# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 11:01:37 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: (2R,3R)-4-(4-amino-1H-imidazo[4,5-c]pyridin-1-yl)-2,3-dihydroxybutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccc2n(C[C@@H](O)[C@@H](O)C(O)=O)cnc12
#
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
 3DD  3DD  '(2R,3R)-4-(4-amino-1H-imidazo[4,5-c]pyridin-1-yl)-2,3-dihydroxybutanoic acid'  ligand  30  18  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3DD
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
 3DD  N9    N  NR5   0  -0.507   0.6733  -0.7209   0.8709
 3DD  C8    C  CR15  0   0.102   1.2460  -1.9398   0.6569
 3DD  N7    N  N     0  -0.456   2.4533  -1.8688   0.1808
 3DD  C5    C  CR56  0  -0.021   2.6910  -0.5220   0.0559
 3DD  C6    C  CR6   0   0.390   3.8292   0.1665  -0.4090
 3DD  N6    N  NH2   0  -0.828   4.9479  -0.5039  -0.7813
 3DD  N1    N  N     0  -0.472   3.8280   1.4917  -0.4486
 3DD  C2    C  CR16  0  -0.089   2.7442   2.1702  -0.0373
 3DD  C3    C  CR16  0  -0.398   1.5798   1.6120   0.4405
 3DD  C4    C  CR56  0   0.429   1.5874   0.2135   0.4760
 3DD  C1'   C  CH2   0  -0.351  -0.6826  -0.4704   1.2959
 3DD  C2'   C  CH1   0  -0.009  -1.6166  -0.3100   0.0980
 3DD  O2'   O  OH1   0  -0.647  -1.6550  -1.4655  -0.6933
 3DD  C3'   C  CH1   0  -0.099  -3.0192   0.1250   0.5663
 3DD  O3'   O  OH1   0  -0.647  -2.9919   1.3858   1.1693
 3DD  C4'   C  C     0   0.521  -3.9516   0.1213  -0.6362
 3DD  O4A   O  OH1   0  -0.577  -4.6327  -1.0021  -0.7599
 3DD  O4B   O  O     0  -0.439  -4.0338   1.0580  -1.3901
 3DD  H8    H  HCR5  0   0.289   0.7184  -2.8527   0.8911
 3DD  HN61  H  HNH2  0   0.387   5.6259   0.0003  -1.3279
 3DD  HN62  H  HNH2  0   0.393   4.8623  -1.4822  -0.9994
 3DD  H2    H  HCR6  0   0.254   2.8247   3.2497  -0.1012
 3DD  H3    H  HCR6  0   0.264   0.7439   2.2221   0.7533
 3DD  H1'1  H  HCH2  0   0.289  -1.0073  -1.3041   1.9223
 3DD  H1'2  H  HCH2  0   0.285  -0.6971   0.4216   1.9208
 3DD  H2'   H  HCH1  0   0.262  -1.2221   0.4787  -0.5525
 3DD  HO2'  H  HOH1  0   0.454  -2.0149  -2.1983  -0.1797
 3DD  H3'   H  HCH1  0   0.283  -3.3896  -0.5783   1.3189
 3DD  HO3'  H  HOH1  0   0.452  -2.7905   2.0507   0.4994
 3DD  HO4A  H  HOH1  0   0.487  -5.1763  -0.9846  -1.5633

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
 3DD  N9   C8    aromatic  1.364  0.020  1.364
 3DD  N9   C4    aromatic  1.365  0.020  1.365
 3DD  N9   C1'   single    1.443  0.020  1.443
 3DD  C8   N7    aromatic  1.300  0.020  1.300
 3DD  C8   H8    single    0.930  0.020  1.080
 3DD  N7   C5    aromatic  1.373  0.020  1.373
 3DD  C5   C6    aromatic  1.409  0.020  1.409
 3DD  C5   C4    aromatic  1.391  0.020  1.391
 3DD  C6   N6    single    1.356  0.020  1.356
 3DD  C6   N1    aromatic  1.326  0.020  1.326
 3DD  N6   HN61  single    0.890  0.020  1.040
 3DD  N6   HN62  single    0.890  0.020  1.040
 3DD  N1   C2    aromatic  1.343  0.020  1.343
 3DD  C2   C3    aromatic  1.377  0.020  1.377
 3DD  C2   H2    single    0.930  0.020  1.080
 3DD  C3   C4    aromatic  1.399  0.020  1.399
 3DD  C3   H3    single    0.930  0.020  1.080
 3DD  C1'  C2'   single    1.527  0.020  1.527
 3DD  C1'  H1'1  single    0.970  0.020  1.090
 3DD  C1'  H1'2  single    0.970  0.020  1.090
 3DD  C2'  O2'   single    1.401  0.020  1.401
 3DD  C2'  C3'   single    1.541  0.020  1.541
 3DD  C2'  H2'   single    0.970  0.020  1.090
 3DD  O2'  HO2'  single    0.850  0.020  0.980
 3DD  C3'  O3'   single    1.398  0.020  1.398
 3DD  C3'  C4'   single    1.522  0.020  1.522
 3DD  C3'  H3'   single    0.970  0.020  1.090
 3DD  O3'  HO3'  single    0.850  0.020  0.980
 3DD  C4'  O4A   single    1.320  0.020  1.320
 3DD  C4'  O4B   double    1.205  0.020  1.205
 3DD  O4A  HO4A  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
 3DD  C1'   N9   C4    126.54  3.000
 3DD  C1'   N9   C8    126.59  3.000
 3DD  C4    N9   C8    106.57  3.000
 3DD  H8    C8   N7    125.41  3.000
 3DD  H8    C8   N9    121.08  3.000
 3DD  N7    C8   N9    113.50  3.000
 3DD  C5    N7   C8    104.34  3.000
 3DD  C4    C5   C6    118.82  3.000
 3DD  C4    C5   N7    110.72  3.000
 3DD  C6    C5   N7    130.47  3.000
 3DD  N1    C6   N6    119.12  3.000
 3DD  N1    C6   C5    119.84  3.000
 3DD  N6    C6   C5    121.01  3.000
 3DD  HN62  N6   HN61  115.26  3.000
 3DD  HN62  N6   C6    118.04  3.000
 3DD  HN61  N6   C6    117.21  3.000
 3DD  C2    N1   C6    119.77  3.000
 3DD  H2    C2   C3    119.13  3.000
 3DD  H2    C2   N1    115.15  3.000
 3DD  C3    C2   N1    125.72  3.000
 3DD  H3    C3   C4    124.13  3.000
 3DD  H3    C3   C2    121.70  3.000
 3DD  C4    C3   C2    114.17  3.000
 3DD  C3    C4   C5    121.68  3.000
 3DD  C3    C4   N9    133.45  3.000
 3DD  C5    C4   N9    104.87  3.000
 3DD  H1'2  C1'  H1'1  106.98  3.000
 3DD  H1'2  C1'  C2'   110.84  3.000
 3DD  H1'1  C1'  C2'   110.37  3.000
 3DD  H1'2  C1'  N9    108.89  3.000
 3DD  H1'1  C1'  N9    108.41  3.000
 3DD  C2'   C1'  N9    111.21  3.000
 3DD  H2'   C2'  C3'   107.74  3.000
 3DD  H2'   C2'  O2'   105.56  3.000
 3DD  C3'   C2'  O2'   112.30  3.000
 3DD  H2'   C2'  C1'   108.72  3.000
 3DD  C3'   C2'  C1'   110.35  3.000
 3DD  O2'   C2'  C1'   111.91  3.000
 3DD  HO2'  O2'  C2'   109.64  3.000
 3DD  H3'   C3'  C4'   109.54  3.000
 3DD  H3'   C3'  O3'   106.83  3.000
 3DD  C4'   C3'  O3'   110.80  3.000
 3DD  H3'   C3'  C2'   109.60  3.000
 3DD  C4'   C3'  C2'   108.47  3.000
 3DD  O3'   C3'  C2'   111.58  3.000
 3DD  HO3'  O3'  C3'   109.03  3.000
 3DD  O4B   C4'  O4A   124.60  3.000
 3DD  O4B   C4'  C3'   122.29  3.000
 3DD  O4A   C4'  C3'   113.11  3.000
 3DD  HO4A  O4A  C4'   110.58  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
 3DD  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 3DD  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 3DD  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 3DD  CONST_04  C2    C3   C4   N9   180.00   0.0  0
 3DD  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 3DD  CONST_06  C3    C4   N9   C8   180.00   0.0  0
 3DD  CONST_07  C6    C5   N7   C8   180.00   0.0  0
 3DD  CONST_08  C4    C5   N7   C8     0.00   0.0  0
 3DD  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 3DD  CONST_10  N1    C6   C5   N7   180.00   0.0  0
 3DD  CONST_11  C3    C4   C5   N7   180.00   0.0  0
 3DD  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 3DD  CONST_13  C2    C3   C4   C5     0.00   0.0  0
 3DD  CONST_14  C3    C4   C5   C6     0.00   0.0  0
 3DD  CONST_15  C3    C2   N1   C6     0.00   0.0  0
 3DD  CONST_16  C4    C5   C6   N1     0.00   0.0  0
 3DD  CONST_17  C4    C3   C2   N1     0.00   0.0  0
 3DD  CONST_18  C1'   N9   C8   N7   180.00   0.0  0
 3DD  CONST_19  N6    C6   C5   N7     0.00   0.0  0
 3DD  CONST_20  C1'   N9   C4   C5   180.00   0.0  0
 3DD  CONST_21  C4    C5   C6   N6   180.00   0.0  0
 3DD  CONST_22  C2    N1   C6   N6   180.00   0.0  0
 3DD  CONST_23  C1'   N9   C4   C3     0.00   0.0  0
 3DD  CONST_24  H3    C3   C4   N9     0.00   0.0  0
 3DD  CONST_25  H8    C8   N7   C5   180.00   0.0  0
 3DD  CONST_26  H2    C2   N1   C6   180.00   0.0  0
 3DD  CONST_29  HO4A  O4A  C4'  C3'  180.00   0.0  0
 3DD  Var_01    C2'   C1'  N9   C8   -90.92  30.0  2

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
 3DD  chir_01  C2'  C1'  O2'  C3'  negativ
 3DD  chir_02  C3'  O3'  C2'  C4'  positiv

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
 3DD  plan-1  N9    0.020
 3DD  plan-1  C8    0.020
 3DD  plan-1  N7    0.020
 3DD  plan-1  C5    0.020
 3DD  plan-1  C6    0.020
 3DD  plan-1  N6    0.020
 3DD  plan-1  N1    0.020
 3DD  plan-1  C2    0.020
 3DD  plan-1  C3    0.020
 3DD  plan-1  C4    0.020
 3DD  plan-1  C1'   0.020
 3DD  plan-1  H8    0.020
 3DD  plan-1  H2    0.020
 3DD  plan-1  H3    0.020
 3DD  plan-2  C6    0.020
 3DD  plan-2  N6    0.020
 3DD  plan-2  HN61  0.020
 3DD  plan-2  HN62  0.020
 3DD  plan-3  C3'   0.020
 3DD  plan-3  C4'   0.020
 3DD  plan-3  O4A   0.020
 3DD  plan-3  O4B   0.020
 3DD  plan-3  HO4A  0.020

