# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:16:01 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: (3R)-3-aminocyclohex-1-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCCC(=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
 GBC  GBC  '(3R)-3-aminocyclohex-1-ene-1-carboxylic acid'  ligand  20  10  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GBC
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
 GBC  C1    C  C      0  -0.102  -0.0909  -0.0634   0.5642
 GBC  C2    C  C1     0  -0.253   0.8326  -0.2634  -0.3774
 GBC  C3    C  CH1    0  -0.093   0.5577  -0.3555  -1.8511
 GBC  C4    C  CH2    0  -0.436  -0.8108   0.2248  -2.1782
 GBC  C5    C  CH2    0  -0.450  -1.8556  -0.3248  -1.2183
 GBC  C6    C  CH2    0  -0.474  -1.5471   0.0847   0.2188
 GBC  C7    C  C      0   0.384   0.3126   0.0565   2.0274
 GBC  N3    N  NH2    0  -0.805   1.6000   0.3614  -2.5835
 GBC  O1    O  O      0  -0.603   1.5131  -0.1215   2.3195
 GBC  O2    O  OC    -1  -0.603  -0.6051   0.3364   2.8264
 GBC  H2    H  H      0   0.226   1.8675  -0.3811  -0.0690
 GBC  H3    H  HCH1   0   0.202   0.5375  -1.4266  -2.1181
 GBC  H41   H  HCH2   0   0.210  -0.7610   1.3152  -2.0874
 GBC  H42   H  HCH2   0   0.226  -1.0751   0.0009  -3.2155
 GBC  H51   H  HCH2   0   0.228  -2.8533   0.0190  -1.4990
 GBC  H52   H  HCH2   0   0.213  -1.8734  -1.4172  -1.2940
 GBC  H61   H  HCH2   0   0.220  -1.8533   1.1244   0.3817
 GBC  H62   H  HCH2   0   0.228  -2.1525  -0.5024   0.9128
 GBC  HN31  H  HNH2   0   0.340   2.4993  -0.0624  -2.3859
 GBC  HN32  H  HNH2   0   0.341   1.4548   0.2239  -3.5772

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
 GBC  C1  C2    double  1.334  0.020  1.334
 GBC  C1  C6    single  1.504  0.020  1.504
 GBC  C1  C7    single  1.523  0.020  1.523
 GBC  C2  C3    single  1.502  0.020  1.502
 GBC  C2  H2    single  0.930  0.020  1.080
 GBC  C3  C4    single  1.522  0.020  1.522
 GBC  C3  N3    single  1.462  0.020  1.462
 GBC  C3  H3    single  0.970  0.020  1.090
 GBC  C4  C5    single  1.522  0.020  1.522
 GBC  C4  H41   single  0.970  0.020  1.090
 GBC  C4  H42   single  0.970  0.020  1.090
 GBC  C5  C6    single  1.526  0.020  1.526
 GBC  C5  H51   single  0.970  0.020  1.090
 GBC  C5  H52   single  0.970  0.020  1.090
 GBC  C6  H61   single  0.970  0.020  1.090
 GBC  C6  H62   single  0.970  0.020  1.090
 GBC  C7  O1    deloc   1.248  0.020  1.248
 GBC  C7  O2    deloc   1.249  0.020  1.249
 GBC  N3  HN31  single  0.890  0.020  1.040
 GBC  N3  HN32  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
 GBC  C7    C1  C6    118.01  3.000
 GBC  C7    C1  C2    120.44  3.000
 GBC  C6    C1  C2    121.53  3.000
 GBC  H2    C2  C3    116.51  3.000
 GBC  H2    C2  C1    118.38  3.000
 GBC  C3    C2  C1    125.10  3.000
 GBC  H3    C3  N3    111.56  3.000
 GBC  H3    C3  C4    107.55  3.000
 GBC  N3    C3  C4    110.27  3.000
 GBC  H3    C3  C2    107.47  3.000
 GBC  N3    C3  C2    109.33  3.000
 GBC  C4    C3  C2    110.62  3.000
 GBC  H42   C4  H41   107.06  3.000
 GBC  H42   C4  C5    111.01  3.000
 GBC  H41   C4  C5    109.79  3.000
 GBC  H42   C4  C3    110.06  3.000
 GBC  H41   C4  C3    108.71  3.000
 GBC  C5    C4  C3    110.13  3.000
 GBC  H52   C5  H51   106.34  3.000
 GBC  H52   C5  C6    109.64  3.000
 GBC  H51   C5  C6    110.02  3.000
 GBC  H52   C5  C4    109.14  3.000
 GBC  H51   C5  C4    110.58  3.000
 GBC  C6    C5  C4    111.00  3.000
 GBC  H62   C6  H61   105.11  3.000
 GBC  H62   C6  C5    110.00  3.000
 GBC  H61   C6  C5    109.76  3.000
 GBC  H62   C6  C1    109.75  3.000
 GBC  H61   C6  C1    109.26  3.000
 GBC  C5    C6  C1    112.69  3.000
 GBC  O2    C7  O1    126.09  3.000
 GBC  O2    C7  C1    115.96  3.000
 GBC  O1    C7  C1    117.94  3.000
 GBC  HN32  N3  HN31  105.16  3.000
 GBC  HN32  N3  C3    108.81  3.000
 GBC  HN31  N3  C3    109.27  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
 GBC  Var_01  C4  C5  C6  C1  -43.71  30.0  1
 GBC  Var_02  C5  C6  C1  C2   12.84  30.0  1
 GBC  Var_03  C6  C1  C2  C3    0.39  30.0  1
 GBC  Var_04  C6  C5  C4  C3   62.47  30.0  1
 GBC  Var_05  O1  C7  C1  C2   -4.41  30.0  2

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
 GBC  chir_01  C3  C2  C4  N3  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
 GBC  plan-1  C1  0.020
 GBC  plan-1  C7  0.020
 GBC  plan-1  O1  0.020
 GBC  plan-1  O2  0.020

