# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 19:05:46 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (6-bromo-1'H,4H-spiro[1,3-benzodioxine-2,4'-piperidin]-1'-yl)methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCN1CCC2(CC1)OCc3cc(Br)ccc3O2
#
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
 QKV  QKV  (6-bromo-1'H,4H-spiro[1,3-benzodioxine-2,4'-piperidin]-1'-yl)methanol  ligand  34  18  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QKV
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
 QKV  N1    N   NT    0  -0.432  -4.5137   0.3945   0.5534
 QKV  C4    C   CR6   0   0.385   0.3804  -1.0901   0.0088
 QKV  C5    C   CH2   0  -0.499  -2.1171   0.2613   1.0103
 QKV  C6    C   CH2   0  -0.481  -3.1777  -1.3346  -0.5661
 QKV  C8    C   CH2   0  -0.302  -4.3605  -0.3813  -0.6656
 QKV  C10   C   CH2   0  -0.201  -0.3830   0.9382  -1.2224
 QKV  C13   C   CR16  0  -0.353   1.3678  -1.8706   0.6014
 QKV  C15   C   CR16  0  -0.227   2.6775  -1.4251   0.6357
 QKV  C14   C   CR6   0  -0.123   2.9906  -0.1913   0.0793
 QKV  C3    C   CR6   0  -0.073   0.7017   0.1371  -0.5639
 QKV  C11   C   CR16  0  -0.262   2.0150   0.5872  -0.5194
 QKV  O1    O   O2    0  -0.498  -0.8859  -1.5605  -0.0038
 QKV  C2    C   CT    0   0.450  -1.8981  -0.5865  -0.2417
 QKV  O2    O   O2    0  -0.485  -1.5579   0.1687  -1.3662
 QKV  C9    C   CH2   0  -0.288  -3.3207   1.1735   0.8329
 QKV  C1    C   CH2   0  -0.025  -5.6863   1.2392   0.5179
 QKV  O3    O   OH1   0  -0.674  -6.8701   0.4939   0.5739
 QKV  H5    H   HCH2  0   0.258  -2.3029  -0.4173   1.8460
 QKV  H5A   H   HCH2  0   0.261  -1.2385   0.8529   1.2784
 QKV  H6    H   HCH2  0   0.249  -3.3652  -2.0654   0.2233
 QKV  H6A   H   HCH2  0   0.257  -3.0655  -1.8850  -1.5032
 QKV  H8    H   HCH2  0   0.245  -5.2616  -0.9737  -0.8308
 QKV  H8A   H   HCH2  0   0.203  -4.2434   0.2733  -1.5454
 QKV  H10   H   HCH2  0   0.244  -0.5754   1.8636  -0.6653
 QKV  H10A  H   HCH2  0   0.276  -0.0795   1.2309  -2.2289
 QKV  H13   H   HCR6  0   0.276   1.1080  -2.8266   1.0377
 QKV  H15   H   HCR6  0   0.281   3.4367  -2.0380   1.1022
 QKV  H11   H   HCR6  0   0.281   2.2627   1.5436  -0.9637
 QKV  H9    H   HCH2  0   0.205  -3.1182   1.9150   0.0416
 QKV  H9A   H   HCH2  0   0.248  -3.4753   1.7396   1.7543
 QKV  H1    H   HCH2  0   0.218  -5.6492   1.8830   1.4009
 QKV  H1A   H   HCH2  0   0.184  -5.6830   1.8946  -0.3704
 QKV  HO3   H   HOH1  0   0.456  -7.2325   0.4069  -0.3109
 QKV  BR1   BR  BR    0  -0.054   4.7750   0.4286   0.1340

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
 QKV  C8   N1    single    1.453  0.020  1.453
 QKV  N1   C1    single    1.446  0.020  1.446
 QKV  N1   C9    single    1.452  0.020  1.452
 QKV  C13  C4    aromatic  1.391  0.020  1.391
 QKV  O1   C4    single    1.351  0.020  1.351
 QKV  C4   C3    aromatic  1.392  0.020  1.392
 QKV  C5   C2    single    1.528  0.020  1.528
 QKV  C5   C9    single    1.521  0.020  1.521
 QKV  C5   H5    single    0.970  0.020  1.090
 QKV  C5   H5A   single    0.970  0.020  1.090
 QKV  C8   C6    single    1.522  0.020  1.522
 QKV  C6   C2    single    1.517  0.020  1.517
 QKV  C6   H6    single    0.970  0.020  1.090
 QKV  C6   H6A   single    0.970  0.020  1.090
 QKV  C8   H8    single    0.970  0.020  1.090
 QKV  C8   H8A   single    0.970  0.020  1.090
 QKV  C3   C10   single    1.501  0.020  1.501
 QKV  O2   C10   single    1.412  0.020  1.412
 QKV  C10  H10   single    0.970  0.020  1.090
 QKV  C10  H10A  single    0.970  0.020  1.090
 QKV  C13  C15   aromatic  1.384  0.020  1.384
 QKV  C13  H13   single    0.930  0.020  1.080
 QKV  C15  C14   aromatic  1.389  0.020  1.389
 QKV  C15  H15   single    0.930  0.020  1.080
 QKV  C14  BR1   single    1.890  0.020  1.890
 QKV  C14  C11   aromatic  1.384  0.020  1.384
 QKV  C3   C11   aromatic  1.389  0.020  1.389
 QKV  C11  H11   single    0.930  0.020  1.080
 QKV  O1   C2    single    1.425  0.020  1.425
 QKV  C2   O2    single    1.397  0.020  1.397
 QKV  C9   H9    single    0.970  0.020  1.090
 QKV  C9   H9A   single    0.970  0.020  1.090
 QKV  C1   O3    single    1.400  0.020  1.400
 QKV  C1   H1    single    0.970  0.020  1.090
 QKV  C1   H1A   single    0.970  0.020  1.090
 QKV  O3   HO3   single    0.850  0.020  0.980

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
 QKV  C1    N1   C9   110.96  3.000
 QKV  C9    N1   C8   111.18  3.000
 QKV  C1    N1   C8   112.14  3.000
 QKV  O1    C4   C3   121.30  3.000
 QKV  C3    C4   C13  120.41  3.000
 QKV  O1    C4   C13  118.29  3.000
 QKV  H5A   C5   H5   106.58  3.000
 QKV  H5A   C5   C9   109.89  3.000
 QKV  H5    C5   C9   109.10  3.000
 QKV  H5A   C5   C2   112.72  3.000
 QKV  H5    C5   C2   107.85  3.000
 QKV  C9    C5   C2   110.53  3.000
 QKV  H6A   C6   H6   107.49  3.000
 QKV  H6A   C6   C2   110.19  3.000
 QKV  H6    C6   C2   108.67  3.000
 QKV  H6A   C6   C8   109.83  3.000
 QKV  H6    C6   C8   109.44  3.000
 QKV  C2    C6   C8   111.13  3.000
 QKV  H8A   C8   H8   106.81  3.000
 QKV  H8A   C8   C6   109.96  3.000
 QKV  H8    C8   C6   108.16  3.000
 QKV  H8A   C8   N1   111.32  3.000
 QKV  H8    C8   N1   109.26  3.000
 QKV  C6    C8   N1   111.18  3.000
 QKV  H10A  C10  H10  106.92  3.000
 QKV  H10A  C10  O2   106.48  3.000
 QKV  H10   C10  O2   111.44  3.000
 QKV  H10A  C10  C3   110.30  3.000
 QKV  H10   C10  C3   110.74  3.000
 QKV  O2    C10  C3   110.81  3.000
 QKV  H13   C13  C15  120.10  3.000
 QKV  H13   C13  C4   119.79  3.000
 QKV  C15   C13  C4   120.11  3.000
 QKV  H15   C15  C14  121.19  3.000
 QKV  H15   C15  C13  119.51  3.000
 QKV  C14   C15  C13  119.30  3.000
 QKV  C11   C14  BR1  119.57  3.000
 QKV  C11   C14  C15  120.92  3.000
 QKV  BR1   C14  C15  119.51  3.000
 QKV  C11   C3   C10  121.63  3.000
 QKV  C11   C3   C4   119.39  3.000
 QKV  C10   C3   C4   118.98  3.000
 QKV  H11   C11  C3   119.28  3.000
 QKV  H11   C11  C14  120.85  3.000
 QKV  C3    C11  C14  119.87  3.000
 QKV  C2    O1   C4   115.43  3.000
 QKV  O2    C2   O1   109.34  3.000
 QKV  O2    C2   C6   107.45  3.000
 QKV  O1    C2   C6   107.33  3.000
 QKV  O2    C2   C5   113.24  3.000
 QKV  O1    C2   C5   110.14  3.000
 QKV  C6    C2   C5   109.14  3.000
 QKV  C2    O2   C10  114.55  3.000
 QKV  H9A   C9   H9   106.42  3.000
 QKV  H9A   C9   C5   108.93  3.000
 QKV  H9    C9   C5   109.98  3.000
 QKV  H9A   C9   N1   108.91  3.000
 QKV  H9    C9   N1   111.92  3.000
 QKV  C5    C9   N1   110.54  3.000
 QKV  H1A   C1   H1   107.47  3.000
 QKV  H1A   C1   O3   110.54  3.000
 QKV  H1    C1   O3   108.05  3.000
 QKV  H1A   C1   N1   111.36  3.000
 QKV  H1    C1   N1   107.25  3.000
 QKV  O3    C1   N1   111.95  3.000
 QKV  HO3   O3   C1   109.29  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
 QKV  CONST_01  C14  C15  C13  C4     0.00   0.0  0
 QKV  CONST_02  C14  C11  C3   C4     0.00   0.0  0
 QKV  CONST_03  C11  C3   C4   C13    0.00   0.0  0
 QKV  CONST_04  C11  C14  C15  C13    0.00   0.0  0
 QKV  CONST_05  C3   C4   C13  C15    0.00   0.0  0
 QKV  CONST_06  C3   C11  C14  C15    0.00   0.0  0
 QKV  CONST_07  BR1  C14  C15  C13  180.00   0.0  0
 QKV  CONST_08  C3   C11  C14  BR1  180.00   0.0  0
 QKV  CONST_09  H15  C15  C13  C4   180.00   0.0  0
 QKV  CONST_10  H11  C11  C3   C4   180.00   0.0  0
 QKV  CONST_11  H13  C13  C15  C14  180.00   0.0  0
 QKV  Var_01    C2   C6   C8   N1   -56.19  30.0  1
 QKV  Var_02    C2   C5   C9   N1    58.30  30.0  1
 QKV  Var_03    C5   C2   O1   C4   -75.36  30.0  1
 QKV  Var_04    O2   C10  C3   C4   -10.96  30.0  1
 QKV  Var_05    C8   C6   C2   C5    53.56  30.0  3
 QKV  Var_06    C8   N1   C9   C5   -60.30  30.0  1
 QKV  Var_07    C9   N1   C8   C6    59.17  30.0  1
 QKV  Var_08    C9   C5   C2   C6   -54.66  30.0  3
 QKV  Var_09    O3   C1   N1   C8    69.39  30.0  3

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
 QKV  plan-1  C4   0.020
 QKV  plan-1  C10  0.020
 QKV  plan-1  C13  0.020
 QKV  plan-1  C15  0.020
 QKV  plan-1  C14  0.020
 QKV  plan-1  C3   0.020
 QKV  plan-1  C11  0.020
 QKV  plan-1  O1   0.020
 QKV  plan-1  H13  0.020
 QKV  plan-1  H15  0.020
 QKV  plan-1  H11  0.020
 QKV  plan-1  BR1  0.020

