# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 03:05:23 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(CC)O[C@@H]1C=C(C[C@H](N)[C@H]1NC(C)=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
 G39  G39  '(3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid'  ligand  43  20  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G39
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
 G39  C1    C  C      0   0.389   3.7385  -0.5930  -0.0740
 G39  O1A   O  O      0  -0.596   3.8356  -1.7841  -0.4288
 G39  O1B   O  OC    -1  -0.600   4.6632   0.1343   0.3432
 G39  C2    C  C      0  -0.107   2.3621   0.0558  -0.1374
 G39  C3    C  CH2    0  -0.486   2.2564   1.5177   0.1794
 G39  C4    C  CH1    0  -0.078   0.9298   2.1269  -0.2545
 G39  C5    C  CH1    0  -0.101  -0.2179   1.2277   0.2002
 G39  N5    N  NH1    0  -0.637  -1.4990   1.8349  -0.0774
 G39  C10   C  C      0   0.522  -2.5113   1.9416   0.8022
 G39  O10   O  O      0  -0.504  -2.4228   1.6266   1.9805
 G39  C11   C  CH3    0  -0.785  -3.7946   2.4924   0.2285
 G39  C6    C  CH1    0   0.052  -0.1183  -0.1384  -0.4761
 G39  C7    C  C1     0  -0.259   1.2839  -0.6712  -0.4284
 G39  O7    O  O2     0  -0.502  -1.0318  -0.9914   0.1799
 G39  C8    C  CH1    0   0.055  -1.4211  -2.1778  -0.4955
 G39  C9    C  CH2    0  -0.430  -1.3972  -3.3245   0.5102
 G39  C81   C  CH2    0  -0.410  -2.8081  -2.0258  -1.1151
 G39  C82   C  CH3    0  -0.679  -2.9137  -0.9697  -2.2060
 G39  C91   C  CH3    0  -0.668  -0.0178  -3.6261   1.0767
 G39  N4    N  NH2    0  -0.800   0.7915   3.4462   0.3400
 G39  H31   H  HCH2   0   0.229   2.3764   1.6744   1.2578
 G39  H32   H  HCH2   0   0.239   3.0779   2.0634  -0.2913
 G39  H4    H  HCH1   0   0.202   0.9149   2.1562  -1.3580
 G39  H5    H  HCH1   0   0.250  -0.1414   1.0934   1.2815
 G39  HN5   H  HNH1   0   0.395  -1.6826   2.0910  -1.0354
 G39  H111  H  HCH3   0   0.246  -3.6980   2.8580  -0.7924
 G39  H112  H  HCH3   0   0.265  -4.5553   1.7110   0.2394
 G39  H113  H  HCH3   0   0.265  -4.1569   3.3063   0.8551
 G39  H6    H  HCH1   0   0.212  -0.4098  -0.0155  -1.5319
 G39  H7    H  H      0   0.238   1.4179  -1.7235  -0.6532
 G39  H8    H  HCH1   0   0.199  -0.7051  -2.4108  -1.2988
 G39  H91   H  HCH2   0   0.215  -2.0973  -3.0974   1.3209
 G39  H92   H  HCH2   0   0.217  -1.7873  -4.2172   0.0147
 G39  H811  H  HCH2   0   0.214  -3.0904  -2.9967  -1.5322
 G39  H812  H  HCH2   0   0.215  -3.5304  -1.8141  -0.3200
 G39  H821  H  HCH3   0   0.217  -2.7547   0.0348  -1.8154
 G39  H822  H  HCH3   0   0.218  -2.1832  -1.1426  -2.9989
 G39  H823  H  HCH3   0   0.233  -3.9034  -0.9844  -2.6642
 G39  H911  H  HCH3   0   0.215   0.6827  -3.8933   0.2827
 G39  H912  H  HCH3   0   0.224   0.3974  -2.7695   1.6067
 G39  H913  H  HCH3   0   0.228  -0.0580  -4.4625   1.7751
 G39  HN41  H  HNH2   0   0.346   1.5696   4.0225   0.0426
 G39  HN42  H  HNH2   0   0.343  -0.0372   3.9035  -0.0196

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
 G39  C1   O1A   deloc   1.247  0.020  1.247
 G39  C1   O1B   deloc   1.248  0.020  1.248
 G39  C1   C2    single  1.523  0.020  1.523
 G39  C2   C3    single  1.500  0.020  1.500
 G39  C2   C7    double  1.333  0.020  1.333
 G39  C3   C4    single  1.523  0.020  1.523
 G39  C3   H31   single  0.970  0.020  1.090
 G39  C3   H32   single  0.970  0.020  1.090
 G39  C4   C5    single  1.527  0.020  1.527
 G39  C4   N4    single  1.454  0.020  1.454
 G39  C4   H4    single  0.970  0.020  1.090
 G39  C5   N5    single  1.445  0.020  1.445
 G39  C5   C6    single  1.528  0.020  1.528
 G39  C5   H5    single  0.970  0.020  1.090
 G39  N5   C10   single  1.345  0.020  1.345
 G39  N5   HN5   single  0.860  0.020  1.020
 G39  C10  O10   double  1.223  0.020  1.223
 G39  C10  C11   single  1.510  0.020  1.510
 G39  C11  H111  single  0.970  0.020  1.090
 G39  C11  H112  single  0.970  0.020  1.090
 G39  C11  H113  single  0.970  0.020  1.090
 G39  C6   C7    single  1.501  0.020  1.501
 G39  C6   O7    single  1.411  0.020  1.411
 G39  C6   H6    single  0.970  0.020  1.090
 G39  C7   H7    single  0.930  0.020  1.080
 G39  O7   C8    single  1.420  0.020  1.420
 G39  C8   C9    single  1.525  0.020  1.525
 G39  C8   C81   single  1.527  0.020  1.527
 G39  C8   H8    single  0.970  0.020  1.090
 G39  C9   C91   single  1.521  0.020  1.521
 G39  C9   H91   single  0.970  0.020  1.090
 G39  C9   H92   single  0.970  0.020  1.090
 G39  C81  C82   single  1.522  0.020  1.522
 G39  C81  H811  single  0.970  0.020  1.090
 G39  C81  H812  single  0.970  0.020  1.090
 G39  C82  H821  single  0.970  0.020  1.090
 G39  C82  H822  single  0.970  0.020  1.090
 G39  C82  H823  single  0.970  0.020  1.090
 G39  C91  H911  single  0.970  0.020  1.090
 G39  C91  H912  single  0.970  0.020  1.090
 G39  C91  H913  single  0.970  0.020  1.090
 G39  N4   HN41  single  0.890  0.020  1.040
 G39  N4   HN42  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
 G39  C2    C1   O1B   115.79  3.000
 G39  C2    C1   O1A   117.75  3.000
 G39  O1B   C1   O1A   126.46  3.000
 G39  C7    C2   C3    121.39  3.000
 G39  C7    C2   C1    120.52  3.000
 G39  C3    C2   C1    118.05  3.000
 G39  H32   C3   H31   105.66  3.000
 G39  H32   C3   C4    109.41  3.000
 G39  H31   C3   C4    108.57  3.000
 G39  H32   C3   C2    110.05  3.000
 G39  H31   C3   C2    109.85  3.000
 G39  C4    C3   C2    113.03  3.000
 G39  H4    C4   N4    112.55  3.000
 G39  H4    C4   C5    107.64  3.000
 G39  N4    C4   C5    109.94  3.000
 G39  H4    C4   C3    107.89  3.000
 G39  N4    C4   C3    109.23  3.000
 G39  C5    C4   C3    109.52  3.000
 G39  H5    C5   C6    108.89  3.000
 G39  H5    C5   N5    107.70  3.000
 G39  C6    C5   N5    110.41  3.000
 G39  H5    C5   C4    108.33  3.000
 G39  C6    C5   C4    110.23  3.000
 G39  N5    C5   C4    111.20  3.000
 G39  HN5   N5   C10   117.64  3.000
 G39  HN5   N5   C5    116.79  3.000
 G39  C10   N5   C5    125.10  3.000
 G39  C11   C10  O10   121.44  3.000
 G39  C11   C10  N5    114.84  3.000
 G39  O10   C10  N5    123.72  3.000
 G39  H113  C11  H112  107.31  3.000
 G39  H113  C11  H111  108.55  3.000
 G39  H112  C11  H111  108.17  3.000
 G39  H113  C11  C10   109.68  3.000
 G39  H112  C11  C10   109.13  3.000
 G39  H111  C11  C10   113.80  3.000
 G39  H6    C6   O7    109.97  3.000
 G39  H6    C6   C7    108.49  3.000
 G39  O7    C6   C7    112.05  3.000
 G39  H6    C6   C5    107.88  3.000
 G39  O7    C6   C5    107.00  3.000
 G39  C7    C6   C5    111.36  3.000
 G39  H7    C7   C6    116.96  3.000
 G39  H7    C7   C2    118.34  3.000
 G39  C6    C7   C2    124.70  3.000
 G39  C8    O7   C6    117.48  3.000
 G39  H8    C8   C81   108.41  3.000
 G39  H8    C8   C9    108.17  3.000
 G39  C81   C8   C9    110.89  3.000
 G39  H8    C8   O7    110.22  3.000
 G39  C81   C8   O7    111.04  3.000
 G39  C9    C8   O7    108.08  3.000
 G39  H92   C9   H91   106.08  3.000
 G39  H92   C9   C91   109.30  3.000
 G39  H91   C9   C91   110.19  3.000
 G39  H92   C9   C8    108.03  3.000
 G39  H91   C9   C8    108.80  3.000
 G39  C91   C9   C8    114.12  3.000
 G39  H812  C81  H811  106.16  3.000
 G39  H812  C81  C82   109.91  3.000
 G39  H811  C81  C82   108.94  3.000
 G39  H812  C81  C8    108.90  3.000
 G39  H811  C81  C8    107.51  3.000
 G39  C82   C81  C8    115.03  3.000
 G39  H823  C82  H822  107.45  3.000
 G39  H823  C82  H821  107.18  3.000
 G39  H822  C82  H821  107.98  3.000
 G39  H823  C82  C81   110.78  3.000
 G39  H822  C82  C81   111.36  3.000
 G39  H821  C82  C81   111.88  3.000
 G39  H913  C91  H912  107.79  3.000
 G39  H913  C91  H911  107.56  3.000
 G39  H912  C91  H911  107.55  3.000
 G39  H913  C91  C9    110.93  3.000
 G39  H912  C91  C9    111.76  3.000
 G39  H911  C91  C9    111.07  3.000
 G39  HN42  N4   HN41  105.52  3.000
 G39  HN42  N4   C4    110.03  3.000
 G39  HN41  N4   C4    108.85  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
 G39  CONST_01  O10   C10  N5   C5      0.00   0.0  0
 G39  CONST_02  C11   C10  N5   C5    180.00   0.0  0
 G39  CONST_03  HN5   N5   C10  O10   180.00   0.0  0
 G39  Var_01    C6    C7   C2   C3      0.10  30.0  1
 G39  Var_02    C7    C2   C3   C4    -16.66  30.0  1
 G39  Var_03    C3    C2   C1   O1A  -175.07  30.0  2
 G39  Var_04    C9    C8   O7   C6    136.07  30.0  3
 G39  Var_05    C91   C9   C8   O7    -63.52  30.0  3
 G39  Var_06    C82   C81  C8   O7     63.92  30.0  3
 G39  Var_07    H111  C11  C10  N5     -7.77  30.0  3
 G39  Var_08    H911  C91  C9   C8    -59.50  30.0  3
 G39  Var_09    H821  C82  C81  C8    -65.85  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
 G39  chir_01  C4  C3  C5  N4  negativ
 G39  chir_02  C5  N5  C6  C4  negativ
 G39  chir_03  C6  O7  C7  C5  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
 G39  plan-1  C5   0.020
 G39  plan-1  N5   0.020
 G39  plan-1  C10  0.020
 G39  plan-1  O10  0.020
 G39  plan-1  C11  0.020
 G39  plan-1  HN5  0.020
 G39  plan-2  C1   0.020
 G39  plan-2  O1A  0.020
 G39  plan-2  O1B  0.020
 G39  plan-2  C2   0.020

