# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 03:29:42 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-L-isoleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[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
 UBV  UBV  N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-L-isoleucine  peptide  64  32  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UBV
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
 UBV  C3    C  CR16   0  -0.294  -7.1711  -1.7410   0.9359
 UBV  C2    C  CR16   0  -0.242  -8.4875  -1.6644   0.5007
 UBV  C1    C  CR16   0  -0.262  -8.7682  -1.6096  -0.8581
 UBV  C6    C  CR16   0  -0.242  -7.7280  -1.6333  -1.7789
 UBV  C5    C  CR16   0  -0.289  -6.4138  -1.7107  -1.3398
 UBV  C4    C  CR6    0   0.076  -6.1232  -1.7669   0.0209
 UBV  C7    C  CH2    0  -0.233  -4.7011  -1.8253   0.4911
 UBV  O8    O  O2     0  -0.486  -4.2273  -0.4778   0.5568
 UBV  C9    C  C      0   0.745  -2.9538  -0.3029   0.9494
 UBV  O21   O  O      0  -0.526  -2.2099  -1.2221   1.2292
 UBV  N10   N  NH1    0  -0.648  -2.6545   1.0035   1.0191
 UBV  C11   C  CH2    0  -0.564  -1.2962   1.4902   1.1519
 UBV  P12   P  P      0   1.234  -0.6421   1.9872  -0.4990
 UBV  O22   O  O      0  -0.815  -1.5455   3.0916  -1.0022
 UBV  O23   O  OP    -1  -0.806  -0.4309   0.7378  -1.3180
 UBV  N13   N  NH1    0  -0.809   0.8776   2.6668  -0.1167
 UBV  C14   C  CH1    0  -0.175   2.1003   1.9931  -0.4761
 UBV  C15   C  C      0   0.577   2.2507   0.6817   0.2873
 UBV  O28   O  O      0  -0.508   1.8847   0.5500   1.4466
 UBV  C24   C  CH2    0  -0.411   3.3246   2.8487  -0.1274
 UBV  C25   C  CH1    0  -0.251   3.4101   4.2056  -0.8320
 UBV  C26   C  CH3    0  -0.648   4.7263   4.8834  -0.4622
 UBV  C27   C  CH3    0  -0.662   3.2670   4.0918  -2.3459
 UBV  N16   N  NH1    0  -0.641   2.8740  -0.2926  -0.3908
 UBV  C17   C  CH1    0  -0.122   3.4250  -1.4500   0.2799
 UBV  C18   C  C      0   0.405   4.4728  -1.0530   1.3505
 UBV  O19   O  O      0  -0.594   5.1097  -0.0016   1.1640
 UBV  C29   C  CH1    0  -0.275   4.0147  -2.4100  -0.7720
 UBV  C30   C  CH2    0  -0.405   4.2436  -3.8064  -0.1897
 UBV  C     C  CH3    0  -0.667   5.2788  -1.8600  -1.4314
 UBV  C31   C  CH3    0  -0.672   4.6296  -4.8494  -1.2306
 UBV  O20   O  OC    -1  -0.614   4.6082  -1.8530   2.2995
 UBV  H3    H  HCR6   0   0.254  -6.9593  -1.7866   1.9978
 UBV  H2    H  HCR6   0   0.258  -9.2931  -1.6496   1.2231
 UBV  H1    H  HCR6   0   0.258  -9.7942  -1.5524  -1.1987
 UBV  H6    H  HCR6   0   0.258  -7.9396  -1.5949  -2.8397
 UBV  H5    H  HCR6   0   0.255  -5.6065  -1.7336  -2.0622
 UBV  H7    H  HCH2   0   0.243  -4.6406  -2.2980   1.4739
 UBV  H7A   H  HCH2   0   0.243  -4.0901  -2.4079  -0.2021
 UBV  HN10  H  HNH1   0   0.388  -3.3322   1.6565   0.6567
 UBV  H11   H  HCH2   0   0.236  -1.2868   2.3407   1.8375
 UBV  H11A  H  HCH2   0   0.261  -0.6738   0.7144   1.5898
 UBV  HN13  H  HNH1   0   0.366   0.9144   3.6646  -0.2644
 UBV  H14   H  HCH1   0   0.221   2.1464   1.7620  -1.5500
 UBV  H24   H  HCH2   0   0.226   3.3459   3.0078   0.9551
 UBV  H24A  H  HCH2   0   0.229   4.2196   2.2668  -0.3679
 UBV  H25   H  HCH1   0   0.213   2.6022   4.8491  -0.4631
 UBV  H26   H  HCH3   0   0.214   5.5774   4.3248  -0.8594
 UBV  H26A  H  HCH3   0   0.226   4.7779   5.8962  -0.8646
 UBV  H26B  H  HCH3   0   0.224   4.8499   4.9500   0.6203
 UBV  H27   H  HCH3   0   0.216   4.0004   3.3945  -2.7583
 UBV  H27A  H  HCH3   0   0.228   2.2751   3.7450  -2.6391
 UBV  H27B  H  HCH3   0   0.229   3.4263   5.0598  -2.8238
 UBV  HN16  H  HNH1   0   0.379   3.2131  -0.0727  -1.3135
 UBV  H17   H  HCH1   0   0.220   2.6048  -1.9758   0.7787
 UBV  H29   H  HCH1   0   0.220   3.2473  -2.5105  -1.5512
 UBV  H30   H  HCH2   0   0.219   5.0100  -3.7572   0.5861
 UBV  H30A  H  HCH2   0   0.212   3.3257  -4.1298   0.3100
 UBV  H     H  HCH3   0   0.222   5.1603  -0.8298  -1.7709
 UBV  HA    H  HCH3   0   0.220   6.1272  -1.8767  -0.7455
 UBV  HB    H  HCH3   0   0.228   5.5501  -2.4504  -2.3066
 UBV  H31   H  HCH3   0   0.214   3.8936  -4.9000  -2.0362
 UBV  H31A  H  HCH3   0   0.220   5.5989  -4.6401  -1.6841
 UBV  H31B  H  HCH3   0   0.227   4.6921  -5.8409  -0.7802

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
 UBV  C    C29   single    1.528  0.020  1.528
 UBV  C    H     single    0.970  0.020  1.090
 UBV  C    HA    single    0.970  0.020  1.090
 UBV  C    HB    single    0.970  0.020  1.090
 UBV  C6   C1    aromatic  1.389  0.020  1.389
 UBV  C1   C2    aromatic  1.389  0.020  1.389
 UBV  C1   H1    single    0.930  0.020  1.080
 UBV  C3   C2    aromatic  1.389  0.020  1.389
 UBV  C2   H2    single    0.930  0.020  1.080
 UBV  C4   C3    aromatic  1.391  0.020  1.391
 UBV  C3   H3    single    0.930  0.020  1.080
 UBV  C5   C4    aromatic  1.392  0.020  1.392
 UBV  C7   C4    single    1.499  0.020  1.499
 UBV  C5   C6    aromatic  1.388  0.020  1.388
 UBV  C5   H5    single    0.930  0.020  1.080
 UBV  C6   H6    single    0.930  0.020  1.080
 UBV  O8   C7    single    1.430  0.020  1.430
 UBV  C7   H7    single    0.970  0.020  1.090
 UBV  C7   H7A   single    0.970  0.020  1.090
 UBV  C9   O8    single    1.344  0.020  1.344
 UBV  N10  C9    single    1.342  0.020  1.342
 UBV  O21  C9    double    1.215  0.020  1.215
 UBV  C11  N10   single    1.449  0.020  1.449
 UBV  N10  HN10  single    0.890  0.020  1.040
 UBV  P12  C11   single    1.844  0.020  1.844
 UBV  C11  H11   single    0.970  0.020  1.090
 UBV  C11  H11A  single    0.970  0.020  1.090
 UBV  N13  P12   single    1.708  0.020  1.708
 UBV  P12  O22   deloc     1.513  0.020  1.513
 UBV  P12  O23   deloc     1.509  0.020  1.509
 UBV  C14  N13   single    1.442  0.020  1.442
 UBV  N13  HN13  single    0.890  0.020  1.040
 UBV  C24  C14   single    1.534  0.020  1.534
 UBV  C14  C15   single    1.525  0.020  1.525
 UBV  C14  H14   single    0.970  0.020  1.090
 UBV  C15  O28   double    1.223  0.020  1.223
 UBV  C15  N16   single    1.341  0.020  1.341
 UBV  N16  C17   single    1.447  0.020  1.447
 UBV  N16  HN16  single    0.860  0.020  1.020
 UBV  C29  C17   single    1.541  0.020  1.541
 UBV  C17  C18   single    1.550  0.020  1.550
 UBV  C17  H17   single    0.970  0.020  1.090
 UBV  C18  O19   deloc     1.243  0.020  1.243
 UBV  C18  O20   deloc     1.249  0.020  1.249
 UBV  C25  C24   single    1.531  0.020  1.531
 UBV  C24  H24   single    0.970  0.020  1.090
 UBV  C24  H24A  single    0.970  0.020  1.090
 UBV  C27  C25   single    1.525  0.020  1.525
 UBV  C25  C26   single    1.526  0.020  1.526
 UBV  C25  H25   single    0.970  0.020  1.090
 UBV  C26  H26   single    0.970  0.020  1.090
 UBV  C26  H26A  single    0.970  0.020  1.090
 UBV  C26  H26B  single    0.970  0.020  1.090
 UBV  C27  H27   single    0.970  0.020  1.090
 UBV  C27  H27A  single    0.970  0.020  1.090
 UBV  C27  H27B  single    0.970  0.020  1.090
 UBV  C30  C29   single    1.530  0.020  1.530
 UBV  C29  H29   single    0.970  0.020  1.090
 UBV  C31  C30   single    1.523  0.020  1.523
 UBV  C30  H30   single    0.970  0.020  1.090
 UBV  C30  H30A  single    0.970  0.020  1.090
 UBV  C31  H31   single    0.970  0.020  1.090
 UBV  C31  H31A  single    0.970  0.020  1.090
 UBV  C31  H31B  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
 UBV  H3    C3   C4    119.76  3.000
 UBV  H3    C3   C2    119.65  3.000
 UBV  C4    C3   C2    120.59  3.000
 UBV  H2    C2   C1    120.14  3.000
 UBV  H2    C2   C3    119.82  3.000
 UBV  C1    C2   C3    120.03  3.000
 UBV  H1    C1   C6    120.13  3.000
 UBV  H1    C1   C2    120.10  3.000
 UBV  C6    C1   C2    119.76  3.000
 UBV  H6    C6   C5    119.82  3.000
 UBV  H6    C6   C1    120.16  3.000
 UBV  C5    C6   C1    120.02  3.000
 UBV  H5    C5   C4    119.68  3.000
 UBV  H5    C5   C6    119.72  3.000
 UBV  C4    C5   C6    120.61  3.000
 UBV  C7    C4   C5    120.40  3.000
 UBV  C7    C4   C3    120.59  3.000
 UBV  C5    C4   C3    118.99  3.000
 UBV  H7A   C7   H7    108.01  3.000
 UBV  H7A   C7   O8    110.27  3.000
 UBV  H7    C7   O8    110.37  3.000
 UBV  H7A   C7   C4    110.64  3.000
 UBV  H7    C7   C4    110.59  3.000
 UBV  O8    C7   C4    106.98  3.000
 UBV  C9    O8   C7    116.75  3.000
 UBV  N10   C9   O21   126.00  3.000
 UBV  O21   C9   O8    123.29  3.000
 UBV  N10   C9   O8    110.68  3.000
 UBV  HN10  N10  C11   116.45  3.000
 UBV  HN10  N10  C9    117.50  3.000
 UBV  C11   N10  C9    122.74  3.000
 UBV  H11A  C11  H11   107.34  3.000
 UBV  H11A  C11  P12   110.49  3.000
 UBV  H11   C11  P12   110.42  3.000
 UBV  H11A  C11  N10   109.51  3.000
 UBV  H11   C11  N10   109.10  3.000
 UBV  P12   C11  N10   109.93  3.000
 UBV  N13   P12  O23   109.05  3.000
 UBV  O23   P12  O22   120.50  3.000
 UBV  N13   P12  O22   108.37  3.000
 UBV  O23   P12  C11   108.21  3.000
 UBV  O22   P12  C11   106.42  3.000
 UBV  N13   P12  C11   102.85  3.000
 UBV  HN13  N13  C14   113.24  3.000
 UBV  HN13  N13  P12   113.14  3.000
 UBV  C14   N13  P12   120.85  3.000
 UBV  H14   C14  C24   107.81  3.000
 UBV  H14   C14  C15   107.70  3.000
 UBV  C24   C14  C15   106.69  3.000
 UBV  H14   C14  N13   112.17  3.000
 UBV  C15   C14  N13   111.15  3.000
 UBV  C24   C14  N13   111.08  3.000
 UBV  N16   C15  O28   122.71  3.000
 UBV  N16   C15  C14   114.68  3.000
 UBV  O28   C15  C14   122.53  3.000
 UBV  H24A  C24  H24   106.19  3.000
 UBV  H24A  C24  C25   108.92  3.000
 UBV  H24   C24  C25   108.98  3.000
 UBV  H24A  C24  C14   107.84  3.000
 UBV  H24   C24  C14   108.76  3.000
 UBV  C25   C24  C14   115.74  3.000
 UBV  H25   C25  C27   107.97  3.000
 UBV  H25   C25  C26   107.05  3.000
 UBV  C27   C25  C26   110.78  3.000
 UBV  H25   C25  C24   108.91  3.000
 UBV  C26   C25  C24   109.29  3.000
 UBV  C27   C25  C24   112.67  3.000
 UBV  H26B  C26  H26A  107.69  3.000
 UBV  H26B  C26  H26   107.67  3.000
 UBV  H26A  C26  H26   107.67  3.000
 UBV  H26B  C26  C25   111.42  3.000
 UBV  H26A  C26  C25   111.33  3.000
 UBV  H26   C26  C25   110.89  3.000
 UBV  H27B  C27  H27A  107.28  3.000
 UBV  H27B  C27  H27   107.62  3.000
 UBV  H27A  C27  H27   107.82  3.000
 UBV  H27B  C27  C25   110.79  3.000
 UBV  H27A  C27  C25   112.08  3.000
 UBV  H27   C27  C25   111.05  3.000
 UBV  HN16  N16  C17   118.10  3.000
 UBV  HN16  N16  C15   117.47  3.000
 UBV  C17   N16  C15   121.59  3.000
 UBV  H17   C17  C29   107.37  3.000
 UBV  H17   C17  C18   108.35  3.000
 UBV  C29   C17  C18   111.86  3.000
 UBV  H17   C17  N16   108.07  3.000
 UBV  C18   C17  N16   111.89  3.000
 UBV  C29   C17  N16   109.12  3.000
 UBV  O20   C18  O19   126.89  3.000
 UBV  O20   C18  C17   115.74  3.000
 UBV  O19   C18  C17   117.34  3.000
 UBV  H29   C29  C     107.75  3.000
 UBV  H29   C29  C30   106.91  3.000
 UBV  C     C29  C30   111.65  3.000
 UBV  H29   C29  C17   105.89  3.000
 UBV  C30   C29  C17   111.47  3.000
 UBV  C     C29  C17   112.76  3.000
 UBV  H30A  C30  H30   106.13  3.000
 UBV  H30A  C30  C31   108.80  3.000
 UBV  H30   C30  C31   109.79  3.000
 UBV  H30A  C30  C29   108.55  3.000
 UBV  H30   C30  C29   109.53  3.000
 UBV  C31   C30  C29   113.75  3.000
 UBV  HB    C    HA    107.64  3.000
 UBV  HB    C    H     106.78  3.000
 UBV  HA    C    H     107.12  3.000
 UBV  HB    C    C29   110.94  3.000
 UBV  HA    C    C29   111.49  3.000
 UBV  H     C    C29   112.60  3.000
 UBV  H31B  C31  H31A  107.18  3.000
 UBV  H31B  C31  H31   107.52  3.000
 UBV  H31A  C31  H31   107.52  3.000
 UBV  H31B  C31  C30   110.78  3.000
 UBV  H31A  C31  C30   112.21  3.000
 UBV  H31   C31  C30   111.40  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
 UBV  CONST_01  C6    C1   C2   C3      0.00   0.0  0
 UBV  CONST_02  C6    C5   C4   C3      0.00   0.0  0
 UBV  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 UBV  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 UBV  CONST_05  C4    C5   C6   C1      0.00   0.0  0
 UBV  CONST_06  C4    C3   C2   C1      0.00   0.0  0
 UBV  CONST_07  C7    C4   C3   C2    180.00   0.0  0
 UBV  CONST_08  C7    C4   C5   C6    180.00   0.0  0
 UBV  CONST_09  H1    C1   C2   C3    180.00   0.0  0
 UBV  CONST_10  H5    C5   C4   C3    180.00   0.0  0
 UBV  CONST_11  H6    C6   C1   C2    180.00   0.0  0
 UBV  CONST_12  H3    C3   C2   C1    180.00   0.0  0
 UBV  CONST_13  H2    C2   C1   C6    180.00   0.0  0
 UBV  CONST_15  C17   N16  C15  O28     0.00   0.0  0
 UBV  CONST_16  HN16  N16  C15  C14     0.00   0.0  0
 UBV  Var_01    O8    C7   C4   C3    -93.70  30.0  2
 UBV  Var_02    N10   C9   O8   C7   -177.54  30.0  1
 UBV  Var_03    C11   N10  C9   O8   -167.31  30.0  2
 UBV  Var_04    P12   C11  N10  C9     98.04  30.0  1
 UBV  Var_05    N13   P12  C11  N10   174.54  30.0  2
 UBV  Var_06    C14   N13  P12  C11   109.84  30.0  1
 UBV  Var_07    C27   C25  C24  C14   -52.18  30.0  1
 UBV  Var_08    H27   C27  C25  C24   -55.10  30.0  3
 UBV  Var_09    H26   C26  C25  C24    65.91  30.0  3
 UBV  Var_10    H31   C31  C30  C29   -55.22  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
 UBV  chir_02  C14  N13  C24  C15  negativ
 UBV  chir_03  C17  N16  C29  C18  negativ
 UBV  chir_04  C29  C30  C17  C    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
 UBV  plan-1  C3    0.020
 UBV  plan-1  C2    0.020
 UBV  plan-1  C1    0.020
 UBV  plan-1  C6    0.020
 UBV  plan-1  C5    0.020
 UBV  plan-1  C4    0.020
 UBV  plan-1  C7    0.020
 UBV  plan-1  H3    0.020
 UBV  plan-1  H2    0.020
 UBV  plan-1  H1    0.020
 UBV  plan-1  H6    0.020
 UBV  plan-1  H5    0.020
 UBV  plan-2  C14   0.020
 UBV  plan-2  C15   0.020
 UBV  plan-2  O28   0.020
 UBV  plan-2  N16   0.020
 UBV  plan-2  C17   0.020
 UBV  plan-2  HN16  0.020
 UBV  plan-3  C17   0.020
 UBV  plan-3  C18   0.020
 UBV  plan-3  O19   0.020
 UBV  plan-3  O20   0.020
 UBV  plan-4  O8    0.020
 UBV  plan-4  C9    0.020
 UBV  plan-4  O21   0.020
 UBV  plan-4  N10   0.020

