# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:29:27 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: [(3R)-7-nitro-1,2,3,4-tetrahydroisoquinolin-3-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1Cc2ccc(cc2CN1)[N+]([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
 HNT  HNT  '[(3R)-7-nitro-1,2,3,4-tetrahydroisoquinolin-3-yl]methanol'  ligand  27  15  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HNT
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
 HNT  C1    C  CH2    0  -0.481   1.8239  -1.2825   0.0572
 HNT  C2    C  CH1    0  -0.126   2.7611  -0.1384  -0.3037
 HNT  O2    O  O     -1  -0.383  -4.5225  -0.6155  -0.0145
 HNT  C4    C  CH2    0  -0.337   1.0901   1.5504  -0.0036
 HNT  C5    C  CR16   0  -0.309  -1.3108   0.8460   0.0046
 HNT  C6    C  CR6    0   0.250  -2.2879  -0.1353   0.0065
 HNT  C7    C  CR16   0  -0.271  -1.9605  -1.4851   0.0259
 HNT  C8    C  CR16   0  -0.292  -0.6251  -1.8335   0.0412
 HNT  C22   C  CH2    0  -0.146   4.1910  -0.5182   0.0213
 HNT  C8A   C  CR6    0   0.096   0.3810  -0.8669   0.0392
 HNT  N1    N  N      1   0.327  -3.6853   0.2574  -0.0113
 HNT  O3    O  O      0  -0.383  -3.9483   1.4379  -0.0228
 HNT  C4A   C  CR6    0   0.058   0.0290   0.4839   0.0256
 HNT  N41   N  NH1    0  -0.608   2.3577   1.0301   0.4586
 HNT  H11   H  HCH2   0   0.258   1.9716  -2.1209  -0.6273
 HNT  H12   H  HCH2   0   0.257   2.0694  -1.6513   1.0595
 HNT  H2    H  HCH1   0   0.215   2.6892   0.0388  -1.3916
 HNT  H41A  H  HCH2   0   0.227   1.1406   1.9510  -1.0292
 HNT  H42   H  HCH2   0   0.257   0.7877   2.3823   0.6363
 HNT  H5    H  HCR6   0   0.287  -1.5783   1.8942  -0.0084
 HNT  H7    H  HCR6   0   0.293  -2.7216  -2.2509   0.0269
 HNT  H8    H  HCR6   0   0.265  -0.3555  -2.8824   0.0506
 HNT  H22   H  HOH1   0   0.459   5.9315   0.3366  -0.0721
 HNT  H221  H  HCH2   0   0.203   4.4288  -1.4626  -0.4851
 HNT  H222  H  HCH2   0   0.198   4.2707  -0.6987   1.1016
 HNT  H41   H  HNH1   0   0.359   3.0592   1.7539   0.3707
 HNT  O22   O  OH1    0  -0.673   5.0459   0.5229  -0.3959

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
 HNT  C1   C2    single    1.522  0.020  1.522
 HNT  C1   C8A   single    1.502  0.020  1.502
 HNT  C1   H11   single    0.970  0.020  1.090
 HNT  C1   H12   single    0.970  0.020  1.090
 HNT  C2   C22   single    1.515  0.020  1.515
 HNT  C2   N41   single    1.452  0.020  1.452
 HNT  C2   H2    single    0.970  0.020  1.090
 HNT  O2   N1    single    1.210  0.020  1.210
 HNT  C4   C4A   single    1.505  0.020  1.505
 HNT  C4   N41   single    1.446  0.020  1.446
 HNT  C4   H41A  single    0.970  0.020  1.090
 HNT  C4   H42   single    0.970  0.020  1.090
 HNT  C5   C6    aromatic  1.385  0.020  1.385
 HNT  C5   C4A   aromatic  1.388  0.020  1.388
 HNT  C5   H5    single    0.930  0.020  1.080
 HNT  C6   C7    aromatic  1.389  0.020  1.389
 HNT  C6   N1    single    1.452  0.020  1.452
 HNT  C7   C8    aromatic  1.380  0.020  1.380
 HNT  C7   H7    single    0.930  0.020  1.080
 HNT  C8   C8A   aromatic  1.395  0.020  1.395
 HNT  C8   H8    single    0.930  0.020  1.080
 HNT  O22  C22   single    1.410  0.020  1.410
 HNT  O22  H22   single    0.850  0.020  0.980
 HNT  C22  H221  single    0.970  0.020  1.090
 HNT  C22  H222  single    0.970  0.020  1.090
 HNT  C8A  C4A   aromatic  1.396  0.020  1.396
 HNT  N1   O3    double    1.210  0.020  1.210
 HNT  N41  H41   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
 HNT  H12   C1   H11   106.53  3.000
 HNT  H12   C1   C8A   108.62  3.000
 HNT  H11   C1   C8A   109.56  3.000
 HNT  H12   C1   C2    109.38  3.000
 HNT  H11   C1   C2    110.18  3.000
 HNT  C8A   C1   C2    112.38  3.000
 HNT  H2    C2   N41   111.71  3.000
 HNT  H2    C2   C22   108.24  3.000
 HNT  N41   C2   C22   110.56  3.000
 HNT  H2    C2   C1    108.30  3.000
 HNT  N41   C2   C1    108.01  3.000
 HNT  C22   C2   C1    109.99  3.000
 HNT  H42   C4   H41A  106.32  3.000
 HNT  H42   C4   N41   109.23  3.000
 HNT  H41A  C4   N41   112.83  3.000
 HNT  H42   C4   C4A   109.47  3.000
 HNT  H41A  C4   C4A   107.94  3.000
 HNT  N41   C4   C4A   110.91  3.000
 HNT  H5    C5   C4A   119.44  3.000
 HNT  H5    C5   C6    120.81  3.000
 HNT  C4A   C5   C6    119.75  3.000
 HNT  N1    C6   C7    119.33  3.000
 HNT  N1    C6   C5    119.18  3.000
 HNT  C7    C6   C5    121.49  3.000
 HNT  H7    C7   C8    120.20  3.000
 HNT  H7    C7   C6    121.54  3.000
 HNT  C8    C7   C6    118.26  3.000
 HNT  H8    C8   C8A   119.44  3.000
 HNT  H8    C8   C7    119.04  3.000
 HNT  C8A   C8   C7    121.52  3.000
 HNT  H222  C22  H221  107.26  3.000
 HNT  H222  C22  O22   111.62  3.000
 HNT  H221  C22  O22   111.55  3.000
 HNT  H222  C22  C2    108.71  3.000
 HNT  H221  C22  C2    108.73  3.000
 HNT  O22   C22  C2    108.88  3.000
 HNT  C4A   C8A  C8    119.25  3.000
 HNT  C4A   C8A  C1    120.67  3.000
 HNT  C8    C8A  C1    120.08  3.000
 HNT  O3    N1   C6    118.26  3.000
 HNT  O3    N1   O2    123.63  3.000
 HNT  C6    N1   O2    118.11  3.000
 HNT  C8A   C4A  C5    119.73  3.000
 HNT  C8A   C4A  C4    120.55  3.000
 HNT  C5    C4A  C4    119.70  3.000
 HNT  H41   N41  C4    108.82  3.000
 HNT  H41   N41  C2    109.72  3.000
 HNT  C4    N41  C2    111.42  3.000
 HNT  H22   O22  C22   108.41  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
 HNT  CONST_01  C8   C7   C6   C5    0.00   0.0  0
 HNT  CONST_02  C8   C8A  C4A  C5    0.00   0.0  0
 HNT  CONST_03  C8A  C4A  C5   C6    0.00   0.0  0
 HNT  CONST_04  C8A  C8   C7   C6    0.00   0.0  0
 HNT  CONST_05  C4A  C5   C6   C7    0.00   0.0  0
 HNT  CONST_06  C4A  C8A  C8   C7    0.00   0.0  0
 HNT  CONST_07  N1   C6   C7   C8  180.00   0.0  0
 HNT  CONST_08  C4A  C5   C6   N1  180.00   0.0  0
 HNT  CONST_09  H8   C8   C8A  C1    0.00   0.0  0
 HNT  CONST_10  H5   C5   C4A  C4    0.00   0.0  0
 HNT  CONST_11  H7   C7   C6   C5  180.00   0.0  0
 HNT  CONST_12  C5   C6   N1   O2  180.00   0.0  0
 HNT  CONST_13  C7   C6   N1   O2    0.00   0.0  0
 HNT  CONST_14  O3   N1   C6   C5    0.00   0.0  0
 HNT  CONST_15  O3   N1   C6   C7  180.00   0.0  0
 HNT  Var_01    C8   C8A  C1   C2  165.34  30.0  1
 HNT  Var_02    C4A  C4   N41  C2   55.35  30.0  1
 HNT  Var_03    N41  C4   C4A  C5  161.17  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
 HNT  chir_01  C2  C1  C22  N41  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
 HNT  plan-1  C1   0.020
 HNT  plan-1  C4   0.020
 HNT  plan-1  C5   0.020
 HNT  plan-1  C6   0.020
 HNT  plan-1  C7   0.020
 HNT  plan-1  C8   0.020
 HNT  plan-1  C8A  0.020
 HNT  plan-1  N1   0.020
 HNT  plan-1  C4A  0.020
 HNT  plan-1  H5   0.020
 HNT  plan-1  H7   0.020
 HNT  plan-1  H8   0.020
 HNT  plan-2  O2   0.020
 HNT  plan-2  C6   0.020
 HNT  plan-2  N1   0.020
 HNT  plan-2  O3   0.020

