# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 02:33:03 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: ~{N}-[(1~{S})-1-(2,3-dihydro-1,4-benzodioxin-6-yl)ethyl]-2-methyl-pyridin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1cccnc1C)c2ccc3OCCOc3c2
#
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
 6RY  6RY  ~{N}-[(1~{S})-1-(2,3-dihydro-1,4-benzodioxin-6-yl)ethyl]-2-methyl-pyridin-3-amine  ligand  38  20  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6RY
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
 6RY  C01  C  CH3   0  -0.657  -1.0474  -0.8205  -2.3701
 6RY  C02  C  CH1   0  -0.198  -0.6802  -0.6746  -0.8934
 6RY  N03  N  NH1   0  -0.692  -1.5748   0.2110  -0.1650
 6RY  C04  C  CR6   0   0.283  -2.8824  -0.1083   0.1018
 6RY  C05  C  CR6   0   0.169  -3.7684   0.8916   0.5731
 6RY  C06  C  CH3   0  -0.766  -3.2937   2.3046   0.7335
 6RY  N07  N  N     0  -0.409  -5.0243   0.6283   0.8930
 6RY  C08  C  CR16  0  -0.124  -5.4949  -0.6112   0.7784
 6RY  C09  C  CR16  0  -0.314  -4.7094  -1.6548   0.3288
 6RY  C10  C  CR16  0  -0.257  -3.3908  -1.4028  -0.0182
 6RY  C11  C  CR6   0   0.162   0.7391  -0.1901  -0.7052
 6RY  C12  C  CR16  0  -0.442   1.6250  -0.9162   0.0785
 6RY  C13  C  CR6   0   0.336   2.9316  -0.4871   0.2747
 6RY  C14  C  CR6   0   0.304   3.3652   0.7047  -0.3129
 6RY  O15  O  O2    0  -0.480   4.6245   1.1718  -0.1407
 6RY  C16  C  CH2   0  -0.226   5.3295   0.5630   0.9307
 6RY  C17  C  CH2   0  -0.227   5.1303  -0.9332   0.9032
 6RY  O18  O  O2    0  -0.481   3.7524  -1.2480   1.0366
 6RY  C19  C  CR16  0  -0.349   2.4822   1.4332  -1.0993
 6RY  C20  C  CR16  0  -0.319   1.1866   0.9871  -1.3022
 6RY  H1   H  HCH3  0   0.237  -0.3853  -1.5364  -2.8577
 6RY  H2   H  HCH3  0   0.240  -2.0705  -1.1791  -2.4872
 6RY  H3   H  HCH3  0   0.229  -0.9670   0.1293  -2.9001
 6RY  H4   H  HCH1  0   0.260  -0.7474  -1.6621  -0.4296
 6RY  H5   H  HNH1  0   0.390  -1.3841   1.1919  -0.2958
 6RY  H6   H  HCH3  0   0.247  -3.0001   2.7494  -0.2219
 6RY  H7   H  HCH3  0   0.262  -4.0869   2.9191   1.1531
 6RY  H8   H  HCH3  0   0.248  -2.4258   2.3686   1.3946
 6RY  H9   H  HCR6  0   0.247  -6.5310  -0.7689   1.0554
 6RY  H10  H  HCR6  0   0.261  -5.1155  -2.6540   0.2442
 6RY  H11  H  HCR6  0   0.275  -2.7740  -2.2166  -0.3756
 6RY  H12  H  HCR6  0   0.263   1.3094  -1.8416   0.5466
 6RY  H13  H  HCH2  0   0.261   6.3830   0.8080   0.8034
 6RY  H14  H  HCH2  0   0.243   4.9917   0.9769   1.8870
 6RY  H15  H  HCH2  0   0.244   5.5233  -1.3535  -0.0286
 6RY  H16  H  HCH2  0   0.261   5.6501  -1.4006   1.7382
 6RY  H17  H  HCR6  0   0.267   2.8224   2.3548  -1.5552
 6RY  H18  H  HCR6  0   0.252   0.5284   1.5741  -1.9309

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
 6RY  C01  C02  single    1.529  0.020  1.529
 6RY  C02  N03  single    1.454  0.020  1.454
 6RY  C02  C11  single    1.512  0.020  1.512
 6RY  C12  C11  aromatic  1.388  0.020  1.388
 6RY  C12  C13  aromatic  1.389  0.020  1.389
 6RY  N03  C04  single    1.372  0.020  1.372
 6RY  C11  C20  aromatic  1.394  0.020  1.394
 6RY  C10  C04  aromatic  1.396  0.020  1.396
 6RY  C10  C09  aromatic  1.387  0.020  1.387
 6RY  O18  C13  single    1.354  0.020  1.354
 6RY  O18  C17  single    1.420  0.020  1.420
 6RY  C04  C05  aromatic  1.417  0.020  1.417
 6RY  C09  C08  aromatic  1.381  0.020  1.381
 6RY  C13  C14  aromatic  1.398  0.020  1.398
 6RY  C05  C06  single    1.499  0.020  1.499
 6RY  C05  N07  aromatic  1.322  0.020  1.322
 6RY  C08  N07  aromatic  1.331  0.020  1.331
 6RY  C17  C16  single    1.510  0.020  1.510
 6RY  C20  C19  aromatic  1.385  0.020  1.385
 6RY  C14  C19  aromatic  1.389  0.020  1.389
 6RY  C14  O15  single    1.354  0.020  1.354
 6RY  C16  O15  single    1.420  0.020  1.420
 6RY  C01  H1   single    0.970  0.020  1.090
 6RY  C01  H2   single    0.970  0.020  1.090
 6RY  C01  H3   single    0.970  0.020  1.090
 6RY  C02  H4   single    0.970  0.020  1.090
 6RY  N03  H5   single    0.890  0.020  1.040
 6RY  C06  H6   single    0.970  0.020  1.090
 6RY  C06  H7   single    0.970  0.020  1.090
 6RY  C06  H8   single    0.970  0.020  1.090
 6RY  C08  H9   single    0.930  0.020  1.080
 6RY  C09  H10  single    0.930  0.020  1.080
 6RY  C10  H11  single    0.930  0.020  1.080
 6RY  C12  H12  single    0.930  0.020  1.080
 6RY  C16  H13  single    0.970  0.020  1.090
 6RY  C16  H14  single    0.970  0.020  1.090
 6RY  C17  H15  single    0.970  0.020  1.090
 6RY  C17  H16  single    0.970  0.020  1.090
 6RY  C19  H17  single    0.930  0.020  1.080
 6RY  C20  H18  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
 6RY  H3   C01  H2   107.66  3.000
 6RY  H3   C01  H1   108.05  3.000
 6RY  H2   C01  H1   107.81  3.000
 6RY  H3   C01  C02  111.63  3.000
 6RY  H2   C01  C02  111.13  3.000
 6RY  H1   C01  C02  110.41  3.000
 6RY  H4   C02  C11  107.13  3.000
 6RY  H4   C02  N03  107.44  3.000
 6RY  C11  C02  N03  108.67  3.000
 6RY  H4   C02  C01  108.00  3.000
 6RY  C11  C02  C01  112.11  3.000
 6RY  N03  C02  C01  113.21  3.000
 6RY  H5   N03  C04  115.60  3.000
 6RY  H5   N03  C02  114.29  3.000
 6RY  C04  N03  C02  122.81  3.000
 6RY  C10  C04  C05  117.08  3.000
 6RY  C05  C04  N03  119.77  3.000
 6RY  C10  C04  N03  123.10  3.000
 6RY  N07  C05  C06  117.55  3.000
 6RY  N07  C05  C04  122.27  3.000
 6RY  C06  C05  C04  120.18  3.000
 6RY  H8   C06  H7   108.22  3.000
 6RY  H8   C06  H6   106.93  3.000
 6RY  H7   C06  H6   107.64  3.000
 6RY  H8   C06  C05  111.80  3.000
 6RY  H7   C06  C05  110.05  3.000
 6RY  H6   C06  C05  112.01  3.000
 6RY  C08  N07  C05  120.03  3.000
 6RY  H9   C08  C09  121.11  3.000
 6RY  H9   C08  N07  116.84  3.000
 6RY  C09  C08  N07  122.04  3.000
 6RY  H10  C09  C10  120.35  3.000
 6RY  H10  C09  C08  120.64  3.000
 6RY  C10  C09  C08  119.01  3.000
 6RY  H11  C10  C09  119.22  3.000
 6RY  H11  C10  C04  121.21  3.000
 6RY  C09  C10  C04  119.56  3.000
 6RY  C20  C11  C12  118.61  3.000
 6RY  C20  C11  C02  121.26  3.000
 6RY  C12  C11  C02  120.13  3.000
 6RY  H12  C12  C13  118.47  3.000
 6RY  H12  C12  C11  120.30  3.000
 6RY  C13  C12  C11  121.23  3.000
 6RY  O18  C13  C14  121.85  3.000
 6RY  C14  C13  C12  119.72  3.000
 6RY  O18  C13  C12  118.43  3.000
 6RY  C19  C14  O15  118.84  3.000
 6RY  O15  C14  C13  121.95  3.000
 6RY  C19  C14  C13  119.21  3.000
 6RY  C16  O15  C14  114.19  3.000
 6RY  H14  C16  H13  108.38  3.000
 6RY  H14  C16  C17  110.47  3.000
 6RY  H13  C16  C17  110.40  3.000
 6RY  H14  C16  O15  110.10  3.000
 6RY  H13  C16  O15  107.20  3.000
 6RY  C17  C16  O15  110.23  3.000
 6RY  H16  C17  H15  108.44  3.000
 6RY  H16  C17  O18  107.22  3.000
 6RY  H15  C17  O18  110.06  3.000
 6RY  H16  C17  C16  110.40  3.000
 6RY  H15  C17  C16  110.40  3.000
 6RY  O18  C17  C16  110.25  3.000
 6RY  C17  O18  C13  114.26  3.000
 6RY  H17  C19  C20  120.41  3.000
 6RY  H17  C19  C14  119.01  3.000
 6RY  C20  C19  C14  120.58  3.000
 6RY  H18  C20  C19  118.61  3.000
 6RY  H18  C20  C11  120.75  3.000
 6RY  C19  C20  C11  120.63  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
 6RY  CONST_01  C08  C09  C10  C04    0.00   0.0  0
 6RY  CONST_02  C08  N07  C05  C04    0.00   0.0  0
 6RY  CONST_03  C09  C10  C04  C05    0.00   0.0  0
 6RY  CONST_04  C09  C08  N07  C05    0.00   0.0  0
 6RY  CONST_05  C10  C04  C05  N07    0.00   0.0  0
 6RY  CONST_06  C10  C09  C08  N07    0.00   0.0  0
 6RY  CONST_07  C14  C13  C12  C11    0.00   0.0  0
 6RY  CONST_08  C14  C19  C20  C11    0.00   0.0  0
 6RY  CONST_09  C19  C20  C11  C12    0.00   0.0  0
 6RY  CONST_10  C19  C14  C13  C12    0.00   0.0  0
 6RY  CONST_11  C20  C11  C12  C13    0.00   0.0  0
 6RY  CONST_12  C20  C19  C14  C13    0.00   0.0  0
 6RY  CONST_13  C13  C12  C11  C02  180.00   0.0  0
 6RY  CONST_14  C19  C20  C11  C02  180.00   0.0  0
 6RY  CONST_15  C09  C10  C04  N03  180.00   0.0  0
 6RY  CONST_16  N07  C05  C04  N03  180.00   0.0  0
 6RY  CONST_17  C10  C04  C05  C06  180.00   0.0  0
 6RY  CONST_18  C08  N07  C05  C06  180.00   0.0  0
 6RY  CONST_19  H10  C09  C10  C04  180.00   0.0  0
 6RY  CONST_20  H11  C10  C04  C05  180.00   0.0  0
 6RY  CONST_21  H9   C08  N07  C05  180.00   0.0  0
 6RY  CONST_22  H17  C19  C20  C11  180.00   0.0  0
 6RY  CONST_23  H18  C20  C11  C12  180.00   0.0  0
 6RY  CONST_24  H12  C12  C13  C14  180.00   0.0  0
 6RY  CONST_26  C05  C04  N03  C02  180.00   0.0  0
 6RY  Var_01    C16  C17  O18  C13   44.60  30.0  1
 6RY  Var_02    C17  C16  O15  C14   44.68  30.0  1
 6RY  Var_03    O18  C17  C16  O15  -60.34  30.0  1
 6RY  Var_04    C19  C14  O15  C16  164.59  30.0  1
 6RY  Var_05    H6   C06  C05  C04   63.32  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
 6RY  chir_01  C02  C01  N03  C11  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
 6RY  plan-1  N03  0.020
 6RY  plan-1  C04  0.020
 6RY  plan-1  C05  0.020
 6RY  plan-1  C06  0.020
 6RY  plan-1  N07  0.020
 6RY  plan-1  C08  0.020
 6RY  plan-1  C09  0.020
 6RY  plan-1  C10  0.020
 6RY  plan-1  H9   0.020
 6RY  plan-1  H10  0.020
 6RY  plan-1  H11  0.020
 6RY  plan-2  C02  0.020
 6RY  plan-2  C11  0.020
 6RY  plan-2  C12  0.020
 6RY  plan-2  C13  0.020
 6RY  plan-2  C14  0.020
 6RY  plan-2  O15  0.020
 6RY  plan-2  O18  0.020
 6RY  plan-2  C19  0.020
 6RY  plan-2  C20  0.020
 6RY  plan-2  H12  0.020
 6RY  plan-2  H17  0.020
 6RY  plan-2  H18  0.020
 6RY  plan-3  C02  0.020
 6RY  plan-3  N03  0.020
 6RY  plan-3  C04  0.020
 6RY  plan-3  H5   0.020

