  0.020  1.390
 062  C3   C10   aromatic  1.462  0.020  1.462
 062  C4   C5    aromatic  1.376  0.020  1.376
 062  C4   C12   single    1.518  0.020  1.518
 062  C5   C6    aromatic  1.381  0.020  1.381
 062  C5   H5    single    0.930  0.020  1.080
 062  C6   H6    single    0.930  0.020  1.080
 062  C10  C11   aromatic  1.396  0.020  1.396
 062  C10  C13   aromatic  1.385  0.020  1.385
 062  C11  C12   single    1.521  0.020  1.521
 062  C11  C16   aromatic  1.380  0.020  1.380
 062  C12  O21   single    1.397  0.020  1.397
 062  C12  C22   single    1.541  0.020  1.541
 062  C13  C14   aromatic  1.391  0.020  1.391
 062  C13  H13   single    0.930  0.020  1.080
 062  C14  C15   aromatic  1.390  0.020  1.390
 062  C14  H14   single    0.930  0.020  1.080
 062  C15  C16   aromatic  1.393  0.020  1.393
 062  C15  H15   single    0.930  0.020  1.080
 062  C16  H16   single    0.930  0.020  1.080
 062  O21  H21   single    0.850  0.020  0.980
 062  C22  N23   single    1.339  0.020  1.339
 062  C22  O63   double    1.224  0.020  1.224
 062  N23  C24   single    1.457  0.020  1.457
 062  N23  C27   single    1.466  0.020  1.466
 062  C24  C25   single    1.534  0.020  1.534
 062  C24  C34   single    1.523  0.020  1.523
 062  C24  H24   single    0.970  0.020  1.090
 062  C25  C26   single    1.521  0.020  1.521
 062  C25  H251  single    0.970  0.020  1.090
 062  C25  H252  single    0.970  0.020  1.090
 062  C26  C27   single    1.521  0.020  1.521
 062  C26  H261  single    0.970  0.020  1.090
 062  C26  H262  single    0.970  0.020  1.090
 062  C27  H271  single    0.970  0.020  1.090
 062  C27  H272  single    0.970  0.020  1.090
 062  C34  N36   single    1.341  0.020  1.341
 062  C34  O64   double    1.220  0.020  1.220
 062  N36  C37   single    1.446  0.020  1.446
 062  N36  H36   single    0.860  0.020  1.020
 062  C37  C38   single    1.507  0.020  1.507
 062  C37  H371  single    0.970  0.020  1.090
 062  C37  H372  single    0.970  0.020  1.090
 062  C38  C41   aromatic  1.390  0.020  1.390
 062  C38  C45   aromatic  1.403  0.020  1.403
 062  C41  C42   aromatic  1.385  0.020  1.385
 062  C41  H41   single    0.930  0.020  1.080
 062  C42  C43   aromatic  1.382  0.020  1.382
 062  C42  CL1   single    1.735  0.020  1.735
 062  C43  C44   aromatic  1.388  0.020  1.388
 062  C43  H43   single    0.930  0.020  1.080
 062  C44  C45   aromatic  1.391  0.020  1.391
 062  C44  H44   single    0.930  0.020  1.080
 062  C45  C53   single    1.510  0.020  1.510
 062  C53  N54   single    1.451  0.020  1.451
 062  C53  H531  single    0.970  0.020  1.090
 062  C53  H532  single    0.970  0.020  1.090
 062  N54  H541  single    0.890  0.020  1.040
 062  N54  H542  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
 062  O60   N1   C6    120.21  3.000
 062  O60   N1   C2    120.09  3.000
 062  C6    N1   C2    119.71  3.000
 062  H2    C2   C3    124.60  3.000
 062  H2    C2   N1    115.56  3.000
 062  C3    C2   N1    119.83  3.000
 062  C10   C3   C4    108.81  3.000
 062  C10   C3   C2    130.35  3.000
 062  C4    C3   C2    120.84  3.000
 062  C12   C4   C5    130.18  3.000
 062  C12   C4   C3    110.92  3.000
 062  C5    C4   C3    118.88  3.000
 062  H5    C5   C6    118.20  3.000
 062  H5    C5   C4    122.98  3.000
 062  C6    C5   C4    118.82  3.000
 062  H6    C6   C5    122.95  3.000
 062  H6    C6   N1    115.13  3.000
 062  C5    C6   N1    121.92  3.000
 062  C13   C10  C11   120.90  3.000
 062  C13   C10  C3    130.87  3.000
 062  C11   C10  C3    108.23  3.000
 062  C16   C11  C12   128.35  3.000
 062  C16   C11  C10   120.74  3.000
 062  C12   C11  C10   110.91  3.000
 062  C22   C12  O21   116.19  3.000
 062  C22   C12  C11   108.23  3.000
 062  O21   C12  C11   109.11  3.000
 062  C22   C12  C4    108.50  3.000
 062  O21   C12  C4    112.55  3.000
 062  C11   C12  C4    101.13  3.000
 062  H13   C13  C14   120.35  3.000
 062  H13   C13  C10   121.28  3.000
 062  C14   C13  C10   118.37  3.000
 062  H14   C14  C15   119.64  3.000
 062  H14   C14  C13   119.63  3.000
 062  C15   C14  C13   120.73  3.000
 062  H15   C15  C16   119.56  3.000
 062  H15   C15  C14   119.70  3.000
 062  C16   C15  C14   120.73  3.000
 062  H16   C16  C15   119.84  3.000
 062  H16   C16  C11   121.63  3.000
 062  C15   C16  C11   118.52  3.000
 062  H21   O21  C12   109.99  3.000
 062  O63   C22  N23   121.34  3.000
 062  O63   C22  C12   117.61  3.000
 062  N23   C22  C12   121.04  3.000
 062  C27   N23  C24   111.89  3.000
 062  C27   N23  C22   130.96  3.000
 062  C24   N23  C22   117.10  3.000
 062  H24   C24  C34   110.70  3.000
 062  H24   C24  C25   110.30  3.000
 062  C34   C24  C25   110.71  3.000
 062  H24   C24  N23   110.01  3.000
 062  C34   C24  N23   110.99  3.000
 062  C25   C24  N23   103.95  3.000
 062  H252  C25  H251  108.02  3.000
 062  H252  C25  C26   113.73  3.000
 062  H251  C25  C26   109.85  3.000
 062  H252  C25  C24   111.58  3.000
 062  H251  C25  C24   110.38  3.000
 062  C26   C25  C24   103.24  3.000
 062  H262  C26  H261  108.03  3.000
 062  H262  C26  C27   110.36  3.000
 062  H261  C26  C27   111.87  3.000
 062  H262  C26  C25   110.68  3.000
 062  H261  C26  C25   112.97  3.000
 062  C27   C26  C25   102.91  3.000
 062  H272  C27  H271  108.25  3.000
 062  H272  C27  C26   112.16  3.000
 062  H271  C27  C26   110.57  3.000
 062  H272  C27  N23   112.31  3.000
 062  H271  C27  N23   110.85  3.000
 062  C26   C27  N23   102.67  3.000
 062  O64   C34  N36   124.22  3.000
 062  O64   C34  C24   121.37  3.000
 062  N36   C34  C24   114.24  3.000
 062  H36   N36  C37   117.07  3.000
 062  H36   N36  C34   118.58  3.000
 062  C37   N36  C34   124.16  3.000
 062  H372  C37  H371  106.76  3.000
 062  H372  C37  C38   110.63  3.000
 062  H371  C37  C38   109.60  3.000
 062  H372  C37  N36   108.17  3.000
 062  H371  C37  N36   110.23  3.000
 062  C38   C37  N36   111.34  3.000
 062  C45   C38  C41   119.98  3.000
 062  C45   C38  C37   121.68  3.000
 062  C41   C38  C37   118.33  3.000
 062  H41   C41  C42   120.05  3.000
 062  H41   C41  C38   119.76  3.000
 062  C42   C41  C38   120.19  3.000
 062  CL1   C42  C43   119.81  3.000
 062  CL1   C42  C41   119.42  3.000
 062  C43   C42  C41   120.77  3.000
 062  H43   C43  C44   120.38  3.000
 062  H43   C43  C42   120.82  3.000
 062  C44   C43  C42   118.79  3.000
 062  H44   C44  C45   119.08  3.000
 062  H44   C44  C43   119.09  3.000
 062  C45   C44  C43   121.83  3.000
 062  C53   C45  C44   120.41  3.000
 062  C53   C45  C38   121.14  3.000
 062  C44   C45  C38   118.44  3.000
 062  H532  C53  H531  105.64  3.000
 062  H532  C53  N54   107.82  3.000
 062  H531  C53  N54   113.19  3.000
 062  H532  C53  C45   108.23  3.000
 062  H531  C53  C45   109.09  3.000
 062  N54   C53  C45   112.52  3.000
 062  H542  N54  H541  105.94  3.000
 062  H542  N54  C53   109.60  3.000
 062  H541  N54  C53   108.91  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
 062  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 062  CONST_02  C10   C3   C2   N1    180.00   0.0  0
 062  CONST_03  C4    C5   C6   N1      0.00   0.0  0
 062  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 062  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 062  CONST_06  C11   C10  C3   C2    180.00   0.0  0
 062  CONST_07  C13   C10  C3   C2      0.00   0.0  0
 062  CONST_08  C6    N1   C2   C3      0.00   0.0  0
 062  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 062  CONST_10  C16   C11  C10  C3    180.00   0.0  0
 062  CONST_11  C14   C13  C10  C3    180.00   0.0  0
 062  CONST_12  C11   C10  C3   C4      0.00   0.0  0
 062  CONST_13  C13   C10  C3   C4    180.00   0.0  0
 062  CONST_14  C10   C3   C4   C5    180.00   0.0  0
 062  CONST_15  C15   C16  C11  C10     0.00   0.0  0
 062  CONST_16  C15   C14  C13  C10     0.00   0.0  0
 062  CONST_17  C14   C13  C10  C11     0.00   0.0  0
 062  CONST_18  C14   C15  C16  C11     0.00   0.0  0
 062  CONST_19  C16   C11  C10  C13     0.00   0.0  0
 062  CONST_20  C16   C15  C14  C13     0.00   0.0  0
 062  CONST_21  C43   C42  C41  C38     0.00   0.0  0
 062  CONST_22  C43   C44  C45  C38     0.00   0.0  0
 062  CONST_23  C44   C45  C38  C41     0.00   0.0  0
 062  CONST_24  C44   C43  C42  C41     0.00   0.0  0
 062  CONST_25  C45   C38  C41  C42     0.00   0.0  0
 062  CONST_26  C45   C44  C43  C42     0.00   0.0  0
 062  CONST_27  O60   N1   C2   C3    180.00   0.0  0
 062  CONST_28  O60   N1   C6   C5    180.00   0.0  0
 062  CONST_29  C42   C41  C38  C37   180.00   0.0  0
 062  CONST_30  C44   C45  C38  C37   180.00   0.0  0
 062  CONST_31  CL1   C42  C41  C38   180.00   0.0  0
 062  CONST_32  C53   C45  C38  C41   180.00   0.0  0
 062  CONST_33  C53   C45  C44  C43   180.00   0.0  0
 062  CONST_34  CL1   C42  C43  C44   180.00   0.0  0
 062  CONST_35  C24   N23  C22  C12   180.00   0.0  0
 062  CONST_36  C27   N23  C22  C12     0.00   0.0  0
 062  CONST_37  H5    C5   C6   N1    180.00   0.0  0
 062  CONST_38  H6    C6   N1   C2    180.00   0.0  0
 062  CONST_39  H13   C13  C10  C3      0.00   0.0  0
 062  CONST_40  H2    C2   C3   C4    180.00   0.0  0
 062  CONST_41  H16   C16  C11  C10   180.00   0.0  0
 062  CONST_42  H14   C14  C13  C10   180.00   0.0  0
 062  CONST_43  H15   C15  C16  C11   180.00   0.0  0
 062  CONST_44  H44   C44  C45  C38   180.00   0.0  0
 062  CONST_45  H43   C43  C42  C41   180.00   0.0  0
 062  CONST_46  H41   C41  C42  C43   180.00   0.0  0
 062  CONST_47  O63   C22  N23  C24     0.00   0.0  0
 062  CONST_48  O63   C22  N23  C27   180.00   0.0  0
 062  CONST_49  C37   N36  C34  C24   180.00   0.0  0
 062  CONST_50  H36   N36  C34  C24     0.00   0.0  0
 062  CONST_51  O64   C34  N36  C37     0.00   0.0  0
 062  Var_01    C25   C26  C27  N23   -35.47  30.0  1
 062  Var_02    C26   C27  N23  C24    19.48  30.0  1
 062  Var_03    C27   C26  C25  C24    38.66  30.0  1
 062  Var_04    C41   C38  C37  N36  -114.13  30.0  2
 062  Var_05    N54   C53  C45  C38   160.98  30.0  2
 062  Var_06    C38   C37  N36  C34  -137.45  30.0  3
 062  Var_07    H541  N54  C53  C45   171.93  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
 062  chir_01  C12  C11  C4   C22  negativ
 062  chir_02  C24  N23  C34  C25  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
 062  plan-1  C37  0.020
 062  plan-1  C38  0.020
 062  plan-1  C41  0.020
 062  plan-1  C42  0.020
 062  plan-1  C43  0.020
 062  plan-1  C44  0.020
 062  plan-1  C45  0.020
 062  plan-1  CL1  0.020
 062  plan-1  C53  0.020
 062  plan-1  H41  0.020
 062  plan-1  H43  0.020
 062  plan-1  H44  0.020
 062  plan-2  N1   0.020
 062  plan-2  C2   0.020
 062  plan-2  C3   0.020
 062  plan-2  C4   0.020
 062  plan-2  C5   0.020
 062  plan-2  C6   0.020
 062  plan-2  C10  0.020
 062  plan-2  C11  0.020
 062  plan-2  C12  0.020
 062  plan-2  C13  0.020
 062  plan-2  C14  0.020
 062  plan-2  C15  0.020
 062  plan-2  C16  0.020
 062  plan-2  O60  0.020
 062  plan-2  H2   0.020
 062  plan-2  H5   0.020
 062  plan-2  H6   0.020
 062  plan-2  H13  0.020
 062  plan-2  H14  0.020
 062  plan-2  H15  0.020
 062  plan-2  H16  0.020
 062  plan-3  C12  0.020
 062  plan-3  C22  0.020
 062  plan-3  N23  0.020
 062  plan-3  C24  0.020
 062  plan-3  C27  0.020
 062  plan-3  O63  0.020
 062  plan-4  C24  0.020
 062  plan-4  C34  0.020
 062  plan-4  N36  0.020
 062  plan-4  C37  0.020
 062  plan-4  O64  0.020
 062  plan-4  H36  0.020

