# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 06:48:47 2021
#   Inital geometry file: a 128 line input string
#   Ligand name: ~{N}-[(2~{S})-1-(aminomethylamino)-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid;hydrogen
#   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)NCN
#
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
 8L5  8L5  '~{N}-[(2~{S})-1-(aminomethylamino)-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid;hydrogen'  ligand  53  26  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8L5
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
 8L5  C10  C  CH2   0  -0.258  13.2652  39.5089  -10.7808
 8L5  C11  C  CR6   0   0.071  14.1487  40.7207  -10.8693
 8L5  C12  C  CR16  0  -0.286  13.6253  41.9980  -10.7050
 8L5  C13  C  CR16  0  -0.244  14.4463  43.1151  -10.7943
 8L5  C14  C  CR16  0  -0.264  15.8043  42.9618  -11.0369
 8L5  C15  C  CR16  0  -0.244  16.3366  41.6877  -11.1965
 8L5  C16  C  CR16  0  -0.283  15.5123  40.5749  -11.1161
 8L5  O01  O  O     0  -0.708  10.9424  37.4596   -6.6562
 8L5  P01  P  P     0   1.332  12.0920  37.3304   -5.7220
 8L5  N01  N  NH1   0  -0.816  11.6696  37.7429   -4.1647
 8L5  C01  C  CH1   0  -0.138  10.3080  38.1124   -3.8063
 8L5  C02  C  CH2   0  -0.451  10.2826  38.4391   -2.3080
 8L5  C03  C  CH1   0  -0.246   8.9348  38.8782   -1.7354
 8L5  C04  C  CH3   0  -0.661   7.8567  37.8141   -1.9146
 8L5  C05  C  CH3   0  -0.649   9.1078  39.2179   -0.2577
 8L5  C06  C  C     0   0.536   9.8228  39.3130   -4.6162
 8L5  O02  O  O     0  -0.495   8.6680  39.3848   -5.0102
 8L5  O03  O  OH1   0  -0.745  12.8024  35.8815   -5.6694
 8L5  C08  C  CH2   0  -0.560  13.5422  38.3491   -6.1525
 8L5  N04  N  NH1   0  -0.655  13.8783  38.2395   -7.5447
 8L5  C09  C  C     0   0.759  13.3284  39.0586   -8.4658
 8L5  O04  O  O2    0  -0.482  13.6430  38.6515   -9.7017
 8L5  O05  O  O     0  -0.493  12.6597  40.0375   -8.2185
 8L5  N02  N  NH1   0  -0.619  10.7323  40.2803   -4.8090
 8L5  C07  C  CH2   0  -0.154  10.4561  41.4928   -5.5378
 8L5  N03  N  NH2   0  -0.795   9.9664  42.5418   -4.6653
 8L5  H22  H  HCH2  0   0.254  12.2157  39.7961  -10.7007
 8L5  H21  H  HCH2  0   0.264  13.3741  38.8868  -11.6688
 8L5  H23  H  HCR6  0   0.252  12.5678  42.1213  -10.5066
 8L5  H24  H  HCR6  0   0.256  14.0261  44.1043  -10.6654
 8L5  H25  H  HCR6  0   0.257  16.4468  43.8302  -11.1040
 8L5  H26  H  HCR6  0   0.256  17.3946  41.5620  -11.3876
 8L5  H27  H  HCR6  0   0.255  15.9345  39.5860  -11.2524
 8L5  H02  H  HCH1  0   0.264   9.6029  37.3009   -4.0073
 8L5  H03  H  HCH2  0   0.242  10.6154  37.5448   -1.7689
 8L5  H04  H  HCH2  0   0.240  11.0301  39.2139   -2.1108
 8L5  H05  H  HCH1  0   0.227   8.6128  39.7889   -2.2511
 8L5  H06  H  HCH3  0   0.229   6.9258  38.1231   -1.4365
 8L5  H08  H  HCH3  0   0.231   7.6346  37.6243   -2.9642
 8L5  H07  H  HCH3  0   0.215   8.1654  36.8692   -1.4599
 8L5  H09  H  HCH3  0   0.229   8.1693  39.5627    0.1788
 8L5  H11  H  HCH3  0   0.215   9.4339  38.3419    0.3087
 8L5  H10  H  HCH3  0   0.226   9.8511  40.0033   -0.1094
 8L5  H2   H  HOH1  0   0.489  12.1848  35.1496   -5.5332
 8L5  H20  H  HNH1  0   0.408  14.3786  37.4215   -7.8543
 8L5  H12  H  HNH1  0   0.395  11.6370  40.1790   -4.3773
 8L5  H13  H  HCH2  0   0.244  11.3911  41.8256   -5.9861
 8L5  H14  H  HCH2  0   0.218   9.7795  41.2382   -6.3579
 8L5  H16  H  HNH2  0   0.351   9.9628  43.4164   -5.1751
 8L5  H3   H  HNH2  0   0.345   9.0005  42.3581   -4.4225
 8L5  H01  H  HNH1  0   0.405  12.2363  37.3863   -3.4080
 8L5  H18  H  HCH2  0   0.299  14.3986  38.0698   -5.5373
 8L5  H19  H  HCH2  0   0.284  13.3039  39.3845   -5.9158

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
 8L5  C10  C11  single    1.502  0.020  1.502
 8L5  C10  O04  single    1.429  0.020  1.429
 8L5  C11  C12  aromatic  1.390  0.020  1.390
 8L5  C11  C16  aromatic  1.393  0.020  1.393
 8L5  C12  C13  aromatic  1.389  0.020  1.389
 8L5  C13  C14  aromatic  1.388  0.020  1.388
 8L5  C14  C15  aromatic  1.390  0.020  1.390
 8L5  C15  C16  aromatic  1.387  0.020  1.387
 8L5  O01  P01  double    1.487  0.020  1.487
 8L5  P01  N01  single    1.665  0.020  1.665
 8L5  P01  O03  single    1.615  0.020  1.615
 8L5  P01  C08  single    1.824  0.020  1.824
 8L5  N01  C01  single    1.456  0.020  1.456
 8L5  C01  C02  single    1.534  0.020  1.534
 8L5  C01  C06  single    1.527  0.020  1.527
 8L5  C02  C03  single    1.529  0.020  1.529
 8L5  C03  C04  single    1.525  0.020  1.525
 8L5  C03  C05  single    1.526  0.020  1.526
 8L5  C06  O02  double    1.222  0.020  1.222
 8L5  C06  N02  single    1.342  0.020  1.342
 8L5  C08  N04  single    1.436  0.020  1.436
 8L5  N04  C09  single    1.350  0.020  1.350
 8L5  C09  O04  single    1.339  0.020  1.339
 8L5  C09  O05  double    1.211  0.020  1.211
 8L5  N02  C07  single    1.441  0.020  1.441
 8L5  C07  N03  single    1.450  0.020  1.450
 8L5  C10  H22  single    0.970  0.020  1.090
 8L5  C10  H21  single    0.970  0.020  1.090
 8L5  C12  H23  single    0.930  0.020  1.080
 8L5  C13  H24  single    0.930  0.020  1.080
 8L5  C14  H25  single    0.930  0.020  1.080
 8L5  C15  H26  single    0.930  0.020  1.080
 8L5  C16  H27  single    0.930  0.020  1.080
 8L5  N01  H01  single    0.890  0.020  1.040
 8L5  C01  H02  single    0.970  0.020  1.090
 8L5  C02  H03  single    0.970  0.020  1.090
 8L5  C02  H04  single    0.970  0.020  1.090
 8L5  C03  H05  single    0.970  0.020  1.090
 8L5  C04  H06  single    0.970  0.020  1.090
 8L5  C04  H08  single    0.970  0.020  1.090
 8L5  C04  H07  single    0.970  0.020  1.090
 8L5  C05  H09  single    0.970  0.020  1.090
 8L5  C05  H11  single    0.970  0.020  1.090
 8L5  C05  H10  single    0.970  0.020  1.090
 8L5  O03  H2   single    0.850  0.020  0.980
 8L5  C08  H18  single    0.970  0.020  1.090
 8L5  C08  H19  single    0.970  0.020  1.090
 8L5  N04  H20  single    0.860  0.020  1.020
 8L5  N02  H12  single    0.860  0.020  1.020
 8L5  C07  H13  single    0.970  0.020  1.090
 8L5  C07  H14  single    0.970  0.020  1.090
 8L5  N03  H16  single    0.890  0.020  1.040
 8L5  N03  H3   single    0.890  0.020  1.040

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
 8L5  H21  C10  H22  107.84  3.000
 8L5  H21  C10  O04  104.26  3.000
 8L5  H22  C10  O04  110.90  3.000
 8L5  H21  C10  C11  110.71  3.000
 8L5  H22  C10  C11  110.96  3.000
 8L5  O04  C10  C11  111.90  3.000
 8L5  C16  C11  C12  119.04  3.000
 8L5  C16  C11  C10  120.11  3.000
 8L5  C12  C11  C10  120.85  3.000
 8L5  H23  C12  C13  119.82  3.000
 8L5  H23  C12  C11  119.60  3.000
 8L5  C13  C12  C11  120.59  3.000
 8L5  H24  C13  C14  120.10  3.000
 8L5  H24  C13  C12  119.86  3.000
 8L5  C14  C13  C12  120.04  3.000
 8L5  H25  C14  C15  120.06  3.000
 8L5  H25  C14  C13  120.20  3.000
 8L5  C15  C14  C13  119.74  3.000
 8L5  H26  C15  C16  119.86  3.000
 8L5  H26  C15  C14  120.07  3.000
 8L5  C16  C15  C14  120.07  3.000
 8L5  H27  C16  C15  119.55  3.000
 8L5  H27  C16  C11  119.93  3.000
 8L5  C15  C16  C11  120.52  3.000
 8L5  C08  P01  O03   99.15  3.000
 8L5  C08  P01  N01  106.50  3.000
 8L5  O03  P01  N01  107.66  3.000
 8L5  C08  P01  O01  114.70  3.000
 8L5  O03  P01  O01  116.01  3.000
 8L5  N01  P01  O01  111.71  3.000
 8L5  H01  N01  C01  115.45  3.000
 8L5  H01  N01  P01  118.08  3.000
 8L5  C01  N01  P01  122.03  3.000
 8L5  H02  C01  C06  106.32  3.000
 8L5  H02  C01  C02  109.08  3.000
 8L5  C06  C01  C02  110.20  3.000
 8L5  H02  C01  N01  111.68  3.000
 8L5  C06  C01  N01  111.48  3.000
 8L5  C02  C01  N01  108.07  3.000
 8L5  H04  C02  H03  106.36  3.000
 8L5  H04  C02  C03  109.35  3.000
 8L5  H03  C02  C03  108.53  3.000
 8L5  H04  C02  C01  108.39  3.000
 8L5  H03  C02  C01  107.56  3.000
 8L5  C03  C02  C01  116.21  3.000
 8L5  H05  C03  C05  107.72  3.000
 8L5  H05  C03  C04  108.48  3.000
 8L5  C05  C03  C04  110.44  3.000
 8L5  H05  C03  C02  108.76  3.000
 8L5  C05  C03  C02  109.07  3.000
 8L5  C04  C03  C02  112.25  3.000
 8L5  H07  C04  H08  107.93  3.000
 8L5  H07  C04  H06  107.67  3.000
 8L5  H08  C04  H06  107.31  3.000
 8L5  H07  C04  C03  110.77  3.000
 8L5  H08  C04  C03  112.26  3.000
 8L5  H06  C04  C03  110.73  3.000
 8L5  H10  C05  H11  107.65  3.000
 8L5  H10  C05  H09  107.70  3.000
 8L5  H11  C05  H09  107.62  3.000
 8L5  H10  C05  C03  111.65  3.000
 8L5  H11  C05  C03  110.93  3.000
 8L5  H09  C05  C03  111.11  3.000
 8L5  N02  C06  O02  123.49  3.000
 8L5  N02  C06  C01  115.32  3.000
 8L5  O02  C06  C01  121.15  3.000
 8L5  H2   O03  P01  113.75  3.000
 8L5  H19  C08  H18  107.02  3.000
 8L5  H19  C08  N04  109.55  3.000
 8L5  H18  C08  N04  110.08  3.000
 8L5  H19  C08  P01  107.81  3.000
 8L5  H18  C08  P01  110.37  3.000
 8L5  N04  C08  P01  111.86  3.000
 8L5  H20  N04  C09  119.03  3.000
 8L5  H20  N04  C08  118.42  3.000
 8L5  C09  N04  C08  121.32  3.000
 8L5  O05  C09  O04  124.34  3.000
 8L5  O05  C09  N04  125.19  3.000
 8L5  O04  C09  N04  110.47  3.000
 8L5  C09  O04  C10  116.90  3.000
 8L5  H12  N02  C07  118.24  3.000
 8L5  H12  N02  C06  118.34  3.000
 8L5  C07  N02  C06  123.32  3.000
 8L5  H14  C07  H13  107.09  3.000
 8L5  H14  C07  N03  114.26  3.000
 8L5  H13  C07  N03  108.46  3.000
 8L5  H14  C07  N02  107.57  3.000
 8L5  H13  C07  N02  107.50  3.000
 8L5  N03  C07  N02  111.66  3.000
 8L5  H3   N03  H16  105.91  3.000
 8L5  H3   N03  C07  109.59  3.000
 8L5  H16  N03  C07  108.86  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
 8L5  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 8L5  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 8L5  CONST_03  C15  C16  C11  C12     0.00   0.0  0
 8L5  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 8L5  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 8L5  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 8L5  CONST_07  C13  C12  C11  C10   180.00   0.0  0
 8L5  CONST_08  C15  C16  C11  C10   180.00   0.0  0
 8L5  CONST_09  H24  C13  C12  C11   180.00   0.0  0
 8L5  CONST_10  H26  C15  C16  C11   180.00   0.0  0
 8L5  CONST_11  H27  C16  C11  C12   180.00   0.0  0
 8L5  CONST_12  H25  C14  C13  C12   180.00   0.0  0
 8L5  CONST_13  H23  C12  C13  C14   180.00   0.0  0
 8L5  CONST_14  C07  N02  C06  C01   180.00   0.0  0
 8L5  CONST_15  C07  N02  C06  O02     0.00   0.0  0
 8L5  CONST_16  H12  N02  C06  C01     0.00   0.0  0
 8L5  Var_01    O04  C10  C11  C12  -117.70  30.0  3
 8L5  Var_02    N04  C09  O04  C10  -172.79  30.0  2
 8L5  Var_03    C01  N01  P01  O01     2.87  30.0  3
 8L5  Var_04    N04  C08  P01  O01   -46.82  30.0  3
 8L5  Var_05    C09  N04  C08  P01    88.74  30.0  3
 8L5  Var_06    C04  C03  C02  C01    59.70  30.0  3
 8L5  Var_07    N03  C07  N02  C06    90.25  30.0  3
 8L5  Var_08    O04  C09  N04  C08  -171.33  30.0  2
 8L5  Var_09    H06  C04  C03  C02   176.03  30.0  3
 8L5  Var_10    H09  C05  C03  C02   178.43  30.0  3
 8L5  Var_11    H16  N03  C07  N02   168.80  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
 8L5  chir_02  C01  N01  C02  C06  negativ
 8L5  chir_03  P01  N01  O03  C08  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
 8L5  plan-1  C10  0.020
 8L5  plan-1  C11  0.020
 8L5  plan-1  C12  0.020
 8L5  plan-1  C13  0.020
 8L5  plan-1  C14  0.020
 8L5  plan-1  C15  0.020
 8L5  plan-1  C16  0.020
 8L5  plan-1  H23  0.020
 8L5  plan-1  H24  0.020
 8L5  plan-1  H25  0.020
 8L5  plan-1  H26  0.020
 8L5  plan-1  H27  0.020
 8L5  plan-2  C01  0.020
 8L5  plan-2  C06  0.020
 8L5  plan-2  O02  0.020
 8L5  plan-2  N02  0.020
 8L5  plan-2  C07  0.020
 8L5  plan-2  H12  0.020
 8L5  plan-3  N04  0.020
 8L5  plan-3  C09  0.020
 8L5  plan-3  O04  0.020
 8L5  plan-3  O05  0.020

