# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 04:06:56 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  66  32  .  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_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  -0.300  -7.8886  -0.8978   0.7836
 UBV  C2    C  CR16  0  -0.241  -8.9771  -1.2407  -0.0100
 UBV  C1    C  CR16  0  -0.262  -8.7742  -1.8219  -1.2532
 UBV  C6    C  CR16  0  -0.242  -7.4795  -2.0647  -1.6987
 UBV  C5    C  CR16  0  -0.283  -6.3961  -1.7266  -0.9025
 UBV  C4    C  CR6   0   0.075  -6.5917  -1.1395   0.3465
 UBV  C7    C  CH2   0  -0.238  -5.4136  -0.7728   1.1973
 UBV  O8    O  O2    0  -0.475  -4.7645   0.3370   0.5642
 UBV  C9    C  C     0   0.769  -3.5738   0.6994   1.0414
 UBV  O21   O  O     0  -0.520  -3.0243   0.1721   1.9882
 UBV  N10   N  NH1   0  -0.654  -3.0719   1.7393   0.3465
 UBV  C11   C  CH2   0  -0.579  -1.7554   2.2554   0.6042
 UBV  P12   P  P     0   1.313  -0.4850   1.3479  -0.3431
 UBV  O22   O  O     0  -0.716  -0.5494   1.4957  -1.8219
 UBV  O23   O  OH1   0  -0.745  -0.7135  -0.2172   0.0012
 UBV  N13   N  NH1   0  -0.758   0.9330   1.9053   0.3151
 UBV  C14   C  CH1   0  -0.251   2.2044   1.5000  -0.2484
 UBV  C15   C  C     0   0.587   2.6863   0.1963   0.3807
 UBV  O28   O  O     0  -0.487   2.4409  -0.0899   1.5430
 UBV  C24   C  CH2   0  -0.402   3.2710   2.5801  -0.0402
 UBV  C25   C  CH1   0  -0.226   2.8880   3.9556  -0.5872
 UBV  C26   C  CH3   0  -0.653   4.0095   4.9490  -0.2989
 UBV  C27   C  CH3   0  -0.672   2.5732   3.9143  -2.0783
 UBV  N16   N  NH1   0  -0.651   3.4326  -0.5871  -0.4097
 UBV  C17   C  CH1   0  -0.123   4.0258  -1.8015   0.0873
 UBV  C18   C  C     0   0.538   4.9578  -1.4740   1.2440
 UBV  O19   O  O     0  -0.433   5.5980  -0.4593   1.3357
 UBV  C29   C  CH1   0  -0.294   4.7541  -2.5379  -1.0573
 UBV  C30   C  CH2   0  -0.415   5.1297  -3.9690  -0.6632
 UBV  C     C  CH3   0  -0.669   5.9528  -1.7645  -1.6013
 UBV  C31   C  CH3   0  -0.670   5.5086  -4.8350  -1.8577
 UBV  O20   O  OH1   0  -0.587   5.0076  -2.4607   2.1281
 UBV  H3    H  HCR6  0   0.256  -8.0543  -0.4408   1.7518
 UBV  H2    H  HCR6  0   0.259  -9.9820  -1.0516   0.3444
 UBV  H1    H  HCR6  0   0.259  -9.6208  -2.0876  -1.8731
 UBV  H6    H  HCR6  0   0.258  -7.3146  -2.5235  -2.6650
 UBV  H5    H  HCR6  0   0.256  -5.3904  -1.9266  -1.2530
 UBV  H7    H  HCH2  0   0.252  -5.7317  -0.4962   2.2048
 UBV  H7A   H  HCH2  0   0.251  -4.7209  -1.6129   1.2788
 UBV  HN10  H  HNH1  0   0.414  -3.5692   2.0793  -0.4611
 UBV  H11   H  HCH2  0   0.313  -1.7154   3.3025   0.3047
 UBV  H11A  H  HCH2  0   0.295  -1.5348   2.2242   1.6724
 UBV  HO23  H  HOH1  0   0.477  -0.7694  -0.4267   0.9428
 UBV  HN13  H  HNH1  0   0.395   0.9534   2.0199   1.3213
 UBV  H14   H  HCH1  0   0.276   2.0611   1.3495  -1.3214
 UBV  H24   H  HCH2  0   0.239   3.4845   2.6646   1.0303
 UBV  H24A  H  HCH2  0   0.233   4.1995   2.2456  -0.5148
 UBV  H25   H  HCH1  0   0.225   1.9909   4.2900  -0.0571
 UBV  H26   H  HCH3  0   0.214   4.9336   4.6538  -0.8021
 UBV  H26A  H  HCH3  0   0.227   3.7477   5.9492  -0.6475
 UBV  H26B  H  HCH3  0   0.225   4.2217   5.0141   0.7698
 UBV  H27   H  HCH3  0   0.214   3.4233   3.5299  -2.6483
 UBV  H27A  H  HCH3  0   0.232   1.7104   3.2846  -2.3002
 UBV  H27B  H  HCH3  0   0.230   2.3493   4.9140  -2.4544
 UBV  HN16  H  HNH1  0   0.407   3.5844  -0.3255  -1.3708
 UBV  H17   H  HCH1  0   0.286   3.2360  -2.4617   0.4592
 UBV  H29   H  HCH1  0   0.255   4.0034  -2.6129  -1.8535
 UBV  H30   H  HCH2  0   0.224   5.9582  -3.9587   0.0496
 UBV  H30A  H  HCH2  0   0.229   4.2842  -4.4321  -0.1470
 UBV  H     H  HCH3  0   0.233   5.7121  -0.7288  -1.8433
 UBV  HA    H  HCH3  0   0.229   6.7814  -1.7529  -0.8918
 UBV  HB    H  HCH3  0   0.245   6.3128  -2.2268  -2.5193
 UBV  H31   H  HCH3  0   0.221   4.7101  -4.8547  -2.6016
 UBV  H31A  H  HCH3  0   0.225   6.4140  -4.4822  -2.3521
 UBV  H31B  H  HCH3  0   0.234   5.6919  -5.8625  -1.5430
 UBV  HO20  H  HOH1  0   0.481   5.6475  -2.2512   2.8256

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    1.527  0.020  1.527
 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  1.391  0.020  1.391
 UBV  C1   C2    aromatic  1.387  0.020  1.387
 UBV  C1   H1    single    0.930  0.020  1.080
 UBV  C3   C2    aromatic  1.390  0.020  1.390
 UBV  C2   H2    single    0.930  0.020  1.080
 UBV  C4   C3    aromatic  1.390  0.020  1.390
 UBV  C3   H3    single    0.930  0.020  1.080
 UBV  C5   C4    aromatic  1.394  0.020  1.394
 UBV  C7   C4    single    1.499  0.020  1.499
 UBV  C5   C6    aromatic  1.386  0.020  1.386
 UBV  C5   H5    single    0.930  0.020  1.080
 UBV  C6   H6    single    0.930  0.020  1.080
 UBV  O8   C7    single    1.433  0.020  1.433
 UBV  C7   H7    single    0.970  0.020  1.090
 UBV  C7   H7A   single    0.970  0.020  1.090
 UBV  C9   O8    single    1.333  0.020  1.333
 UBV  N10  C9    single    1.348  0.020  1.348
 UBV  O21  C9    double    1.215  0.020  1.215
 UBV  C11  N10   single    1.437  0.020  1.437
 UBV  N10  HN10  single    0.860  0.020  1.020
 UBV  P12  C11   single    1.826  0.020  1.826
 UBV  C11  H11   single    0.970  0.020  1.090
 UBV  C11  H11A  single    0.970  0.020  1.090
 UBV  N13  P12   single    1.660  0.020  1.660
 UBV  P12  O22   double    1.488  0.020  1.488
 UBV  P12  O23   single    1.619  0.020  1.619
 UBV  C14  N13   single    1.449  0.020  1.449
 UBV  N13  HN13  single    0.890  0.020  1.040
 UBV  C24  C14   single    1.532  0.020  1.532
 UBV  C14  C15   single    1.526  0.020  1.526
 UBV  C14  H14   single    0.970  0.020  1.090
 UBV  C15  O28   double    1.222  0.020  1.222
 UBV  C15  N16   single    1.340  0.020  1.340
 UBV  N16  C17   single    1.440  0.020  1.440
 UBV  N16  HN16  single    0.860  0.020  1.020
 UBV  C29  C17   single    1.544  0.020  1.544
 UBV  C17  C18   single    1.521  0.020  1.521
 UBV  C17  H17   single    0.970  0.020  1.090
 UBV  C18  O19   double    1.203  0.020  1.203
 UBV  C18  O20   single    1.326  0.020  1.326
 UBV  O20  HO20  single    0.850  0.020  0.980
 UBV  O23  HO23  single    0.850  0.020  0.980
 UBV  C25  C24   single    1.529  0.020  1.529
 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    1.531  0.020  1.531
 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    119.80  3.000
 UBV  H3    C3   C2    119.64  3.000
 UBV  C4    C3   C2    120.56  3.000
 UBV  H2    C2   C1    120.16  3.000
 UBV  H2    C2   C3    119.81  3.000
 UBV  C1    C2   C3    120.03  3.000
 UBV  H1    C1   C6    120.12  3.000
 UBV  H1    C1   C2    120.11  3.000
 UBV  C6    C1   C2    119.76  3.000
 UBV  H6    C6   C5    119.81  3.000
 UBV  H6    C6   C1    120.12  3.000
 UBV  C5    C6   C1    120.07  3.000
 UBV  H5    C5   C4    119.85  3.000
 UBV  H5    C5   C6    119.64  3.000
 UBV  C4    C5   C6    120.51  3.000
 UBV  C7    C4   C5    120.10  3.000
 UBV  C7    C4   C3    120.83  3.000
 UBV  C5    C4   C3    119.07  3.000
 UBV  H7A   C7   H7    108.11  3.000
 UBV  H7A   C7   O8    109.97  3.000
 UBV  H7    C7   O8    110.08  3.000
 UBV  H7A   C7   C4    110.66  3.000
 UBV  H7    C7   C4    110.90  3.000
 UBV  O8    C7   C4    107.14  3.000
 UBV  C9    O8   C7    117.19  3.000
 UBV  N10   C9   O21   124.63  3.000
 UBV  O21   C9   O8    124.40  3.000
 UBV  N10   C9   O8    110.97  3.000
 UBV  HN10  N10  C11   118.34  3.000
 UBV  HN10  N10  C9    119.33  3.000
 UBV  C11   N10  C9    121.72  3.000
 UBV  H11A  C11  H11   106.80  3.000
 UBV  H11A  C11  P12   110.67  3.000
 UBV  H11   C11  P12   108.02  3.000
 UBV  H11A  C11  N10   110.51  3.000
 UBV  H11   C11  N10   109.23  3.000
 UBV  P12   C11  N10   111.45  3.000
 UBV  N13   P12  O23   111.16  3.000
 UBV  O23   P12  O22   107.54  3.000
 UBV  N13   P12  O22   113.45  3.000
 UBV  O23   P12  C11   105.78  3.000
 UBV  O22   P12  C11   115.86  3.000
 UBV  N13   P12  C11   102.81  3.000
 UBV  HO23  O23  P12   115.15  3.000
 UBV  HN13  N13  C14   113.61  3.000
 UBV  HN13  N13  P12   116.69  3.000
 UBV  C14   N13  P12   120.11  3.000
 UBV  H14   C14  C24   108.77  3.000
 UBV  H14   C14  C15   109.19  3.000
 UBV  C24   C14  C15   109.05  3.000
 UBV  H14   C14  N13   107.78  3.000
 UBV  C15   C14  N13   110.85  3.000
 UBV  C24   C14  N13   111.15  3.000
 UBV  N16   C15  O28   122.41  3.000
 UBV  N16   C15  C14   115.61  3.000
 UBV  O28   C15  C14   121.94  3.000
 UBV  H24A  C24  H24   106.38  3.000
 UBV  H24A  C24  C25   109.39  3.000
 UBV  H24   C24  C25   109.22  3.000
 UBV  H24A  C24  C14   108.42  3.000
 UBV  H24   C24  C14   108.85  3.000
 UBV  C25   C24  C14   114.28  3.000
 UBV  H25   C25  C27   108.23  3.000
 UBV  H25   C25  C26   108.19  3.000
 UBV  C27   C25  C26   110.75  3.000
 UBV  H25   C25  C24   107.88  3.000
 UBV  C26   C25  C24   109.51  3.000
 UBV  C27   C25  C24   112.16  3.000
 UBV  H26B  C26  H26A  107.74  3.000
 UBV  H26B  C26  H26   107.61  3.000
 UBV  H26A  C26  H26   107.66  3.000
 UBV  H26B  C26  C25   111.52  3.000
 UBV  H26A  C26  C25   111.11  3.000
 UBV  H26   C26  C25   111.02  3.000
 UBV  H27B  C27  H27A  107.24  3.000
 UBV  H27B  C27  H27   107.57  3.000
 UBV  H27A  C27  H27   107.81  3.000
 UBV  H27B  C27  C25   110.77  3.000
 UBV  H27A  C27  C25   112.20  3.000
 UBV  H27   C27  C25   111.03  3.000
 UBV  HN16  N16  C17   119.09  3.000
 UBV  HN16  N16  C15   119.65  3.000
 UBV  C17   N16  C15   121.26  3.000
 UBV  H17   C17  C29   107.74  3.000
 UBV  H17   C17  C18   108.28  3.000
 UBV  C29   C17  C18   112.18  3.000
 UBV  H17   C17  N16   109.19  3.000
 UBV  C18   C17  N16   109.47  3.000
 UBV  C29   C17  N16   109.92  3.000
 UBV  O20   C18  O19   123.84  3.000
 UBV  O20   C18  C17   111.70  3.000
 UBV  O19   C18  C17   124.43  3.000
 UBV  H29   C29  C     108.26  3.000
 UBV  H29   C29  C30   106.91  3.000
 UBV  C     C29  C30   111.88  3.000
 UBV  H29   C29  C17   104.35  3.000
 UBV  C30   C29  C17   111.76  3.000
 UBV  C     C29  C17   113.14  3.000
 UBV  H30A  C30  H30   106.39  3.000
 UBV  H30A  C30  C31   108.77  3.000
 UBV  H30   C30  C31   109.15  3.000
 UBV  H30A  C30  C29   109.13  3.000
 UBV  H30   C30  C29   110.19  3.000
 UBV  C31   C30  C29   112.99  3.000
 UBV  HB    C    HA    107.56  3.000
 UBV  HB    C    H     106.80  3.000
 UBV  HA    C    H     107.57  3.000
 UBV  HB    C    C29   110.17  3.000
 UBV  HA    C    C29   111.72  3.000
 UBV  H     C    C29   112.76  3.000
 UBV  H31B  C31  H31A  107.24  3.000
 UBV  H31B  C31  H31   107.62  3.000
 UBV  H31A  C31  H31   107.71  3.000
 UBV  H31B  C31  C30   110.57  3.000
 UBV  H31A  C31  C30   112.22  3.000
 UBV  H31   C31  C30   111.26  3.000
 UBV  HO20  O20  C18   110.10  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_14  C17   N16  C15  C14   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  CONST_17  HO20  O20  C18  C17   180.00   0.0  0
 UBV  Var_01    O8    C7   C4   C3   -109.65  30.0  2
 UBV  Var_02    N10   C9   O8   C7    179.20  30.0  1
 UBV  Var_03    C11   N10  C9   O8   -175.47  30.0  2
 UBV  Var_04    P12   C11  N10  C9     86.45  30.0  2
 UBV  Var_05    N13   P12  C11  N10  -169.77  30.0  2
 UBV  Var_06    C14   N13  P12  C11  -174.91  30.0  1
 UBV  Var_07    C27   C25  C24  C14   -57.72  30.0  1
 UBV  Var_08    H27   C27  C25  C24   -57.85  30.0  3
 UBV  Var_09    H26   C26  C25  C24    62.24  30.0  3
 UBV  Var_10    H31   C31  C30  C29   -56.01  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
 UBV  chir_05  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
 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-3  HO20  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

