# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 02:54:21 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-alanyl-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@H](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
 UB2  UB2  N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-alanyl-L-leucine  peptide  57  29  .  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_UB2
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
 UB2  C3    C  CR16  0  -0.290  -7.1119  -0.6966   0.1569
 UB2  C2    C  CR16  0  -0.242  -8.0446  -1.5828  -0.3651
 UB2  C1    C  CR16  0  -0.260  -7.7584  -2.9406  -0.4188
 UB2  H29   H  HCR6  0   0.259  -6.3113  -4.4669   0.0145
 UB2  H28   H  HCR6  0   0.257  -4.6597  -2.8904   0.9441
 UB2  H5    H  HCH2  0   0.256  -5.3527   0.6934   1.5740
 UB2  H5A   H  HCH2  0   0.256  -4.2840  -0.6623   1.9672
 UB2  C29   C  CR16  0  -0.242  -6.5377  -3.4092   0.0509
 UB2  C28   C  CR16  0  -0.287  -5.6081  -2.5207   0.5727
 UB2  C4    C  CR6   0   0.076  -5.8882  -1.1583   0.6315
 UB2  C5    C  CH2   0  -0.245  -4.8723  -0.2002   1.1722
 UB2  O6    O  O2    0  -0.466  -4.0141   0.1589   0.0755
 UB2  C7    C  C     0   0.801  -2.9941   0.9634   0.3367
 UB2  O27   O  O     0  -0.553  -2.7760   1.4434   1.4440
 UB2  N8    N  NH1   0  -0.650  -2.2364   1.1902  -0.7423
 UB2  C9    C  CH2   0  -0.565  -1.1246   2.1105  -0.7272
 UB2  P10   P  P     0   1.301   0.2722   1.5698   0.3342
 UB2  O12   O  O     0  -0.704   0.6318   0.1489   0.0744
 UB2  O11   O  OH1   0  -0.774  -0.1780   1.9635   1.8221
 UB2  N13   N  NH1   0  -0.764   1.5129   2.6353   0.0261
 UB2  C14   C  CH1   0  -0.210   2.7392   2.1593  -0.5804
 UB2  C16   C  C     0   0.581   3.4631   1.1662   0.3258
 UB2  O26   O  O     0  -0.495   3.4662   1.2866   1.5402
 UB2  C15   C  CH3   0  -0.666   3.6642   3.3374  -0.8659
 UB2  N17   N  NH1   0  -0.634   4.1238   0.1884  -0.3120
 UB2  C18   C  CH1   0  -0.196   4.9017  -0.7850   0.3978
 UB2  C22   C  CH2   0  -0.451   5.1659  -2.0172  -0.4740
 UB2  C23   C  CH1   0  -0.229   3.9019  -2.6852  -1.0231
 UB2  C25   C  CH3   0  -0.653   4.2986  -3.9434  -1.7889
 UB2  C24   C  CH3   0  -0.674   2.8908  -3.0069   0.0719
 UB2  C19   C  C     0   0.551   6.2149  -0.1763   0.8644
 UB2  O21   O  O     0  -0.429   6.6845   0.8468   0.4407
 UB2  O20   O  OH1   0  -0.593   6.7939  -0.9329   1.7873
 UB2  H3    H  HCR6  0   0.256  -7.3407   0.3617   0.1996
 UB2  H2    H  HCR6  0   0.260  -8.9948  -1.2138  -0.7282
 UB2  H1    H  HCR6  0   0.260  -8.4868  -3.6329  -0.8212
 UB2  HN8   H  HNH1  0   0.420  -2.4631   0.7268  -1.6076
 UB2  H9    H  HCH2  0   0.303  -0.7421   2.1730  -1.7448
 UB2  H9A   H  HCH2  0   0.287  -1.4392   3.1196  -0.4472
 UB2  HO11  H  HOH1  0   0.490  -1.1538   1.8581   1.9111
 UB2  HN13  H  HNH1  0   0.399   1.6296   3.3979   0.6787
 UB2  H14   H  HCH1  0   0.266   2.4971   1.6731  -1.5289
 UB2  H15   H  HCH3  0   0.247   4.5809   3.0011  -1.3485
 UB2  H15A  H  HCH3  0   0.253   3.1735   4.0516  -1.5259
 UB2  H15B  H  HCH3  0   0.238   3.9374   3.8503   0.0578
 UB2  HN17  H  HNH1  0   0.404   4.1155   0.1612  -1.3191
 UB2  H18   H  HCH1  0   0.287   4.3481  -1.0983   1.2873
 UB2  H22   H  HCH2  0   0.248   5.8184  -1.7386  -1.3082
 UB2  H22A  H  HCH2  0   0.251   5.7184  -2.7456   0.1249
 UB2  H23   H  HCH1  0   0.223   3.4214  -2.0027  -1.7316
 UB2  H25   H  HCH3  0   0.216   4.7748  -4.6700  -1.1261
 UB2  H25A  H  HCH3  0   0.229   3.4272  -4.4230  -2.2364
 UB2  H25B  H  HCH3  0   0.227   5.0027  -3.7177  -2.5916
 UB2  H24   H  HCH3  0   0.215   3.3439  -3.6023   0.8687
 UB2  H24A  H  HCH3  0   0.243   2.4690  -2.1040   0.5152
 UB2  H24B  H  HCH3  0   0.231   2.0574  -3.5826  -0.3341
 UB2  HO20  H  HOH1  0   0.484   7.6478  -0.5549   2.0463

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
 UB2  C28  C29   aromatic  1.388  0.020  1.388
 UB2  C29  C1    aromatic  1.389  0.020  1.389
 UB2  C29  H29   single    0.930  0.020  1.080
 UB2  C28  C4    aromatic  1.392  0.020  1.392
 UB2  C28  H28   single    0.930  0.020  1.080
 UB2  C5   C4    single    1.497  0.020  1.497
 UB2  C4   C3    aromatic  1.391  0.020  1.391
 UB2  O6   C5    single    1.438  0.020  1.438
 UB2  C5   H5    single    0.970  0.020  1.090
 UB2  C5   H5A   single    0.970  0.020  1.090
 UB2  C7   O6    single    1.325  0.020  1.325
 UB2  N8   C7    single    1.338  0.020  1.338
 UB2  O27  C7    double    1.226  0.020  1.226
 UB2  C9   N8    single    1.443  0.020  1.443
 UB2  N8   HN8   single    0.860  0.020  1.020
 UB2  P10  C9    single    1.836  0.020  1.836
 UB2  C9   H9    single    0.970  0.020  1.090
 UB2  C9   H9A   single    0.970  0.020  1.090
 UB2  N13  P10   single    1.664  0.020  1.664
 UB2  P10  O12   double    1.489  0.020  1.489
 UB2  P10  O11   single    1.604  0.020  1.604
 UB2  C14  N13   single    1.449  0.020  1.449
 UB2  N13  HN13  single    0.890  0.020  1.040
 UB2  C15  C14   single    1.525  0.020  1.525
 UB2  C14  C16   single    1.527  0.020  1.527
 UB2  C14  H14   single    0.970  0.020  1.090
 UB2  O26  C16   double    1.220  0.020  1.220
 UB2  C16  N17   single    1.341  0.020  1.341
 UB2  N17  C18   single    1.434  0.020  1.434
 UB2  N17  HN17  single    0.860  0.020  1.020
 UB2  C22  C18   single    1.532  0.020  1.532
 UB2  C18  C19   single    1.521  0.020  1.521
 UB2  C18  H18   single    0.970  0.020  1.090
 UB2  C23  C22   single    1.531  0.020  1.531
 UB2  C22  H22   single    0.970  0.020  1.090
 UB2  C22  H22A  single    0.970  0.020  1.090
 UB2  C24  C23   single    1.525  0.020  1.525
 UB2  C25  C23   single    1.525  0.020  1.525
 UB2  C23  H23   single    0.970  0.020  1.090
 UB2  C25  H25   single    0.970  0.020  1.090
 UB2  C25  H25A  single    0.970  0.020  1.090
 UB2  C25  H25B  single    0.970  0.020  1.090
 UB2  C24  H24   single    0.970  0.020  1.090
 UB2  C24  H24A  single    0.970  0.020  1.090
 UB2  C24  H24B  single    0.970  0.020  1.090
 UB2  C19  O21   double    1.203  0.020  1.203
 UB2  C19  O20   single    1.326  0.020  1.326
 UB2  O20  HO20  single    0.850  0.020  0.980
 UB2  C15  H15   single    0.970  0.020  1.090
 UB2  C15  H15A  single    0.970  0.020  1.090
 UB2  C15  H15B  single    0.970  0.020  1.090
 UB2  O11  HO11  single    0.850  0.020  0.980
 UB2  C3   C2    aromatic  1.388  0.020  1.388
 UB2  C3   H3    single    0.930  0.020  1.080
 UB2  C1   C2    aromatic  1.389  0.020  1.389
 UB2  C2   H2    single    0.930  0.020  1.080
 UB2  C1   H1    single    0.930  0.020  1.080

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
 UB2  H3    C3   C4    119.76  3.000
 UB2  H3    C3   C2    119.76  3.000
 UB2  C4    C3   C2    120.48  3.000
 UB2  H2    C2   C1    120.10  3.000
 UB2  H2    C2   C3    119.89  3.000
 UB2  C1    C2   C3    120.01  3.000
 UB2  H1    C1   C29   120.08  3.000
 UB2  H1    C1   C2    120.07  3.000
 UB2  C29   C1   C2    119.85  3.000
 UB2  C28   C29  H29   119.88  3.000
 UB2  H29   C29  C1    120.14  3.000
 UB2  C28   C29  C1    119.98  3.000
 UB2  C4    C28  C29   120.51  3.000
 UB2  C4    C28  H28   119.70  3.000
 UB2  C29   C28  H28   119.79  3.000
 UB2  C5    C4   C28   120.33  3.000
 UB2  C5    C4   C3    120.50  3.000
 UB2  C28   C4   C3    119.16  3.000
 UB2  O6    C5   C4    106.81  3.000
 UB2  O6    C5   H5A   109.84  3.000
 UB2  C4    C5   H5A   110.97  3.000
 UB2  H5A   C5   H5    108.40  3.000
 UB2  O6    C5   H5    109.81  3.000
 UB2  C4    C5   H5    110.99  3.000
 UB2  C7    O6   C5    117.43  3.000
 UB2  N8    C7   O27   124.13  3.000
 UB2  O27   C7   O6    123.54  3.000
 UB2  N8    C7   O6    112.33  3.000
 UB2  HN8   N8   C9    118.40  3.000
 UB2  HN8   N8   C7    119.17  3.000
 UB2  C9    N8   C7    122.40  3.000
 UB2  H9A   C9   H9    106.70  3.000
 UB2  H9A   C9   P10   110.04  3.000
 UB2  H9    C9   P10   106.86  3.000
 UB2  H9A   C9   N8    111.68  3.000
 UB2  H9    C9   N8    107.30  3.000
 UB2  P10   C9   N8    113.85  3.000
 UB2  N13   P10  O11   102.94  3.000
 UB2  O11   P10  O12   117.65  3.000
 UB2  N13   P10  O12   113.50  3.000
 UB2  O11   P10  C9    104.51  3.000
 UB2  O12   P10  C9    111.35  3.000
 UB2  N13   P10  C9    105.76  3.000
 UB2  HO11  O11  P10   109.60  3.000
 UB2  HN13  N13  C14   114.87  3.000
 UB2  HN13  N13  P10   116.73  3.000
 UB2  C14   N13  P10   119.89  3.000
 UB2  H14   C14  C15   108.40  3.000
 UB2  H14   C14  C16   109.31  3.000
 UB2  C15   C14  C16   109.03  3.000
 UB2  H14   C14  N13   108.78  3.000
 UB2  C16   C14  N13   111.51  3.000
 UB2  C15   C14  N13   109.76  3.000
 UB2  N17   C16  O26   122.94  3.000
 UB2  N17   C16  C14   115.18  3.000
 UB2  O26   C16  C14   121.84  3.000
 UB2  H15B  C15  H15A  108.51  3.000
 UB2  H15B  C15  H15   108.03  3.000
 UB2  H15A  C15  H15   108.25  3.000
 UB2  H15B  C15  C14   110.89  3.000
 UB2  H15A  C15  C14   110.29  3.000
 UB2  H15   C15  C14   110.79  3.000
 UB2  HN17  N17  C18   118.74  3.000
 UB2  HN17  N17  C16   119.40  3.000
 UB2  C18   N17  C16   121.78  3.000
 UB2  H18   C18  C19   107.60  3.000
 UB2  H18   C18  C22   108.65  3.000
 UB2  C19   C18  C22   110.34  3.000
 UB2  H18   C18  N17   108.81  3.000
 UB2  C19   C18  N17   110.40  3.000
 UB2  C22   C18  N17   110.96  3.000
 UB2  H22A  C22  H22   106.60  3.000
 UB2  H22A  C22  C23   108.84  3.000
 UB2  H22   C22  C23   109.25  3.000
 UB2  H22A  C22  C18   108.14  3.000
 UB2  H22   C22  C18   109.36  3.000
 UB2  C23   C22  C18   114.36  3.000
 UB2  H23   C23  C24   107.77  3.000
 UB2  H23   C23  C25   107.66  3.000
 UB2  C24   C23  C25   111.03  3.000
 UB2  H23   C23  C22   108.81  3.000
 UB2  C25   C23  C22   108.97  3.000
 UB2  C24   C23  C22   112.45  3.000
 UB2  H25B  C25  H25A  107.73  3.000
 UB2  H25B  C25  H25   107.61  3.000
 UB2  H25A  C25  H25   107.74  3.000
 UB2  H25B  C25  C23   111.49  3.000
 UB2  H25A  C25  C23   111.16  3.000
 UB2  H25   C25  C23   110.93  3.000
 UB2  H24B  C24  H24A  107.01  3.000
 UB2  H24B  C24  H24   107.48  3.000
 UB2  H24A  C24  H24   108.36  3.000
 UB2  H24B  C24  C23   110.52  3.000
 UB2  H24A  C24  C23   111.94  3.000
 UB2  H24   C24  C23   111.32  3.000
 UB2  O20   C19  O21   124.04  3.000
 UB2  O20   C19  C18   111.23  3.000
 UB2  O21   C19  C18   124.72  3.000
 UB2  HO20  O20  C19   110.37  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
 UB2  CONST_01  C29   C28  C4   C3      0.00   0.0  0
 UB2  CONST_02  C29   C1   C2   C3      0.00   0.0  0
 UB2  CONST_03  C28   C4   C3   C2      0.00   0.0  0
 UB2  CONST_04  C28   C29  C1   C2      0.00   0.0  0
 UB2  CONST_05  C4    C28  C29  C1      0.00   0.0  0
 UB2  CONST_06  C4    C3   C2   C1      0.00   0.0  0
 UB2  CONST_07  C5    C4   C3   C2    180.00   0.0  0
 UB2  CONST_08  C5    C4   C28  C29   180.00   0.0  0
 UB2  CONST_09  H28   C28  C4   C3    180.00   0.0  0
 UB2  CONST_10  H1    C1   C2   C3    180.00   0.0  0
 UB2  CONST_11  H29   C29  C1   C2    180.00   0.0  0
 UB2  CONST_12  H3    C3   C2   C1    180.00   0.0  0
 UB2  CONST_13  H2    C2   C1   C29   180.00   0.0  0
 UB2  CONST_14  C18   N17  C16  C14   180.00   0.0  0
 UB2  CONST_15  C18   N17  C16  O26     0.00   0.0  0
 UB2  CONST_16  HN17  N17  C16  C14     0.00   0.0  0
 UB2  CONST_17  HO20  O20  C19  C18   180.00   0.0  0
 UB2  Var_01    O6    C5   C4   C3    -92.44  30.0  2
 UB2  Var_02    N8    C7   O6   C5    177.66  30.0  1
 UB2  Var_03    C9    N8   C7   O6    175.46  30.0  2
 UB2  Var_04    P10   C9   N8   C7     66.98  30.0  1
 UB2  Var_05    N13   P10  C9   N8    171.58  30.0  2
 UB2  Var_06    C14   N13  P10  C9   -115.83  30.0  1
 UB2  Var_07    C24   C23  C22  C18   -52.65  30.0  1
 UB2  Var_08    H24   C24  C23  C22   -54.11  30.0  3
 UB2  Var_09    H25   C25  C23  C22    62.83  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
 UB2  chir_02  C14  N13  C15  C16  negativ
 UB2  chir_03  C18  N17  C22  C19  negativ
 UB2  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
 UB2  plan-1  C3    0.020
 UB2  plan-1  C2    0.020
 UB2  plan-1  C1    0.020
 UB2  plan-1  H29   0.020
 UB2  plan-1  H28   0.020
 UB2  plan-1  C29   0.020
 UB2  plan-1  C28   0.020
 UB2  plan-1  C4    0.020
 UB2  plan-1  C5    0.020
 UB2  plan-1  H3    0.020
 UB2  plan-1  H2    0.020
 UB2  plan-1  H1    0.020
 UB2  plan-2  C14   0.020
 UB2  plan-2  C16   0.020
 UB2  plan-2  O26   0.020
 UB2  plan-2  N17   0.020
 UB2  plan-2  C18   0.020
 UB2  plan-2  HN17  0.020
 UB2  plan-3  C18   0.020
 UB2  plan-3  C19   0.020
 UB2  plan-3  O21   0.020
 UB2  plan-3  O20   0.020
 UB2  plan-3  HO20  0.020
 UB2  plan-4  O6    0.020
 UB2  plan-4  C7    0.020
 UB2  plan-4  O27   0.020
 UB2  plan-4  N8    0.020

