# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 16:09:31 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (1S,2S,3R,6S)-6-amino-4-(hydroxymethyl)cyclohex-4-ene-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1C=C(CO)[C@@H](O)[C@H](O)[C@H]1O
#
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
 CMN  CMN  (1S,2S,3R,6S)-6-amino-4-(hydroxymethyl)cyclohex-4-ene-1,2,3-triol  ligand  25  12  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CMN
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
 CMN  C1    C  CH1   0  -0.187  -1.6152   0.1256  -0.6451
 CMN  C2    C  CH1   0   0.048  -0.4119   0.5753  -1.4785
 CMN  C3    C  CH1   0   0.044   0.8214  -0.1935  -1.0449
 CMN  C4    C  CH1   0  -0.064   1.1607   0.1883   0.3923
 CMN  C5    C  C     0   0.025  -0.0453   0.1516   1.3000
 CMN  C6    C  CH2   0  -0.183   0.2684   0.1834   2.7666
 CMN  C7    C  C1    0  -0.266  -1.2852   0.1508   0.8192
 CMN  N1    N  NH2   0  -0.790  -2.0236  -1.2242  -1.0269
 CMN  O2    O  OH1   0  -0.671  -0.6199   0.3730  -2.8555
 CMN  O3    O  OH1   0  -0.674   1.8909   0.1123  -1.9069
 CMN  O4    O  OH1   0  -0.673   2.1815  -0.6913   0.8360
 CMN  O6    O  OH1   0  -0.666  -0.8954   0.3862   3.5250
 CMN  H1    H  HCH1  0   0.224  -2.4204   0.8589  -0.8144
 CMN  H2    H  HCH1  0   0.209  -0.2461   1.6438  -1.2674
 CMN  H3    H  HCH1  0   0.207   0.5891  -1.2684  -1.0711
 CMN  H4    H  HCH1  0   0.236   1.5416   1.2204   0.3814
 CMN  H62   H  HCH2  0   0.219   0.7645  -0.7566   3.0402
 CMN  H61   H  HCH2  0   0.206   1.0090   0.9789   2.9450
 CMN  H7    H  H     0   0.251  -2.1296   0.1525   1.4988
 CMN  H12   H  HNH2  0   0.347  -2.7806  -1.5249  -0.4249
 CMN  H11   H  HNH2  0   0.342  -2.4095  -1.2056  -1.9628
 CMN  H2O1  H  HOH1  0   0.450  -1.3334   0.9553  -3.1357
 CMN  H3O1  H  HOH1  0   0.445   2.6632  -0.3663  -1.5872
 CMN  H4O1  H  HOH1  0   0.462   2.8279  -0.1942   1.3439
 CMN  H6    H  HOH1  0   0.460  -0.6650   0.2879   4.4529

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
 CMN  C1  C2    single  1.531  0.020  1.531
 CMN  C1  C7    single  1.501  0.020  1.501
 CMN  C1  N1    single  1.461  0.020  1.461
 CMN  C1  H1    single  0.970  0.020  1.090
 CMN  C2  C3    single  1.517  0.020  1.517
 CMN  C2  O2    single  1.407  0.020  1.407
 CMN  C2  H2    single  0.970  0.020  1.090
 CMN  C3  C4    single  1.525  0.020  1.525
 CMN  C3  O3    single  1.407  0.020  1.407
 CMN  C3  H3    single  0.970  0.020  1.090
 CMN  C4  C5    single  1.510  0.020  1.510
 CMN  C4  O4    single  1.419  0.020  1.419
 CMN  C4  H4    single  0.970  0.020  1.090
 CMN  C5  C6    single  1.500  0.020  1.500
 CMN  C5  C7    double  1.330  0.020  1.330
 CMN  C6  O6    single  1.404  0.020  1.404
 CMN  C6  H62   single  0.970  0.020  1.090
 CMN  C6  H61   single  0.970  0.020  1.090
 CMN  C7  H7    single  0.930  0.020  1.080
 CMN  N1  H12   single  0.890  0.020  1.040
 CMN  N1  H11   single  0.890  0.020  1.040
 CMN  O2  H2O1  single  0.850  0.020  0.980
 CMN  O3  H3O1  single  0.850  0.020  0.980
 CMN  O4  H4O1  single  0.850  0.020  0.980
 CMN  O6  H6    single  0.850  0.020  0.980

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
 CMN  H1    C1  N1   111.74  3.000
 CMN  H1    C1  C7   107.41  3.000
 CMN  N1    C1  C7   109.38  3.000
 CMN  H1    C1  C2   107.16  3.000
 CMN  N1    C1  C2   110.41  3.000
 CMN  C7    C1  C2   110.68  3.000
 CMN  H2    C2  O2   110.44  3.000
 CMN  H2    C2  C3   108.33  3.000
 CMN  O2    C2  C3   109.09  3.000
 CMN  H2    C2  C1   107.39  3.000
 CMN  O2    C2  C1   111.97  3.000
 CMN  C3    C2  C1   109.55  3.000
 CMN  H3    C3  O3   110.99  3.000
 CMN  H3    C3  C4   108.30  3.000
 CMN  O3    C3  C4   110.71  3.000
 CMN  H3    C3  C2   108.47  3.000
 CMN  O3    C3  C2   109.44  3.000
 CMN  C4    C3  C2   108.87  3.000
 CMN  H4    C4  O4   109.61  3.000
 CMN  H4    C4  C5   107.78  3.000
 CMN  O4    C4  C5   111.81  3.000
 CMN  H4    C4  C3   107.61  3.000
 CMN  O4    C4  C3   107.43  3.000
 CMN  C5    C4  C3   112.50  3.000
 CMN  C7    C5  C6   123.26  3.000
 CMN  C7    C5  C4   121.82  3.000
 CMN  C6    C5  C4   114.85  3.000
 CMN  H61   C6  H62  105.91  3.000
 CMN  H61   C6  O6   111.45  3.000
 CMN  H62   C6  O6   111.33  3.000
 CMN  H61   C6  C5   108.32  3.000
 CMN  H62   C6  C5   108.66  3.000
 CMN  O6    C6  C5   110.97  3.000
 CMN  H7    C7  C5   119.97  3.000
 CMN  H7    C7  C1   116.13  3.000
 CMN  C5    C7  C1   123.89  3.000
 CMN  H11   N1  H12  105.67  3.000
 CMN  H11   N1  C1   109.33  3.000
 CMN  H12   N1  C1   109.14  3.000
 CMN  H2O1  O2  C2   107.90  3.000
 CMN  H3O1  O3  C3   107.34  3.000
 CMN  H4O1  O4  C4   109.19  3.000
 CMN  H6    O6  C6   107.95  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
 CMN  Var_01  C4  C5  C7  C1    2.76  30.0  1
 CMN  Var_02  O6  C6  C5  C4  169.47  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
 CMN  chir_01  C1  C2  C7  N1  positiv
 CMN  chir_02  C2  O2  C1  C3  negativ
 CMN  chir_03  C3  O3  C2  C4  positiv
 CMN  chir_04  C4  O4  C3  C5  negativ

