# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 11:00:48 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: N-[(2-nitrophenyl)methyl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNCc1ccccc1[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
 EZY  EZY  N-[(2-nitrophenyl)methyl]glycine  ligand  24  15  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EZY
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
 EZY  N    N  NH1    0  -0.588   1.2570   0.6188   0.1520
 EZY  CA   C  CH2    0  -0.408   2.5697   0.5467   0.7576
 EZY  C    C  C      0   0.391   3.6974   0.3897  -0.2781
 EZY  O    O  O      0  -0.607   3.3768  -0.0251  -1.4087
 EZY  C01  C  CH2    0  -0.335   0.1934   0.4406   1.1159
 EZY  C02  C  CR6    0   0.180  -1.9590  -0.4449   0.0043
 EZY  C03  C  CR16   0  -0.252  -3.2137  -0.2402  -0.5575
 EZY  C04  C  CR16   0  -0.271  -3.6782   1.0516  -0.7167
 EZY  C05  C  CR16   0  -0.218  -2.8977   2.1177  -0.2883
 EZY  C06  C  CR16   0  -0.300  -1.6621   1.8858   0.2924
 EZY  C07  C  CR6    0   0.137  -1.1543   0.5986   0.4577
 EZY  O01  O  O      0  -0.372  -0.3585  -2.0732  -0.1748
 EZY  O02  O  O     -1  -0.373  -2.3261  -2.6623   0.4079
 EZY  H    H  HNH1   0   0.334   1.1983  -0.0936  -0.5639
 EZY  HA2  H  HCH2   0   0.217   2.7433   1.4471   1.3552
 EZY  HA3  H  HCH2   0   0.196   2.6622  -0.2985   1.4645
 EZY  H08  H  HCH2   0   0.213   0.2559  -0.5029   1.6758
 EZY  H05  H  HCH2   0   0.243   0.2790   1.2310   1.8665
 EZY  H14  H  HCR6   0   0.292  -3.8114  -1.0777  -0.8895
 EZY  H10  H  HCR6   0   0.276  -4.6442   1.2241  -1.1706
 EZY  H11  H  HCR6   0   0.274  -3.2560   3.1320  -0.4017
 EZY  H12  H  HCR6   0   0.268  -1.0719   2.7222   0.6453
 EZY  OXT  O  OC    -1  -0.623   4.8467   0.6558   0.1242
 EZY  N01  N  N      1   0.326  -1.5115  -1.8273   0.0934

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
 EZY  C04  C03  aromatic  1.382  0.020  1.382
 EZY  C04  C05  aromatic  1.389  0.020  1.389
 EZY  C03  C02  aromatic  1.390  0.020  1.390
 EZY  O01  N01  double    1.209  0.020  1.209
 EZY  C05  C06  aromatic  1.385  0.020  1.385
 EZY  C02  N01  single    1.456  0.020  1.456
 EZY  C02  C07  aromatic  1.394  0.020  1.394
 EZY  N01  O02  single    1.208  0.020  1.208
 EZY  C06  C07  aromatic  1.394  0.020  1.394
 EZY  C07  C01  single    1.508  0.020  1.508
 EZY  C01  N    single    1.446  0.020  1.446
 EZY  CA   N    single    1.447  0.020  1.447
 EZY  CA   C    single    1.539  0.020  1.539
 EZY  C    O    deloc     1.246  0.020  1.246
 EZY  N    H    single    0.860  0.020  1.020
 EZY  CA   HA2  single    0.970  0.020  1.090
 EZY  CA   HA3  single    0.970  0.020  1.090
 EZY  C01  H08  single    0.970  0.020  1.090
 EZY  C01  H05  single    0.970  0.020  1.090
 EZY  C03  H14  single    0.930  0.020  1.080
 EZY  C04  H10  single    0.930  0.020  1.080
 EZY  C05  H11  single    0.930  0.020  1.080
 EZY  C06  H12  single    0.930  0.020  1.080
 EZY  C    OXT  deloc     1.246  0.020  1.246

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
 EZY  H    N    C01  110.01  3.000
 EZY  H    N    CA   108.28  3.000
 EZY  C01  N    CA   112.46  3.000
 EZY  HA3  CA   HA2  105.46  3.000
 EZY  HA3  CA   C    106.91  3.000
 EZY  HA2  CA   C    109.58  3.000
 EZY  HA3  CA   N    112.42  3.000
 EZY  HA2  CA   N    109.35  3.000
 EZY  C    CA   N    112.83  3.000
 EZY  OXT  C    O    126.95  3.000
 EZY  OXT  C    CA   115.89  3.000
 EZY  O    C    CA   117.12  3.000
 EZY  H05  C01  H08  105.45  3.000
 EZY  H05  C01  C07  107.09  3.000
 EZY  H08  C01  C07  111.29  3.000
 EZY  H05  C01  N    108.11  3.000
 EZY  H08  C01  N    113.80  3.000
 EZY  C07  C01  N    110.70  3.000
 EZY  N01  C02  C07  120.91  3.000
 EZY  C07  C02  C03  122.85  3.000
 EZY  N01  C02  C03  116.24  3.000
 EZY  H14  C03  C04  120.19  3.000
 EZY  H14  C03  C02  120.60  3.000
 EZY  C04  C03  C02  119.19  3.000
 EZY  H10  C04  C05  120.61  3.000
 EZY  H10  C04  C03  119.85  3.000
 EZY  C05  C04  C03  119.54  3.000
 EZY  H11  C05  C06  119.77  3.000
 EZY  H11  C05  C04  120.08  3.000
 EZY  C06  C05  C04  120.14  3.000
 EZY  H12  C06  C07  118.44  3.000
 EZY  H12  C06  C05  119.58  3.000
 EZY  C07  C06  C05  121.98  3.000
 EZY  C06  C07  C02  116.27  3.000
 EZY  C06  C07  C01  118.30  3.000
 EZY  C02  C07  C01  125.42  3.000
 EZY  O02  N01  O01  124.07  3.000
 EZY  O02  N01  C02  117.71  3.000
 EZY  O01  N01  C02  118.21  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
 EZY  CONST_01  C05  C04  C03  C02    0.00   0.0  0
 EZY  CONST_02  C05  C06  C07  C02    0.00   0.0  0
 EZY  CONST_03  C06  C05  C04  C03    0.00   0.0  0
 EZY  CONST_04  C06  C07  C02  C03    0.00   0.0  0
 EZY  CONST_05  C07  C02  C03  C04    0.00   0.0  0
 EZY  CONST_06  C07  C06  C05  C04    0.00   0.0  0
 EZY  CONST_07  C03  C02  C07  C01  180.00   0.0  0
 EZY  CONST_08  C05  C06  C07  C01  180.00   0.0  0
 EZY  CONST_09  N01  C02  C03  C04  180.00   0.0  0
 EZY  CONST_10  N01  C02  C07  C06  180.00   0.0  0
 EZY  CONST_11  H10  C04  C03  C02  180.00   0.0  0
 EZY  CONST_12  H12  C06  C07  C02  180.00   0.0  0
 EZY  CONST_13  H11  C05  C04  C03  180.00   0.0  0
 EZY  CONST_14  H14  C03  C04  C05  180.00   0.0  0
 EZY  Var_01    C02  C07  C01  N     97.18  30.0  2
 EZY  Var_02    C07  C01  N    CA   176.87  30.0  1
 EZY  Var_03    O    C    CA   N    -19.50  30.0  3
 EZY  Var_04    C01  N    CA   C    165.98  30.0  3

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
 EZY  plan-1  C01  0.020
 EZY  plan-1  C02  0.020
 EZY  plan-1  C03  0.020
 EZY  plan-1  C04  0.020
 EZY  plan-1  C05  0.020
 EZY  plan-1  C06  0.020
 EZY  plan-1  C07  0.020
 EZY  plan-1  H14  0.020
 EZY  plan-1  H10  0.020
 EZY  plan-1  H11  0.020
 EZY  plan-1  H12  0.020
 EZY  plan-1  N01  0.020
 EZY  plan-2  C02  0.020
 EZY  plan-2  O01  0.020
 EZY  plan-2  O02  0.020
 EZY  plan-2  N01  0.020
 EZY  plan-3  CA   0.020
 EZY  plan-3  C    0.020
 EZY  plan-3  O    0.020
 EZY  plan-3  OXT  0.020

