# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 12:10:27 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(2,3-dihydro-1,4-benzodioxin-6-yl)-1H-pyrrole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1COc2cc(ccc2O1)c3[nH]ccc3
#
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
 YEY  YEY  2-(2,3-dihydro-1,4-benzodioxin-6-yl)-1H-pyrrole  ligand  26  15  .  2022-03-29  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YEY
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
 YEY  C4    C  CR16  0  -0.455  71.3401  39.2861  35.5687
 YEY  C5    C  CR6   0   0.074  72.5309  38.7212  36.0255
 YEY  C6    C  CR16  0  -0.326  72.5531  38.1780  37.3130
 YEY  C7    C  CR16  0  -0.348  71.4162  38.1857  38.1035
 YEY  C8    C  CR5   0   0.332  73.7056  38.7126  35.1602
 YEY  C9    C  CR15  0  -0.073  75.8746  38.6335  34.6179
 YEY  C10   C  CR15  0  -0.343  75.1690  38.7078  33.4416
 YEY  C11   C  CR15  0  -0.398  73.7972  38.7578  33.7829
 YEY  N     N  NR15  0  -0.641  74.9811  38.6334  35.6405
 YEY  C3    C  CR6   0   0.351  70.1988  39.2937  36.3549
 YEY  O     O  O2    0  -0.478  69.0787  39.8662  35.8546
 YEY  C2    C  CR6   0   0.301  70.2295  38.7325  37.6366
 YEY  O1    O  O2    0  -0.475  69.1361  38.7050  38.4350
 YEY  C1    C  CH2   0  -0.227  67.9179  38.9644  37.7562
 YEY  C     C  CH2   0  -0.226  68.0802  40.1416  36.8250
 YEY  H41   H  HCR6  0   0.257  71.2915  39.7464  34.5892
 YEY  H61   H  HCR6  0   0.247  73.4492  37.7134  37.7041
 YEY  H71   H  HCR6  0   0.265  71.4397  37.7510  39.0953
 YEY  H91   H  HCR5  0   0.267  76.9351  38.5889  34.8034
 YEY  H101  H  HCR5  0   0.241  75.5906  38.7181  32.4490
 YEY  H111  H  HCR5  0   0.242  72.9638  38.7961  33.0984
 YEY  H1    H  HNR5  0   0.410  75.2375  38.6290  36.6144
 YEY  H11   H  HCH2  0   0.260  67.1658  39.1794  38.5144
 YEY  H12   H  HCH2  0   0.241  67.6004  38.0768  37.1979
 YEY  HC2   H  HCH2  0   0.242  68.3427  41.0419  37.3911
 YEY  HC3   H  HCH2  0   0.259  67.1524  40.3327  36.2872

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
 YEY  N    C8    aromatic  1.365  0.020  1.365
 YEY  N    C9    aromatic  1.358  0.020  1.358
 YEY  C    O     single    1.419  0.020  1.419
 YEY  C    C1    single    1.510  0.020  1.510
 YEY  O    C3    single    1.354  0.020  1.354
 YEY  C1   O1    single    1.418  0.020  1.418
 YEY  C10  C11   aromatic  1.414  0.020  1.414
 YEY  C10  C9    aromatic  1.374  0.020  1.374
 YEY  C11  C8    aromatic  1.381  0.020  1.381
 YEY  C2   C3    aromatic  1.400  0.020  1.400
 YEY  C2   C7    aromatic  1.388  0.020  1.388
 YEY  C2   O1    single    1.354  0.020  1.354
 YEY  C3   C4    aromatic  1.386  0.020  1.386
 YEY  C4   C5    aromatic  1.395  0.020  1.395
 YEY  C5   C6    aromatic  1.398  0.020  1.398
 YEY  C5   C8    single    1.459  0.020  1.459
 YEY  C6   C7    aromatic  1.385  0.020  1.385
 YEY  C4   H41   single    0.930  0.020  1.080
 YEY  C6   H61   single    0.930  0.020  1.080
 YEY  C7   H71   single    0.930  0.020  1.080
 YEY  C9   H91   single    0.930  0.020  1.080
 YEY  C10  H101  single    0.930  0.020  1.080
 YEY  C11  H111  single    0.930  0.020  1.080
 YEY  N    H1    single    0.860  0.020  1.020
 YEY  C1   H11   single    0.970  0.020  1.090
 YEY  C1   H12   single    0.970  0.020  1.090
 YEY  C    HC2   single    0.970  0.020  1.090
 YEY  C    HC3   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
 YEY  H41   C4   C3   118.27  3.000
 YEY  H41   C4   C5   120.43  3.000
 YEY  C3    C4   C5   121.30  3.000
 YEY  C8    C5   C6   122.09  3.000
 YEY  C8    C5   C4   119.70  3.000
 YEY  C6    C5   C4   118.21  3.000
 YEY  H61   C6   C7   118.41  3.000
 YEY  H61   C6   C5   120.85  3.000
 YEY  C7    C6   C5   120.71  3.000
 YEY  H71   C7   C2   119.00  3.000
 YEY  H71   C7   C6   120.18  3.000
 YEY  C2    C7   C6   120.82  3.000
 YEY  N     C8   C11  106.90  3.000
 YEY  C11   C8   C5   130.14  3.000
 YEY  N     C8   C5   122.95  3.000
 YEY  H91   C9   N    121.20  3.000
 YEY  H91   C9   C10  130.93  3.000
 YEY  N     C9   C10  107.87  3.000
 YEY  H101  C10  C11  126.93  3.000
 YEY  H101  C10  C9   126.00  3.000
 YEY  C11   C10  C9   107.06  3.000
 YEY  H111  C11  C10  126.67  3.000
 YEY  H111  C11  C8   125.62  3.000
 YEY  C10   C11  C8   107.69  3.000
 YEY  H1    N    C9   124.10  3.000
 YEY  H1    N    C8   125.33  3.000
 YEY  C9    N    C8   110.48  3.000
 YEY  C2    C3   O    121.74  3.000
 YEY  C2    C3   C4   119.95  3.000
 YEY  O     C3   C4   118.30  3.000
 YEY  C     O    C3   114.30  3.000
 YEY  O1    C2   C3   122.03  3.000
 YEY  O1    C2   C7   118.96  3.000
 YEY  C3    C2   C7   119.01  3.000
 YEY  C1    O1   C2   114.06  3.000
 YEY  H12   C1   H11  108.33  3.000
 YEY  H12   C1   C    110.39  3.000
 YEY  H11   C1   C    110.47  3.000
 YEY  H12   C1   O1   110.16  3.000
 YEY  H11   C1   O1   107.22  3.000
 YEY  C     C1   O1   110.21  3.000
 YEY  HC3   C    HC2  108.36  3.000
 YEY  HC3   C    C1   110.48  3.000
 YEY  HC2   C    C1   110.35  3.000
 YEY  HC3   C    O    107.20  3.000
 YEY  HC2   C    O    110.13  3.000
 YEY  C1    C    O    110.25  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
 YEY  CONST_01  C7    C2   C3   C4     0.00   0.0  0
 YEY  CONST_02  C7    C6   C5   C4     0.00   0.0  0
 YEY  CONST_05  C2    C3   C4   C5     0.00   0.0  0
 YEY  CONST_06  C2    C7   C6   C5     0.00   0.0  0
 YEY  CONST_07  C9    N    C8   C5   180.00   0.0  0
 YEY  CONST_08  C10   C11  C8   C5   180.00   0.0  0
 YEY  CONST_09  C3    C4   C5   C6     0.00   0.0  0
 YEY  CONST_12  C3    C2   C7   C6     0.00   0.0  0
 YEY  CONST_13  C8    C5   C6   C7   180.00   0.0  0
 YEY  CONST_14  C10   C9   N    C8     0.00   0.0  0
 YEY  CONST_15  C9    C10  C11  C8     0.00   0.0  0
 YEY  CONST_16  C3    C4   C5   C8   180.00   0.0  0
 YEY  CONST_17  C11   C8   N    C9     0.00   0.0  0
 YEY  CONST_18  N     C8   C11  C10    0.00   0.0  0
 YEY  CONST_19  N     C9   C10  C11    0.00   0.0  0
 YEY  CONST_20  H61   C6   C5   C4   180.00   0.0  0
 YEY  CONST_21  H71   C7   C6   C5   180.00   0.0  0
 YEY  CONST_22  H1    N    C8   C5     0.00   0.0  0
 YEY  CONST_23  H111  C11  C8   C5     0.00   0.0  0
 YEY  CONST_24  H41   C4   C5   C6   180.00   0.0  0
 YEY  CONST_25  H91   C9   N    C8   180.00   0.0  0
 YEY  CONST_26  H101  C10  C11  C8   180.00   0.0  0
 YEY  Var_01    C1    C    O    C3   -44.38  30.0  1
 YEY  Var_02    O1    C1   C    O     60.61  30.0  1
 YEY  Var_03    C     C1   O1   C2   -44.89  30.0  1

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
 YEY  plan-1  C5    0.020
 YEY  plan-1  C8    0.020
 YEY  plan-1  C9    0.020
 YEY  plan-1  C10   0.020
 YEY  plan-1  C11   0.020
 YEY  plan-1  N     0.020
 YEY  plan-1  H91   0.020
 YEY  plan-1  H101  0.020
 YEY  plan-1  H111  0.020
 YEY  plan-1  H1    0.020
 YEY  plan-2  C4    0.020
 YEY  plan-2  C5    0.020
 YEY  plan-2  C6    0.020
 YEY  plan-2  C7    0.020
 YEY  plan-2  C8    0.020
 YEY  plan-2  C3    0.020
 YEY  plan-2  O     0.020
 YEY  plan-2  C2    0.020
 YEY  plan-2  O1    0.020
 YEY  plan-2  H41   0.020
 YEY  plan-2  H61   0.020
 YEY  plan-2  H71   0.020

