# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 18:38:43 2020
#   Inital geometry file: a 165 line input string
#   Ligand name: N-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-L-phenylalanine
#   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](Cc2ccccc2)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
 X32  X32  N-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-L-phenylalanine  peptide  65  35  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X32
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
 X32  C3    C  CR16   0  -0.290  -6.3415  -2.4833  -0.7919
 X32  C2    C  CR16   0  -0.242  -7.5074  -2.5879  -1.5375
 X32  C1    C  CR16   0  -0.262  -8.5786  -1.7431  -1.2751
 X32  C6    C  CR16   0  -0.242  -8.4786  -0.7955  -0.2649
 X32  C5    C  CR16   0  -0.292  -7.3100  -0.6935   0.4782
 X32  C4    C  CR6    0   0.078  -6.2328  -1.5367   0.2232
 X32  C7    C  CH2    0  -0.238  -4.9610  -1.4073   1.0058
 X32  O8    O  O2     0  -0.486  -4.1114  -0.5207   0.2742
 X32  C9    C  C      0   0.764  -2.8724  -0.3306   0.7589
 X32  O22   O  O      0  -0.524  -2.4531  -0.8741   1.7615
 X32  N10   N  NH1    0  -0.664  -2.1793   0.5153  -0.0169
 X32  C11   C  CH2    0  -0.558  -0.8324   0.9342   0.3028
 X32  P12   P  P      0   1.233  -0.1289   1.8642  -1.1311
 X32  O24   O  O      0  -0.795   0.3121   0.9194  -2.2226
 X32  O23   O  OP    -1  -0.810  -1.1590   2.9277  -1.4408
 X32  N13   N  NH1    0  -0.774   1.2605   2.5936  -0.4842
 X32  C14   C  CH1    0  -0.200   2.5810   2.0610  -0.6776
 X32  C15   C  C      0   0.561   2.8721   0.8146   0.1649
 X32  O29   O  O      0  -0.503   2.3512   0.6328   1.2569
 X32  C25   C  CH2    0  -0.419   3.6440   3.1190  -0.3514
 X32  C26   C  CH1    0  -0.215   3.4717   4.4435  -1.0954
 X32  C27   C  CH3    0  -0.652   4.5844   5.4096  -0.7000
 X32  C28   C  CH3    0  -0.666   3.4327   4.2493  -2.6062
 X32  N16   N  NH1    0  -0.610   3.7746  -0.0072  -0.3875
 X32  C17   C  CH1    0  -0.208   4.3825  -1.1557   0.2338
 X32  C18   C  C      0   0.419   5.9252  -1.1076   0.0750
 X32  O37   O  O      0  -0.595   6.3857  -0.2966  -0.7499
 X32  C30   C  CH2    0  -0.515   3.8629  -2.4690  -0.3827
 X32  C31   C  CR6    0   0.159   2.3951  -2.7110  -0.1753
 X32  C36   C  CR16   0  -0.331   1.9627  -3.6199   0.7886
 X32  C32   C  CR16   0  -0.289   1.4319  -2.0368  -0.9239
 X32  C35   C  CR16   0  -0.247   0.6096  -3.8552   0.9984
 X32  C33   C  CR16   0  -0.243   0.0795  -2.2614  -0.7117
 X32  C34   C  CR16   0  -0.263  -0.3391  -3.1739   0.2478
 X32  O19   O  OC    -1  -0.608   6.5617  -1.9191   0.7720
 X32  H3    H  HCR6   0   0.254  -5.5114  -3.1491  -0.9981
 X32  H2    H  HCR6   0   0.258  -7.5805  -3.3302  -2.3216
 X32  H1    H  HCR6   0   0.258  -9.4899  -1.8262  -1.8534
 X32  H6    H  HCR6   0   0.258  -9.3112  -0.1370  -0.0532
 X32  H5    H  HCR6   0   0.255  -7.2370   0.0451   1.2676
 X32  H7    H  HCH2   0   0.243  -5.1593  -1.0058   2.0023
 X32  H7A   H  HCH2   0   0.242  -4.4815  -2.3815   1.1242
 X32  HN10  H  HNH1   0   0.385  -2.6753   1.0346  -0.7253
 X32  H11   H  HCH2   0   0.226  -0.8219   1.5845   1.1857
 X32  H11A  H  HCH2   0   0.269  -0.2121   0.0685   0.5289
 X32  HN13  H  HNH1   0   0.356   1.1414   3.0774   0.3950
 X32  H14   H  HCH1   0   0.244   2.6780   1.7851  -1.7298
 X32  H25   H  HCH2   0   0.226   3.6320   3.3115   0.7277
 X32  H25A  H  HCH2   0   0.221   4.6336   2.7064  -0.5779
 X32  H26   H  HCH1   0   0.216   2.5175   4.8809  -0.7874
 X32  H27   H  HCH3   0   0.211   5.5614   5.0401  -1.0212
 X32  H27A  H  HCH3   0   0.223   4.4366   6.3898  -1.1573
 X32  H27B  H  HCH3   0   0.221   4.6242   5.5527   0.3818
 X32  H28   H  HCH3   0   0.231   2.5680   3.6603  -2.9153
 X32  H28A  H  HCH3   0   0.224   3.3729   5.2090  -3.1229
 X32  H28B  H  HCH3   0   0.210   4.3319   3.7384  -2.9604
 X32  HN16  H  HNH1   0   0.377   4.2180   0.2838  -1.2456
 X32  H17   H  HCH1   0   0.243   4.1317  -1.1448   1.2963
 X32  H30   H  HCH2   0   0.237   4.0920  -2.4582  -1.4534
 X32  H30A  H  HCH2   0   0.243   4.4312  -3.2925   0.0527
 X32  H36   H  HCR6   0   0.238   2.6951  -4.1569   1.3813
 X32  H32   H  HCR6   0   0.237   1.7274  -1.3058  -1.6643
 X32  H35   H  HCR6   0   0.244   0.2983  -4.5697   1.7505
 X32  H33   H  HCR6   0   0.242  -0.6428  -1.6983  -1.2884
 X32  H34   H  HCR6   0   0.237  -1.3939  -3.3463   0.4156

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
 X32  C2   C1    aromatic  1.389  0.020  1.389
 X32  C1   C6    aromatic  1.389  0.020  1.389
 X32  C1   H1    single    0.930  0.020  1.080
 X32  C2   C3    aromatic  1.388  0.020  1.388
 X32  C2   H2    single    0.930  0.020  1.080
 X32  C3   C4    aromatic  1.392  0.020  1.392
 X32  C3   H3    single    0.930  0.020  1.080
 X32  C4   C7    single    1.499  0.020  1.499
 X32  C4   C5    aromatic  1.391  0.020  1.391
 X32  C6   C5    aromatic  1.389  0.020  1.389
 X32  C5   H5    single    0.930  0.020  1.080
 X32  C6   H6    single    0.930  0.020  1.080
 X32  C7   O8    single    1.429  0.020  1.429
 X32  C7   H7    single    0.970  0.020  1.090
 X32  C7   H7A   single    0.970  0.020  1.090
 X32  O8   C9    single    1.344  0.020  1.344
 X32  C9   O22   double    1.215  0.020  1.215
 X32  C9   N10   single    1.341  0.020  1.341
 X32  N10  C11   single    1.446  0.020  1.446
 X32  N10  HN10  single    0.860  0.020  1.020
 X32  C11  P12   single    1.848  0.020  1.848
 X32  C11  H11   single    0.970  0.020  1.090
 X32  C11  H11A  single    0.970  0.020  1.090
 X32  O24  P12   deloc     1.509  0.020  1.509
 X32  O23  P12   deloc     1.513  0.020  1.513
 X32  P12  N13   single    1.697  0.020  1.697
 X32  N13  C14   single    1.437  0.020  1.437
 X32  N13  HN13  single    0.890  0.020  1.040
 X32  C15  C14   single    1.532  0.020  1.532
 X32  C14  C25   single    1.535  0.020  1.535
 X32  C14  H14   single    0.970  0.020  1.090
 X32  N16  C15   single    1.340  0.020  1.340
 X32  C15  O29   double    1.224  0.020  1.224
 X32  C17  N16   single    1.440  0.020  1.440
 X32  N16  HN16  single    0.860  0.020  1.020
 X32  C18  C17   single    1.552  0.020  1.552
 X32  C17  C30   single    1.541  0.020  1.541
 X32  C17  H17   single    0.970  0.020  1.090
 X32  O37  C18   deloc     1.245  0.020  1.245
 X32  O19  C18   deloc     1.245  0.020  1.245
 X32  C25  C26   single    1.529  0.020  1.529
 X32  C25  H25   single    0.970  0.020  1.090
 X32  C25  H25A  single    0.970  0.020  1.090
 X32  C28  C26   single    1.524  0.020  1.524
 X32  C26  C27   single    1.526  0.020  1.526
 X32  C26  H26   single    0.970  0.020  1.090
 X32  C27  H27   single    0.970  0.020  1.090
 X32  C27  H27A  single    0.970  0.020  1.090
 X32  C27  H27B  single    0.970  0.020  1.090
 X32  C28  H28   single    0.970  0.020  1.090
 X32  C28  H28A  single    0.970  0.020  1.090
 X32  C28  H28B  single    0.970  0.020  1.090
 X32  C30  C31   single    1.502  0.020  1.502
 X32  C30  H30   single    0.970  0.020  1.090
 X32  C30  H30A  single    0.970  0.020  1.090
 X32  C36  C31   aromatic  1.394  0.020  1.394
 X32  C31  C32   aromatic  1.394  0.020  1.394
 X32  C32  C33   aromatic  1.387  0.020  1.387
 X32  C32  H32   single    0.930  0.020  1.080
 X32  C34  C33   aromatic  1.389  0.020  1.389
 X32  C33  H33   single    0.930  0.020  1.080
 X32  C35  C34   aromatic  1.388  0.020  1.388
 X32  C34  H34   single    0.930  0.020  1.080
 X32  C36  C35   aromatic  1.389  0.020  1.389
 X32  C35  H35   single    0.930  0.020  1.080
 X32  C36  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
 X32  H3    C3   C4    119.77  3.000
 X32  H3    C3   C2    119.66  3.000
 X32  C4    C3   C2    120.56  3.000
 X32  H2    C2   C1    120.12  3.000
 X32  H2    C2   C3    119.85  3.000
 X32  C1    C2   C3    120.03  3.000
 X32  H1    C1   C6    120.11  3.000
 X32  H1    C1   C2    120.10  3.000
 X32  C6    C1   C2    119.79  3.000
 X32  H6    C6   C5    119.87  3.000
 X32  H6    C6   C1    120.13  3.000
 X32  C5    C6   C1    120.00  3.000
 X32  H5    C5   C4    119.63  3.000
 X32  H5    C5   C6    119.77  3.000
 X32  C4    C5   C6    120.59  3.000
 X32  C7    C4   C5    120.59  3.000
 X32  C5    C4   C3    119.03  3.000
 X32  C7    C4   C3    120.37  3.000
 X32  H7A   C7   H7    107.97  3.000
 X32  H7A   C7   O8    110.35  3.000
 X32  H7    C7   O8    110.29  3.000
 X32  H7A   C7   C4    110.62  3.000
 X32  H7    C7   C4    110.73  3.000
 X32  O8    C7   C4    106.90  3.000
 X32  C9    O8   C7    116.82  3.000
 X32  N10   C9   O22   125.54  3.000
 X32  N10   C9   O8    110.92  3.000
 X32  O22   C9   O8    123.53  3.000
 X32  HN10  N10  C11   117.65  3.000
 X32  HN10  N10  C9    118.49  3.000
 X32  C11   N10  C9    122.42  3.000
 X32  H11A  C11  H11   107.39  3.000
 X32  H11A  C11  P12   110.14  3.000
 X32  H11   C11  P12   108.82  3.000
 X32  H11A  C11  N10   110.26  3.000
 X32  H11   C11  N10   111.02  3.000
 X32  P12   C11  N10   109.19  3.000
 X32  N13   P12  O23   109.47  3.000
 X32  N13   P12  O24   107.78  3.000
 X32  O23   P12  O24   119.41  3.000
 X32  N13   P12  C11   103.42  3.000
 X32  O23   P12  C11   104.68  3.000
 X32  O24   P12  C11   110.93  3.000
 X32  HN13  N13  C14   113.76  3.000
 X32  HN13  N13  P12   116.16  3.000
 X32  C14   N13  P12   122.80  3.000
 X32  H14   C14  C25   108.51  3.000
 X32  H14   C14  C15   107.90  3.000
 X32  C25   C14  C15   108.19  3.000
 X32  H14   C14  N13   107.75  3.000
 X32  C25   C14  N13   110.63  3.000
 X32  C15   C14  N13   113.71  3.000
 X32  N16   C15  O29   124.31  3.000
 X32  O29   C15  C14   122.06  3.000
 X32  N16   C15  C14   113.59  3.000
 X32  H25A  C25  H25   106.23  3.000
 X32  H25A  C25  C26   109.11  3.000
 X32  H25   C25  C26   109.01  3.000
 X32  H25A  C25  C14   108.78  3.000
 X32  H25   C25  C14   108.83  3.000
 X32  C26   C25  C14   114.56  3.000
 X32  H26   C26  C28   107.92  3.000
 X32  H26   C26  C27   108.06  3.000
 X32  C28   C26  C27   110.88  3.000
 X32  H26   C26  C25   107.92  3.000
 X32  C27   C26  C25   109.90  3.000
 X32  C28   C26  C25   112.02  3.000
 X32  H27B  C27  H27A  107.60  3.000
 X32  H27B  C27  H27   107.63  3.000
 X32  H27A  C27  H27   107.55  3.000
 X32  H27B  C27  C26   111.49  3.000
 X32  H27A  C27  C26   111.18  3.000
 X32  H27   C27  C26   111.21  3.000
 X32  H28B  C28  H28A  107.61  3.000
 X32  H28B  C28  H28   107.93  3.000
 X32  H28A  C28  H28   107.28  3.000
 X32  H28B  C28  C26   111.09  3.000
 X32  H28A  C28  C26   111.01  3.000
 X32  H28   C28  C26   111.72  3.000
 X32  HN16  N16  C17   114.30  3.000
 X32  HN16  N16  C15   118.02  3.000
 X32  C17   N16  C15   126.55  3.000
 X32  H17   C17  C30   108.68  3.000
 X32  H17   C17  C18   109.13  3.000
 X32  C30   C17  C18   108.71  3.000
 X32  H17   C17  N16   108.35  3.000
 X32  C30   C17  N16   111.38  3.000
 X32  C18   C17  N16   110.53  3.000
 X32  O19   C18  O37   127.33  3.000
 X32  O19   C18  C17   115.53  3.000
 X32  O37   C18  C17   117.11  3.000
 X32  H30A  C30  H30   106.78  3.000
 X32  H30A  C30  C31   109.40  3.000
 X32  H30   C30  C31   109.94  3.000
 X32  H30A  C30  C17   107.93  3.000
 X32  H30   C30  C17   108.20  3.000
 X32  C31   C30  C17   114.31  3.000
 X32  C32   C31  C36   118.20  3.000
 X32  C32   C31  C30   121.55  3.000
 X32  C36   C31  C30   120.25  3.000
 X32  H36   C36  C35   119.43  3.000
 X32  H36   C36  C31   119.43  3.000
 X32  C35   C36  C31   121.13  3.000
 X32  H32   C32  C33   118.72  3.000
 X32  H32   C32  C31   120.38  3.000
 X32  C33   C32  C31   120.88  3.000
 X32  H35   C35  C34   120.18  3.000
 X32  H35   C35  C36   119.77  3.000
 X32  C34   C35  C36   120.05  3.000
 X32  H33   C33  C34   120.59  3.000
 X32  H33   C33  C32   119.00  3.000
 X32  C34   C33  C32   120.39  3.000
 X32  H34   C34  C33   120.38  3.000
 X32  H34   C34  C35   120.28  3.000
 X32  C33   C34  C35   119.34  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
 X32  CONST_01  C6    C1   C2   C3      0.00   0.0  0
 X32  CONST_02  C6    C5   C4   C3      0.00   0.0  0
 X32  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 X32  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 X32  CONST_05  C4    C3   C2   C1      0.00   0.0  0
 X32  CONST_06  C4    C5   C6   C1      0.00   0.0  0
 X32  CONST_07  C34   C35  C36  C31     0.00   0.0  0
 X32  CONST_08  C34   C33  C32  C31     0.00   0.0  0
 X32  CONST_09  C33   C32  C31  C36     0.00   0.0  0
 X32  CONST_10  C33   C34  C35  C36     0.00   0.0  0
 X32  CONST_11  C35   C36  C31  C32     0.00   0.0  0
 X32  CONST_12  C35   C34  C33  C32     0.00   0.0  0
 X32  CONST_13  C7    C4   C3   C2    180.00   0.0  0
 X32  CONST_14  C7    C4   C5   C6    180.00   0.0  0
 X32  CONST_15  C35   C36  C31  C30   180.00   0.0  0
 X32  CONST_16  C33   C32  C31  C30   180.00   0.0  0
 X32  CONST_17  H1    C1   C2   C3    180.00   0.0  0
 X32  CONST_18  H5    C5   C4   C3    180.00   0.0  0
 X32  CONST_19  H6    C6   C1   C2    180.00   0.0  0
 X32  CONST_20  H3    C3   C2   C1    180.00   0.0  0
 X32  CONST_21  H2    C2   C1   C6    180.00   0.0  0
 X32  CONST_22  H35   C35  C36  C31   180.00   0.0  0
 X32  CONST_23  H33   C33  C32  C31   180.00   0.0  0
 X32  CONST_24  H32   C32  C31  C36   180.00   0.0  0
 X32  CONST_25  H34   C34  C35  C36   180.00   0.0  0
 X32  CONST_26  H36   C36  C31  C32   180.00   0.0  0
 X32  CONST_27  C17   N16  C15  C14   180.00   0.0  0
 X32  CONST_28  C17   N16  C15  O29     0.00   0.0  0
 X32  CONST_29  HN16  N16  C15  C14     0.00   0.0  0
 X32  Var_01    O8    C7   C4   C3     86.39  30.0  2
 X32  Var_02    C36   C31  C30  C17  -102.94  30.0  2
 X32  Var_03    O22   C9   O8   C7      0.51  30.0  3
 X32  Var_04    C11   N10  C9   O8    177.62  30.0  2
 X32  Var_05    P12   C11  N10  C9    170.77  30.0  3
 X32  Var_06    O24   P12  C11  N10   -77.80  30.0  3
 X32  Var_07    C14   N13  P12  C11   100.00  30.0  3
 X32  Var_08    C28   C26  C25  C14   -55.94  30.0  3
 X32  Var_09    H28   C28  C26  C25    63.87  30.0  3
 X32  Var_10    H27   C27  C26  C25    64.77  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
 X32  chir_02  C14  N13  C15  C25  positiv
 X32  chir_03  C17  N16  C18  C30  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
 X32  plan-1  C3    0.020
 X32  plan-1  C2    0.020
 X32  plan-1  C1    0.020
 X32  plan-1  C6    0.020
 X32  plan-1  C5    0.020
 X32  plan-1  C4    0.020
 X32  plan-1  C7    0.020
 X32  plan-1  H3    0.020
 X32  plan-1  H2    0.020
 X32  plan-1  H1    0.020
 X32  plan-1  H6    0.020
 X32  plan-1  H5    0.020
 X32  plan-2  C30   0.020
 X32  plan-2  C31   0.020
 X32  plan-2  C36   0.020
 X32  plan-2  C32   0.020
 X32  plan-2  C35   0.020
 X32  plan-2  C33   0.020
 X32  plan-2  C34   0.020
 X32  plan-2  H36   0.020
 X32  plan-2  H32   0.020
 X32  plan-2  H35   0.020
 X32  plan-2  H33   0.020
 X32  plan-2  H34   0.020
 X32  plan-3  C14   0.020
 X32  plan-3  C15   0.020
 X32  plan-3  O29   0.020
 X32  plan-3  N16   0.020
 X32  plan-3  C17   0.020
 X32  plan-3  HN16  0.020
 X32  plan-4  C17   0.020
 X32  plan-4  C18   0.020
 X32  plan-4  O37   0.020
 X32  plan-4  O19   0.020
 X32  plan-5  O8    0.020
 X32  plan-5  C9    0.020
 X32  plan-5  O22   0.020
 X32  plan-5  N10   0.020

