# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 16:52:19 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: tert-butyl (2-{[(2R)-2-(cyclopentylamino)-3-oxo-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}ethyl)carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)OC(=O)NCCSC[C@H](NC1CCCC1)C(=O)NCc2cccnc2
#
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
 D7M  D7M  'tert-butyl (2-{[(2R)-2-(cyclopentylamino)-3-oxo-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}ethyl)carbamate'  ligand  63  29  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D7M
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
 D7M  C20  C  C     0   0.555  -3.2068  -0.5679  -0.5805
 D7M  C10  C  CH2   0  -0.553   1.8302  -0.2484   0.7709
 D7M  C12  C  CH2   0  -0.541  -0.7781  -0.5897  -0.0894
 D7M  C13  C  CH1   0  -0.216  -2.0813  -1.3629   0.0950
 D7M  C15  C  CH1   0  -0.113  -3.0003  -3.6302  -0.1098
 D7M  C16  C  CH2   0  -0.459  -2.7468  -4.9303  -0.8682
 D7M  C17  C  CH2   0  -0.434  -1.5985  -5.6040  -0.1025
 D7M  C18  C  CH2   0  -0.432  -1.6915  -5.0579   1.3404
 D7M  C19  C  CH2   0  -0.441  -2.8871  -4.0949   1.3415
 D7M  C01  C  CH3   0  -0.671   6.4663   2.2564  -1.2657
 D7M  C02  C  CT    0   0.191   6.9229   1.8086   0.1177
 D7M  C03  C  CH3   0  -0.673   7.9617   0.6962   0.0440
 D7M  C04  C  CH3   0  -0.659   7.5011   2.9985   0.8754
 D7M  O05  O  O2    0  -0.504   5.7941   1.4116   0.9405
 D7M  C06  C  C     0   0.758   5.0132   0.3746   0.6369
 D7M  O07  O  O     0  -0.519   5.0977  -0.3079  -0.3646
 D7M  N08  N  NH1   0  -0.652   4.1082   0.1682   1.6173
 D7M  C09  C  CH2   0  -0.285   3.0520  -0.8053   1.4959
 D7M  N14  N  NH1   0  -0.568  -1.9331  -2.6933  -0.4277
 D7M  O21  O  O     0  -0.493  -3.4104  -0.6581  -1.7830
 D7M  N22  N  NH1   0  -0.615  -3.9123   0.2280   0.2357
 D7M  C23  C  CH2   0  -0.401  -4.9386   1.1436  -0.2186
 D7M  C24  C  CR6   0   0.036  -4.3887   2.5050  -0.5532
 D7M  C25  C  CR16  0  -0.181  -3.7530   2.7653  -1.7630
 D7M  C26  C  CR16  0  -0.319  -3.2412   4.0308  -1.9974
 D7M  C27  C  CR16  0  -0.069  -3.3838   4.9971  -1.0115
 D7M  N28  N  N     0  -0.402  -3.9919   4.7679   0.1457
 D7M  C29  C  CR16  0  -0.097  -4.4782   3.5509   0.3586
 D7M  H1   H  HCH2  0   0.261   1.4226   0.6003   1.3239
 D7M  H2   H  HCH2  0   0.263   2.1121   0.0960  -0.2259
 D7M  H3   H  HCH2  0   0.270  -0.5809  -0.4110  -1.1491
 D7M  H4   H  HCH2  0   0.275  -0.8367   0.3787   0.4113
 D7M  H5   H  HCH1  0   0.263  -2.2787  -1.4303   1.1685
 D7M  H6   H  HCH1  0   0.218  -4.0008  -3.2281  -0.3316
 D7M  H7   H  HCH2  0   0.230  -3.6504  -5.5432  -0.8250
 D7M  H8   H  HCH2  0   0.233  -2.5251  -4.7680  -1.9260
 D7M  H9   H  HCH2  0   0.222  -1.6784  -6.6912  -0.1401
 D7M  H10  H  HCH2  0   0.224  -0.6382  -5.3425  -0.5475
 D7M  H11  H  HCH2  0   0.221  -1.8190  -5.8535   2.0754
 D7M  H12  H  HCH2  0   0.226  -0.7790  -4.5241   1.6063
 D7M  H13  H  HCH2  0   0.233  -2.7717  -3.2787   2.0572
 D7M  H14  H  HCH2  0   0.224  -3.8086  -4.6159   1.6138
 D7M  H15  H  HCH3  0   0.246   6.0859   1.4337  -1.8663
 D7M  H16  H  HCH3  0   0.234   5.6937   3.0230  -1.1908
 D7M  H17  H  HCH3  0   0.233   7.3128   2.6935  -1.7970
 D7M  H18  H  HCH3  0   0.234   8.8624   1.0775  -0.4387
 D7M  H19  H  HCH3  0   0.235   8.2417   0.3577   1.0429
 D7M  H20  H  HCH3  0   0.246   7.6174  -0.1607  -0.5307
 D7M  H21  H  HCH3  0   0.237   6.7808   3.8153   0.9447
 D7M  H22  H  HCH3  0   0.237   7.8047   2.7183   1.8852
 D7M  H23  H  HCH3  0   0.230   8.3815   3.3718   0.3527
 D7M  H24  H  HNH1  0   0.399   4.0625   0.8223   2.3818
 D7M  H25  H  HCH2  0   0.260   2.7732  -1.1244   2.5004
 D7M  H26  H  HCH2  0   0.251   3.4312  -1.6841   0.9743
 D7M  H27  H  HNH1  0   0.343  -1.8030  -2.6456  -1.4318
 D7M  H29  H  HNH1  0   0.406  -3.6593   0.2656   1.2101
 D7M  H30  H  HCH2  0   0.272  -5.4357   0.7101  -1.0857
 D7M  H31  H  HCH2  0   0.277  -5.6841   1.2276   0.5719
 D7M  H32  H  HCR6  0   0.271  -3.6637   1.9882  -2.5114
 D7M  H33  H  HCR6  0   0.271  -2.7429   4.2707  -2.9267
 D7M  H34  H  HCR6  0   0.264  -2.9937   5.9971  -1.1661
 D7M  H35  H  HCR6  0   0.259  -4.9758   3.3923   1.3112
 D7M  S11  S  S2    0  -0.014   0.5764  -1.5560   0.6370

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
 D7M  C04  C02  single    1.525  0.020  1.525
 D7M  O05  C02  single    1.452  0.020  1.452
 D7M  O05  C06  single    1.333  0.020  1.333
 D7M  C02  C01  single    1.524  0.020  1.524
 D7M  C02  C03  single    1.524  0.020  1.524
 D7M  N08  C06  single    1.350  0.020  1.350
 D7M  N08  C09  single    1.442  0.020  1.442
 D7M  C06  O07  double    1.215  0.020  1.215
 D7M  C09  C10  single    1.526  0.020  1.526
 D7M  C10  S11  single    1.817  0.020  1.817
 D7M  C26  C27  aromatic  1.388  0.020  1.388
 D7M  C26  C25  aromatic  1.385  0.020  1.385
 D7M  C27  N28  aromatic  1.327  0.020  1.327
 D7M  S11  C12  single    1.815  0.020  1.815
 D7M  N28  C29  aromatic  1.328  0.020  1.328
 D7M  C25  C24  aromatic  1.391  0.020  1.391
 D7M  C12  C13  single    1.526  0.020  1.526
 D7M  C29  C24  aromatic  1.390  0.020  1.390
 D7M  C24  C23  single    1.506  0.020  1.506
 D7M  C13  C20  single    1.535  0.020  1.535
 D7M  C13  N14  single    1.437  0.020  1.437
 D7M  O21  C20  double    1.223  0.020  1.223
 D7M  C20  N22  single    1.341  0.020  1.341
 D7M  N22  C23  single    1.448  0.020  1.448
 D7M  N14  C15  single    1.455  0.020  1.455
 D7M  C15  C16  single    1.526  0.020  1.526
 D7M  C15  C19  single    1.528  0.020  1.528
 D7M  C16  C17  single    1.536  0.020  1.536
 D7M  C17  C18  single    1.546  0.020  1.546
 D7M  C19  C18  single    1.535  0.020  1.535
 D7M  C10  H1   single    0.970  0.020  1.090
 D7M  C10  H2   single    0.970  0.020  1.090
 D7M  C12  H3   single    0.970  0.020  1.090
 D7M  C12  H4   single    0.970  0.020  1.090
 D7M  C13  H5   single    0.970  0.020  1.090
 D7M  C15  H6   single    0.970  0.020  1.090
 D7M  C16  H7   single    0.970  0.020  1.090
 D7M  C16  H8   single    0.970  0.020  1.090
 D7M  C17  H9   single    0.970  0.020  1.090
 D7M  C17  H10  single    0.970  0.020  1.090
 D7M  C18  H11  single    0.970  0.020  1.090
 D7M  C18  H12  single    0.970  0.020  1.090
 D7M  C19  H13  single    0.970  0.020  1.090
 D7M  C19  H14  single    0.970  0.020  1.090
 D7M  C01  H15  single    0.970  0.020  1.090
 D7M  C01  H16  single    0.970  0.020  1.090
 D7M  C01  H17  single    0.970  0.020  1.090
 D7M  C03  H18  single    0.970  0.020  1.090
 D7M  C03  H19  single    0.970  0.020  1.090
 D7M  C03  H20  single    0.970  0.020  1.090
 D7M  C04  H21  single    0.970  0.020  1.090
 D7M  C04  H22  single    0.970  0.020  1.090
 D7M  C04  H23  single    0.970  0.020  1.090
 D7M  N08  H24  single    0.860  0.020  1.020
 D7M  C09  H25  single    0.970  0.020  1.090
 D7M  C09  H26  single    0.970  0.020  1.090
 D7M  N14  H27  single    0.890  0.020  1.040
 D7M  N22  H29  single    0.860  0.020  1.020
 D7M  C23  H30  single    0.970  0.020  1.090
 D7M  C23  H31  single    0.970  0.020  1.090
 D7M  C25  H32  single    0.930  0.020  1.080
 D7M  C26  H33  single    0.930  0.020  1.080
 D7M  C27  H34  single    0.930  0.020  1.080
 D7M  C29  H35  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
 D7M  N22  C20  O21  123.70  3.000
 D7M  N22  C20  C13  115.18  3.000
 D7M  O21  C20  C13  121.11  3.000
 D7M  H2   C10  H1   108.28  3.000
 D7M  H2   C10  S11  109.75  3.000
 D7M  H1   C10  S11  109.82  3.000
 D7M  H2   C10  C09  110.02  3.000
 D7M  H1   C10  C09  110.00  3.000
 D7M  S11  C10  C09  108.96  3.000
 D7M  H4   C12  H3   108.03  3.000
 D7M  H4   C12  S11  109.19  3.000
 D7M  H3   C12  S11  109.90  3.000
 D7M  H4   C12  C13  110.37  3.000
 D7M  H3   C12  C13  110.73  3.000
 D7M  S11  C12  C13  108.60  3.000
 D7M  H5   C13  N14  108.58  3.000
 D7M  H5   C13  C12  107.69  3.000
 D7M  N14  C13  C12  109.69  3.000
 D7M  H5   C13  C20  109.37  3.000
 D7M  N14  C13  C20  113.27  3.000
 D7M  C12  C13  C20  108.09  3.000
 D7M  H6   C15  N14  112.79  3.000
 D7M  H6   C15  C19  111.70  3.000
 D7M  N14  C15  C19  110.42  3.000
 D7M  H6   C15  C16  111.22  3.000
 D7M  C19  C15  C16  101.57  3.000
 D7M  N14  C15  C16  108.54  3.000
 D7M  H8   C16  H7   106.82  3.000
 D7M  H8   C16  C17  113.33  3.000
 D7M  H7   C16  C17  110.64  3.000
 D7M  H8   C16  C15  112.83  3.000
 D7M  H7   C16  C15  108.71  3.000
 D7M  C17  C16  C15  104.48  3.000
 D7M  H10  C17  H9   106.84  3.000
 D7M  H10  C17  C18  110.44  3.000
 D7M  H9   C17  C18  112.33  3.000
 D7M  H10  C17  C16  110.48  3.000
 D7M  H9   C17  C16  111.42  3.000
 D7M  C18  C17  C16  105.39  3.000
 D7M  H12  C18  H11  106.90  3.000
 D7M  H12  C18  C19  110.16  3.000
 D7M  H11  C18  C19  111.47  3.000
 D7M  H12  C18  C17  110.51  3.000
 D7M  H11  C18  C17  112.23  3.000
 D7M  C19  C18  C17  105.62  3.000
 D7M  H14  C19  H13  106.39  3.000
 D7M  H14  C19  C18  110.97  3.000
 D7M  H13  C19  C18  112.78  3.000
 D7M  H14  C19  C15  108.61  3.000
 D7M  H13  C19  C15  113.77  3.000
 D7M  C18  C19  C15  104.35  3.000
 D7M  H17  C01  H16  107.54  3.000
 D7M  H17  C01  H15  107.81  3.000
 D7M  H16  C01  H15  108.77  3.000
 D7M  H17  C01  C02  109.11  3.000
 D7M  H16  C01  C02  110.87  3.000
 D7M  H15  C01  C02  112.57  3.000
 D7M  O05  C02  C04  103.10  3.000
 D7M  O05  C02  C03  110.96  3.000
 D7M  C04  C02  C03  109.59  3.000
 D7M  C03  C02  C01  112.01  3.000
 D7M  O05  C02  C01  111.21  3.000
 D7M  C04  C02  C01  109.60  3.000
 D7M  H20  C03  H19  108.69  3.000
 D7M  H20  C03  H18  107.64  3.000
 D7M  H19  C03  H18  107.56  3.000
 D7M  H20  C03  C02  112.64  3.000
 D7M  H19  C03  C02  110.92  3.000
 D7M  H18  C03  C02  109.22  3.000
 D7M  H23  C04  H22  107.88  3.000
 D7M  H23  C04  H21  107.89  3.000
 D7M  H22  C04  H21  108.49  3.000
 D7M  H23  C04  C02  109.60  3.000
 D7M  H22  C04  C02  111.41  3.000
 D7M  H21  C04  C02  111.44  3.000
 D7M  C06  O05  C02  122.61  3.000
 D7M  N08  C06  O07  124.01  3.000
 D7M  O07  C06  O05  125.73  3.000
 D7M  N08  C06  O05  110.26  3.000
 D7M  H24  N08  C09  117.98  3.000
 D7M  H24  N08  C06  118.84  3.000
 D7M  C09  N08  C06  122.23  3.000
 D7M  H26  C09  H25  107.09  3.000
 D7M  H26  C09  N08  109.26  3.000
 D7M  H25  C09  N08  107.90  3.000
 D7M  H26  C09  C10  110.21  3.000
 D7M  H25  C09  C10  109.87  3.000
 D7M  N08  C09  C10  112.35  3.000
 D7M  H27  N14  C15  109.93  3.000
 D7M  H27  N14  C13  109.27  3.000
 D7M  C15  N14  C13  116.16  3.000
 D7M  H29  N22  C23  117.24  3.000
 D7M  H29  N22  C20  118.61  3.000
 D7M  C23  N22  C20  123.86  3.000
 D7M  H31  C23  H30  107.21  3.000
 D7M  H31  C23  C24  109.95  3.000
 D7M  H30  C23  C24  110.46  3.000
 D7M  H31  C23  N22  107.81  3.000
 D7M  H30  C23  N22  108.75  3.000
 D7M  C24  C23  N22  112.49  3.000
 D7M  C29  C24  C25  117.32  3.000
 D7M  C29  C24  C23  120.72  3.000
 D7M  C25  C24  C23  121.95  3.000
 D7M  H32  C25  C26  120.55  3.000
 D7M  H32  C25  C24  120.31  3.000
 D7M  C26  C25  C24  119.14  3.000
 D7M  H33  C26  C27  120.22  3.000
 D7M  H33  C26  C25  121.23  3.000
 D7M  C27  C26  C25  118.55  3.000
 D7M  H34  C27  N28  116.63  3.000
 D7M  H34  C27  C26  120.26  3.000
 D7M  N28  C27  C26  123.11  3.000
 D7M  C29  N28  C27  117.77  3.000
 D7M  H35  C29  N28  116.24  3.000
 D7M  H35  C29  C24  119.65  3.000
 D7M  N28  C29  C24  124.11  3.000
 D7M  C12  S11  C10   99.29  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
 D7M  CONST_01  C27  C26  C25  C24     0.00   0.0  0
 D7M  CONST_02  C27  N28  C29  C24     0.00   0.0  0
 D7M  CONST_03  N28  C27  C26  C25     0.00   0.0  0
 D7M  CONST_04  N28  C29  C24  C25     0.00   0.0  0
 D7M  CONST_05  C29  N28  C27  C26     0.00   0.0  0
 D7M  CONST_06  C29  C24  C25  C26     0.00   0.0  0
 D7M  CONST_07  C26  C25  C24  C23   180.00   0.0  0
 D7M  CONST_08  N28  C29  C24  C23   180.00   0.0  0
 D7M  CONST_09  H33  C26  C25  C24   180.00   0.0  0
 D7M  CONST_10  H34  C27  C26  C25   180.00   0.0  0
 D7M  CONST_11  H35  C29  C24  C25   180.00   0.0  0
 D7M  CONST_12  H32  C25  C26  C27   180.00   0.0  0
 D7M  CONST_13  C23  N22  C20  C13   180.00   0.0  0
 D7M  CONST_14  C23  N22  C20  O21     0.00   0.0  0
 D7M  CONST_15  H29  N22  C20  C13     0.00   0.0  0
 D7M  Var_01    C18  C17  C16  C15    25.69  30.0  1
 D7M  Var_02    C17  C18  C19  C15   -25.61  30.0  1
 D7M  Var_03    C19  C18  C17  C16    -0.02  30.0  1
 D7M  Var_04    C25  C24  C23  N22    80.07  30.0  2
 D7M  Var_05    C24  C23  N22  C20   -89.72  30.0  3
 D7M  Var_06    C06  N08  C09  C10   -85.10  30.0  1
 D7M  Var_07    C13  C12  S11  C10  -162.80  30.0  3
 D7M  Var_08    C09  C10  S11  C12   174.65  30.0  1
 D7M  Var_09    N08  C06  O05  C02   175.39  30.0  3
 D7M  Var_10    C09  N08  C06  O05   173.83  30.0  2
 D7M  Var_11    S11  C10  C09  N08   178.76  30.0  3
 D7M  Var_12    H21  C04  C02  C01    56.61  30.0  3
 D7M  Var_13    H18  C03  C02  C01    64.24  30.0  3
 D7M  Var_14    H15  C01  C02  C03    55.54  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
 D7M  chir_01  C13  C12  C20  N14  negativ
 D7M  chir_02  C15  N14  C16  C19  negativ

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
 D7M  plan-1  C23  0.020
 D7M  plan-1  C24  0.020
 D7M  plan-1  C25  0.020
 D7M  plan-1  C26  0.020
 D7M  plan-1  C27  0.020
 D7M  plan-1  N28  0.020
 D7M  plan-1  C29  0.020
 D7M  plan-1  H32  0.020
 D7M  plan-1  H33  0.020
 D7M  plan-1  H34  0.020
 D7M  plan-1  H35  0.020
 D7M  plan-2  C20  0.020
 D7M  plan-2  C13  0.020
 D7M  plan-2  O21  0.020
 D7M  plan-2  N22  0.020
 D7M  plan-2  C23  0.020
 D7M  plan-2  H29  0.020
 D7M  plan-3  O05  0.020
 D7M  plan-3  C06  0.020
 D7M  plan-3  O07  0.020
 D7M  plan-3  N08  0.020

