# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 12:43:44 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: 3-[(3E)-3-(2-carbamimidoylhydrazinylidene)-4-hydroxy-6-oxocyclohexa-1,4-dien-1-yl]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1=CC(=N/NC(N)=N)\C(=CC1=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
 AGQ  AGQ  3-[(3E)-3-(2-carbamimidoylhydrazinylidene)-4-hydroxy-6-oxocyclohexa-1,4-dien-1-yl]-L-alanine  L-peptide  31  19  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_AGQ
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
 AGQ  OXT  O  OC    -1  -0.601  -21.9832   -6.2406  26.0204
 AGQ  C    C  C      0   0.417  -22.1720   -6.1133  24.7962
 AGQ  N    N  NH2    0  -0.809  -22.1046   -7.1676  22.5551
 AGQ  O    O  O      0  -0.597  -22.3246   -5.0456  24.1700
 AGQ  N6   N  NH1    0  -0.495  -19.1823  -11.1077  20.3783
 AGQ  C7   C  C      0   0.578  -18.5382  -11.6320  19.2508
 AGQ  N8   N  N      0  -0.657  -19.0538  -12.6112  18.6282
 AGQ  N9   N  NH2    0  -0.837  -17.4145  -10.9178  18.9405
 AGQ  CA   C  CH1    0  -0.220  -22.2882   -7.4253  23.9730
 AGQ  CB   C  CH2    0  -0.473  -21.2785   -8.4794  24.4547
 AGQ  CG   C  CR6    0  -0.010  -21.4379   -9.7676  23.7165
 AGQ  CZ   C  CR6    0   0.367  -21.9673  -12.1878  22.2951
 AGQ  CD1  C  CR6    0   0.375  -22.5233  -10.6920  24.1427
 AGQ  CD2  C  CR16   0  -0.357  -20.6721  -10.0830  22.6569
 AGQ  CE1  C  CR16   0  -0.509  -22.7412  -11.8905  23.3623
 AGQ  CE2  C  CR6    0   0.197  -20.8752  -11.2976  21.9013
 AGQ  H    H  HNH2   0   0.332  -22.6339   -7.8274  22.0021
 AGQ  H2   H  HNH2   0   0.335  -22.4745   -6.2463  22.3605
 AGQ  H6   H  HNH1   0   0.427  -18.8612  -10.2264  20.7617
 AGQ  H8   H  H      0   0.336  -18.4544  -12.9076  17.8672
 AGQ  H91  H  HNH2   0   0.401  -16.8281  -11.3126  18.2227
 AGQ  H92  H  HNH2   0   0.399  -16.8845  -10.5064  19.6940
 AGQ  HA   H  HCH1   0   0.210  -23.2953   -7.8135  24.1959
 AGQ  HB2  H  HCH2   0   0.229  -20.2691   -8.0934  24.2946
 AGQ  HB3  H  HCH2   0   0.234  -21.4070   -8.6370  25.5241
 AGQ  HH   H  HOH1   0   0.475  -21.5046  -13.3128  20.8660
 AGQ  HD2  H  HCR6   0   0.273  -19.8845   -9.3988  22.3639
 AGQ  HE1  H  HCR6   0   0.262  -23.5430  -12.5540  23.6619
 AGQ  OH   O  OH1    0  -0.598  -22.1648  -13.2874  21.5800
 AGQ  N5   N  N      0  -0.240  -20.2073  -11.7294  20.8856
 AGQ  OZ   O  O      0  -0.442  -23.2070  -10.4331  25.1279

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
 AGQ  OXT  C    deloc   1.245  0.020  1.245
 AGQ  C    O    deloc   1.231  0.020  1.231
 AGQ  C    CA   single  1.525  0.021  1.525
 AGQ  N    CA   single  1.458  0.019  1.458
 AGQ  N5   N6   single  1.302  0.020  1.302
 AGQ  N5   CE2  double  1.290  0.020  1.290
 AGQ  N6   C7   single  1.400  0.020  1.400
 AGQ  C7   N8   double  1.270  0.020  1.270
 AGQ  C7   N9   single  1.367  0.020  1.367
 AGQ  CA   CB   single  1.530  0.020  1.530
 AGQ  CB   CG   single  1.493  0.020  1.493
 AGQ  CG   CD1  single  1.488  0.020  1.488
 AGQ  CG   CD2  double  1.345  0.020  1.345
 AGQ  OH   CZ   single  1.327  0.020  1.327
 AGQ  CZ   CE1  double  1.351  0.020  1.351
 AGQ  CZ   CE2  single  1.463  0.020  1.463
 AGQ  OZ   CD1  double  1.227  0.020  1.227
 AGQ  CD1  CE1  single  1.447  0.020  1.447
 AGQ  CD2  CE2  single  1.445  0.020  1.445
 AGQ  N    H    single  0.860  0.020  0.860
 AGQ  N    H2   single  0.890  0.020  1.040
 AGQ  N6   H6   single  0.860  0.020  1.020
 AGQ  N8   H8   single  0.890  0.020  1.040
 AGQ  N9   H91  single  0.890  0.020  1.040
 AGQ  N9   H92  single  0.890  0.020  1.040
 AGQ  CA   HA   single  0.970  0.020  0.970
 AGQ  CB   HB2  single  0.970  0.020  1.090
 AGQ  CB   HB3  single  0.970  0.020  1.090
 AGQ  OH   HH   single  0.850  0.020  0.980
 AGQ  CD2  HD2  single  0.930  0.020  1.080
 AGQ  CE1  HE1  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
 AGQ  CA   C    O    120.80  1.700
 AGQ  CA   C    OXT  116.49  3.000
 AGQ  O    C    OXT  126.85  3.000
 AGQ  H2   N    H    107.33  3.000
 AGQ  H2   N    CA   107.64  3.000
 AGQ  H    N    CA   114.00  3.000
 AGQ  H6   N6   C7   118.98  3.000
 AGQ  H6   N6   N5   121.16  3.000
 AGQ  C7   N6   N5   119.81  3.000
 AGQ  N9   C7   N8   128.70  3.000
 AGQ  N9   C7   N6   111.42  3.000
 AGQ  N8   C7   N6   119.79  3.000
 AGQ  H8   N8   C7   110.71  3.000
 AGQ  H92  N9   H91  112.72  3.000
 AGQ  H92  N9   C7   118.37  3.000
 AGQ  H91  N9   C7   115.81  3.000
 AGQ  HA   CA   CB   109.00  3.000
 AGQ  HA   CA   N    110.00  3.000
 AGQ  CB   CA   N    110.50  1.700
 AGQ  HA   CA   C    109.00  3.000
 AGQ  CB   CA   C    110.10  1.900
 AGQ  N    CA   C    111.00  2.800
 AGQ  HB3  CB   HB2  107.70  3.000
 AGQ  HB3  CB   CG   110.38  3.000
 AGQ  HB2  CB   CG   109.33  3.000
 AGQ  HB3  CB   CA   109.25  3.000
 AGQ  HB2  CB   CA   108.58  3.000
 AGQ  CG   CB   CA   111.50  3.000
 AGQ  CD2  CG   CD1  119.69  3.000
 AGQ  CD2  CG   CB   122.07  3.000
 AGQ  CD1  CG   CB   118.18  3.000
 AGQ  CE2  CZ   CE1  120.41  3.000
 AGQ  CE2  CZ   OH   118.06  3.000
 AGQ  CE1  CZ   OH   121.52  3.000
 AGQ  CE1  CD1  OZ   121.61  3.000
 AGQ  CE1  CD1  CG   118.03  3.000
 AGQ  OZ   CD1  CG   120.36  3.000
 AGQ  HD2  CD2  CE2  119.44  3.000
 AGQ  HD2  CD2  CG   118.61  3.000
 AGQ  CE2  CD2  CG   121.95  3.000
 AGQ  HE1  CE1  CD1  118.02  3.000
 AGQ  HE1  CE1  CZ   120.51  3.000
 AGQ  CD1  CE1  CZ   121.47  3.000
 AGQ  CD2  CE2  CZ   118.40  3.000
 AGQ  CD2  CE2  N5   128.34  3.000
 AGQ  CZ   CE2  N5   113.25  3.000
 AGQ  HH   OH   CZ   108.44  3.000
 AGQ  CE2  N5   N6   123.69  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
 AGQ  CONST_01  N8   C7   N6  N5     0.00   0.0  0
 AGQ  CONST_02  N9   C7   N6  N5   180.00   0.0  0
 AGQ  CONST_03  H8   N8   C7  N6   180.00   0.0  0
 AGQ  CONST_04  H91  N9   C7  N6   180.00   0.0  0
 AGQ  CONST_06  H6   N6   C7  N8   180.00   0.0  0
 AGQ  Var_01    CZ   CE2  N5  N6  -178.96   0.0  2
 AGQ  Var_02    CD1  CG   CB  CA   -80.43  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
 AGQ  chir_01  CA  C  N  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
 AGQ  plan-1  N6   0.020
 AGQ  plan-1  CB   0.020
 AGQ  plan-1  CG   0.020
 AGQ  plan-1  CZ   0.020
 AGQ  plan-1  CD1  0.020
 AGQ  plan-1  CD2  0.020
 AGQ  plan-1  CE1  0.020
 AGQ  plan-1  CE2  0.020
 AGQ  plan-1  HD2  0.020
 AGQ  plan-1  HE1  0.020
 AGQ  plan-1  OH   0.020
 AGQ  plan-1  N5   0.020
 AGQ  plan-1  OZ   0.020
 AGQ  plan-2  N6   0.020
 AGQ  plan-2  C7   0.020
 AGQ  plan-2  N8   0.020
 AGQ  plan-2  N9   0.020
 AGQ  plan-2  H6   0.020
 AGQ  plan-2  H8   0.020
 AGQ  plan-2  H91  0.020
 AGQ  plan-2  H92  0.020
 AGQ  plan-2  N5   0.020
 AGQ  plan-3  OXT  0.020
 AGQ  plan-3  C    0.020
 AGQ  plan-3  O    0.020
 AGQ  plan-3  CA   0.020

