# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:07:14 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: 4-[(1R)-2-(methylamino)-1-oxidanyl-ethyl]benzene-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC[C@H](O)c1ccc(O)c(O)c1
#
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
 ALE  ALE  4-[(1R)-2-(methylamino)-1-oxidanyl-ethyl]benzene-1,2-diol  ligand  26  13  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ALE
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
 ALE  C1    C  CR6   0   0.137  -0.0364   0.1226   0.2556
 ALE  C2    C  CR16  0  -0.442   0.9060  -0.8667   0.5228
 ALE  C3    C  CR6   0   0.278   2.2200  -0.7389   0.1011
 ALE  C4    C  CR6   0   0.278   2.6202   0.4051  -0.5998
 ALE  C5    C  CR16  0  -0.329   1.6835   1.3916  -0.8668
 ALE  C6    C  CR16  0  -0.340   0.3675   1.2526  -0.4458
 ALE  O1    O  OH1   0  -0.646   3.1793  -1.6653   0.3297
 ALE  O2    O  OH1   0  -0.635   3.8923   0.5713  -1.0220
 ALE  O3    O  OH1   0  -0.658  -1.8910   1.0178   1.5502
 ALE  C9    C  CH3   0  -0.516  -4.6671  -0.6956  -1.1484
 ALE  C8    C  CH2   0  -0.273  -2.4029  -0.2388  -0.4707
 ALE  C7    C  CH1   0  -0.090  -1.4656  -0.0442   0.7168
 ALE  H2    H  HCR6  0   0.270   0.6105  -1.7558   1.0713
 ALE  H6    H  HCR6  0   0.246  -0.3356   2.0430  -0.6811
 ALE  H7    H  HCH1  0   0.241  -1.5284  -0.9401   1.3414
 ALE  H1    H  HOH1  0   0.482   2.8271  -2.4095   0.8300
 ALE  H5    H  HCR6  0   0.264   1.9930   2.2763  -1.4097
 ALE  HA    H  HOH1  0   0.472   4.4428  -0.1646  -0.7303
 ALE  H3    H  HOH1  0   0.446  -1.9074   1.8310   1.0342
 ALE  H91C  H  HCH3  0   0.220  -4.4139  -1.5960  -1.7117
 ALE  H92C  H  HCH3  0   0.232  -5.6829  -0.8197  -0.7732
 ALE  H93C  H  HCH3  0   0.193  -4.6701   0.1447  -1.8568
 ALE  HB    H  HNH1  0   0.341  -4.0795   0.2310   0.5444
 ALE  H81C  H  HCH2  0   0.231  -2.0328  -1.0829  -1.0599
 ALE  H82C  H  HCH2  0   0.193  -2.3424   0.6447  -1.1321
 ALE  N1    N  NH1   0  -0.595  -3.7520  -0.5285  -0.0383

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
 ALE  C1  C2    aromatic  1.392  0.020  1.392
 ALE  C1  C6    aromatic  1.390  0.020  1.390
 ALE  C1  C7    single    1.511  0.020  1.511
 ALE  C2  C3    aromatic  1.386  0.020  1.386
 ALE  C3  C4    aromatic  1.400  0.020  1.400
 ALE  C3  O1    single    1.353  0.020  1.353
 ALE  C4  C5    aromatic  1.386  0.020  1.386
 ALE  C4  O2    single    1.351  0.020  1.351
 ALE  C5  C6    aromatic  1.389  0.020  1.389
 ALE  O3  C7    single    1.415  0.020  1.415
 ALE  C9  N1    single    1.448  0.020  1.448
 ALE  N1  C8    single    1.446  0.020  1.446
 ALE  C8  C7    single    1.525  0.020  1.525
 ALE  C2  H2    single    0.930  0.020  1.080
 ALE  C6  H6    single    0.930  0.020  1.080
 ALE  C7  H7    single    0.970  0.020  1.090
 ALE  O1  H1    single    0.850  0.020  0.980
 ALE  C5  H5    single    0.930  0.020  1.080
 ALE  O2  HA    single    0.850  0.020  0.980
 ALE  O3  H3    single    0.850  0.020  0.980
 ALE  C9  H91C  single    0.970  0.020  1.090
 ALE  C9  H92C  single    0.970  0.020  1.090
 ALE  C9  H93C  single    0.970  0.020  1.090
 ALE  N1  HB    single    0.890  0.020  1.040
 ALE  C8  H81C  single    0.970  0.020  1.090
 ALE  C8  H82C  single    0.970  0.020  1.090

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
 ALE  C7    C1  C6    121.24  3.000
 ALE  C7    C1  C2    120.21  3.000
 ALE  C6    C1  C2    118.54  3.000
 ALE  H2    C2  C3    119.16  3.000
 ALE  H2    C2  C1    119.65  3.000
 ALE  C3    C2  C1    121.19  3.000
 ALE  O1    C3  C4    116.19  3.000
 ALE  O1    C3  C2    123.90  3.000
 ALE  C4    C3  C2    119.91  3.000
 ALE  O2    C4  C5    119.25  3.000
 ALE  O2    C4  C3    121.75  3.000
 ALE  C5    C4  C3    119.00  3.000
 ALE  H5    C5  C6    120.30  3.000
 ALE  H5    C5  C4    118.99  3.000
 ALE  C6    C5  C4    120.70  3.000
 ALE  H6    C6  C5    118.42  3.000
 ALE  H6    C6  C1    120.93  3.000
 ALE  C5    C6  C1    120.65  3.000
 ALE  H1    O1  C3    110.94  3.000
 ALE  HA    O2  C4    110.44  3.000
 ALE  H3    O3  C7    108.85  3.000
 ALE  H93C  C9  H92C  107.84  3.000
 ALE  H93C  C9  H91C  107.37  3.000
 ALE  H92C  C9  H91C  107.44  3.000
 ALE  H93C  C9  N1    114.05  3.000
 ALE  H92C  C9  N1    109.77  3.000
 ALE  H91C  C9  N1    110.12  3.000
 ALE  H82C  C8  H81C  106.02  3.000
 ALE  H82C  C8  C7    109.28  3.000
 ALE  H81C  C8  C7    108.05  3.000
 ALE  H82C  C8  N1    112.97  3.000
 ALE  H81C  C8  N1    108.79  3.000
 ALE  C7    C8  N1    111.47  3.000
 ALE  H7    C7  C8    107.74  3.000
 ALE  H7    C7  O3    105.14  3.000
 ALE  C8    C7  O3    111.68  3.000
 ALE  H7    C7  C1    108.60  3.000
 ALE  C8    C7  C1    110.96  3.000
 ALE  O3    C7  C1    112.41  3.000
 ALE  HB    N1  C8    108.90  3.000
 ALE  HB    N1  C9    108.87  3.000
 ALE  C8    N1  C9    112.54  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
 ALE  CONST_01  C4    C3  C2  C1    0.00   0.0  0
 ALE  CONST_02  C4    C5  C6  C1    0.00   0.0  0
 ALE  CONST_03  C5    C6  C1  C2    0.00   0.0  0
 ALE  CONST_04  C5    C4  C3  C2    0.00   0.0  0
 ALE  CONST_05  C6    C1  C2  C3    0.00   0.0  0
 ALE  CONST_06  C6    C5  C4  C3    0.00   0.0  0
 ALE  CONST_07  O1    C3  C2  C1  180.00   0.0  0
 ALE  CONST_08  O2    C4  C3  C2  180.00   0.0  0
 ALE  CONST_09  C7    C1  C2  C3  180.00   0.0  0
 ALE  CONST_10  O1    C3  C4  C5  180.00   0.0  0
 ALE  CONST_11  C7    C1  C6  C5  180.00   0.0  0
 ALE  CONST_12  O2    C4  C5  C6  180.00   0.0  0
 ALE  CONST_13  H5    C5  C6  C1  180.00   0.0  0
 ALE  CONST_14  H6    C6  C1  C2  180.00   0.0  0
 ALE  CONST_15  H2    C2  C3  C4  180.00   0.0  0
 ALE  Var_01    C7    C8  N1  C9  179.03  30.0  3
 ALE  Var_02    H91C  C9  N1  C8   67.11  30.0  3

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
 ALE  chir_01  C7  C1  O3  C8  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
 ALE  plan-1  C1  0.020
 ALE  plan-1  C2  0.020
 ALE  plan-1  C3  0.020
 ALE  plan-1  C4  0.020
 ALE  plan-1  C5  0.020
 ALE  plan-1  C6  0.020
 ALE  plan-1  O1  0.020
 ALE  plan-1  O2  0.020
 ALE  plan-1  C7  0.020
 ALE  plan-1  H2  0.020
 ALE  plan-1  H6  0.020
 ALE  plan-1  H5  0.020

