# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 18:42:55 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: 5-[(4-nitrobenzyl)(phosphonomethyl)amino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCN(Cc1ccc(cc1)[N+]([O-])=O)C[P](O)(O)=O
#
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
 AAH  AAH  '5-[(4-nitrobenzyl)(phosphonomethyl)amino]pentanoic acid'  ligand  39  23  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AAH
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
 AAH  C1    C  C1     0  -0.260  61.6017  47.4195  15.7256
 AAH  C2    C  C1     0  -0.312  61.4588  46.0432  15.7447
 AAH  C3    C  C      0   0.109  62.3063  45.2236  14.9958
 AAH  C4    C  C1     0  -0.298  63.2910  45.8222  14.2111
 AAH  C5    C  C1     0  -0.259  63.4444  47.1964  14.1701
 AAH  C6    C  C      0   0.231  62.5974  47.9835  14.9380
 AAH  N7    N  N      1   0.325  62.7519  49.4265  14.9067
 AAH  O8    O  O      0  -0.383  62.0327  50.0950  15.6134
 AAH  O9    O  O     -1  -0.383  63.5935  49.8946  14.1741
 AAH  C10   C  CH2    0  -0.404  62.1905  43.7178  15.0716
 AAH  N11   N  NT    -1  -0.386  62.8491  43.1147  16.2178
 AAH  C12   C  CH2    0  -0.582  62.2007  43.3523  17.4993
 AAH  P13   P  P      0   1.171  60.4148  42.7951  17.7137
 AAH  O14   O  O      0  -0.872  59.5283  43.7401  16.8758
 AAH  O15   O  OP    -1  -0.888  60.3670  41.3417  17.2231
 AAH  O16   O  OP    -1  -0.894  60.2182  42.9619  19.2254
 AAH  C17   C  CH2    0  -0.264  64.2750  43.3786  16.2316
 AAH  C18   C  CH2    0  -0.443  65.1136  42.3951  17.0432
 AAH  C19   C  CH2    0  -0.416  64.9819  40.9287  16.6154
 AAH  C20   C  CH2    0  -0.559  63.9772  40.1151  17.4299
 AAH  C21   C  C      0   0.389  64.3913  39.9682  18.9067
 AAH  O22   O  OC    -1  -0.617  63.5725  40.3401  19.7751
 AAH  O23   O  O      0  -0.620  65.5223  39.4805  19.1226
 AAH  H1    H  H      0   0.283  60.9386  48.0394  16.3115
 AAH  H2    H  H      0   0.295  60.6758  45.5748  16.3329
 AAH  H4    H  H      0   0.261  63.9497  45.2019  13.6155
 AAH  H5    H  H      0   0.287  64.2114  47.6374  13.5502
 AAH  H101  H  HCH2   0   0.250  61.1368  43.4450  15.0999
 AAH  H102  H  HCH2   0   0.231  62.6247  43.2874  14.1639
 AAH  H121  H  HCH2   0   0.204  62.7598  42.7873  18.2495
 AAH  H122  H  HCH2   0   0.162  62.2890  44.4108  17.8102
 AAH  H171  H  HCH2   0   0.210  64.6295  43.3327  15.1958
 AAH  H172  H  HCH2   0   0.179  64.5031  44.3997  16.5857
 AAH  H181  H  HCH2   0   0.217  66.1515  42.7197  16.9221
 AAH  H182  H  HCH2   0   0.217  64.9050  42.5003  18.1118
 AAH  H191  H  HCH2   0   0.202  64.7120  40.8884  15.5550
 AAH  H192  H  HCH2   0   0.200  65.9561  40.4409  16.6931
 AAH  H201  H  HCH2   0   0.214  62.9831  40.5563  17.3523
 AAH  H202  H  HCH2   0   0.202  63.9140  39.1114  16.9917

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
 AAH  C1   C2    aromatic  1.384  0.020  1.384
 AAH  C1   C6    aromatic  1.389  0.020  1.389
 AAH  C1   H1    single    0.930  0.020  1.080
 AAH  C2   C3    aromatic  1.397  0.020  1.397
 AAH  C2   H2    single    0.930  0.020  1.080
 AAH  C3   C4    aromatic  1.394  0.020  1.394
 AAH  C3   C10   single    1.512  0.020  1.512
 AAH  C4   C5    aromatic  1.383  0.020  1.383
 AAH  C4   H4    single    0.930  0.020  1.080
 AAH  C5   C6    aromatic  1.388  0.020  1.388
 AAH  C5   H5    single    0.930  0.020  1.080
 AAH  C6   N7    single    1.452  0.020  1.452
 AAH  N7   O8    double    1.210  0.020  1.210
 AAH  N7   O9    single    1.210  0.020  1.210
 AAH  C10  N11   single    1.453  0.020  1.453
 AAH  C10  H101  single    0.970  0.020  1.090
 AAH  C10  H102  single    0.970  0.020  1.090
 AAH  N11  C12   single    1.456  0.020  1.456
 AAH  N11  C17   single    1.450  0.020  1.450
 AAH  C12  P13   single    1.883  0.020  1.883
 AAH  C12  H121  single    0.970  0.020  1.090
 AAH  C12  H122  single    0.970  0.020  1.090
 AAH  P13  O14   deloc     1.543  0.020  1.543
 AAH  P13  O15   deloc     1.535  0.020  1.535
 AAH  P13  O16   deloc     1.534  0.020  1.534
 AAH  C17  C18   single    1.526  0.020  1.526
 AAH  C17  H171  single    0.970  0.020  1.090
 AAH  C17  H172  single    0.970  0.020  1.090
 AAH  C18  C19   single    1.533  0.020  1.533
 AAH  C18  H181  single    0.970  0.020  1.090
 AAH  C18  H182  single    0.970  0.020  1.090
 AAH  C19  C20   single    1.528  0.020  1.528
 AAH  C19  H191  single    0.970  0.020  1.090
 AAH  C19  H192  single    0.970  0.020  1.090
 AAH  C20  C21   single    1.541  0.020  1.541
 AAH  C20  H201  single    0.970  0.020  1.090
 AAH  C20  H202  single    0.970  0.020  1.090
 AAH  C21  O22   deloc     1.250  0.020  1.250
 AAH  C21  O23   deloc     1.250  0.020  1.250

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
 AAH  H1    C1   C6    120.95  3.000
 AAH  H1    C1   C2    119.99  3.000
 AAH  C6    C1   C2    119.06  3.000
 AAH  H2    C2   C3    118.36  3.000
 AAH  H2    C2   C1    120.73  3.000
 AAH  C3    C2   C1    120.90  3.000
 AAH  C10   C3   C4    120.65  3.000
 AAH  C10   C3   C2    120.73  3.000
 AAH  C4    C3   C2    118.58  3.000
 AAH  H4    C4   C5    119.02  3.000
 AAH  H4    C4   C3    119.54  3.000
 AAH  C5    C4   C3    121.43  3.000
 AAH  H5    C5   C6    121.28  3.000
 AAH  H5    C5   C4    120.08  3.000
 AAH  C6    C5   C4    118.64  3.000
 AAH  N7    C6   C5    119.13  3.000
 AAH  N7    C6   C1    119.48  3.000
 AAH  C5    C6   C1    121.38  3.000
 AAH  O9    N7   O8    123.60  3.000
 AAH  O9    N7   C6    118.14  3.000
 AAH  O8    N7   C6    118.26  3.000
 AAH  H102  C10  H101  107.88  3.000
 AAH  H102  C10  N11   108.13  3.000
 AAH  H101  C10  N11   108.31  3.000
 AAH  H102  C10  C3    108.64  3.000
 AAH  H101  C10  C3    108.95  3.000
 AAH  N11   C10  C3    114.72  3.000
 AAH  C17   N11  C12   113.57  3.000
 AAH  C17   N11  C10   112.18  3.000
 AAH  C12   N11  C10   115.14  3.000
 AAH  H122  C12  H121  105.11  3.000
 AAH  H122  C12  P13   109.07  3.000
 AAH  H121  C12  P13   104.72  3.000
 AAH  H122  C12  N11   111.58  3.000
 AAH  H121  C12  N11   106.98  3.000
 AAH  P13   C12  N11   118.32  3.000
 AAH  O16   P13  O15   114.47  3.000
 AAH  O16   P13  O14   113.26  3.000
 AAH  O15   P13  O14   112.86  3.000
 AAH  O16   P13  C12   101.63  3.000
 AAH  O15   P13  C12   105.86  3.000
 AAH  O14   P13  C12   107.57  3.000
 AAH  H172  C17  H171  105.96  3.000
 AAH  H172  C17  C18   108.16  3.000
 AAH  H171  C17  C18   107.33  3.000
 AAH  H172  C17  N11   111.99  3.000
 AAH  H171  C17  N11   107.55  3.000
 AAH  C18   C17  N11   115.34  3.000
 AAH  H182  C18  H181  105.10  3.000
 AAH  H182  C18  C19   110.37  3.000
 AAH  H181  C18  C19   109.53  3.000
 AAH  H182  C18  C17   110.66  3.000
 AAH  H181  C18  C17   105.74  3.000
 AAH  C19   C18  C17   114.88  3.000
 AAH  H192  C19  H191  105.81  3.000
 AAH  H192  C19  C20   108.10  3.000
 AAH  H191  C19  C20   109.55  3.000
 AAH  H192  C19  C18   109.31  3.000
 AAH  H191  C19  C18   109.06  3.000
 AAH  C20   C19  C18   114.65  3.000
 AAH  H202  C20  H201  106.82  3.000
 AAH  H202  C20  C21   108.13  3.000
 AAH  H201  C20  C21   110.60  3.000
 AAH  H202  C20  C19   108.18  3.000
 AAH  H201  C20  C19   110.24  3.000
 AAH  C21   C20  C19   112.64  3.000
 AAH  O23   C21  O22   126.05  3.000
 AAH  O23   C21  C20   116.48  3.000
 AAH  O22   C21  C20   117.48  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
 AAH  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 AAH  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 AAH  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 AAH  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 AAH  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 AAH  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 AAH  CONST_07  C10  C3   C2   C1   180.00   0.0  0
 AAH  CONST_08  N7   C6   C1   C2   180.00   0.0  0
 AAH  CONST_09  N7   C6   C5   C4   180.00   0.0  0
 AAH  CONST_10  C10  C3   C4   C5   180.00   0.0  0
 AAH  CONST_11  H5   C5   C6   C1   180.00   0.0  0
 AAH  CONST_12  H4   C4   C3   C2   180.00   0.0  0
 AAH  CONST_13  H1   C1   C2   C3   180.00   0.0  0
 AAH  CONST_14  H2   C2   C3   C4   180.00   0.0  0
 AAH  CONST_15  O8   N7   C6   C1     0.00   0.0  0
 AAH  CONST_16  O9   N7   C6   C1   180.00   0.0  0
 AAH  CONST_17  O8   N7   C6   C5   180.00   0.0  0
 AAH  CONST_18  O9   N7   C6   C5     0.00   0.0  0
 AAH  Var_01    N11  C10  C3   C2   -81.30  30.0  2
 AAH  Var_02    O14  P13  C12  N11  -71.57  30.0  3
 AAH  Var_03    C19  C18  C17  N11   57.43  30.0  3
 AAH  Var_04    C20  C19  C18  C17  -96.25  30.0  3
 AAH  Var_05    C21  C20  C19  C18  -64.60  30.0  3
 AAH  Var_06    O22  C21  C20  C19  124.60  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
 AAH  chir_01  N11  C10  C12  C17  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
 AAH  plan-1  C1   0.020
 AAH  plan-1  C2   0.020
 AAH  plan-1  C3   0.020
 AAH  plan-1  C4   0.020
 AAH  plan-1  C5   0.020
 AAH  plan-1  C6   0.020
 AAH  plan-1  N7   0.020
 AAH  plan-1  C10  0.020
 AAH  plan-1  H1   0.020
 AAH  plan-1  H2   0.020
 AAH  plan-1  H4   0.020
 AAH  plan-1  H5   0.020
 AAH  plan-2  C6   0.020
 AAH  plan-2  N7   0.020
 AAH  plan-2  O8   0.020
 AAH  plan-2  O9   0.020
 AAH  plan-3  C20  0.020
 AAH  plan-3  C21  0.020
 AAH  plan-3  O22  0.020
 AAH  plan-3  O23  0.020

