# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 04:16:09 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: (5R,6R,7S,8R)-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-6,7,8-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)c2nccn12
#
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
 MVL  MVL  (5R,6R,7S,8R)-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-6,7,8-triol  ligand  26  14  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MVL
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
 MVL  C1    C  CR5   0   0.443   0.2238   1.4247   0.1734
 MVL  N10   N  NR5   0  -0.475   0.9994   0.3146   0.2269
 MVL  C3    C  CH1   0   0.018  -1.7415   0.0198   0.5432
 MVL  C4    C  CH1   0   0.012  -0.9645  -1.1223  -0.1085
 MVL  C5    C  CH1   0  -0.106   0.5235  -1.0658   0.2504
 MVL  C6    C  CH2   0  -0.152   1.3211  -1.9557  -0.6924
 MVL  C7    C  CR15  0  -0.230   2.2325   2.1053   0.3474
 MVL  C8    C  CR15  0  -0.101   2.2954   0.7421   0.3491
 MVL  N1    N  N     0  -0.465   0.9381   2.5202   0.2405
 MVL  O3    O  OH1   0  -0.671  -3.1037  -0.2014   0.2841
 MVL  O2    O  OH1   0  -0.662  -1.6286   1.4527  -1.3572
 MVL  O4    O  OH1   0  -0.669  -1.4241  -2.3709   0.3413
 MVL  C2    C  CH1   0  -0.085  -1.2574   1.3587  -0.0011
 MVL  O6    O  OH1   0  -0.665   2.5835  -2.2277  -0.1311
 MVL  H2    H  HCH1  0   0.243  -1.7030   2.1738   0.5841
 MVL  H5    H  HCH1  0   0.275   0.6316  -1.4407   1.2740
 MVL  H8    H  HCR5  0   0.291   3.1244   0.0623   0.4288
 MVL  H3    H  HCH1  0   0.239  -1.5378   0.0055   1.6234
 MVL  H4    H  HCH1  0   0.228  -1.0691  -1.0363  -1.2003
 MVL  HA    H  HOH1  0   0.461  -3.6251   0.2202   0.9731
 MVL  HB    H  HOH1  0   0.454  -2.3706  -2.4147   0.1662
 MVL  H6C1  H  HCH2  0   0.227   0.7536  -2.8794  -0.8500
 MVL  H6C2  H  HCH2  0   0.215   1.4014  -1.4532  -1.6640
 MVL  H6    H  HOH1  0   0.461   3.1323  -2.6341  -0.8080
 MVL  H7    H  HCR5  0   0.249   3.0526   2.8023   0.4248
 MVL  HC    H  HOH1  0   0.465  -1.3398   2.3093  -1.6894

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
 MVL  C1   N10   aromatic  1.355  0.020  1.355
 MVL  C1   N1    aromatic  1.310  0.020  1.310
 MVL  C1   C2    single    1.493  0.020  1.493
 MVL  N10  C5    single    1.460  0.020  1.460
 MVL  N10  C8    aromatic  1.370  0.020  1.370
 MVL  C3   C4    single    1.527  0.020  1.527
 MVL  C3   O3    single    1.404  0.020  1.404
 MVL  C3   C2    single    1.524  0.020  1.524
 MVL  C4   C5    single    1.532  0.020  1.532
 MVL  C4   O4    single    1.404  0.020  1.404
 MVL  C5   C6    single    1.522  0.020  1.522
 MVL  C6   O6    single    1.408  0.020  1.408
 MVL  C7   C8    aromatic  1.365  0.020  1.365
 MVL  C7   N1    aromatic  1.364  0.020  1.364
 MVL  O2   C2    single    1.409  0.020  1.409
 MVL  C2   H2    single    0.970  0.020  1.090
 MVL  C5   H5    single    0.970  0.020  1.090
 MVL  C8   H8    single    0.930  0.020  1.080
 MVL  C3   H3    single    0.970  0.020  1.090
 MVL  C4   H4    single    0.970  0.020  1.090
 MVL  O3   HA    single    0.850  0.020  0.980
 MVL  O4   HB    single    0.850  0.020  0.980
 MVL  C6   H6C1  single    0.970  0.020  1.090
 MVL  C6   H6C2  single    0.970  0.020  1.090
 MVL  O6   H6    single    0.850  0.020  0.980
 MVL  C7   H7    single    0.930  0.020  1.080
 MVL  O2   HC    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
 MVL  C2    C1   N1    125.74  3.000
 MVL  C2    C1   N10   122.43  3.000
 MVL  N1    C1   N10   111.78  3.000
 MVL  C8    N10  C5    127.00  3.000
 MVL  C8    N10  C1    106.81  3.000
 MVL  C5    N10  C1    126.04  3.000
 MVL  H3    C3   C2    107.67  3.000
 MVL  H3    C3   O3    111.04  3.000
 MVL  C2    C3   O3    112.37  3.000
 MVL  H3    C3   C4    108.37  3.000
 MVL  C2    C3   C4    110.06  3.000
 MVL  O3    C3   C4    107.27  3.000
 MVL  H4    C4   O4    110.87  3.000
 MVL  H4    C4   C5    108.78  3.000
 MVL  O4    C4   C5    106.00  3.000
 MVL  H4    C4   C3    108.46  3.000
 MVL  O4    C4   C3    111.20  3.000
 MVL  C5    C4   C3    111.51  3.000
 MVL  H5    C5   C6    109.09  3.000
 MVL  H5    C5   C4    107.59  3.000
 MVL  C6    C5   C4    110.02  3.000
 MVL  H5    C5   N10   107.84  3.000
 MVL  C6    C5   N10   111.83  3.000
 MVL  C4    C5   N10   110.35  3.000
 MVL  H6C2  C6   H6C1  107.27  3.000
 MVL  H6C2  C6   O6    112.08  3.000
 MVL  H6C1  C6   O6    111.04  3.000
 MVL  H6C2  C6   C5    108.61  3.000
 MVL  H6C1  C6   C5    108.10  3.000
 MVL  O6    C6   C5    109.62  3.000
 MVL  H7    C7   N1    122.04  3.000
 MVL  H7    C7   C8    127.60  3.000
 MVL  N1    C7   C8    110.36  3.000
 MVL  H8    C8   C7    131.86  3.000
 MVL  H8    C8   N10   122.59  3.000
 MVL  C7    C8   N10   105.55  3.000
 MVL  C7    N1   C1    105.50  3.000
 MVL  HA    O3   C3    108.96  3.000
 MVL  HC    O2   C2    108.19  3.000
 MVL  HB    O4   C4    107.68  3.000
 MVL  H2    C2   O2    110.89  3.000
 MVL  H2    C2   C3    109.44  3.000
 MVL  O2    C2   C3    108.57  3.000
 MVL  H2    C2   C1    107.91  3.000
 MVL  O2    C2   C1    111.77  3.000
 MVL  C3    C2   C1    108.19  3.000
 MVL  H6    O6   C6    108.22  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
 MVL  CONST_01  C7  C8  N10  C1     0.00  0.0  0
 MVL  CONST_02  C8  C7  N1   C1     0.00  0.0  0
 MVL  CONST_03  C7  N1  C1   N10    0.00  0.0  0
 MVL  CONST_04  N1  C7  C8   N10    0.00  0.0  0
 MVL  CONST_05  N1  C1  N10  C8     0.00  0.0  0
 MVL  CONST_06  H8  C8  N10  C1   180.00  0.0  0
 MVL  CONST_07  H7  C7  N1   C1   180.00  0.0  0

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
 MVL  chir_01  C3  C4   O3  C2  positiv
 MVL  chir_02  C4  O4   C3  C5  negativ
 MVL  chir_03  C5  N10  C4  C6  negativ
 MVL  chir_04  C2  O2   C3  C1  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 MVL  plan-1  C1   0.020
 MVL  plan-1  N10  0.020
 MVL  plan-1  C5   0.020
 MVL  plan-1  C7   0.020
 MVL  plan-1  C8   0.020
 MVL  plan-1  N1   0.020
 MVL  plan-1  C2   0.020
 MVL  plan-1  H8   0.020
 MVL  plan-1  H7   0.020

