# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 12:41:13 2020
#   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  52  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.252  13.4507  39.9997  -11.4219
 8L5  C11  C  C      0   0.071  14.7606  40.7185  -11.2593
 8L5  C12  C  C1     0  -0.287  14.8115  42.1070  -11.2264
 8L5  C13  C  C1     0  -0.244  16.0268  42.7677  -11.0976
 8L5  C14  C  C1     0  -0.265  17.2044  42.0416  -10.9852
 8L5  C15  C  C1     0  -0.244  17.1614  40.6524  -11.0090
 8L5  C16  C  C1     0  -0.284  15.9471  39.9963  -11.1481
 8L5  O01  O  O      0  -0.796  10.0427  37.5925   -6.5676
 8L5  P01  P  P      0   1.234  11.4759  37.5991   -6.1019
 8L5  N01  N  NH1    0  -0.815  11.4801  38.0246   -4.4437
 8L5  C01  C  CH1    0  -0.145  10.2294  38.1377   -3.7198
 8L5  C02  C  CH2    0  -0.438  10.5475  38.3188   -2.2280
 8L5  C03  C  CH1    0  -0.245   9.3645  38.5730   -1.2925
 8L5  C04  C  CH3    0  -0.657   8.3269  37.4560   -1.3371
 8L5  C05  C  CH3    0  -0.648   9.8794  38.7655    0.1313
 8L5  C06  C  C      0   0.541   9.4132  39.3259   -4.2147
 8L5  O02  O  O      0  -0.509   8.1907  39.2898   -4.2803
 8L5  O03  O  OP    -1  -0.801  12.3687  36.4023   -6.3333
 8L5  C08  C  CH2    0  -0.543  12.3543  39.0417   -6.8478
 8L5  N04  N  NH1    0  -0.658  12.7178  38.7355   -8.2124
 8L5  C09  C  C      0   0.749  12.8271  39.6678   -9.1694
 8L5  O04  O  O2     0  -0.488  13.1879  39.1103  -10.3387
 8L5  O05  O  O      0  -0.515  12.6129  40.8548   -9.0285
 8L5  N02  N  NH1    0  -0.615  10.1236  40.4294   -4.4942
 8L5  C07  C  CH2    0  -0.158   9.5055  41.6832   -4.8421
 8L5  N03  N  NH2    0  -0.796   8.9779  42.3692   -3.6765
 8L5  H22  H  HCH2   0   0.249  12.6326  40.7104  -11.5540
 8L5  H21  H  HCH2   0   0.260  13.4763  39.3557  -12.3013
 8L5  H23  H  H      0   0.250  13.8944  42.6781  -11.3032
 8L5  H24  H  H      0   0.255  16.0520  43.8496  -11.0767
 8L5  H25  H  H      0   0.256  18.1516  42.5546  -10.8787
 8L5  H26  H  H      0   0.255  18.0756  40.0792  -10.9224
 8L5  H27  H  H      0   0.254  15.9260  38.9131  -11.1729
 8L5  H02  H  HCH1   0   0.237   9.5860  37.2593   -3.8402
 8L5  H03  H  HCH2   0   0.231  11.0694  37.4145   -1.8935
 8L5  H04  H  HCH2   0   0.228  11.2639  39.1409   -2.1280
 8L5  H05  H  HCH1   0   0.221   8.8790  39.5072   -1.5940
 8L5  H06  H  HCH3   0   0.223   7.5316  37.6404   -0.6126
 8L5  H08  H  HCH3   0   0.230   7.8611  37.3682   -2.3178
 8L5  H07  H  HCH3   0   0.211   8.7786  36.4917   -1.0903
 8L5  H09  H  HCH3   0   0.226   9.0632  39.0063    0.8147
 8L5  H11  H  HCH3   0   0.213  10.3618  37.8573    0.5006
 8L5  H10  H  HCH3   0   0.224  10.6090  39.5755    0.1891
 8L5  H20  H  HNH1   0   0.390  12.9963  37.7885   -8.4188
 8L5  H12  H  HNH1   0   0.394  11.1226  40.3874   -4.3678
 8L5  H13  H  HCH2   0   0.242  10.2741  42.3095   -5.2917
 8L5  H14  H  HCH2   0   0.215   8.7549  41.4897   -5.6152
 8L5  H16  H  HNH2   0   0.349   8.7231  43.3125   -3.9417
 8L5  H3   H  HNH2   0   0.345   8.1157  41.9215   -3.3915
 8L5  H01  H  HNH1   0   0.370  12.2097  37.5799   -3.9036
 8L5  H18  H  HCH2   0   0.235  13.2386  39.2884   -6.2493
 8L5  H19  H  HCH2   0   0.245  11.7034  39.9153   -6.8334

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    1.503  0.020  1.503
 8L5  C10  O04  single    1.426  0.020  1.426
 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  deloc     1.507  0.020  1.507
 8L5  P01  N01  single    1.712  0.020  1.712
 8L5  P01  O03  deloc     1.511  0.020  1.511
 8L5  P01  C08  single    1.846  0.020  1.846
 8L5  N01  C01  single    1.450  0.020  1.450
 8L5  C01  C02  single    1.536  0.020  1.536
 8L5  C01  C06  single    1.524  0.020  1.524
 8L5  C02  C03  single    1.530  0.020  1.530
 8L5  C03  C04  single    1.525  0.020  1.525
 8L5  C03  C05  single    1.526  0.020  1.526
 8L5  C06  O02  double    1.225  0.020  1.225
 8L5  C06  N02  single    1.342  0.020  1.342
 8L5  C08  N04  single    1.445  0.020  1.445
 8L5  N04  C09  single    1.340  0.020  1.340
 8L5  C09  O04  single    1.345  0.020  1.345
 8L5  C09  O05  double    1.214  0.020  1.214
 8L5  N02  C07  single    1.441  0.020  1.441
 8L5  C07  N03  single    1.452  0.020  1.452
 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  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  107.73  3.000
 8L5  H21  C10  O04  104.40  3.000
 8L5  H22  C10  O04  111.09  3.000
 8L5  H21  C10  C11  110.44  3.000
 8L5  H22  C10  C11  110.78  3.000
 8L5  O04  C10  C11  112.13  3.000
 8L5  C16  C11  C12  118.99  3.000
 8L5  C16  C11  C10  120.19  3.000
 8L5  C12  C11  C10  120.82  3.000
 8L5  H23  C12  C13  119.77  3.000
 8L5  H23  C12  C11  119.61  3.000
 8L5  C13  C12  C11  120.62  3.000
 8L5  H24  C13  C14  120.11  3.000
 8L5  H24  C13  C12  119.84  3.000
 8L5  C14  C13  C12  120.06  3.000
 8L5  H25  C14  C15  120.15  3.000
 8L5  H25  C14  C13  120.16  3.000
 8L5  C15  C14  C13  119.69  3.000
 8L5  H26  C15  C16  119.79  3.000
 8L5  H26  C15  C14  120.12  3.000
 8L5  C16  C15  C14  120.09  3.000
 8L5  H27  C16  C15  119.48  3.000
 8L5  H27  C16  C11  119.97  3.000
 8L5  C15  C16  C11  120.55  3.000
 8L5  C08  P01  O03  106.02  3.000
 8L5  C08  P01  N01  101.30  3.000
 8L5  O03  P01  N01  110.11  3.000
 8L5  C08  P01  O01  109.33  3.000
 8L5  O03  P01  O01  120.74  3.000
 8L5  N01  P01  O01  107.62  3.000
 8L5  H01  N01  C01  112.97  3.000
 8L5  H01  N01  P01  114.20  3.000
 8L5  C01  N01  P01  120.07  3.000
 8L5  H02  C01  C06  105.96  3.000
 8L5  H02  C01  C02  108.84  3.000
 8L5  C06  C01  C02  109.54  3.000
 8L5  H02  C01  N01  112.91  3.000
 8L5  C06  C01  N01  111.15  3.000
 8L5  C02  C01  N01  108.39  3.000
 8L5  H04  C02  H03  106.26  3.000
 8L5  H04  C02  C03  108.99  3.000
 8L5  H03  C02  C03  108.58  3.000
 8L5  H04  C02  C01  108.22  3.000
 8L5  H03  C02  C01  107.32  3.000
 8L5  C03  C02  C01  116.96  3.000
 8L5  H05  C03  C05  107.38  3.000
 8L5  H05  C03  C04  108.37  3.000
 8L5  C05  C03  C04  110.44  3.000
 8L5  H05  C03  C02  108.44  3.000
 8L5  C05  C03  C02  109.31  3.000
 8L5  C04  C03  C02  112.74  3.000
 8L5  H07  C04  H08  107.99  3.000
 8L5  H07  C04  H06  107.47  3.000
 8L5  H08  C04  H06  107.43  3.000
 8L5  H07  C04  C03  111.00  3.000
 8L5  H08  C04  C03  112.10  3.000
 8L5  H06  C04  C03  110.64  3.000
 8L5  H10  C05  H11  107.68  3.000
 8L5  H10  C05  H09  107.63  3.000
 8L5  H11  C05  H09  107.57  3.000
 8L5  H10  C05  C03  111.63  3.000
 8L5  H11  C05  C03  111.06  3.000
 8L5  H09  C05  C03  111.08  3.000
 8L5  N02  C06  O02  122.79  3.000
 8L5  N02  C06  C01  115.17  3.000
 8L5  O02  C06  C01  121.93  3.000
 8L5  H19  C08  H18  107.12  3.000
 8L5  H19  C08  N04  109.43  3.000
 8L5  H18  C08  N04  111.13  3.000
 8L5  H19  C08  P01  109.69  3.000
 8L5  H18  C08  P01  109.83  3.000
 8L5  N04  C08  P01  109.61  3.000
 8L5  H20  N04  C09  118.98  3.000
 8L5  H20  N04  C08  117.50  3.000
 8L5  C09  N04  C08  123.18  3.000
 8L5  O05  C09  O04  123.60  3.000
 8L5  O05  C09  N04  125.64  3.000
 8L5  O04  C09  N04  110.75  3.000
 8L5  C09  O04  C10  116.83  3.000
 8L5  H12  N02  C07  119.47  3.000
 8L5  H12  N02  C06  117.67  3.000
 8L5  C07  N02  C06  122.61  3.000
 8L5  H14  C07  H13  107.10  3.000
 8L5  H14  C07  N03  113.66  3.000
 8L5  H13  C07  N03  108.44  3.000
 8L5  H14  C07  N02  108.11  3.000
 8L5  H13  C07  N02  107.31  3.000
 8L5  N03  C07  N02  111.92  3.000
 8L5  H3   N03  H16  105.75  3.000
 8L5  H3   N03  C07  109.06  3.000
 8L5  H16  N03  C07  108.75  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  -121.78  30.0  3
 8L5  Var_02    N04  C09  O04  C10  -174.92  30.0  2
 8L5  Var_03    C01  N01  P01  O01     7.58  30.0  3
 8L5  Var_04    N04  C08  P01  O01   -79.33  30.0  3
 8L5  Var_05    C09  N04  C08  P01   150.61  30.0  3
 8L5  Var_06    C04  C03  C02  C01    58.38  30.0  3
 8L5  Var_07    N03  C07  N02  C06    77.27  30.0  3
 8L5  Var_08    O04  C09  N04  C08   179.47  30.0  2
 8L5  Var_09    H06  C04  C03  C02   176.41  30.0  3
 8L5  Var_10    H09  C05  C03  C02   176.73  30.0  3
 8L5  Var_11    H16  N03  C07  N02   168.95  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

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

