# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 06:06:25 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (2S,3R,4S)-2-amino-1-cyclohexyl-6-methylheptane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](O)[C@H](O)[C@@H](N)CC1CCCCC1
#
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
 XAO  XAO  (2S,3R,4S)-2-amino-1-cyclohexyl-6-methylheptane-3,4-diol  ligand  46  17  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XAO
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
 XAO  C1    C  CH1   0  -0.138  -0.1399  -0.2841  -0.2782
 XAO  N     N  NH2   0  -0.833  -0.3097  -1.7370  -0.2794
 XAO  C2    C  CH1   0   0.047  -0.7427   0.2333   1.0439
 XAO  O2    O  OH1   0  -0.684  -1.9931  -0.3796   1.2450
 XAO  C3    C  CH1   0   0.007   0.1921   0.0069   2.2464
 XAO  O3    O  OH1   0  -0.667   1.4118   0.6990   2.0527
 XAO  C4    C  CH2   0  -0.435  -0.4757   0.3918   3.5630
 XAO  C5    C  CH1   0  -0.223   0.4169   0.2890   4.8017
 XAO  C6    C  CH3   0  -0.651  -0.3615   0.7361   6.0359
 XAO  C7    C  CH3   0  -0.663   0.9627  -1.1217   5.0029
 XAO  C7'   C  CH2   0  -0.402  -0.8518   0.3494  -1.4716
 XAO  C1'   C  CH1   0  -0.254  -0.3868  -0.1090  -2.8547
 XAO  C2'   C  CH2   0  -0.408  -1.1427   0.6578  -3.9414
 XAO  C6'   C  CH2   0  -0.423   1.1215   0.0389  -3.0567
 XAO  C3'   C  CH2   0  -0.431  -0.7185   0.2399  -5.3453
 XAO  C5'   C  CH2   0  -0.428   1.5510  -0.3796  -4.4601
 XAO  C4'   C  CH2   0  -0.429   0.7875   0.3868  -5.5344
 XAO  H1    H  HCH1  0   0.227   0.9149   0.0088  -0.3149
 XAO  HN1   H  HNH2  0   0.366  -0.2614  -2.1127  -1.2164
 XAO  HN2   H  HNH2  0   0.360   0.4347  -2.1842   0.2398
 XAO  H2    H  HCH1  0   0.208  -0.9059   1.3176   0.9564
 XAO  HO2   H  HOH1  0   0.435  -1.8759  -1.2616   0.8463
 XAO  H3    H  HCH1  0   0.217   0.4646  -1.0543   2.2885
 XAO  HO3   H  HOH1  0   0.440   1.2278   1.6442   2.0876
 XAO  H41   H  HCH2  0   0.221  -1.3530  -0.2442   3.7086
 XAO  H42   H  HCH2  0   0.213  -0.8561   1.4189   3.4829
 XAO  H5    H  HCH1  0   0.211   1.2652   0.9703   4.6796
 XAO  H61   H  HCH3  0   0.223   0.2673   0.7254   6.9282
 XAO  H62   H  HCH3  0   0.222  -0.7501   1.7499   5.9202
 XAO  H63   H  HCH3  0   0.211  -1.2124   0.0761   6.2230
 XAO  H71   H  HCH3  0   0.211   0.1487  -1.8476   5.0794
 XAO  H72   H  HCH3  0   0.228   1.6099  -1.4359   4.1834
 XAO  H73   H  HCH3  0   0.225   1.5488  -1.1862   5.9215
 XAO  H7'1  H  HCH2  0   0.222  -1.9298   0.1765  -1.3868
 XAO  H7'2  H  HCH2  0   0.218  -0.7095   1.4333  -1.4007
 XAO  H1'   H  HCH1  0   0.204  -0.6401  -1.1715  -2.9844
 XAO  H2'1  H  HCH2  0   0.223  -2.2197   0.5122  -3.8135
 XAO  H2'2  H  HCH2  0   0.205  -0.9600   1.7317  -3.8108
 XAO  H6'1  H  HCH2  0   0.205   1.4050   1.0844  -2.8817
 XAO  H6'2  H  HCH2  0   0.228   1.6677  -0.5544  -2.3185
 XAO  H3'1  H  HCH2  0   0.207  -1.0057  -0.8037  -5.5146
 XAO  H3'2  H  HCH2  0   0.224  -1.2546   0.8319  -6.0914
 XAO  H5'1  H  HCH2  0   0.207   1.3716  -1.4537  -4.5840
 XAO  H5'2  H  HCH2  0   0.225   2.6274  -0.2328  -4.5803
 XAO  H4'1  H  HCH2  0   0.224   1.0817   0.0410  -6.5284
 XAO  H4'2  H  HCH2  0   0.206   1.0565   1.4478  -5.4817

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
 XAO  C1   N     single  1.463  0.020  1.463
 XAO  C1   C2    single  1.542  0.020  1.542
 XAO  C1   C7'   single  1.527  0.020  1.527
 XAO  C1   H1    single  0.970  0.020  1.090
 XAO  N    HN1   single  0.890  0.020  1.040
 XAO  N    HN2   single  0.890  0.020  1.040
 XAO  C2   O2    single  1.407  0.020  1.407
 XAO  C2   C3    single  1.540  0.020  1.540
 XAO  C2   H2    single  0.970  0.020  1.090
 XAO  O2   HO2   single  0.850  0.020  0.980
 XAO  C3   O3    single  1.416  0.020  1.416
 XAO  C3   C4    single  1.526  0.020  1.526
 XAO  C3   H3    single  0.970  0.020  1.090
 XAO  O3   HO3   single  0.850  0.020  0.980
 XAO  C4   C5    single  1.530  0.020  1.530
 XAO  C4   H41   single  0.970  0.020  1.090
 XAO  C4   H42   single  0.970  0.020  1.090
 XAO  C5   C6    single  1.526  0.020  1.526
 XAO  C5   C7    single  1.526  0.020  1.526
 XAO  C5   H5    single  0.970  0.020  1.090
 XAO  C6   H61   single  0.970  0.020  1.090
 XAO  C6   H62   single  0.970  0.020  1.090
 XAO  C6   H63   single  0.970  0.020  1.090
 XAO  C7   H71   single  0.970  0.020  1.090
 XAO  C7   H72   single  0.970  0.020  1.090
 XAO  C7   H73   single  0.970  0.020  1.090
 XAO  C7'  C1'   single  1.529  0.020  1.529
 XAO  C7'  H7'1  single  0.970  0.020  1.090
 XAO  C7'  H7'2  single  0.970  0.020  1.090
 XAO  C1'  C2'   single  1.530  0.020  1.530
 XAO  C1'  C6'   single  1.529  0.020  1.529
 XAO  C1'  H1'   single  0.970  0.020  1.090
 XAO  C2'  C3'   single  1.525  0.020  1.525
 XAO  C2'  H2'1  single  0.970  0.020  1.090
 XAO  C2'  H2'2  single  0.970  0.020  1.090
 XAO  C6'  C5'   single  1.526  0.020  1.526
 XAO  C6'  H6'1  single  0.970  0.020  1.090
 XAO  C6'  H6'2  single  0.970  0.020  1.090
 XAO  C3'  C4'   single  1.525  0.020  1.525
 XAO  C3'  H3'1  single  0.970  0.020  1.090
 XAO  C3'  H3'2  single  0.970  0.020  1.090
 XAO  C5'  C4'   single  1.525  0.020  1.525
 XAO  C5'  H5'1  single  0.970  0.020  1.090
 XAO  C5'  H5'2  single  0.970  0.020  1.090
 XAO  C4'  H4'1  single  0.970  0.020  1.090
 XAO  C4'  H4'2  single  0.970  0.020  1.090

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
 XAO  H1    C1   C7'   108.17  3.000
 XAO  H1    C1   C2    108.39  3.000
 XAO  C7'   C1   C2    110.39  3.000
 XAO  H1    C1   N     112.17  3.000
 XAO  C7'   C1   N     110.93  3.000
 XAO  C2    C1   N     106.77  3.000
 XAO  HN2   N    HN1   106.04  3.000
 XAO  HN2   N    C1    110.67  3.000
 XAO  HN1   N    C1    111.37  3.000
 XAO  H2    C2   C3    107.29  3.000
 XAO  H2    C2   O2    107.99  3.000
 XAO  C3    C2   O2    111.34  3.000
 XAO  H2    C2   C1    108.69  3.000
 XAO  C3    C2   C1    112.51  3.000
 XAO  O2    C2   C1    108.89  3.000
 XAO  HO2   O2   C2    103.23  3.000
 XAO  H3    C3   C4    108.65  3.000
 XAO  H3    C3   O3    105.33  3.000
 XAO  C4    C3   O3    111.83  3.000
 XAO  H3    C3   C2    108.85  3.000
 XAO  C4    C3   C2    111.78  3.000
 XAO  O3    C3   C2    110.13  3.000
 XAO  HO3   O3   C3    108.07  3.000
 XAO  H42   C4   H41   106.01  3.000
 XAO  H42   C4   C5    108.90  3.000
 XAO  H41   C4   C5    108.74  3.000
 XAO  H42   C4   C3    108.94  3.000
 XAO  H41   C4   C3    108.63  3.000
 XAO  C5    C4   C3    115.23  3.000
 XAO  H5    C5   C7    108.22  3.000
 XAO  H5    C5   C6    107.65  3.000
 XAO  C7    C5   C6    110.28  3.000
 XAO  H5    C5   C4    108.66  3.000
 XAO  C7    C5   C4    112.17  3.000
 XAO  C6    C5   C4    109.72  3.000
 XAO  H63   C6   H62   107.56  3.000
 XAO  H63   C6   H61   107.61  3.000
 XAO  H62   C6   H61   107.50  3.000
 XAO  H63   C6   C5    111.02  3.000
 XAO  H62   C6   C5    111.58  3.000
 XAO  H61   C6   C5    111.37  3.000
 XAO  H73   C7   H72   107.26  3.000
 XAO  H73   C7   H71   107.55  3.000
 XAO  H72   C7   H71   107.65  3.000
 XAO  H73   C7   C5    110.96  3.000
 XAO  H72   C7   C5    112.31  3.000
 XAO  H71   C7   C5    110.90  3.000
 XAO  H7'2  C7'  H7'1  106.21  3.000
 XAO  H7'2  C7'  C1'   108.40  3.000
 XAO  H7'1  C7'  C1'   108.78  3.000
 XAO  H7'2  C7'  C1    107.41  3.000
 XAO  H7'1  C7'  C1    109.45  3.000
 XAO  C1'   C7'  C1    116.14  3.000
 XAO  H1'   C1'  C6'   107.77  3.000
 XAO  H1'   C1'  C2'   106.65  3.000
 XAO  C6'   C1'  C2'   110.19  3.000
 XAO  H1'   C1'  C7'   109.04  3.000
 XAO  C6'   C1'  C7'   112.98  3.000
 XAO  C2'   C1'  C7'   109.99  3.000
 XAO  H2'2  C2'  H2'1  106.27  3.000
 XAO  H2'2  C2'  C3'   109.36  3.000
 XAO  H2'1  C2'  C3'   110.18  3.000
 XAO  H2'2  C2'  C1'   108.89  3.000
 XAO  H2'1  C2'  C1'   109.67  3.000
 XAO  C3'   C2'  C1'   112.28  3.000
 XAO  H6'2  C6'  H6'1  106.28  3.000
 XAO  H6'2  C6'  C5'   109.36  3.000
 XAO  H6'1  C6'  C5'   109.58  3.000
 XAO  H6'2  C6'  C1'   110.55  3.000
 XAO  H6'1  C6'  C1'   109.03  3.000
 XAO  C5'   C6'  C1'   111.88  3.000
 XAO  H3'2  C3'  H3'1  106.37  3.000
 XAO  H3'2  C3'  C4'   110.34  3.000
 XAO  H3'1  C3'  C4'   109.36  3.000
 XAO  H3'2  C3'  C2'   110.10  3.000
 XAO  H3'1  C3'  C2'   109.29  3.000
 XAO  C4'   C3'  C2'   111.25  3.000
 XAO  H5'2  C5'  H5'1  106.28  3.000
 XAO  H5'2  C5'  C4'   110.38  3.000
 XAO  H5'1  C5'  C4'   109.33  3.000
 XAO  H5'2  C5'  C6'   109.97  3.000
 XAO  H5'1  C5'  C6'   109.07  3.000
 XAO  C4'   C5'  C6'   111.67  3.000
 XAO  H4'2  C4'  H4'1  106.50  3.000
 XAO  H4'2  C4'  C5'   109.26  3.000
 XAO  H4'1  C4'  C5'   110.31  3.000
 XAO  H4'2  C4'  C3'   109.26  3.000
 XAO  H4'1  C4'  C3'   110.38  3.000
 XAO  C5'   C4'  C3'   111.02  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
 XAO  Var_01  C4'  C3'  C2'  C1'   -55.45  30.0  1
 XAO  Var_02  C4'  C5'  C6'  C1'    55.39  30.0  1
 XAO  Var_03  C5'  C4'  C3'  C2'    54.78  30.0  1
 XAO  Var_04  C3'  C4'  C5'  C6'   -54.97  30.0  1
 XAO  Var_05  C6   C5   C4   C3    178.50  30.0  3
 XAO  Var_06  H61  C6   C5   C4   -176.89  30.0  3
 XAO  Var_07  H71  C7   C5   C4    -57.28  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
 XAO  chir_01  C1   N    C2   C7'  positiv
 XAO  chir_02  C2   O2   C1   C3   positiv
 XAO  chir_03  C3   O3   C2   C4   positiv
 XAO  chir_04  C1'  C6'  C2'  C7'  positiv

