# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 08:58:56 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
 CYL  CYL  (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_CYL
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
 CYL  C1    C  CH1   0  -0.184  -1.6204   0.1823  -0.6802
 CYL  C2    C  CH1   0   0.049  -0.4106   0.5895  -1.5281
 CYL  C3    C  CH1   0   0.043   0.8179  -0.1793  -1.0825
 CYL  C4    C  CH1   0  -0.061   1.1599   0.2219   0.3486
 CYL  C5    C  C     0   0.020  -0.0417   0.1691   1.2609
 CYL  C6    C  CH2   0  -0.184   0.2735   0.1702   2.7276
 CYL  N1    N  NH2   0  -0.791  -2.0839  -1.1484  -1.0643
 CYL  O2    O  OH1   0  -0.671  -0.6280   0.3517  -2.8983
 CYL  O3    O  OH1   0  -0.674   1.8880   0.1137  -1.9483
 CYL  O4    O  OH1   0  -0.673   2.2013  -0.6345   0.7881
 CYL  C7    C  C1    0  -0.264  -1.2820   0.1832   0.7819
 CYL  O6    O  OH1   0  -0.666  -0.8925   0.3294   3.4929
 CYL  H1    H  HCH1  0   0.223  -2.3949   0.9507  -0.8389
 CYL  H2    H  HCH1  0   0.210  -0.2300   1.6615  -1.3509
 CYL  H3    H  HCH1  0   0.206   0.5831  -1.2543  -1.0958
 CYL  H4    H  HCH1  0   0.236   1.5217   1.2607   0.3245
 CYL  H61   H  HCH2  0   0.221   0.7914  -0.7643   2.9775
 CYL  H62   H  HCH2  0   0.205   0.9961   0.9782   2.9249
 CYL  HN11  H  HNH2  0   0.346  -2.8464  -1.4236  -0.4570
 CYL  HN12  H  HNH2  0   0.342  -2.4756  -1.1126  -1.9971
 CYL  HO2   H  HOH1  0   0.451  -1.3112   0.9589  -3.1999
 CYL  HO3   H  HOH1  0   0.445   2.6663  -0.3392  -1.6060
 CYL  HO4   H  HOH1  0   0.462   2.8152  -0.1327   1.3310
 CYL  H7    H  H     0   0.251  -2.1246   0.1694   1.4638
 CYL  HO6   H  HOH1  0   0.460  -0.6748   0.1397   4.4094

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
 CYL  C1  C2    single  1.532  0.020  1.532
 CYL  C1  N1    single  1.461  0.020  1.461
 CYL  C1  C7    single  1.501  0.020  1.501
 CYL  C1  H1    single  0.970  0.020  1.090
 CYL  C2  C3    single  1.516  0.020  1.516
 CYL  C2  O2    single  1.408  0.020  1.408
 CYL  C2  H2    single  0.970  0.020  1.090
 CYL  C3  C4    single  1.525  0.020  1.525
 CYL  C3  O3    single  1.407  0.020  1.407
 CYL  C3  H3    single  0.970  0.020  1.090
 CYL  C4  C5    single  1.510  0.020  1.510
 CYL  C4  O4    single  1.418  0.020  1.418
 CYL  C4  H4    single  0.970  0.020  1.090
 CYL  C5  C6    single  1.500  0.020  1.500
 CYL  C5  C7    double  1.330  0.020  1.330
 CYL  C6  O6    single  1.404  0.020  1.404
 CYL  C6  H61   single  0.970  0.020  1.090
 CYL  C6  H62   single  0.970  0.020  1.090
 CYL  N1  HN11  single  0.890  0.020  1.040
 CYL  N1  HN12  single  0.890  0.020  1.040
 CYL  O2  HO2   single  0.850  0.020  0.980
 CYL  O3  HO3   single  0.850  0.020  0.980
 CYL  O4  HO4   single  0.850  0.020  0.980
 CYL  C7  H7    single  0.930  0.020  1.080
 CYL  O6  HO6   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
 CYL  H1    C1  C7    107.35  3.000
 CYL  H1    C1  N1    111.97  3.000
 CYL  C7    C1  N1    109.17  3.000
 CYL  H1    C1  C2    106.85  3.000
 CYL  C7    C1  C2    111.16  3.000
 CYL  N1    C1  C2    110.31  3.000
 CYL  H2    C2  O2    110.27  3.000
 CYL  H2    C2  C3    108.26  3.000
 CYL  O2    C2  C3    109.00  3.000
 CYL  H2    C2  C1    107.40  3.000
 CYL  O2    C2  C1    111.83  3.000
 CYL  C3    C2  C1    110.02  3.000
 CYL  H3    C3  O3    110.99  3.000
 CYL  H3    C3  C4    108.43  3.000
 CYL  O3    C3  C4    110.61  3.000
 CYL  H3    C3  C2    108.59  3.000
 CYL  O3    C3  C2    109.25  3.000
 CYL  C4    C3  C2    108.91  3.000
 CYL  H4    C4  O4    109.60  3.000
 CYL  H4    C4  C5    107.94  3.000
 CYL  O4    C4  C5    112.09  3.000
 CYL  H4    C4  C3    107.55  3.000
 CYL  O4    C4  C3    107.25  3.000
 CYL  C5    C4  C3    112.30  3.000
 CYL  C7    C5  C6    123.24  3.000
 CYL  C7    C5  C4    121.63  3.000
 CYL  C6    C5  C4    115.06  3.000
 CYL  H62   C6  H61   105.91  3.000
 CYL  H62   C6  O6    111.35  3.000
 CYL  H61   C6  O6    111.38  3.000
 CYL  H62   C6  C5    108.26  3.000
 CYL  H61   C6  C5    108.73  3.000
 CYL  O6    C6  C5    111.01  3.000
 CYL  HN12  N1  HN11  105.71  3.000
 CYL  HN12  N1  C1    109.45  3.000
 CYL  HN11  N1  C1    109.19  3.000
 CYL  HO2   O2  C2    107.94  3.000
 CYL  HO3   O3  C3    107.33  3.000
 CYL  HO4   O4  C4    109.20  3.000
 CYL  H7    C7  C5    119.89  3.000
 CYL  H7    C7  C1    115.95  3.000
 CYL  C5    C7  C1    124.15  3.000
 CYL  HO6   O6  C6    108.02  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
 CYL  Var_01  C4  C5  C7  C1    3.19  30.0  1
 CYL  Var_02  O6  C6  C5  C4  170.81  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
 CYL  chir_01  C1  C2  N1  C7  negativ
 CYL  chir_02  C2  O2  C1  C3  negativ
 CYL  chir_03  C3  O3  C2  C4  positiv
 CYL  chir_04  C4  O4  C3  C5  negativ

