# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 14:43:00 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (1R,2S,3S,4R,5R)-4-[(cyclohexylmethyl)amino]-5-(hydroxymethyl)cyclopentane-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1NCC2CCCCC2
#
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
 VM2  VM2  (1R,2S,3S,4R,5R)-4-[(cyclohexylmethyl)amino]-5-(hydroxymethyl)cyclopentane-1,2,3-triol  ligand  43  18  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VM2
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
 VM2  C1    C  CH1   0  -0.246  -2.7422  -0.2040  -0.3981
 VM2  C2    C  CH2   0  -0.418  -3.8754   0.5281  -1.1189
 VM2  C3    C  CH2   0  -0.430  -5.2529   0.0027  -0.7297
 VM2  C4    C  CH2   0  -0.429  -5.4589   0.0551   0.7799
 VM2  C5    C  CH2   0  -0.428  -4.3478  -0.6953   1.5047
 VM2  C6    C  CH2   0  -0.429  -2.9690  -0.1704   1.1151
 VM2  C2B   C  CH1   0   0.043   1.5388   1.4162  -0.0409
 VM2  C3B   C  CH1   0  -0.020   3.0475   1.2586  -0.0496
 VM2  C4B   C  CH1   0   0.059   3.2262  -0.1984   0.3634
 VM2  C5B   C  CH1   0  -0.322   2.1723  -0.9222  -0.4777
 VM2  C6B   C  CH2   0  -0.131   1.6886  -2.2411   0.0963
 VM2  O2B   O  OH1   0  -0.669   1.0630   2.5548  -0.7130
 VM2  O3B   O  OH1   0  -0.676   3.6558   2.2024   0.8008
 VM2  O4B   O  OH1   0  -0.668   4.5162  -0.7059   0.1295
 VM2  O6B   O  OH1   0  -0.670   2.7766  -3.1358   0.1798
 VM2  CAR   C  CH1   0  -0.087   1.0265   0.1222  -0.6944
 VM2  N2B   N  NH1   0  -0.612  -0.2750  -0.3333  -0.2491
 VM2  C7B   C  CH2   0  -0.235  -1.4014   0.4045  -0.7943
 VM2  H1    H  HCH1  0   0.205  -2.7482  -1.2531  -0.7218
 VM2  H21C  H  HCH2  0   0.204  -3.8166   1.5969  -0.8786
 VM2  H22C  H  HCH2  0   0.224  -3.7358   0.4495  -2.2013
 VM2  H61C  H  HCH2  0   0.222  -2.2058  -0.7579   1.6331
 VM2  H62C  H  HCH2  0   0.205  -2.8593   0.8632   1.4666
 VM2  H7B1  H  HCH2  0   0.217  -1.3124   0.3821  -1.8856
 VM2  H7B2  H  HCH2  0   0.189  -1.4053   1.4676  -0.5111
 VM2  H31C  H  HCH2  0   0.224  -6.0298   0.5769  -1.2403
 VM2  H32C  H  HCH2  0   0.207  -5.3587  -1.0326  -1.0724
 VM2  H41C  H  HCH2  0   0.206  -5.4650   1.1003   1.1085
 VM2  H42C  H  HCH2  0   0.225  -6.4339  -0.3603   1.0462
 VM2  H51C  H  HCH2  0   0.225  -4.4809  -0.6232   2.5872
 VM2  H52C  H  HCH2  0   0.208  -4.4105  -1.7606   1.2563
 VM2  H2B   H  HCH1  0   0.197   1.2106   1.4226   1.0129
 VM2  H3B   H  HCH1  0   0.210   3.4062   1.3723  -1.0841
 VM2  HA    H  HOH1  0   0.448   1.3733   3.3328  -0.2384
 VM2  HAR   H  HCH1  0   0.243   0.9416   0.3057  -1.7696
 VM2  H4B   H  HCH1  0   0.192   2.9602  -0.2854   1.4300
 VM2  HB    H  HOH1  0   0.456   4.5629   2.3427   0.5160
 VM2  H5B   H  HCH1  0   0.243   2.6220  -1.1295  -1.4553
 VM2  HC    H  HOH1  0   0.445   5.1220  -0.2838   0.7463
 VM2  H6B1  H  HCH2  0   0.180   1.2405  -2.0744   1.0856
 VM2  H6B2  H  HCH2  0   0.204   0.8923  -2.6371  -0.5439
 VM2  H6B   H  HOH1  0   0.449   2.4439  -3.9654   0.5338
 VM2  HD    H  HNH1  0   0.340  -0.3116  -0.3083   0.7623

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
 VM2  C1   C2    single  1.530  0.020  1.530
 VM2  C1   C6    single  1.531  0.020  1.531
 VM2  C1   C7B   single  1.525  0.020  1.525
 VM2  C2   C3    single  1.525  0.020  1.525
 VM2  C3   C4    single  1.524  0.020  1.524
 VM2  C4   C5    single  1.524  0.020  1.524
 VM2  C5   C6    single  1.526  0.020  1.526
 VM2  C2B  C3B   single  1.517  0.020  1.517
 VM2  C2B  O2B   single  1.405  0.020  1.405
 VM2  C2B  CAR   single  1.538  0.020  1.538
 VM2  C3B  C4B   single  1.525  0.020  1.525
 VM2  C3B  O3B   single  1.409  0.020  1.409
 VM2  C4B  C5B   single  1.530  0.020  1.530
 VM2  C4B  O4B   single  1.406  0.020  1.406
 VM2  C5B  C6B   single  1.518  0.020  1.518
 VM2  C5B  CAR   single  1.565  0.020  1.565
 VM2  C6B  O6B   single  1.411  0.020  1.411
 VM2  N2B  C7B   single  1.453  0.020  1.453
 VM2  N2B  CAR   single  1.449  0.020  1.449
 VM2  C1   H1    single  0.970  0.020  1.090
 VM2  C2   H21C  single  0.970  0.020  1.090
 VM2  C2   H22C  single  0.970  0.020  1.090
 VM2  C6   H61C  single  0.970  0.020  1.090
 VM2  C6   H62C  single  0.970  0.020  1.090
 VM2  C7B  H7B1  single  0.970  0.020  1.090
 VM2  C7B  H7B2  single  0.970  0.020  1.090
 VM2  C3   H31C  single  0.970  0.020  1.090
 VM2  C3   H32C  single  0.970  0.020  1.090
 VM2  C4   H41C  single  0.970  0.020  1.090
 VM2  C4   H42C  single  0.970  0.020  1.090
 VM2  C5   H51C  single  0.970  0.020  1.090
 VM2  C5   H52C  single  0.970  0.020  1.090
 VM2  C2B  H2B   single  0.970  0.020  1.090
 VM2  C3B  H3B   single  0.970  0.020  1.090
 VM2  O2B  HA    single  0.850  0.020  0.980
 VM2  CAR  HAR   single  0.970  0.020  1.090
 VM2  C4B  H4B   single  0.970  0.020  1.090
 VM2  O3B  HB    single  0.850  0.020  0.980
 VM2  C5B  H5B   single  0.970  0.020  1.090
 VM2  O4B  HC    single  0.850  0.020  0.980
 VM2  C6B  H6B1  single  0.970  0.020  1.090
 VM2  C6B  H6B2  single  0.970  0.020  1.090
 VM2  O6B  H6B   single  0.850  0.020  0.980
 VM2  N2B  HD    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
 VM2  H1    C1   C7B   108.03  3.000
 VM2  H1    C1   C6    108.15  3.000
 VM2  C7B   C1   C6    112.24  3.000
 VM2  H1    C1   C2    108.32  3.000
 VM2  C7B   C1   C2    109.76  3.000
 VM2  C6    C1   C2    110.22  3.000
 VM2  H22C  C2   H21C  106.25  3.000
 VM2  H22C  C2   C3    110.06  3.000
 VM2  H21C  C2   C3    109.16  3.000
 VM2  H22C  C2   C1    109.71  3.000
 VM2  H21C  C2   C1    108.86  3.000
 VM2  C3    C2   C1    112.59  3.000
 VM2  H32C  C3   H31C  106.36  3.000
 VM2  H32C  C3   C4    109.21  3.000
 VM2  H31C  C3   C4    110.41  3.000
 VM2  H32C  C3   C2    109.44  3.000
 VM2  H31C  C3   C2    110.00  3.000
 VM2  C4    C3   C2    111.29  3.000
 VM2  H42C  C4   H41C  106.53  3.000
 VM2  H42C  C4   C5    110.33  3.000
 VM2  H41C  C4   C5    109.33  3.000
 VM2  H42C  C4   C3    110.42  3.000
 VM2  H41C  C4   C3    109.30  3.000
 VM2  C5    C4   C3    110.83  3.000
 VM2  H52C  C5   H51C  106.36  3.000
 VM2  H52C  C5   C6    109.16  3.000
 VM2  H51C  C5   C6    109.89  3.000
 VM2  H52C  C5   C4    109.21  3.000
 VM2  H51C  C5   C4    110.48  3.000
 VM2  C6    C5   C4    111.59  3.000
 VM2  H62C  C6   H61C  106.53  3.000
 VM2  H62C  C6   C5    109.42  3.000
 VM2  H61C  C6   C5    108.96  3.000
 VM2  H62C  C6   C1    108.82  3.000
 VM2  H61C  C6   C1    110.68  3.000
 VM2  C5    C6   C1    112.26  3.000
 VM2  H2B   C2B  CAR   108.15  3.000
 VM2  H2B   C2B  O2B   110.57  3.000
 VM2  CAR   C2B  O2B   111.46  3.000
 VM2  H2B   C2B  C3B   107.57  3.000
 VM2  CAR   C2B  C3B   103.97  3.000
 VM2  O2B   C2B  C3B   114.72  3.000
 VM2  H3B   C3B  O3B   110.94  3.000
 VM2  H3B   C3B  C4B   108.36  3.000
 VM2  O3B   C3B  C4B   115.21  3.000
 VM2  H3B   C3B  C2B   108.59  3.000
 VM2  O3B   C3B  C2B   110.88  3.000
 VM2  C4B   C3B  C2B   102.37  3.000
 VM2  H4B   C4B  O4B   110.72  3.000
 VM2  H4B   C4B  C5B   109.15  3.000
 VM2  O4B   C4B  C5B   111.70  3.000
 VM2  H4B   C4B  C3B   108.01  3.000
 VM2  O4B   C4B  C3B   114.04  3.000
 VM2  C5B   C4B  C3B   102.85  3.000
 VM2  H5B   C5B  CAR   107.65  3.000
 VM2  H5B   C5B  C6B   107.69  3.000
 VM2  CAR   C5B  C6B   113.51  3.000
 VM2  H5B   C5B  C4B   107.28  3.000
 VM2  CAR   C5B  C4B   105.34  3.000
 VM2  C6B   C5B  C4B   115.01  3.000
 VM2  H6B2  C6B  H6B1  106.53  3.000
 VM2  H6B2  C6B  O6B   111.45  3.000
 VM2  H6B1  C6B  O6B   110.94  3.000
 VM2  H6B2  C6B  C5B   108.95  3.000
 VM2  H6B1  C6B  C5B   109.80  3.000
 VM2  O6B   C6B  C5B   109.13  3.000
 VM2  HA    O2B  C2B   108.05  3.000
 VM2  HB    O3B  C3B   109.06  3.000
 VM2  HC    O4B  C4B   108.23  3.000
 VM2  H6B   O6B  C6B   107.59  3.000
 VM2  HAR   CAR  N2B   106.56  3.000
 VM2  HAR   CAR  C5B   107.74  3.000
 VM2  N2B   CAR  C5B   113.90  3.000
 VM2  HAR   CAR  C2B   107.60  3.000
 VM2  N2B   CAR  C2B   115.67  3.000
 VM2  C5B   CAR  C2B   105.00  3.000
 VM2  HD    N2B  C7B   109.53  3.000
 VM2  HD    N2B  CAR   109.37  3.000
 VM2  C7B   N2B  CAR   114.93  3.000
 VM2  H7B2  C7B  H7B1  106.05  3.000
 VM2  H7B2  C7B  N2B   113.38  3.000
 VM2  H7B1  C7B  N2B   107.49  3.000
 VM2  H7B2  C7B  C1    108.40  3.000
 VM2  H7B1  C7B  C1    108.80  3.000
 VM2  N2B   C7B  C1    112.44  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
 VM2  Var_01  C4   C3   C2   C1   55.32  30.0  1
 VM2  Var_02  C4   C5   C6   C1  -55.22  30.0  1
 VM2  Var_03  C5   C4   C3   C2  -55.23  30.0  1
 VM2  Var_04  C6   C5   C4   C3   55.36  30.0  1
 VM2  Var_05  CAR  N2B  C7B  C1  174.44  30.0  1

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
 VM2  chir_01  C1   C2   C6   C7B  positiv
 VM2  chir_02  C2B  O2B  C3B  CAR  positiv
 VM2  chir_03  C3B  O3B  C2B  C4B  positiv
 VM2  chir_04  C4B  O4B  C3B  C5B  negativ
 VM2  chir_05  C5B  C4B  C6B  CAR  negativ
 VM2  chir_06  CAR  N2B  C2B  C5B  negativ

