# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:33:29 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: (5R,6R,7S,8S)-5-(hydroxymethyl)-2-phenyl-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)c2nc(cn12)c3ccccc3
#
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
 IDD  IDD  (5R,6R,7S,8S)-5-(hydroxymethyl)-2-phenyl-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-6,7,8-triol  ligand  36  20  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_IDD
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
 IDD  C1    C  CR6   0   0.038   2.8582  -0.1253  -0.0116
 IDD  C2    C  CR16  0  -0.308   3.5217  -1.3164   0.2895
 IDD  C3    C  CR16  0  -0.239   4.9076  -1.3788   0.2762
 IDD  C4    C  CR16  0  -0.273   5.6589  -0.2541  -0.0378
 IDD  C5    C  CR16  0  -0.236   5.0082   0.9361  -0.3408
 IDD  C6    C  CR16  0  -0.344   3.6238   0.9997  -0.3295
 IDD  C1B   C  CR5   0   0.447  -0.6083  -0.7847   0.1242
 IDD  C2B   C  CH1   0  -0.055  -1.8117  -1.6673   0.2353
 IDD  C3B   C  CH1   0   0.014  -2.9930  -0.9662  -0.4163
 IDD  C4B   C  CH1   0   0.007  -3.1323   0.4336   0.1778
 IDD  C5B   C  CH1   0  -0.110  -1.9322   1.3229  -0.1621
 IDD  C6B   C  CH2   0  -0.149  -1.9294   2.5562   0.7309
 IDD  O2B   O  OH1   0  -0.660  -1.6066  -2.8979  -0.4048
 IDD  O3B   O  OH1   0  -0.673  -4.2012  -1.6377  -0.1664
 IDD  O4B   O  OH1   0  -0.664  -4.2617   1.0909  -0.3307
 IDD  N1B   N  NR5   0  -0.489  -0.6969   0.5570  -0.0317
 IDD  O6B   O  OH1   0  -0.665  -1.0662   3.5261   0.1878
 IDD  N2B   N  N     0  -0.490   0.6306  -1.1903   0.1594
 IDD  C7B   C  CR5   0   0.126   1.3976  -0.0677   0.0046
 IDD  C8B   C  CR15  0  -0.102   0.5852   1.0298  -0.1165
 IDD  H21   H  HCR6  0   0.247   2.9459  -2.1983   0.5386
 IDD  H31   H  HCR6  0   0.254   5.4022  -2.3116   0.5156
 IDD  H41   H  HCR6  0   0.254   6.7399  -0.3035  -0.0486
 IDD  H51   H  HCR6  0   0.255   5.5811   1.8194  -0.5927
 IDD  H61   H  HCR6  0   0.246   3.1373   1.9344  -0.5806
 IDD  H2B1  H  HCH1  0   0.239  -2.0468  -1.8139   1.3013
 IDD  H3B1  H  HCH1  0   0.236  -2.8027  -0.8769  -1.4967
 IDD  H4B1  H  HCH1  0   0.228  -3.1970   0.3311   1.2741
 IDD  H5B1  H  HCH1  0   0.281  -2.0304   1.6350  -1.2073
 IDD  H6B1  H  HCH2  0   0.215  -1.6297   2.2541   1.7419
 IDD  H6B2  H  HCH2  0   0.229  -2.9558   2.9333   0.7951
 IDD  HO21  H  HOH1  0   0.458  -0.8463  -3.3275   0.0016
 IDD  HO31  H  HOH1  0   0.463  -4.2543  -2.4103  -0.7370
 IDD  HO41  H  HOH1  0   0.457  -5.0299   0.5363  -0.1555
 IDD  HO61  H  HOH1  0   0.463  -0.9512   4.2264   0.8367
 IDD  H8B1  H  HCR5  0   0.298   0.8006   2.0750  -0.2470

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
 IDD  C1   C2    aromatic  1.396  0.020  1.396
 IDD  C1   C6    aromatic  1.397  0.020  1.397
 IDD  C1   C7B   single    1.462  0.020  1.462
 IDD  C2   C3    aromatic  1.387  0.020  1.387
 IDD  C2   H21   single    0.930  0.020  1.080
 IDD  C3   C4    aromatic  1.389  0.020  1.389
 IDD  C3   H31   single    0.930  0.020  1.080
 IDD  C4   C5    aromatic  1.390  0.020  1.390
 IDD  C4   H41   single    0.930  0.020  1.080
 IDD  C5   C6    aromatic  1.386  0.020  1.386
 IDD  C5   H51   single    0.930  0.020  1.080
 IDD  C6   H61   single    0.930  0.020  1.080
 IDD  C1B  C2B   single    1.496  0.020  1.496
 IDD  C1B  N1B   aromatic  1.354  0.020  1.354
 IDD  C1B  N2B   aromatic  1.304  0.020  1.304
 IDD  C2B  C3B   single    1.520  0.020  1.520
 IDD  C2B  O2B   single    1.402  0.020  1.402
 IDD  C2B  H2B1  single    0.970  0.020  1.090
 IDD  C3B  C4B   single    1.527  0.020  1.527
 IDD  C3B  O3B   single    1.405  0.020  1.405
 IDD  C3B  H3B1  single    0.970  0.020  1.090
 IDD  C4B  C5B   single    1.532  0.020  1.532
 IDD  C4B  O4B   single    1.402  0.020  1.402
 IDD  C4B  H4B1  single    0.970  0.020  1.090
 IDD  C5B  C6B   single    1.523  0.020  1.523
 IDD  C5B  N1B   single    1.459  0.020  1.459
 IDD  C5B  H5B1  single    0.970  0.020  1.090
 IDD  C6B  O6B   single    1.407  0.020  1.407
 IDD  C6B  H6B1  single    0.970  0.020  1.090
 IDD  C6B  H6B2  single    0.970  0.020  1.090
 IDD  O2B  HO21  single    0.850  0.020  0.980
 IDD  O3B  HO31  single    0.850  0.020  0.980
 IDD  O4B  HO41  single    0.850  0.020  0.980
 IDD  N1B  C8B   aromatic  1.369  0.020  1.369
 IDD  O6B  HO61  single    0.850  0.020  0.980
 IDD  N2B  C7B   aromatic  1.368  0.020  1.368
 IDD  C7B  C8B   aromatic  1.371  0.020  1.371
 IDD  C8B  H8B1  single    0.930  0.020  1.080

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
 IDD  C7B   C1   C6    121.21  3.000
 IDD  C7B   C1   C2    120.40  3.000
 IDD  C6    C1   C2    118.39  3.000
 IDD  H21   C2   C3    119.80  3.000
 IDD  H21   C2   C1    119.47  3.000
 IDD  C3    C2   C1    120.73  3.000
 IDD  H31   C3   C4    120.05  3.000
 IDD  H31   C3   C2    119.54  3.000
 IDD  C4    C3   C2    120.41  3.000
 IDD  H41   C4   C5    120.31  3.000
 IDD  H41   C4   C3    120.38  3.000
 IDD  C5    C4   C3    119.31  3.000
 IDD  H51   C5   C6    119.54  3.000
 IDD  H51   C5   C4    120.11  3.000
 IDD  C6    C5   C4    120.34  3.000
 IDD  H61   C6   C5    119.10  3.000
 IDD  H61   C6   C1    120.09  3.000
 IDD  C5    C6   C1    120.81  3.000
 IDD  N2B   C1B  N1B   111.94  3.000
 IDD  N2B   C1B  C2B   125.34  3.000
 IDD  N1B   C1B  C2B   122.72  3.000
 IDD  H2B1  C2B  O2B   110.87  3.000
 IDD  H2B1  C2B  C3B   108.08  3.000
 IDD  O2B   C2B  C3B   108.82  3.000
 IDD  H2B1  C2B  C1B   108.78  3.000
 IDD  O2B   C2B  C1B   111.48  3.000
 IDD  C3B   C2B  C1B   108.73  3.000
 IDD  H3B1  C3B  O3B   111.23  3.000
 IDD  H3B1  C3B  C4B   108.86  3.000
 IDD  O3B   C3B  C4B   106.89  3.000
 IDD  H3B1  C3B  C2B   108.89  3.000
 IDD  O3B   C3B  C2B   111.82  3.000
 IDD  C4B   C3B  C2B   109.08  3.000
 IDD  H4B1  C4B  O4B   110.90  3.000
 IDD  H4B1  C4B  C5B   108.69  3.000
 IDD  O4B   C4B  C5B   106.17  3.000
 IDD  H4B1  C4B  C3B   107.87  3.000
 IDD  O4B   C4B  C3B   111.23  3.000
 IDD  C5B   C4B  C3B   111.99  3.000
 IDD  H5B1  C5B  N1B   108.10  3.000
 IDD  H5B1  C5B  C6B   109.21  3.000
 IDD  N1B   C5B  C6B   111.79  3.000
 IDD  H5B1  C5B  C4B   107.87  3.000
 IDD  N1B   C5B  C4B   109.80  3.000
 IDD  C6B   C5B  C4B   109.97  3.000
 IDD  H6B2  C6B  H6B1  107.27  3.000
 IDD  H6B2  C6B  O6B   111.11  3.000
 IDD  H6B1  C6B  O6B   112.20  3.000
 IDD  H6B2  C6B  C5B   108.15  3.000
 IDD  H6B1  C6B  C5B   108.54  3.000
 IDD  O6B   C6B  C5B   109.45  3.000
 IDD  HO21  O2B  C2B   108.32  3.000
 IDD  HO31  O3B  C3B   109.03  3.000
 IDD  HO41  O4B  C4B   107.84  3.000
 IDD  C8B   N1B  C5B   127.29  3.000
 IDD  C8B   N1B  C1B   106.75  3.000
 IDD  C5B   N1B  C1B   125.87  3.000
 IDD  HO61  O6B  C6B   108.35  3.000
 IDD  C7B   N2B  C1B   105.92  3.000
 IDD  C8B   C7B  N2B   109.55  3.000
 IDD  C8B   C7B  C1    128.52  3.000
 IDD  N2B   C7B  C1    121.94  3.000
 IDD  H8B1  C8B  C7B   132.09  3.000
 IDD  H8B1  C8B  N1B   122.06  3.000
 IDD  C7B   C8B  N1B   105.85  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
 IDD  CONST_01  C4    C3   C2   C1     0.00  0.0  0
 IDD  CONST_02  C4    C5   C6   C1     0.00  0.0  0
 IDD  CONST_03  C1B   N2B  C7B  C1   180.00  0.0  0
 IDD  CONST_04  N1B   C8B  C7B  C1   180.00  0.0  0
 IDD  CONST_05  C5    C6   C1   C2     0.00  0.0  0
 IDD  CONST_06  N2B   C7B  C1   C2     0.00  0.0  0
 IDD  CONST_07  C8B   C7B  C1   C2   180.00  0.0  0
 IDD  CONST_08  C5    C4   C3   C2     0.00  0.0  0
 IDD  CONST_09  C6    C1   C2   C3     0.00  0.0  0
 IDD  CONST_10  C7B   C1   C2   C3   180.00  0.0  0
 IDD  CONST_11  C6    C5   C4   C3     0.00  0.0  0
 IDD  CONST_12  C7B   C1   C6   C5   180.00  0.0  0
 IDD  CONST_13  N2B   C7B  C1   C6   180.00  0.0  0
 IDD  CONST_14  C8B   C7B  C1   C6     0.00  0.0  0
 IDD  CONST_15  C7B   C8B  N1B  C1B    0.00  0.0  0
 IDD  CONST_16  C8B   C7B  N2B  C1B    0.00  0.0  0
 IDD  CONST_17  C7B   N2B  C1B  N1B    0.00  0.0  0
 IDD  CONST_18  N2B   C7B  C8B  N1B    0.00  0.0  0
 IDD  CONST_19  C8B   N1B  C1B  N2B    0.00  0.0  0
 IDD  CONST_20  H31   C3   C2   C1   180.00  0.0  0
 IDD  CONST_21  H51   C5   C6   C1   180.00  0.0  0
 IDD  CONST_22  H8B1  C8B  C7B  C1     0.00  0.0  0
 IDD  CONST_23  H61   C6   C1   C2   180.00  0.0  0
 IDD  CONST_24  H41   C4   C3   C2   180.00  0.0  0
 IDD  CONST_25  H21   C2   C3   C4   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
 IDD  chir_01  C2B  C1B  C3B  O2B  negativ
 IDD  chir_02  C3B  O3B  C2B  C4B  positiv
 IDD  chir_03  C4B  O4B  C5B  C3B  positiv
 IDD  chir_04  C5B  N1B  C4B  C6B  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
 IDD  plan-1  C1    0.020
 IDD  plan-1  C2    0.020
 IDD  plan-1  C3    0.020
 IDD  plan-1  C4    0.020
 IDD  plan-1  C5    0.020
 IDD  plan-1  C6    0.020
 IDD  plan-1  C7B   0.020
 IDD  plan-1  H21   0.020
 IDD  plan-1  H31   0.020
 IDD  plan-1  H41   0.020
 IDD  plan-1  H51   0.020
 IDD  plan-1  H61   0.020
 IDD  plan-2  C1    0.020
 IDD  plan-2  C1B   0.020
 IDD  plan-2  C2B   0.020
 IDD  plan-2  C5B   0.020
 IDD  plan-2  N1B   0.020
 IDD  plan-2  N2B   0.020
 IDD  plan-2  C7B   0.020
 IDD  plan-2  C8B   0.020
 IDD  plan-2  H8B1  0.020

