# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 13:49:32 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  63  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   0.766   3.5748  -0.1189   0.9728
 UB3  O29   O  O     0  -0.517   3.0099   0.8483   1.4412
 UB3  O6    O  O2    0  -0.476   4.8478  -0.1276   0.5746
 UB3  C5    C  CH2   0  -0.241   5.5803   1.0974   0.7153
 UB3  C4    C  CR6   0   0.075   6.9631   0.8380   0.2009
 UB3  C30   C  CR16  0  -0.293   7.9802   0.4546   1.0695
 UB3  C31   C  CR16  0  -0.242   9.2562   0.1914   0.5893
 UB3  C1    C  CR16  0  -0.261   9.5244   0.3058  -0.7684
 UB3  C2    C  CR16  0  -0.242   8.5141   0.6866  -1.6429
 UB3  C3    C  CR16  0  -0.286   7.2407   0.9508  -1.1589
 UB3  N8    N  NH1   0  -0.655   3.0114  -1.3326   0.8057
 UB3  C9    C  CH2   0  -0.574   1.6184  -1.5618   1.0747
 UB3  P10   P  P     0   1.313   0.6102  -1.2252  -0.4119
 UB3  O12   O  O     0  -0.715   0.9630  -2.0681  -1.5869
 UB3  O11   O  OH1   0  -0.747   0.8755   0.3135  -0.8210
 UB3  N13   N  NH1   0  -0.796  -0.9381  -1.2593   0.1875
 UB3  C14   C  CH1   0  -0.199  -2.1006  -0.9709  -0.6317
 UB3  C18   C  C     0   0.589  -3.2064  -0.4971   0.3044
 UB3  O28   O  O     0  -0.487  -3.3369  -0.9523   1.4299
 UB3  C15   C  CH1   0  -0.229  -2.5547  -2.1590  -1.5128
 UB3  C16   C  CH3   0  -0.669  -3.0342  -3.3601  -0.7063
 UB3  C17   C  CH3   0  -0.683  -3.5992  -1.7403  -2.5420
 UB3  N19   N  NH1   0  -0.642  -4.0291   0.4412  -0.1891
 UB3  C20   C  CH1   0  -0.183  -5.1612   0.9201   0.5563
 UB3  C21   C  C     0   0.551  -6.1798  -0.1907   0.7592
 UB3  O22   O  O     0  -0.426  -6.3192  -1.1389   0.0321
 UB3  C24   C  CH2   0  -0.460  -5.8210   2.0932  -0.1760
 UB3  C25   C  CH1   0  -0.241  -4.9176   3.3175  -0.3552
 UB3  C26   C  CH3   0  -0.652  -5.6663   4.3775  -1.1571
 UB3  C27   C  CH3   0  -0.661  -4.4425   3.8830   0.9784
 UB3  O23   O  OH1   0  -0.590  -6.9323   0.0449   1.8246
 UB3  H5    H  HCH2  0   0.251   5.6063   1.4012   1.7636
 UB3  H5A   H  HCH2  0   0.250   5.0947   1.8894   0.1418
 UB3  H30   H  HCR6  0   0.256   7.7764   0.3672   2.1303
 UB3  H31   H  HCR6  0   0.259  10.0412  -0.1001   1.2752
 UB3  H1    H  HCR6  0   0.259  10.5191   0.1021  -1.1434
 UB3  H2    H  HCR6  0   0.259   8.7186   0.7804  -2.7015
 UB3  H3    H  HCR6  0   0.255   6.4565   1.2524  -1.8438
 UB3  HN8   H  HNH1  0   0.413   3.5368  -2.0623   0.3513
 UB3  H9    H  HCH2  0   0.310   1.4755  -2.6037   1.3644
 UB3  H9A   H  HCH2  0   0.296   1.2835  -0.9486   1.9113
 UB3  HO11  H  HOH1  0   0.481   0.7242   0.9521  -0.1122
 UB3  HN13  H  HNH1  0   0.403  -1.1154  -1.8889   0.9594
 UB3  H14   H  HCH1  0   0.275  -1.8379  -0.1478  -1.3038
 UB3  H15   H  HCH1  0   0.247  -1.6540  -2.4563  -2.0567
 UB3  H16   H  HCH3  0   0.226  -3.9901  -3.1647  -0.2182
 UB3  H16A  H  HCH3  0   0.235  -3.1722  -4.2169  -1.3668
 UB3  H16B  H  HCH3  0   0.224  -2.3177  -3.6597   0.0601
 UB3  H17   H  HCH3  0   0.228  -3.2686  -0.8750  -3.1207
 UB3  H17A  H  HCH3  0   0.239  -3.7753  -2.5525  -3.2482
 UB3  H17B  H  HCH3  0   0.230  -4.5561  -1.4971  -2.0785
 UB3  HN19  H  HNH1  0   0.407  -3.9041   0.7603  -1.1365
 UB3  H20   H  HCH1  0   0.286  -4.8314   1.2554   1.5431
 UB3  H24   H  HCH2  0   0.252  -6.1685   1.7484  -1.1555
 UB3  H24A  H  HCH2  0   0.257  -6.7121   2.3919   0.3824
 UB3  H25   H  HCH1  0   0.226  -4.0350   3.0241  -0.9342
 UB3  H26   H  HCH3  0   0.218  -6.5697   4.6957  -0.6319
 UB3  H26A  H  HCH3  0   0.231  -5.0464   5.2609  -1.3152
 UB3  H26B  H  HCH3  0   0.229  -5.9660   3.9993  -2.1359
 UB3  H27   H  HCH3  0   0.231  -3.8377   3.1716   1.5427
 UB3  H27A  H  HCH3  0   0.235  -3.8293   4.7714   0.8218
 UB3  H27B  H  HCH3  0   0.219  -5.2901   4.1725   1.6047
 UB3  HO23  H  HOH1  0   0.485  -7.6135  -0.6383   1.9146

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  1.389  0.020  1.389
 UB3  C1   C31   aromatic  1.389  0.020  1.389
 UB3  C1   H1    single    0.930  0.020  1.080
 UB3  C3   C2    aromatic  1.388  0.020  1.388
 UB3  C2   H2    single    0.930  0.020  1.080
 UB3  C3   C4    aromatic  1.392  0.020  1.392
 UB3  C3   H3    single    0.930  0.020  1.080
 UB3  C5   C4    single    1.498  0.020  1.498
 UB3  C4   C30   aromatic  1.391  0.020  1.391
 UB3  O6   C5    single    1.434  0.020  1.434
 UB3  C5   H5    single    0.970  0.020  1.090
 UB3  C5   H5A   single    0.970  0.020  1.090
 UB3  C7   O6    single    1.334  0.020  1.334
 UB3  N8   C7    single    1.348  0.020  1.348
 UB3  O29  C7    double    1.214  0.020  1.214
 UB3  C9   N8    single    1.437  0.020  1.437
 UB3  N8   HN8   single    0.860  0.020  1.020
 UB3  P10  C9    single    1.828  0.020  1.828
 UB3  C9   H9    single    0.970  0.020  1.090
 UB3  C9   H9A   single    0.970  0.020  1.090
 UB3  N13  P10   single    1.661  0.020  1.661
 UB3  P10  O12   double    1.489  0.020  1.489
 UB3  P10  O11   single    1.614  0.020  1.614
 UB3  O11  HO11  single    0.850  0.020  0.980
 UB3  C14  N13   single    1.451  0.020  1.451
 UB3  N13  HN13  single    0.890  0.020  1.040
 UB3  C15  C14   single    1.547  0.020  1.547
 UB3  C14  C18   single    1.524  0.020  1.524
 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    1.221  0.020  1.221
 UB3  C18  N19   single    1.342  0.020  1.342
 UB3  N19  C20   single    1.438  0.020  1.438
 UB3  N19  HN19  single    0.860  0.020  1.020
 UB3  C24  C20   single    1.532  0.020  1.532
 UB3  C20  C21   single    1.521  0.020  1.521
 UB3  C20  H20   single    0.970  0.020  1.090
 UB3  C21  O22   double    1.203  0.020  1.203
 UB3  C21  O23   single    1.325  0.020  1.325
 UB3  O23  HO23  single    0.850  0.020  0.980
 UB3  C30  C31   aromatic  1.389  0.020  1.389
 UB3  C30  H30   single    0.930  0.020  1.080
 UB3  C31  H31   single    0.930  0.020  1.080
 UB3  C25  C24   single    1.532  0.020  1.532
 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    1.526  0.020  1.526
 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    110.85  3.000
 UB3  N8    C7   O29   124.78  3.000
 UB3  O6    C7   O29   124.36  3.000
 UB3  C5    O6   C7    116.91  3.000
 UB3  H5A   C5   H5    108.24  3.000
 UB3  H5A   C5   C4    110.84  3.000
 UB3  H5    C5   C4    110.85  3.000
 UB3  H5A   C5   O6    109.93  3.000
 UB3  H5    C5   O6    110.13  3.000
 UB3  C4    C5   O6    106.85  3.000
 UB3  C3    C4   C30   119.10  3.000
 UB3  C30   C4   C5    120.53  3.000
 UB3  C3    C4   C5    120.35  3.000
 UB3  H30   C30  C31   119.74  3.000
 UB3  H30   C30  C4    119.73  3.000
 UB3  C31   C30  C4    120.53  3.000
 UB3  H31   C31  C1    120.11  3.000
 UB3  H31   C31  C30   119.89  3.000
 UB3  C1    C31  C30   120.00  3.000
 UB3  H1    C1   C2    120.11  3.000
 UB3  H1    C1   C31   120.05  3.000
 UB3  C2    C1   C31   119.83  3.000
 UB3  H2    C2   C3    119.87  3.000
 UB3  H2    C2   C1    120.13  3.000
 UB3  C3    C2   C1    119.99  3.000
 UB3  H3    C3   C2    119.77  3.000
 UB3  H3    C3   C4    119.69  3.000
 UB3  C2    C3   C4    120.54  3.000
 UB3  HN8   N8   C9    118.32  3.000
 UB3  HN8   N8   C7    119.34  3.000
 UB3  C9    N8   C7    121.69  3.000
 UB3  H9A   C9   H9    107.06  3.000
 UB3  H9A   C9   P10   110.56  3.000
 UB3  H9    C9   P10   108.64  3.000
 UB3  H9A   C9   N8    110.59  3.000
 UB3  H9    C9   N8    109.21  3.000
 UB3  P10   C9   N8    110.68  3.000
 UB3  N13   P10  O11   105.33  3.000
 UB3  O11   P10  O12   107.50  3.000
 UB3  N13   P10  O12   119.62  3.000
 UB3  O11   P10  C9    106.93  3.000
 UB3  O12   P10  C9    114.02  3.000
 UB3  N13   P10  C9    102.54  3.000
 UB3  HO11  O11  P10   114.73  3.000
 UB3  HN13  N13  C14   114.46  3.000
 UB3  HN13  N13  P10   116.84  3.000
 UB3  C14   N13  P10   122.62  3.000
 UB3  H14   C14  C15   107.35  3.000
 UB3  H14   C14  C18   108.51  3.000
 UB3  C15   C14  C18   112.05  3.000
 UB3  H14   C14  N13   107.69  3.000
 UB3  C18   C14  N13   107.23  3.000
 UB3  C15   C14  N13   113.83  3.000
 UB3  N19   C18  O28   122.28  3.000
 UB3  N19   C18  C14   115.86  3.000
 UB3  O28   C18  C14   121.85  3.000
 UB3  H15   C15  C17   107.65  3.000
 UB3  H15   C15  C16   107.94  3.000
 UB3  C17   C15  C16   110.98  3.000
 UB3  H15   C15  C14   104.49  3.000
 UB3  C17   C15  C14   112.00  3.000
 UB3  C16   C15  C14   113.34  3.000
 UB3  H16B  C16  H16A  107.02  3.000
 UB3  H16B  C16  H16   108.07  3.000
 UB3  H16A  C16  H16   107.50  3.000
 UB3  H16B  C16  C15   112.43  3.000
 UB3  H16A  C16  C15   109.79  3.000
 UB3  H16   C16  C15   111.79  3.000
 UB3  H17B  C17  H17A  107.44  3.000
 UB3  H17B  C17  H17   108.31  3.000
 UB3  H17A  C17  H17   107.20  3.000
 UB3  H17B  C17  C15   112.04  3.000
 UB3  H17A  C17  C15   110.07  3.000
 UB3  H17   C17  C15   111.58  3.000
 UB3  HN19  N19  C20   118.67  3.000
 UB3  HN19  N19  C18   119.42  3.000
 UB3  C20   N19  C18   121.67  3.000
 UB3  H20   C20  C24   109.06  3.000
 UB3  H20   C20  C21   107.80  3.000
 UB3  C24   C20  C21   109.55  3.000
 UB3  H20   C20  N19   109.43  3.000
 UB3  C21   C20  N19   110.69  3.000
 UB3  C24   C20  N19   110.27  3.000
 UB3  O23   C21  O22   124.07  3.000
 UB3  O23   C21  C20   110.96  3.000
 UB3  O22   C21  C20   124.93  3.000
 UB3  H24A  C24  H24   106.51  3.000
 UB3  H24A  C24  C25   108.78  3.000
 UB3  H24   C24  C25   109.52  3.000
 UB3  H24A  C24  C20   108.43  3.000
 UB3  H24   C24  C20   108.85  3.000
 UB3  C25   C24  C20   114.45  3.000
 UB3  H25   C25  C27   108.09  3.000
 UB3  H25   C25  C26   107.68  3.000
 UB3  C27   C25  C26   110.80  3.000
 UB3  H25   C25  C24   108.83  3.000
 UB3  C26   C25  C24   109.11  3.000
 UB3  C27   C25  C24   112.20  3.000
 UB3  H26B  C26  H26A  107.86  3.000
 UB3  H26B  C26  H26   107.76  3.000
 UB3  H26A  C26  H26   107.68  3.000
 UB3  H26B  C26  C25   111.44  3.000
 UB3  H26A  C26  C25   111.10  3.000
 UB3  H26   C26  C25   110.83  3.000
 UB3  H27B  C27  H27A  107.61  3.000
 UB3  H27B  C27  H27   107.83  3.000
 UB3  H27A  C27  H27   107.08  3.000
 UB3  H27B  C27  C25   110.97  3.000
 UB3  H27A  C27  C25   110.59  3.000
 UB3  H27   C27  C25   112.54  3.000
 UB3  HO23  O23  C21   110.39  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  CONST_17  HO23  O23  C21  C20   180.00   0.0  0
 UB3  Var_01    C3    C4   C5   O6     85.05  30.0  2
 UB3  Var_02    C4    C5   O6   C7   -179.76  30.0  3
 UB3  Var_03    P10   C9   N8   C7     88.56  30.0  1
 UB3  Var_04    C9    N8   C7   O29     5.36  30.0  2
 UB3  Var_05    N8    C7   O6   C5   -179.05  30.0  1
 UB3  Var_06    N13   P10  C9   N8   -169.48  30.0  2
 UB3  Var_07    C14   N13  P10  C9    176.72  30.0  1
 UB3  Var_08    C27   C25  C24  C20   -59.74  30.0  1
 UB3  Var_09    H16   C16  C15  C14    70.67  30.0  3
 UB3  Var_10    H17   C17  C15  C14    51.80  30.0  3
 UB3  Var_11    H27   C27  C25  C24    62.14  30.0  3
 UB3  Var_12    H26   C26  C25  C24    61.05  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
 UB3  chir_04  P10  N13  O12  O11  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
 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-3  HO23  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

