# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 21:44:32 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-valyl-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@@H](N[P](O)(=O)CNC(=O)OCc1ccccc1)C(C)C)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
 UB3  UB3  N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-valyl-L-leucine  ligand  61  31  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UB3
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
 UB3  C7    C  C      0   0.753   1.9276   0.5644   0.0954
 UB3  O29   O  O      0  -0.513   1.2493   1.1492  -0.7241
 UB3  O6    O  O2     0  -0.487   3.2499   0.7659   0.2359
 UB3  C5    C  CH2    0  -0.233   3.8293   1.7839  -0.5833
 UB3  C4    C  CR6    0   0.076   5.2945   1.8267  -0.2693
 UB3  C30   C  CR16   0  -0.283   5.7442   2.4199   0.9085
 UB3  C31   C  CR16   0  -0.243   7.0980   2.4540   1.2078
 UB3  C1    C  CR16   0  -0.263   8.0200   1.8951   0.3300
 UB3  C2    C  CR16   0  -0.240   7.5808   1.3031  -0.8457
 UB3  C3    C  CR16   0  -0.301   6.2234   1.2677  -1.1402
 UB3  N8    N  NH1    0  -0.650   1.4837  -0.3251   0.9983
 UB3  C9    C  CH2    0  -0.571   0.1630  -0.9095   0.9205
 UB3  P10   P  P      0   1.211   0.1915  -2.5430   0.0526
 UB3  O12   O  O      0  -0.815   0.8194  -3.5533   0.9824
 UB3  O11   O  OP    -1  -0.807   0.7613  -2.3111  -1.3241
 UB3  N13   N  NH1    0  -0.773  -1.4531  -2.9651  -0.1124
 UB3  C14   C  CH1    0  -0.188  -2.3375  -2.1439  -0.9139
 UB3  C18   C  C      0   0.558  -3.1387  -1.2001  -0.0145
 UB3  O28   O  O      0  -0.515  -3.5943  -1.5862   1.0576
 UB3  C15   C  CH1    0  -0.213  -3.2470  -3.0024  -1.8184
 UB3  C16   C  CH3    0  -0.662  -4.1632  -3.9417  -1.0432
 UB3  C17   C  CH3    0  -0.700  -4.0413  -2.1431  -2.7967
 UB3  N19   N  NH1    0  -0.610  -3.2605   0.0598  -0.4459
 UB3  C20   C  CH1    0  -0.208  -4.0224   1.0728   0.2450
 UB3  C21   C  C      0   0.419  -5.5408   1.0262  -0.0647
 UB3  O22   O  O      0  -0.579  -5.9380   0.2551  -0.9543
 UB3  C24   C  CH2    0  -0.436  -3.4471   2.4552  -0.0675
 UB3  C25   C  CH1    0  -0.232  -1.9573   2.6304   0.2404
 UB3  C26   C  CH3    0  -0.649  -1.5175   4.0468  -0.1164
 UB3  C27   C  CH3    0  -0.662  -1.6237   2.3119   1.6932
 UB3  O23   O  OC    -1  -0.619  -6.2371   1.7972   0.6272
 UB3  H5    H  HCH2   0   0.241   3.3632   2.7483  -0.3667
 UB3  H5A   H  HCH2   0   0.244   3.6698   1.5630  -1.6407
 UB3  H30   H  HCR6   0   0.254   5.0319   2.8659   1.5928
 UB3  H31   H  HCR6   0   0.258   7.4362   2.9202   2.1241
 UB3  H1    H  HCR6   0   0.258   9.0767   1.9258   0.5620
 UB3  H2    H  HCR6   0   0.257   8.2933   0.8696  -1.5357
 UB3  H3    H  HCR6   0   0.255   5.8858   0.8065  -2.0607
 UB3  HN8   H  HNH1   0   0.391   2.1685  -0.8083   1.5581
 UB3  H9    H  HCH2   0   0.241  -0.2388  -1.0212   1.9303
 UB3  H9A   H  HCH2   0   0.260  -0.4893  -0.2109   0.3992
 UB3  HN13  H  HNH1   0   0.356  -1.8934  -3.2664   0.7475
 UB3  H14   H  HCH1   0   0.241  -1.7141  -1.5482  -1.5893
 UB3  H15   H  HCH1   0   0.221  -2.5490  -3.6189  -2.3954
 UB3  H16   H  HCH3   0   0.220  -4.9115  -3.3971  -0.4662
 UB3  H16A  H  HCH3   0   0.222  -4.6957  -4.5992  -1.7325
 UB3  H16B  H  HCH3   0   0.221  -3.6044  -4.5788  -0.3560
 UB3  H17   H  HCH3   0   0.217  -3.3817  -1.5089  -3.3938
 UB3  H17A  H  HCH3   0   0.224  -4.6029  -2.7714  -3.4899
 UB3  H17B  H  HCH3   0   0.251  -4.7503  -1.4920  -2.2828
 UB3  HN19  H  HNH1   0   0.384  -2.9237   0.2768  -1.3702
 UB3  H20   H  HCH1   0   0.236  -3.9114   0.8893   1.3167
 UB3  H24   H  HCH2   0   0.219  -3.6190   2.6869  -1.1260
 UB3  H24A  H  HCH2   0   0.225  -4.0210   3.1893   0.5028
 UB3  H25   H  HCH1   0   0.227  -1.3819   1.9440  -0.3881
 UB3  H26   H  HCH3   0   0.209  -2.0349   4.7894   0.4964
 UB3  H26A  H  HCH3   0   0.222  -0.4451   4.1750   0.0406
 UB3  H26B  H  HCH3   0   0.220  -1.7277   4.2772  -1.1628
 UB3  H27   H  HCH3   0   0.226  -1.8258   1.2688   1.9371
 UB3  H27A  H  HCH3   0   0.225  -0.5656   2.4879   1.8934
 UB3  H27B  H  HCH3   0   0.211  -2.2031   2.9343   2.3804

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
 UB3  C2   C1    aromatic  1.388  0.020  1.388
 UB3  C1   C31   aromatic  1.390  0.020  1.390
 UB3  C1   H1    single    0.930  0.020  1.080
 UB3  C3   C2    aromatic  1.389  0.020  1.389
 UB3  C2   H2    single    0.930  0.020  1.080
 UB3  C3   C4    aromatic  1.391  0.020  1.391
 UB3  C3   H3    single    0.930  0.020  1.080
 UB3  C5   C4    single    1.499  0.020  1.499
 UB3  C4   C30   aromatic  1.393  0.020  1.393
 UB3  O6   C5    single    1.429  0.020  1.429
 UB3  C5   H5    single    0.970  0.020  1.090
 UB3  C5   H5A   single    0.970  0.020  1.090
 UB3  C7   O6    single    1.345  0.020  1.345
 UB3  N8   C7    single    1.343  0.020  1.343
 UB3  O29  C7    double    1.214  0.020  1.214
 UB3  C9   N8    single    1.446  0.020  1.446
 UB3  N8   HN8   single    0.860  0.020  1.020
 UB3  P10  C9    single    1.850  0.020  1.850
 UB3  C9   H9    single    0.970  0.020  1.090
 UB3  C9   H9A   single    0.970  0.020  1.090
 UB3  N13  P10   single    1.706  0.020  1.706
 UB3  P10  O12   deloc     1.510  0.020  1.510
 UB3  P10  O11   deloc     1.508  0.020  1.508
 UB3  C14  N13   single    1.449  0.020  1.449
 UB3  N13  HN13  single    0.890  0.020  1.040
 UB3  C15  C14   single    1.543  0.020  1.543
 UB3  C14  C18   single    1.530  0.020  1.530
 UB3  C14  H14   single    0.970  0.020  1.090
 UB3  C16  C15   single    1.524  0.020  1.524
 UB3  C17  C15   single    1.525  0.020  1.525
 UB3  C15  H15   single    0.970  0.020  1.090
 UB3  C16  H16   single    0.970  0.020  1.090
 UB3  C16  H16A  single    0.970  0.020  1.090
 UB3  C16  H16B  single    0.970  0.020  1.090
 UB3  C17  H17   single    0.970  0.020  1.090
 UB3  C17  H17A  single    0.970  0.020  1.090
 UB3  C17  H17B  single    0.970  0.020  1.090
 UB3  O28  C18   double    1.227  0.020  1.227
 UB3  C18  N19   single    1.337  0.020  1.337
 UB3  N19  C20   single    1.444  0.020  1.444
 UB3  N19  HN19  single    0.860  0.020  1.020
 UB3  C24  C20   single    1.530  0.020  1.530
 UB3  C20  C21   single    1.550  0.020  1.550
 UB3  C20  H20   single    0.970  0.020  1.090
 UB3  C21  O22   deloc     1.243  0.020  1.243
 UB3  C21  O23   deloc     1.248  0.020  1.248
 UB3  C30  C31   aromatic  1.387  0.020  1.387
 UB3  C30  H30   single    0.930  0.020  1.080
 UB3  C31  H31   single    0.930  0.020  1.080
 UB3  C25  C24   single    1.531  0.020  1.531
 UB3  C24  H24   single    0.970  0.020  1.090
 UB3  C24  H24A  single    0.970  0.020  1.090
 UB3  C27  C25   single    1.524  0.020  1.524
 UB3  C26  C25   single    1.525  0.020  1.525
 UB3  C25  H25   single    0.970  0.020  1.090
 UB3  C26  H26   single    0.970  0.020  1.090
 UB3  C26  H26A  single    0.970  0.020  1.090
 UB3  C26  H26B  single    0.970  0.020  1.090
 UB3  C27  H27   single    0.970  0.020  1.090
 UB3  C27  H27A  single    0.970  0.020  1.090
 UB3  C27  H27B  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
 UB3  N8    C7   O6    110.73  3.000
 UB3  N8    C7   O29   126.03  3.000
 UB3  O6    C7   O29   123.21  3.000
 UB3  C5    O6   C7    116.45  3.000
 UB3  H5A   C5   H5    107.95  3.000
 UB3  H5A   C5   C4    110.57  3.000
 UB3  H5    C5   C4    110.49  3.000
 UB3  H5A   C5   O6    110.60  3.000
 UB3  H5    C5   O6    110.00  3.000
 UB3  C4    C5   O6    107.25  3.000
 UB3  C3    C4   C30   119.01  3.000
 UB3  C30   C4   C5    120.32  3.000
 UB3  C3    C4   C5    120.68  3.000
 UB3  H30   C30  C31   119.68  3.000
 UB3  H30   C30  C4    119.79  3.000
 UB3  C31   C30  C4    120.53  3.000
 UB3  H31   C31  C1    120.04  3.000
 UB3  H31   C31  C30   119.89  3.000
 UB3  C1    C31  C30   120.07  3.000
 UB3  H1    C1   C2    120.17  3.000
 UB3  H1    C1   C31   120.05  3.000
 UB3  C2    C1   C31   119.78  3.000
 UB3  H2    C2   C3    119.85  3.000
 UB3  H2    C2   C1    120.18  3.000
 UB3  C3    C2   C1    119.97  3.000
 UB3  H3    C3   C2    119.69  3.000
 UB3  H3    C3   C4    119.67  3.000
 UB3  C2    C3   C4    120.64  3.000
 UB3  HN8   N8   C9    117.17  3.000
 UB3  HN8   N8   C7    117.80  3.000
 UB3  C9    N8   C7    122.23  3.000
 UB3  H9A   C9   H9    106.72  3.000
 UB3  H9A   C9   P10   110.56  3.000
 UB3  H9    C9   P10   110.43  3.000
 UB3  H9A   C9   N8    108.28  3.000
 UB3  H9    C9   N8    109.11  3.000
 UB3  P10   C9   N8    111.59  3.000
 UB3  N13   P10  O11   108.30  3.000
 UB3  O11   P10  O12   120.54  3.000
 UB3  N13   P10  O12   107.15  3.000
 UB3  O11   P10  C9    107.36  3.000
 UB3  O12   P10  C9    107.96  3.000
 UB3  N13   P10  C9    104.42  3.000
 UB3  HN13  N13  C14   111.91  3.000
 UB3  HN13  N13  P10   114.26  3.000
 UB3  C14   N13  P10   120.12  3.000
 UB3  H14   C14  C15   106.06  3.000
 UB3  H14   C14  C18   108.96  3.000
 UB3  C15   C14  C18   112.27  3.000
 UB3  H14   C14  N13   107.58  3.000
 UB3  C18   C14  N13   110.13  3.000
 UB3  C15   C14  N13   111.63  3.000
 UB3  N19   C18  O28   122.99  3.000
 UB3  N19   C18  C14   116.05  3.000
 UB3  O28   C18  C14   120.91  3.000
 UB3  H15   C15  C17   108.12  3.000
 UB3  H15   C15  C16   107.71  3.000
 UB3  C17   C15  C16   111.12  3.000
 UB3  H15   C15  C14   104.25  3.000
 UB3  C17   C15  C14   111.67  3.000
 UB3  C16   C15  C14   113.52  3.000
 UB3  H16B  C16  H16A  107.22  3.000
 UB3  H16B  C16  H16   108.04  3.000
 UB3  H16A  C16  H16   107.47  3.000
 UB3  H16B  C16  C15   111.86  3.000
 UB3  H16A  C16  C15   110.08  3.000
 UB3  H16   C16  C15   111.95  3.000
 UB3  H17B  C17  H17A  107.96  3.000
 UB3  H17B  C17  H17   107.66  3.000
 UB3  H17A  C17  H17   107.32  3.000
 UB3  H17B  C17  C15   111.87  3.000
 UB3  H17A  C17  C15   110.55  3.000
 UB3  H17   C17  C15   111.29  3.000
 UB3  HN19  N19  C20   117.67  3.000
 UB3  HN19  N19  C18   117.93  3.000
 UB3  C20   N19  C18   123.70  3.000
 UB3  H20   C20  C24   108.29  3.000
 UB3  H20   C20  C21   106.87  3.000
 UB3  C24   C20  C21   110.78  3.000
 UB3  H20   C20  N19   107.33  3.000
 UB3  C21   C20  N19   113.59  3.000
 UB3  C24   C20  N19   109.75  3.000
 UB3  O23   C21  O22   127.00  3.000
 UB3  O23   C21  C20   114.65  3.000
 UB3  O22   C21  C20   118.35  3.000
 UB3  H24A  C24  H24   106.22  3.000
 UB3  H24A  C24  C25   109.22  3.000
 UB3  H24   C24  C25   108.80  3.000
 UB3  H24A  C24  C20   107.64  3.000
 UB3  H24   C24  C20   109.21  3.000
 UB3  C25   C24  C20   115.36  3.000
 UB3  H25   C25  C27   107.54  3.000
 UB3  H25   C25  C26   107.24  3.000
 UB3  C27   C25  C26   110.73  3.000
 UB3  H25   C25  C24   108.92  3.000
 UB3  C26   C25  C24   109.86  3.000
 UB3  C27   C25  C24   112.37  3.000
 UB3  H26B  C26  H26A  107.59  3.000
 UB3  H26B  C26  H26   107.62  3.000
 UB3  H26A  C26  H26   107.73  3.000
 UB3  H26B  C26  C25   111.39  3.000
 UB3  H26A  C26  C25   111.02  3.000
 UB3  H26   C26  C25   111.30  3.000
 UB3  H27B  C27  H27A  107.86  3.000
 UB3  H27B  C27  H27   107.81  3.000
 UB3  H27A  C27  H27   107.04  3.000
 UB3  H27B  C27  C25   111.36  3.000
 UB3  H27A  C27  C25   110.70  3.000
 UB3  H27   C27  C25   111.88  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
 UB3  CONST_01  C1    C2   C3   C4      0.00   0.0  0
 UB3  CONST_02  C1    C31  C30  C4      0.00   0.0  0
 UB3  CONST_03  C2    C3   C4   C30     0.00   0.0  0
 UB3  CONST_04  C2    C1   C31  C30     0.00   0.0  0
 UB3  CONST_05  C3    C2   C1   C31     0.00   0.0  0
 UB3  CONST_06  C3    C4   C30  C31     0.00   0.0  0
 UB3  CONST_07  C2    C3   C4   C5    180.00   0.0  0
 UB3  CONST_08  C31   C30  C4   C5    180.00   0.0  0
 UB3  CONST_09  H2    C2   C3   C4    180.00   0.0  0
 UB3  CONST_10  H31   C31  C30  C4    180.00   0.0  0
 UB3  CONST_11  H3    C3   C4   C30   180.00   0.0  0
 UB3  CONST_12  H1    C1   C31  C30   180.00   0.0  0
 UB3  CONST_13  H30   C30  C31  C1    180.00   0.0  0
 UB3  CONST_14  C20   N19  C18  C14   180.00   0.0  0
 UB3  CONST_15  C20   N19  C18  O28     0.00   0.0  0
 UB3  CONST_16  HN19  N19  C18  C14     0.00   0.0  0
 UB3  Var_01    C3    C4   C5   O6    103.53  30.0  2
 UB3  Var_02    C4    C5   O6   C7   -179.64  30.0  3
 UB3  Var_03    P10   C9   N8   C7     94.97  30.0  1
 UB3  Var_04    C9    N8   C7   O29    13.35  30.0  2
 UB3  Var_05    N8    C7   O6   C5   -174.41  30.0  1
 UB3  Var_06    N13   P10  C9   N8   -173.02  30.0  1
 UB3  Var_07    C14   N13  P10  C9     63.38  30.0  2
 UB3  Var_08    C27   C25  C24  C20   -56.25  30.0  2
 UB3  Var_09    H16   C16  C15  C14    66.97  30.0  3
 UB3  Var_10    H17   C17  C15  C14    55.34  30.0  3
 UB3  Var_11    H27   C27  C25  C24    63.22  30.0  3
 UB3  Var_12    H26   C26  C25  C24    63.32  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
 UB3  chir_02  C14  N13  C15  C18  negativ
 UB3  chir_03  C20  N19  C24  C21  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
 UB3  plan-1  C5    0.020
 UB3  plan-1  C4    0.020
 UB3  plan-1  C30   0.020
 UB3  plan-1  C31   0.020
 UB3  plan-1  C1    0.020
 UB3  plan-1  C2    0.020
 UB3  plan-1  C3    0.020
 UB3  plan-1  H30   0.020
 UB3  plan-1  H31   0.020
 UB3  plan-1  H1    0.020
 UB3  plan-1  H2    0.020
 UB3  plan-1  H3    0.020
 UB3  plan-2  C14   0.020
 UB3  plan-2  C18   0.020
 UB3  plan-2  O28   0.020
 UB3  plan-2  N19   0.020
 UB3  plan-2  C20   0.020
 UB3  plan-2  HN19  0.020
 UB3  plan-3  C20   0.020
 UB3  plan-3  C21   0.020
 UB3  plan-3  O22   0.020
 UB3  plan-3  O23   0.020
 UB3  plan-4  C7    0.020
 UB3  plan-4  O29   0.020
 UB3  plan-4  O6    0.020
 UB3  plan-4  N8    0.020

