# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:10:42 2022
#   Inital geometry file: a 163 line input string
#   Ligand name: N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-4-methyl-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N[P](O)(=O)CNC(=O)OCc1ccccc1)C(=O)N[C@@H](CC(C)(C)C)C(O)=O
#
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
 5H9  5H9  N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-4-methyl-L-leucine  ligand  67  33  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5H9
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
 5H9  C1   C  CR16   0  -0.262   7.7274  -3.4587   0.7670
 5H9  C2   C  CR16   0  -0.242   6.5011  -3.8247   0.2273
 5H9  C3   C  CR16   0  -0.292   5.7238  -2.8821  -0.4320
 5H9  C9   C  C      0   0.750   3.6369   1.0096  -0.6493
 5H9  C11  C  CH2    0  -0.553   1.7745   2.3150   0.2289
 5H9  C14  C  CH1    0  -0.200  -2.2653   2.1301   0.2723
 5H9  C15  C  C      0   0.573  -2.9445   0.9429  -0.4073
 5H9  O17  O  O      0  -0.524   3.5119   1.3460  -1.8089
 5H9  C20  C  CH2    0  -0.401  -3.0702   3.4059   0.0452
 5H9  C21  C  CH1    0  -0.250  -4.5215   3.3639   0.5266
 5H9  C22  C  CH3    0  -0.654  -4.6275   3.0255   2.0104
 5H9  C30  C  CH3    0  -0.656  -1.2242  -2.4495   1.0773
 5H9  C31  C  C      0   0.401  -5.4131  -0.9507  -0.2957
 5H9  C4   C  CR6    0   0.077   6.1633  -1.5679  -0.5624
 5H9  O8   O  O2     0  -0.485   4.4975   0.0631  -0.2424
 5H9  N10  N  NH1    0  -0.649   2.9942   1.5524   0.4010
 5H9  P12  P  P      0   1.238   0.3047   1.1930   0.2801
 5H9  O19  O  O      0  -0.805   0.0193   0.8315   1.7186
 5H9  O18  O  OP    -1  -0.791   0.5508   0.1115  -0.7445
 5H9  N13  N  NH1    0  -0.782  -0.9090   2.3003  -0.2204
 5H9  C23  C  CH3    0  -0.652  -5.1966   4.6992   0.2286
 5H9  O24  O  O      0  -0.534  -3.2261   0.9746  -1.6033
 5H9  N16  N  NH1    0  -0.612  -3.1670  -0.1214   0.3641
 5H9  C25  C  CH1    0  -0.172  -3.9085  -1.2745  -0.0854
 5H9  C26  C  CH2    0  -0.437  -3.7687  -2.4262   0.9156
 5H9  C29  C  CH3    0  -0.642  -2.3927  -4.0082  -0.4833
 5H9  C28  C  CH3    0  -0.639  -2.5878  -4.3235   1.9741
 5H9  C5   C  CR16   0  -0.290   7.3936  -1.2099  -0.0185
 5H9  C6   C  CR16   0  -0.243   8.1734  -2.1490   0.6423
 5H9  H1   H  HCR6   0   0.258   8.3354  -4.1928   1.2797
 5H9  H2   H  HCR6   0   0.258   6.1513  -4.8450   0.3173
 5H9  H3   H  HCR6   0   0.255   4.7690  -3.1721  -0.8542
 5H9  H4   H  HCH2   0   0.243   5.9291   0.2068  -1.7428
 5H9  H5   H  HCH2   0   0.243   4.6808  -1.0158  -2.0093
 5H9  H6   H  HCH2   0   0.248   1.7132   3.0675   1.0169
 5H9  H7   H  HCH2   0   0.248   1.8229   2.8508  -0.7189
 5H9  H8   H  HCH1   0   0.238  -2.1876   1.9433   1.3449
 5H9  H9   H  HCH2   0   0.216  -2.5459   4.2231   0.5526
 5H9  H10  H  HCH2   0   0.213  -3.0554   3.6454  -1.0233
 5H9  H11  H  HCH1   0   0.235  -5.0517   2.5811  -0.0248
 5H9  H12  H  HCH3   0   0.220  -5.6582   3.1194   2.3575
 5H9  H13  H  HCH3   0   0.224  -4.3160   2.0015   2.2139
 5H9  H14  H  HCH3   0   0.206  -4.0117   3.6965   2.6151
 5H9  H15  H  HCH3   0   0.207  -1.2582  -1.8992   2.0205
 5H9  H16  H  HCH3   0   0.204  -0.3490  -3.1044   1.1159
 5H9  H17  H  HCH3   0   0.257  -1.0500  -1.7153   0.2924
 5H9  H18  H  HNH1   0   0.390   3.1169   1.1021   1.2949
 5H9  H20  H  HNH1   0   0.351  -0.9042   2.4636  -1.2208
 5H9  H21  H  HCH3   0   0.220  -5.1454   4.9437  -0.8345
 5H9  H22  H  HCH3   0   0.222  -6.2499   4.6844   0.5139
 5H9  H23  H  HCH3   0   0.209  -4.7159   5.5135   0.7768
 5H9  H24  H  HNH1   0   0.381  -2.9060  -0.0640   1.3343
 5H9  H25  H  HCH1   0   0.225  -3.5078  -1.5920  -1.0516
 5H9  H27  H  HCH2   0   0.231  -4.6134  -3.1033   0.7641
 5H9  H28  H  HCH2   0   0.219  -3.8877  -2.0263   1.9311
 5H9  H29  H  HCH3   0   0.220  -1.5064  -4.6464  -0.5121
 5H9  H30  H  HCH3   0   0.216  -3.2638  -4.6460  -0.6534
 5H9  H31  H  HCH3   0   0.223  -2.3186  -3.3151  -1.3233
 5H9  H32  H  HCH3   0   0.219  -2.6392  -3.8477   2.9562
 5H9  H33  H  HCH3   0   0.217  -3.4774  -4.9474   1.8598
 5H9  H34  H  HCH3   0   0.220  -1.7165  -4.9819   1.9698
 5H9  H35  H  HCR6   0   0.254   7.7481  -0.1904  -0.1171
 5H9  H36  H  HCR6   0   0.258   9.1300  -1.8597   1.0575
 5H9  C7   C  CH2    0  -0.234   5.3094  -0.5458  -1.2500
 5H9  O33  O  O      0  -0.582  -5.8836   0.0358   0.2945
 5H9  C27  C  CT     0  -0.083  -2.4878  -3.2795   0.8588
 5H9  O32  O  OC    -1  -0.621  -6.0270  -1.7547  -1.0276

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
 5H9  C22  C21  single    1.526  0.020  1.526
 5H9  C29  C27  single    1.530  0.020  1.530
 5H9  C28  C27  single    1.531  0.020  1.531
 5H9  C21  C23  single    1.526  0.020  1.526
 5H9  C21  C20  single    1.530  0.020  1.530
 5H9  C27  C30  single    1.528  0.020  1.528
 5H9  C27  C26  single    1.540  0.020  1.540
 5H9  C20  C14  single    1.525  0.020  1.525
 5H9  C26  C25  single    1.532  0.020  1.532
 5H9  C14  C15  single    1.527  0.020  1.527
 5H9  C14  N13  single    1.453  0.020  1.453
 5H9  O24  C15  double    1.229  0.020  1.229
 5H9  C15  N16  single    1.333  0.020  1.333
 5H9  N16  C25  single    1.443  0.020  1.443
 5H9  C25  C31  single    1.553  0.020  1.553
 5H9  N13  P12  single    1.717  0.020  1.717
 5H9  C31  O33  deloc     1.242  0.020  1.242
 5H9  C31  O32  deloc     1.249  0.020  1.249
 5H9  P12  O19  deloc     1.510  0.020  1.510
 5H9  P12  O18  deloc     1.510  0.020  1.510
 5H9  P12  C11  single    1.850  0.020  1.850
 5H9  C11  N10  single    1.449  0.020  1.449
 5H9  N10  C9   single    1.346  0.020  1.346
 5H9  O17  C9   double    1.214  0.020  1.214
 5H9  C9   O8   single    1.342  0.020  1.342
 5H9  O8   C7   single    1.430  0.020  1.430
 5H9  C5   C6   aromatic  1.388  0.020  1.388
 5H9  C5   C4   aromatic  1.392  0.020  1.392
 5H9  C6   C1   aromatic  1.389  0.020  1.389
 5H9  C7   C4   single    1.499  0.020  1.499
 5H9  C4   C3   aromatic  1.392  0.020  1.392
 5H9  C1   C2   aromatic  1.389  0.020  1.389
 5H9  C3   C2   aromatic  1.388  0.020  1.388
 5H9  C1   H1   single    0.930  0.020  1.080
 5H9  C2   H2   single    0.930  0.020  1.080
 5H9  C3   H3   single    0.930  0.020  1.080
 5H9  C7   H4   single    0.970  0.020  1.090
 5H9  C7   H5   single    0.970  0.020  1.090
 5H9  C11  H6   single    0.970  0.020  1.090
 5H9  C11  H7   single    0.970  0.020  1.090
 5H9  C14  H8   single    0.970  0.020  1.090
 5H9  C20  H9   single    0.970  0.020  1.090
 5H9  C20  H10  single    0.970  0.020  1.090
 5H9  C21  H11  single    0.970  0.020  1.090
 5H9  C22  H12  single    0.970  0.020  1.090
 5H9  C22  H13  single    0.970  0.020  1.090
 5H9  C22  H14  single    0.970  0.020  1.090
 5H9  C30  H15  single    0.970  0.020  1.090
 5H9  C30  H16  single    0.970  0.020  1.090
 5H9  C30  H17  single    0.970  0.020  1.090
 5H9  N10  H18  single    0.890  0.020  1.040
 5H9  N13  H20  single    0.890  0.020  1.040
 5H9  C23  H21  single    0.970  0.020  1.090
 5H9  C23  H22  single    0.970  0.020  1.090
 5H9  C23  H23  single    0.970  0.020  1.090
 5H9  N16  H24  single    0.860  0.020  1.020
 5H9  C25  H25  single    0.970  0.020  1.090
 5H9  C26  H27  single    0.970  0.020  1.090
 5H9  C26  H28  single    0.970  0.020  1.090
 5H9  C29  H29  single    0.970  0.020  1.090
 5H9  C29  H30  single    0.970  0.020  1.090
 5H9  C29  H31  single    0.970  0.020  1.090
 5H9  C28  H32  single    0.970  0.020  1.090
 5H9  C28  H33  single    0.970  0.020  1.090
 5H9  C28  H34  single    0.970  0.020  1.090
 5H9  C5   H35  single    0.930  0.020  1.080
 5H9  C6   H36  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
 5H9  H1   C1   C6   120.11  3.000
 5H9  H1   C1   C2   120.09  3.000
 5H9  C6   C1   C2   119.81  3.000
 5H9  H2   C2   C3   119.91  3.000
 5H9  H2   C2   C1   120.10  3.000
 5H9  C3   C2   C1   120.00  3.000
 5H9  H3   C3   C4   119.64  3.000
 5H9  H3   C3   C2   119.78  3.000
 5H9  C4   C3   C2   120.58  3.000
 5H9  N10  C9   O8   110.73  3.000
 5H9  O8   C9   O17  123.43  3.000
 5H9  N10  C9   O17  125.78  3.000
 5H9  H7   C11  H6   106.95  3.000
 5H9  H7   C11  P12  110.95  3.000
 5H9  H6   C11  P12  110.71  3.000
 5H9  H7   C11  N10  108.95  3.000
 5H9  H6   C11  N10  108.94  3.000
 5H9  P12  C11  N10  110.26  3.000
 5H9  H8   C14  N13  106.67  3.000
 5H9  H8   C14  C20  109.08  3.000
 5H9  N13  C14  C20  110.12  3.000
 5H9  H8   C14  C15  109.63  3.000
 5H9  N13  C14  C15  110.81  3.000
 5H9  C20  C14  C15  110.44  3.000
 5H9  N16  C15  O24  123.05  3.000
 5H9  N16  C15  C14  115.93  3.000
 5H9  O24  C15  C14  120.99  3.000
 5H9  H10  C20  H9   106.40  3.000
 5H9  H10  C20  C21  109.02  3.000
 5H9  H9   C20  C21  109.20  3.000
 5H9  H10  C20  C14  108.72  3.000
 5H9  H9   C20  C14  107.61  3.000
 5H9  C21  C20  C14  115.52  3.000
 5H9  H11  C21  C23  108.25  3.000
 5H9  H11  C21  C22  107.32  3.000
 5H9  C23  C21  C22  110.69  3.000
 5H9  H11  C21  C20  108.71  3.000
 5H9  C23  C21  C20  109.53  3.000
 5H9  C22  C21  C20  112.21  3.000
 5H9  H14  C22  H13  108.21  3.000
 5H9  H14  C22  H12  107.65  3.000
 5H9  H13  C22  H12  106.94  3.000
 5H9  H14  C22  C21  111.27  3.000
 5H9  H13  C22  C21  111.73  3.000
 5H9  H12  C22  C21  110.84  3.000
 5H9  H17  C30  H16  107.53  3.000
 5H9  H17  C30  H15  106.72  3.000
 5H9  H16  C30  H15  107.22  3.000
 5H9  H17  C30  C27  113.30  3.000
 5H9  H16  C30  C27  109.98  3.000
 5H9  H15  C30  C27  111.81  3.000
 5H9  O32  C31  O33  127.14  3.000
 5H9  O32  C31  C25  114.92  3.000
 5H9  O33  C31  C25  117.91  3.000
 5H9  C5   C4   C7   120.49  3.000
 5H9  C7   C4   C3   120.46  3.000
 5H9  C5   C4   C3   119.04  3.000
 5H9  C9   O8   C7   116.78  3.000
 5H9  H18  N10  C11  116.28  3.000
 5H9  H18  N10  C9   116.98  3.000
 5H9  C11  N10  C9   121.45  3.000
 5H9  N13  P12  O18  112.29  3.000
 5H9  O18  P12  O19  120.37  3.000
 5H9  N13  P12  O19  107.36  3.000
 5H9  O18  P12  C11  106.63  3.000
 5H9  O19  P12  C11  108.76  3.000
 5H9  N13  P12  C11   99.34  3.000
 5H9  H20  N13  P12  112.84  3.000
 5H9  H20  N13  C14  110.97  3.000
 5H9  P12  N13  C14  119.03  3.000
 5H9  H23  C23  H22  107.67  3.000
 5H9  H23  C23  H21  107.51  3.000
 5H9  H22  C23  H21  107.62  3.000
 5H9  H23  C23  C21  111.07  3.000
 5H9  H22  C23  C21  111.35  3.000
 5H9  H21  C23  C21  111.43  3.000
 5H9  H24  N16  C25  118.64  3.000
 5H9  H24  N16  C15  117.97  3.000
 5H9  C25  N16  C15  122.93  3.000
 5H9  H25  C25  C26  109.01  3.000
 5H9  H25  C25  N16  108.61  3.000
 5H9  C26  C25  N16  110.50  3.000
 5H9  H25  C25  C31  107.21  3.000
 5H9  N16  C25  C31  111.93  3.000
 5H9  C26  C25  C31  109.48  3.000
 5H9  H28  C26  H27  105.66  3.000
 5H9  H28  C26  C25  108.70  3.000
 5H9  H27  C26  C25  107.73  3.000
 5H9  H28  C26  C27  109.03  3.000
 5H9  H27  C26  C27  107.12  3.000
 5H9  C25  C26  C27  117.92  3.000
 5H9  H31  C29  H30  107.75  3.000
 5H9  H31  C29  H29  107.19  3.000
 5H9  H30  C29  H29  107.55  3.000
 5H9  H31  C29  C27  112.14  3.000
 5H9  H30  C29  C27  111.40  3.000
 5H9  H29  C29  C27  110.60  3.000
 5H9  H34  C28  H33  107.76  3.000
 5H9  H34  C28  H32  107.68  3.000
 5H9  H33  C28  H32  107.72  3.000
 5H9  H34  C28  C27  110.86  3.000
 5H9  H33  C28  C27  111.49  3.000
 5H9  H32  C28  C27  111.16  3.000
 5H9  H35  C5   C6   119.73  3.000
 5H9  H35  C5   C4   119.70  3.000
 5H9  C6   C5   C4   120.57  3.000
 5H9  H36  C6   C5   119.89  3.000
 5H9  H36  C6   C1   120.09  3.000
 5H9  C5   C6   C1   120.01  3.000
 5H9  H5   C7   H4   108.02  3.000
 5H9  H5   C7   O8   110.26  3.000
 5H9  H4   C7   O8   110.28  3.000
 5H9  H5   C7   C4   110.70  3.000
 5H9  H4   C7   C4   110.71  3.000
 5H9  O8   C7   C4   106.89  3.000
 5H9  C28  C27  C29  108.56  3.000
 5H9  C28  C27  C26  107.26  3.000
 5H9  C29  C27  C26  110.36  3.000
 5H9  C26  C27  C30  112.43  3.000
 5H9  C28  C27  C30  108.68  3.000
 5H9  C29  C27  C30  109.44  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
 5H9  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 5H9  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 5H9  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 5H9  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 5H9  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 5H9  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 5H9  CONST_07  C7   C4   C3   C2    180.00   0.0  0
 5H9  CONST_08  C6   C5   C4   C7    180.00   0.0  0
 5H9  CONST_09  H35  C5   C6   C1    180.00   0.0  0
 5H9  CONST_10  H3   C3   C2   C1    180.00   0.0  0
 5H9  CONST_11  H36  C6   C1   C2    180.00   0.0  0
 5H9  CONST_12  H1   C1   C2   C3    180.00   0.0  0
 5H9  CONST_13  H2   C2   C3   C4    180.00   0.0  0
 5H9  CONST_14  C25  N16  C15  C14   180.00   0.0  0
 5H9  CONST_15  C25  N16  C15  O24     0.00   0.0  0
 5H9  CONST_16  H24  N16  C15  C14     0.00   0.0  0
 5H9  Var_01    O8   C7   C4   C3     90.66  30.0  3
 5H9  Var_02    C4   C7   O8   C9   -179.30  30.0  3
 5H9  Var_03    N10  C9   O8   C7   -176.43  30.0  1
 5H9  Var_04    P12  C11  N10  C9     88.26  30.0  1
 5H9  Var_05    C14  N13  P12  C11  -149.50  30.0  1
 5H9  Var_06    C22  C21  C20  C14    56.88  30.0  1
 5H9  Var_07    C25  C26  C27  C30    59.21  30.0  3
 5H9  Var_08    N13  P12  C11  N10  -170.41  30.0  1
 5H9  Var_09    H12  C22  C21  C20   173.16  30.0  3
 5H9  Var_10    H21  C23  C21  C20    56.90  30.0  3
 5H9  Var_11    H29  C29  C27  C30    58.07  30.0  3
 5H9  Var_12    H32  C28  C27  C30    59.98  30.0  3
 5H9  Var_13    H15  C30  C27  C26    56.11  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
 5H9  chir_01  C14  C20  C15  N13  negativ
 5H9  chir_03  C25  C26  N16  C31  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
 5H9  plan-1  C1   0.020
 5H9  plan-1  C2   0.020
 5H9  plan-1  C3   0.020
 5H9  plan-1  C4   0.020
 5H9  plan-1  C5   0.020
 5H9  plan-1  C6   0.020
 5H9  plan-1  H1   0.020
 5H9  plan-1  H2   0.020
 5H9  plan-1  H3   0.020
 5H9  plan-1  H35  0.020
 5H9  plan-1  H36  0.020
 5H9  plan-1  C7   0.020
 5H9  plan-2  C14  0.020
 5H9  plan-2  C15  0.020
 5H9  plan-2  O24  0.020
 5H9  plan-2  N16  0.020
 5H9  plan-2  C25  0.020
 5H9  plan-2  H24  0.020
 5H9  plan-3  C31  0.020
 5H9  plan-3  C25  0.020
 5H9  plan-3  O33  0.020
 5H9  plan-3  O32  0.020
 5H9  plan-4  C9   0.020
 5H9  plan-4  O17  0.020
 5H9  plan-4  O8   0.020
 5H9  plan-4  N10  0.020

