# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 19:09:13 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (2S)-2-({(1S,2S,4S)-4-chloro-2-[(R)-hydroxy(methoxy)methyl]cyclohexyl}amino)ethane-1,1,2-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H](O)[C@H]1C[C@@H](Cl)CC[C@@H]1N[C@@H](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
 RB2  RB2  (2S)-2-({(1S,2S,4S)-4-chloro-2-[(R)-hydroxy(methoxy)methyl]cyclohexyl}amino)ethane-1,1,2-triol  ligand  37  17  .  2021-08-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RB2
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
 RB2  O17   O   OH1   0  -0.633   3.8051  -0.2848   1.7342
 RB2  C15   C   CH1   0   0.265   3.8536  -0.2747   0.3418
 RB2  O16   O   OH1   0  -0.640   4.8543  -1.1020  -0.1648
 RB2  C13   C   CH1   0   0.084   2.5374  -0.7364  -0.3042
 RB2  O14   O   OH1   0  -0.631   2.6146  -0.6407  -1.7099
 RB2  N12   N   NH1   0  -0.624   1.4459  -0.0314   0.2984
 RB2  C6    C   CH1   0   0.001   0.1094  -0.2684  -0.2334
 RB2  C5    C   CH1   0  -0.307  -0.9361   0.4320   0.6535
 RB2  C8    C   CH1   0   0.301  -0.6464   1.9219   0.8734
 RB2  O10   O   OH1   0  -0.643  -1.5638   2.5399   1.7261
 RB2  O9    O   O2    0  -0.485  -0.5732   2.5391  -0.3739
 RB2  C11   C   CH3   0  -0.378  -0.0586   3.8536  -0.3502
 RB2  C4    C   CH2   0  -0.413  -2.3422   0.1918   0.0930
 RB2  C3    C   CH1   0  -0.278  -2.6293  -1.2952   0.0325
 RB2  CL    CL  CL    0  -0.131  -4.2897  -1.5578  -0.6541
 RB2  C2    C   CH2   0  -0.400  -1.6100  -2.0317  -0.8068
 RB2  C1    C   CH2   0  -0.473  -0.2025  -1.7640  -0.2838
 RB2  H17   H   HOH1  0   0.429   3.4193  -1.1156   2.0363
 RB2  H15   H   HCH1  0   0.174   4.0372   0.7757   0.0728
 RB2  H16   H   HOH1  0   0.439   5.7118  -0.7271   0.0620
 RB2  H13   H   HCH1  0   0.226   2.4237  -1.8069  -0.1057
 RB2  H14   H   HOH1  0   0.414   2.6989   0.2878  -1.9561
 RB2  H12   H   HNH1  0   0.326   1.6480   0.9611   0.3005
 RB2  H6    H   HCH1  0   0.210   0.0015   0.1184  -1.2571
 RB2  H5    H   HCH1  0   0.236  -0.8767  -0.0272   1.6481
 RB2  H8    H   HCH1  0   0.195   0.3087   2.0280   1.4069
 RB2  H10   H   HOH1  0   0.429  -2.4487   2.4931   1.3458
 RB2  H111  H   HCH3  0   0.214  -0.7421   4.5629   0.1231
 RB2  H112  H   HCH3  0   0.188   0.9020   3.9002   0.1753
 RB2  H113  H   HCH3  0   0.222   0.0984   4.1625  -1.3823
 RB2  H41   H   HCH2  0   0.227  -3.1007   0.6624   0.7221
 RB2  H42   H   HCH2  0   0.246  -2.4354   0.6187  -0.9088
 RB2  H3    H   HCH1  0   0.261  -2.6695  -1.7132   1.0399
 RB2  H21   H   HCH2  0   0.249  -1.8128  -3.1037  -0.8004
 RB2  H22   H   HCH2  0   0.231  -1.6878  -1.6942  -1.8442
 RB2  H11   H   HCH2  0   0.216  -0.0776  -2.1943   0.7154
 RB2  H12A  H   HCH2  0   0.253   0.4978  -2.2820  -0.9406

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
 RB2  O17  C15   single  1.393  0.020  1.393
 RB2  O17  H17   single  0.850  0.020  0.980
 RB2  C15  O16   single  1.394  0.020  1.394
 RB2  C15  C13   single  1.537  0.020  1.537
 RB2  C15  H15   single  0.970  0.020  1.090
 RB2  O16  H16   single  0.850  0.020  0.980
 RB2  C13  O14   single  1.411  0.020  1.411
 RB2  C13  N12   single  1.432  0.020  1.432
 RB2  C13  H13   single  0.970  0.020  1.090
 RB2  O14  H14   single  0.850  0.020  0.980
 RB2  N12  C6    single  1.458  0.020  1.458
 RB2  N12  H12   single  0.890  0.020  1.040
 RB2  C6   C5    single  1.540  0.020  1.540
 RB2  C6   C1    single  1.529  0.020  1.529
 RB2  C6   H6    single  0.970  0.020  1.090
 RB2  C5   C8    single  1.534  0.020  1.534
 RB2  C5   C4    single  1.533  0.020  1.533
 RB2  C5   H5    single  0.970  0.020  1.090
 RB2  C8   O10   single  1.397  0.020  1.397
 RB2  C8   O9    single  1.394  0.020  1.394
 RB2  C8   H8    single  0.970  0.020  1.090
 RB2  O10  H10   single  0.850  0.020  0.980
 RB2  O9   C11   single  1.412  0.020  1.412
 RB2  C11  H111  single  0.970  0.020  1.090
 RB2  C11  H112  single  0.970  0.020  1.090
 RB2  C11  H113  single  0.970  0.020  1.090
 RB2  C4   C3    single  1.516  0.020  1.516
 RB2  C4   H41   single  0.970  0.020  1.090
 RB2  C4   H42   single  0.970  0.020  1.090
 RB2  C3   CL    single  1.816  0.020  1.816
 RB2  C3   C2    single  1.512  0.020  1.512
 RB2  C3   H3    single  0.970  0.020  1.090
 RB2  C2   C1    single  1.525  0.020  1.525
 RB2  C2   H21   single  0.970  0.020  1.090
 RB2  C2   H22   single  0.970  0.020  1.090
 RB2  C1   H11   single  0.970  0.020  1.090
 RB2  C1   H12A  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
 RB2  H17   O17  C15   109.46  3.000
 RB2  H15   C15  C13   109.09  3.000
 RB2  H15   C15  O16   110.99  3.000
 RB2  C13   C15  O16   106.49  3.000
 RB2  H15   C15  O17   104.90  3.000
 RB2  C13   C15  O17   112.83  3.000
 RB2  O16   C15  O17   112.58  3.000
 RB2  H16   O16  C15   108.83  3.000
 RB2  H13   C13  N12   109.02  3.000
 RB2  H13   C13  O14   104.64  3.000
 RB2  N12   C13  O14   115.30  3.000
 RB2  H13   C13  C15   107.85  3.000
 RB2  N12   C13  C15   109.14  3.000
 RB2  O14   C13  C15   110.57  3.000
 RB2  H14   O14  C13   108.93  3.000
 RB2  H12   N12  C6    110.06  3.000
 RB2  H12   N12  C13   109.34  3.000
 RB2  C6    N12  C13   117.72  3.000
 RB2  H6    C6   C1    107.07  3.000
 RB2  H6    C6   C5    108.04  3.000
 RB2  C1    C6   C5    109.00  3.000
 RB2  H6    C6   N12   111.86  3.000
 RB2  C1    C6   N12   110.98  3.000
 RB2  C5    C6   N12   109.78  3.000
 RB2  H5    C5   C4    108.40  3.000
 RB2  H5    C5   C8    105.45  3.000
 RB2  C4    C5   C8    112.21  3.000
 RB2  H5    C5   C6    107.16  3.000
 RB2  C4    C5   C6    109.94  3.000
 RB2  C8    C5   C6    113.35  3.000
 RB2  H8    C8   O9    110.25  3.000
 RB2  H8    C8   O10   103.39  3.000
 RB2  O9    C8   O10   112.64  3.000
 RB2  H8    C8   C5    109.12  3.000
 RB2  O9    C8   C5    108.17  3.000
 RB2  O10   C8   C5    113.16  3.000
 RB2  H10   O10  C8    109.91  3.000
 RB2  C11   O9   C8    114.61  3.000
 RB2  H113  C11  H112  108.42  3.000
 RB2  H113  C11  H111  108.46  3.000
 RB2  H112  C11  H111  108.24  3.000
 RB2  H113  C11  O9    107.50  3.000
 RB2  H112  C11  O9    111.54  3.000
 RB2  H111  C11  O9    112.56  3.000
 RB2  H42   C4   H41   107.49  3.000
 RB2  H42   C4   C3    109.30  3.000
 RB2  H41   C4   C3    108.32  3.000
 RB2  H42   C4   C5    110.62  3.000
 RB2  H41   C4   C5    111.04  3.000
 RB2  C3    C4   C5    110.01  3.000
 RB2  H3    C3   C2    110.53  3.000
 RB2  H3    C3   CL    105.07  3.000
 RB2  C2    C3   CL    109.64  3.000
 RB2  H3    C3   C4    110.24  3.000
 RB2  C2    C3   C4    111.86  3.000
 RB2  CL    C3   C4    109.28  3.000
 RB2  H22   C2   H21   107.19  3.000
 RB2  H22   C2   C1    109.68  3.000
 RB2  H21   C2   C1    110.00  3.000
 RB2  H22   C2   C3    109.16  3.000
 RB2  H21   C2   C3    110.49  3.000
 RB2  C1    C2   C3    110.26  3.000
 RB2  H12A  C1   H11   106.83  3.000
 RB2  H12A  C1   C2    107.61  3.000
 RB2  H11   C1   C2    110.44  3.000
 RB2  H12A  C1   C6    110.70  3.000
 RB2  H11   C1   C6    109.34  3.000
 RB2  C2    C1   C6    111.80  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
 RB2  Var_01  C3    C2   C1  C6  -56.09  30.0  1
 RB2  Var_02  H111  C11  O9  C8  -69.59  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
 RB2  chir_01  C13  C15  O14  N12  positiv
 RB2  chir_02  C6   N12  C5   C1   positiv
 RB2  chir_03  C5   C6   C8   C4   negativ
 RB2  chir_04  C8   O9   O10  C5   negativ
 RB2  chir_05  C3   CL   C2   C4   negativ

