# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 10:54:31 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N-[(1R,2R)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]-L-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
 EZG  EZG  N-[(1R,2R)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]-L-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_EZG
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
 EZG  CG   C  CR5    0   0.172  -4.2439   0.8287  -0.3908
 EZG  CB   C  CH2    0  -0.521  -3.0979   0.0079  -0.8692
 EZG  CA   C  CH1    0  -0.225  -1.8247   0.2504  -0.0488
 EZG  C    C  C      0   0.563  -0.7526  -0.7391  -0.5001
 EZG  O    O  O      0  -0.484  -0.2006  -0.6238  -1.5829
 EZG  N    N  NH2    0  -0.772  -1.3951   1.6259  -0.1859
 EZG  CAG  C  CR16   0  -0.312   2.1132   0.1197   0.9742
 EZG  CAI  C  CR16   0  -0.257   2.5164   1.3266   0.4306
 EZG  CAU  C  CR6    0   0.237   3.1863   1.3260  -0.7836
 EZG  NAY  N  N      1   0.328   3.6176   2.5886  -1.3567
 EZG  OAF  O  O     -1  -0.383   3.3815   3.6041  -0.7438
 EZG  OAC  O  O      0  -0.382   4.1919   2.5654  -2.4206
 EZG  CAJ  C  CR16   0  -0.253   3.4614   0.1446  -1.4586
 EZG  CAH  C  CR16   0  -0.272   3.0413  -1.0480  -0.9028
 EZG  CAT  C  CR6    0   0.122   2.3589  -1.0775   0.3096
 EZG  CAW  C  CH1    0  -0.007   1.8529  -2.3969   0.8468
 EZG  OAE  O  OH1    0  -0.653   1.7861  -2.4142   2.2471
 EZG  CAX  C  CH1    0  -0.157   0.5178  -2.7511   0.1540
 EZG  CAM  C  CH2    0  -0.160  -0.0341  -4.1164   0.5417
 EZG  OAD  O  OH1    0  -0.671  -0.5547  -4.0771   1.8508
 EZG  NAP  N  NH1    0  -0.652  -0.4776  -1.7269   0.3749
 EZG  CD2  C  CR15   0  -0.138  -4.8701   1.8634  -1.0271
 EZG  NE2  N  NR15   0  -0.562  -5.8450   2.2852  -0.1684
 EZG  CE1  C  CR15   0   0.079  -5.7769   1.5131   0.9312
 EZG  ND1  N  N      0  -0.465  -4.8212   0.6225   0.8332
 EZG  H1   H  HCH2   0   0.250  -3.3550  -1.0545  -0.8181
 EZG  H2   H  HCH2   0   0.248  -2.8971   0.2314  -1.9203
 EZG  H3   H  HCH1   0   0.256  -2.0621   0.0773   1.0050
 EZG  H4   H  HNH2   0   0.348  -0.6129   1.8112   0.4294
 EZG  H5   H  HNH2   0   0.341  -1.0618   1.7846  -1.1295
 EZG  H8   H  HCR6   0   0.296   2.3130   2.2481   0.9568
 EZG  H9   H  HCR6   0   0.294   3.9947   0.1447  -2.3980
 EZG  H10  H  HCR6   0   0.266   3.2492  -1.9736  -1.4254
 EZG  H11  H  HCH1   0   0.261   2.5701  -3.1754   0.5646
 EZG  H12  H  HOH1   0   0.449   0.9576  -2.0265   2.5460
 EZG  H13  H  HCH1   0   0.283   0.7247  -2.7940  -0.9171
 EZG  H14  H  HCH2   0   0.228  -0.8108  -4.3782  -0.1845
 EZG  H15  H  HCH2   0   0.212   0.7663  -4.8600   0.4404
 EZG  H16  H  HOH1   0   0.464  -1.1870  -4.7940   1.9487
 EZG  H17  H  HNH1   0   0.398  -1.0467  -1.7962   1.2046
 EZG  H18  H  HCR5   0   0.279  -4.7077   2.3194  -1.9891
 EZG  H19  H  HNR5   0   0.418  -6.4992   3.0339  -0.3298
 EZG  H20  H  HCR5   0   0.274  -6.4435   1.6404   1.7701
 EZG  H7   H  HCR6   0   0.262   1.6023   0.1300   1.9274

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
 EZG  OAD  CAM  single    1.409  0.020  1.409
 EZG  O    C    double    1.221  0.020  1.221
 EZG  C    CA   single    1.527  0.020  1.527
 EZG  C    NAP  single    1.348  0.020  1.348
 EZG  CAX  CAM  single    1.523  0.020  1.523
 EZG  CAX  NAP  single    1.445  0.020  1.445
 EZG  CAX  CAW  single    1.545  0.020  1.545
 EZG  CA   N    single    1.448  0.020  1.448
 EZG  CA   CB   single    1.534  0.020  1.534
 EZG  CAH  CAJ  aromatic  1.381  0.020  1.381
 EZG  CAH  CAT  aromatic  1.392  0.020  1.392
 EZG  CAJ  CAU  aromatic  1.388  0.020  1.388
 EZG  CD2  NE2  aromatic  1.366  0.020  1.366
 EZG  CD2  CG   aromatic  1.367  0.020  1.367
 EZG  NE2  CE1  aromatic  1.345  0.020  1.345
 EZG  CAW  CAT  single    1.512  0.020  1.512
 EZG  CAW  OAE  single    1.402  0.020  1.402
 EZG  CAT  CAG  aromatic  1.391  0.020  1.391
 EZG  OAC  NAY  double    1.209  0.020  1.209
 EZG  CG   CB   single    1.489  0.020  1.489
 EZG  CG   ND1  aromatic  1.369  0.020  1.369
 EZG  CE1  ND1  aromatic  1.310  0.020  1.310
 EZG  CAU  NAY  single    1.452  0.020  1.452
 EZG  CAU  CAI  aromatic  1.387  0.020  1.387
 EZG  NAY  OAF  single    1.209  0.020  1.209
 EZG  CAG  CAI  aromatic  1.384  0.020  1.384
 EZG  CB   H1   single    0.970  0.020  1.090
 EZG  CB   H2   single    0.970  0.020  1.090
 EZG  CA   H3   single    0.970  0.020  1.090
 EZG  N    H4   single    0.890  0.020  1.040
 EZG  N    H5   single    0.890  0.020  1.040
 EZG  CAG  H7   single    0.930  0.020  1.080
 EZG  CAI  H8   single    0.930  0.020  1.080
 EZG  CAJ  H9   single    0.930  0.020  1.080
 EZG  CAH  H10  single    0.930  0.020  1.080
 EZG  CAW  H11  single    0.970  0.020  1.090
 EZG  OAE  H12  single    0.850  0.020  0.980
 EZG  CAX  H13  single    0.970  0.020  1.090
 EZG  CAM  H14  single    0.970  0.020  1.090
 EZG  CAM  H15  single    0.970  0.020  1.090
 EZG  OAD  H16  single    0.850  0.020  0.980
 EZG  NAP  H17  single    0.860  0.020  1.020
 EZG  CD2  H18  single    0.930  0.020  1.080
 EZG  NE2  H19  single    0.860  0.020  1.020
 EZG  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
 EZG  ND1  CG   CD2  109.70  3.000
 EZG  ND1  CG   CB   121.93  3.000
 EZG  CD2  CG   CB   128.36  3.000
 EZG  H2   CB   H1   106.65  3.000
 EZG  H2   CB   CA   109.23  3.000
 EZG  H1   CB   CA   108.88  3.000
 EZG  H2   CB   CG   109.73  3.000
 EZG  H1   CB   CG   109.84  3.000
 EZG  CA   CB   CG   112.33  3.000
 EZG  H3   CA   N    107.82  3.000
 EZG  H3   CA   C    109.54  3.000
 EZG  N    CA   C    112.30  3.000
 EZG  H3   CA   CB   108.06  3.000
 EZG  N    CA   CB   110.24  3.000
 EZG  C    CA   CB   108.80  3.000
 EZG  NAP  C    O    123.55  3.000
 EZG  NAP  C    CA   115.23  3.000
 EZG  O    C    CA   121.22  3.000
 EZG  H5   N    H4   106.45  3.000
 EZG  H5   N    CA   109.55  3.000
 EZG  H4   N    CA   110.23  3.000
 EZG  H7   CAG  CAT  120.84  3.000
 EZG  H7   CAG  CAI  118.40  3.000
 EZG  CAT  CAG  CAI  120.76  3.000
 EZG  H8   CAI  CAU  121.18  3.000
 EZG  H8   CAI  CAG  119.85  3.000
 EZG  CAU  CAI  CAG  118.97  3.000
 EZG  CAJ  CAU  NAY  119.29  3.000
 EZG  NAY  CAU  CAI  119.25  3.000
 EZG  CAJ  CAU  CAI  121.46  3.000
 EZG  OAC  NAY  OAF  123.69  3.000
 EZG  OAF  NAY  CAU  118.17  3.000
 EZG  OAC  NAY  CAU  118.14  3.000
 EZG  H9   CAJ  CAH  120.02  3.000
 EZG  H9   CAJ  CAU  121.37  3.000
 EZG  CAH  CAJ  CAU  118.61  3.000
 EZG  H10  CAH  CAT  119.76  3.000
 EZG  H10  CAH  CAJ  119.03  3.000
 EZG  CAT  CAH  CAJ  121.21  3.000
 EZG  CAW  CAT  CAH  119.49  3.000
 EZG  CAW  CAT  CAG  121.48  3.000
 EZG  CAH  CAT  CAG  118.99  3.000
 EZG  H11  CAW  CAX  106.70  3.000
 EZG  H11  CAW  OAE  106.25  3.000
 EZG  CAX  CAW  OAE  113.81  3.000
 EZG  H11  CAW  CAT  108.03  3.000
 EZG  OAE  CAW  CAT  112.44  3.000
 EZG  CAX  CAW  CAT  109.26  3.000
 EZG  H12  OAE  CAW  110.27  3.000
 EZG  H13  CAX  NAP  107.95  3.000
 EZG  H13  CAX  CAM  106.45  3.000
 EZG  NAP  CAX  CAM  110.29  3.000
 EZG  H13  CAX  CAW  106.57  3.000
 EZG  NAP  CAX  CAW  111.36  3.000
 EZG  CAM  CAX  CAW  113.86  3.000
 EZG  H15  CAM  H14  107.10  3.000
 EZG  H15  CAM  OAD  111.97  3.000
 EZG  H14  CAM  OAD  111.14  3.000
 EZG  H15  CAM  CAX  108.65  3.000
 EZG  H14  CAM  CAX  107.61  3.000
 EZG  OAD  CAM  CAX  110.21  3.000
 EZG  H16  OAD  CAM  108.48  3.000
 EZG  H17  NAP  CAX  117.76  3.000
 EZG  H17  NAP  C    117.99  3.000
 EZG  CAX  NAP  C    124.10  3.000
 EZG  H18  CD2  NE2  122.58  3.000
 EZG  H18  CD2  CG   131.87  3.000
 EZG  NE2  CD2  CG   105.56  3.000
 EZG  H19  NE2  CE1  126.19  3.000
 EZG  H19  NE2  CD2  126.32  3.000
 EZG  CE1  NE2  CD2  107.48  3.000
 EZG  H20  CE1  ND1  126.09  3.000
 EZG  H20  CE1  NE2  122.44  3.000
 EZG  ND1  CE1  NE2  111.47  3.000
 EZG  CE1  ND1  CG   105.79  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
 EZG  CONST_01  CE1  NE2  CD2  CG     0.00   0.0  0
 EZG  CONST_02  NE2  CE1  ND1  CG     0.00   0.0  0
 EZG  CONST_03  CAJ  CAH  CAT  CAG    0.00   0.0  0
 EZG  CONST_04  CAJ  CAU  CAI  CAG    0.00   0.0  0
 EZG  CONST_05  CAH  CAJ  CAU  CAI    0.00   0.0  0
 EZG  CONST_06  CAH  CAT  CAG  CAI    0.00   0.0  0
 EZG  CONST_07  CAT  CAH  CAJ  CAU    0.00   0.0  0
 EZG  CONST_08  CAT  CAG  CAI  CAU    0.00   0.0  0
 EZG  CONST_09  ND1  CE1  NE2  CD2    0.00   0.0  0
 EZG  CONST_10  CE1  ND1  CG   CD2    0.00   0.0  0
 EZG  CONST_11  ND1  CG   CD2  NE2    0.00   0.0  0
 EZG  CONST_12  NE2  CD2  CG   CB   180.00   0.0  0
 EZG  CONST_13  CE1  ND1  CG   CB   180.00   0.0  0
 EZG  CONST_14  NAY  CAU  CAI  CAG  180.00   0.0  0
 EZG  CONST_15  CAW  CAT  CAG  CAI  180.00   0.0  0
 EZG  CONST_16  CAH  CAJ  CAU  NAY  180.00   0.0  0
 EZG  CONST_17  CAW  CAT  CAH  CAJ  180.00   0.0  0
 EZG  CONST_18  H19  NE2  CD2  CG   180.00   0.0  0
 EZG  CONST_19  H20  CE1  ND1  CG   180.00   0.0  0
 EZG  CONST_20  H10  CAH  CAT  CAG  180.00   0.0  0
 EZG  CONST_21  H9   CAJ  CAU  CAI  180.00   0.0  0
 EZG  CONST_22  H7   CAG  CAI  CAU  180.00   0.0  0
 EZG  CONST_23  H8   CAI  CAU  CAJ  180.00   0.0  0
 EZG  CONST_24  H18  CD2  NE2  CE1  180.00   0.0  0
 EZG  CONST_25  OAC  NAY  CAU  CAI  180.00   0.0  0
 EZG  CONST_26  OAF  NAY  CAU  CAI    0.00   0.0  0
 EZG  CONST_27  CAJ  CAU  NAY  OAF  180.00   0.0  0
 EZG  CONST_28  CAJ  CAU  NAY  OAC    0.00   0.0  0
 EZG  CONST_29  CAX  NAP  C    CA   180.00   0.0  0
 EZG  CONST_30  CAX  NAP  C    O      0.00   0.0  0
 EZG  CONST_31  H17  NAP  C    CA     0.00   0.0  0
 EZG  Var_01    CD2  CG   CB   CA   112.18  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
 EZG  chir_01  CA   C    N    CB   negativ
 EZG  chir_02  CAW  OAE  CAX  CAT  negativ
 EZG  chir_03  CAX  NAP  CAW  CAM  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
 EZG  plan-1  CG   0.020
 EZG  plan-1  CB   0.020
 EZG  plan-1  CD2  0.020
 EZG  plan-1  NE2  0.020
 EZG  plan-1  CE1  0.020
 EZG  plan-1  ND1  0.020
 EZG  plan-1  H18  0.020
 EZG  plan-1  H19  0.020
 EZG  plan-1  H20  0.020
 EZG  plan-2  CAG  0.020
 EZG  plan-2  CAI  0.020
 EZG  plan-2  CAU  0.020
 EZG  plan-2  NAY  0.020
 EZG  plan-2  CAJ  0.020
 EZG  plan-2  CAH  0.020
 EZG  plan-2  CAT  0.020
 EZG  plan-2  CAW  0.020
 EZG  plan-2  H8   0.020
 EZG  plan-2  H9   0.020
 EZG  plan-2  H10  0.020
 EZG  plan-2  H7   0.020
 EZG  plan-3  CA   0.020
 EZG  plan-3  C    0.020
 EZG  plan-3  O    0.020
 EZG  plan-3  CAX  0.020
 EZG  plan-3  NAP  0.020
 EZG  plan-3  H17  0.020
 EZG  plan-4  CAU  0.020
 EZG  plan-4  NAY  0.020
 EZG  plan-4  OAF  0.020
 EZG  plan-4  OAC  0.020

