# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 05:13:19 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2R)-1-(2,6-dimethylphenoxy)propan-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N)COc1c(C)cccc1C
#
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
 505  505  (2R)-1-(2,6-dimethylphenoxy)propan-2-amine  ligand  30  13  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_505
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
 505  C1    C  CH3   0  -0.654  31.6953   3.5589  27.7279
 505  C2    C  CH1   0  -0.140  32.5893   4.7929  27.7175
 505  N3    N  NH2   0  -0.788  33.2539   4.9103  26.4265
 505  C4    C  CH2   0  -0.167  31.8292   6.0431  28.1416
 505  O5    O  O2    0  -0.491  30.7651   6.2641  27.2233
 505  C6    C  CR6   0   0.286  30.0446   7.4034  27.4353
 505  C7    C  CR6   0   0.020  28.9098   7.3440  28.2472
 505  C8    C  CH3   0  -0.720  28.4902   6.0533  28.8882
 505  C9    C  CR16  0  -0.321  28.1713   8.5101  28.4301
 505  C10   C  CR16  0  -0.245  28.5538   9.6982  27.8253
 505  C11   C  CR16  0  -0.321  29.6763   9.7291  27.0116
 505  C12   C  CR6   0   0.022  30.4412   8.5842  26.8033
 505  C13   C  CH3   0  -0.722  31.6458   8.6118  25.9074
 505  H1C1  H  HCH3  0   0.222  31.1971   3.4462  28.6914
 505  H1C2  H  HCH3  0   0.223  30.9231   3.6192  26.9599
 505  H1C3  H  HCH3  0   0.231  32.2826   2.6594  27.5440
 505  H2    H  HCH1  0   0.233  33.3677   4.6554  28.4753
 505  H3N1  H  HNH2  0   0.338  32.5648   5.0993  25.7077
 505  H3N2  H  HNH2  0   0.343  33.8760   5.7099  26.4311
 505  H4C1  H  HCH2  0   0.217  31.4397   5.9242  29.1601
 505  H4C2  H  HCH2  0   0.223  32.5101   6.9034  28.1511
 505  H8C1  H  HCH3  0   0.246  28.4819   5.2287  28.1755
 505  H8C2  H  HCH3  0   0.243  29.1629   5.7642  29.6985
 505  H8C3  H  HCH3  0   0.246  27.4919   6.1409  29.3148
 505  H9    H  HCR6  0   0.247  27.2859   8.4841  29.0544
 505  H10   H  HCR6  0   0.249  27.9691  10.5965  27.9765
 505  H11   H  HCR6  0   0.247  29.9656  10.6540  26.5266
 505  H131  H  HCH3  0   0.245  31.6548   7.7709  25.2145
 505  H132  H  HCH3  0   0.247  31.6711   9.5318  25.3252
 505  H133  H  HCH3  0   0.242  32.5765   8.5640  26.4767

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
 505  C1   C2    single    1.524  0.020  1.524
 505  C2   N3    single    1.457  0.020  1.457
 505  C2   C4    single    1.523  0.020  1.523
 505  C4   O5    single    1.423  0.020  1.423
 505  O5   C6    single    1.365  0.020  1.365
 505  C6   C7    aromatic  1.397  0.020  1.397
 505  C6   C12   aromatic  1.397  0.020  1.397
 505  C7   C8    single    1.501  0.020  1.501
 505  C7   C9    aromatic  1.392  0.020  1.392
 505  C9   C10   aromatic  1.387  0.020  1.387
 505  C10  C11   aromatic  1.387  0.020  1.387
 505  C11  C12   aromatic  1.393  0.020  1.393
 505  C12  C13   single    1.501  0.020  1.501
 505  C1   H1C1  single    0.970  0.020  1.090
 505  C1   H1C2  single    0.970  0.020  1.090
 505  C1   H1C3  single    0.970  0.020  1.090
 505  C2   H2    single    0.970  0.020  1.090
 505  N3   H3N1  single    0.890  0.020  1.040
 505  N3   H3N2  single    0.890  0.020  1.040
 505  C4   H4C1  single    0.970  0.020  1.090
 505  C4   H4C2  single    0.970  0.020  1.090
 505  C8   H8C1  single    0.970  0.020  1.090
 505  C8   H8C2  single    0.970  0.020  1.090
 505  C8   H8C3  single    0.970  0.020  1.090
 505  C9   H9    single    0.930  0.020  1.080
 505  C10  H10   single    0.930  0.020  1.080
 505  C11  H11   single    0.930  0.020  1.080
 505  C13  H131  single    0.970  0.020  1.090
 505  C13  H132  single    0.970  0.020  1.090
 505  C13  H133  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
 505  H1C3  C1   H1C2  107.96  3.000
 505  H1C3  C1   H1C1  108.05  3.000
 505  H1C2  C1   H1C1  107.73  3.000
 505  H1C3  C1   C2    110.55  3.000
 505  H1C2  C1   C2    111.46  3.000
 505  H1C1  C1   C2    110.96  3.000
 505  H2    C2   C4    105.37  3.000
 505  H2    C2   N3    107.40  3.000
 505  C4    C2   N3    114.09  3.000
 505  H2    C2   C1    108.10  3.000
 505  C4    C2   C1    111.72  3.000
 505  N3    C2   C1    109.82  3.000
 505  H3N2  N3   H3N1  105.88  3.000
 505  H3N2  N3   C2    109.86  3.000
 505  H3N1  N3   C2    109.47  3.000
 505  H4C2  C4   H4C1  107.30  3.000
 505  H4C2  C4   O5    110.35  3.000
 505  H4C1  C4   O5    110.52  3.000
 505  H4C2  C4   C2    109.65  3.000
 505  H4C1  C4   C2    110.29  3.000
 505  O5    C4   C2    108.72  3.000
 505  C6    O5   C4    115.11  3.000
 505  C12   C6   C7    121.99  3.000
 505  C12   C6   O5    119.05  3.000
 505  C7    C6   O5    118.94  3.000
 505  C9    C7   C8    121.05  3.000
 505  C9    C7   C6    118.15  3.000
 505  C8    C7   C6    120.80  3.000
 505  H8C3  C8   H8C2  107.17  3.000
 505  H8C3  C8   H8C1  108.05  3.000
 505  H8C2  C8   H8C1  106.84  3.000
 505  H8C3  C8   C7    110.75  3.000
 505  H8C2  C8   C7    111.86  3.000
 505  H8C1  C8   C7    111.92  3.000
 505  H9    C9   C10   119.81  3.000
 505  H9    C9   C7    119.27  3.000
 505  C10   C9   C7    120.92  3.000
 505  H10   C10  C11   120.04  3.000
 505  H10   C10  C9    120.07  3.000
 505  C11   C10  C9    119.88  3.000
 505  H11   C11  C12   119.22  3.000
 505  H11   C11  C10   119.85  3.000
 505  C12   C11  C10   120.93  3.000
 505  C13   C12  C11   120.98  3.000
 505  C13   C12  C6    120.89  3.000
 505  C11   C12  C6    118.12  3.000
 505  H133  C13  H132  107.21  3.000
 505  H133  C13  H131  106.89  3.000
 505  H132  C13  H131  108.17  3.000
 505  H133  C13  C12   111.83  3.000
 505  H132  C13  C12   110.68  3.000
 505  H131  C13  C12   111.83  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
 505  CONST_01  C10   C9   C7   C6     0.00   0.0  0
 505  CONST_02  C10   C11  C12  C6     0.00   0.0  0
 505  CONST_03  C11   C12  C6   C7     0.00   0.0  0
 505  CONST_04  C11   C10  C9   C7     0.00   0.0  0
 505  CONST_05  C12   C6   C7   C9     0.00   0.0  0
 505  CONST_06  C12   C11  C10  C9     0.00   0.0  0
 505  CONST_07  C9    C7   C6   O5   180.00   0.0  0
 505  CONST_08  C11   C12  C6   O5   180.00   0.0  0
 505  CONST_09  C13   C12  C6   C7   180.00   0.0  0
 505  CONST_10  C12   C6   C7   C8   180.00   0.0  0
 505  CONST_11  C10   C9   C7   C8   180.00   0.0  0
 505  CONST_12  C13   C12  C11  C10  180.00   0.0  0
 505  CONST_13  H9    C9   C7   C6   180.00   0.0  0
 505  CONST_14  H11   C11  C12  C6   180.00   0.0  0
 505  CONST_15  H10   C10  C9   C7   180.00   0.0  0
 505  Var_01    C7    C6   O5   C4   -91.49  30.0  2
 505  Var_02    H8C1  C8   C7   C6   -48.03  30.0  2
 505  Var_03    H131  C13  C12  C6    46.02  30.0  2
 505  Var_04    H4C1  C4   O5   C6    62.62  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
 505  chir_01  C2  C1  N3  C4  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
 505  plan-1  O5   0.020
 505  plan-1  C6   0.020
 505  plan-1  C7   0.020
 505  plan-1  C8   0.020
 505  plan-1  C9   0.020
 505  plan-1  C10  0.020
 505  plan-1  C11  0.020
 505  plan-1  C12  0.020
 505  plan-1  C13  0.020
 505  plan-1  H9   0.020
 505  plan-1  H10  0.020
 505  plan-1  H11  0.020

