# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 11:41:24 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: (2S)-2-({N-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl}amino)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](NC(=O)[C@H](CC(C)C)N[P](O)(=O)CNC(=O)OCc1ccccc1)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
 UBZ  UBZ  '(2S)-2-({N-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl}amino)butanoic acid'  peptide  60  30  .  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_UBZ
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
 UBZ  C3    C  CR16  0  -0.285   -6.7883  -0.2029  -1.5084
 UBZ  C2    C  CR16  0  -0.242   -8.0428   0.3327  -1.7609
 UBZ  C1    C  CR16  0  -0.261   -9.0977   0.0710  -0.8946
 UBZ  C6    C  CR16  0  -0.242   -8.8926  -0.7295   0.2209
 UBZ  C5    C  CR16  0  -0.295   -7.6343  -1.2621   0.4717
 UBZ  C4    C  CR6   0   0.076   -6.5733  -1.0049  -0.3901
 UBZ  C7    C  CH2   0  -0.240   -5.2088  -1.5560  -0.1095
 UBZ  O8    O  O2    0  -0.478   -4.4599  -0.5101   0.5233
 UBZ  C9    C  C     0   0.764   -3.1827  -0.7725   0.8115
 UBZ  O21   O  O     0  -0.513   -2.6307  -1.8258   0.5749
 UBZ  N10   N  NH1   0  -0.656   -2.6064   0.2830   1.4234
 UBZ  C11   C  CH2   0  -0.568   -1.2004   0.3103   1.7202
 UBZ  P12   P  P     0   1.309   -0.2604   0.9660   0.3004
 UBZ  O22   O  O     0  -0.713   -0.4607   0.2532  -0.9880
 UBZ  O23   O  OH1   0  -0.751   -0.7985   2.4838   0.1192
 UBZ  N13   N  NH1   0  -0.779    1.3090   0.9435   0.8340
 UBZ  C14   C  CH1   0  -0.213    2.4370   1.0806  -0.0767
 UBZ  C15   C  C     0   0.593    3.5204   0.1266   0.4145
 UBZ  O24   O  O     0  -0.489    3.9851   0.2256   1.5399
 UBZ  C20   C  CH2   0  -0.404    2.9616   2.5138  -0.1427
 UBZ  C21   C  CH1   0  -0.263    4.1292   2.7365  -1.1056
 UBZ  C22   C  CH3   0  -0.660    3.7611   2.3920  -2.5452
 UBZ  C23   C  CH3   0  -0.649    4.6025   4.1834  -1.0069
 UBZ  N16   N  NH1   0  -0.641    3.9046  -0.8283  -0.4445
 UBZ  C17   C  CH1   0  -0.175    4.9139  -1.7936  -0.1002
 UBZ  C18   C  C     0   0.546    6.2810  -1.1324  -0.0172
 UBZ  O32   O  O     0  -0.426    6.5824  -0.1090  -0.5725
 UBZ  C25   C  CH2   0  -0.471    4.9403  -2.9256  -1.1327
 UBZ  C26   C  CH3   0  -0.662    3.6424  -3.7208  -1.1646
 UBZ  O19   O  OH1   0  -0.591    7.1169  -1.8552   0.7146
 UBZ  H3    H  HCR6  0   0.255   -5.9706  -0.0005  -2.1905
 UBZ  H2    H  HCR6  0   0.258   -8.1992   0.9515  -2.6349
 UBZ  H1    H  HCR6  0   0.259  -10.0774   0.4867  -1.0919
 UBZ  H6    H  HCR6  0   0.258   -9.7115  -0.9404   0.8964
 UBZ  H5    H  HCR6  0   0.255   -7.4789  -1.8880   1.3425
 UBZ  H7    H  HCH2  0   0.250   -5.2667  -2.4264   0.5472
 UBZ  H7A   H  HCH2  0   0.249   -4.7157  -1.8604  -1.0347
 UBZ  HN10  H  HNH1  0   0.410   -3.1370   1.1311   1.5416
 UBZ  H11   H  HCH2  0   0.304   -1.0275   0.9235   2.6065
 UBZ  H11A  H  HCH2  0   0.297   -0.8400  -0.6919   1.9482
 UBZ  HO23  H  HOH1  0   0.484   -0.6344   3.0715   0.8676
 UBZ  HN13  H  HNH1  0   0.402    1.4926   1.2662   1.7761
 UBZ  H14   H  HCH1  0   0.264    2.0892   0.7714  -1.0644
 UBZ  H20   H  HCH2  0   0.233    2.1277   3.1616  -0.4329
 UBZ  H20A  H  HCH2  0   0.233    3.2577   2.8194   0.8657
 UBZ  H21   H  HCH1  0   0.237    4.9618   2.0920  -0.8042
 UBZ  H22   H  HCH3  0   0.233    4.5940   2.6007  -3.2181
 UBZ  H22A  H  HCH3  0   0.221    3.5048   1.3394  -2.6745
 UBZ  H22B  H  HCH3  0   0.219    2.9061   2.9832  -2.8820
 UBZ  H23   H  HCH3  0   0.226    4.9075   4.4344   0.0104
 UBZ  H23A  H  HCH3  0   0.227    5.4527   4.3663  -1.6659
 UBZ  H23B  H  HCH3  0   0.215    3.8074   4.8754  -1.2957
 UBZ  HN16  H  HNH1  0   0.407    3.5407  -0.8289  -1.3841
 UBZ  H17   H  HCH1  0   0.286    4.6800  -2.2207   0.8791
 UBZ  H25   H  HCH2  0   0.247    5.1555  -2.5083  -2.1207
 UBZ  H25A  H  HCH2  0   0.262    5.7676  -3.5947  -0.8932
 UBZ  H26   H  HCH3  0   0.228    2.7907  -3.1135  -1.4719
 UBZ  H26A  H  HCH3  0   0.243    3.7247  -4.5468  -1.8701
 UBZ  H26B  H  HCH3  0   0.230    3.4168  -4.1404  -0.1833
 UBZ  HO19  H  HOH1  0   0.485    7.9987  -1.4526   0.7140

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
 UBZ  C2   C1    aromatic  1.390  0.020  1.390
 UBZ  C1   C6    aromatic  1.388  0.020  1.388
 UBZ  C1   H1    single    0.930  0.020  1.080
 UBZ  C2   C3    aromatic  1.387  0.020  1.387
 UBZ  C2   H2    single    0.930  0.020  1.080
 UBZ  C3   C4    aromatic  1.393  0.020  1.393
 UBZ  C3   H3    single    0.930  0.020  1.080
 UBZ  C4   C7    single    1.498  0.020  1.498
 UBZ  C4   C5    aromatic  1.391  0.020  1.391
 UBZ  C6   C5    aromatic  1.389  0.020  1.389
 UBZ  C5   H5    single    0.930  0.020  1.080
 UBZ  C6   H6    single    0.930  0.020  1.080
 UBZ  C7   O8    single    1.434  0.020  1.434
 UBZ  C7   H7    single    0.970  0.020  1.090
 UBZ  C7   H7A   single    0.970  0.020  1.090
 UBZ  O8   C9    single    1.335  0.020  1.335
 UBZ  C9   O21   double    1.213  0.020  1.213
 UBZ  C9   N10   single    1.349  0.020  1.349
 UBZ  N10  C11   single    1.437  0.020  1.437
 UBZ  N10  HN10  single    0.860  0.020  1.020
 UBZ  C11  P12   single    1.825  0.020  1.825
 UBZ  C11  H11   single    0.970  0.020  1.090
 UBZ  C11  H11A  single    0.970  0.020  1.090
 UBZ  O22  P12   double    1.486  0.020  1.486
 UBZ  O23  P12   single    1.621  0.020  1.621
 UBZ  P12  N13   single    1.658  0.020  1.658
 UBZ  N13  C14   single    1.456  0.020  1.456
 UBZ  N13  HN13  single    0.890  0.020  1.040
 UBZ  C15  C14   single    1.525  0.020  1.525
 UBZ  C14  C20   single    1.528  0.020  1.528
 UBZ  C14  H14   single    0.970  0.020  1.090
 UBZ  N16  C15   single    1.341  0.020  1.341
 UBZ  C15  O24   double    1.222  0.020  1.222
 UBZ  C17  N16   single    1.438  0.020  1.438
 UBZ  N16  HN16  single    0.860  0.020  1.020
 UBZ  C18  C17   single    1.521  0.020  1.521
 UBZ  C17  C25   single    1.532  0.020  1.532
 UBZ  C17  H17   single    0.970  0.020  1.090
 UBZ  O32  C18   double    1.203  0.020  1.203
 UBZ  O19  C18   single    1.325  0.020  1.325
 UBZ  O19  HO19  single    0.850  0.020  0.980
 UBZ  C20  C21   single    1.530  0.020  1.530
 UBZ  C20  H20   single    0.970  0.020  1.090
 UBZ  C20  H20A  single    0.970  0.020  1.090
 UBZ  C23  C21   single    1.526  0.020  1.526
 UBZ  C21  C22   single    1.525  0.020  1.525
 UBZ  C21  H21   single    0.970  0.020  1.090
 UBZ  C22  H22   single    0.970  0.020  1.090
 UBZ  C22  H22A  single    0.970  0.020  1.090
 UBZ  C22  H22B  single    0.970  0.020  1.090
 UBZ  C23  H23   single    0.970  0.020  1.090
 UBZ  C23  H23A  single    0.970  0.020  1.090
 UBZ  C23  H23B  single    0.970  0.020  1.090
 UBZ  O23  HO23  single    0.850  0.020  0.980
 UBZ  C25  C26   single    1.522  0.020  1.522
 UBZ  C25  H25   single    0.970  0.020  1.090
 UBZ  C25  H25A  single    0.970  0.020  1.090
 UBZ  C26  H26   single    0.970  0.020  1.090
 UBZ  C26  H26A  single    0.970  0.020  1.090
 UBZ  C26  H26B  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
 UBZ  H3    C3   C4    119.76  3.000
 UBZ  H3    C3   C2    119.71  3.000
 UBZ  C4    C3   C2    120.53  3.000
 UBZ  H2    C2   C1    120.09  3.000
 UBZ  H2    C2   C3    119.89  3.000
 UBZ  C1    C2   C3    120.02  3.000
 UBZ  H1    C1   C6    120.11  3.000
 UBZ  H1    C1   C2    120.07  3.000
 UBZ  C6    C1   C2    119.82  3.000
 UBZ  H6    C6   C5    119.87  3.000
 UBZ  H6    C6   C1    120.14  3.000
 UBZ  C5    C6   C1    119.99  3.000
 UBZ  H5    C5   C4    119.69  3.000
 UBZ  H5    C5   C6    119.76  3.000
 UBZ  C4    C5   C6    120.55  3.000
 UBZ  C7    C4   C5    120.71  3.000
 UBZ  C5    C4   C3    119.09  3.000
 UBZ  C7    C4   C3    120.18  3.000
 UBZ  H7A   C7   H7    108.14  3.000
 UBZ  H7A   C7   O8    109.97  3.000
 UBZ  H7    C7   O8    110.11  3.000
 UBZ  H7A   C7   C4    110.80  3.000
 UBZ  H7    C7   C4    110.95  3.000
 UBZ  O8    C7   C4    106.86  3.000
 UBZ  C9    O8   C7    116.84  3.000
 UBZ  N10   C9   O21   125.00  3.000
 UBZ  N10   C9   O8    110.66  3.000
 UBZ  O21   C9   O8    124.34  3.000
 UBZ  HN10  N10  C11   118.36  3.000
 UBZ  HN10  N10  C9    119.13  3.000
 UBZ  C11   N10  C9    121.76  3.000
 UBZ  H11A  C11  H11   107.13  3.000
 UBZ  H11A  C11  P12   108.85  3.000
 UBZ  H11   C11  P12   110.39  3.000
 UBZ  H11A  C11  N10   110.45  3.000
 UBZ  H11   C11  N10   109.47  3.000
 UBZ  P12   C11  N10   110.50  3.000
 UBZ  N13   P12  O23   111.29  3.000
 UBZ  N13   P12  O22   113.59  3.000
 UBZ  O23   P12  O22   107.91  3.000
 UBZ  N13   P12  C11   103.44  3.000
 UBZ  O23   P12  C11   104.63  3.000
 UBZ  O22   P12  C11   115.65  3.000
 UBZ  HO23  O23  P12   115.28  3.000
 UBZ  HN13  N13  C14   114.30  3.000
 UBZ  HN13  N13  P12   117.82  3.000
 UBZ  C14   N13  P12   122.06  3.000
 UBZ  H14   C14  C20   109.63  3.000
 UBZ  H14   C14  C15   109.91  3.000
 UBZ  C20   C14  C15   110.91  3.000
 UBZ  H14   C14  N13   107.00  3.000
 UBZ  C20   C14  N13   112.42  3.000
 UBZ  C15   C14  N13   106.86  3.000
 UBZ  N16   C15  O24   122.61  3.000
 UBZ  O24   C15  C14   121.09  3.000
 UBZ  N16   C15  C14   116.28  3.000
 UBZ  H20A  C20  H20   106.56  3.000
 UBZ  H20A  C20  C21   109.44  3.000
 UBZ  H20   C20  C21   109.17  3.000
 UBZ  H20A  C20  C14   108.36  3.000
 UBZ  H20   C20  C14   107.75  3.000
 UBZ  C21   C20  C14   115.21  3.000
 UBZ  H21   C21  C23   107.72  3.000
 UBZ  H21   C21  C22   108.08  3.000
 UBZ  C23   C21  C22   110.49  3.000
 UBZ  H21   C21  C20   108.75  3.000
 UBZ  C22   C21  C20   112.15  3.000
 UBZ  C23   C21  C20   109.52  3.000
 UBZ  H22B  C22  H22A  107.55  3.000
 UBZ  H22B  C22  H22   107.69  3.000
 UBZ  H22A  C22  H22   106.91  3.000
 UBZ  H22B  C22  C21   110.95  3.000
 UBZ  H22A  C22  C21   112.73  3.000
 UBZ  H22   C22  C21   110.78  3.000
 UBZ  H23B  C23  H23A  107.53  3.000
 UBZ  H23B  C23  H23   107.70  3.000
 UBZ  H23A  C23  H23   107.86  3.000
 UBZ  H23B  C23  C21   110.96  3.000
 UBZ  H23A  C23  C21   111.20  3.000
 UBZ  H23   C23  C21   111.42  3.000
 UBZ  HN16  N16  C17   118.44  3.000
 UBZ  HN16  N16  C15   119.63  3.000
 UBZ  C17   N16  C15   121.72  3.000
 UBZ  H17   C17  C25   108.58  3.000
 UBZ  H17   C17  C18   108.25  3.000
 UBZ  C25   C17  C18   110.03  3.000
 UBZ  H17   C17  N16   109.04  3.000
 UBZ  C25   C17  N16   110.28  3.000
 UBZ  C18   C17  N16   110.61  3.000
 UBZ  O19   C18  O32   124.11  3.000
 UBZ  O19   C18  C17   111.10  3.000
 UBZ  O32   C18  C17   124.75  3.000
 UBZ  H25A  C25  H25   106.45  3.000
 UBZ  H25A  C25  C26   109.32  3.000
 UBZ  H25   C25  C26   110.36  3.000
 UBZ  H25A  C25  C17   108.56  3.000
 UBZ  H25   C25  C17   109.28  3.000
 UBZ  C26   C25  C17   112.66  3.000
 UBZ  H26B  C26  H26A  107.85  3.000
 UBZ  H26B  C26  H26   107.84  3.000
 UBZ  H26A  C26  H26   107.38  3.000
 UBZ  H26B  C26  C25   111.00  3.000
 UBZ  H26A  C26  C25   110.19  3.000
 UBZ  H26   C26  C25   112.39  3.000
 UBZ  HO19  O19  C18   110.30  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
 UBZ  CONST_01  C6    C1   C2   C3      0.00   0.0  0
 UBZ  CONST_02  C6    C5   C4   C3      0.00   0.0  0
 UBZ  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 UBZ  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 UBZ  CONST_05  C4    C3   C2   C1      0.00   0.0  0
 UBZ  CONST_06  C4    C5   C6   C1      0.00   0.0  0
 UBZ  CONST_07  C7    C4   C3   C2    180.00   0.0  0
 UBZ  CONST_08  C7    C4   C5   C6    180.00   0.0  0
 UBZ  CONST_09  H1    C1   C2   C3    180.00   0.0  0
 UBZ  CONST_10  H5    C5   C4   C3    180.00   0.0  0
 UBZ  CONST_11  H6    C6   C1   C2    180.00   0.0  0
 UBZ  CONST_12  H3    C3   C2   C1    180.00   0.0  0
 UBZ  CONST_13  H2    C2   C1   C6    180.00   0.0  0
 UBZ  CONST_14  C17   N16  C15  C14   180.00   0.0  0
 UBZ  CONST_15  C17   N16  C15  O24     0.00   0.0  0
 UBZ  CONST_16  HN16  N16  C15  C14     0.00   0.0  0
 UBZ  CONST_17  HO19  O19  C18  C17   180.00   0.0  0
 UBZ  Var_01    O8    C7   C4   C3     80.89  30.0  2
 UBZ  Var_02    O21   C9   O8   C7     -0.11  30.0  3
 UBZ  Var_03    C11   N10  C9   O8   -173.72  30.0  2
 UBZ  Var_04    P12   C11  N10  C9     87.40  30.0  3
 UBZ  Var_05    O22   P12  C11  N10   -56.05  30.0  3
 UBZ  Var_06    C14   N13  P12  C11   164.98  30.0  3
 UBZ  Var_07    C23   C21  C20  C14  -176.60  30.0  3
 UBZ  Var_08    H23   C23  C21  C20    58.23  30.0  3
 UBZ  Var_09    H22   C22  C21  C20   177.48  30.0  3
 UBZ  Var_10    H26   C26  C25  C17    63.42  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
 UBZ  chir_02  C14  N13  C15  C20  positiv
 UBZ  chir_03  C17  N16  C18  C25  positiv
 UBZ  chir_04  P12  O22  O23  N13  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
 UBZ  plan-1  C3    0.020
 UBZ  plan-1  C2    0.020
 UBZ  plan-1  C1    0.020
 UBZ  plan-1  C6    0.020
 UBZ  plan-1  C5    0.020
 UBZ  plan-1  C4    0.020
 UBZ  plan-1  C7    0.020
 UBZ  plan-1  H3    0.020
 UBZ  plan-1  H2    0.020
 UBZ  plan-1  H1    0.020
 UBZ  plan-1  H6    0.020
 UBZ  plan-1  H5    0.020
 UBZ  plan-2  C14   0.020
 UBZ  plan-2  C15   0.020
 UBZ  plan-2  O24   0.020
 UBZ  plan-2  N16   0.020
 UBZ  plan-2  C17   0.020
 UBZ  plan-2  HN16  0.020
 UBZ  plan-3  C17   0.020
 UBZ  plan-3  C18   0.020
 UBZ  plan-3  O32   0.020
 UBZ  plan-3  O19   0.020
 UBZ  plan-3  HO19  0.020
 UBZ  plan-4  O8    0.020
 UBZ  plan-4  C9    0.020
 UBZ  plan-4  O21   0.020
 UBZ  plan-4  N10   0.020

