# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 23:57:23 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  54  28  .  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_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  -0.283   7.2786   0.4983   0.7581
 UBT  C2    C  CR16  0  -0.242   8.5252  -0.0812   0.5766
 UBT  C1    C  CR16  0  -0.262   8.9754  -0.3773  -0.7052
 UBT  C6    C  CR16  0  -0.241   8.1737  -0.0905  -1.8009
 UBT  C5    C  CR16  0  -0.299   6.9228   0.4854  -1.6149
 UBT  C4    C  CR6   0   0.074   6.4660   0.7862  -0.3367
 UBT  C7    C  CH2   0  -0.237   5.1144   1.4003  -0.1321
 UBT  O8    O  O2    0  -0.478   4.2607   0.3762   0.3923
 UBT  C9    C  C     0   0.763   3.0243   0.7405   0.7414
 UBT  O19   O  O     0  -0.513   2.5814   1.8624   0.6181
 UBT  N10   N  NH1   0  -0.655   2.3528  -0.3034   1.2703
 UBT  C11   C  CH2   0  -0.569   0.9591  -0.2149   1.6106
 UBT  P12   P  P     0   1.311  -0.0812  -0.6493   0.1766
 UBT  O20   O  O     0  -0.713   0.1156   0.1815  -1.0395
 UBT  O21   O  OH1   0  -0.751   0.3463  -2.1705  -0.1863
 UBT  N13   N  NH1   0  -0.780  -1.6223  -0.5852   0.7831
 UBT  C14   C  CH1   0  -0.206  -2.7892  -0.5341  -0.0844
 UBT  C15   C  C     0   0.581  -3.8582   0.2705   0.6457
 UBT  O23   O  O     0  -0.487  -4.1543   0.0218   1.8043
 UBT  C18   C  CH2   0  -0.408  -3.3169  -1.9282  -0.4375
 UBT  C20   C  CH1   0  -0.267  -4.4935  -1.9617  -1.4144
 UBT  C22   C  CH3   0  -0.661  -4.1207  -1.3761  -2.7737
 UBT  C24   C  CH3   0  -0.649  -4.9809  -3.3987  -1.5755
 UBT  N16   N  NH1   0  -0.626  -4.4458   1.2516  -0.0540
 UBT  C17   C  CH2   0  -0.422  -5.4660   2.0733   0.5235
 UBT  C27   C  C     0   0.539  -6.7763   1.3386   0.7169
 UBT  O28   O  O     0  -0.426  -7.0425   0.2611   0.2554
 UBT  O31   O  OH1   0  -0.591  -7.6115   2.0630   1.4485
 UBT  H3    H  HCR6  0   0.255   6.9368   0.7337   1.7591
 UBT  H2    H  HCR6  0   0.258   9.1484  -0.2984   1.4344
 UBT  H1    H  HCR6  0   0.259   9.9490  -0.8279  -0.8484
 UBT  H6    H  HCR6  0   0.259   8.5202  -0.3146  -2.8012
 UBT  H5    H  HCR6  0   0.255   6.2997   0.7050  -2.4738
 UBT  H7    H  HCH2  0   0.249   5.1707   2.2348   0.5698
 UBT  H7A   H  HCH2  0   0.250   4.7141   1.7768  -1.0758
 UBT  HN10  H  HNH1  0   0.410   2.7914  -1.2102   1.2865
 UBT  H11   H  HCH2  0   0.304   0.7458  -0.8812   2.4484
 UBT  H11A  H  HCH2  0   0.297   0.7100   0.7952   1.9328
 UBT  HO21  H  HOH1  0   0.484   0.1495  -2.8284   0.4926
 UBT  HN13  H  HNH1  0   0.400  -1.7938  -1.0149   1.6841
 UBT  H14   H  HCH1  0   0.269  -2.4880  -0.0121  -0.9947
 UBT  H18   H  HCH2  0   0.233  -2.4855  -2.4994  -0.8634
 UBT  H18A  H  HCH2  0   0.233  -3.5970  -2.4348   0.4916
 UBT  H20   H  HCH1  0   0.238  -5.3175  -1.3730  -0.9979
 UBT  H22   H  HCH3  0   0.234  -4.9606  -1.4369  -3.4666
 UBT  H22A  H  HCH3  0   0.222  -3.8290  -0.3264  -2.7153
 UBT  H22B  H  HCH3  0   0.219  -3.2847  -1.9250  -3.2141
 UBT  H24   H  HCH3  0   0.227  -5.2894  -3.8270  -0.6204
 UBT  H24A  H  HCH3  0   0.228  -5.8343  -3.4522  -2.2535
 UBT  H24B  H  HCH3  0   0.214  -4.1912  -4.0337  -1.9849
 UBT  HN16  H  HNH1  0   0.413  -4.1769   1.4248  -1.0079
 UBT  H17   H  HCH2  0   0.290  -5.1421   2.4922   1.4785
 UBT  H17A  H  HCH2  0   0.316  -5.6464   2.9186  -0.1426
 UBT  HO31  H  HOH1  0   0.485  -8.4618   1.6069   1.5378

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  1.388  0.020  1.388
 UBT  C1   C2    aromatic  1.390  0.020  1.390
 UBT  C1   H1    single    0.930  0.020  1.080
 UBT  C2   C3    aromatic  1.387  0.020  1.387
 UBT  C2   H2    single    0.930  0.020  1.080
 UBT  C4   C3    aromatic  1.394  0.020  1.394
 UBT  C3   H3    single    0.930  0.020  1.080
 UBT  C5   C4    aromatic  1.390  0.020  1.390
 UBT  C4   C7    single    1.499  0.020  1.499
 UBT  C6   C5    aromatic  1.390  0.020  1.390
 UBT  C5   H5    single    0.930  0.020  1.080
 UBT  C6   H6    single    0.930  0.020  1.080
 UBT  C7   O8    single    1.433  0.020  1.433
 UBT  C7   H7    single    0.970  0.020  1.090
 UBT  C7   H7A   single    0.970  0.020  1.090
 UBT  O8   C9    single    1.335  0.020  1.335
 UBT  C9   O19   double    1.212  0.020  1.212
 UBT  C9   N10   single    1.349  0.020  1.349
 UBT  N10  C11   single    1.437  0.020  1.437
 UBT  N10  HN10  single    0.860  0.020  1.020
 UBT  C11  P12   single    1.824  0.020  1.824
 UBT  C11  H11   single    0.970  0.020  1.090
 UBT  C11  H11A  single    0.970  0.020  1.090
 UBT  O20  P12   double    1.486  0.020  1.486
 UBT  O21  P12   single    1.621  0.020  1.621
 UBT  P12  N13   single    1.657  0.020  1.657
 UBT  N13  C14   single    1.455  0.020  1.455
 UBT  N13  HN13  single    0.890  0.020  1.040
 UBT  C15  C14   single    1.524  0.020  1.524
 UBT  C14  C18   single    1.532  0.020  1.532
 UBT  C14  H14   single    0.970  0.020  1.090
 UBT  N16  C15   single    1.341  0.020  1.341
 UBT  O23  C15   double    1.221  0.020  1.221
 UBT  C17  N16   single    1.432  0.020  1.432
 UBT  N16  HN16  single    0.860  0.020  1.020
 UBT  C27  C17   single    1.515  0.020  1.515
 UBT  C17  H17   single    0.970  0.020  1.090
 UBT  C17  H17A  single    0.970  0.020  1.090
 UBT  C18  C20   single    1.530  0.020  1.530
 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  O21  HO21  single    0.850  0.020  0.980
 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   double    1.202  0.020  1.202
 UBT  O31  C27   single    1.326  0.020  1.326
 UBT  O31  HO31  single    0.850  0.020  0.980

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    119.80  3.000
 UBT  H3    C3   C2    119.69  3.000
 UBT  C4    C3   C2    120.51  3.000
 UBT  H2    C2   C1    120.10  3.000
 UBT  H2    C2   C3    119.85  3.000
 UBT  C1    C2   C3    120.05  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    119.85  3.000
 UBT  H6    C6   C1    120.14  3.000
 UBT  C5    C6   C1    120.00  3.000
 UBT  H5    C5   C4    119.73  3.000
 UBT  H5    C5   C6    119.70  3.000
 UBT  C4    C5   C6    120.56  3.000
 UBT  C7    C4   C5    120.70  3.000
 UBT  C7    C4   C3    120.22  3.000
 UBT  C5    C4   C3    119.08  3.000
 UBT  H7A   C7   H7    108.11  3.000
 UBT  H7A   C7   O8    110.14  3.000
 UBT  H7    C7   O8    109.98  3.000
 UBT  H7A   C7   C4    110.73  3.000
 UBT  H7    C7   C4    110.76  3.000
 UBT  O8    C7   C4    107.13  3.000
 UBT  C9    O8   C7    116.90  3.000
 UBT  N10   C9   O19   125.03  3.000
 UBT  N10   C9   O8    110.62  3.000
 UBT  O19   C9   O8    124.33  3.000
 UBT  HN10  N10  C11   118.28  3.000
 UBT  HN10  N10  C9    119.08  3.000
 UBT  C11   N10  C9    121.85  3.000
 UBT  H11A  C11  H11   107.12  3.000
 UBT  H11A  C11  P12   108.85  3.000
 UBT  H11   C11  P12   110.28  3.000
 UBT  H11A  C11  N10   110.42  3.000
 UBT  H11   C11  N10   109.49  3.000
 UBT  P12   C11  N10   110.62  3.000
 UBT  N13   P12  O21   111.31  3.000
 UBT  N13   P12  O20   113.64  3.000
 UBT  O21   P12  O20   107.85  3.000
 UBT  N13   P12  C11   103.50  3.000
 UBT  O21   P12  C11   104.42  3.000
 UBT  O20   P12  C11   115.77  3.000
 UBT  HO21  O21  P12   115.35  3.000
 UBT  HN13  N13  C14   114.17  3.000
 UBT  HN13  N13  P12   117.81  3.000
 UBT  C14   N13  P12   121.93  3.000
 UBT  H14   C14  C18   109.76  3.000
 UBT  H14   C14  C15   109.90  3.000
 UBT  C18   C14  C15   110.44  3.000
 UBT  H14   C14  N13   107.02  3.000
 UBT  C18   C14  N13   112.44  3.000
 UBT  C15   C14  N13   107.18  3.000
 UBT  N16   C15  O23   122.53  3.000
 UBT  O23   C15  C14   121.13  3.000
 UBT  N16   C15  C14   116.34  3.000
 UBT  H18A  C18  H18   106.44  3.000
 UBT  H18A  C18  C20   109.58  3.000
 UBT  H18   C18  C20   108.92  3.000
 UBT  H18A  C18  C14   108.28  3.000
 UBT  H18   C18  C14   107.62  3.000
 UBT  C20   C18  C14   115.60  3.000
 UBT  H20   C20  C24   107.82  3.000
 UBT  H20   C20  C22   108.43  3.000
 UBT  C24   C20  C22   110.20  3.000
 UBT  H20   C20  C18   108.92  3.000
 UBT  C24   C20  C18   109.50  3.000
 UBT  C22   C20  C18   111.87  3.000
 UBT  H22B  C22  H22A  107.48  3.000
 UBT  H22B  C22  H22   107.77  3.000
 UBT  H22A  C22  H22   107.07  3.000
 UBT  H22B  C22  C20   110.67  3.000
 UBT  H22A  C22  C20   112.75  3.000
 UBT  H22   C22  C20   110.88  3.000
 UBT  H24B  C24  H24A  107.69  3.000
 UBT  H24B  C24  H24   107.71  3.000
 UBT  H24A  C24  H24   107.66  3.000
 UBT  H24B  C24  C20   110.85  3.000
 UBT  H24A  C24  C20   111.20  3.000
 UBT  H24   C24  C20   111.56  3.000
 UBT  HN16  N16  C17   118.30  3.000
 UBT  HN16  N16  C15   120.24  3.000
 UBT  C17   N16  C15   121.46  3.000
 UBT  H17A  C17  H17   106.60  3.000
 UBT  H17A  C17  C27   108.10  3.000
 UBT  H17   C17  C27   109.33  3.000
 UBT  H17A  C17  N16   108.44  3.000
 UBT  H17   C17  N16   111.19  3.000
 UBT  C27   C17  N16   112.93  3.000
 UBT  O31   C27  O28   124.21  3.000
 UBT  O31   C27  C17   110.51  3.000
 UBT  O28   C27  C17   125.27  3.000
 UBT  HO31  O31  C27   110.27  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  CONST_17  HO31  O31  C27  C17   180.00   0.0  0
 UBT  Var_01    O8    C7   C4   C3    -73.39  30.0  2
 UBT  Var_02    O19   C9   O8   C7      1.48  30.0  3
 UBT  Var_03    C11   N10  C9   O8   -173.96  30.0  2
 UBT  Var_04    P12   C11  N10  C9     88.13  30.0  3
 UBT  Var_05    O20   P12  C11  N10   -58.46  30.0  3
 UBT  Var_06    C14   N13  P12  C11   164.27  30.0  3
 UBT  Var_07    C22   C20  C18  C14    62.30  30.0  3
 UBT  Var_08    C27   C17  N16  C15   -71.77  30.0  1
 UBT  Var_09    O28   C27  C17  N16   -11.65  30.0  2
 UBT  Var_10    H22   C22  C20  C18   178.20  30.0  3
 UBT  Var_11    H24   C24  C20  C18    58.69  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
 UBT  chir_03  P12  O20  O21  N13  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
 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-3  HO31  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

