# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 10:13:47 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-L-alanine
#   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](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
 UBY  UBY  N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-L-alanine  peptide  57  29  .  2022-03-23  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UBY
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
 UBY  C3    C  CR16  0  -0.298  -7.6788  -1.1326   0.3088
 UBY  C2    C  CR16  0  -0.241  -8.8998  -0.5840  -0.0640
 UBY  C1    C  CR16  0  -0.261  -8.9867   0.2080  -1.2003
 UBY  C6    C  CR16  0  -0.242  -7.8506   0.4461  -1.9654
 UBY  C5    C  CR16  0  -0.282  -6.6343  -0.1059  -1.5923
 UBY  C4    C  CR6   0   0.075  -6.5380  -0.8997  -0.4513
 UBY  C7    C  CH2   0  -0.240  -5.2141  -1.4696  -0.0424
 UBY  O8    O  O2    0  -0.476  -4.4659  -0.3992   0.5493
 UBY  C9    C  C     0   0.765  -3.2145  -0.6695   0.9237
 UBY  O21   O  O     0  -0.515  -2.6935  -1.7624   0.8368
 UBY  N10   N  NH1   0  -0.655  -2.6196   0.4296   1.4310
 UBY  C11   C  CH2   0  -0.570  -1.2373   0.4284   1.8253
 UBY  P12   P  P     0   1.309  -0.1666   0.8581   0.4086
 UBY  O22   O  O     0  -0.715  -0.5020   2.1604  -0.2292
 UBY  O23   O  OH1   0  -0.746  -0.3609  -0.2971  -0.6995
 UBY  N13   N  NH1   0  -0.783   1.3651   0.6170   1.0167
 UBY  C14   C  CH1   0  -0.220   2.5374   0.8302   0.1778
 UBY  C15   C  C     0   0.584   3.6354  -0.1028   0.6746
 UBY  O24   O  O     0  -0.491   3.9767  -0.0986   1.8481
 UBY  C20   C  CH2   0  -0.408   3.0300   2.2797   0.2149
 UBY  C21   C  CH1   0  -0.253   4.2447   2.5877  -0.6627
 UBY  C22   C  CH3   0  -0.657   3.9627   2.3499  -2.1434
 UBY  C23   C  CH3   0  -0.649   4.6862   4.0291  -0.4295
 UBY  N16   N  NH1   0  -0.637   4.2017  -0.8774  -0.2598
 UBY  C17   C  CH1   0  -0.204   5.2937  -1.7758   0.0216
 UBY  C18   C  C     0   0.551   6.1268  -1.9273  -1.2357
 UBY  O32   O  O     0  -0.432   5.7965  -1.5290  -2.3235
 UBY  C25   C  CH3   0  -0.653   4.8103  -3.1411   0.5188
 UBY  O19   O  OH1   0  -0.585   7.2527  -2.5760  -0.9937
 UBY  H3    H  HCR6  0   0.256  -7.6170  -1.7497   1.1974
 UBY  H2    H  HCR6  0   0.259  -9.7816  -0.7751   0.5337
 UBY  H1    H  HCR6  0   0.259  -9.9368   0.6367  -1.4918
 UBY  H6    H  HCR6  0   0.259  -7.9142   1.0598  -2.8546
 UBY  H5    H  HCR6  0   0.255  -5.7531   0.0771  -2.1959
 UBY  H7    H  HCH2  0   0.251  -5.3431  -2.2809   0.6763
 UBY  H7A   H  HCH2  0   0.250  -4.6772  -1.8629  -0.9081
 UBY  HN10  H  HNH1  0   0.412  -3.1045   1.3119   1.3976
 UBY  H11   H  HCH2  0   0.309  -1.0884   1.1679   2.6130
 UBY  H11A  H  HCH2  0   0.297  -0.9573  -0.5406   2.2381
 UBY  HO23  H  HOH1  0   0.482  -0.2250  -1.1958  -0.3730
 UBY  HN13  H  HNH1  0   0.401   1.5019   0.9107   1.9768
 UBY  H14   H  HCH1  0   0.267   2.2642   0.5644  -0.8464
 UBY  H20   H  HCH2  0   0.241   2.1961   2.9201  -0.0876
 UBY  H20A  H  HCH2  0   0.232   3.2576   2.5338   1.2552
 UBY  H21   H  HCH1  0   0.225   5.0746   1.9373  -0.3633
 UBY  H22   H  HCH3  0   0.233   4.8274   2.6213  -2.7507
 UBY  H22A  H  HCH3  0   0.219   3.7283   1.3086  -2.3689
 UBY  H22B  H  HCH3  0   0.219   3.1181   2.9564  -2.4793
 UBY  H23   H  HCH3  0   0.227   4.9335   4.2043   0.6187
 UBY  H23A  H  HCH3  0   0.228   5.5659   4.2754  -1.0261
 UBY  H23B  H  HCH3  0   0.216   3.8945   4.7300  -0.7055
 UBY  HN16  H  HNH1  0   0.404   3.8336  -0.8697  -1.1984
 UBY  H17   H  HCH1  0   0.297   5.9228  -1.3212   0.7906
 UBY  H25   H  HCH3  0   0.248   5.6472  -3.7829   0.7888
 UBY  H25A  H  HCH3  0   0.255   4.1938  -3.0054   1.4056
 UBY  H25B  H  HCH3  0   0.240   4.2137  -3.6462  -0.2410
 UBY  HO19  H  HOH1  0   0.489   7.7537  -2.6969  -1.8148

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
 UBY  C6   C1    aromatic  1.390  0.020  1.390
 UBY  C1   C2    aromatic  1.388  0.020  1.388
 UBY  C1   H1    single    0.930  0.020  1.080
 UBY  C3   C2    aromatic  1.390  0.020  1.390
 UBY  C2   H2    single    0.930  0.020  1.080
 UBY  C4   C3    aromatic  1.390  0.020  1.390
 UBY  C3   H3    single    0.930  0.020  1.080
 UBY  C5   C4    aromatic  1.393  0.020  1.393
 UBY  C7   C4    single    1.498  0.020  1.498
 UBY  C5   C6    aromatic  1.387  0.020  1.387
 UBY  C5   H5    single    0.930  0.020  1.080
 UBY  C6   H6    single    0.930  0.020  1.080
 UBY  O8   C7    single    1.434  0.020  1.434
 UBY  C7   H7    single    0.970  0.020  1.090
 UBY  C7   H7A   single    0.970  0.020  1.090
 UBY  C9   O8    single    1.334  0.020  1.334
 UBY  N10  C9    single    1.349  0.020  1.349
 UBY  O21  C9    double    1.214  0.020  1.214
 UBY  C11  N10   single    1.437  0.020  1.437
 UBY  N10  HN10  single    0.860  0.020  1.020
 UBY  P12  C11   single    1.827  0.020  1.827
 UBY  C11  H11   single    0.970  0.020  1.090
 UBY  C11  H11A  single    0.970  0.020  1.090
 UBY  N13  P12   single    1.666  0.020  1.666
 UBY  P12  O22   double    1.488  0.020  1.488
 UBY  P12  O23   single    1.612  0.020  1.612
 UBY  C14  N13   single    1.457  0.020  1.457
 UBY  N13  HN13  single    0.890  0.020  1.040
 UBY  C20  C14   single    1.531  0.020  1.531
 UBY  C14  C15   single    1.524  0.020  1.524
 UBY  C14  H14   single    0.970  0.020  1.090
 UBY  C15  O24   double    1.222  0.020  1.222
 UBY  C15  N16   single    1.339  0.020  1.339
 UBY  N16  C17   single    1.442  0.020  1.442
 UBY  N16  HN16  single    0.860  0.020  1.020
 UBY  C25  C17   single    1.531  0.020  1.531
 UBY  C17  C18   single    1.516  0.020  1.516
 UBY  C17  H17   single    0.970  0.020  1.090
 UBY  C18  O32   double    1.205  0.020  1.205
 UBY  C18  O19   single    1.322  0.020  1.322
 UBY  O19  HO19  single    0.850  0.020  0.980
 UBY  C21  C20   single    1.530  0.020  1.530
 UBY  C20  H20   single    0.970  0.020  1.090
 UBY  C20  H20A  single    0.970  0.020  1.090
 UBY  C22  C21   single    1.526  0.020  1.526
 UBY  C21  C23   single    1.525  0.020  1.525
 UBY  C21  H21   single    0.970  0.020  1.090
 UBY  C22  H22   single    0.970  0.020  1.090
 UBY  C22  H22A  single    0.970  0.020  1.090
 UBY  C22  H22B  single    0.970  0.020  1.090
 UBY  C23  H23   single    0.970  0.020  1.090
 UBY  C23  H23A  single    0.970  0.020  1.090
 UBY  C23  H23B  single    0.970  0.020  1.090
 UBY  O23  HO23  single    0.850  0.020  0.980
 UBY  C25  H25   single    0.970  0.020  1.090
 UBY  C25  H25A  single    0.970  0.020  1.090
 UBY  C25  H25B  single    0.970  0.020  1.090

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
 UBY  H3    C3   C4    119.79  3.000
 UBY  H3    C3   C2    119.66  3.000
 UBY  C4    C3   C2    120.54  3.000
 UBY  H2    C2   C1    120.13  3.000
 UBY  H2    C2   C3    119.87  3.000
 UBY  C1    C2   C3    120.00  3.000
 UBY  H1    C1   C6    120.08  3.000
 UBY  H1    C1   C2    120.10  3.000
 UBY  C6    C1   C2    119.82  3.000
 UBY  H6    C6   C5    119.88  3.000
 UBY  H6    C6   C1    120.09  3.000
 UBY  C5    C6   C1    120.03  3.000
 UBY  H5    C5   C4    119.74  3.000
 UBY  H5    C5   C6    119.74  3.000
 UBY  C4    C5   C6    120.51  3.000
 UBY  C7    C4   C5    120.09  3.000
 UBY  C7    C4   C3    120.80  3.000
 UBY  C5    C4   C3    119.10  3.000
 UBY  H7A   C7   H7    108.21  3.000
 UBY  H7A   C7   O8    109.85  3.000
 UBY  H7    C7   O8    110.17  3.000
 UBY  H7A   C7   C4    110.80  3.000
 UBY  H7    C7   C4    110.97  3.000
 UBY  O8    C7   C4    106.85  3.000
 UBY  C9    O8   C7    117.01  3.000
 UBY  N10   C9   O21   124.84  3.000
 UBY  O21   C9   O8    124.41  3.000
 UBY  N10   C9   O8    110.75  3.000
 UBY  HN10  N10  C11   118.21  3.000
 UBY  HN10  N10  C9    119.27  3.000
 UBY  C11   N10  C9    121.78  3.000
 UBY  H11A  C11  H11   107.11  3.000
 UBY  H11A  C11  P12   110.62  3.000
 UBY  H11   C11  P12   108.69  3.000
 UBY  H11A  C11  N10   110.59  3.000
 UBY  H11   C11  N10   109.20  3.000
 UBY  P12   C11  N10   110.52  3.000
 UBY  N13   P12  O23   104.95  3.000
 UBY  O23   P12  O22   107.77  3.000
 UBY  N13   P12  O22   119.37  3.000
 UBY  O23   P12  C11   107.08  3.000
 UBY  O22   P12  C11   113.96  3.000
 UBY  N13   P12  C11   102.81  3.000
 UBY  HO23  O23  P12   114.67  3.000
 UBY  HN13  N13  C14   113.23  3.000
 UBY  HN13  N13  P12   115.35  3.000
 UBY  C14   N13  P12   120.56  3.000
 UBY  H14   C14  C20   109.48  3.000
 UBY  H14   C14  C15   109.68  3.000
 UBY  C20   C14  C15   109.86  3.000
 UBY  H14   C14  N13   107.63  3.000
 UBY  C15   C14  N13   107.60  3.000
 UBY  C20   C14  N13   112.54  3.000
 UBY  N16   C15  O24   123.62  3.000
 UBY  N16   C15  C14   115.55  3.000
 UBY  O24   C15  C14   120.81  3.000
 UBY  H20A  C20  H20   106.58  3.000
 UBY  H20A  C20  C21   109.47  3.000
 UBY  H20   C20  C21   109.19  3.000
 UBY  H20A  C20  C14   108.04  3.000
 UBY  H20   C20  C14   107.59  3.000
 UBY  C21   C20  C14   115.60  3.000
 UBY  H21   C21  C23   107.45  3.000
 UBY  H21   C21  C22   108.21  3.000
 UBY  C23   C21  C22   110.43  3.000
 UBY  H21   C21  C20   108.97  3.000
 UBY  C23   C21  C20   109.41  3.000
 UBY  C22   C21  C20   112.24  3.000
 UBY  H22B  C22  H22A  107.47  3.000
 UBY  H22B  C22  H22   107.67  3.000
 UBY  H22A  C22  H22   107.02  3.000
 UBY  H22B  C22  C21   110.77  3.000
 UBY  H22A  C22  C21   112.89  3.000
 UBY  H22   C22  C21   110.79  3.000
 UBY  H23B  C23  H23A  107.54  3.000
 UBY  H23B  C23  H23   107.69  3.000
 UBY  H23A  C23  H23   107.83  3.000
 UBY  H23B  C23  C21   110.97  3.000
 UBY  H23A  C23  C21   111.29  3.000
 UBY  H23   C23  C21   111.35  3.000
 UBY  HN16  N16  C17   117.58  3.000
 UBY  HN16  N16  C15   119.38  3.000
 UBY  C17   N16  C15   122.99  3.000
 UBY  H17   C17  C25   108.92  3.000
 UBY  H17   C17  C18   107.99  3.000
 UBY  C25   C17  C18   110.72  3.000
 UBY  H17   C17  N16   108.31  3.000
 UBY  C18   C17  N16   108.46  3.000
 UBY  C25   C17  N16   112.32  3.000
 UBY  O19   C18  O32   124.14  3.000
 UBY  O19   C18  C17   111.43  3.000
 UBY  O32   C18  C17   124.42  3.000
 UBY  H25B  C25  H25A  108.40  3.000
 UBY  H25B  C25  H25   108.68  3.000
 UBY  H25A  C25  H25   107.87  3.000
 UBY  H25B  C25  C17   111.07  3.000
 UBY  H25A  C25  C17   109.41  3.000
 UBY  H25   C25  C17   111.31  3.000
 UBY  HO19  O19  C18   110.26  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
 UBY  CONST_01  C6    C1   C2   C3      0.00   0.0  0
 UBY  CONST_02  C6    C5   C4   C3      0.00   0.0  0
 UBY  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 UBY  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 UBY  CONST_05  C4    C5   C6   C1      0.00   0.0  0
 UBY  CONST_06  C4    C3   C2   C1      0.00   0.0  0
 UBY  CONST_07  C7    C4   C3   C2    180.00   0.0  0
 UBY  CONST_08  C7    C4   C5   C6    180.00   0.0  0
 UBY  CONST_09  H1    C1   C2   C3    180.00   0.0  0
 UBY  CONST_10  H5    C5   C4   C3    180.00   0.0  0
 UBY  CONST_11  H6    C6   C1   C2    180.00   0.0  0
 UBY  CONST_12  H3    C3   C2   C1    180.00   0.0  0
 UBY  CONST_13  H2    C2   C1   C6    180.00   0.0  0
 UBY  CONST_14  C17   N16  C15  C14   180.00   0.0  0
 UBY  CONST_15  C17   N16  C15  O24     0.00   0.0  0
 UBY  CONST_16  HN16  N16  C15  C14     0.00   0.0  0
 UBY  CONST_17  HO19  O19  C18  C17   180.00   0.0  0
 UBY  Var_01    O8    C7   C4   C3   -102.59  30.0  2
 UBY  Var_02    N10   C9   O8   C7    178.47  30.0  1
 UBY  Var_03    C11   N10  C9   O8   -175.76  30.0  1
 UBY  Var_04    P12   C11  N10  C9     88.12  30.0  1
 UBY  Var_05    N13   P12  C11  N10  -173.26  30.0  1
 UBY  Var_06    C14   N13  P12  C11   178.87  30.0  1
 UBY  Var_07    C22   C21  C20  C14    61.84  30.0  2
 UBY  Var_08    H22   C22  C21  C20   177.32  30.0  3
 UBY  Var_09    H23   C23  C21  C20    58.44  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
 UBY  chir_02  C14  N13  C20  C15  negativ
 UBY  chir_03  C17  N16  C25  C18  negativ
 UBY  chir_04  P12  N13  O22  O23  both

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
 UBY  plan-1  C3    0.020
 UBY  plan-1  C2    0.020
 UBY  plan-1  C1    0.020
 UBY  plan-1  C6    0.020
 UBY  plan-1  C5    0.020
 UBY  plan-1  C4    0.020
 UBY  plan-1  C7    0.020
 UBY  plan-1  H3    0.020
 UBY  plan-1  H2    0.020
 UBY  plan-1  H1    0.020
 UBY  plan-1  H6    0.020
 UBY  plan-1  H5    0.020
 UBY  plan-2  C14   0.020
 UBY  plan-2  C15   0.020
 UBY  plan-2  O24   0.020
 UBY  plan-2  N16   0.020
 UBY  plan-2  C17   0.020
 UBY  plan-2  HN16  0.020
 UBY  plan-3  C17   0.020
 UBY  plan-3  C18   0.020
 UBY  plan-3  O32   0.020
 UBY  plan-3  O19   0.020
 UBY  plan-3  HO19  0.020
 UBY  plan-4  O8    0.020
 UBY  plan-4  C9    0.020
 UBY  plan-4  O21   0.020
 UBY  plan-4  N10   0.020

