# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 15:43:27 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: (2~{S})-2-azanyl-3-[1-(dioxidanyl)-4-oxidanylidene-cyclohexa-2,5-dien-1-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1(OO)C=CC(=O)C=C1)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
 F7Q  F7Q  '(2~{S})-2-azanyl-3-[1-(dioxidanyl)-4-oxidanylidene-cyclohexa-2,5-dien-1-yl]propanoic acid'  L-peptide  25  15  .  2019-03-22  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_F7Q
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
 F7Q  C    C  C      0   0.423   -5.6215   -8.6975  -22.8096
 F7Q  O    O  O      0  -0.593   -4.4341   -8.5796  -22.4486
 F7Q  CA   C  CH1    0  -0.239   -6.4877   -9.7346  -22.0291
 F7Q  N    N  NH2    0  -0.812   -5.8365  -10.1222  -20.7872
 F7Q  CB   C  CH2    0  -0.446   -7.8871   -9.1744  -21.7809
 F7Q  CAG  C  CR6    0   0.148   -8.9392  -10.2039  -21.3268
 F7Q  OAA  O  O2     0  -0.298  -10.1291   -9.4169  -21.2131
 F7Q  OAB  O  OH1    0  -0.448  -11.2101  -10.2456  -20.8580
 F7Q  CAJ  C  CR16   0  -0.167   -8.6057  -10.7919  -19.9904
 F7Q  CAM  C  CR16   0  -0.365   -8.4524  -12.0979  -19.7787
 F7Q  CAO  C  CR6    0   0.389   -8.5806  -13.0754  -20.8690
 F7Q  OAE  O  O      0  -0.419   -8.4085  -14.2682  -20.6846
 F7Q  CAL  C  CR16   0  -0.359   -8.9405  -12.5438  -22.1928
 F7Q  CAK  C  CR16   0  -0.162   -9.1242  -11.2407  -22.3920
 F7Q  H2   H  HCH1   0   0.215   -6.5843  -10.5882  -22.7193
 F7Q  H3   H  HNH2   0   0.338   -5.9183  -11.1162  -20.6298
 F7Q  H4   H  HNH2   0   0.338   -4.8506   -9.9157  -20.8985
 F7Q  H6   H  HCH2   0   0.238   -7.8227   -8.3881  -21.0224
 F7Q  H7   H  HCH2   0   0.247   -8.2569   -8.7196  -22.7015
 F7Q  H8   H  HOH1   0   0.472  -11.2838  -10.1064  -19.9023
 F7Q  H9   H  HCR6   0   0.280   -8.5007  -10.0882  -19.1715
 F7Q  H10  H  HCR6   0   0.267   -8.2094  -12.4808  -18.7947
 F7Q  H11  H  HCR6   0   0.268   -9.0640  -13.2576  -22.9985
 F7Q  H12  H  HCR6   0   0.282   -9.4056  -10.8709  -23.3730
 F7Q  OXT  O  OC    -1  -0.596   -6.1794   -8.1060  -23.7519

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
 F7Q  C    O    deloc   1.231  0.020  1.231
 F7Q  C    CA   single  1.525  0.021  1.525
 F7Q  CAK  CAL  double  1.331  0.020  1.331
 F7Q  CAK  CAG  single  1.498  0.020  1.498
 F7Q  CAL  CAO  single  1.471  0.020  1.471
 F7Q  CA   CB   single  1.530  0.020  1.530
 F7Q  CA   N    single  1.458  0.019  1.458
 F7Q  CB   CAG  single  1.540  0.020  1.540
 F7Q  CAG  OAA  single  1.431  0.020  1.431
 F7Q  CAG  CAJ  single  1.498  0.020  1.498
 F7Q  OAA  OAB  single  1.408  0.020  1.408
 F7Q  CAO  OAE  double  1.219  0.020  1.219
 F7Q  CAO  CAM  single  1.470  0.020  1.470
 F7Q  CAJ  CAM  double  1.332  0.020  1.332
 F7Q  CA   H2   single  0.970  0.020  1.090
 F7Q  N    H3   single  0.890  0.020  1.040
 F7Q  N    H4   single  0.890  0.020  1.040
 F7Q  CB   H6   single  0.970  0.020  1.090
 F7Q  CB   H7   single  0.970  0.020  1.090
 F7Q  OAB  H8   single  0.850  0.020  0.980
 F7Q  CAJ  H9   single  0.930  0.020  1.080
 F7Q  CAM  H10  single  0.930  0.020  1.080
 F7Q  CAL  H11  single  0.930  0.020  1.080
 F7Q  CAK  H12  single  0.930  0.020  1.080
 F7Q  C    OXT  deloc   1.245  0.020  1.245

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
 F7Q  OXT  C    CA   116.47  3.000
 F7Q  OXT  C    O    126.96  3.000
 F7Q  CA   C    O    120.80  1.700
 F7Q  H2   CA   CB   107.79  3.000
 F7Q  H2   CA   N    111.56  3.000
 F7Q  CB   CA   N    110.50  1.700
 F7Q  H2   CA   C    104.49  3.000
 F7Q  N    CA   C    111.00  2.800
 F7Q  CB   CA   C    110.10  1.900
 F7Q  H4   N    H3   107.25  3.000
 F7Q  H4   N    CA   106.70  3.000
 F7Q  H3   N    CA   111.05  3.000
 F7Q  H7   CB   H6   107.76  3.000
 F7Q  H7   CB   CAG  107.20  3.000
 F7Q  H6   CB   CAG  108.43  3.000
 F7Q  H7   CB   CA   109.03  3.000
 F7Q  H6   CB   CA   108.79  3.000
 F7Q  CAG  CB   CA   115.37  3.000
 F7Q  CAK  CAG  CAJ  112.97  3.000
 F7Q  CAJ  CAG  OAA  109.28  3.000
 F7Q  CAK  CAG  OAA  109.54  3.000
 F7Q  CAJ  CAG  CB   111.92  3.000
 F7Q  OAA  CAG  CB   102.93  3.000
 F7Q  CAK  CAG  CB   109.71  3.000
 F7Q  OAB  OAA  CAG  109.56  3.000
 F7Q  H8   OAB  OAA  102.88  3.000
 F7Q  H9   CAJ  CAM  120.33  3.000
 F7Q  H9   CAJ  CAG  116.13  3.000
 F7Q  CAM  CAJ  CAG  123.54  3.000
 F7Q  H10  CAM  CAO  117.27  3.000
 F7Q  H10  CAM  CAJ  121.11  3.000
 F7Q  CAO  CAM  CAJ  121.61  3.000
 F7Q  CAL  CAO  OAE  121.61  3.000
 F7Q  OAE  CAO  CAM  121.75  3.000
 F7Q  CAL  CAO  CAM  116.64  3.000
 F7Q  H11  CAL  CAK  121.20  3.000
 F7Q  H11  CAL  CAO  117.32  3.000
 F7Q  CAK  CAL  CAO  121.48  3.000
 F7Q  H12  CAK  CAL  120.31  3.000
 F7Q  H12  CAK  CAG  116.03  3.000
 F7Q  CAL  CAK  CAG  123.66  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
 F7Q  Var_01  CAO  CAL  CAK  CAG   2.25  30.0  1
 F7Q  Var_02  CAO  CAM  CAJ  CAG   1.04  30.0  1
 F7Q  Var_03  CAL  CAO  CAM  CAJ  -2.42  30.0  1
 F7Q  Var_04  CAK  CAL  CAO  CAM   0.77  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
 F7Q  chir_01  CA   C    CB  N    positiv
 F7Q  chir_02  CAG  CAJ  CB  CAK  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
 F7Q  plan-1  CAM  0.020
 F7Q  plan-1  CAO  0.020
 F7Q  plan-1  OAE  0.020
 F7Q  plan-1  CAL  0.020
 F7Q  plan-2  C    0.020
 F7Q  plan-2  O    0.020
 F7Q  plan-2  CA   0.020
 F7Q  plan-2  OXT  0.020

