# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 03:03:52 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  44  20  .  2021-08-10  2022-11-17
;
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   0.524   3.6657  -0.5950  -0.0828
 G39  O1A   O  O     0  -0.442   3.8565  -1.7546  -0.3658
 G39  O1B   O  OH1   0  -0.593   4.6327   0.2138   0.3321
 G39  C2    C  C     0  -0.082   2.3481   0.0898  -0.1428
 G39  C3    C  CH2   0  -0.486   2.2528   1.5590   0.1487
 G39  C4    C  CH1   0  -0.081   0.9158   2.1494  -0.2853
 G39  C5    C  CH1   0  -0.105  -0.2234   1.2483   0.1894
 G39  N5    N  NH1   0  -0.640  -1.5083   1.8456  -0.0808
 G39  C10   C  C     0   0.524  -2.5143   1.9430   0.8101
 G39  O10   O  O     0  -0.500  -2.4100   1.6225   1.9845
 G39  C11   C  CH3   0  -0.786  -3.8053   2.4877   0.2503
 G39  C6    C  CH1   0   0.042  -0.1235  -0.1212  -0.4816
 G39  C7    C  C1    0  -0.213   1.2777  -0.6541  -0.4249
 G39  O7    O  O2    0  -0.497  -1.0261  -0.9784   0.1714
 G39  C8    C  CH1   0   0.045  -1.4242  -2.1619  -0.5110
 G39  C9    C  CH2   0  -0.429  -1.3996  -3.3120   0.4898
 G39  C81   C  CH2   0  -0.410  -2.8112  -1.9984  -1.1250
 G39  C82   C  CH3   0  -0.681  -2.9131  -0.9404  -2.2144
 G39  C91   C  CH3   0  -0.673  -0.0206  -3.6146   1.0570
 G39  N4    N  NH2   0  -0.799   0.7779   3.4715   0.2982
 G39  HO1   H  HOH1  0   0.485   5.4741  -0.2658   0.3613
 G39  H31   H  HCH2  0   0.254   2.3827   1.7354   1.2221
 G39  H32   H  HCH2  0   0.262   3.0583   2.1028  -0.3508
 G39  H4    H  HCH1  0   0.216   0.8954   2.1645  -1.3884
 G39  H5    H  HCH1  0   0.260  -0.1360   1.1196   1.2707
 G39  HN5   H  HNH1  0   0.398  -1.6999   2.1069  -1.0358
 G39  H111  H  HCH3  0   0.248  -3.7210   2.8545  -0.7711
 G39  H112  H  HCH3  0   0.267  -4.5616   1.7023   0.2683
 G39  H113  H  HCH3  0   0.267  -4.1653   3.2989   0.8815
 G39  H6    H  HCH1  0   0.234  -0.3954  -0.0041  -1.5428
 G39  H7    H  H     0   0.268   1.4070  -1.7113  -0.6281
 G39  H8    H  HCH1  0   0.204  -0.7110  -2.3920  -1.3176
 G39  H91   H  HCH2  0   0.219  -2.1017  -3.0910   1.3002
 G39  H92   H  HCH2  0   0.221  -1.7865  -4.2022  -0.0122
 G39  H811  H  HCH2  0   0.217  -3.0994  -2.9669  -1.5432
 G39  H812  H  HCH2  0   0.218  -3.5298  -1.7848  -0.3273
 G39  H821  H  HCH3  0   0.217  -2.7543   0.0642  -1.8236
 G39  H822  H  HCH3  0   0.220  -2.1826  -1.1138  -3.0071
 G39  H823  H  HCH3  0   0.236  -3.9023  -0.9533  -2.6735
 G39  H911  H  HCH3  0   0.216   0.6853  -3.8652   0.2619
 G39  H912  H  HCH3  0   0.224   0.3865  -2.7672   1.6087
 G39  H913  H  HCH3  0   0.233  -0.0588  -4.4640   1.7393
 G39  HN41  H  HNH2  0   0.350   1.5406   4.0556  -0.0232
 G39  HN42  H  HNH2  0   0.348  -0.0656   3.9145  -0.0441

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   double  1.209  0.020  1.209
 G39  C1   O1B   single  1.327  0.020  1.327
 G39  C1   C2    single  1.486  0.020  1.486
 G39  O1B  HO1   single  0.850  0.020  0.980
 G39  C2   C3    single  1.501  0.020  1.501
 G39  C2   C7    double  1.334  0.020  1.334
 G39  C3   C4    single  1.525  0.020  1.525
 G39  C3   H31   single  0.970  0.020  1.090
 G39  C3   H32   single  0.970  0.020  1.090
 G39  C4   C5    single  1.528  0.020  1.528
 G39  C4   N4    single  1.452  0.020  1.452
 G39  C4   H4    single  0.970  0.020  1.090
 G39  C5   N5    single  1.442  0.020  1.442
 G39  C5   C6    single  1.528  0.020  1.528
 G39  C5   H5    single  0.970  0.020  1.090
 G39  N5   C10   single  1.347  0.020  1.347
 G39  N5   HN5   single  0.860  0.020  1.020
 G39  C10  O10   double  1.222  0.020  1.222
 G39  C10  C11   single  1.509  0.020  1.509
 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  1.500  0.020  1.500
 G39  C6   O7    single  1.406  0.020  1.406
 G39  C6   H6    single  0.970  0.020  1.090
 G39  C7   H7    single  0.930  0.020  1.080
 G39  O7   C8    single  1.423  0.020  1.423
 G39  C8   C9    single  1.525  0.020  1.525
 G39  C8   C81   single  1.526  0.020  1.526
 G39  C8   H8    single  0.970  0.020  1.090
 G39  C9   C91   single  1.522  0.020  1.522
 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   112.20  3.000
 G39  C2    C1   O1A   124.93  3.000
 G39  O1B   C1   O1A   122.87  3.000
 G39  HO1   O1B  C1    109.91  3.000
 G39  C7    C2   C3    122.42  3.000
 G39  C7    C2   C1    117.58  3.000
 G39  C3    C2   C1    119.97  3.000
 G39  H32   C3   H31   106.28  3.000
 G39  H32   C3   C4    108.88  3.000
 G39  H31   C3   C4    108.70  3.000
 G39  H32   C3   C2    110.58  3.000
 G39  H31   C3   C2    109.90  3.000
 G39  C4    C3   C2    112.30  3.000
 G39  H4    C4   N4    112.81  3.000
 G39  H4    C4   C5    107.75  3.000
 G39  N4    C4   C5    109.96  3.000
 G39  H4    C4   C3    107.82  3.000
 G39  N4    C4   C3    108.76  3.000
 G39  C5    C4   C3    109.69  3.000
 G39  H5    C5   C6    108.89  3.000
 G39  H5    C5   N5    107.79  3.000
 G39  C6    C5   N5    110.31  3.000
 G39  H5    C5   C4    108.50  3.000
 G39  C6    C5   C4    110.07  3.000
 G39  N5    C5   C4    111.20  3.000
 G39  HN5   N5   C10   117.75  3.000
 G39  HN5   N5   C5    117.00  3.000
 G39  C10   N5   C5    124.83  3.000
 G39  C11   C10  O10   121.62  3.000
 G39  C11   C10  N5    114.81  3.000
 G39  O10   C10  N5    123.56  3.000
 G39  H113  C11  H112  107.32  3.000
 G39  H113  C11  H111  108.57  3.000
 G39  H112  C11  H111  108.18  3.000
 G39  H113  C11  C10   109.67  3.000
 G39  H112  C11  C10   109.10  3.000
 G39  H111  C11  C10   113.79  3.000
 G39  H6    C6   O7    110.72  3.000
 G39  H6    C6   C7    107.74  3.000
 G39  O7    C6   C7    111.45  3.000
 G39  H6    C6   C5    108.15  3.000
 G39  O7    C6   C5    107.49  3.000
 G39  C7    C6   C5    111.27  3.000
 G39  H7    C7   C6    116.79  3.000
 G39  H7    C7   C2    119.20  3.000
 G39  C6    C7   C2    124.02  3.000
 G39  C8    O7   C6    117.65  3.000
 G39  H8    C8   C81   108.45  3.000
 G39  H8    C8   C9    108.23  3.000
 G39  C81   C8   C9    111.08  3.000
 G39  H8    C8   O7    110.12  3.000
 G39  C81   C8   O7    110.99  3.000
 G39  C9    C8   O7    107.94  3.000
 G39  H92   C9   H91   106.11  3.000
 G39  H92   C9   C91   109.28  3.000
 G39  H91   C9   C91   110.21  3.000
 G39  H92   C9   C8    107.90  3.000
 G39  H91   C9   C8    108.86  3.000
 G39  C91   C9   C8    114.16  3.000
 G39  H812  C81  H811  106.17  3.000
 G39  H812  C81  C82   110.00  3.000
 G39  H811  C81  C82   108.92  3.000
 G39  H812  C81  C8    108.93  3.000
 G39  H811  C81  C8    107.37  3.000
 G39  C82   C81  C8    115.05  3.000
 G39  H823  C82  H822  107.42  3.000
 G39  H823  C82  H821  107.10  3.000
 G39  H822  C82  H821  108.02  3.000
 G39  H823  C82  C81   110.72  3.000
 G39  H822  C82  C81   111.37  3.000
 G39  H821  C82  C81   111.99  3.000
 G39  H913  C91  H912  107.58  3.000
 G39  H913  C91  H911  107.42  3.000
 G39  H912  C91  H911  107.79  3.000
 G39  H913  C91  C9    110.88  3.000
 G39  H912  C91  C9    111.87  3.000
 G39  H911  C91  C9    111.10  3.000
 G39  HN42  N4   HN41  105.53  3.000
 G39  HN42  N4   C4    109.98  3.000
 G39  HN41  N4   C4    109.03  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  HO1   O1B  C1   C2    180.00   0.0  0
 G39  CONST_04  HN5   N5   C10  O10   180.00   0.0  0
 G39  Var_01    C6    C7   C2   C3     -0.09  30.0  1
 G39  Var_02    C7    C2   C3   C4    -15.81  30.0  1
 G39  Var_03    C3    C2   C1   O1A  -176.04  30.0  2
 G39  Var_04    C9    C8   O7   C6    136.53  30.0  3
 G39  Var_05    C91   C9   C8   O7    -63.08  30.0  3
 G39  Var_06    C82   C81  C8   O7     64.22  30.0  3
 G39  Var_07    H111  C11  C10  N5     -7.59  30.0  3
 G39  Var_08    H911  C91  C9   C8    -58.75  30.0  3
 G39  Var_09    H821  C82  C81  C8    -66.38  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
 G39  plan-2  HO1  0.020

