# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 07:39:46 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (6aR)-2,3,6a,7,8,9-hexahydro-11H-[1,4]dioxino[2,3-g]pyrrolo[2,1-b][1,3]benzoxazin-11-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N2CCC[C@H]2Oc3cc4OCCOc4cc13
#
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
 CX6  CX6  (6aR)-2,3,6a,7,8,9-hexahydro-11H-[1,4]dioxino[2,3-g]pyrrolo[2,1-b][1,3]benzoxazin-11-one  ligand  31  18  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CX6
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
 CX6  O1    O  O     0  -0.482   1.3363   1.5285  -0.2207
 CX6  O2    O  O     0  -0.486   1.6244  -2.4736  -0.2151
 CX6  N1    N  NR6   0  -0.539   2.5778  -0.4470   0.1054
 CX6  C1    C  CR16  0   0.241   2.4091   0.9423   0.4806
 CX6  C2    C  CH2   0  -0.517   3.7415   1.5675   0.1219
 CX6  C3    C  CH2   0  -0.494   4.7238   0.4231   0.3655
 CX6  C4    C  CH2   0  -0.258   3.9675  -0.8202  -0.1043
 CX6  C5    C  CR6   0   0.594   1.5234  -1.2715  -0.0094
 CX6  C6    C  CR66  0  -0.192   0.2254  -0.5648   0.0689
 CX6  C7    C  CR66  0   0.378   0.1862   0.8207  -0.0987
 CX6  C8    C  CR16  0  -0.471  -1.0228   1.4879  -0.1892
 CX6  C9    C  CR6   0   0.348  -2.2091   0.7720  -0.0971
 CX6  C10   C  CR6   0   0.323  -2.1840  -0.6171   0.1126
 CX6  C11   C  CR16  0  -0.404  -0.9694  -1.2693   0.1769
 CX6  O3    O  O2    0  -0.473  -3.3640   1.4521  -0.2030
 CX6  O4    O  O2    0  -0.481  -3.3269  -1.3348   0.2449
 CX6  C12   C  CH2   0  -0.234  -4.4633  -0.5462   0.5607
 CX6  C13   C  CH2   0  -0.224  -4.5301   0.6496  -0.3562
 CX6  H1    H  HCR6  0   0.247   2.1996   1.0217   1.5564
 CX6  H21   H  HCH2  0   0.269   3.9579   2.4554   0.7134
 CX6  H22   H  HCH2  0   0.254   3.7341   1.8484  -0.9340
 CX6  H31   H  HCH2  0   0.250   4.9533   0.3425   1.4293
 CX6  H32   H  HCH2  0   0.265   5.6635   0.5586  -0.1665
 CX6  H41   H  HCH2  0   0.255   4.2307  -1.7108   0.4658
 CX6  H42   H  HCH2  0   0.247   4.1488  -1.0303  -1.1612
 CX6  H8    H  HCR6  0   0.284  -1.0519   2.5602  -0.3375
 CX6  H11   H  HCR6  0   0.274  -0.9501  -2.3445   0.3053
 CX6  H121  H  HCH2  0   0.246  -4.4229  -0.2247   1.6072
 CX6  H122  H  HCH2  0   0.266  -5.3412  -1.1763   0.4285
 CX6  H131  H  HCH2  0   0.265  -5.3836   1.2786  -0.1086
 CX6  H132  H  HCH2  0   0.250  -4.6256   0.3302  -1.3985

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
 CX6  O1   C1    single    1.409  0.020  1.409
 CX6  O1   C7    single    1.356  0.020  1.356
 CX6  O2   C5    double    1.224  0.020  1.224
 CX6  N1   C1    single    1.449  0.020  1.449
 CX6  N1   C4    single    1.454  0.020  1.454
 CX6  N1   C5    single    1.343  0.020  1.343
 CX6  C1   C2    single    1.515  0.020  1.515
 CX6  C1   H1    single    0.970  0.020  1.090
 CX6  C2   C3    single    1.528  0.020  1.528
 CX6  C2   H21   single    0.970  0.020  1.090
 CX6  C2   H22   single    0.970  0.020  1.090
 CX6  C3   C4    single    1.529  0.020  1.529
 CX6  C3   H31   single    0.970  0.020  1.090
 CX6  C3   H32   single    0.970  0.020  1.090
 CX6  C4   H41   single    0.970  0.020  1.090
 CX6  C4   H42   single    0.970  0.020  1.090
 CX6  C5   C6    single    1.480  0.020  1.480
 CX6  C6   C7    aromatic  1.396  0.020  1.396
 CX6  C6   C11   aromatic  1.391  0.020  1.391
 CX6  C7   C8    aromatic  1.384  0.020  1.384
 CX6  C8   C9    aromatic  1.389  0.020  1.389
 CX6  C8   H8    single    0.930  0.020  1.080
 CX6  C9   C10   aromatic  1.405  0.020  1.405
 CX6  C9   O3    single    1.345  0.020  1.345
 CX6  C10  C11   aromatic  1.380  0.020  1.380
 CX6  C10  O4    single    1.356  0.020  1.356
 CX6  C11  H11   single    0.930  0.020  1.080
 CX6  O3   C13   single    1.424  0.020  1.424
 CX6  O4   C12   single    1.419  0.020  1.419
 CX6  C12  C13   single    1.508  0.020  1.508
 CX6  C12  H121  single    0.970  0.020  1.090
 CX6  C12  H122  single    0.970  0.020  1.090
 CX6  C13  H131  single    0.970  0.020  1.090
 CX6  C13  H132  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
 CX6  C7    O1   C1    112.56  3.000
 CX6  C5    N1   C4    125.47  3.000
 CX6  C5    N1   C1    121.27  3.000
 CX6  C4    N1   C1    113.25  3.000
 CX6  H1    C1   C2    111.70  3.000
 CX6  H1    C1   N1    110.19  3.000
 CX6  C2    C1   N1    103.41  3.000
 CX6  H1    C1   O1    108.18  3.000
 CX6  C2    C1   O1    112.33  3.000
 CX6  N1    C1   O1    111.02  3.000
 CX6  H22   C2   H21   108.46  3.000
 CX6  H22   C2   C3    110.56  3.000
 CX6  H21   C2   C3    113.36  3.000
 CX6  H22   C2   C1    109.21  3.000
 CX6  H21   C2   C1    112.51  3.000
 CX6  C3    C2   C1    102.63  3.000
 CX6  H32   C3   H31   107.70  3.000
 CX6  H32   C3   C4    112.22  3.000
 CX6  H31   C3   C4    110.09  3.000
 CX6  H32   C3   C2    112.58  3.000
 CX6  H31   C3   C2    110.24  3.000
 CX6  C4    C3   C2    104.00  3.000
 CX6  H42   C4   H41   107.98  3.000
 CX6  H42   C4   C3    111.80  3.000
 CX6  H41   C4   C3    112.60  3.000
 CX6  H42   C4   N1    110.33  3.000
 CX6  H41   C4   N1    111.41  3.000
 CX6  C3    C4   N1    102.69  3.000
 CX6  C6    C5   N1    113.01  3.000
 CX6  C6    C5   O2    123.39  3.000
 CX6  N1    C5   O2    123.53  3.000
 CX6  C11   C6   C7    119.20  3.000
 CX6  C11   C6   C5    121.03  3.000
 CX6  C7    C6   C5    119.48  3.000
 CX6  C8    C7   C6    120.72  3.000
 CX6  C8    C7   O1    118.91  3.000
 CX6  C6    C7   O1    120.34  3.000
 CX6  H8    C8   C9    119.78  3.000
 CX6  H8    C8   C7    120.66  3.000
 CX6  C9    C8   C7    119.57  3.000
 CX6  O3    C9   C10   121.82  3.000
 CX6  O3    C9   C8    117.89  3.000
 CX6  C10   C9   C8    120.29  3.000
 CX6  O4    C10  C11   119.15  3.000
 CX6  O4    C10  C9    121.52  3.000
 CX6  C11   C10  C9    119.33  3.000
 CX6  H11   C11  C10   119.36  3.000
 CX6  H11   C11  C6    119.78  3.000
 CX6  C10   C11  C6    120.85  3.000
 CX6  C13   O3   C9    115.27  3.000
 CX6  C12   O4   C10   113.74  3.000
 CX6  H122  C12  H121  108.39  3.000
 CX6  H122  C12  C13   110.45  3.000
 CX6  H121  C12  C13   110.47  3.000
 CX6  H122  C12  O4    107.28  3.000
 CX6  H121  C12  O4    110.26  3.000
 CX6  C13   C12  O4    109.93  3.000
 CX6  H132  C13  H131  108.47  3.000
 CX6  H132  C13  C12   110.58  3.000
 CX6  H131  C13  C12   110.77  3.000
 CX6  H132  C13  O3    109.78  3.000
 CX6  H131  C13  O3    106.97  3.000
 CX6  C12   C13  O3    110.19  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
 CX6  CONST_01  C9   C8   C7   C6     0.00   0.0  0
 CX6  CONST_02  C9   C10  C11  C6     0.00   0.0  0
 CX6  CONST_03  C10  C11  C6   C7     0.00   0.0  0
 CX6  CONST_04  C10  C9   C8   C7     0.00   0.0  0
 CX6  CONST_05  C11  C6   C7   C8     0.00   0.0  0
 CX6  CONST_06  C11  C10  C9   C8     0.00   0.0  0
 CX6  CONST_07  C6   C5   N1   C1     0.00   0.0  0
 CX6  CONST_08  C6   C5   N1   C4   180.00   0.0  0
 CX6  CONST_09  C1   N1   C5   O2   180.00   0.0  0
 CX6  CONST_10  C4   N1   C5   O2     0.00   0.0  0
 CX6  CONST_11  H8   C8   C7   O1     0.00   0.0  0
 CX6  CONST_12  H11  C11  C6   C5     0.00   0.0  0
 CX6  Var_01    C2   C3   C4   N1   -27.85  30.0  1
 CX6  Var_02    C7   C6   C5   N1    16.31  30.0  1
 CX6  Var_03    C6   C7   O1   C1   -30.37  30.0  1
 CX6  Var_04    C3   C4   N1   C1     7.71  30.0  1
 CX6  Var_05    C4   C3   C2   C1    37.54  30.0  1
 CX6  Var_06    C12  C13  O3   C9    41.63  30.0  1
 CX6  Var_07    C13  C12  O4   C10   47.73  30.0  1
 CX6  Var_08    O4   C12  C13  O3   -60.36  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
 CX6  chir_01  C1  O1  N1  C2  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
 CX6  plan-1  O2   0.020
 CX6  plan-1  N1   0.020
 CX6  plan-1  C1   0.020
 CX6  plan-1  C4   0.020
 CX6  plan-1  C5   0.020
 CX6  plan-1  C6   0.020
 CX6  plan-2  O1   0.020
 CX6  plan-2  C5   0.020
 CX6  plan-2  C6   0.020
 CX6  plan-2  C7   0.020
 CX6  plan-2  C8   0.020
 CX6  plan-2  C9   0.020
 CX6  plan-2  C10  0.020
 CX6  plan-2  C11  0.020
 CX6  plan-2  O3   0.020
 CX6  plan-2  O4   0.020
 CX6  plan-2  H8   0.020
 CX6  plan-2  H11  0.020

