# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 17:09:28 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: ~{N}-[[(3~{R})-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]furan-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NC[C@@H]1COc2ccccc2O1)c3occc3
#
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
 9RK  9RK  ~{N}-[[(3~{R})-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]furan-2-carboxamide  ligand  32  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9RK
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
 9RK  C1   C  CR16  0  -0.265  -5.0200   1.4830   0.4599
 9RK  C2   C  CR16  0  -0.267  -4.0829   2.3368  -0.1087
 9RK  C3   C  CR16  0  -0.360  -2.8215   1.8615  -0.4344
 9RK  C4   C  CR6   0   0.314  -2.4935   0.5312  -0.2072
 9RK  C5   C  CR6   0   0.313  -3.4416  -0.3319   0.3488
 9RK  C6   C  CR16  0  -0.363  -4.7005   0.1518   0.6812
 9RK  C8   C  CH1   0  -0.030  -0.8718  -1.1419   0.0417
 9RK  C11  C  CH2   0  -0.302   0.3706  -1.6278  -0.6792
 9RK  C16  C  CR15  0  -0.322   4.9014   0.0023   0.6500
 9RK  O7   O  O2    0  -0.491  -1.2484   0.1037  -0.5319
 9RK  C9   C  CH2   0  -0.194  -2.0168  -2.1260  -0.0905
 9RK  O10  O  O2    0  -0.479  -3.1657  -1.6383   0.5791
 9RK  N12  N  NH1   0  -0.651   1.4737  -0.7110  -0.5360
 9RK  C13  C  C     0   0.493   2.6328  -1.0342   0.0648
 9RK  C14  C  CR5   0   0.226   3.6509   0.0249   0.1202
 9RK  C17  C  CR15  0  -0.332   5.4482   1.2957   0.4274
 9RK  C18  C  CR15  0   0.018   4.4880   2.0015  -0.2199
 9RK  O19  O  O     0  -0.411   3.3964   1.2418  -0.4106
 9RK  H1   H  HCR6  0   0.257  -6.0036   1.8468   0.7247
 9RK  H2   H  HCR6  0   0.256  -4.3259   3.3751  -0.2900
 9RK  H3   H  HCR6  0   0.266  -2.0770   2.5179  -0.8680
 9RK  H4   H  HCR6  0   0.267  -5.4253  -0.5263   1.1150
 9RK  H5   H  HCH1  0   0.259  -0.6416  -0.9956   1.1050
 9RK  H6   H  HCH2  0   0.271   0.6599  -2.5898  -0.2603
 9RK  H7   H  HCH2  0   0.264   0.1534  -1.7839  -1.7393
 9RK  H9   H  HCH2  0   0.240  -2.2428  -2.3068  -1.1476
 9RK  H10  H  HCH2  0   0.264  -1.7571  -3.0767   0.3736
 9RK  H11  H  HNH1  0   0.408   1.3577   0.2142  -0.9189
 9RK  H12  H  HCR5  0   0.274   6.4246   1.6526   0.7102
 9RK  H13  H  HCR5  0   0.289   4.4448   3.0125  -0.5915
 9RK  H8   H  HCR5  0   0.275   5.3743  -0.8333   1.1389
 9RK  O15  O  O     0  -0.484   2.8749  -2.1307   0.5514

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
 9RK  C17  C18  aromatic  1.356  0.020  1.356
 9RK  C17  C16  aromatic  1.422  0.020  1.422
 9RK  C18  O19  aromatic  1.343  0.020  1.343
 9RK  C16  C14  aromatic  1.358  0.020  1.358
 9RK  O19  C14  aromatic  1.352  0.020  1.352
 9RK  C14  C13  single    1.470  0.020  1.470
 9RK  C1   C6   aromatic  1.387  0.020  1.387
 9RK  C1   C2   aromatic  1.389  0.020  1.389
 9RK  C6   C5   aromatic  1.389  0.020  1.389
 9RK  C13  N12  single    1.345  0.020  1.345
 9RK  C13  O15  double    1.224  0.020  1.224
 9RK  O10  C5   single    1.355  0.020  1.355
 9RK  O10  C9   single    1.416  0.020  1.416
 9RK  C2   C3   aromatic  1.387  0.020  1.387
 9RK  C5   C4   aromatic  1.397  0.020  1.397
 9RK  N12  C11  single    1.442  0.020  1.442
 9RK  C9   C8   single    1.516  0.020  1.516
 9RK  C4   C3   aromatic  1.389  0.020  1.389
 9RK  C4   O7   single    1.356  0.020  1.356
 9RK  O7   C8   single    1.422  0.020  1.422
 9RK  C8   C11  single    1.516  0.020  1.516
 9RK  C1   H1   single    0.930  0.020  1.080
 9RK  C2   H2   single    0.930  0.020  1.080
 9RK  C3   H3   single    0.930  0.020  1.080
 9RK  C6   H4   single    0.930  0.020  1.080
 9RK  C8   H5   single    0.970  0.020  1.090
 9RK  C11  H6   single    0.970  0.020  1.090
 9RK  C11  H7   single    0.970  0.020  1.090
 9RK  C16  H8   single    0.930  0.020  1.080
 9RK  C9   H9   single    0.970  0.020  1.090
 9RK  C9   H10  single    0.970  0.020  1.090
 9RK  N12  H11  single    0.860  0.020  1.020
 9RK  C17  H12  single    0.930  0.020  1.080
 9RK  C18  H13  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
 9RK  H1   C1   C6   119.56  3.000
 9RK  H1   C1   C2   120.45  3.000
 9RK  C6   C1   C2   119.99  3.000
 9RK  H2   C2   C3   119.60  3.000
 9RK  H2   C2   C1   120.46  3.000
 9RK  C3   C2   C1   119.93  3.000
 9RK  H3   C3   C4   118.92  3.000
 9RK  H3   C3   C2   120.77  3.000
 9RK  C4   C3   C2   120.31  3.000
 9RK  O7   C4   C5   121.57  3.000
 9RK  O7   C4   C3   118.67  3.000
 9RK  C5   C4   C3   119.76  3.000
 9RK  O10  C5   C6   118.66  3.000
 9RK  O10  C5   C4   121.67  3.000
 9RK  C6   C5   C4   119.68  3.000
 9RK  H4   C6   C5   118.97  3.000
 9RK  H4   C6   C1   120.71  3.000
 9RK  C5   C6   C1   120.32  3.000
 9RK  H5   C8   C9   109.24  3.000
 9RK  H5   C8   O7   109.24  3.000
 9RK  C9   C8   O7   109.48  3.000
 9RK  H5   C8   C11  109.35  3.000
 9RK  O7   C8   C11  107.82  3.000
 9RK  C9   C8   C11  111.68  3.000
 9RK  H7   C11  H6   107.45  3.000
 9RK  H7   C11  N12  109.82  3.000
 9RK  H6   C11  N12  108.70  3.000
 9RK  H7   C11  C8   110.11  3.000
 9RK  H6   C11  C8   108.55  3.000
 9RK  N12  C11  C8   112.08  3.000
 9RK  H8   C16  C17  127.42  3.000
 9RK  H8   C16  C14  126.44  3.000
 9RK  C17  C16  C14  106.14  3.000
 9RK  C8   O7   C4   115.01  3.000
 9RK  H10  C9   H9   108.43  3.000
 9RK  H10  C9   O10  107.01  3.000
 9RK  H9   C9   O10  110.21  3.000
 9RK  H10  C9   C8   110.45  3.000
 9RK  H9   C9   C8   110.31  3.000
 9RK  O10  C9   C8   110.36  3.000
 9RK  C9   O10  C5   114.63  3.000
 9RK  H11  N12  C13  119.30  3.000
 9RK  H11  N12  C11  117.26  3.000
 9RK  C13  N12  C11  123.44  3.000
 9RK  C14  C13  N12  116.14  3.000
 9RK  N12  C13  O15  124.29  3.000
 9RK  C14  C13  O15  119.57  3.000
 9RK  O19  C14  C13  120.22  3.000
 9RK  C13  C14  C16  129.81  3.000
 9RK  O19  C14  C16  109.96  3.000
 9RK  H12  C17  C18  126.48  3.000
 9RK  H12  C17  C16  127.50  3.000
 9RK  C18  C17  C16  106.01  3.000
 9RK  H13  C18  O19  116.67  3.000
 9RK  H13  C18  C17  132.92  3.000
 9RK  O19  C18  C17  110.41  3.000
 9RK  C18  O19  C14  107.48  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
 9RK  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 9RK  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 9RK  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 9RK  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 9RK  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 9RK  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 9RK  CONST_07  O19  C18  C17  C16    0.00   0.0  0
 9RK  CONST_08  C18  O19  C14  C16    0.00   0.0  0
 9RK  CONST_09  C18  C17  C16  C14    0.00   0.0  0
 9RK  CONST_10  C17  C18  O19  C14    0.00   0.0  0
 9RK  CONST_11  O19  C14  C16  C17    0.00   0.0  0
 9RK  CONST_12  C17  C16  C14  C13  180.00   0.0  0
 9RK  CONST_13  C18  O19  C14  C13  180.00   0.0  0
 9RK  CONST_14  H3   C3   C2   C1   180.00   0.0  0
 9RK  CONST_15  H4   C6   C1   C2   180.00   0.0  0
 9RK  CONST_16  H1   C1   C2   C3   180.00   0.0  0
 9RK  CONST_17  H2   C2   C3   C4   180.00   0.0  0
 9RK  CONST_18  H13  C18  C17  C16  180.00   0.0  0
 9RK  CONST_19  H12  C17  C16  C14  180.00   0.0  0
 9RK  CONST_20  H8   C16  C17  C18  180.00   0.0  0
 9RK  CONST_21  C14  C13  N12  C11  180.00   0.0  0
 9RK  CONST_22  H11  N12  C13  C14    0.00   0.0  0
 9RK  CONST_23  O15  C13  N12  C11    0.00   0.0  0
 9RK  Var_01    C8   C9   O10  C5    45.01  30.0  1
 9RK  Var_02    C16  C14  C13  O15    0.13  30.0  2
 9RK  Var_03    C13  N12  C11  C8   118.05  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
 9RK  chir_01  C8  C9  O7  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
 9RK  plan-1  C16  0.020
 9RK  plan-1  C13  0.020
 9RK  plan-1  C14  0.020
 9RK  plan-1  C17  0.020
 9RK  plan-1  C18  0.020
 9RK  plan-1  O19  0.020
 9RK  plan-1  H12  0.020
 9RK  plan-1  H13  0.020
 9RK  plan-1  H8   0.020
 9RK  plan-2  C1   0.020
 9RK  plan-2  C2   0.020
 9RK  plan-2  C3   0.020
 9RK  plan-2  C4   0.020
 9RK  plan-2  C5   0.020
 9RK  plan-2  C6   0.020
 9RK  plan-2  O7   0.020
 9RK  plan-2  O10  0.020
 9RK  plan-2  H1   0.020
 9RK  plan-2  H2   0.020
 9RK  plan-2  H3   0.020
 9RK  plan-2  H4   0.020
 9RK  plan-3  C11  0.020
 9RK  plan-3  N12  0.020
 9RK  plan-3  C13  0.020
 9RK  plan-3  C14  0.020
 9RK  plan-3  H11  0.020
 9RK  plan-3  O15  0.020

