# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 18:50:35 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: (2S)-2-({N-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl}amino)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[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
 UBZ  UBZ  '(2S)-2-({N-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl}amino)butanoic acid'  peptide  58  30  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UBZ
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
 UBZ  C3    C  CR16   0  -0.289   -6.9381   0.3487  -1.4244
 UBZ  C2    C  CR16   0  -0.243   -8.0939   1.1126  -1.5023
 UBZ  C1    C  CR16   0  -0.262   -9.1324   0.8956  -0.6050
 UBZ  C6    C  CR16   0  -0.242   -9.0096  -0.0875   0.3678
 UBZ  C5    C  CR16   0  -0.294   -7.8507  -0.8491   0.4431
 UBZ  C4    C  CR6    0   0.077   -6.8068  -0.6398  -0.4526
 UBZ  C7    C  CH2    0  -0.235   -5.5449  -1.4429  -0.3581
 UBZ  O8    O  O2     0  -0.484   -4.6275  -0.6849   0.4351
 UBZ  C9    C  C      0   0.746   -3.3818  -1.1709   0.5532
 UBZ  O21   O  O      0  -0.526   -3.0086  -2.1963   0.0180
 UBZ  N10   N  NH1    0  -0.647   -2.6436  -0.3914   1.3598
 UBZ  C11   C  CH2    0  -0.552   -1.2061  -0.5224   1.4760
 UBZ  P12   P  P      0   1.220   -0.3655   0.7465   0.4323
 UBZ  O22   O  O      0  -0.808   -0.4853   0.3690  -1.0239
 UBZ  O23   O  OP    -1  -0.812   -0.8829   2.0897   0.8963
 UBZ  N13   N  NH1    0  -0.791    1.2567   0.4743   0.9107
 UBZ  C14   C  CH1    0  -0.195    2.3333   0.7185  -0.0336
 UBZ  C15   C  C      0   0.569    3.5902   0.0617   0.5280
 UBZ  O24   O  O      0  -0.518    3.9624   0.2921   1.6739
 UBZ  C20   C  CH2    0  -0.413    2.5852   2.2090  -0.2901
 UBZ  C21   C  CH1    0  -0.278    3.6610   2.5362  -1.3270
 UBZ  C22   C  CH3    0  -0.654    3.2750   2.0490  -2.7210
 UBZ  C23   C  CH3    0  -0.649    3.9120   4.0414  -1.3501
 UBZ  N16   N  NH1    0  -0.624    4.2215  -0.7890  -0.2864
 UBZ  C17   C  CH1    0  -0.175    5.4637  -1.4390   0.0613
 UBZ  C18   C  C      0   0.410    6.6865  -0.4849   0.0678
 UBZ  O32   O  O      0  -0.579    6.5702   0.6288  -0.4702
 UBZ  C25   C  CH2    0  -0.465    5.7110  -2.6126  -0.8874
 UBZ  C26   C  CH3    0  -0.659    4.6348  -3.6886  -0.8315
 UBZ  O19   O  OC    -1  -0.619    7.7081  -0.9583   0.6058
 UBZ  H3    H  HCR6   0   0.255   -6.1339   0.5187  -2.1309
 UBZ  H2    H  HCR6   0   0.258   -8.1854   1.8752  -2.2647
 UBZ  H1    H  HCR6   0   0.258  -10.0361   1.4882  -0.6672
 UBZ  H6    H  HCR6   0   0.258   -9.8169  -0.2640   1.0668
 UBZ  H5    H  HCR6   0   0.255   -7.7608  -1.6179   1.2013
 UBZ  H7    H  HCH2   0   0.244   -5.7366  -2.4121   0.1083
 UBZ  H7A   H  HCH2   0   0.244   -5.1284  -1.6226  -1.3511
 UBZ  HN10  H  HNH1   0   0.391   -3.0358   0.4938   1.6420
 UBZ  H11   H  HCH2   0   0.247   -0.9228  -0.4006   2.5248
 UBZ  H11A  H  HCH2   0   0.252   -0.9116  -1.5281   1.1821
 UBZ  HN13  H  HNH1   0   0.353    1.4761   0.8753   1.8151
 UBZ  H14   H  HCH1   0   0.242    2.0536   0.2351  -0.9719
 UBZ  H20   H  HCH2   0   0.222    1.6363   2.6570  -0.6046
 UBZ  H20A  H  HCH2   0   0.212    2.8444   2.6784   0.6654
 UBZ  H21   H  HCH1   0   0.253    4.5932   2.0405  -1.0378
 UBZ  H22   H  HCH3   0   0.224    4.0373   2.3190  -3.4541
 UBZ  H22A  H  HCH3   0   0.218    3.1539   0.9656  -2.7713
 UBZ  H22B  H  HCH3   0   0.212    2.3322   2.4995  -3.0417
 UBZ  H23   H  HCH3   0   0.222    4.2225   4.4092  -0.3704
 UBZ  H23A  H  HCH3   0   0.221    4.6930   4.3032  -2.0666
 UBZ  H23B  H  HCH3   0   0.209    3.0074   4.5845  -1.6364
 UBZ  HN16  H  HNH1   0   0.387    3.9061  -0.8478  -1.2412
 UBZ  H17   H  HCH1   0   0.227    5.3587  -1.8443   1.0728
 UBZ  H25   H  HCH2   0   0.221    5.8109  -2.2368  -1.9119
 UBZ  H25A  H  HCH2   0   0.237    6.6757  -3.0482  -0.6259
 UBZ  H26   H  HCH3   0   0.220    3.6615  -3.3186  -1.1552
 UBZ  H26A  H  HCH3   0   0.229    4.8940  -4.5288  -1.4766
 UBZ  H26B  H  HCH3   0   0.219    4.5205  -4.0751   0.1830

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
 UBZ  C2   C1    aromatic  1.389  0.020  1.389
 UBZ  C1   C6    aromatic  1.389  0.020  1.389
 UBZ  C1   H1    single    0.930  0.020  1.080
 UBZ  C2   C3    aromatic  1.388  0.020  1.388
 UBZ  C2   H2    single    0.930  0.020  1.080
 UBZ  C3   C4    aromatic  1.392  0.020  1.392
 UBZ  C3   H3    single    0.930  0.020  1.080
 UBZ  C4   C7    single    1.499  0.020  1.499
 UBZ  C4   C5    aromatic  1.391  0.020  1.391
 UBZ  C6   C5    aromatic  1.389  0.020  1.389
 UBZ  C5   H5    single    0.930  0.020  1.080
 UBZ  C6   H6    single    0.930  0.020  1.080
 UBZ  C7   O8    single    1.430  0.020  1.430
 UBZ  C7   H7    single    0.970  0.020  1.090
 UBZ  C7   H7A   single    0.970  0.020  1.090
 UBZ  O8   C9    single    1.342  0.020  1.342
 UBZ  C9   O21   double    1.215  0.020  1.215
 UBZ  C9   N10   single    1.343  0.020  1.343
 UBZ  N10  C11   single    1.448  0.020  1.448
 UBZ  N10  HN10  single    0.890  0.020  1.040
 UBZ  C11  P12   single    1.846  0.020  1.846
 UBZ  C11  H11   single    0.970  0.020  1.090
 UBZ  C11  H11A  single    0.970  0.020  1.090
 UBZ  O22  P12   deloc     1.509  0.020  1.509
 UBZ  O23  P12   deloc     1.512  0.020  1.512
 UBZ  P12  N13   single    1.713  0.020  1.713
 UBZ  N13  C14   single    1.453  0.020  1.453
 UBZ  N13  HN13  single    0.890  0.020  1.040
 UBZ  C15  C14   single    1.525  0.020  1.525
 UBZ  C14  C20   single    1.533  0.020  1.533
 UBZ  C14  H14   single    0.970  0.020  1.090
 UBZ  N16  C15   single    1.336  0.020  1.336
 UBZ  C15  O24   double    1.227  0.020  1.227
 UBZ  C17  N16   single    1.445  0.020  1.445
 UBZ  N16  HN16  single    0.860  0.020  1.020
 UBZ  C18  C17   single    1.551  0.020  1.551
 UBZ  C17  C25   single    1.529  0.020  1.529
 UBZ  C17  H17   single    0.970  0.020  1.090
 UBZ  O32  C18   deloc     1.242  0.020  1.242
 UBZ  O19  C18   deloc     1.248  0.020  1.248
 UBZ  C20  C21   single    1.530  0.020  1.530
 UBZ  C20  H20   single    0.970  0.020  1.090
 UBZ  C20  H20A  single    0.970  0.020  1.090
 UBZ  C23  C21   single    1.526  0.020  1.526
 UBZ  C21  C22   single    1.526  0.020  1.526
 UBZ  C21  H21   single    0.970  0.020  1.090
 UBZ  C22  H22   single    0.970  0.020  1.090
 UBZ  C22  H22A  single    0.970  0.020  1.090
 UBZ  C22  H22B  single    0.970  0.020  1.090
 UBZ  C23  H23   single    0.970  0.020  1.090
 UBZ  C23  H23A  single    0.970  0.020  1.090
 UBZ  C23  H23B  single    0.970  0.020  1.090
 UBZ  C25  C26   single    1.523  0.020  1.523
 UBZ  C25  H25   single    0.970  0.020  1.090
 UBZ  C25  H25A  single    0.970  0.020  1.090
 UBZ  C26  H26   single    0.970  0.020  1.090
 UBZ  C26  H26A  single    0.970  0.020  1.090
 UBZ  C26  H26B  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
 UBZ  H3    C3   C4    119.76  3.000
 UBZ  H3    C3   C2    119.68  3.000
 UBZ  C4    C3   C2    120.56  3.000
 UBZ  H2    C2   C1    120.12  3.000
 UBZ  H2    C2   C3    119.86  3.000
 UBZ  C1    C2   C3    120.03  3.000
 UBZ  H1    C1   C6    120.11  3.000
 UBZ  H1    C1   C2    120.09  3.000
 UBZ  C6    C1   C2    119.80  3.000
 UBZ  H6    C6   C5    119.87  3.000
 UBZ  H6    C6   C1    120.13  3.000
 UBZ  C5    C6   C1    120.00  3.000
 UBZ  H5    C5   C4    119.67  3.000
 UBZ  H5    C5   C6    119.75  3.000
 UBZ  C4    C5   C6    120.58  3.000
 UBZ  C7    C4   C5    120.70  3.000
 UBZ  C5    C4   C3    119.03  3.000
 UBZ  C7    C4   C3    120.25  3.000
 UBZ  H7A   C7   H7    108.02  3.000
 UBZ  H7A   C7   O8    110.31  3.000
 UBZ  H7    C7   O8    110.25  3.000
 UBZ  H7A   C7   C4    110.61  3.000
 UBZ  H7    C7   C4    110.76  3.000
 UBZ  O8    C7   C4    106.92  3.000
 UBZ  C9    O8   C7    116.88  3.000
 UBZ  N10   C9   O21   125.84  3.000
 UBZ  N10   C9   O8    110.66  3.000
 UBZ  O21   C9   O8    123.48  3.000
 UBZ  HN10  N10  C11   116.30  3.000
 UBZ  HN10  N10  C9    117.63  3.000
 UBZ  C11   N10  C9    122.77  3.000
 UBZ  H11A  C11  H11   106.98  3.000
 UBZ  H11A  C11  P12   111.06  3.000
 UBZ  H11   C11  P12   110.36  3.000
 UBZ  H11A  C11  N10   109.30  3.000
 UBZ  H11   C11  N10   108.92  3.000
 UBZ  P12   C11  N10   110.15  3.000
 UBZ  N13   P12  O23   112.30  3.000
 UBZ  N13   P12  O22   107.75  3.000
 UBZ  O23   P12  O22   119.41  3.000
 UBZ  N13   P12  C11    99.45  3.000
 UBZ  O23   P12  C11   106.34  3.000
 UBZ  O22   P12  C11   109.73  3.000
 UBZ  HN13  N13  C14   110.68  3.000
 UBZ  HN13  N13  P12   113.05  3.000
 UBZ  C14   N13  P12   119.58  3.000
 UBZ  H14   C14  C20   109.19  3.000
 UBZ  H14   C14  C15   109.68  3.000
 UBZ  C20   C14  C15   110.17  3.000
 UBZ  H14   C14  N13   107.12  3.000
 UBZ  C20   C14  N13   113.20  3.000
 UBZ  C15   C14  N13   107.40  3.000
 UBZ  N16   C15  O24   123.07  3.000
 UBZ  O24   C15  C14   120.87  3.000
 UBZ  N16   C15  C14   116.04  3.000
 UBZ  H20A  C20  H20   106.26  3.000
 UBZ  H20A  C20  C21   109.46  3.000
 UBZ  H20   C20  C21   109.10  3.000
 UBZ  H20A  C20  C14   108.03  3.000
 UBZ  H20   C20  C14   107.66  3.000
 UBZ  C21   C20  C14   115.91  3.000
 UBZ  H21   C21  C23   108.09  3.000
 UBZ  H21   C21  C22   108.18  3.000
 UBZ  C23   C21  C22   110.03  3.000
 UBZ  H21   C21  C20   108.85  3.000
 UBZ  C22   C21  C20   111.90  3.000
 UBZ  C23   C21  C20   109.69  3.000
 UBZ  H22B  C22  H22A  107.45  3.000
 UBZ  H22B  C22  H22   107.66  3.000
 UBZ  H22A  C22  H22   106.99  3.000
 UBZ  H22B  C22  C21   110.76  3.000
 UBZ  H22A  C22  C21   112.77  3.000
 UBZ  H22   C22  C21   110.97  3.000
 UBZ  H23B  C23  H23A  107.51  3.000
 UBZ  H23B  C23  H23   107.63  3.000
 UBZ  H23A  C23  H23   107.75  3.000
 UBZ  H23B  C23  C21   110.97  3.000
 UBZ  H23A  C23  C21   111.36  3.000
 UBZ  H23   C23  C21   111.44  3.000
 UBZ  HN16  N16  C17   118.11  3.000
 UBZ  HN16  N16  C15   117.84  3.000
 UBZ  C17   N16  C15   123.10  3.000
 UBZ  H17   C17  C25   107.74  3.000
 UBZ  H17   C17  C18   107.43  3.000
 UBZ  C25   C17  C18   110.32  3.000
 UBZ  H17   C17  N16   107.85  3.000
 UBZ  C25   C17  N16   109.58  3.000
 UBZ  C18   C17  N16   113.71  3.000
 UBZ  O19   C18  O32   127.12  3.000
 UBZ  O19   C18  C17   114.44  3.000
 UBZ  O32   C18  C17   118.42  3.000
 UBZ  H25A  C25  H25   106.29  3.000
 UBZ  H25A  C25  C26   109.52  3.000
 UBZ  H25   C25  C26   109.94  3.000
 UBZ  H25A  C25  C17   107.51  3.000
 UBZ  H25   C25  C17   109.37  3.000
 UBZ  C26   C25  C17   113.90  3.000
 UBZ  H26B  C26  H26A  107.57  3.000
 UBZ  H26B  C26  H26   107.61  3.000
 UBZ  H26A  C26  H26   107.34  3.000
 UBZ  H26B  C26  C25   111.00  3.000
 UBZ  H26A  C26  C25   110.77  3.000
 UBZ  H26   C26  C25   112.34  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
 UBZ  CONST_01  C6    C1   C2   C3      0.00   0.0  0
 UBZ  CONST_02  C6    C5   C4   C3      0.00   0.0  0
 UBZ  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 UBZ  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 UBZ  CONST_05  C4    C3   C2   C1      0.00   0.0  0
 UBZ  CONST_06  C4    C5   C6   C1      0.00   0.0  0
 UBZ  CONST_07  C7    C4   C3   C2    180.00   0.0  0
 UBZ  CONST_08  C7    C4   C5   C6    180.00   0.0  0
 UBZ  CONST_09  H1    C1   C2   C3    180.00   0.0  0
 UBZ  CONST_10  H5    C5   C4   C3    180.00   0.0  0
 UBZ  CONST_11  H6    C6   C1   C2    180.00   0.0  0
 UBZ  CONST_12  H3    C3   C2   C1    180.00   0.0  0
 UBZ  CONST_13  H2    C2   C1   C6    180.00   0.0  0
 UBZ  CONST_14  C17   N16  C15  C14   180.00   0.0  0
 UBZ  CONST_15  C17   N16  C15  O24     0.00   0.0  0
 UBZ  CONST_16  HN16  N16  C15  C14     0.00   0.0  0
 UBZ  Var_01    O8    C7   C4   C3     84.77  30.0  2
 UBZ  Var_02    O21   C9   O8   C7      0.64  30.0  3
 UBZ  Var_03    C11   N10  C9   O8   -168.17  30.0  2
 UBZ  Var_04    P12   C11  N10  C9     98.99  30.0  3
 UBZ  Var_05    O22   P12  C11  N10   -73.57  30.0  3
 UBZ  Var_06    C14   N13  P12  C11   149.57  30.0  3
 UBZ  Var_07    C23   C21  C20  C14  -173.29  30.0  3
 UBZ  Var_08    H23   C23  C21  C20    58.38  30.0  3
 UBZ  Var_09    H22   C22  C21  C20   178.13  30.0  3
 UBZ  Var_10    H26   C26  C25  C17    63.71  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
 UBZ  chir_02  C14  N13  C15  C20  positiv
 UBZ  chir_03  C17  N16  C18  C25  positiv

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
 UBZ  plan-1  C3    0.020
 UBZ  plan-1  C2    0.020
 UBZ  plan-1  C1    0.020
 UBZ  plan-1  C6    0.020
 UBZ  plan-1  C5    0.020
 UBZ  plan-1  C4    0.020
 UBZ  plan-1  C7    0.020
 UBZ  plan-1  H3    0.020
 UBZ  plan-1  H2    0.020
 UBZ  plan-1  H1    0.020
 UBZ  plan-1  H6    0.020
 UBZ  plan-1  H5    0.020
 UBZ  plan-2  C14   0.020
 UBZ  plan-2  C15   0.020
 UBZ  plan-2  O24   0.020
 UBZ  plan-2  N16   0.020
 UBZ  plan-2  C17   0.020
 UBZ  plan-2  HN16  0.020
 UBZ  plan-3  C17   0.020
 UBZ  plan-3  C18   0.020
 UBZ  plan-3  O32   0.020
 UBZ  plan-3  O19   0.020
 UBZ  plan-4  O8    0.020
 UBZ  plan-4  C9    0.020
 UBZ  plan-4  O21   0.020
 UBZ  plan-4  N10   0.020

