# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 12:20:18 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: ~{N}-[(2~{S})-1-(4-azanylbutylamino)-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid
#   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)NCCCCN
#
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
 8JH  8JH  '~{N}-[(2~{S})-1-(4-azanylbutylamino)-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid'  ligand  61  29  .  2021-08-06  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8JH
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
 8JH  C10  C  CH2    0  -0.271   8.2644  -3.3475  -1.3889
 8JH  C11  C  CH2    0  -0.562  -1.1492   1.7502   0.5654
 8JH  C12  C  C      0   0.747  -3.5253   1.2550   0.8893
 8JH  C13  C  CH2    0  -0.233  -5.7473   0.4500   0.9716
 8JH  C14  C  CR6    0   0.076  -6.6875  -0.2798   0.0600
 8JH  C15  C  CR16   0  -0.283  -6.4739  -1.6243  -0.2374
 8JH  C16  C  CR16   0  -0.243  -7.3250  -2.2987  -1.0999
 8JH  C19  C  CR16   0  -0.301  -7.7682   0.3758  -0.5192
 8JH  P01  P  P      0   1.234  -0.1734   0.2128   0.8714
 8JH  C01  C  CH1    0  -0.214   2.5364   0.6624   0.5633
 8JH  N01  N  NH1    0  -0.777   1.3404   0.8309   1.3428
 8JH  O01  O  O      0  -0.814  -0.0164  -0.4794  -0.4635
 8JH  C02  C  CH2    0  -0.389   3.3570   1.9552   0.4641
 8JH  N02  N  NH1    0  -0.635   4.1077  -1.1383   0.2089
 8JH  O02  O  O      0  -0.505   3.5466  -0.6211   2.3362
 8JH  C03  C  CH1    0  -0.227   2.6190   3.1137  -0.2054
 8JH  N03  N  NH2    0  -0.801   9.1866  -4.4502  -1.1591
 8JH  O03  O  OP    -1  -0.802  -0.8163  -0.5039   2.0327
 8JH  C04  C  CH3    0  -0.651   3.5056   4.3554  -0.2130
 8JH  N04  N  NH1    0  -0.647  -2.4703   1.4156   0.0730
 8JH  O04  O  O2     0  -0.485  -4.5392   0.6626   0.2381
 8JH  C05  C  CH3    0  -0.674   2.1709   2.7659  -1.6223
 8JH  O05  O  O      0  -0.526  -3.5947   1.6216   2.0453
 8JH  C06  C  C      0   0.546   3.4308  -0.4379   1.1308
 8JH  C07  C  CH2    0  -0.242   5.0802  -2.1696   0.4992
 8JH  C08  C  CH2    0  -0.461   6.1801  -2.1868  -0.5510
 8JH  C09  C  CH2    0  -0.431   7.1711  -3.3216  -0.3323
 8JH  C17  C  CR16   0  -0.263  -8.4039  -1.6357  -1.6741
 8JH  C18  C  CR16   0  -0.241  -8.6259  -0.2979  -1.3805
 8JH  H1   H  HCH2   0   0.213   8.8313  -2.4136  -1.3396
 8JH  H2   H  HCH2   0   0.188   7.7949  -3.3674  -2.3837
 8JH  H3   H  HCH2   0   0.246  -1.2433   2.3446   1.4734
 8JH  H4   H  HCH2   0   0.248  -0.6482   2.3779  -0.1748
 8JH  H5   H  HCH2   0   0.245  -6.1778   1.4036   1.2849
 8JH  H6   H  HCH2   0   0.244  -5.5434  -0.1385   1.8690
 8JH  H7   H  HCR6   0   0.255  -5.6386  -2.1490   0.2113
 8JH  H8   H  HCR6   0   0.258  -7.1490  -3.3429  -1.3238
 8JH  H9   H  HCR6   0   0.255  -7.9447   1.4210  -0.2944
 8JH  H10  H  HCH1   0   0.250   2.2299   0.3677  -0.4413
 8JH  H11  H  HNH1   0   0.357   1.5076   0.8934   2.3369
 8JH  H12  H  HCH2   0   0.224   3.6711   2.2570   1.4693
 8JH  H13  H  HCH2   0   0.213   4.2771   1.7480  -0.0956
 8JH  H14  H  HNH1   0   0.394   3.8959  -0.9690  -0.7616
 8JH  H15  H  HCH1   0   0.220   1.7258   3.3342   0.3887
 8JH  H16  H  HNH2   0   0.337   8.7043  -5.3269  -1.3161
 8JH  H17  H  HNH2   0   0.345   9.9264  -4.4207  -1.8490
 8JH  H20  H  HCH3   0   0.224   2.9862   5.2119  -0.6460
 8JH  H21  H  HCH3   0   0.222   3.8149   4.6322   0.7966
 8JH  H22  H  HCH3   0   0.211   4.4112   4.1861  -0.8014
 8JH  H23  H  HNH1   0   0.390  -2.5052   0.9522  -0.8218
 8JH  H24  H  HCH3   0   0.214   3.0209   2.4543  -2.2356
 8JH  H25  H  HCH3   0   0.229   1.4371   1.9585  -1.6389
 8JH  H26  H  HCH3   0   0.227   1.7120   3.6286  -2.1083
 8JH  H27  H  HCH2   0   0.239   5.5027  -1.9802   1.4859
 8JH  H28  H  HCH2   0   0.228   4.5944  -3.1506   0.5438
 8JH  H29  H  HCH2   0   0.224   5.7308  -2.2858  -1.5453
 8JH  H30  H  HCH2   0   0.228   6.7039  -1.2262  -0.5415
 8JH  H31  H  HCH2   0   0.216   6.6347  -4.2772  -0.3423
 8JH  H32  H  HCH2   0   0.219   7.6298  -3.2350   0.6573
 8JH  H33  H  HCR6   0   0.258  -9.0690  -2.1629  -2.3457
 8JH  H34  H  HCR6   0   0.258  -9.4647   0.2241  -1.8223

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
 8JH  C04  C03  single    1.526  0.020  1.526
 8JH  C03  C05  single    1.526  0.020  1.526
 8JH  C03  C02  single    1.528  0.020  1.528
 8JH  N03  C10  single    1.456  0.020  1.456
 8JH  C10  C09  single    1.521  0.020  1.521
 8JH  C02  C01  single    1.534  0.020  1.534
 8JH  C09  C08  single    1.522  0.020  1.522
 8JH  C08  C07  single    1.521  0.020  1.521
 8JH  C01  C06  single    1.527  0.020  1.527
 8JH  C01  N01  single    1.437  0.020  1.437
 8JH  O02  C06  double    1.225  0.020  1.225
 8JH  C06  N02  single    1.341  0.020  1.341
 8JH  N02  C07  single    1.447  0.020  1.447
 8JH  N01  P01  single    1.702  0.020  1.702
 8JH  P01  O01  deloc     1.512  0.020  1.512
 8JH  P01  O03  deloc     1.508  0.020  1.508
 8JH  P01  C11  single    1.846  0.020  1.846
 8JH  C11  N04  single    1.449  0.020  1.449
 8JH  N04  C12  single    1.344  0.020  1.344
 8JH  C12  O05  double    1.215  0.020  1.215
 8JH  C12  O04  single    1.343  0.020  1.343
 8JH  O04  C13  single    1.429  0.020  1.429
 8JH  C19  C18  aromatic  1.390  0.020  1.390
 8JH  C19  C14  aromatic  1.390  0.020  1.390
 8JH  C18  C17  aromatic  1.388  0.020  1.388
 8JH  C13  C14  single    1.499  0.020  1.499
 8JH  C14  C15  aromatic  1.394  0.020  1.394
 8JH  C17  C16  aromatic  1.390  0.020  1.390
 8JH  C15  C16  aromatic  1.387  0.020  1.387
 8JH  C10  H1   single    0.970  0.020  1.090
 8JH  C10  H2   single    0.970  0.020  1.090
 8JH  C11  H3   single    0.970  0.020  1.090
 8JH  C11  H4   single    0.970  0.020  1.090
 8JH  C13  H5   single    0.970  0.020  1.090
 8JH  C13  H6   single    0.970  0.020  1.090
 8JH  C15  H7   single    0.930  0.020  1.080
 8JH  C16  H8   single    0.930  0.020  1.080
 8JH  C19  H9   single    0.930  0.020  1.080
 8JH  C01  H10  single    0.970  0.020  1.090
 8JH  N01  H11  single    0.890  0.020  1.040
 8JH  C02  H12  single    0.970  0.020  1.090
 8JH  C02  H13  single    0.970  0.020  1.090
 8JH  N02  H14  single    0.860  0.020  1.020
 8JH  C03  H15  single    0.970  0.020  1.090
 8JH  N03  H16  single    0.890  0.020  1.040
 8JH  N03  H17  single    0.890  0.020  1.040
 8JH  C04  H20  single    0.970  0.020  1.090
 8JH  C04  H21  single    0.970  0.020  1.090
 8JH  C04  H22  single    0.970  0.020  1.090
 8JH  N04  H23  single    0.890  0.020  1.040
 8JH  C05  H24  single    0.970  0.020  1.090
 8JH  C05  H25  single    0.970  0.020  1.090
 8JH  C05  H26  single    0.970  0.020  1.090
 8JH  C07  H27  single    0.970  0.020  1.090
 8JH  C07  H28  single    0.970  0.020  1.090
 8JH  C08  H29  single    0.970  0.020  1.090
 8JH  C08  H30  single    0.970  0.020  1.090
 8JH  C09  H31  single    0.970  0.020  1.090
 8JH  C09  H32  single    0.970  0.020  1.090
 8JH  C17  H33  single    0.930  0.020  1.080
 8JH  C18  H34  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
 8JH  H2   C10  H1   106.10  3.000
 8JH  H2   C10  C09  108.77  3.000
 8JH  H1   C10  C09  109.07  3.000
 8JH  H2   C10  N03  113.54  3.000
 8JH  H1   C10  N03  108.14  3.000
 8JH  C09  C10  N03  111.02  3.000
 8JH  H4   C11  H3   106.91  3.000
 8JH  H4   C11  N04  108.70  3.000
 8JH  H3   C11  N04  109.29  3.000
 8JH  H4   C11  P01  110.39  3.000
 8JH  H3   C11  P01  111.21  3.000
 8JH  N04  C11  P01  110.23  3.000
 8JH  O05  C12  O04  123.47  3.000
 8JH  O04  C12  N04  110.55  3.000
 8JH  O05  C12  N04  125.94  3.000
 8JH  H6   C13  H5   107.96  3.000
 8JH  H6   C13  O04  110.12  3.000
 8JH  H5   C13  O04  110.53  3.000
 8JH  H6   C13  C14  110.75  3.000
 8JH  H5   C13  C14  110.62  3.000
 8JH  O04  C13  C14  106.88  3.000
 8JH  C19  C14  C15  119.02  3.000
 8JH  C15  C14  C13  120.22  3.000
 8JH  C19  C14  C13  120.75  3.000
 8JH  H7   C15  C16  119.68  3.000
 8JH  H7   C15  C14  119.80  3.000
 8JH  C16  C15  C14  120.53  3.000
 8JH  H8   C16  C17  120.05  3.000
 8JH  H8   C16  C15  119.87  3.000
 8JH  C17  C16  C15  120.08  3.000
 8JH  H9   C19  C18  119.71  3.000
 8JH  H9   C19  C14  119.67  3.000
 8JH  C18  C19  C14  120.62  3.000
 8JH  O03  P01  O01  120.43  3.000
 8JH  O03  P01  N01  109.78  3.000
 8JH  O01  P01  N01  108.57  3.000
 8JH  O03  P01  C11  107.33  3.000
 8JH  O01  P01  C11  106.85  3.000
 8JH  N01  P01  C11  102.33  3.000
 8JH  H10  C01  C06  108.18  3.000
 8JH  H10  C01  C02  108.56  3.000
 8JH  C06  C01  C02  108.53  3.000
 8JH  H10  C01  N01  107.30  3.000
 8JH  C06  C01  N01  111.73  3.000
 8JH  C02  C01  N01  112.41  3.000
 8JH  H11  N01  C01  113.78  3.000
 8JH  H11  N01  P01  116.26  3.000
 8JH  C01  N01  P01  123.18  3.000
 8JH  H13  C02  H12  106.25  3.000
 8JH  H13  C02  C03  108.95  3.000
 8JH  H12  C02  C03  109.37  3.000
 8JH  H13  C02  C01  108.81  3.000
 8JH  H12  C02  C01  109.03  3.000
 8JH  C03  C02  C01  114.13  3.000
 8JH  H14  N02  C07  117.01  3.000
 8JH  H14  N02  C06  117.92  3.000
 8JH  C07  N02  C06  125.00  3.000
 8JH  H15  C03  C05  108.06  3.000
 8JH  H15  C03  C04  108.22  3.000
 8JH  C05  C03  C04  110.58  3.000
 8JH  H15  C03  C02  107.99  3.000
 8JH  C05  C03  C02  112.08  3.000
 8JH  C04  C03  C02  109.78  3.000
 8JH  H17  N03  H16  105.53  3.000
 8JH  H17  N03  C10  109.48  3.000
 8JH  H16  N03  C10  109.24  3.000
 8JH  H22  C04  H21  107.60  3.000
 8JH  H22  C04  H20  107.59  3.000
 8JH  H21  C04  H20  107.62  3.000
 8JH  H22  C04  C03  110.98  3.000
 8JH  H21  C04  C03  111.50  3.000
 8JH  H20  C04  C03  111.35  3.000
 8JH  H23  N04  C12  117.19  3.000
 8JH  H23  N04  C11  116.06  3.000
 8JH  C12  N04  C11  122.49  3.000
 8JH  C13  O04  C12  117.06  3.000
 8JH  H26  C05  H25  107.18  3.000
 8JH  H26  C05  H24  107.60  3.000
 8JH  H25  C05  H24  107.66  3.000
 8JH  H26  C05  C03  110.90  3.000
 8JH  H25  C05  C03  112.34  3.000
 8JH  H24  C05  C03  110.94  3.000
 8JH  O02  C06  N02  123.42  3.000
 8JH  N02  C06  C01  114.61  3.000
 8JH  O02  C06  C01  121.92  3.000
 8JH  H28  C07  H27  106.89  3.000
 8JH  H28  C07  C08  109.80  3.000
 8JH  H27  C07  C08  110.29  3.000
 8JH  H28  C07  N02  110.38  3.000
 8JH  H27  C07  N02  108.56  3.000
 8JH  C08  C07  N02  110.83  3.000
 8JH  H30  C08  H29  106.47  3.000
 8JH  H30  C08  C09  109.97  3.000
 8JH  H29  C08  C09  109.27  3.000
 8JH  H30  C08  C07  109.29  3.000
 8JH  H29  C08  C07  109.34  3.000
 8JH  C09  C08  C07  112.33  3.000
 8JH  H32  C09  H31  106.40  3.000
 8JH  H32  C09  C08  110.11  3.000
 8JH  H31  C09  C08  109.27  3.000
 8JH  H32  C09  C10  109.17  3.000
 8JH  H31  C09  C10  109.32  3.000
 8JH  C08  C09  C10  112.39  3.000
 8JH  H33  C17  C18  120.17  3.000
 8JH  H33  C17  C16  120.06  3.000
 8JH  C18  C17  C16  119.77  3.000
 8JH  H34  C18  C17  120.18  3.000
 8JH  H34  C18  C19  119.84  3.000
 8JH  C17  C18  C19  119.98  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
 8JH  CONST_01  C17  C18  C19  C14     0.00   0.0  0
 8JH  CONST_02  C17  C16  C15  C14     0.00   0.0  0
 8JH  CONST_03  C18  C19  C14  C15     0.00   0.0  0
 8JH  CONST_04  C18  C17  C16  C15     0.00   0.0  0
 8JH  CONST_05  C19  C18  C17  C16     0.00   0.0  0
 8JH  CONST_06  C19  C14  C15  C16     0.00   0.0  0
 8JH  CONST_07  C18  C19  C14  C13   180.00   0.0  0
 8JH  CONST_08  C16  C15  C14  C13   180.00   0.0  0
 8JH  CONST_09  H34  C18  C19  C14   180.00   0.0  0
 8JH  CONST_10  H8   C16  C15  C14   180.00   0.0  0
 8JH  CONST_11  H9   C19  C14  C15   180.00   0.0  0
 8JH  CONST_12  H33  C17  C16  C15   180.00   0.0  0
 8JH  CONST_13  H7   C15  C14  C19   180.00   0.0  0
 8JH  CONST_14  C07  N02  C06  C01   180.00   0.0  0
 8JH  CONST_15  C07  N02  C06  O02     0.00   0.0  0
 8JH  CONST_16  H14  N02  C06  C01     0.00   0.0  0
 8JH  Var_01    O04  C13  C14  C15    73.00  30.0  2
 8JH  Var_02    C14  C13  O04  C12  -177.14  30.0  3
 8JH  Var_03    C07  C08  C09  C10   179.49  30.0  3
 8JH  Var_04    C01  N01  P01  C11  -113.84  30.0  2
 8JH  Var_05    O05  C12  N04  C11    16.08  30.0  2
 8JH  Var_06    P01  C11  N04  C12    92.10  30.0  2
 8JH  Var_07    N04  C12  O04  C13  -178.68  30.0  1
 8JH  Var_08    C04  C03  C02  C01   178.26  30.0  1
 8JH  Var_09    N04  C11  P01  N01   176.75  30.0  3
 8JH  Var_10    C09  C08  C07  N02  -176.07  30.0  1
 8JH  Var_11    C08  C09  C10  N03  -179.45  30.0  3
 8JH  Var_12    C08  C07  N02  C06  -146.93  30.0  3
 8JH  Var_13    H20  C04  C03  C02  -177.46  30.0  3
 8JH  Var_14    H24  C05  C03  C02   -56.31  30.0  3
 8JH  Var_15    H16  N03  C10  C09    67.44  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
 8JH  chir_02  C01  C02  C06  N01  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
 8JH  plan-1  C13  0.020
 8JH  plan-1  C14  0.020
 8JH  plan-1  C15  0.020
 8JH  plan-1  C16  0.020
 8JH  plan-1  C19  0.020
 8JH  plan-1  C17  0.020
 8JH  plan-1  C18  0.020
 8JH  plan-1  H7   0.020
 8JH  plan-1  H8   0.020
 8JH  plan-1  H9   0.020
 8JH  plan-1  H33  0.020
 8JH  plan-1  H34  0.020
 8JH  plan-2  C01  0.020
 8JH  plan-2  N02  0.020
 8JH  plan-2  O02  0.020
 8JH  plan-2  C06  0.020
 8JH  plan-2  C07  0.020
 8JH  plan-2  H14  0.020
 8JH  plan-3  C12  0.020
 8JH  plan-3  N04  0.020
 8JH  plan-3  O04  0.020
 8JH  plan-3  O05  0.020

