# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 23:32:49 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-ethyl-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)[C@H](CC(C)C)N[P](O)(=O)CNC(=O)OCc1ccccc1
#
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
 UBU  UBU  N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-ethyl-L-leucinamide  peptide  53  26  .  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_UBU
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
 UBU  C23   C  CR16   0  -0.282  -5.3140  -0.6057  -1.4857
 UBU  C22   C  CR16   0  -0.242  -6.5913  -0.1617  -1.7928
 UBU  C21   C  CR16   0  -0.263  -7.6356  -0.3721  -0.8993
 UBU  C20   C  CR16   0  -0.241  -7.3952  -1.0273   0.2999
 UBU  C19   C  CR16   0  -0.301  -6.1129  -1.4668   0.6064
 UBU  C1    C  CR6    0   0.074  -5.0633  -1.2624  -0.2823
 UBU  C2    C  CH2    0  -0.231  -3.6771  -1.7267   0.0512
 UBU  O3    O  O2     0  -0.485  -2.9051  -0.5617   0.3504
 UBU  C4    C  C      0   0.748  -1.6185  -0.7566   0.6837
 UBU  O26   O  O      0  -0.515  -1.1018  -1.8549   0.7431
 UBU  N5    N  NH1    0  -0.647  -1.0226   0.4120   0.9656
 UBU  C6    C  CH2    0  -0.566   0.4012   0.5485   1.1816
 UBU  P7    P  P      0   1.243   1.2094   1.3252  -0.2871
 UBU  O24   O  O      0  -0.801   1.2546   0.3213  -1.4215
 UBU  O8    O  OP    -1  -0.798   0.5172   2.6509  -0.4817
 UBU  N9    N  NH1    0  -0.779   2.8119   1.5773   0.2191
 UBU  C10   C  CH1    0  -0.215   3.9195   0.7169  -0.1478
 UBU  C11   C  C      0   0.571   3.8962  -0.5878   0.6587
 UBU  N12   N  NH1    0  -0.651   3.0592  -1.5163   0.1690
 UBU  C13   C  CH2    0  -0.267   2.7728  -2.7564   0.8614
 UBU  C14   C  CH3    0  -0.704   1.9282  -3.6650  -0.0109
 UBU  C15   C  CH2    0  -0.412   5.2518   1.4374   0.0037
 UBU  C16   C  CH1    0  -0.216   5.3574   2.7472  -0.7791
 UBU  C17   C  CH3    0  -0.652   6.7475   3.3469  -0.5906
 UBU  C18   C  CH3    0  -0.669   5.0429   2.5652  -2.2599
 UBU  O25   O  O      0  -0.511   4.5642  -0.7623   1.6718
 UBU  H23   H  HCR6   0   0.254  -4.5064  -0.4452  -2.1903
 UBU  H22   H  HCR6   0   0.258  -6.7753   0.3462  -2.7308
 UBU  H21   H  HCR6   0   0.258  -8.6333  -0.0290  -1.1408
 UBU  H20   H  HCR6   0   0.258  -8.2044  -1.1968   0.9984
 UBU  H19   H  HCR6   0   0.254  -5.9296  -1.9776   1.5444
 UBU  H2    H  HCH2   0   0.244  -3.6954  -2.4055   0.9063
 UBU  H2A   H  HCH2   0   0.243  -3.2360  -2.2615  -0.7934
 UBU  HN5   H  HNH1   0   0.392  -1.5332   1.2603   0.7758
 UBU  H6    H  HCH2   0   0.245   0.5698   1.1695   2.0658
 UBU  H6A   H  HCH2   0   0.260   0.8259  -0.4313   1.3932
 UBU  HN9   H  HNH1   0   0.364   2.9525   2.0952   1.0755
 UBU  H10   H  HCH1   0   0.251   3.7881   0.4489  -1.1977
 UBU  HN12  H  HNH1   0   0.396   2.4252  -1.2211  -0.5678
 UBU  H13   H  HCH2   0   0.233   3.7124  -3.2482   1.1187
 UBU  H13A  H  HCH2   0   0.222   2.2521  -2.5600   1.8045
 UBU  H14   H  HCH3   0   0.241   0.9726  -3.1984  -0.2493
 UBU  H14A  H  HCH3   0   0.228   2.4392  -3.9062  -0.9435
 UBU  H14B  H  HCH3   0   0.237   1.7204  -4.5985   0.5106
 UBU  H15   H  HCH2   0   0.222   5.4425   1.6364   1.0629
 UBU  H15A  H  HCH2   0   0.220   6.0484   0.7614  -0.3263
 UBU  H16   H  HCH1   0   0.214   4.6284   3.4504  -0.3648
 UBU  H17   H  HCH3   0   0.210   7.5166   2.7042  -1.0266
 UBU  H17A  H  HCH3   0   0.223   6.8258   4.3248  -1.0689
 UBU  H17B  H  HCH3   0   0.221   6.9855   3.4751   0.4673
 UBU  H18   H  HCH3   0   0.211   5.6802   1.7966  -2.7053
 UBU  H18A  H  HCH3   0   0.231   4.0038   2.2752  -2.4217
 UBU  H18B  H  HCH3   0   0.224   5.2117   3.4915  -2.8120

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
 UBU  C23  C1    aromatic  1.394  0.020  1.394
 UBU  C1   C2    single    1.499  0.020  1.499
 UBU  C1   C19   aromatic  1.390  0.020  1.390
 UBU  C2   O3    single    1.429  0.020  1.429
 UBU  C2   H2    single    0.970  0.020  1.090
 UBU  C2   H2A   single    0.970  0.020  1.090
 UBU  O3   C4    single    1.343  0.020  1.343
 UBU  C4   O26   double    1.215  0.020  1.215
 UBU  C4   N5    single    1.342  0.020  1.342
 UBU  N5   C6    single    1.447  0.020  1.447
 UBU  N5   HN5   single    0.860  0.020  1.020
 UBU  C6   P7    single    1.848  0.020  1.848
 UBU  C6   H6    single    0.970  0.020  1.090
 UBU  C6   H6A   single    0.970  0.020  1.090
 UBU  O24  P7    deloc     1.515  0.020  1.515
 UBU  O8   P7    deloc     1.508  0.020  1.508
 UBU  P7   N9    single    1.699  0.020  1.699
 UBU  N9   C10   single    1.450  0.020  1.450
 UBU  N9   HN9   single    0.890  0.020  1.040
 UBU  C11  C10   single    1.534  0.020  1.534
 UBU  C10  C15   single    1.522  0.020  1.522
 UBU  C10  H10   single    0.970  0.020  1.090
 UBU  N12  C11   single    1.343  0.020  1.343
 UBU  O25  C11   double    1.226  0.020  1.226
 UBU  C13  N12   single    1.449  0.020  1.449
 UBU  N12  HN12  single    0.860  0.020  1.020
 UBU  C13  C14   single    1.516  0.020  1.516
 UBU  C13  H13   single    0.970  0.020  1.090
 UBU  C13  H13A  single    0.970  0.020  1.090
 UBU  C14  H14   single    0.970  0.020  1.090
 UBU  C14  H14A  single    0.970  0.020  1.090
 UBU  C14  H14B  single    0.970  0.020  1.090
 UBU  C15  C16   single    1.529  0.020  1.529
 UBU  C15  H15   single    0.970  0.020  1.090
 UBU  C15  H15A  single    0.970  0.020  1.090
 UBU  C17  C16   single    1.526  0.020  1.526
 UBU  C16  C18   single    1.525  0.020  1.525
 UBU  C16  H16   single    0.970  0.020  1.090
 UBU  C17  H17   single    0.970  0.020  1.090
 UBU  C17  H17A  single    0.970  0.020  1.090
 UBU  C17  H17B  single    0.970  0.020  1.090
 UBU  C18  H18   single    0.970  0.020  1.090
 UBU  C18  H18A  single    0.970  0.020  1.090
 UBU  C18  H18B  single    0.970  0.020  1.090
 UBU  C20  C19   aromatic  1.390  0.020  1.390
 UBU  C19  H19   single    0.930  0.020  1.080
 UBU  C21  C20   aromatic  1.388  0.020  1.388
 UBU  C20  H20   single    0.930  0.020  1.080
 UBU  C22  C21   aromatic  1.390  0.020  1.390
 UBU  C21  H21   single    0.930  0.020  1.080
 UBU  C22  C23   aromatic  1.387  0.020  1.387
 UBU  C22  H22   single    0.930  0.020  1.080
 UBU  C23  H23   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
 UBU  H23   C23  C1    119.81  3.000
 UBU  H23   C23  C22   119.67  3.000
 UBU  C1    C23  C22   120.52  3.000
 UBU  H22   C22  C21   120.01  3.000
 UBU  H22   C22  C23   119.92  3.000
 UBU  C21   C22  C23   120.07  3.000
 UBU  H21   C21  C20   120.15  3.000
 UBU  H21   C21  C22   120.07  3.000
 UBU  C20   C21  C22   119.79  3.000
 UBU  H20   C20  C19   119.87  3.000
 UBU  H20   C20  C21   120.15  3.000
 UBU  C19   C20  C21   119.98  3.000
 UBU  H19   C19  C1    119.66  3.000
 UBU  H19   C19  C20   119.73  3.000
 UBU  C1    C19  C20   120.61  3.000
 UBU  C2    C1   C19   120.68  3.000
 UBU  C19   C1   C23   119.03  3.000
 UBU  C2    C1   C23   120.28  3.000
 UBU  H2A   C2   H2    107.92  3.000
 UBU  H2A   C2   O3    110.05  3.000
 UBU  H2    C2   O3    110.60  3.000
 UBU  H2A   C2   C1    110.67  3.000
 UBU  H2    C2   C1    110.56  3.000
 UBU  O3    C2   C1    107.07  3.000
 UBU  C4    O3   C2    116.80  3.000
 UBU  N5    C4   O26   126.02  3.000
 UBU  N5    C4   O3    110.55  3.000
 UBU  O26   C4   O3    123.41  3.000
 UBU  HN5   N5   C6    116.57  3.000
 UBU  HN5   N5   C4    117.93  3.000
 UBU  C6    N5   C4    123.41  3.000
 UBU  H6A   C6   H6    107.08  3.000
 UBU  H6A   C6   P7    111.24  3.000
 UBU  H6    C6   P7    109.67  3.000
 UBU  H6A   C6   N5    109.15  3.000
 UBU  H6    C6   N5    109.03  3.000
 UBU  P7    C6   N5    110.58  3.000
 UBU  N9    P7   O8    109.93  3.000
 UBU  N9    P7   O24   107.05  3.000
 UBU  O8    P7   O24   119.96  3.000
 UBU  N9    P7   C6    103.77  3.000
 UBU  O8    P7   C6    105.74  3.000
 UBU  O24   P7   C6    109.25  3.000
 UBU  HN9   N9   C10   114.35  3.000
 UBU  HN9   N9   P7    117.36  3.000
 UBU  C10   N9   P7    123.85  3.000
 UBU  H10   C10  C15   108.50  3.000
 UBU  H10   C10  C11   107.16  3.000
 UBU  C15   C10  C11   111.32  3.000
 UBU  H10   C10  N9    107.29  3.000
 UBU  C15   C10  N9    111.26  3.000
 UBU  C11   C10  N9    111.11  3.000
 UBU  O25   C11  N12   122.86  3.000
 UBU  O25   C11  C10   123.18  3.000
 UBU  N12   C11  C10   113.95  3.000
 UBU  HN12  N12  C13   118.16  3.000
 UBU  HN12  N12  C11   116.91  3.000
 UBU  C13   N12  C11   122.74  3.000
 UBU  H13A  C13  H13   106.69  3.000
 UBU  H13A  C13  C14   109.76  3.000
 UBU  H13   C13  C14   110.19  3.000
 UBU  H13A  C13  N12   110.62  3.000
 UBU  H13   C13  N12   109.16  3.000
 UBU  C14   C13  N12   110.37  3.000
 UBU  H14B  C14  H14A  108.01  3.000
 UBU  H14B  C14  H14   107.72  3.000
 UBU  H14A  C14  H14   108.57  3.000
 UBU  H14B  C14  C13   110.14  3.000
 UBU  H14A  C14  C13   111.32  3.000
 UBU  H14   C14  C13   110.95  3.000
 UBU  H15A  C15  H15   106.08  3.000
 UBU  H15A  C15  C16   108.91  3.000
 UBU  H15   C15  C16   109.12  3.000
 UBU  H15A  C15  C10   108.32  3.000
 UBU  H15   C15  C10   109.56  3.000
 UBU  C16   C15  C10   114.51  3.000
 UBU  H16   C16  C18   107.88  3.000
 UBU  H16   C16  C17   107.91  3.000
 UBU  C18   C16  C17   110.78  3.000
 UBU  H16   C16  C15   108.10  3.000
 UBU  C18   C16  C15   112.37  3.000
 UBU  C17   C16  C15   109.65  3.000
 UBU  H17B  C17  H17A  107.69  3.000
 UBU  H17B  C17  H17   107.58  3.000
 UBU  H17A  C17  H17   107.55  3.000
 UBU  H17B  C17  C16   111.37  3.000
 UBU  H17A  C17  C16   111.31  3.000
 UBU  H17   C17  C16   111.14  3.000
 UBU  H18B  C18  H18A  107.33  3.000
 UBU  H18B  C18  H18   107.49  3.000
 UBU  H18A  C18  H18   107.94  3.000
 UBU  H18B  C18  C16   110.98  3.000
 UBU  H18A  C18  C16   111.85  3.000
 UBU  H18   C18  C16   111.06  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
 UBU  CONST_01  C20   C19  C1   C23     0.00   0.0  0
 UBU  CONST_02  C20   C21  C22  C23     0.00   0.0  0
 UBU  CONST_03  C19   C20  C21  C22     0.00   0.0  0
 UBU  CONST_04  C19   C1   C23  C22     0.00   0.0  0
 UBU  CONST_05  C1    C19  C20  C21     0.00   0.0  0
 UBU  CONST_06  C1    C23  C22  C21     0.00   0.0  0
 UBU  CONST_07  C2    C1   C23  C22   180.00   0.0  0
 UBU  CONST_08  C2    C1   C19  C20   180.00   0.0  0
 UBU  CONST_09  H19   C19  C1   C23   180.00   0.0  0
 UBU  CONST_10  H21   C21  C22  C23   180.00   0.0  0
 UBU  CONST_11  H20   C20  C21  C22   180.00   0.0  0
 UBU  CONST_12  H23   C23  C22  C21   180.00   0.0  0
 UBU  CONST_13  H22   C22  C21  C20   180.00   0.0  0
 UBU  CONST_14  C13   N12  C11  C10   180.00   0.0  0
 UBU  CONST_15  O25   C11  N12  C13     0.00   0.0  0
 UBU  CONST_16  HN12  N12  C11  C10     0.00   0.0  0
 UBU  Var_01    O3    C2   C1   C23    72.07  30.0  2
 UBU  Var_02    O26   C4   O3   C2     -0.25  30.0  3
 UBU  Var_03    C6    N5   C4   O3   -171.38  30.0  2
 UBU  Var_04    P7    C6   N5   C4    104.82  30.0  3
 UBU  Var_05    O24   P7   C6   N5    -72.84  30.0  3
 UBU  Var_06    C10   N9   P7   C6    100.95  30.0  3
 UBU  Var_07    C17   C16  C15  C10  -177.93  30.0  3
 UBU  Var_08    C14   C13  N12  C11  -173.30  30.0  1
 UBU  Var_09    H14   C14  C13  N12   -61.18  30.0  3
 UBU  Var_10    H17   C17  C16  C15    64.93  30.0  3
 UBU  Var_11    H18   C18  C16  C15   -55.40  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
 UBU  chir_02  C10  N9  C11  C15  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
 UBU  plan-1  C23   0.020
 UBU  plan-1  C22   0.020
 UBU  plan-1  C21   0.020
 UBU  plan-1  C20   0.020
 UBU  plan-1  C19   0.020
 UBU  plan-1  C1    0.020
 UBU  plan-1  C2    0.020
 UBU  plan-1  H23   0.020
 UBU  plan-1  H22   0.020
 UBU  plan-1  H21   0.020
 UBU  plan-1  H20   0.020
 UBU  plan-1  H19   0.020
 UBU  plan-2  C10   0.020
 UBU  plan-2  C11   0.020
 UBU  plan-2  N12   0.020
 UBU  plan-2  C13   0.020
 UBU  plan-2  O25   0.020
 UBU  plan-2  HN12  0.020
 UBU  plan-3  O3    0.020
 UBU  plan-3  C4    0.020
 UBU  plan-3  O26   0.020
 UBU  plan-3  N5    0.020

