# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 09:03:18 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N-[(1R,2R)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]-L-lysinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](N)C(=O)N[C@H](CO)[C@H](O)c1ccc(cc1)[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
 EZM  EZM  N-[(1R,2R)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]-L-lysinamide  ligand  48  24  .  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_EZM
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
 EZM  CAG  C  CR16   0  -0.311  -2.4010  -0.0613   0.9790
 EZM  CAI  C  CR16   0  -0.252  -3.0176  -1.1835   0.4536
 EZM  CAU  C  CR6    0   0.237  -3.6660  -1.0838  -0.7683
 EZM  NAY  N  N      1   0.328  -4.3153  -2.2565  -1.3261
 EZM  OAF  O  O     -1  -0.383  -4.2363  -3.2975  -0.7157
 EZM  OAC  O  O      0  -0.383  -4.9027  -2.1377  -2.3766
 EZM  CAJ  C  CR16   0  -0.253  -3.7139   0.1149  -1.4667
 EZM  CAH  C  CR16   0  -0.275  -3.0813   1.2188  -0.9301
 EZM  CAT  C  CR6    0   0.127  -2.4112   1.1456   0.2877
 EZM  CAW  C  CH1    0  -0.011  -1.6649   2.3571   0.7970
 EZM  OAE  O  OH1    0  -0.652  -1.5870   2.3941   2.1957
 EZM  CAX  C  CH1    0  -0.148  -0.2894   2.4384   0.0994
 EZM  CAM  C  CH2    0  -0.164   0.4932   3.7030   0.4317
 EZM  OAD  O  OH1    0  -0.670   0.9927   3.6403   1.7489
 EZM  NAP  N  NH1    0  -0.650   0.5140   1.2721   0.3851
 EZM  C    C  C      0   0.546   0.6425   0.2136  -0.4429
 EZM  O    O  O      0  -0.475   0.0595   0.1199  -1.5097
 EZM  CA   C  CH1    0  -0.231   1.6127  -0.8637   0.0479
 EZM  N    N  NH2    0  -0.772   1.2604  -2.1930  -0.3999
 EZM  CB   C  CH2    0  -0.413   3.0283  -0.4915  -0.4066
 EZM  CG   C  CH2    0  -0.416   4.1043  -1.3970   0.1762
 EZM  CD   C  CH2    0  -0.427   5.5058  -0.9965  -0.2659
 EZM  CE   C  CH2    0  -0.272   6.5868  -1.8739   0.3456
 EZM  NZ   N  NH2    0  -0.801   7.9095  -1.4724  -0.1133
 EZM  H1   H  HCR6   0   0.259  -1.9114  -0.1490   1.9391
 EZM  H2   H  HCR6   0   0.294  -2.9894  -2.1154   0.9992
 EZM  H3   H  HCR6   0   0.293  -4.2328   0.1953  -2.4105
 EZM  H4   H  HCR6   0   0.266  -3.1109   2.1562  -1.4723
 EZM  H5   H  HCH1   0   0.261  -2.2228   3.2502   0.4965
 EZM  H6   H  HOH1   0   0.448  -0.8772   1.8193   2.5001
 EZM  H7   H  HCH1   0   0.281  -0.4815   2.4656  -0.9754
 EZM  H8   H  HCH2   0   0.230   1.3073   3.7877  -0.2952
 EZM  H9   H  HCH2   0   0.212  -0.1623   4.5708   0.2862
 EZM  H10  H  HOH1   0   0.463   1.7956   4.1657   1.7939
 EZM  H11  H  HNH1   0   0.396   1.1075   1.3124   1.2000
 EZM  H12  H  HCH1   0   0.247   1.5997  -0.8665   1.1438
 EZM  H13  H  HNH2   0   0.346   0.3526  -2.4509  -0.0326
 EZM  H14  H  HNH2   0   0.339   1.1608  -2.1923  -1.4086
 EZM  H16  H  HCH2   0   0.225   3.0708  -0.5168  -1.5013
 EZM  H17  H  HCH2   0   0.228   3.2331   0.5437  -0.1170
 EZM  H18  H  HCH2   0   0.210   4.0422  -1.3672   1.2697
 EZM  H19  H  HCH2   0   0.222   3.9079  -2.4315  -0.1139
 EZM  H20  H  HCH2   0   0.212   5.5802  -1.0459  -1.3568
 EZM  H21  H  HCH2   0   0.210   5.6891   0.0483   0.0100
 EZM  H22  H  HCH2   0   0.186   6.4787  -1.8578   1.4404
 EZM  H23  H  HCH2   0   0.211   6.4204  -2.9108   0.0402
 EZM  H24  H  HNH2   0   0.336   8.1253  -0.5551   0.2577
 EZM  H25  H  HNH2   0   0.345   8.6053  -2.0930   0.2802

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
 EZM  OAD  CAM  single    1.410  0.020  1.410
 EZM  CE   NZ   single    1.456  0.020  1.456
 EZM  CE   CD   single    1.521  0.020  1.521
 EZM  CG   CD   single    1.523  0.020  1.523
 EZM  CG   CB   single    1.522  0.020  1.522
 EZM  O    C    double    1.219  0.020  1.219
 EZM  CAM  CAX  single    1.524  0.020  1.524
 EZM  CAX  NAP  single    1.445  0.020  1.445
 EZM  CAX  CAW  single    1.544  0.020  1.544
 EZM  CB   CA   single    1.533  0.020  1.533
 EZM  C    NAP  single    1.350  0.020  1.350
 EZM  C    CA   single    1.531  0.020  1.531
 EZM  CAH  CAJ  aromatic  1.381  0.020  1.381
 EZM  CAH  CAT  aromatic  1.392  0.020  1.392
 EZM  CAW  CAT  single    1.511  0.020  1.511
 EZM  CAW  OAE  single    1.401  0.020  1.401
 EZM  CA   N    single    1.446  0.020  1.446
 EZM  CAJ  CAU  aromatic  1.388  0.020  1.388
 EZM  CAT  CAG  aromatic  1.391  0.020  1.391
 EZM  OAC  NAY  double    1.209  0.020  1.209
 EZM  CAU  NAY  single    1.452  0.020  1.452
 EZM  CAU  CAI  aromatic  1.387  0.020  1.387
 EZM  CAG  CAI  aromatic  1.384  0.020  1.384
 EZM  NAY  OAF  single    1.209  0.020  1.209
 EZM  CAG  H1   single    0.930  0.020  1.080
 EZM  CAI  H2   single    0.930  0.020  1.080
 EZM  CAJ  H3   single    0.930  0.020  1.080
 EZM  CAH  H4   single    0.930  0.020  1.080
 EZM  CAW  H5   single    0.970  0.020  1.090
 EZM  OAE  H6   single    0.850  0.020  0.980
 EZM  CAX  H7   single    0.970  0.020  1.090
 EZM  CAM  H8   single    0.970  0.020  1.090
 EZM  CAM  H9   single    0.970  0.020  1.090
 EZM  OAD  H10  single    0.850  0.020  0.980
 EZM  NAP  H11  single    0.860  0.020  1.020
 EZM  CA   H12  single    0.970  0.020  1.090
 EZM  N    H13  single    0.890  0.020  1.040
 EZM  N    H14  single    0.890  0.020  1.040
 EZM  CB   H16  single    0.970  0.020  1.090
 EZM  CB   H17  single    0.970  0.020  1.090
 EZM  CG   H18  single    0.970  0.020  1.090
 EZM  CG   H19  single    0.970  0.020  1.090
 EZM  CD   H20  single    0.970  0.020  1.090
 EZM  CD   H21  single    0.970  0.020  1.090
 EZM  CE   H22  single    0.970  0.020  1.090
 EZM  CE   H23  single    0.970  0.020  1.090
 EZM  NZ   H24  single    0.890  0.020  1.040
 EZM  NZ   H25  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
 EZM  H1   CAG  CAT  120.99  3.000
 EZM  H1   CAG  CAI  118.24  3.000
 EZM  CAT  CAG  CAI  120.77  3.000
 EZM  H2   CAI  CAU  121.28  3.000
 EZM  H2   CAI  CAG  119.74  3.000
 EZM  CAU  CAI  CAG  118.98  3.000
 EZM  CAJ  CAU  NAY  119.26  3.000
 EZM  NAY  CAU  CAI  119.31  3.000
 EZM  CAJ  CAU  CAI  121.43  3.000
 EZM  OAC  NAY  OAF  123.69  3.000
 EZM  OAF  NAY  CAU  118.18  3.000
 EZM  OAC  NAY  CAU  118.13  3.000
 EZM  H3   CAJ  CAH  120.01  3.000
 EZM  H3   CAJ  CAU  121.37  3.000
 EZM  CAH  CAJ  CAU  118.62  3.000
 EZM  H4   CAH  CAT  119.77  3.000
 EZM  H4   CAH  CAJ  119.00  3.000
 EZM  CAT  CAH  CAJ  121.23  3.000
 EZM  CAW  CAT  CAH  119.36  3.000
 EZM  CAW  CAT  CAG  121.63  3.000
 EZM  CAH  CAT  CAG  118.95  3.000
 EZM  H5   CAW  CAX  106.67  3.000
 EZM  H5   CAW  OAE  106.31  3.000
 EZM  CAX  CAW  OAE  113.57  3.000
 EZM  H5   CAW  CAT  108.05  3.000
 EZM  OAE  CAW  CAT  112.64  3.000
 EZM  CAX  CAW  CAT  109.25  3.000
 EZM  H6   OAE  CAW  109.93  3.000
 EZM  H7   CAX  NAP  108.21  3.000
 EZM  H7   CAX  CAM  106.52  3.000
 EZM  NAP  CAX  CAM  109.95  3.000
 EZM  H7   CAX  CAW  106.80  3.000
 EZM  NAP  CAX  CAW  111.31  3.000
 EZM  CAM  CAX  CAW  113.74  3.000
 EZM  H9   CAM  H8   107.16  3.000
 EZM  H9   CAM  OAD  111.75  3.000
 EZM  H8   CAM  OAD  111.12  3.000
 EZM  H9   CAM  CAX  108.70  3.000
 EZM  H8   CAM  CAX  107.54  3.000
 EZM  OAD  CAM  CAX  110.41  3.000
 EZM  H10  OAD  CAM  108.39  3.000
 EZM  H11  NAP  C    118.08  3.000
 EZM  H11  NAP  CAX  117.04  3.000
 EZM  C    NAP  CAX  124.37  3.000
 EZM  CA   C    O    121.97  3.000
 EZM  CA   C    NAP  114.55  3.000
 EZM  O    C    NAP  123.46  3.000
 EZM  H12  CA   CB   107.95  3.000
 EZM  H12  CA   N    107.72  3.000
 EZM  CB   CA   N    110.87  3.000
 EZM  H12  CA   C    108.36  3.000
 EZM  N    CA   C    113.16  3.000
 EZM  CB   CA   C    108.63  3.000
 EZM  H14  N    H13  105.84  3.000
 EZM  H14  N    CA   109.36  3.000
 EZM  H13  N    CA   109.88  3.000
 EZM  H17  CB   H16  106.20  3.000
 EZM  H17  CB   CG   109.21  3.000
 EZM  H16  CB   CG   109.96  3.000
 EZM  H17  CB   CA   108.91  3.000
 EZM  H16  CB   CA   109.05  3.000
 EZM  CG   CB   CA   113.26  3.000
 EZM  H19  CG   H18  106.30  3.000
 EZM  H19  CG   CD   109.72  3.000
 EZM  H18  CG   CD   109.55  3.000
 EZM  H19  CG   CB   109.55  3.000
 EZM  H18  CG   CB   109.01  3.000
 EZM  CD   CG   CB   112.51  3.000
 EZM  H21  CD   H20  106.42  3.000
 EZM  H21  CD   CE   109.27  3.000
 EZM  H20  CD   CE   109.05  3.000
 EZM  H21  CD   CG   109.36  3.000
 EZM  H20  CD   CG   109.87  3.000
 EZM  CE   CD   CG   112.68  3.000
 EZM  H23  CE   H22  106.07  3.000
 EZM  H23  CE   NZ   108.15  3.000
 EZM  H22  CE   NZ   113.50  3.000
 EZM  H23  CE   CD   109.06  3.000
 EZM  H22  CE   CD   108.77  3.000
 EZM  NZ   CE   CD   111.09  3.000
 EZM  H25  NZ   H24  105.45  3.000
 EZM  H25  NZ   CE   109.44  3.000
 EZM  H24  NZ   CE   109.13  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
 EZM  CONST_01  CAJ  CAH  CAT  CAG     0.00   0.0  0
 EZM  CONST_02  CAJ  CAU  CAI  CAG     0.00   0.0  0
 EZM  CONST_03  CAH  CAJ  CAU  CAI     0.00   0.0  0
 EZM  CONST_04  CAH  CAT  CAG  CAI     0.00   0.0  0
 EZM  CONST_05  CAT  CAH  CAJ  CAU     0.00   0.0  0
 EZM  CONST_06  CAT  CAG  CAI  CAU     0.00   0.0  0
 EZM  CONST_07  NAY  CAU  CAI  CAG   180.00   0.0  0
 EZM  CONST_08  CAW  CAT  CAG  CAI   180.00   0.0  0
 EZM  CONST_09  CAH  CAJ  CAU  NAY   180.00   0.0  0
 EZM  CONST_10  CAW  CAT  CAH  CAJ   180.00   0.0  0
 EZM  CONST_11  H4   CAH  CAT  CAG   180.00   0.0  0
 EZM  CONST_12  H3   CAJ  CAU  CAI   180.00   0.0  0
 EZM  CONST_13  H1   CAG  CAI  CAU   180.00   0.0  0
 EZM  CONST_14  H2   CAI  CAU  CAJ   180.00   0.0  0
 EZM  CONST_15  OAC  NAY  CAU  CAI   180.00   0.0  0
 EZM  CONST_16  OAF  NAY  CAU  CAI     0.00   0.0  0
 EZM  CONST_17  CAJ  CAU  NAY  OAF   180.00   0.0  0
 EZM  CONST_18  CAJ  CAU  NAY  OAC     0.00   0.0  0
 EZM  CONST_19  O    C    NAP  CAX     0.00   0.0  0
 EZM  CONST_20  CA   C    NAP  CAX   180.00   0.0  0
 EZM  CONST_21  H11  NAP  C    O     180.00   0.0  0
 EZM  Var_01    CD   CG   CB   CA   -178.94  30.0  1
 EZM  Var_02    CE   CD   CG   CB    178.36  30.0  3
 EZM  Var_03    NZ   CE   CD   CG    179.25  30.0  1
 EZM  Var_04    H24  NZ   CE   CD     67.18  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
 EZM  chir_01  CAW  CAX  CAT  OAE  negativ
 EZM  chir_02  CAX  NAP  CAW  CAM  negativ
 EZM  chir_03  CA   N    C    CB   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
 EZM  plan-1  CAG  0.020
 EZM  plan-1  CAI  0.020
 EZM  plan-1  CAU  0.020
 EZM  plan-1  NAY  0.020
 EZM  plan-1  CAJ  0.020
 EZM  plan-1  CAH  0.020
 EZM  plan-1  CAT  0.020
 EZM  plan-1  CAW  0.020
 EZM  plan-1  H1   0.020
 EZM  plan-1  H2   0.020
 EZM  plan-1  H3   0.020
 EZM  plan-1  H4   0.020
 EZM  plan-2  CAX  0.020
 EZM  plan-2  NAP  0.020
 EZM  plan-2  C    0.020
 EZM  plan-2  O    0.020
 EZM  plan-2  CA   0.020
 EZM  plan-2  H11  0.020
 EZM  plan-3  CAU  0.020
 EZM  plan-3  NAY  0.020
 EZM  plan-3  OAF  0.020
 EZM  plan-3  OAC  0.020

