# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 09:18:29 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 4-(4-nitrophenyl)-L-threonine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@H](O)Cc1ccc(cc1)[N+]([O-])=O)C(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
 KFJ  KFJ  4-(4-nitrophenyl)-L-threonine  ligand  28  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KFJ
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
 KFJ  C02   C  CH1    0  -0.243   3.2938  -0.0230  -0.6500
 KFJ  C03   C  C      0   0.414   4.1763   0.6506   0.4301
 KFJ  C06   C  CH1    0   0.031   1.8277   0.0464  -0.1835
 KFJ  C08   C  CH2    0  -0.563   0.8534  -0.4594  -1.2584
 KFJ  C09   C  C      0   0.180  -0.5706  -0.2833  -0.8342
 KFJ  C10   C  C1     0  -0.305  -1.2434  -1.2904  -0.1442
 KFJ  C11   C  C1     0  -0.253  -2.5488  -1.1204   0.2787
 KFJ  C12   C  C      0   0.230  -3.1886   0.0828   0.0129
 KFJ  C16   C  C1     0  -0.251  -2.5454   1.1081  -0.6672
 KFJ  C17   C  C1     0  -0.301  -1.2411   0.9139  -1.0836
 KFJ  N01   N  NH2    0  -0.808   3.7815  -1.3518  -0.9595
 KFJ  N13   N  N      1   0.329  -4.5591   0.2703   0.4503
 KFJ  O04   O  OC    -1  -0.618   3.9883   1.8728   0.5906
 KFJ  O05   O  O      0  -0.598   4.9750  -0.0700   1.0564
 KFJ  O07   O  OH1    0  -0.658   1.6348  -0.6306   1.0381
 KFJ  O14   O  O      0  -0.384  -5.0960   1.3272   0.2097
 KFJ  O15   O  O     -1  -0.384  -5.1016  -0.6387   1.0358
 KFJ  H021  H  HCH1   0   0.218   3.3577   0.5928  -1.5554
 KFJ  H061  H  HCH1   0   0.236   1.5961   1.0967   0.0142
 KFJ  H081  H  HCH2   0   0.259   1.0390   0.0911  -2.1838
 KFJ  H082  H  HCH2   0   0.246   1.0422  -1.5164  -1.4702
 KFJ  H101  H  H      0   0.262  -0.7464  -2.2304   0.0559
 KFJ  H111  H  H      0   0.294  -3.0514  -1.9173   0.8070
 KFJ  H161  H  H      0   0.294  -3.0442   2.0433  -0.8766
 KFJ  H171  H  H      0   0.266  -0.7356   1.7090  -1.6174
 KFJ  H1    H  HNH2   0   0.335   4.0230  -1.8479  -0.1129
 KFJ  H011  H  HNH2   0   0.342   3.1149  -1.9020  -1.4840
 KFJ  H071  H  HOH1   0   0.431   1.9500  -1.5350   0.9318

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
 KFJ  O05  C03   deloc     1.245  0.020  1.245
 KFJ  C03  O04   deloc     1.247  0.020  1.247
 KFJ  C03  C02   single    1.549  0.020  1.549
 KFJ  O07  C06   single    1.410  0.020  1.410
 KFJ  C06  C02   single    1.540  0.020  1.540
 KFJ  C06  C08   single    1.536  0.020  1.536
 KFJ  C02  N01   single    1.449  0.020  1.449
 KFJ  C10  C11   aromatic  1.383  0.020  1.383
 KFJ  C10  C09   aromatic  1.394  0.020  1.394
 KFJ  C11  C12   aromatic  1.388  0.020  1.388
 KFJ  O14  N13   double    1.210  0.020  1.210
 KFJ  C08  C09   single    1.496  0.020  1.496
 KFJ  C09  C17   aromatic  1.395  0.020  1.395
 KFJ  C12  N13   single    1.451  0.020  1.451
 KFJ  C12  C16   aromatic  1.388  0.020  1.388
 KFJ  N13  O15   single    1.210  0.020  1.210
 KFJ  C17  C16   aromatic  1.383  0.020  1.383
 KFJ  C02  H021  single    0.970  0.020  1.090
 KFJ  C06  H061  single    0.970  0.020  1.090
 KFJ  C08  H081  single    0.970  0.020  1.090
 KFJ  C08  H082  single    0.970  0.020  1.090
 KFJ  C10  H101  single    0.930  0.020  1.080
 KFJ  C11  H111  single    0.930  0.020  1.080
 KFJ  C16  H161  single    0.930  0.020  1.080
 KFJ  C17  H171  single    0.930  0.020  1.080
 KFJ  N01  H1    single    0.890  0.020  1.040
 KFJ  N01  H011  single    0.890  0.020  1.040
 KFJ  O07  H071  single    0.850  0.020  0.980

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
 KFJ  H021  C02  N01   108.60  3.000
 KFJ  H021  C02  C06   106.27  3.000
 KFJ  N01   C02  C06   115.24  3.000
 KFJ  H021  C02  C03   107.35  3.000
 KFJ  N01   C02  C03   110.85  3.000
 KFJ  C06   C02  C03   108.15  3.000
 KFJ  O05   C03  O04   126.82  3.000
 KFJ  O04   C03  C02   115.48  3.000
 KFJ  O05   C03  C02   117.69  3.000
 KFJ  H061  C06  O07   106.00  3.000
 KFJ  H061  C06  C08   107.96  3.000
 KFJ  O07   C06  C08   111.18  3.000
 KFJ  H061  C06  C02   107.44  3.000
 KFJ  C08   C06  C02   112.14  3.000
 KFJ  O07   C06  C02   111.78  3.000
 KFJ  H082  C08  H081  107.06  3.000
 KFJ  H082  C08  C09   109.43  3.000
 KFJ  H081  C08  C09   110.03  3.000
 KFJ  H082  C08  C06   110.12  3.000
 KFJ  H081  C08  C06   108.61  3.000
 KFJ  C09   C08  C06   111.50  3.000
 KFJ  C17   C09  C10   118.47  3.000
 KFJ  C17   C09  C08   120.53  3.000
 KFJ  C10   C09  C08   120.98  3.000
 KFJ  H101  C10  C11   118.94  3.000
 KFJ  H101  C10  C09   119.84  3.000
 KFJ  C11   C10  C09   121.22  3.000
 KFJ  H111  C11  C12   121.23  3.000
 KFJ  H111  C11  C10   119.89  3.000
 KFJ  C12   C11  C10   118.88  3.000
 KFJ  N13   C12  C16   119.33  3.000
 KFJ  C16   C12  C11   121.36  3.000
 KFJ  N13   C12  C11   119.31  3.000
 KFJ  H161  C16  C17   119.91  3.000
 KFJ  H161  C16  C12   121.36  3.000
 KFJ  C17   C16  C12   118.73  3.000
 KFJ  H171  C17  C16   119.05  3.000
 KFJ  H171  C17  C09   119.60  3.000
 KFJ  C16   C17  C09   121.34  3.000
 KFJ  H011  N01  H1    108.97  3.000
 KFJ  H011  N01  C02   112.83  3.000
 KFJ  H1    N01  C02   110.59  3.000
 KFJ  O15   N13  O14   123.63  3.000
 KFJ  O15   N13  C12   118.19  3.000
 KFJ  O14   N13  C12   118.18  3.000
 KFJ  H071  O07  C06   108.08  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
 KFJ  CONST_01  C12   C11  C10  C09    0.00   0.0  0
 KFJ  CONST_02  C12   C16  C17  C09    0.00   0.0  0
 KFJ  CONST_03  C16   C12  C11  C10    0.00   0.0  0
 KFJ  CONST_04  C16   C17  C09  C10    0.00   0.0  0
 KFJ  CONST_05  C17   C09  C10  C11    0.00   0.0  0
 KFJ  CONST_06  C17   C16  C12  C11    0.00   0.0  0
 KFJ  CONST_07  C11   C10  C09  C08  180.00   0.0  0
 KFJ  CONST_08  C16   C17  C09  C08  180.00   0.0  0
 KFJ  CONST_09  N13   C12  C11  C10  180.00   0.0  0
 KFJ  CONST_10  N13   C12  C16  C17  180.00   0.0  0
 KFJ  CONST_11  H111  C11  C10  C09  180.00   0.0  0
 KFJ  CONST_12  H161  C16  C17  C09  180.00   0.0  0
 KFJ  CONST_13  H171  C17  C09  C10  180.00   0.0  0
 KFJ  CONST_14  H101  C10  C11  C12  180.00   0.0  0
 KFJ  CONST_15  O14   N13  C12  C11  180.00   0.0  0
 KFJ  CONST_16  O15   N13  C12  C11    0.00   0.0  0
 KFJ  CONST_17  O14   N13  C12  C16    0.00   0.0  0
 KFJ  CONST_18  O15   N13  C12  C16  180.00   0.0  0
 KFJ  Var_01    C10   C09  C08  C06  -90.65  30.0  2

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
 KFJ  chir_01  C02  C03  C06  N01  positiv
 KFJ  chir_02  C06  O07  C02  C08  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
 KFJ  plan-1  C08   0.020
 KFJ  plan-1  C09   0.020
 KFJ  plan-1  C10   0.020
 KFJ  plan-1  C11   0.020
 KFJ  plan-1  C12   0.020
 KFJ  plan-1  C16   0.020
 KFJ  plan-1  C17   0.020
 KFJ  plan-1  N13   0.020
 KFJ  plan-1  H101  0.020
 KFJ  plan-1  H111  0.020
 KFJ  plan-1  H161  0.020
 KFJ  plan-1  H171  0.020
 KFJ  plan-2  C12   0.020
 KFJ  plan-2  N13   0.020
 KFJ  plan-2  O14   0.020
 KFJ  plan-2  O15   0.020
 KFJ  plan-3  C02   0.020
 KFJ  plan-3  C03   0.020
 KFJ  plan-3  O04   0.020
 KFJ  plan-3  O05   0.020

