# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 20:05:05 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: tert-butyl (2-{[(2R)-3-oxo-2-[(propan-2-yl)amino]-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}ethyl)carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)N[C@@H](CSCCNC(=O)OC(C)(C)C)C(=O)NCc1cccnc1
#
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
 D7Y  D7Y  'tert-butyl (2-{[(2R)-3-oxo-2-[(propan-2-yl)amino]-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}ethyl)carbamate'  ligand  59  27  .  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_D7Y
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
 D7Y  C15  C  CH3   0  -0.672  -7.3596  -1.1506   1.3578
 D7Y  C17  C  CH3   0  -0.671  -5.4952  -2.8529   1.3457
 D7Y  C21  C  CH2   0  -0.385   4.2575  -0.7876   1.4186
 D7Y  C22  C  CR6   0   0.027   4.0093  -1.9531   0.4966
 D7Y  C24  C  CR16  0  -0.321   4.5334  -3.2993  -1.4121
 D7Y  C02  C  CH1   0  -0.077   2.9114   4.1084   0.1253
 D7Y  C03  C  CH3   0  -0.676   3.5049   5.0934  -0.8692
 D7Y  C06  C  CH2   0  -0.541   0.8153   1.0669  -0.5962
 D7Y  C08  C  CH2   0  -0.556  -1.9118   0.7539  -0.8883
 D7Y  C09  C  CH2   0  -0.283  -3.2971   1.3669  -1.0655
 D7Y  O12  O  O     0  -0.519  -4.5722   0.0570   1.0621
 D7Y  C14  C  CT    0   0.189  -6.4403  -2.0099   0.4978
 D7Y  C16  C  CH3   0  -0.659  -7.2758  -2.9168  -0.3982
 D7Y  C18  C  C     0   0.554   3.1520   1.0099   0.1948
 D7Y  O19  O  O     0  -0.480   3.9826   0.9929  -0.7009
 D7Y  C23  C  CR16  0  -0.178   4.8296  -2.2224  -0.5895
 D7Y  C25  C  CR16  0  -0.073   3.4164  -4.0656  -1.1198
 D7Y  C27  C  CR16  0  -0.088   2.9167  -2.7918   0.6966
 D7Y  C01  C  CH3   0  -0.642   2.0460   4.8337   1.1476
 D7Y  N04  N  NH1   0  -0.576   2.1165   3.1202  -0.6011
 D7Y  C05  C  CH1   0  -0.220   1.8956   1.8860   0.1055
 D7Y  S07  S  S2    0  -0.017  -0.6773   2.0828  -0.7791
 D7Y  N10  N  NH1   0  -0.653  -4.3313   0.3676  -1.1683
 D7Y  C11  C  C     0   0.759  -4.8488  -0.2448  -0.0821
 D7Y  O13  O  O2    0  -0.504  -5.7024  -1.1987  -0.4538
 D7Y  N20  N  NH1   0  -0.623   3.2439   0.2374   1.2873
 D7Y  N26  N  N     0  -0.404   2.6193  -3.8212  -0.0843
 D7Y  H1   H  HCH3  0   0.247  -6.8113  -0.5182   2.0522
 D7Y  H2   H  HCH3  0   0.235  -7.9974  -0.5191   0.7372
 D7Y  H3   H  HCH3  0   0.234  -8.0100  -1.8020   1.9425
 D7Y  H4   H  HCH3  0   0.233  -6.0800  -3.5464   1.9516
 D7Y  H5   H  HCH3  0   0.234  -4.8290  -3.4452   0.7163
 D7Y  H6   H  HCH3  0   0.247  -4.8934  -2.2479   2.0196
 D7Y  H7   H  HCH2  0   0.281   4.2497  -1.1183   2.4567
 D7Y  H8   H  HCH2  0   0.267   5.2432  -0.3631   1.2249
 D7Y  H9   H  HCR6  0   0.270   5.1515  -3.5387  -2.2666
 D7Y  H10  H  HCH1  0   0.200   3.7495   3.6322   0.6589
 D7Y  H11  H  HCH3  0   0.232   4.0972   5.8510  -0.3560
 D7Y  H12  H  HCH3  0   0.230   4.1583   4.5898  -1.5845
 D7Y  H13  H  HCH3  0   0.222   2.7168   5.6017  -1.4284
 D7Y  H14  H  HCH2  0   0.271   1.1619   0.7327  -1.5768
 D7Y  H15  H  HCH2  0   0.275   0.5668   0.1804  -0.0099
 D7Y  H16  H  HCH2  0   0.264  -1.8789   0.1522   0.0220
 D7Y  H17  H  HCH2  0   0.262  -1.6844   0.1048  -1.7359
 D7Y  H18  H  HCH2  0   0.250  -3.5196   2.0390  -0.2361
 D7Y  H19  H  HCH2  0   0.261  -3.3248   1.9649  -1.9763
 D7Y  H20  H  HCH3  0   0.237  -7.9469  -2.3384  -1.0354
 D7Y  H21  H  HCH3  0   0.237  -6.6440  -3.5376  -1.0351
 D7Y  H22  H  HCH3  0   0.230  -7.8863  -3.5795   0.2149
 D7Y  H23  H  HCR6  0   0.266   5.6917  -1.5979  -0.7883
 D7Y  H24  H  HCR6  0   0.263   3.1541  -4.9123  -1.7447
 D7Y  H25  H  HCR6  0   0.258   2.2485  -2.6201   1.5363
 D7Y  H26  H  HCH3  0   0.217   1.2685   5.4134   0.6468
 D7Y  H27  H  HCH3  0   0.227   1.5553   4.1456   1.8372
 D7Y  H28  H  HCH3  0   0.221   2.6508   5.5162   1.7459
 D7Y  H29  H  HNH1  0   0.345   2.5670   2.9063  -1.4845
 D7Y  H31  H  HCH1  0   0.265   1.5381   2.1142   1.1142
 D7Y  H32  H  HNH1  0   0.399  -4.5456  -0.0000  -2.0811
 D7Y  H33  H  HNH1  0   0.407   2.5251   0.2894   1.9902

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
 D7Y  C17  C14  single    1.524  0.020  1.524
 D7Y  O12  C11  double    1.215  0.020  1.215
 D7Y  C15  C14  single    1.524  0.020  1.524
 D7Y  C14  O13  single    1.452  0.020  1.452
 D7Y  C14  C16  single    1.524  0.020  1.524
 D7Y  C11  O13  single    1.333  0.020  1.333
 D7Y  C11  N10  single    1.350  0.020  1.350
 D7Y  N10  C09  single    1.442  0.020  1.442
 D7Y  C09  C08  single    1.525  0.020  1.525
 D7Y  C25  C24  aromatic  1.386  0.020  1.386
 D7Y  C25  N26  aromatic  1.329  0.020  1.329
 D7Y  C24  C23  aromatic  1.387  0.020  1.387
 D7Y  C08  S07  single    1.817  0.020  1.817
 D7Y  N26  C27  aromatic  1.326  0.020  1.326
 D7Y  C23  C22  aromatic  1.387  0.020  1.387
 D7Y  S07  C06  single    1.815  0.020  1.815
 D7Y  C27  C22  aromatic  1.392  0.020  1.392
 D7Y  C22  C21  single    1.507  0.020  1.507
 D7Y  C06  C05  single    1.527  0.020  1.527
 D7Y  C05  N04  single    1.439  0.020  1.439
 D7Y  C05  C18  single    1.534  0.020  1.534
 D7Y  N04  C02  single    1.462  0.020  1.462
 D7Y  N20  C21  single    1.447  0.020  1.447
 D7Y  N20  C18  single    1.341  0.020  1.341
 D7Y  C18  O19  double    1.222  0.020  1.222
 D7Y  C03  C02  single    1.520  0.020  1.520
 D7Y  C02  C01  single    1.523  0.020  1.523
 D7Y  C15  H1   single    0.970  0.020  1.090
 D7Y  C15  H2   single    0.970  0.020  1.090
 D7Y  C15  H3   single    0.970  0.020  1.090
 D7Y  C17  H4   single    0.970  0.020  1.090
 D7Y  C17  H5   single    0.970  0.020  1.090
 D7Y  C17  H6   single    0.970  0.020  1.090
 D7Y  C21  H7   single    0.970  0.020  1.090
 D7Y  C21  H8   single    0.970  0.020  1.090
 D7Y  C24  H9   single    0.930  0.020  1.080
 D7Y  C02  H10  single    0.970  0.020  1.090
 D7Y  C03  H11  single    0.970  0.020  1.090
 D7Y  C03  H12  single    0.970  0.020  1.090
 D7Y  C03  H13  single    0.970  0.020  1.090
 D7Y  C06  H14  single    0.970  0.020  1.090
 D7Y  C06  H15  single    0.970  0.020  1.090
 D7Y  C08  H16  single    0.970  0.020  1.090
 D7Y  C08  H17  single    0.970  0.020  1.090
 D7Y  C09  H18  single    0.970  0.020  1.090
 D7Y  C09  H19  single    0.970  0.020  1.090
 D7Y  C16  H20  single    0.970  0.020  1.090
 D7Y  C16  H21  single    0.970  0.020  1.090
 D7Y  C16  H22  single    0.970  0.020  1.090
 D7Y  C23  H23  single    0.930  0.020  1.080
 D7Y  C25  H24  single    0.930  0.020  1.080
 D7Y  C27  H25  single    0.930  0.020  1.080
 D7Y  C01  H26  single    0.970  0.020  1.090
 D7Y  C01  H27  single    0.970  0.020  1.090
 D7Y  C01  H28  single    0.970  0.020  1.090
 D7Y  N04  H29  single    0.890  0.020  1.040
 D7Y  C05  H31  single    0.970  0.020  1.090
 D7Y  N10  H32  single    0.860  0.020  1.020
 D7Y  N20  H33  single    0.860  0.020  1.020

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
 D7Y  H3   C15  H2   107.58  3.000
 D7Y  H3   C15  H1   107.80  3.000
 D7Y  H2   C15  H1   108.75  3.000
 D7Y  H3   C15  C14  108.99  3.000
 D7Y  H2   C15  C14  110.97  3.000
 D7Y  H1   C15  C14  112.59  3.000
 D7Y  H6   C17  H5   108.76  3.000
 D7Y  H6   C17  H4   107.83  3.000
 D7Y  H5   C17  H4   107.61  3.000
 D7Y  H6   C17  C14  112.35  3.000
 D7Y  H5   C17  C14  110.97  3.000
 D7Y  H4   C17  C14  109.16  3.000
 D7Y  H8   C21  H7   107.08  3.000
 D7Y  H8   C21  N20  109.95  3.000
 D7Y  H7   C21  N20  107.24  3.000
 D7Y  H8   C21  C22  109.95  3.000
 D7Y  H7   C21  C22  110.31  3.000
 D7Y  N20  C21  C22  112.15  3.000
 D7Y  C27  C22  C23  117.37  3.000
 D7Y  C27  C22  C21  120.50  3.000
 D7Y  C23  C22  C21  122.13  3.000
 D7Y  H9   C24  C25  120.33  3.000
 D7Y  H9   C24  C23  121.22  3.000
 D7Y  C25  C24  C23  118.45  3.000
 D7Y  H10  C02  N04  111.24  3.000
 D7Y  H10  C02  C01  108.23  3.000
 D7Y  N04  C02  C01  110.28  3.000
 D7Y  H10  C02  C03  107.45  3.000
 D7Y  C01  C02  C03  110.63  3.000
 D7Y  N04  C02  C03  108.98  3.000
 D7Y  H13  C03  H12  108.13  3.000
 D7Y  H13  C03  H11  108.04  3.000
 D7Y  H12  C03  H11  107.69  3.000
 D7Y  H13  C03  C02  110.79  3.000
 D7Y  H12  C03  C02  111.30  3.000
 D7Y  H11  C03  C02  110.76  3.000
 D7Y  H15  C06  H14  107.81  3.000
 D7Y  H15  C06  S07  108.75  3.000
 D7Y  H14  C06  S07  109.98  3.000
 D7Y  H15  C06  C05  110.49  3.000
 D7Y  H14  C06  C05  110.63  3.000
 D7Y  S07  C06  C05  109.15  3.000
 D7Y  H17  C08  H16  108.27  3.000
 D7Y  H17  C08  S07  109.88  3.000
 D7Y  H16  C08  S07  109.42  3.000
 D7Y  H17  C08  C09  109.76  3.000
 D7Y  H16  C08  C09  110.23  3.000
 D7Y  S07  C08  C09  109.28  3.000
 D7Y  H19  C09  H18  106.99  3.000
 D7Y  H19  C09  N10  107.60  3.000
 D7Y  H18  C09  N10  109.58  3.000
 D7Y  H19  C09  C08  109.92  3.000
 D7Y  H18  C09  C08  110.16  3.000
 D7Y  N10  C09  C08  112.41  3.000
 D7Y  O13  C14  C16  103.05  3.000
 D7Y  C16  C14  C17  109.75  3.000
 D7Y  O13  C14  C17  111.01  3.000
 D7Y  C16  C14  C15  109.66  3.000
 D7Y  O13  C14  C15  111.18  3.000
 D7Y  C17  C14  C15  111.83  3.000
 D7Y  H22  C16  H21  107.86  3.000
 D7Y  H22  C16  H20  107.84  3.000
 D7Y  H21  C16  H20  108.47  3.000
 D7Y  H22  C16  C14  109.76  3.000
 D7Y  H21  C16  C14  111.36  3.000
 D7Y  H20  C16  C14  111.41  3.000
 D7Y  N20  C18  C05  115.62  3.000
 D7Y  N20  C18  O19  122.86  3.000
 D7Y  C05  C18  O19  121.47  3.000
 D7Y  H23  C23  C24  120.59  3.000
 D7Y  H23  C23  C22  120.16  3.000
 D7Y  C24  C23  C22  119.25  3.000
 D7Y  H24  C25  N26  116.57  3.000
 D7Y  H24  C25  C24  120.34  3.000
 D7Y  N26  C25  C24  123.08  3.000
 D7Y  H25  C27  N26  116.09  3.000
 D7Y  H25  C27  C22  119.90  3.000
 D7Y  N26  C27  C22  124.00  3.000
 D7Y  H28  C01  H27  107.30  3.000
 D7Y  H28  C01  H26  108.33  3.000
 D7Y  H27  C01  H26  107.73  3.000
 D7Y  H28  C01  C02  110.56  3.000
 D7Y  H27  C01  C02  112.30  3.000
 D7Y  H26  C01  C02  110.46  3.000
 D7Y  H29  N04  C05  108.36  3.000
 D7Y  H29  N04  C02  109.50  3.000
 D7Y  C05  N04  C02  114.79  3.000
 D7Y  H31  C05  N04  108.90  3.000
 D7Y  H31  C05  C18  109.45  3.000
 D7Y  N04  C05  C18  113.11  3.000
 D7Y  H31  C05  C06  107.72  3.000
 D7Y  C18  C05  C06  107.45  3.000
 D7Y  N04  C05  C06  110.06  3.000
 D7Y  C08  S07  C06   98.94  3.000
 D7Y  H32  N10  C11  118.82  3.000
 D7Y  H32  N10  C09  118.05  3.000
 D7Y  C11  N10  C09  122.14  3.000
 D7Y  O13  C11  N10  110.22  3.000
 D7Y  N10  C11  O12  123.89  3.000
 D7Y  O13  C11  O12  125.88  3.000
 D7Y  C11  O13  C14  122.85  3.000
 D7Y  H33  N20  C18  119.34  3.000
 D7Y  H33  N20  C21  118.25  3.000
 D7Y  C18  N20  C21  121.99  3.000
 D7Y  C27  N26  C25  117.84  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
 D7Y  CONST_01  C25  C24  C23  C22     0.00   0.0  0
 D7Y  CONST_02  C25  N26  C27  C22     0.00   0.0  0
 D7Y  CONST_03  C27  N26  C25  C24     0.00   0.0  0
 D7Y  CONST_04  C27  C22  C23  C24     0.00   0.0  0
 D7Y  CONST_05  N26  C25  C24  C23     0.00   0.0  0
 D7Y  CONST_06  N26  C27  C22  C23     0.00   0.0  0
 D7Y  CONST_07  C24  C23  C22  C21   180.00   0.0  0
 D7Y  CONST_08  N26  C27  C22  C21   180.00   0.0  0
 D7Y  CONST_09  H9   C24  C23  C22   180.00   0.0  0
 D7Y  CONST_10  H24  C25  C24  C23   180.00   0.0  0
 D7Y  CONST_11  H25  C27  C22  C23   180.00   0.0  0
 D7Y  CONST_12  H23  C23  C24  C25   180.00   0.0  0
 D7Y  CONST_13  C05  C18  N20  C21   180.00   0.0  0
 D7Y  CONST_14  O19  C18  N20  C21     0.00   0.0  0
 D7Y  CONST_15  H33  N20  C18  O19   180.00   0.0  0
 D7Y  Var_01    N20  C21  C22  C23   110.91  30.0  2
 D7Y  Var_02    C18  N20  C21  C22   -70.37  30.0  2
 D7Y  Var_03    C05  N04  C02  C03   158.78  30.0  1
 D7Y  Var_04    C09  C08  S07  C06  -179.45  30.0  2
 D7Y  Var_05    C11  N10  C09  C08    80.40  30.0  2
 D7Y  Var_06    C05  C06  S07  C08  -155.60  30.0  3
 D7Y  Var_07    O12  C11  N10  C09     5.89  30.0  2
 D7Y  Var_08    N10  C11  O13  C14  -178.55  30.0  3
 D7Y  Var_09    N10  C09  C08  S07   179.64  30.0  2
 D7Y  Var_10    H4   C17  C14  C15    62.83  30.0  3
 D7Y  Var_11    H20  C16  C14  C15    58.12  30.0  3
 D7Y  Var_12    H1   C15  C14  C17    55.20  30.0  3
 D7Y  Var_13    H26  C01  C02  C03    56.08  30.0  3
 D7Y  Var_14    H11  C03  C02  C01    58.05  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
 D7Y  chir_01  C05  C06  N04  C18  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
 D7Y  plan-1  C21  0.020
 D7Y  plan-1  C22  0.020
 D7Y  plan-1  C24  0.020
 D7Y  plan-1  C23  0.020
 D7Y  plan-1  C25  0.020
 D7Y  plan-1  C27  0.020
 D7Y  plan-1  N26  0.020
 D7Y  plan-1  H9   0.020
 D7Y  plan-1  H23  0.020
 D7Y  plan-1  H24  0.020
 D7Y  plan-1  H25  0.020
 D7Y  plan-2  C21  0.020
 D7Y  plan-2  C18  0.020
 D7Y  plan-2  O19  0.020
 D7Y  plan-2  C05  0.020
 D7Y  plan-2  N20  0.020
 D7Y  plan-2  H33  0.020
 D7Y  plan-3  O12  0.020
 D7Y  plan-3  N10  0.020
 D7Y  plan-3  C11  0.020
 D7Y  plan-3  O13  0.020

