# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 12:05:46 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: ~{N}-[(2~{S})-1-(2-azanylethylamino)-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)NCCN
#
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
 8JQ  8JQ  '~{N}-[(2~{S})-1-(2-azanylethylamino)-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid'  ligand  55  27  .  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_8JQ
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
 8JQ  C10  C  C      0   0.781   0.9243   0.6639   1.0746
 8JQ  C11  C  CH2    0  -0.235   2.3453   0.9962  -0.7801
 8JQ  C12  C  CR6    0   0.077   3.7724   0.7111  -1.1392
 8JQ  C13  C  CR16   0  -0.283   4.2050  -0.6044  -1.2969
 8JQ  C14  C  CR16   0  -0.243   5.5241  -0.8773  -1.6252
 8JQ  C15  C  CR16   0  -0.263   6.4278   0.1646  -1.8022
 8JQ  C16  C  CR16   0  -0.241   6.0052   1.4771  -1.6478
 8JQ  O01  O  OP    -1  -0.815  -0.9779  -2.5232   4.1034
 8JQ  P01  P  P      0   1.235  -0.8215  -1.8443   2.7643
 8JQ  N01  N  NH1    0  -0.795  -2.4017  -1.6787   2.1309
 8JQ  C01  C  CH1    0  -0.221  -2.5710  -1.3121   0.7379
 8JQ  C02  C  CH2    0  -0.403  -2.9547  -2.4856  -0.1547
 8JQ  C03  C  CH1    0  -0.247  -3.1040  -2.1457  -1.6394
 8JQ  C04  C  CH3    0  -0.657  -1.8171  -1.5756  -2.2319
 8JQ  C05  C  CH3    0  -0.649  -3.5433  -3.3832  -2.4168
 8JQ  C06  C  C      0   0.571  -3.6006  -0.1887   0.6744
 8JQ  O02  O  O      0  -0.516  -4.8033  -0.4015   0.7824
 8JQ  O03  O  O      0  -0.795   0.1324  -2.3898   1.7316
 8JQ  C09  C  CH2    0  -0.599  -0.3397  -0.0523   3.0295
 8JQ  N04  N  NH1    0  -0.626   0.8915   0.3154   2.3688
 8JQ  O04  O  O2     0  -0.480   2.1699   0.6191   0.5886
 8JQ  C17  C  CR16   0  -0.301   4.6832   1.7466  -1.3143
 8JQ  O05  O  O      0  -0.528  -0.0303   1.0326   0.4103
 8JQ  N02  N  NH1    0  -0.660  -3.0773   1.0394   0.5424
 8JQ  C07  C  CH2    0  -0.298  -3.8670   2.2464   0.4838
 8JQ  C08  C  CH2    0  -0.281  -4.3502   2.5589  -0.9283
 8JQ  N03  N  NH2    0  -0.802  -5.0974   3.8061  -0.9328
 8JQ  H1   H  HCH2   0   0.247   2.1160   2.0556  -0.9150
 8JQ  H2   H  HCH2   0   0.245   1.6677   0.4218  -1.4156
 8JQ  H3   H  HCR6   0   0.253   3.5037  -1.4209  -1.1704
 8JQ  H4   H  HCR6   0   0.258   5.8478  -1.9026  -1.7491
 8JQ  H5   H  HCR6   0   0.259   7.4566  -0.0486  -2.0620
 8JQ  H6   H  HCR6   0   0.258   6.7028   2.2928  -1.7854
 8JQ  H8   H  HNH1   0   0.358  -3.0685  -2.3631   2.4603
 8JQ  H9   H  HCH1   0   0.261  -1.6107  -0.9290   0.3908
 8JQ  H10  H  HCH2   0   0.224  -2.1788  -3.2491  -0.0348
 8JQ  H11  H  HCH2   0   0.213  -3.8899  -2.9225   0.2108
 8JQ  H12  H  HCH1   0   0.217  -3.8930  -1.3923  -1.7468
 8JQ  H13  H  HCH3   0   0.213  -0.9933  -2.2853  -2.1215
 8JQ  H14  H  HCH3   0   0.225  -1.9362  -1.3685  -3.2968
 8JQ  H15  H  HCH3   0   0.223  -1.5134  -0.6438  -1.7539
 8JQ  H16  H  HCH3   0   0.223  -4.4721  -3.7975  -2.0199
 8JQ  H17  H  HCH3   0   0.224  -3.7077  -3.1521  -3.4707
 8JQ  H18  H  HCH3   0   0.212  -2.7828  -4.1664  -2.3657
 8JQ  H19  H  HCH2   0   0.256  -1.1402   0.6076   2.6965
 8JQ  H20  H  HCH2   0   0.260  -0.2166   0.1284   4.0982
 8JQ  H21  H  HNH1   0   0.394   1.7371  -0.0814   2.7473
 8JQ  H22  H  HCR6   0   0.255   4.3588   2.7731  -1.1924
 8JQ  H23  H  HNH1   0   0.414  -2.0715   1.1212   0.4679
 8JQ  H24  H  HCH2   0   0.235  -4.7218   2.1655   1.1567
 8JQ  H25  H  HCH2   0   0.239  -3.2469   3.0664   0.8520
 8JQ  H26  H  HCH2   0   0.195  -3.4857   2.5505  -1.6067
 8JQ  H27  H  HCH2   0   0.222  -5.0129   1.7560  -1.2579
 8JQ  H28  H  HNH2   0   0.341  -4.4597   4.5821  -0.8037
 8JQ  H29  H  HNH2   0   0.350  -5.5148   3.9459  -1.8434

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
 8JQ  C16  C17  aromatic  1.390  0.020  1.390
 8JQ  C16  C15  aromatic  1.387  0.020  1.387
 8JQ  C17  C12  aromatic  1.390  0.020  1.390
 8JQ  C15  C14  aromatic  1.391  0.020  1.391
 8JQ  C12  C11  single    1.499  0.020  1.499
 8JQ  C12  C13  aromatic  1.394  0.020  1.394
 8JQ  C11  O04  single    1.431  0.020  1.431
 8JQ  C14  C13  aromatic  1.386  0.020  1.386
 8JQ  O04  C10  single    1.338  0.020  1.338
 8JQ  O05  C10  double    1.220  0.020  1.220
 8JQ  C10  N04  single    1.341  0.020  1.341
 8JQ  N04  C09  single    1.445  0.020  1.445
 8JQ  C09  P01  single    1.874  0.020  1.874
 8JQ  O03  P01  deloc     1.508  0.020  1.508
 8JQ  O01  P01  deloc     1.509  0.020  1.509
 8JQ  P01  N01  single    1.710  0.020  1.710
 8JQ  N01  C01  single    1.450  0.020  1.450
 8JQ  C07  N02  single    1.444  0.020  1.444
 8JQ  C07  C08  single    1.525  0.020  1.525
 8JQ  N02  C06  single    1.341  0.020  1.341
 8JQ  C06  O02  double    1.226  0.020  1.226
 8JQ  C06  C01  single    1.525  0.020  1.525
 8JQ  C01  C02  single    1.523  0.020  1.523
 8JQ  C08  N03  single    1.454  0.020  1.454
 8JQ  C02  C03  single    1.530  0.020  1.530
 8JQ  C04  C03  single    1.527  0.020  1.527
 8JQ  C03  C05  single    1.526  0.020  1.526
 8JQ  C11  H1   single    0.970  0.020  1.090
 8JQ  C11  H2   single    0.970  0.020  1.090
 8JQ  C13  H3   single    0.930  0.020  1.080
 8JQ  C14  H4   single    0.930  0.020  1.080
 8JQ  C15  H5   single    0.930  0.020  1.080
 8JQ  C16  H6   single    0.930  0.020  1.080
 8JQ  N01  H8   single    0.890  0.020  1.040
 8JQ  C01  H9   single    0.970  0.020  1.090
 8JQ  C02  H10  single    0.970  0.020  1.090
 8JQ  C02  H11  single    0.970  0.020  1.090
 8JQ  C03  H12  single    0.970  0.020  1.090
 8JQ  C04  H13  single    0.970  0.020  1.090
 8JQ  C04  H14  single    0.970  0.020  1.090
 8JQ  C04  H15  single    0.970  0.020  1.090
 8JQ  C05  H16  single    0.970  0.020  1.090
 8JQ  C05  H17  single    0.970  0.020  1.090
 8JQ  C05  H18  single    0.970  0.020  1.090
 8JQ  C09  H19  single    0.970  0.020  1.090
 8JQ  C09  H20  single    0.970  0.020  1.090
 8JQ  N04  H21  single    0.890  0.020  1.040
 8JQ  C17  H22  single    0.930  0.020  1.080
 8JQ  N02  H23  single    0.860  0.020  1.020
 8JQ  C07  H24  single    0.970  0.020  1.090
 8JQ  C07  H25  single    0.970  0.020  1.090
 8JQ  C08  H26  single    0.970  0.020  1.090
 8JQ  C08  H27  single    0.970  0.020  1.090
 8JQ  N03  H28  single    0.890  0.020  1.040
 8JQ  N03  H29  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
 8JQ  O05  C10  O04  122.74  3.000
 8JQ  O05  C10  N04  125.81  3.000
 8JQ  O04  C10  N04  111.39  3.000
 8JQ  H2   C11  H1   107.93  3.000
 8JQ  H2   C11  O04  110.00  3.000
 8JQ  H1   C11  O04  110.37  3.000
 8JQ  H2   C11  C12  110.57  3.000
 8JQ  H1   C11  C12  110.78  3.000
 8JQ  O04  C11  C12  107.21  3.000
 8JQ  C17  C12  C13  119.04  3.000
 8JQ  C13  C12  C11  120.14  3.000
 8JQ  C17  C12  C11  120.81  3.000
 8JQ  H3   C13  C14  119.67  3.000
 8JQ  H3   C13  C12  119.81  3.000
 8JQ  C14  C13  C12  120.52  3.000
 8JQ  H4   C14  C15  120.06  3.000
 8JQ  H4   C14  C13  119.88  3.000
 8JQ  C15  C14  C13  120.06  3.000
 8JQ  H5   C15  C16  120.17  3.000
 8JQ  H5   C15  C14  120.05  3.000
 8JQ  C16  C15  C14  119.78  3.000
 8JQ  H6   C16  C17  119.84  3.000
 8JQ  H6   C16  C15  120.17  3.000
 8JQ  C17  C16  C15  119.99  3.000
 8JQ  C09  P01  O03  106.27  3.000
 8JQ  O03  P01  N01  111.46  3.000
 8JQ  C09  P01  N01  101.38  3.000
 8JQ  N01  P01  O01  106.04  3.000
 8JQ  O03  P01  O01  120.68  3.000
 8JQ  C09  P01  O01  109.33  3.000
 8JQ  H8   N01  C01  114.03  3.000
 8JQ  H8   N01  P01  115.04  3.000
 8JQ  C01  N01  P01  119.21  3.000
 8JQ  H9   C01  C06  108.81  3.000
 8JQ  H9   C01  C02  107.80  3.000
 8JQ  C06  C01  C02  111.90  3.000
 8JQ  H9   C01  N01  106.96  3.000
 8JQ  C02  C01  N01  113.42  3.000
 8JQ  C06  C01  N01  107.76  3.000
 8JQ  H11  C02  H10  106.88  3.000
 8JQ  H11  C02  C03  109.21  3.000
 8JQ  H10  C02  C03  109.28  3.000
 8JQ  H11  C02  C01  109.07  3.000
 8JQ  H10  C02  C01  107.13  3.000
 8JQ  C03  C02  C01  114.96  3.000
 8JQ  H12  C03  C05  107.48  3.000
 8JQ  H12  C03  C04  108.18  3.000
 8JQ  C05  C03  C04  110.34  3.000
 8JQ  H12  C03  C02  108.53  3.000
 8JQ  C05  C03  C02  110.01  3.000
 8JQ  C04  C03  C02  112.15  3.000
 8JQ  H15  C04  H14  107.22  3.000
 8JQ  H15  C04  H13  107.49  3.000
 8JQ  H14  C04  H13  107.70  3.000
 8JQ  H15  C04  C03  112.56  3.000
 8JQ  H14  C04  C03  110.94  3.000
 8JQ  H13  C04  C03  110.71  3.000
 8JQ  H18  C05  H17  107.56  3.000
 8JQ  H18  C05  H16  107.64  3.000
 8JQ  H17  C05  H16  107.65  3.000
 8JQ  H18  C05  C03  110.92  3.000
 8JQ  H17  C05  C03  111.32  3.000
 8JQ  H16  C05  C03  111.56  3.000
 8JQ  N02  C06  O02  123.39  3.000
 8JQ  O02  C06  C01  122.05  3.000
 8JQ  N02  C06  C01  114.52  3.000
 8JQ  H20  C09  H19  106.37  3.000
 8JQ  H20  C09  N04  108.04  3.000
 8JQ  H19  C09  N04  109.40  3.000
 8JQ  H20  C09  P01  109.02  3.000
 8JQ  H19  C09  P01  110.30  3.000
 8JQ  N04  C09  P01  113.43  3.000
 8JQ  H21  N04  C09  116.29  3.000
 8JQ  H21  N04  C10  116.38  3.000
 8JQ  C09  N04  C10  121.90  3.000
 8JQ  C11  O04  C10  116.93  3.000
 8JQ  H22  C17  C16  119.71  3.000
 8JQ  H22  C17  C12  119.70  3.000
 8JQ  C16  C17  C12  120.59  3.000
 8JQ  H23  N02  C07  118.24  3.000
 8JQ  H23  N02  C06  117.97  3.000
 8JQ  C07  N02  C06  123.78  3.000
 8JQ  H25  C07  H24  107.02  3.000
 8JQ  H25  C07  C08  109.77  3.000
 8JQ  H24  C07  C08  109.76  3.000
 8JQ  H25  C07  N02  107.67  3.000
 8JQ  H24  C07  N02  109.97  3.000
 8JQ  C08  C07  N02  112.47  3.000
 8JQ  H27  C08  H26  106.59  3.000
 8JQ  H27  C08  N03  108.54  3.000
 8JQ  H26  C08  N03  114.14  3.000
 8JQ  H27  C08  C07  108.73  3.000
 8JQ  H26  C08  C07  108.72  3.000
 8JQ  N03  C08  C07  109.97  3.000
 8JQ  H29  N03  H28  105.59  3.000
 8JQ  H29  N03  C08  109.47  3.000
 8JQ  H28  N03  C08  109.47  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
 8JQ  CONST_01  C15  C16  C17  C12     0.00   0.0  0
 8JQ  CONST_02  C15  C14  C13  C12     0.00   0.0  0
 8JQ  CONST_03  C16  C17  C12  C13     0.00   0.0  0
 8JQ  CONST_04  C16  C15  C14  C13     0.00   0.0  0
 8JQ  CONST_05  C17  C16  C15  C14     0.00   0.0  0
 8JQ  CONST_06  C17  C12  C13  C14     0.00   0.0  0
 8JQ  CONST_07  C16  C17  C12  C11   180.00   0.0  0
 8JQ  CONST_08  C14  C13  C12  C11   180.00   0.0  0
 8JQ  CONST_09  H6   C16  C17  C12   180.00   0.0  0
 8JQ  CONST_10  H4   C14  C13  C12   180.00   0.0  0
 8JQ  CONST_11  H22  C17  C12  C13   180.00   0.0  0
 8JQ  CONST_12  H5   C15  C14  C13   180.00   0.0  0
 8JQ  CONST_13  H3   C13  C14  C15   180.00   0.0  0
 8JQ  CONST_14  C07  N02  C06  C01   180.00   0.0  0
 8JQ  CONST_15  C07  N02  C06  O02     0.00   0.0  0
 8JQ  CONST_16  H23  N02  C06  C01     0.00   0.0  0
 8JQ  Var_01    O04  C11  C12  C13    72.31  30.0  2
 8JQ  Var_02    C12  C11  O04  C10  -173.32  30.0  1
 8JQ  Var_03    P01  C09  N04  C10    83.22  30.0  3
 8JQ  Var_04    O05  C10  O04  C11    -1.52  30.0  3
 8JQ  Var_05    N04  C09  P01  O01   123.41  30.0  1
 8JQ  Var_06    C01  N01  P01  O01  -167.44  30.0  3
 8JQ  Var_07    C04  C03  C02  C01    59.08  30.0  3
 8JQ  Var_08    C08  C07  N02  C06   -85.71  30.0  1
 8JQ  Var_09    O04  C10  N04  C09  -163.58  30.0  1
 8JQ  Var_10    N03  C08  C07  N02  -178.00  30.0  3
 8JQ  Var_11    H13  C04  C03  C02    58.78  30.0  3
 8JQ  Var_12    H16  C05  C03  C02    56.71  30.0  3
 8JQ  Var_13    H28  N03  C08  C07    71.96  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
 8JQ  chir_02  C01  N01  C06  C02  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
 8JQ  plan-1  C11  0.020
 8JQ  plan-1  C12  0.020
 8JQ  plan-1  C13  0.020
 8JQ  plan-1  C14  0.020
 8JQ  plan-1  C15  0.020
 8JQ  plan-1  C16  0.020
 8JQ  plan-1  C17  0.020
 8JQ  plan-1  H3   0.020
 8JQ  plan-1  H4   0.020
 8JQ  plan-1  H5   0.020
 8JQ  plan-1  H6   0.020
 8JQ  plan-1  H22  0.020
 8JQ  plan-2  C01  0.020
 8JQ  plan-2  C06  0.020
 8JQ  plan-2  O02  0.020
 8JQ  plan-2  N02  0.020
 8JQ  plan-2  C07  0.020
 8JQ  plan-2  H23  0.020
 8JQ  plan-3  C10  0.020
 8JQ  plan-3  N04  0.020
 8JQ  plan-3  O04  0.020
 8JQ  plan-3  O05  0.020

