# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 23:16:21 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: N-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-L-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[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
 UBW  UBW  N-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-L-norvaline  peptide  61  31  .  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_UBW
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
 UBW  C3    C  CR16   0  -0.286   7.9205   0.6588   0.8517
 UBW  C2    C  CR16   0  -0.242   9.1360  -0.0006   0.7408
 UBW  C1    C  CR16   0  -0.262   9.5328  -0.5263  -0.4828
 UBW  C6    C  CR16   0  -0.242   8.7104  -0.3874  -1.5928
 UBW  C5    C  CR16   0  -0.294   7.4936   0.2722  -1.4772
 UBW  C4    C  CR6    0   0.075   7.0884   0.8012  -0.2561
 UBW  C7    C  CH2    0  -0.234   5.7597   1.4820  -0.1229
 UBW  O8    O  O2     0  -0.484   4.8413   0.5025   0.3699
 UBW  C9    C  C      0   0.745   3.5870   0.9138   0.6150
 UBW  O21   O  O      0  -0.528   3.2027   2.0491   0.4116
 UBW  N10   N  NH1    0  -0.645   2.8555  -0.0841   1.1336
 UBW  C11   C  CH2    0  -0.554   1.4214  -0.0064   1.3126
 UBW  P12   P  P      0   1.222   0.5537  -0.9484  -0.0170
 UBW  O22   O  O      0  -0.808   0.5626  -0.1528  -1.2991
 UBW  O23   O  OP    -1  -0.811   1.1413  -2.3419   0.0009
 UBW  N13   N  NH1    0  -0.791  -1.0376  -0.9144   0.6114
 UBW  C14   C  CH1    0  -0.194  -2.1770  -0.8684  -0.2853
 UBW  C15   C  C      0   0.570  -3.3874  -0.4353   0.5378
 UBW  O28   O  O      0  -0.518  -3.6488  -0.9761   1.6072
 UBW  C24   C  CH2    0  -0.415  -2.4634  -2.2101  -0.9716
 UBW  C25   C  CH1    0  -0.276  -3.5970  -2.2008  -1.9983
 UBW  C26   C  CH3    0  -0.656  -3.2600  -1.3283  -3.2047
 UBW  C27   C  CH3    0  -0.649  -3.9053  -3.6265  -2.4460
 UBW  N16   N  NH1    0  -0.628  -4.1079   0.5736   0.0385
 UBW  C17   C  CH1    0  -0.172  -5.3162   1.0567   0.6658
 UBW  C29   C  CH2    0  -0.458  -5.7246   2.3901   0.0395
 UBW  C30   C  CH2    0  -0.418  -4.6773   3.4922   0.1595
 UBW  C31   C  CH3    0  -0.662  -5.1708   4.8176  -0.4051
 UBW  C18   C  C      0   0.409  -6.4987   0.0580   0.5875
 UBW  O19   O  O      0  -0.581  -6.4457  -0.8486  -0.2606
 UBW  O20   O  OC    -1  -0.619  -7.4334   0.2942   1.3796
 UBW  H3    H  HCR6   0   0.254   7.6169   1.0699   1.8076
 UBW  H2    H  HCR6   0   0.258   9.7748  -0.1039   1.6084
 UBW  H1    H  HCR6   0   0.258  10.4815  -1.0402  -0.5708
 UBW  H6    H  HCR6   0   0.258   9.0155  -0.7920  -2.5490
 UBW  H5    H  HCR6   0   0.255   6.8558   0.3791  -2.3467
 UBW  H7    H  HCH2   0   0.243   5.8230   2.3233   0.5709
 UBW  H7A   H  HCH2   0   0.244   5.4235   1.8652  -1.0890
 UBW  HN10  H  HNH1   0   0.391   3.2577  -1.0086   1.1416
 UBW  H11   H  HCH2   0   0.247   1.1632  -0.4145   2.2934
 UBW  H11A  H  HCH2   0   0.252   1.1156   1.0383   1.3149
 UBW  HN13  H  HNH1   0   0.353  -1.1894  -1.5881   1.3526
 UBW  H14   H  HCH1   0   0.243  -1.9617  -0.1134  -1.0445
 UBW  H24   H  HCH2   0   0.224  -1.5400  -2.5407  -1.4588
 UBW  H24A  H  HCH2   0   0.213  -2.6779  -2.9496  -0.1918
 UBW  H25   H  HCH1   0   0.251  -4.4986  -1.7969  -1.5264
 UBW  H26   H  HCH3   0   0.225  -4.0697  -1.3426  -3.9361
 UBW  H26A  H  HCH3   0   0.219  -3.0920  -0.2849  -2.9327
 UBW  H26B  H  HCH3   0   0.213  -2.3546  -1.6838  -3.7034
 UBW  H27   H  HCH3   0   0.221  -4.1969  -4.2540  -1.6013
 UBW  H27A  H  HCH3   0   0.222  -4.7222  -3.6480  -3.1699
 UBW  H27B  H  HCH3   0   0.209  -3.0345  -4.0906  -2.9161
 UBW  HN16  H  HNH1   0   0.388  -3.8959   0.8901  -0.8941
 UBW  H17   H  HCH1   0   0.226  -5.0974   1.2328   1.7236
 UBW  H29   H  HCH2   0   0.218  -5.9736   2.2330  -1.0169
 UBW  H29A  H  HCH2   0   0.234  -6.6463   2.7154   0.5267
 UBW  H30   H  HCH2   0   0.214  -4.4095   3.6208   1.2126
 UBW  H30A  H  HCH2   0   0.216  -3.7579   3.1985  -0.3537
 UBW  H31   H  HCH3   0   0.217  -5.4279   4.7272  -1.4622
 UBW  H31A  H  HCH3   0   0.217  -6.0629   5.1608   0.1218
 UBW  H31B  H  HCH3   0   0.228  -4.4132   5.5967  -0.3157

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
 UBW  C6   C1    aromatic  1.388  0.020  1.388
 UBW  C1   C2    aromatic  1.390  0.020  1.390
 UBW  C1   H1    single    0.930  0.020  1.080
 UBW  C2   C3    aromatic  1.387  0.020  1.387
 UBW  C2   H2    single    0.930  0.020  1.080
 UBW  C4   C3    aromatic  1.393  0.020  1.393
 UBW  C3   H3    single    0.930  0.020  1.080
 UBW  C5   C4    aromatic  1.391  0.020  1.391
 UBW  C4   C7    single    1.499  0.020  1.499
 UBW  C6   C5    aromatic  1.389  0.020  1.389
 UBW  C5   H5    single    0.930  0.020  1.080
 UBW  C6   H6    single    0.930  0.020  1.080
 UBW  C7   O8    single    1.430  0.020  1.430
 UBW  C7   H7    single    0.970  0.020  1.090
 UBW  C7   H7A   single    0.970  0.020  1.090
 UBW  O8   C9    single    1.343  0.020  1.343
 UBW  C9   O21   double    1.216  0.020  1.216
 UBW  C9   N10   single    1.342  0.020  1.342
 UBW  N10  C11   single    1.447  0.020  1.447
 UBW  N10  HN10  single    0.860  0.020  1.020
 UBW  C11  P12   single    1.846  0.020  1.846
 UBW  C11  H11   single    0.970  0.020  1.090
 UBW  C11  H11A  single    0.970  0.020  1.090
 UBW  O22  P12   deloc     1.509  0.020  1.509
 UBW  O23  P12   deloc     1.512  0.020  1.512
 UBW  P12  N13   single    1.711  0.020  1.711
 UBW  N13  C14   single    1.451  0.020  1.451
 UBW  N13  HN13  single    0.890  0.020  1.040
 UBW  C15  C14   single    1.526  0.020  1.526
 UBW  C14  C24   single    1.534  0.020  1.534
 UBW  C14  H14   single    0.970  0.020  1.090
 UBW  N16  C15   single    1.337  0.020  1.337
 UBW  O28  C15   double    1.227  0.020  1.227
 UBW  C17  N16   single    1.445  0.020  1.445
 UBW  N16  HN16  single    0.860  0.020  1.020
 UBW  C18  C17   single    1.550  0.020  1.550
 UBW  C17  C29   single    1.529  0.020  1.529
 UBW  C17  H17   single    0.970  0.020  1.090
 UBW  O19  C18   deloc     1.243  0.020  1.243
 UBW  O20  C18   deloc     1.248  0.020  1.248
 UBW  C24  C25   single    1.529  0.020  1.529
 UBW  C24  H24   single    0.970  0.020  1.090
 UBW  C24  H24A  single    0.970  0.020  1.090
 UBW  C27  C25   single    1.526  0.020  1.526
 UBW  C25  C26   single    1.526  0.020  1.526
 UBW  C25  H25   single    0.970  0.020  1.090
 UBW  C26  H26   single    0.970  0.020  1.090
 UBW  C26  H26A  single    0.970  0.020  1.090
 UBW  C26  H26B  single    0.970  0.020  1.090
 UBW  C27  H27   single    0.970  0.020  1.090
 UBW  C27  H27A  single    0.970  0.020  1.090
 UBW  C27  H27B  single    0.970  0.020  1.090
 UBW  C29  C30   single    1.525  0.020  1.525
 UBW  C29  H29   single    0.970  0.020  1.090
 UBW  C29  H29A  single    0.970  0.020  1.090
 UBW  C30  C31   single    1.523  0.020  1.523
 UBW  C30  H30   single    0.970  0.020  1.090
 UBW  C30  H30A  single    0.970  0.020  1.090
 UBW  C31  H31   single    0.970  0.020  1.090
 UBW  C31  H31A  single    0.970  0.020  1.090
 UBW  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
 UBW  H3    C3   C4    119.70  3.000
 UBW  H3    C3   C2    119.74  3.000
 UBW  C4    C3   C2    120.56  3.000
 UBW  H2    C2   C1    120.08  3.000
 UBW  H2    C2   C3    119.89  3.000
 UBW  C1    C2   C3    120.02  3.000
 UBW  H1    C1   C6    120.11  3.000
 UBW  H1    C1   C2    120.09  3.000
 UBW  C6    C1   C2    119.80  3.000
 UBW  H6    C6   C5    119.87  3.000
 UBW  H6    C6   C1    120.13  3.000
 UBW  C5    C6   C1    120.00  3.000
 UBW  H5    C5   C4    119.69  3.000
 UBW  H5    C5   C6    119.72  3.000
 UBW  C4    C5   C6    120.59  3.000
 UBW  C7    C4   C5    120.60  3.000
 UBW  C7    C4   C3    120.35  3.000
 UBW  C5    C4   C3    119.03  3.000
 UBW  H7A   C7   H7    108.03  3.000
 UBW  H7A   C7   O8    110.32  3.000
 UBW  H7    C7   O8    110.23  3.000
 UBW  H7A   C7   C4    110.70  3.000
 UBW  H7    C7   C4    110.79  3.000
 UBW  O8    C7   C4    106.78  3.000
 UBW  C9    O8   C7    116.94  3.000
 UBW  N10   C9   O21   125.95  3.000
 UBW  N10   C9   O8    110.62  3.000
 UBW  O21   C9   O8    123.42  3.000
 UBW  HN10  N10  C11   116.33  3.000
 UBW  HN10  N10  C9    117.88  3.000
 UBW  C11   N10  C9    123.24  3.000
 UBW  H11A  C11  H11   106.86  3.000
 UBW  H11A  C11  P12   111.05  3.000
 UBW  H11   C11  P12   110.16  3.000
 UBW  H11A  C11  N10   109.28  3.000
 UBW  H11   C11  N10   108.96  3.000
 UBW  P12   C11  N10   110.44  3.000
 UBW  N13   P12  O23   112.04  3.000
 UBW  N13   P12  O22   107.88  3.000
 UBW  O23   P12  O22   119.57  3.000
 UBW  N13   P12  C11    99.35  3.000
 UBW  O23   P12  C11   106.20  3.000
 UBW  O22   P12  C11   109.88  3.000
 UBW  HN13  N13  C14   110.84  3.000
 UBW  HN13  N13  P12   113.25  3.000
 UBW  C14   N13  P12   120.27  3.000
 UBW  H14   C14  C24   109.29  3.000
 UBW  H14   C14  C15   109.57  3.000
 UBW  C24   C14  C15   109.96  3.000
 UBW  H14   C14  N13   107.27  3.000
 UBW  C24   C14  N13   113.29  3.000
 UBW  C15   C14  N13   107.37  3.000
 UBW  N16   C15  O28   122.93  3.000
 UBW  O28   C15  C14   120.94  3.000
 UBW  N16   C15  C14   116.12  3.000
 UBW  H24A  C24  H24   106.13  3.000
 UBW  H24A  C24  C25   109.68  3.000
 UBW  H24   C24  C25   109.16  3.000
 UBW  H24A  C24  C14   107.96  3.000
 UBW  H24   C24  C14   107.79  3.000
 UBW  C25   C24  C14   115.68  3.000
 UBW  H25   C25  C27   107.75  3.000
 UBW  H25   C25  C26   108.16  3.000
 UBW  C27   C25  C26   110.29  3.000
 UBW  H25   C25  C24   108.86  3.000
 UBW  C26   C25  C24   111.74  3.000
 UBW  C27   C25  C24   109.94  3.000
 UBW  H26B  C26  H26A  107.29  3.000
 UBW  H26B  C26  H26   107.73  3.000
 UBW  H26A  C26  H26   107.09  3.000
 UBW  H26B  C26  C25   110.95  3.000
 UBW  H26A  C26  C25   112.55  3.000
 UBW  H26   C26  C25   111.00  3.000
 UBW  H27B  C27  H27A  107.61  3.000
 UBW  H27B  C27  H27   107.55  3.000
 UBW  H27A  C27  H27   107.57  3.000
 UBW  H27B  C27  C25   111.23  3.000
 UBW  H27A  C27  C25   111.35  3.000
 UBW  H27   C27  C25   111.34  3.000
 UBW  HN16  N16  C17   118.23  3.000
 UBW  HN16  N16  C15   118.00  3.000
 UBW  C17   N16  C15   122.76  3.000
 UBW  H17   C17  C18   107.76  3.000
 UBW  H17   C17  C29   108.00  3.000
 UBW  C18   C17  C29   109.73  3.000
 UBW  H17   C17  N16   107.84  3.000
 UBW  C29   C17  N16   109.71  3.000
 UBW  C18   C17  N16   113.63  3.000
 UBW  H29A  C29  H29   106.30  3.000
 UBW  H29A  C29  C30   109.22  3.000
 UBW  H29   C29  C30   109.59  3.000
 UBW  H29A  C29  C17   107.61  3.000
 UBW  H29   C29  C17   109.29  3.000
 UBW  C30   C29  C17   114.50  3.000
 UBW  H30A  C30  H30   106.12  3.000
 UBW  H30A  C30  C31   109.41  3.000
 UBW  H30   C30  C31   109.51  3.000
 UBW  H30A  C30  C29   110.27  3.000
 UBW  H30   C30  C29   109.19  3.000
 UBW  C31   C30  C29   112.16  3.000
 UBW  H31B  C31  H31A  107.67  3.000
 UBW  H31B  C31  H31   107.60  3.000
 UBW  H31A  C31  H31   107.52  3.000
 UBW  H31B  C31  C30   111.49  3.000
 UBW  H31A  C31  C30   111.07  3.000
 UBW  H31   C31  C30   111.31  3.000
 UBW  O20   C18  O19   127.11  3.000
 UBW  O20   C18  C17   114.68  3.000
 UBW  O19   C18  C17   118.17  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
 UBW  CONST_01  C6    C1   C2   C3      0.00   0.0  0
 UBW  CONST_02  C6    C5   C4   C3      0.00   0.0  0
 UBW  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 UBW  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 UBW  CONST_05  C4    C5   C6   C1      0.00   0.0  0
 UBW  CONST_06  C4    C3   C2   C1      0.00   0.0  0
 UBW  CONST_07  C7    C4   C3   C2    180.00   0.0  0
 UBW  CONST_08  C7    C4   C5   C6    180.00   0.0  0
 UBW  CONST_09  H1    C1   C2   C3    180.00   0.0  0
 UBW  CONST_10  H5    C5   C4   C3    180.00   0.0  0
 UBW  CONST_11  H6    C6   C1   C2    180.00   0.0  0
 UBW  CONST_12  H3    C3   C2   C1    180.00   0.0  0
 UBW  CONST_13  H2    C2   C1   C6    180.00   0.0  0
 UBW  CONST_14  C17   N16  C15  C14   180.00   0.0  0
 UBW  CONST_15  C17   N16  C15  O28     0.00   0.0  0
 UBW  CONST_16  HN16  N16  C15  C14     0.00   0.0  0
 UBW  Var_01    O8    C7   C4   C3    -82.60  30.0  2
 UBW  Var_02    O21   C9   O8   C7      1.67  30.0  3
 UBW  Var_03    C11   N10  C9   O8   -170.35  30.0  2
 UBW  Var_04    P12   C11  N10  C9    102.23  30.0  3
 UBW  Var_05    O22   P12  C11  N10   -76.79  30.0  3
 UBW  Var_06    C14   N13  P12  C11   147.19  30.0  3
 UBW  Var_07    C27   C25  C24  C14  -171.77  30.0  3
 UBW  Var_08    C31   C30  C29  C17  -176.53  30.0  3
 UBW  Var_09    H27   C27  C25  C24    59.16  30.0  3
 UBW  Var_10    H26   C26  C25  C24   179.12  30.0  3
 UBW  Var_11    H31   C31  C30  C29   -59.73  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
 UBW  chir_02  C14  N13  C15  C24  positiv
 UBW  chir_03  C17  N16  C18  C29  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
 UBW  plan-1  C3    0.020
 UBW  plan-1  C2    0.020
 UBW  plan-1  C1    0.020
 UBW  plan-1  C6    0.020
 UBW  plan-1  C5    0.020
 UBW  plan-1  C4    0.020
 UBW  plan-1  C7    0.020
 UBW  plan-1  H3    0.020
 UBW  plan-1  H2    0.020
 UBW  plan-1  H1    0.020
 UBW  plan-1  H6    0.020
 UBW  plan-1  H5    0.020
 UBW  plan-2  C14   0.020
 UBW  plan-2  C15   0.020
 UBW  plan-2  O28   0.020
 UBW  plan-2  N16   0.020
 UBW  plan-2  C17   0.020
 UBW  plan-2  HN16  0.020
 UBW  plan-3  C17   0.020
 UBW  plan-3  C18   0.020
 UBW  plan-3  O19   0.020
 UBW  plan-3  O20   0.020
 UBW  plan-4  O8    0.020
 UBW  plan-4  C9    0.020
 UBW  plan-4  O21   0.020
 UBW  plan-4  N10   0.020

