# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 12:37:54 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  63  31  .  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_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  -0.284   7.8953   0.5251   0.9859
 UBW  C2    C  CR16  0  -0.242   9.1659   0.0003   0.8018
 UBW  C1    C  CR16  0  -0.261   9.6584  -0.1946  -0.4834
 UBW  C6    C  CR16  0  -0.242   8.8758   0.1394  -1.5800
 UBW  C5    C  CR16  0  -0.296   7.6023   0.6618  -1.3918
 UBW  C4    C  CR6   0   0.075   7.1024   0.8601  -0.1094
 UBW  C7    C  CH2   0  -0.238   5.7214   1.4033   0.0979
 UBW  O8    O  O2    0  -0.479   4.8765   0.2875   0.4066
 UBW  C9    C  C     0   0.763   3.6084   0.5609   0.7251
 UBW  O21   O  O     0  -0.513   3.1291   1.6749   0.7264
 UBW  N10   N  NH1   0  -0.655   2.9505  -0.5659   1.0649
 UBW  C11   C  CH2   0  -0.568   1.5472  -0.5661   1.3742
 UBW  P12   P  P     0   1.313   0.5414  -0.8450  -0.1215
 UBW  O22   O  O     0  -0.714   0.6816   0.1690  -1.1988
 UBW  O23   O  OH1   0  -0.751   1.0561  -2.2692  -0.6990
 UBW  N13   N  NH1   0  -0.781  -0.9986  -0.9616   0.4825
 UBW  C14   C  CH1   0  -0.210  -2.1738  -0.8413  -0.3649
 UBW  C15   C  C     0   0.588  -3.3029  -0.3032   0.5058
 UBW  O28   O  O     0  -0.487  -3.5109  -0.7484   1.6243
 UBW  C24   C  CH2   0  -0.411  -2.5790  -2.1791  -0.9963
 UBW  C25   C  CH1   0  -0.269  -3.7629  -2.1293  -1.9637
 UBW  C26   C  CH3   0  -0.661  -3.4757  -1.2484  -3.1770
 UBW  C27   C  CH3   0  -0.648  -4.1195  -3.5445  -2.4083
 UBW  N16   N  NH1   0  -0.647  -4.0551   0.6685  -0.0295
 UBW  C17   C  CH1   0  -0.163  -5.1669   1.2358   0.6873
 UBW  C29   C  CH2   0  -0.468  -5.7856   2.3905  -0.1071
 UBW  C30   C  CH2   0  -0.427  -4.8484   3.5845  -0.2568
 UBW  C31   C  CH3   0  -0.663  -5.5170   4.7334  -0.9979
 UBW  C18   C  C     0   0.542  -6.2300   0.1823   0.9551
 UBW  O19   O  O     0  -0.428  -6.4527  -0.7654   0.2481
 UBW  O20   O  OH1   0  -0.589  -6.9273   0.4749   2.0434
 UBW  H3    H  HCR6  0   0.255   7.5194   0.6821   1.9900
 UBW  H2    H  HCR6  0   0.258   9.7738  -0.2532   1.6607
 UBW  H1    H  HCR6  0   0.259  10.6502  -0.6025  -0.6293
 UBW  H6    H  HCR6  0   0.259   9.2553  -0.0070  -2.5828
 UBW  H5    H  HCR6  0   0.255   6.9954   0.9201  -2.2516
 UBW  H7    H  HCH2  0   0.249   5.7066   2.1213   0.9202
 UBW  H7A   H  HCH2  0   0.249   5.3638   1.9082  -0.8017
 UBW  HN10  H  HNH1  0   0.410   3.4258  -1.4514   0.9967
 UBW  H11   H  HCH2  0   0.303   1.3392  -1.3390   2.1164
 UBW  H11A  H  HCH2  0   0.297   1.2550   0.3857   1.8163
 UBW  HO23  H  HOH1  0   0.484   0.8962  -3.0281  -0.1235
 UBW  HN13  H  HNH1  0   0.399  -1.1380  -1.5593   1.2886
 UBW  H14   H  HCH1  0   0.271  -1.9383  -0.1185  -1.1492
 UBW  H24   H  HCH2  0   0.235  -1.7056  -2.5715  -1.5264
 UBW  H24A  H  HCH2  0   0.234  -2.7920  -2.8873  -0.1888
 UBW  H25   H  HCH1  0   0.239  -4.6320  -1.7200  -1.4396
 UBW  H26   H  HCH3  0   0.234  -4.3123  -1.2692  -3.8764
 UBW  H26A  H  HCH3  0   0.219  -3.3097  -0.2022  -2.9135
 UBW  H26B  H  HCH3  0   0.221  -2.5874  -1.5956  -3.7101
 UBW  H27   H  HCH3  0   0.226  -4.3709  -4.1788  -1.5562
 UBW  H27A  H  HCH3  0   0.228  -4.9781  -3.5405  -3.0817
 UBW  H27B  H  HCH3  0   0.215  -3.2861  -4.0139  -2.9365
 UBW  HN16  H  HNH1  0   0.409  -3.8699   0.9819  -0.9691
 UBW  H17   H  HCH1  0   0.284  -4.8204   1.6251   1.6497
 UBW  H29   H  HCH2  0   0.245  -6.0973   2.0264  -1.0914
 UBW  H29A  H  HCH2  0   0.261  -6.6933   2.7137   0.4076
 UBW  H30   H  HCH2  0   0.228  -4.5314   3.9169   0.7355
 UBW  H30A  H  HCH2  0   0.226  -3.9382   3.2922  -0.7867
 UBW  H31   H  HCH3  0   0.222  -5.8106   4.4353  -2.0056
 UBW  H31A  H  HCH3  0   0.222  -6.4157   5.0662  -0.4762
 UBW  H31B  H  HCH3  0   0.233  -4.8476   5.5889  -1.0872
 UBW  HO20  H  HOH1  0   0.485  -7.6432  -0.1667   2.1655

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    1.498  0.020  1.498
 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    1.433  0.020  1.433
 UBW  C7   H7    single    0.970  0.020  1.090
 UBW  C7   H7A   single    0.970  0.020  1.090
 UBW  O8   C9    single    1.336  0.020  1.336
 UBW  C9   O21   double    1.213  0.020  1.213
 UBW  C9   N10   single    1.348  0.020  1.348
 UBW  N10  C11   single    1.437  0.020  1.437
 UBW  N10  HN10  single    0.860  0.020  1.020
 UBW  C11  P12   single    1.824  0.020  1.824
 UBW  C11  H11   single    0.970  0.020  1.090
 UBW  C11  H11A  single    0.970  0.020  1.090
 UBW  O22  P12   double    1.486  0.020  1.486
 UBW  O23  P12   single    1.621  0.020  1.621
 UBW  P12  N13   single    1.658  0.020  1.658
 UBW  N13  C14   single    1.454  0.020  1.454
 UBW  N13  HN13  single    0.890  0.020  1.040
 UBW  C15  C14   single    1.524  0.020  1.524
 UBW  C14  C24   single    1.534  0.020  1.534
 UBW  C14  H14   single    0.970  0.020  1.090
 UBW  N16  C15   single    1.340  0.020  1.340
 UBW  O28  C15   double    1.222  0.020  1.222
 UBW  C17  N16   single    1.439  0.020  1.439
 UBW  N16  HN16  single    0.860  0.020  1.020
 UBW  C18  C17   single    1.520  0.020  1.520
 UBW  C17  C29   single    1.532  0.020  1.532
 UBW  C17  H17   single    0.970  0.020  1.090
 UBW  O19  C18   double    1.203  0.020  1.203
 UBW  O20  C18   single    1.325  0.020  1.325
 UBW  O20  HO20  single    0.850  0.020  0.980
 UBW  O23  HO23  single    0.850  0.020  0.980
 UBW  C24  C25   single    1.530  0.020  1.530
 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    1.527  0.020  1.527
 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    1.522  0.020  1.522
 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    119.75  3.000
 UBW  H3    C3   C2    119.71  3.000
 UBW  C4    C3   C2    120.54  3.000
 UBW  H2    C2   C1    120.13  3.000
 UBW  H2    C2   C3    119.85  3.000
 UBW  C1    C2   C3    120.02  3.000
 UBW  H1    C1   C6    120.06  3.000
 UBW  H1    C1   C2    120.14  3.000
 UBW  C6    C1   C2    119.81  3.000
 UBW  H6    C6   C5    119.86  3.000
 UBW  H6    C6   C1    120.12  3.000
 UBW  C5    C6   C1    120.02  3.000
 UBW  H5    C5   C4    119.76  3.000
 UBW  H5    C5   C6    119.71  3.000
 UBW  C4    C5   C6    120.53  3.000
 UBW  C7    C4   C5    120.71  3.000
 UBW  C7    C4   C3    120.20  3.000
 UBW  C5    C4   C3    119.09  3.000
 UBW  H7A   C7   H7    108.18  3.000
 UBW  H7A   C7   O8    110.14  3.000
 UBW  H7    C7   O8    109.99  3.000
 UBW  H7A   C7   C4    110.82  3.000
 UBW  H7    C7   C4    110.80  3.000
 UBW  O8    C7   C4    106.91  3.000
 UBW  C9    O8   C7    116.85  3.000
 UBW  N10   C9   O21   125.07  3.000
 UBW  N10   C9   O8    110.63  3.000
 UBW  O21   C9   O8    124.29  3.000
 UBW  HN10  N10  C11   118.38  3.000
 UBW  HN10  N10  C9    119.17  3.000
 UBW  C11   N10  C9    122.06  3.000
 UBW  H11A  C11  H11   106.95  3.000
 UBW  H11A  C11  P12   108.57  3.000
 UBW  H11   C11  P12   110.13  3.000
 UBW  H11A  C11  N10   110.44  3.000
 UBW  H11   C11  N10   109.42  3.000
 UBW  P12   C11  N10   111.23  3.000
 UBW  N13   P12  O23   111.28  3.000
 UBW  N13   P12  O22   113.56  3.000
 UBW  O23   P12  O22   108.14  3.000
 UBW  N13   P12  C11   102.96  3.000
 UBW  O23   P12  C11   104.56  3.000
 UBW  O22   P12  C11   115.98  3.000
 UBW  HO23  O23  P12   115.19  3.000
 UBW  HN13  N13  C14   113.66  3.000
 UBW  HN13  N13  P12   117.33  3.000
 UBW  C14   N13  P12   122.18  3.000
 UBW  H14   C14  C24   109.79  3.000
 UBW  H14   C14  C15   109.65  3.000
 UBW  C24   C14  C15   110.33  3.000
 UBW  H14   C14  N13   107.40  3.000
 UBW  C24   C14  N13   112.42  3.000
 UBW  C15   C14  N13   107.17  3.000
 UBW  N16   C15  O28   122.30  3.000
 UBW  O28   C15  C14   121.36  3.000
 UBW  N16   C15  C14   116.34  3.000
 UBW  H24A  C24  H24   106.30  3.000
 UBW  H24A  C24  C25   109.69  3.000
 UBW  H24   C24  C25   108.84  3.000
 UBW  H24A  C24  C14   108.18  3.000
 UBW  H24   C24  C14   107.53  3.000
 UBW  C25   C24  C14   115.88  3.000
 UBW  H25   C25  C27   107.51  3.000
 UBW  H25   C25  C26   108.32  3.000
 UBW  C27   C25  C26   110.35  3.000
 UBW  H25   C25  C24   108.90  3.000
 UBW  C26   C25  C24   112.07  3.000
 UBW  C27   C25  C24   109.57  3.000
 UBW  H26B  C26  H26A  107.38  3.000
 UBW  H26B  C26  H26   107.74  3.000
 UBW  H26A  C26  H26   106.84  3.000
 UBW  H26B  C26  C25   110.94  3.000
 UBW  H26A  C26  C25   112.94  3.000
 UBW  H26   C26  C25   110.75  3.000
 UBW  H27B  C27  H27A  107.66  3.000
 UBW  H27B  C27  H27   107.67  3.000
 UBW  H27A  C27  H27   107.61  3.000
 UBW  H27B  C27  C25   111.17  3.000
 UBW  H27A  C27  C25   111.12  3.000
 UBW  H27   C27  C25   111.43  3.000
 UBW  HN16  N16  C17   118.93  3.000
 UBW  HN16  N16  C15   119.65  3.000
 UBW  C17   N16  C15   121.36  3.000
 UBW  H17   C17  C18   108.24  3.000
 UBW  H17   C17  C29   108.41  3.000
 UBW  C18   C17  C29   109.34  3.000
 UBW  H17   C17  N16   109.49  3.000
 UBW  C29   C17  N16   110.53  3.000
 UBW  C18   C17  N16   110.77  3.000
 UBW  H29A  C29  H29   106.58  3.000
 UBW  H29A  C29  C30   108.98  3.000
 UBW  H29   C29  C30   110.31  3.000
 UBW  H29A  C29  C17   108.32  3.000
 UBW  H29   C29  C17   109.30  3.000
 UBW  C30   C29  C17   113.13  3.000
 UBW  H30A  C30  H30   106.25  3.000
 UBW  H30A  C30  C31   109.37  3.000
 UBW  H30   C30  C31   109.87  3.000
 UBW  H30A  C30  C29   110.48  3.000
 UBW  H30   C30  C29   109.09  3.000
 UBW  C31   C30  C29   111.65  3.000
 UBW  H31B  C31  H31A  107.80  3.000
 UBW  H31B  C31  H31   107.70  3.000
 UBW  H31A  C31  H31   107.66  3.000
 UBW  H31B  C31  C30   111.26  3.000
 UBW  H31A  C31  C30   111.05  3.000
 UBW  H31   C31  C30   111.20  3.000
 UBW  O20   C18  O19   123.99  3.000
 UBW  O20   C18  C17   111.07  3.000
 UBW  O19   C18  C17   124.87  3.000
 UBW  HO20  O20  C18   110.24  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  CONST_17  HO20  O20  C18  C17   180.00   0.0  0
 UBW  Var_01    O8    C7   C4   C3    -78.33  30.0  2
 UBW  Var_02    O21   C9   O8   C7      2.43  30.0  3
 UBW  Var_03    C11   N10  C9   O8   -176.19  30.0  2
 UBW  Var_04    P12   C11  N10  C9     89.85  30.0  3
 UBW  Var_05    O22   P12  C11  N10   -60.95  30.0  3
 UBW  Var_06    C14   N13  P12  C11   163.71  30.0  3
 UBW  Var_07    C27   C25  C24  C14  -175.03  30.0  3
 UBW  Var_08    C31   C30  C29  C17  -177.53  30.0  3
 UBW  Var_09    H27   C27  C25  C24    58.62  30.0  3
 UBW  Var_10    H26   C26  C25  C24   177.07  30.0  3
 UBW  Var_11    H31   C31  C30  C29   -60.86  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
 UBW  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
 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-3  HO20  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

