# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 21:56:19 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: tert-butyl (2-{[(2S)-3-oxo-2-(phenylamino)-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](Nc1ccccc1)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
 80K  80K  'tert-butyl (2-{[(2S)-3-oxo-2-(phenylamino)-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}ethyl)carbamate'  ligand  60  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_80K
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
 80K  C01  C  CH3   0  -0.670  -8.5355   0.3578  -0.0442
 80K  C02  C  CT    0   0.190  -7.5096   1.4826  -0.1129
 80K  C03  C  CH3   0  -0.671  -7.0365   1.7261  -1.5411
 80K  C04  C  CH3   0  -0.659  -8.1105   2.7631   0.4547
 80K  C06  C  C     0   0.758  -5.5694   0.1894   0.6286
 80K  C09  C  CH2   0  -0.284  -3.5383  -0.7408   1.6237
 80K  C10  C  CH2   0  -0.552  -2.3995  -0.3368   0.6929
 80K  C12  C  CH2   0  -0.555   0.1430  -0.7778  -0.2949
 80K  C13  C  CH1   0  -0.235   1.5410  -1.3082   0.0006
 80K  C15  C  CR6   0   0.367   2.6687  -3.4794   0.2256
 80K  C16  C  CR16  0  -0.335   3.7296  -2.9637   0.9776
 80K  C17  C  CR16  0  -0.243   4.8164  -3.7663   1.3012
 80K  C18  C  CR16  0  -0.291   4.8816  -5.0871   0.8852
 80K  C19  C  CR16  0  -0.244   3.8317  -5.6015   0.1309
 80K  C20  C  CR16  0  -0.349   2.7420  -4.8146  -0.1953
 80K  C21  C  C     0   0.560   2.5202  -0.6688  -0.9963
 80K  C24  C  CH2   0  -0.325   4.0541   1.2060  -1.3687
 80K  C25  C  CR6   0  -0.036   4.2197   2.5874  -0.8055
 80K  C26  C  CR16  0  -0.179   5.3545   2.9615  -0.0997
 80K  C27  C  CR16  0  -0.318   5.4407   4.2494   0.4081
 80K  C28  C  CR16  0  -0.068   4.3810   5.1158   0.1922
 80K  C30  C  CR16  0  -0.074   3.2167   3.5407  -0.9619
 80K  N08  N  NH1   0  -0.652  -4.6264   0.2036   1.5958
 80K  N14  N  NH1   0  -0.672   1.5405  -2.7407  -0.0792
 80K  N23  N  NH1   0  -0.631   3.1255   0.4423  -0.5571
 80K  N29  N  N     0  -0.401   3.2863   4.7730  -0.4801
 80K  O05  O  O2    0  -0.504  -6.3899   1.2282   0.7748
 80K  O07  O  O     0  -0.518  -5.6469  -0.6654  -0.2312
 80K  O22  O  O     0  -0.481   2.6838  -1.1354  -2.1115
 80K  S11  S  S2    0  -0.020  -1.0470  -1.5393   0.8464
 80K  H1   H  HCH3  0   0.235  -8.8150   0.1428   0.9883
 80K  H2   H  HCH3  0   0.234  -9.4383   0.6691  -0.5716
 80K  H3   H  HCH3  0   0.245  -8.1801  -0.5595  -0.5076
 80K  H4   H  HCH3  0   0.234  -7.8747   2.0928  -2.1354
 80K  H5   H  HCH3  0   0.235  -6.2539   2.4862  -1.5718
 80K  H6   H  HCH3  0   0.246  -6.6631   0.8220  -2.0164
 80K  H7   H  HCH3  0   0.237  -8.4414   2.6258   1.4853
 80K  H8   H  HCH3  0   0.237  -7.3927   3.5844   0.4304
 80K  H9   H  HCH3  0   0.230  -8.9771   3.0580  -0.1367
 80K  H10  H  HCH2  0   0.253  -3.9088  -1.7318   1.3606
 80K  H11  H  HCH2  0   0.262  -3.1756  -0.7969   2.6503
 80K  H12  H  HCH2  0   0.269  -2.7498  -0.3061  -0.3402
 80K  H13  H  HCH2  0   0.266  -2.0304   0.6549   0.9615
 80K  H14  H  HCH2  0   0.290   0.1256   0.3036  -0.1528
 80K  H15  H  HCH2  0   0.281  -0.1407  -0.9876  -1.3288
 80K  H16  H  HCH1  0   0.277   1.7968  -1.0037   1.0207
 80K  H17  H  HCR6  0   0.257   3.7226  -1.9391   1.3250
 80K  H18  H  HCR6  0   0.253   5.6231  -3.3413   1.8850
 80K  H19  H  HCR6  0   0.247   5.7318  -5.7053   1.1406
 80K  H20  H  HCR6  0   0.253   3.8612  -6.6288  -0.2099
 80K  H21  H  HCR6  0   0.257   1.9319  -5.2332  -0.7814
 80K  H22  H  HCH2  0   0.268   3.6675   1.2587  -2.3875
 80K  H23  H  HCH2  0   0.263   5.0243   0.7045  -1.4205
 80K  H24  H  HCR6  0   0.274   6.1620   2.2548   0.0497
 80K  H25  H  HCR6  0   0.274   6.3105   4.5768   0.9606
 80K  H26  H  HCR6  0   0.267   4.4170   6.1293   0.5755
 80K  H27  H  HCR6  0   0.263   2.3149   3.2863  -1.5115
 80K  H28  H  HNH1  0   0.400  -4.5819   0.9955   2.2163
 80K  H29  H  HNH1  0   0.382   1.0095  -3.1089  -0.8547
 80K  H30  H  HNH1  0   0.409   3.0134   0.7107   0.4079

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
 80K  O07  C06  double    1.215  0.020  1.215
 80K  C28  C27  aromatic  1.386  0.020  1.386
 80K  C28  N29  aromatic  1.330  0.020  1.330
 80K  C01  C02  single    1.524  0.020  1.524
 80K  C27  C26  aromatic  1.387  0.020  1.387
 80K  C04  C02  single    1.524  0.020  1.524
 80K  N29  C30  aromatic  1.325  0.020  1.325
 80K  C06  O05  single    1.332  0.020  1.332
 80K  C06  N08  single    1.351  0.020  1.351
 80K  C02  O05  single    1.451  0.020  1.451
 80K  C02  C03  single    1.524  0.020  1.524
 80K  C26  C25  aromatic  1.388  0.020  1.388
 80K  N08  C09  single    1.441  0.020  1.441
 80K  C30  C25  aromatic  1.393  0.020  1.393
 80K  C25  C24  single    1.501  0.020  1.501
 80K  C09  C10  single    1.525  0.020  1.525
 80K  C12  S11  single    1.816  0.020  1.816
 80K  C12  C13  single    1.524  0.020  1.524
 80K  N14  C13  single    1.435  0.020  1.435
 80K  N14  C15  single    1.383  0.020  1.383
 80K  C24  N23  single    1.451  0.020  1.451
 80K  S11  C10  single    1.816  0.020  1.816
 80K  N23  C21  single    1.339  0.020  1.339
 80K  C13  C21  single    1.537  0.020  1.537
 80K  C21  O22  double    1.220  0.020  1.220
 80K  C16  C15  aromatic  1.399  0.020  1.399
 80K  C16  C17  aromatic  1.389  0.020  1.389
 80K  C15  C20  aromatic  1.402  0.020  1.402
 80K  C17  C18  aromatic  1.386  0.020  1.386
 80K  C20  C19  aromatic  1.383  0.020  1.383
 80K  C18  C19  aromatic  1.391  0.020  1.391
 80K  C01  H1   single    0.970  0.020  1.090
 80K  C01  H2   single    0.970  0.020  1.090
 80K  C01  H3   single    0.970  0.020  1.090
 80K  C03  H4   single    0.970  0.020  1.090
 80K  C03  H5   single    0.970  0.020  1.090
 80K  C03  H6   single    0.970  0.020  1.090
 80K  C04  H7   single    0.970  0.020  1.090
 80K  C04  H8   single    0.970  0.020  1.090
 80K  C04  H9   single    0.970  0.020  1.090
 80K  C09  H10  single    0.970  0.020  1.090
 80K  C09  H11  single    0.970  0.020  1.090
 80K  C10  H12  single    0.970  0.020  1.090
 80K  C10  H13  single    0.970  0.020  1.090
 80K  C12  H14  single    0.970  0.020  1.090
 80K  C12  H15  single    0.970  0.020  1.090
 80K  C13  H16  single    0.970  0.020  1.090
 80K  C16  H17  single    0.930  0.020  1.080
 80K  C17  H18  single    0.930  0.020  1.080
 80K  C18  H19  single    0.930  0.020  1.080
 80K  C19  H20  single    0.930  0.020  1.080
 80K  C20  H21  single    0.930  0.020  1.080
 80K  C24  H22  single    0.970  0.020  1.090
 80K  C24  H23  single    0.970  0.020  1.090
 80K  C26  H24  single    0.930  0.020  1.080
 80K  C27  H25  single    0.930  0.020  1.080
 80K  C28  H26  single    0.930  0.020  1.080
 80K  C30  H27  single    0.930  0.020  1.080
 80K  N08  H28  single    0.860  0.020  1.020
 80K  N14  H29  single    0.890  0.020  1.040
 80K  N23  H30  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
 80K  H3   C01  H2   107.77  3.000
 80K  H3   C01  H1   108.71  3.000
 80K  H2   C01  H1   107.56  3.000
 80K  H3   C01  C02  112.54  3.000
 80K  H2   C01  C02  108.95  3.000
 80K  H1   C01  C02  111.13  3.000
 80K  O05  C02  C04  102.92  3.000
 80K  O05  C02  C03  111.20  3.000
 80K  C04  C02  C03  109.70  3.000
 80K  C03  C02  C01  111.66  3.000
 80K  O05  C02  C01  111.25  3.000
 80K  C04  C02  C01  109.75  3.000
 80K  H6   C03  H5   108.69  3.000
 80K  H6   C03  H4   107.76  3.000
 80K  H5   C03  H4   107.55  3.000
 80K  H6   C03  C02  112.54  3.000
 80K  H5   C03  C02  111.12  3.000
 80K  H4   C03  C02  109.00  3.000
 80K  H9   C04  H8   107.90  3.000
 80K  H9   C04  H7   107.78  3.000
 80K  H8   C04  H7   108.37  3.000
 80K  H9   C04  C02  109.80  3.000
 80K  H8   C04  C02  111.40  3.000
 80K  H7   C04  C02  111.45  3.000
 80K  O07  C06  O05  125.96  3.000
 80K  O05  C06  N08  110.07  3.000
 80K  O07  C06  N08  123.96  3.000
 80K  H11  C09  H10  107.07  3.000
 80K  H11  C09  N08  107.65  3.000
 80K  H10  C09  N08  109.54  3.000
 80K  H11  C09  C10  109.87  3.000
 80K  H10  C09  C10  110.31  3.000
 80K  N08  C09  C10  112.23  3.000
 80K  H13  C10  H12  108.42  3.000
 80K  H13  C10  S11  109.20  3.000
 80K  H12  C10  S11  109.74  3.000
 80K  H13  C10  C09  110.05  3.000
 80K  H12  C10  C09  110.21  3.000
 80K  S11  C10  C09  109.21  3.000
 80K  H15  C12  H14  108.03  3.000
 80K  H15  C12  S11  110.12  3.000
 80K  H14  C12  S11  108.87  3.000
 80K  H15  C12  C13  110.78  3.000
 80K  H14  C12  C13  109.53  3.000
 80K  S11  C12  C13  109.47  3.000
 80K  H16  C13  N14  109.24  3.000
 80K  H16  C13  C21  109.86  3.000
 80K  N14  C13  C21  112.30  3.000
 80K  H16  C13  C12  107.35  3.000
 80K  C21  C13  C12  108.30  3.000
 80K  N14  C13  C12  109.66  3.000
 80K  N14  C15  C20  119.04  3.000
 80K  C20  C15  C16  118.21  3.000
 80K  N14  C15  C16  122.71  3.000
 80K  H17  C16  C17  118.52  3.000
 80K  H17  C16  C15  121.11  3.000
 80K  C17  C16  C15  120.37  3.000
 80K  H18  C17  C18  120.05  3.000
 80K  H18  C17  C16  118.80  3.000
 80K  C18  C17  C16  121.15  3.000
 80K  H19  C18  C19  120.65  3.000
 80K  H19  C18  C17  120.70  3.000
 80K  C19  C18  C17  118.65  3.000
 80K  H20  C19  C20  119.15  3.000
 80K  H20  C19  C18  120.05  3.000
 80K  C20  C19  C18  120.80  3.000
 80K  H21  C20  C19  119.77  3.000
 80K  H21  C20  C15  119.41  3.000
 80K  C19  C20  C15  120.82  3.000
 80K  O22  C21  N23  123.81  3.000
 80K  O22  C21  C13  121.29  3.000
 80K  N23  C21  C13  114.86  3.000
 80K  H23  C24  H22  107.00  3.000
 80K  H23  C24  N23  110.68  3.000
 80K  H22  C24  N23  108.73  3.000
 80K  H23  C24  C25  110.00  3.000
 80K  H22  C24  C25  110.18  3.000
 80K  N23  C24  C25  110.19  3.000
 80K  C30  C25  C26  117.49  3.000
 80K  C30  C25  C24  120.56  3.000
 80K  C26  C25  C24  121.95  3.000
 80K  H24  C26  C27  120.59  3.000
 80K  H24  C26  C25  120.25  3.000
 80K  C27  C26  C25  119.16  3.000
 80K  H25  C27  C28  120.37  3.000
 80K  H25  C27  C26  121.21  3.000
 80K  C28  C27  C26  118.42  3.000
 80K  H26  C28  N29  116.56  3.000
 80K  H26  C28  C27  120.27  3.000
 80K  N29  C28  C27  123.18  3.000
 80K  H27  C30  N29  116.45  3.000
 80K  H27  C30  C25  119.63  3.000
 80K  N29  C30  C25  123.92  3.000
 80K  H28  N08  C09  118.04  3.000
 80K  H28  N08  C06  118.71  3.000
 80K  C09  N08  C06  122.28  3.000
 80K  H29  N14  C15  113.81  3.000
 80K  H29  N14  C13  114.03  3.000
 80K  C15  N14  C13  121.40  3.000
 80K  H30  N23  C24  117.82  3.000
 80K  H30  N23  C21  118.99  3.000
 80K  C24  N23  C21  122.86  3.000
 80K  C30  N29  C28  117.83  3.000
 80K  C06  O05  C02  123.02  3.000
 80K  C12  S11  C10   99.05  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
 80K  CONST_01  C18  C17  C16  C15    0.00   0.0  0
 80K  CONST_02  C18  C19  C20  C15    0.00   0.0  0
 80K  CONST_03  C19  C20  C15  C16    0.00   0.0  0
 80K  CONST_04  C19  C18  C17  C16    0.00   0.0  0
 80K  CONST_05  C20  C15  C16  C17    0.00   0.0  0
 80K  CONST_06  C20  C19  C18  C17    0.00   0.0  0
 80K  CONST_07  C28  C27  C26  C25    0.00   0.0  0
 80K  CONST_08  C28  N29  C30  C25    0.00   0.0  0
 80K  CONST_09  N29  C28  C27  C26    0.00   0.0  0
 80K  CONST_10  N29  C30  C25  C26    0.00   0.0  0
 80K  CONST_11  C30  N29  C28  C27    0.00   0.0  0
 80K  CONST_12  C30  C25  C26  C27    0.00   0.0  0
 80K  CONST_13  N14  C15  C16  C17  180.00   0.0  0
 80K  CONST_14  N14  C15  C20  C19  180.00   0.0  0
 80K  CONST_15  C27  C26  C25  C24  180.00   0.0  0
 80K  CONST_16  N29  C30  C25  C24  180.00   0.0  0
 80K  CONST_17  H18  C17  C16  C15  180.00   0.0  0
 80K  CONST_18  H20  C19  C20  C15  180.00   0.0  0
 80K  CONST_19  H21  C20  C15  C16  180.00   0.0  0
 80K  CONST_20  H19  C18  C17  C16  180.00   0.0  0
 80K  CONST_21  H17  C16  C17  C18  180.00   0.0  0
 80K  CONST_22  H25  C27  C26  C25  180.00   0.0  0
 80K  CONST_23  H26  C28  C27  C26  180.00   0.0  0
 80K  CONST_24  H27  C30  C25  C26  180.00   0.0  0
 80K  CONST_25  H24  C26  C27  C28  180.00   0.0  0
 80K  CONST_29  C24  N23  C21  C13  180.00   0.0  0
 80K  CONST_30  O22  C21  N23  C24    0.00   0.0  0
 80K  CONST_31  H30  N23  C21  C13    0.00   0.0  0
 80K  Var_01    N23  C24  C25  C26  104.41  30.0  2
 80K  Var_02    C25  C24  N23  C21  161.85  30.0  1
 80K  Var_03    O07  C06  O05  C02   -0.58  30.0  1
 80K  Var_04    C10  C09  N08  C06   81.55  30.0  3
 80K  Var_05    C13  C12  S11  C10  160.45  30.0  2
 80K  Var_06    S11  C10  C09  N08  177.53  30.0  3
 80K  Var_07    H7   C04  C02  C01   58.08  30.0  3
 80K  Var_08    H4   C03  C02  C01   65.47  30.0  3
 80K  Var_09    H1   C01  C02  C03  175.95  30.0  3
 80K  Var_10    H12  C10  S11  C12   61.09  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
 80K  chir_01  C13  C12  N14  C21  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
 80K  plan-1  C15  0.020
 80K  plan-1  C16  0.020
 80K  plan-1  C17  0.020
 80K  plan-1  C18  0.020
 80K  plan-1  C19  0.020
 80K  plan-1  C20  0.020
 80K  plan-1  N14  0.020
 80K  plan-1  H17  0.020
 80K  plan-1  H18  0.020
 80K  plan-1  H19  0.020
 80K  plan-1  H20  0.020
 80K  plan-1  H21  0.020
 80K  plan-2  C24  0.020
 80K  plan-2  C25  0.020
 80K  plan-2  C26  0.020
 80K  plan-2  C27  0.020
 80K  plan-2  C28  0.020
 80K  plan-2  C30  0.020
 80K  plan-2  N29  0.020
 80K  plan-2  H24  0.020
 80K  plan-2  H25  0.020
 80K  plan-2  H26  0.020
 80K  plan-2  H27  0.020
 80K  plan-3  C13  0.020
 80K  plan-3  C21  0.020
 80K  plan-3  C24  0.020
 80K  plan-3  N23  0.020
 80K  plan-3  O22  0.020
 80K  plan-3  H30  0.020
 80K  plan-4  C13  0.020
 80K  plan-4  C15  0.020
 80K  plan-4  N14  0.020
 80K  plan-4  H29  0.020
 80K  plan-5  C06  0.020
 80K  plan-5  N08  0.020
 80K  plan-5  O05  0.020
 80K  plan-5  O07  0.020

