# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 10:42:39 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N-[(1R,2R)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]-D-histidinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1c[nH]cn1)C(=O)N[C@H](CO)[C@H](O)c2ccc(cc2)[N](=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
 EZP  EZP  N-[(1R,2R)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]-D-histidinamide  ligand  44  25  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EZP
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
 EZP  CAG  C  CR16   0  -0.305   1.4735  -0.2527  -1.4789
 EZP  CAI  C  CR16   0  -0.257   1.3176  -1.6079  -1.2413
 EZP  CAU  C  CR6    0   0.235   1.7873  -2.1412  -0.0511
 EZP  NAY  N  N      1   0.331   1.6054  -3.5574   0.2135
 EZP  OAF  O  O     -1  -0.381   0.9156  -4.1951  -0.5495
 EZP  OAC  O  O      0  -0.376   2.1481  -4.0308   1.1836
 EZP  CAJ  C  CR16   0  -0.255   2.4267  -1.3489   0.8928
 EZP  CAH  C  CR16   0  -0.279   2.5749   0.0011   0.6364
 EZP  CAT  C  CR6    0   0.104   2.0921   0.5685  -0.5411
 EZP  CAW  C  CH1    0  -0.008   2.1949   2.0605  -0.7411
 EZP  OAE  O  OH1    0  -0.675   1.9324   2.3592  -2.0840
 EZP  CAX  C  CH1    0  -0.157   1.2190   2.7674   0.2242
 EZP  CAM  C  CH2    0  -0.153   1.3263   4.2842   0.1678
 EZP  OAD  O  OH1    0  -0.673   0.9929   4.7313  -1.1331
 EZP  NAP  N  NH1    0  -0.629  -0.1224   2.2842  -0.0097
 EZP  C    C  C      0   0.561  -0.9612   1.9244   0.9760
 EZP  O    O  O      0  -0.495  -0.7422   2.1443   2.1588
 EZP  CA   C  CH1    0  -0.224  -2.1770   1.1282   0.5325
 EZP  N    N  NH2    0  -0.797  -3.3608   1.6409   1.1937
 EZP  CB   C  CH2    0  -0.522  -1.8587  -0.3581   0.8144
 EZP  CG   C  CR5    0   0.167  -2.8153  -1.2989   0.1628
 EZP  CD2  C  CR15   0  -0.132  -2.5195  -2.4036  -0.5878
 EZP  NE2  N  NR15   0  -0.564  -3.7235  -2.9278  -0.9609
 EZP  CE1  C  CR15   0   0.099  -4.6854  -2.1442  -0.4441
 EZP  ND1  N  N      0  -0.476  -4.1754  -1.1523   0.2428
 EZP  H1   H  HCR6   0   0.277   1.0991   0.1553  -2.4063
 EZP  H2   H  HCR6   0   0.298   0.8333  -2.2261  -1.9833
 EZP  H3   H  HCR6   0   0.299   2.8014  -1.7655   1.8161
 EZP  H4   H  HCR6   0   0.274   3.0732   0.6197   1.3727
 EZP  H5   H  HCH1   0   0.247   3.2072   2.3801  -0.4499
 EZP  H6   H  HOH1   0   0.458   1.7563   3.3112  -2.1443
 EZP  H7   H  HCH1   0   0.281   1.5033   2.4844   1.2401
 EZP  H8   H  HCH2   0   0.229   0.6535   4.7113   0.9196
 EZP  H9   H  HCH2   0   0.223   2.3483   4.5690   0.4417
 EZP  H10  H  HOH1   0   0.473   1.2357   5.6584  -1.2164
 EZP  H11  H  HNH1   0   0.399  -0.4034   2.1186  -0.9636
 EZP  H12  H  HCH1   0   0.251  -2.3152   1.2446  -0.5471
 EZP  H13  H  HNH2   0   0.358  -4.1283   1.0095   0.9915
 EZP  H14  H  HNH2   0   0.337  -3.2225   1.5955   2.1969
 EZP  H16  H  HCH2   0   0.246  -0.8510  -0.5950   0.4603
 EZP  H17  H  HCH2   0   0.247  -1.8479  -0.5035   1.8994
 EZP  H18  H  HCR5   0   0.266  -1.5814  -2.8532  -0.8674
 EZP  H19  H  HNR5   0   0.421  -3.8658  -3.7538  -1.5196
 EZP  H20  H  HCR5   0   0.279  -5.7360  -2.3382  -0.5944

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
 EZP  OAD  CAM  single    1.415  0.020  1.415
 EZP  CE1  NE2  aromatic  1.344  0.020  1.344
 EZP  CE1  ND1  aromatic  1.310  0.020  1.310
 EZP  NE2  CD2  aromatic  1.365  0.020  1.365
 EZP  ND1  CG   aromatic  1.370  0.020  1.370
 EZP  CD2  CG   aromatic  1.368  0.020  1.368
 EZP  O    C    double    1.223  0.020  1.223
 EZP  CAM  CAX  single    1.522  0.020  1.522
 EZP  CAX  NAP  single    1.445  0.020  1.445
 EZP  CAX  CAW  single    1.544  0.020  1.544
 EZP  CG   CB   single    1.491  0.020  1.491
 EZP  C    NAP  single    1.343  0.020  1.343
 EZP  C    CA   single    1.519  0.020  1.519
 EZP  CA   CB   single    1.546  0.020  1.546
 EZP  CA   N    single    1.450  0.020  1.450
 EZP  CAH  CAJ  aromatic  1.382  0.020  1.382
 EZP  CAH  CAT  aromatic  1.393  0.020  1.393
 EZP  CAW  CAT  single    1.509  0.020  1.509
 EZP  CAW  OAE  single    1.401  0.020  1.401
 EZP  CAJ  CAU  aromatic  1.388  0.020  1.388
 EZP  CAT  CAG  aromatic  1.392  0.020  1.392
 EZP  OAC  NAY  double    1.208  0.020  1.208
 EZP  CAU  NAY  single    1.452  0.020  1.452
 EZP  CAU  CAI  aromatic  1.386  0.020  1.386
 EZP  CAG  CAI  aromatic  1.385  0.020  1.385
 EZP  NAY  OAF  single    1.210  0.020  1.210
 EZP  CAG  H1   single    0.930  0.020  1.080
 EZP  CAI  H2   single    0.930  0.020  1.080
 EZP  CAJ  H3   single    0.930  0.020  1.080
 EZP  CAH  H4   single    0.930  0.020  1.080
 EZP  CAW  H5   single    0.970  0.020  1.090
 EZP  OAE  H6   single    0.850  0.020  0.980
 EZP  CAX  H7   single    0.970  0.020  1.090
 EZP  CAM  H8   single    0.970  0.020  1.090
 EZP  CAM  H9   single    0.970  0.020  1.090
 EZP  OAD  H10  single    0.850  0.020  0.980
 EZP  NAP  H11  single    0.860  0.020  1.020
 EZP  CA   H12  single    0.970  0.020  1.090
 EZP  N    H13  single    0.890  0.020  1.040
 EZP  N    H14  single    0.890  0.020  1.040
 EZP  CB   H16  single    0.970  0.020  1.090
 EZP  CB   H17  single    0.970  0.020  1.090
 EZP  CD2  H18  single    0.930  0.020  1.080
 EZP  NE2  H19  single    0.860  0.020  1.020
 EZP  CE1  H20  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
 EZP  H1   CAG  CAT  120.65  3.000
 EZP  H1   CAG  CAI  118.56  3.000
 EZP  CAT  CAG  CAI  120.79  3.000
 EZP  H2   CAI  CAU  121.43  3.000
 EZP  H2   CAI  CAG  119.51  3.000
 EZP  CAU  CAI  CAG  119.06  3.000
 EZP  CAJ  CAU  NAY  119.36  3.000
 EZP  NAY  CAU  CAI  119.29  3.000
 EZP  CAJ  CAU  CAI  121.35  3.000
 EZP  OAC  NAY  OAF  123.76  3.000
 EZP  OAF  NAY  CAU  118.06  3.000
 EZP  OAC  NAY  CAU  118.18  3.000
 EZP  H3   CAJ  CAH  119.88  3.000
 EZP  H3   CAJ  CAU  121.39  3.000
 EZP  CAH  CAJ  CAU  118.73  3.000
 EZP  H4   CAH  CAT  120.09  3.000
 EZP  H4   CAH  CAJ  118.76  3.000
 EZP  CAT  CAH  CAJ  121.15  3.000
 EZP  CAW  CAT  CAH  119.41  3.000
 EZP  CAW  CAT  CAG  121.63  3.000
 EZP  CAH  CAT  CAG  118.90  3.000
 EZP  H5   CAW  CAX  106.44  3.000
 EZP  H5   CAW  OAE  111.35  3.000
 EZP  CAX  CAW  OAE  112.54  3.000
 EZP  H5   CAW  CAT  108.35  3.000
 EZP  OAE  CAW  CAT  108.98  3.000
 EZP  CAX  CAW  CAT  109.07  3.000
 EZP  H6   OAE  CAW  107.64  3.000
 EZP  H7   CAX  NAP  107.80  3.000
 EZP  H7   CAX  CAM  105.92  3.000
 EZP  NAP  CAX  CAM  113.13  3.000
 EZP  H7   CAX  CAW  107.36  3.000
 EZP  NAP  CAX  CAW  109.42  3.000
 EZP  CAM  CAX  CAW  112.87  3.000
 EZP  H9   CAM  H8   107.45  3.000
 EZP  H9   CAM  OAD  111.55  3.000
 EZP  H8   CAM  OAD  111.28  3.000
 EZP  H9   CAM  CAX  108.39  3.000
 EZP  H8   CAM  CAX  108.65  3.000
 EZP  OAD  CAM  CAX  109.41  3.000
 EZP  H10  OAD  CAM  108.94  3.000
 EZP  H11  NAP  C    118.43  3.000
 EZP  H11  NAP  CAX  117.84  3.000
 EZP  C    NAP  CAX  123.40  3.000
 EZP  CA   C    O    121.32  3.000
 EZP  CA   C    NAP  115.21  3.000
 EZP  O    C    NAP  123.35  3.000
 EZP  H12  CA   CB   107.95  3.000
 EZP  H12  CA   N    108.01  3.000
 EZP  CB   CA   N    115.15  3.000
 EZP  H12  CA   C    109.46  3.000
 EZP  N    CA   C    109.57  3.000
 EZP  CB   CA   C    106.61  3.000
 EZP  H14  N    H13  105.82  3.000
 EZP  H14  N    CA   108.92  3.000
 EZP  H13  N    CA   107.87  3.000
 EZP  H17  CB   H16  106.43  3.000
 EZP  H17  CB   CG   110.82  3.000
 EZP  H16  CB   CG   108.23  3.000
 EZP  H17  CB   CA   108.09  3.000
 EZP  H16  CB   CA   109.80  3.000
 EZP  CG   CB   CA   113.25  3.000
 EZP  ND1  CG   CD2  109.45  3.000
 EZP  CD2  CG   CB   127.62  3.000
 EZP  ND1  CG   CB   122.93  3.000
 EZP  H18  CD2  NE2  122.47  3.000
 EZP  H18  CD2  CG   131.90  3.000
 EZP  NE2  CD2  CG   105.63  3.000
 EZP  H19  NE2  CE1  126.18  3.000
 EZP  H19  NE2  CD2  126.23  3.000
 EZP  CE1  NE2  CD2  107.59  3.000
 EZP  H20  CE1  ND1  126.04  3.000
 EZP  H20  CE1  NE2  122.58  3.000
 EZP  ND1  CE1  NE2  111.38  3.000
 EZP  CE1  ND1  CG   105.95  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
 EZP  CONST_01  CAJ  CAH  CAT  CAG    0.00   0.0  0
 EZP  CONST_02  CAJ  CAU  CAI  CAG    0.00   0.0  0
 EZP  CONST_03  CAH  CAJ  CAU  CAI    0.00   0.0  0
 EZP  CONST_04  CAH  CAT  CAG  CAI    0.00   0.0  0
 EZP  CONST_05  CAT  CAH  CAJ  CAU    0.00   0.0  0
 EZP  CONST_06  CAT  CAG  CAI  CAU    0.00   0.0  0
 EZP  CONST_07  NE2  CE1  ND1  CG     0.00   0.0  0
 EZP  CONST_08  CE1  NE2  CD2  CG     0.00   0.0  0
 EZP  CONST_09  ND1  CE1  NE2  CD2    0.00   0.0  0
 EZP  CONST_10  CE1  ND1  CG   CD2    0.00   0.0  0
 EZP  CONST_11  ND1  CG   CD2  NE2    0.00   0.0  0
 EZP  CONST_12  NAY  CAU  CAI  CAG  180.00   0.0  0
 EZP  CONST_13  CAW  CAT  CAG  CAI  180.00   0.0  0
 EZP  CONST_14  CAH  CAJ  CAU  NAY  180.00   0.0  0
 EZP  CONST_15  CAW  CAT  CAH  CAJ  180.00   0.0  0
 EZP  CONST_16  CE1  ND1  CG   CB   180.00   0.0  0
 EZP  CONST_17  NE2  CD2  CG   CB   180.00   0.0  0
 EZP  CONST_18  H4   CAH  CAT  CAG  180.00   0.0  0
 EZP  CONST_19  H3   CAJ  CAU  CAI  180.00   0.0  0
 EZP  CONST_20  H1   CAG  CAI  CAU  180.00   0.0  0
 EZP  CONST_21  H2   CAI  CAU  CAJ  180.00   0.0  0
 EZP  CONST_22  H20  CE1  ND1  CG   180.00   0.0  0
 EZP  CONST_23  H19  NE2  CD2  CG   180.00   0.0  0
 EZP  CONST_24  H18  CD2  NE2  CE1  180.00   0.0  0
 EZP  CONST_25  OAC  NAY  CAU  CAI  180.00   0.0  0
 EZP  CONST_26  OAF  NAY  CAU  CAI    0.00   0.0  0
 EZP  CONST_27  CAJ  CAU  NAY  OAF  180.00   0.0  0
 EZP  CONST_28  CAJ  CAU  NAY  OAC    0.00   0.0  0
 EZP  CONST_29  O    C    NAP  CAX    0.00   0.0  0
 EZP  CONST_30  CA   C    NAP  CAX  180.00   0.0  0
 EZP  CONST_31  H11  NAP  C    O    180.00   0.0  0
 EZP  Var_01    ND1  CG   CB   CA   -48.49  30.0  1

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
 EZP  chir_01  CAW  CAX  CAT  OAE  negativ
 EZP  chir_02  CAX  NAP  CAW  CAM  negativ
 EZP  chir_03  CA   N    C    CB   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
 EZP  plan-1  CB   0.020
 EZP  plan-1  CG   0.020
 EZP  plan-1  CD2  0.020
 EZP  plan-1  NE2  0.020
 EZP  plan-1  CE1  0.020
 EZP  plan-1  ND1  0.020
 EZP  plan-1  H18  0.020
 EZP  plan-1  H19  0.020
 EZP  plan-1  H20  0.020
 EZP  plan-2  CAG  0.020
 EZP  plan-2  CAI  0.020
 EZP  plan-2  CAU  0.020
 EZP  plan-2  NAY  0.020
 EZP  plan-2  CAJ  0.020
 EZP  plan-2  CAH  0.020
 EZP  plan-2  CAT  0.020
 EZP  plan-2  CAW  0.020
 EZP  plan-2  H1   0.020
 EZP  plan-2  H2   0.020
 EZP  plan-2  H3   0.020
 EZP  plan-2  H4   0.020
 EZP  plan-3  CAX  0.020
 EZP  plan-3  NAP  0.020
 EZP  plan-3  C    0.020
 EZP  plan-3  O    0.020
 EZP  plan-3  CA   0.020
 EZP  plan-3  H11  0.020
 EZP  plan-4  CAU  0.020
 EZP  plan-4  NAY  0.020
 EZP  plan-4  OAF  0.020
 EZP  plan-4  OAC  0.020

