# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 20:43:40 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: N-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N[P](O)(=O)CNC(=O)OCc1ccccc1)C(=O)NCC(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
 UBT  UBT  N-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucylglycine  peptide  52  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UBT
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
 UBT  C3    C  CR16   0  -0.296   7.3684   1.1925   0.3428
 UBT  C2    C  CR16   0  -0.242   8.5962   0.5479   0.2620
 UBT  C1    C  CR16   0  -0.262   8.7840  -0.4744  -0.6581
 UBT  C6    C  CR16   0  -0.243   7.7415  -0.8473  -1.4982
 UBT  C5    C  CR16   0  -0.286   6.5174  -0.1995  -1.4159
 UBT  C4    C  CR6    0   0.076   6.3201   0.8264  -0.4948
 UBT  C7    C  CH2    0  -0.234   4.9853   1.4998  -0.3867
 UBT  O8    O  O2     0  -0.485   4.1598   0.6518   0.4152
 UBT  C9    C  C      0   0.745   2.8830   1.0293   0.5901
 UBT  O19   O  O      0  -0.527   2.4096   2.0374   0.1034
 UBT  N10   N  NH1    0  -0.646   2.2426   0.1646   1.3925
 UBT  C11   C  CH2    0  -0.556   0.8047   0.1628   1.5677
 UBT  P12   P  P      0   1.229   0.0257  -1.1070   0.4768
 UBT  O20   O  O      0  -0.806   0.0318  -0.5998  -0.9438
 UBT  O21   O  OP    -1  -0.811   0.6911  -2.4195   0.8226
 UBT  N13   N  NH1    0  -0.792  -1.5811  -1.0941   1.0598
 UBT  C14   C  CH1    0  -0.178  -2.7153  -0.9111   0.1757
 UBT  C15   C  C      0   0.556  -3.8991  -0.4735   1.0311
 UBT  O23   O  O      0  -0.520  -4.3172  -1.1831   1.9427
 UBT  C18   C  CH2    0  -0.406  -3.0720  -2.1802  -0.6043
 UBT  C20   C  CH1    0  -0.250  -4.2933  -2.0932  -1.5203
 UBT  C22   C  CH3    0  -0.654  -4.1446  -1.0222  -2.5966
 UBT  C24   C  CH3    0  -0.647  -4.5610  -3.4552  -2.1548
 UBT  N16   N  NH1    0  -0.630  -4.4365   0.7056   0.7205
 UBT  C17   C  CH2    0  -0.412  -5.5667   1.2914   1.3926
 UBT  C27   C  C      0   0.399  -5.9279   2.6572   0.7710
 UBT  O28   O  O      0  -0.599  -5.2096   3.0627  -0.1630
 UBT  O31   O  OC    -1  -0.610  -6.9115   3.2250   1.2754
 UBT  H3    H  HCR6   0   0.255   7.2271   1.9907   1.0619
 UBT  H2    H  HCR6   0   0.258   9.4047   0.8447   0.9175
 UBT  H1    H  HCR6   0   0.258   9.7400  -0.9777  -0.7235
 UBT  H6    H  HCR6   0   0.258   7.8825  -1.6417  -2.2196
 UBT  H5    H  HCR6   0   0.254   5.7101  -0.4906  -2.0779
 UBT  H7    H  HCH2   0   0.244   5.0863   2.4830   0.0787
 UBT  H7A   H  HCH2   0   0.244   4.5403   1.6378  -1.3745
 UBT  HN10  H  HNH1   0   0.390   2.7186  -0.6933   1.6252
 UBT  H11   H  HCH2   0   0.245   0.5787  -0.0506   2.6150
 UBT  H11A  H  HCH2   0   0.249   0.4143   1.1567   1.3547
 UBT  HN13  H  HNH1   0   0.356  -1.7619  -1.8016   1.7604
 UBT  H14   H  HCH1   0   0.240  -2.4595  -0.1183  -0.5295
 UBT  H18   H  HCH2   0   0.222  -2.1945  -2.4530  -1.1985
 UBT  H18A  H  HCH2   0   0.213  -3.2233  -2.9909   0.1163
 UBT  H20   H  HCH1   0   0.218  -5.1694  -1.8406  -0.9116
 UBT  H22   H  HCH3   0   0.227  -5.0030  -1.0288  -3.2705
 UBT  H22A  H  HCH3   0   0.218  -4.0754  -0.0175  -2.1782
 UBT  H22B  H  HCH3   0   0.215  -3.2489  -1.1895  -3.1997
 UBT  H24   H  HCH3   0   0.223  -4.7029  -4.2266  -1.3953
 UBT  H24A  H  HCH3   0   0.224  -5.4577  -3.4341  -2.7768
 UBT  H24B  H  HCH3   0   0.212  -3.7263  -3.7646  -2.7885
 UBT  HN16  H  HNH1   0   0.386  -4.0476   1.2756  -0.0171
 UBT  H17   H  HCH2   0   0.239  -6.4369   0.6305   1.3351
 UBT  H17A  H  HCH2   0   0.240  -5.3574   1.4329   2.4578

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
 UBT  C6   C1    aromatic  1.390  0.020  1.390
 UBT  C1   C2    aromatic  1.388  0.020  1.388
 UBT  C1   H1    single    0.930  0.020  1.080
 UBT  C2   C3    aromatic  1.389  0.020  1.389
 UBT  C2   H2    single    0.930  0.020  1.080
 UBT  C4   C3    aromatic  1.391  0.020  1.391
 UBT  C3   H3    single    0.930  0.020  1.080
 UBT  C5   C4    aromatic  1.393  0.020  1.393
 UBT  C4   C7    single    1.499  0.020  1.499
 UBT  C6   C5    aromatic  1.387  0.020  1.387
 UBT  C5   H5    single    0.930  0.020  1.080
 UBT  C6   H6    single    0.930  0.020  1.080
 UBT  C7   O8    single    1.430  0.020  1.430
 UBT  C7   H7    single    0.970  0.020  1.090
 UBT  C7   H7A   single    0.970  0.020  1.090
 UBT  O8   C9    single    1.343  0.020  1.343
 UBT  C9   O19   double    1.215  0.020  1.215
 UBT  C9   N10   single    1.342  0.020  1.342
 UBT  N10  C11   single    1.449  0.020  1.449
 UBT  N10  HN10  single    0.890  0.020  1.040
 UBT  C11  P12   single    1.846  0.020  1.846
 UBT  C11  H11   single    0.970  0.020  1.090
 UBT  C11  H11A  single    0.970  0.020  1.090
 UBT  O20  P12   deloc     1.508  0.020  1.508
 UBT  O21  P12   deloc     1.512  0.020  1.512
 UBT  P12  N13   single    1.709  0.020  1.709
 UBT  N13  C14   single    1.450  0.020  1.450
 UBT  N13  HN13  single    0.890  0.020  1.040
 UBT  C15  C14   single    1.525  0.020  1.525
 UBT  C14  C18   single    1.532  0.020  1.532
 UBT  C14  H14   single    0.970  0.020  1.090
 UBT  N16  C15   single    1.332  0.020  1.332
 UBT  O23  C15   double    1.229  0.020  1.229
 UBT  C17  N16   single    1.440  0.020  1.440
 UBT  N16  HN16  single    0.860  0.020  1.020
 UBT  C27  C17   single    1.543  0.020  1.543
 UBT  C17  H17   single    0.970  0.020  1.090
 UBT  C17  H17A  single    0.970  0.020  1.090
 UBT  C18  C20   single    1.529  0.020  1.529
 UBT  C18  H18   single    0.970  0.020  1.090
 UBT  C18  H18A  single    0.970  0.020  1.090
 UBT  C22  C20   single    1.526  0.020  1.526
 UBT  C20  C24   single    1.526  0.020  1.526
 UBT  C20  H20   single    0.970  0.020  1.090
 UBT  C22  H22   single    0.970  0.020  1.090
 UBT  C22  H22A  single    0.970  0.020  1.090
 UBT  C22  H22B  single    0.970  0.020  1.090
 UBT  C24  H24   single    0.970  0.020  1.090
 UBT  C24  H24A  single    0.970  0.020  1.090
 UBT  C24  H24B  single    0.970  0.020  1.090
 UBT  O28  C27   deloc     1.246  0.020  1.246
 UBT  O31  C27   deloc     1.243  0.020  1.243

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
 UBT  H3    C3   C4    119.69  3.000
 UBT  H3    C3   C2    119.72  3.000
 UBT  C4    C3   C2    120.59  3.000
 UBT  H2    C2   C1    120.15  3.000
 UBT  H2    C2   C3    119.85  3.000
 UBT  C1    C2   C3    119.99  3.000
 UBT  H1    C1   C6    120.08  3.000
 UBT  H1    C1   C2    120.13  3.000
 UBT  C6    C1   C2    119.79  3.000
 UBT  H6    C6   C5    119.82  3.000
 UBT  H6    C6   C1    120.14  3.000
 UBT  C5    C6   C1    120.04  3.000
 UBT  H5    C5   C4    119.75  3.000
 UBT  H5    C5   C6    119.70  3.000
 UBT  C4    C5   C6    120.54  3.000
 UBT  C7    C4   C5    120.32  3.000
 UBT  C7    C4   C3    120.63  3.000
 UBT  C5    C4   C3    119.04  3.000
 UBT  H7A   C7   H7    108.01  3.000
 UBT  H7A   C7   O8    110.31  3.000
 UBT  H7    C7   O8    110.38  3.000
 UBT  H7A   C7   C4    110.76  3.000
 UBT  H7    C7   C4    110.65  3.000
 UBT  O8    C7   C4    106.75  3.000
 UBT  C9    O8   C7    117.09  3.000
 UBT  N10   C9   O19   126.00  3.000
 UBT  N10   C9   O8    110.51  3.000
 UBT  O19   C9   O8    123.46  3.000
 UBT  HN10  N10  C11   116.08  3.000
 UBT  HN10  N10  C9    117.44  3.000
 UBT  C11   N10  C9    123.14  3.000
 UBT  H11A  C11  H11   106.96  3.000
 UBT  H11A  C11  P12   111.15  3.000
 UBT  H11   C11  P12   110.17  3.000
 UBT  H11A  C11  N10   109.34  3.000
 UBT  H11   C11  N10   108.76  3.000
 UBT  P12   C11  N10   110.38  3.000
 UBT  N13   P12  O21   110.01  3.000
 UBT  N13   P12  O20   108.82  3.000
 UBT  O21   P12  O20   120.37  3.000
 UBT  N13   P12  C11   100.95  3.000
 UBT  O21   P12  C11   106.04  3.000
 UBT  O20   P12  C11   108.87  3.000
 UBT  HN13  N13  C14   111.76  3.000
 UBT  HN13  N13  P12   113.51  3.000
 UBT  C14   N13  P12   121.90  3.000
 UBT  H14   C14  C18   109.11  3.000
 UBT  H14   C14  C15   109.63  3.000
 UBT  C18   C14  C15   110.04  3.000
 UBT  H14   C14  N13   107.60  3.000
 UBT  C18   C14  N13   112.84  3.000
 UBT  C15   C14  N13   107.55  3.000
 UBT  N16   C15  O23   123.15  3.000
 UBT  O23   C15  C14   120.98  3.000
 UBT  N16   C15  C14   115.87  3.000
 UBT  H18A  C18  H18   106.48  3.000
 UBT  H18A  C18  C20   109.02  3.000
 UBT  H18   C18  C20   109.23  3.000
 UBT  H18A  C18  C14   108.08  3.000
 UBT  H18   C18  C14   107.24  3.000
 UBT  C20   C18  C14   116.35  3.000
 UBT  H20   C20  C24   107.24  3.000
 UBT  H20   C20  C22   107.93  3.000
 UBT  C24   C20  C22   110.50  3.000
 UBT  H20   C20  C18   108.59  3.000
 UBT  C24   C20  C18   109.77  3.000
 UBT  C22   C20  C18   112.63  3.000
 UBT  H22B  C22  H22A  107.50  3.000
 UBT  H22B  C22  H22   107.64  3.000
 UBT  H22A  C22  H22   107.00  3.000
 UBT  H22B  C22  C20   111.21  3.000
 UBT  H22A  C22  C20   112.47  3.000
 UBT  H22   C22  C20   110.78  3.000
 UBT  H24B  C24  H24A  107.61  3.000
 UBT  H24B  C24  H24   107.62  3.000
 UBT  H24A  C24  H24   107.65  3.000
 UBT  H24B  C24  C20   111.09  3.000
 UBT  H24A  C24  C20   111.33  3.000
 UBT  H24   C24  C20   111.36  3.000
 UBT  HN16  N16  C17   114.43  3.000
 UBT  HN16  N16  C15   120.95  3.000
 UBT  C17   N16  C15   124.61  3.000
 UBT  H17A  C17  H17   106.33  3.000
 UBT  H17A  C17  C27   108.80  3.000
 UBT  H17   C17  C27   109.10  3.000
 UBT  H17A  C17  N16   110.90  3.000
 UBT  H17   C17  N16   110.74  3.000
 UBT  C27   C17  N16   110.84  3.000
 UBT  O31   C27  O28   127.72  3.000
 UBT  O31   C27  C17   115.21  3.000
 UBT  O28   C27  C17   117.06  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
 UBT  CONST_01  C6    C1   C2   C3      0.00   0.0  0
 UBT  CONST_02  C6    C5   C4   C3      0.00   0.0  0
 UBT  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 UBT  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 UBT  CONST_05  C4    C5   C6   C1      0.00   0.0  0
 UBT  CONST_06  C4    C3   C2   C1      0.00   0.0  0
 UBT  CONST_07  C7    C4   C3   C2    180.00   0.0  0
 UBT  CONST_08  C7    C4   C5   C6    180.00   0.0  0
 UBT  CONST_09  H1    C1   C2   C3    180.00   0.0  0
 UBT  CONST_10  H5    C5   C4   C3    180.00   0.0  0
 UBT  CONST_11  H6    C6   C1   C2    180.00   0.0  0
 UBT  CONST_12  H3    C3   C2   C1    180.00   0.0  0
 UBT  CONST_13  H2    C2   C1   C6    180.00   0.0  0
 UBT  CONST_14  C17   N16  C15  C14   180.00   0.0  0
 UBT  CONST_15  C17   N16  C15  O23     0.00   0.0  0
 UBT  CONST_16  HN16  N16  C15  C14     0.00   0.0  0
 UBT  Var_01    O8    C7   C4   C3    -97.44  30.0  2
 UBT  Var_02    O19   C9   O8   C7      0.17  30.0  3
 UBT  Var_03    C11   N10  C9   O8   -168.20  30.0  2
 UBT  Var_04    P12   C11  N10  C9     97.37  30.0  3
 UBT  Var_05    O20   P12  C11  N10   -74.90  30.0  3
 UBT  Var_06    C14   N13  P12  C11   127.14  30.0  3
 UBT  Var_07    C22   C20  C18  C14    59.82  30.0  3
 UBT  Var_08    C27   C17  N16  C15  -179.70  30.0  1
 UBT  Var_09    O28   C27  C17  N16    -1.49  30.0  2
 UBT  Var_10    H22   C22  C20  C18   176.40  30.0  3
 UBT  Var_11    H24   C24  C20  C18    57.08  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
 UBT  chir_02  C14  N13  C15  C18  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
 UBT  plan-1  C3    0.020
 UBT  plan-1  C2    0.020
 UBT  plan-1  C1    0.020
 UBT  plan-1  C6    0.020
 UBT  plan-1  C5    0.020
 UBT  plan-1  C4    0.020
 UBT  plan-1  C7    0.020
 UBT  plan-1  H3    0.020
 UBT  plan-1  H2    0.020
 UBT  plan-1  H1    0.020
 UBT  plan-1  H6    0.020
 UBT  plan-1  H5    0.020
 UBT  plan-2  C14   0.020
 UBT  plan-2  C15   0.020
 UBT  plan-2  O23   0.020
 UBT  plan-2  N16   0.020
 UBT  plan-2  C17   0.020
 UBT  plan-2  HN16  0.020
 UBT  plan-3  C17   0.020
 UBT  plan-3  C27   0.020
 UBT  plan-3  O28   0.020
 UBT  plan-3  O31   0.020
 UBT  plan-4  O8    0.020
 UBT  plan-4  C9    0.020
 UBT  plan-4  O19   0.020
 UBT  plan-4  N10   0.020

