# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 14:17:23 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: tert-butyl [(2S)-1-({3-oxo-3-[(pyridin-3-ylmethyl)amino]propyl}sulfanyl)-3-phenylpropan-2-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)OC(=O)N[C@H](CSCCC(=O)NCc1cccnc1)Cc2ccccc2
#
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
 J9K  J9K  'tert-butyl [(2S)-1-({3-oxo-3-[(pyridin-3-ylmethyl)amino]propyl}sulfanyl)-3-phenylpropan-2-yl]carbamate'  ligand  61  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J9K
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
 J9K  C01   C  CH3   0  -0.674   3.7109  -3.7190   1.2040
 J9K  C02   C  CT    0   0.191   4.5114  -3.0120   0.1156
 J9K  C03   C  CH3   0  -0.663   5.8665  -2.5310   0.6195
 J9K  C04   C  CH3   0  -0.659   4.7061  -3.9548  -1.0661
 J9K  O05   O  O2    0  -0.505   3.7616  -1.9132  -0.4647
 J9K  C06   C  C     0   0.776   3.3586  -0.8638   0.2514
 J9K  O07   O  O     0  -0.511   3.5175  -0.7183   1.4449
 J9K  N08   N  NH1   0  -0.653   2.7052   0.0123  -0.5476
 J9K  C09   C  CH1   0  -0.085   2.3148   1.3307  -0.1093
 J9K  C10   C  CH2   0  -0.546   0.9009   1.6524  -0.5767
 J9K  S11   S  S2    0  -0.021  -0.2301   0.3132  -0.1066
 J9K  C12   C  CH2   0  -0.545  -1.8149   1.1697  -0.3351
 J9K  C13   C  CH2   0  -0.570  -2.9431   0.1514  -0.2588
 J9K  C14   C  C     0   0.573  -4.3011   0.8173  -0.3574
 J9K  O15   O  O     0  -0.498  -4.5587   1.8502   0.2453
 J9K  N16   N  NH1   0  -0.621  -5.1871   0.1839  -1.1428
 J9K  C17   C  CH2   0  -0.402  -6.5627   0.6057  -1.3039
 J9K  C18   C  CR6   0   0.036  -7.4816  -0.0148  -0.2847
 J9K  C19   C  CR16  0  -0.180  -7.6222   0.5080   0.9965
 J9K  C20   C  CR16  0  -0.319  -8.4595  -0.1297   1.8973
 J9K  C21   C  CR16  0  -0.070  -9.1322  -1.2709   1.4843
 J9K  N22   N  N     0  -0.402  -9.0153  -1.7796   0.2638
 J9K  C23   C  CR16  0  -0.096  -8.2095  -1.1597  -0.5898
 J9K  C24   C  CH2   0  -0.508   3.2963   2.4053  -0.6074
 J9K  C25   C  CR6   0   0.143   4.7040   2.1280  -0.1654
 J9K  C26   C  CR16  0  -0.309   5.5723   1.3883  -0.9642
 J9K  C27   C  CR16  0  -0.230   6.8529   1.0783  -0.5262
 J9K  C28   C  CR16  0  -0.270   7.2869   1.5091   0.7197
 J9K  C29   C  CR16  0  -0.241   6.4325   2.2548   1.5220
 J9K  C30   C  CR16  0  -0.301   5.1523   2.5582   1.0813
 J9K  H01   H  HCH3  0   0.246   3.6037  -3.1189   2.1040
 J9K  H01A  H  HCH3  0   0.234   2.7174  -3.9886   0.8415
 J9K  H01B  H  HCH3  0   0.232   4.2227  -4.6426   1.4768
 J9K  H03   H  HCH3  0   0.230   6.4505  -3.3877   0.9590
 J9K  H03A  H  HCH3  0   0.232   6.4258  -2.0421  -0.1792
 J9K  H03B  H  HCH3  0   0.246   5.7787  -1.8335   1.4489
 J9K  H04   H  HCH3  0   0.236   3.7490  -4.3025  -1.4582
 J9K  H04A  H  HCH3  0   0.236   5.2569  -3.4699  -1.8734
 J9K  H04B  H  HCH3  0   0.229   5.2752  -4.8297  -0.7519
 J9K  HN08  H  HNH1  0   0.391   2.7026  -0.1674  -1.5406
 J9K  H09   H  HCH1  0   0.268   2.3252   1.3246   0.9807
 J9K  H10   H  HCH2  0   0.278   0.5717   2.5834  -0.1123
 J9K  H10A  H  HCH2  0   0.264   0.8699   1.7912  -1.6605
 J9K  H12   H  HCH2  0   0.270  -1.9325   1.9353   0.4311
 J9K  H12A  H  HCH2  0   0.270  -1.8152   1.6612  -1.3102
 J9K  H13   H  HCH2  0   0.264  -2.8175  -0.6050  -1.0354
 J9K  H13A  H  HCH2  0   0.280  -2.9086  -0.3736   0.7013
 J9K  HN16  H  HNH1  0   0.405  -4.9168  -0.6853  -1.5735
 J9K  H17   H  HCH2  0   0.272  -6.6079   1.6924  -1.2444
 J9K  H17A  H  HCH2  0   0.277  -6.8787   0.3261  -2.3090
 J9K  H19   H  HCR6  0   0.270  -7.0875   1.4044   1.2833
 J9K  H20   H  HCR6  0   0.272  -8.5946   0.2490   2.9011
 J9K  H21   H  HCR6  0   0.265  -9.7965  -1.7907   2.1657
 J9K  H23   H  HCR6  0   0.259  -8.1376  -1.5924  -1.5837
 J9K  H24   H  HCH2  0   0.248   3.2427   2.4546  -1.6990
 J9K  H24A  H  HCH2  0   0.255   2.9638   3.3760  -0.2315
 J9K  H26   H  HCR6  0   0.243   5.2469   1.0513  -1.9414
 J9K  H27   H  HCR6  0   0.248   7.5120   0.4981  -1.1595
 J9K  H28   H  HCR6  0   0.250   8.2860   1.2704   1.0608
 J9K  H29   H  HCR6  0   0.250   6.7635   2.6025   2.4923
 J9K  H30   H  HCR6  0   0.243   4.4913   3.1394   1.7143

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
 J9K  C01  C02   single    1.525  0.020  1.525
 J9K  C02  C03   single    1.524  0.020  1.524
 J9K  C02  C04   single    1.524  0.020  1.524
 J9K  C02  O05   single    1.451  0.020  1.451
 J9K  O05  C06   single    1.333  0.020  1.333
 J9K  C06  O07   double    1.213  0.020  1.213
 J9K  C06  N08   single    1.354  0.020  1.354
 J9K  N08  C09   single    1.443  0.020  1.443
 J9K  C09  C10   single    1.524  0.020  1.524
 J9K  C09  C24   single    1.538  0.020  1.538
 J9K  C10  S11   single    1.815  0.020  1.815
 J9K  S11  C12   single    1.816  0.020  1.816
 J9K  C12  C13   single    1.522  0.020  1.522
 J9K  C13  C14   single    1.516  0.020  1.516
 J9K  C14  O15   double    1.223  0.020  1.223
 J9K  C14  N16   single    1.343  0.020  1.343
 J9K  N16  C17   single    1.448  0.020  1.448
 J9K  C17  C18   single    1.506  0.020  1.506
 J9K  C18  C19   aromatic  1.391  0.020  1.391
 J9K  C18  C23   aromatic  1.391  0.020  1.391
 J9K  C19  C20   aromatic  1.385  0.020  1.385
 J9K  C20  C21   aromatic  1.388  0.020  1.388
 J9K  C21  N22   aromatic  1.327  0.020  1.327
 J9K  N22  C23   aromatic  1.327  0.020  1.327
 J9K  C24  C25   single    1.501  0.020  1.501
 J9K  C25  C26   aromatic  1.393  0.020  1.393
 J9K  C25  C30   aromatic  1.393  0.020  1.393
 J9K  C26  C27   aromatic  1.388  0.020  1.388
 J9K  C27  C28   aromatic  1.388  0.020  1.388
 J9K  C28  C29   aromatic  1.389  0.020  1.389
 J9K  C29  C30   aromatic  1.387  0.020  1.387
 J9K  C01  H01   single    0.970  0.020  1.090
 J9K  C01  H01A  single    0.970  0.020  1.090
 J9K  C01  H01B  single    0.970  0.020  1.090
 J9K  C03  H03   single    0.970  0.020  1.090
 J9K  C03  H03A  single    0.970  0.020  1.090
 J9K  C03  H03B  single    0.970  0.020  1.090
 J9K  C04  H04   single    0.970  0.020  1.090
 J9K  C04  H04A  single    0.970  0.020  1.090
 J9K  C04  H04B  single    0.970  0.020  1.090
 J9K  N08  HN08  single    0.860  0.020  1.020
 J9K  C09  H09   single    0.970  0.020  1.090
 J9K  C10  H10   single    0.970  0.020  1.090
 J9K  C10  H10A  single    0.970  0.020  1.090
 J9K  C12  H12   single    0.970  0.020  1.090
 J9K  C12  H12A  single    0.970  0.020  1.090
 J9K  C13  H13   single    0.970  0.020  1.090
 J9K  C13  H13A  single    0.970  0.020  1.090
 J9K  N16  HN16  single    0.860  0.020  1.020
 J9K  C17  H17   single    0.970  0.020  1.090
 J9K  C17  H17A  single    0.970  0.020  1.090
 J9K  C19  H19   single    0.930  0.020  1.080
 J9K  C20  H20   single    0.930  0.020  1.080
 J9K  C21  H21   single    0.930  0.020  1.080
 J9K  C23  H23   single    0.930  0.020  1.080
 J9K  C24  H24   single    0.970  0.020  1.090
 J9K  C24  H24A  single    0.970  0.020  1.090
 J9K  C26  H26   single    0.930  0.020  1.080
 J9K  C27  H27   single    0.930  0.020  1.080
 J9K  C28  H28   single    0.930  0.020  1.080
 J9K  C29  H29   single    0.930  0.020  1.080
 J9K  C30  H30   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
 J9K  H01B  C01  H01A  107.52  3.000
 J9K  H01B  C01  H01   107.87  3.000
 J9K  H01A  C01  H01   108.76  3.000
 J9K  H01B  C01  C02   108.96  3.000
 J9K  H01A  C01  C02   110.81  3.000
 J9K  H01   C01  C02   112.75  3.000
 J9K  O05   C02  C04   102.96  3.000
 J9K  O05   C02  C03   110.65  3.000
 J9K  C04   C02  C03   109.76  3.000
 J9K  O05   C02  C01   111.42  3.000
 J9K  C04   C02  C01   109.49  3.000
 J9K  C03   C02  C01   112.16  3.000
 J9K  H03B  C03  H03A  108.21  3.000
 J9K  H03B  C03  H03   108.03  3.000
 J9K  H03A  C03  H03   107.77  3.000
 J9K  H03B  C03  C02   112.52  3.000
 J9K  H03A  C03  C02   110.82  3.000
 J9K  H03   C03  C02   109.34  3.000
 J9K  H04B  C04  H04A  107.85  3.000
 J9K  H04B  C04  H04   107.81  3.000
 J9K  H04A  C04  H04   108.58  3.000
 J9K  H04B  C04  C02   109.86  3.000
 J9K  H04A  C04  C02   111.30  3.000
 J9K  H04   C04  C02   111.32  3.000
 J9K  C06   O05  C02   122.51  3.000
 J9K  N08   C06  O07   124.50  3.000
 J9K  N08   C06  O05   109.77  3.000
 J9K  O07   C06  O05   125.70  3.000
 J9K  HN08  N08  C09   117.44  3.000
 J9K  HN08  N08  C06   117.82  3.000
 J9K  C09   N08  C06   122.85  3.000
 J9K  H09   C09  C24   108.76  3.000
 J9K  H09   C09  C10   108.47  3.000
 J9K  C24   C09  C10   110.20  3.000
 J9K  H09   C09  N08   107.22  3.000
 J9K  C24   C09  N08   111.54  3.000
 J9K  C10   C09  N08   110.54  3.000
 J9K  H10A  C10  H10   107.76  3.000
 J9K  H10A  C10  S11   109.44  3.000
 J9K  H10   C10  S11   109.35  3.000
 J9K  H10A  C10  C09   110.94  3.000
 J9K  H10   C10  C09   109.24  3.000
 J9K  S11   C10  C09   110.07  3.000
 J9K  C12   S11  C10    99.40  3.000
 J9K  H12A  C12  H12   108.16  3.000
 J9K  H12A  C12  C13   110.23  3.000
 J9K  H12   C12  C13   110.79  3.000
 J9K  H12A  C12  S11   108.96  3.000
 J9K  H12   C12  S11   109.70  3.000
 J9K  C13   C12  S11   108.97  3.000
 J9K  H13A  C13  H13   106.74  3.000
 J9K  H13A  C13  C14   107.21  3.000
 J9K  H13   C13  C14   111.18  3.000
 J9K  H13A  C13  C12   109.97  3.000
 J9K  H13   C13  C12   110.05  3.000
 J9K  C14   C13  C12   111.53  3.000
 J9K  N16   C14  O15   123.20  3.000
 J9K  N16   C14  C13   114.96  3.000
 J9K  O15   C14  C13   121.84  3.000
 J9K  HN16  N16  C17   117.32  3.000
 J9K  HN16  N16  C14   118.70  3.000
 J9K  C17   N16  C14   123.68  3.000
 J9K  H17A  C17  H17   107.11  3.000
 J9K  H17A  C17  C18   109.96  3.000
 J9K  H17   C17  C18   110.41  3.000
 J9K  H17A  C17  N16   107.65  3.000
 J9K  H17   C17  N16   108.91  3.000
 J9K  C18   C17  N16   112.61  3.000
 J9K  C23   C18  C19   117.30  3.000
 J9K  C23   C18  C17   120.67  3.000
 J9K  C19   C18  C17   122.02  3.000
 J9K  H19   C19  C20   120.49  3.000
 J9K  H19   C19  C18   120.36  3.000
 J9K  C20   C19  C18   119.15  3.000
 J9K  H20   C20  C21   120.25  3.000
 J9K  H20   C20  C19   121.19  3.000
 J9K  C21   C20  C19   118.56  3.000
 J9K  H21   C21  N22   116.62  3.000
 J9K  H21   C21  C20   120.28  3.000
 J9K  N22   C21  C20   123.10  3.000
 J9K  C23   N22  C21   117.76  3.000
 J9K  H23   C23  N22   116.27  3.000
 J9K  H23   C23  C18   119.60  3.000
 J9K  N22   C23  C18   124.13  3.000
 J9K  H24A  C24  H24   106.76  3.000
 J9K  H24A  C24  C25   110.37  3.000
 J9K  H24   C24  C25   110.37  3.000
 J9K  H24A  C24  C09   108.36  3.000
 J9K  H24   C24  C09   108.86  3.000
 J9K  C25   C24  C09   111.95  3.000
 J9K  C30   C25  C26   118.47  3.000
 J9K  C30   C25  C24   120.55  3.000
 J9K  C26   C25  C24   120.92  3.000
 J9K  H26   C26  C27   119.47  3.000
 J9K  H26   C26  C25   119.69  3.000
 J9K  C27   C26  C25   120.85  3.000
 J9K  H27   C27  C28   120.07  3.000
 J9K  H27   C27  C26   119.78  3.000
 J9K  C28   C27  C26   120.15  3.000
 J9K  H28   C28  C29   120.27  3.000
 J9K  H28   C28  C27   120.20  3.000
 J9K  C29   C28  C27   119.52  3.000
 J9K  H29   C29  C30   119.77  3.000
 J9K  H29   C29  C28   120.13  3.000
 J9K  C30   C29  C28   120.10  3.000
 J9K  H30   C30  C29   119.63  3.000
 J9K  H30   C30  C25   119.46  3.000
 J9K  C29   C30  C25   120.91  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
 J9K  CONST_01  C21   C20  C19  C18     0.00   0.0  0
 J9K  CONST_02  C21   N22  C23  C18     0.00   0.0  0
 J9K  CONST_03  N22   C23  C18  C19     0.00   0.0  0
 J9K  CONST_04  N22   C21  C20  C19     0.00   0.0  0
 J9K  CONST_05  C23   C18  C19  C20     0.00   0.0  0
 J9K  CONST_06  C23   N22  C21  C20     0.00   0.0  0
 J9K  CONST_07  C28   C27  C26  C25     0.00   0.0  0
 J9K  CONST_08  C28   C29  C30  C25     0.00   0.0  0
 J9K  CONST_09  C29   C30  C25  C26     0.00   0.0  0
 J9K  CONST_10  C29   C28  C27  C26     0.00   0.0  0
 J9K  CONST_11  C30   C25  C26  C27     0.00   0.0  0
 J9K  CONST_12  C30   C29  C28  C27     0.00   0.0  0
 J9K  CONST_13  C20   C19  C18  C17   180.00   0.0  0
 J9K  CONST_14  N22   C23  C18  C17   180.00   0.0  0
 J9K  CONST_15  C27   C26  C25  C24   180.00   0.0  0
 J9K  CONST_16  C29   C30  C25  C24   180.00   0.0  0
 J9K  CONST_17  H20   C20  C19  C18   180.00   0.0  0
 J9K  CONST_18  H23   C23  C18  C19   180.00   0.0  0
 J9K  CONST_19  H21   C21  C20  C19   180.00   0.0  0
 J9K  CONST_20  H19   C19  C20  C21   180.00   0.0  0
 J9K  CONST_21  H27   C27  C26  C25   180.00   0.0  0
 J9K  CONST_22  H29   C29  C30  C25   180.00   0.0  0
 J9K  CONST_23  H30   C30  C25  C26   180.00   0.0  0
 J9K  CONST_24  H28   C28  C27  C26   180.00   0.0  0
 J9K  CONST_25  H26   C26  C27  C28   180.00   0.0  0
 J9K  CONST_26  C17   N16  C14  C13   180.00   0.0  0
 J9K  CONST_27  C17   N16  C14  O15     0.00   0.0  0
 J9K  CONST_28  HN16  N16  C14  C13     0.00   0.0  0
 J9K  Var_01    C26   C25  C24  C09    91.47  30.0  2
 J9K  Var_02    C19   C18  C17  N16    82.61  30.0  2
 J9K  Var_03    C18   C17  N16  C14   -89.10  30.0  3
 J9K  Var_04    O07   C06  O05  C02    -2.73  30.0  3
 J9K  Var_05    C09   N08  C06  O05  -170.96  30.0  2
 J9K  Var_06    C13   C12  S11  C10   168.97  30.0  3
 J9K  Var_07    C14   C13  C12  S11   176.50  30.0  3
 J9K  Var_08    O15   C14  C13  C12   -43.01  30.0  3
 J9K  Var_09    H03   C03  C02  C01    60.52  30.0  3
 J9K  Var_10    H04   C04  C02  C01    57.41  30.0  3
 J9K  Var_11    H01   C01  C02  C03    53.65  30.0  3
 J9K  Var_12    H10   C10  S11  C12    44.30  30.0  1

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
 J9K  chir_01  C09  N08  C10  C24  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
 J9K  plan-1  C17   0.020
 J9K  plan-1  C18   0.020
 J9K  plan-1  C19   0.020
 J9K  plan-1  C20   0.020
 J9K  plan-1  C21   0.020
 J9K  plan-1  N22   0.020
 J9K  plan-1  C23   0.020
 J9K  plan-1  H19   0.020
 J9K  plan-1  H20   0.020
 J9K  plan-1  H21   0.020
 J9K  plan-1  H23   0.020
 J9K  plan-2  C24   0.020
 J9K  plan-2  C25   0.020
 J9K  plan-2  C26   0.020
 J9K  plan-2  C27   0.020
 J9K  plan-2  C28   0.020
 J9K  plan-2  C29   0.020
 J9K  plan-2  C30   0.020
 J9K  plan-2  H26   0.020
 J9K  plan-2  H27   0.020
 J9K  plan-2  H28   0.020
 J9K  plan-2  H29   0.020
 J9K  plan-2  H30   0.020
 J9K  plan-3  C13   0.020
 J9K  plan-3  C14   0.020
 J9K  plan-3  O15   0.020
 J9K  plan-3  N16   0.020
 J9K  plan-3  C17   0.020
 J9K  plan-3  HN16  0.020
 J9K  plan-4  O05   0.020
 J9K  plan-4  C06   0.020
 J9K  plan-4  O07   0.020
 J9K  plan-4  N08   0.020

