# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:55:10 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: 3-oxidanyl-~{N}-[[(2~{R})-oxolan-2-yl]methyl]naphthalene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc2ccccc2cc1C(=O)NC[C@H]3CCCO3
#
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
 KBF  KBF  3-oxidanyl-~{N}-[[(2~{R})-oxolan-2-yl]methyl]naphthalene-2-carboxamide  ligand  37  20  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KBF
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
 KBF  C3   C  CR66  0   0.137   3.5418   0.0426  -0.1058
 KBF  C4   C  CR16  0  -0.321   4.8817   0.5034  -0.1010
 KBF  C5   C  CR16  0  -0.250   5.1580   1.8380   0.0098
 KBF  C6   C  CR16  0  -0.267   4.1152   2.7858   0.1203
 KBF  C7   C  CR16  0  -0.301   2.8133   2.3712   0.1207
 KBF  C8   C  CR66  0   0.119   2.4964   0.9952   0.0122
 KBF  C9   C  CR16  0  -0.362   1.1671   0.5363   0.0190
 KBF  C10  C  CR6   0  -0.173   0.8551  -0.7989  -0.0882
 KBF  C1   C  CR6   0   0.367   1.9141  -1.7482  -0.2530
 KBF  O1   O  OH1   0  -0.640   1.6636  -3.0509  -0.4093
 KBF  C2   C  CR16  0  -0.433   3.2207  -1.3206  -0.2396
 KBF  C11  C  C     0   0.613  -0.5471  -1.2981  -0.0697
 KBF  N    N  NH1   0  -0.642  -1.4865  -0.5011   0.4387
 KBF  C12  C  CH2   0  -0.319  -2.8986  -0.8115   0.4618
 KBF  O2   O  O     0  -0.536  -0.8051  -2.4329  -0.4962
 KBF  C15  C  CH2   0  -0.475  -5.8066   1.1061  -0.4182
 KBF  C14  C  CH2   0  -0.504  -5.1904  -0.2910  -0.4899
 KBF  C13  C  CH1   0   0.039  -3.6783  -0.0176  -0.5779
 KBF  O3   O  O2    0  -0.500  -3.4998   1.3773  -0.3696
 KBF  C16  C  CH2   0  -0.176  -4.6790   1.9045   0.2124
 KBF  H2   H  HCR6  0   0.257   5.6856  -0.2173  -0.1873
 KBF  H3   H  HCR6  0   0.261   6.1864   2.1759   0.0124
 KBF  H4   H  HCR6  0   0.259   4.3526   3.8379   0.2042
 KBF  H5   H  HCR6  0   0.259   2.0075   3.0902   0.2045
 KBF  H6   H  HCR6  0   0.259   0.3860   1.2844   0.0905
 KBF  H22  H  HOH1  0   0.475   0.6863  -3.1476  -0.5086
 KBF  H1   H  HCR6  0   0.262   4.0153  -2.0492  -0.3478
 KBF  H21  H  HNH1  0   0.415  -1.2201   0.3883   0.8268
 KBF  H8   H  HCH2  0   0.265  -3.0353  -1.8778   0.2889
 KBF  H7   H  HCH2  0   0.257  -3.2810  -0.5931   1.4622
 KBF  H13  H  HCH2  0   0.245  -6.7240   1.1365   0.1689
 KBF  H10  H  HCH2  0   0.242  -5.4291  -0.8605   0.4121
 KBF  H11  H  HCH2  0   0.256  -5.5489  -0.8690  -1.3404
 KBF  H9   H  HCH1  0   0.238  -3.2837  -0.2552  -1.5711
 KBF  H15  H  HCH2  0   0.234  -4.7221   2.9738   0.0008
 KBF  H14  H  HCH2  0   0.203  -4.6775   1.7770   1.3033
 KBF  H12  H  HCH2  0   0.238  -6.0307   1.4868  -1.4163

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
 KBF  C4   C5   aromatic  1.367  0.020  1.367
 KBF  C4   C3   aromatic  1.417  0.020  1.417
 KBF  C15  C16  single    1.519  0.020  1.519
 KBF  C15  C14  single    1.529  0.020  1.529
 KBF  C5   C6   aromatic  1.413  0.020  1.413
 KBF  C2   C3   aromatic  1.407  0.020  1.407
 KBF  C2   C1   aromatic  1.375  0.020  1.375
 KBF  C3   C8   aromatic  1.419  0.020  1.419
 KBF  O1   C1   single    1.336  0.020  1.336
 KBF  C16  O3   single    1.417  0.020  1.417
 KBF  C1   C10  aromatic  1.432  0.020  1.432
 KBF  C14  C13  single    1.539  0.020  1.539
 KBF  C6   C7   aromatic  1.366  0.020  1.366
 KBF  C8   C7   aromatic  1.416  0.020  1.416
 KBF  C8   C9   aromatic  1.406  0.020  1.406
 KBF  C10  C9   aromatic  1.375  0.020  1.375
 KBF  C10  C11  single    1.489  0.020  1.489
 KBF  O3   C13  single    1.422  0.020  1.422
 KBF  C13  C12  single    1.523  0.020  1.523
 KBF  N    C11  single    1.333  0.020  1.333
 KBF  N    C12  single    1.446  0.020  1.446
 KBF  C11  O2   double    1.239  0.020  1.239
 KBF  C4   H2   single    0.930  0.020  1.080
 KBF  C5   H3   single    0.930  0.020  1.080
 KBF  C6   H4   single    0.930  0.020  1.080
 KBF  C7   H5   single    0.930  0.020  1.080
 KBF  C9   H6   single    0.930  0.020  1.080
 KBF  O1   H22  single    0.850  0.020  0.980
 KBF  C2   H1   single    0.930  0.020  1.080
 KBF  N    H21  single    0.860  0.020  1.020
 KBF  C12  H8   single    0.970  0.020  1.090
 KBF  C12  H7   single    0.970  0.020  1.090
 KBF  C15  H12  single    0.970  0.020  1.090
 KBF  C15  H13  single    0.970  0.020  1.090
 KBF  C14  H10  single    0.970  0.020  1.090
 KBF  C14  H11  single    0.970  0.020  1.090
 KBF  C13  H9   single    0.970  0.020  1.090
 KBF  C16  H15  single    0.970  0.020  1.090
 KBF  C16  H14  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
 KBF  C2   C3   C8   119.35  3.000
 KBF  C8   C3   C4   118.55  3.000
 KBF  C2   C3   C4   122.09  3.000
 KBF  H2   C4   C5   120.39  3.000
 KBF  H2   C4   C3   119.03  3.000
 KBF  C5   C4   C3   120.58  3.000
 KBF  H3   C5   C6   119.43  3.000
 KBF  H3   C5   C4   119.79  3.000
 KBF  C6   C5   C4   120.78  3.000
 KBF  H4   C6   C7   120.27  3.000
 KBF  H4   C6   C5   119.76  3.000
 KBF  C7   C6   C5   119.97  3.000
 KBF  H5   C7   C8   118.97  3.000
 KBF  H5   C7   C6   120.49  3.000
 KBF  C8   C7   C6   120.54  3.000
 KBF  C9   C8   C7   121.89  3.000
 KBF  C9   C8   C3   118.53  3.000
 KBF  C7   C8   C3   119.58  3.000
 KBF  H6   C9   C10  120.78  3.000
 KBF  H6   C9   C8   117.15  3.000
 KBF  C10  C9   C8   122.06  3.000
 KBF  C11  C10  C1   118.41  3.000
 KBF  C11  C10  C9   122.57  3.000
 KBF  C1   C10  C9   119.01  3.000
 KBF  C2   C1   O1   118.86  3.000
 KBF  O1   C1   C10  121.43  3.000
 KBF  C2   C1   C10  119.70  3.000
 KBF  H22  O1   C1   107.04  3.000
 KBF  H1   C2   C1   119.13  3.000
 KBF  H1   C2   C3   119.58  3.000
 KBF  C1   C2   C3   121.28  3.000
 KBF  O2   C11  N    122.14  3.000
 KBF  O2   C11  C10  119.93  3.000
 KBF  N    C11  C10  117.91  3.000
 KBF  H21  N    C12  116.24  3.000
 KBF  H21  N    C11  119.28  3.000
 KBF  C12  N    C11  124.47  3.000
 KBF  H7   C12  H8   107.28  3.000
 KBF  H7   C12  C13  109.97  3.000
 KBF  H8   C12  C13  109.75  3.000
 KBF  H7   C12  N    108.26  3.000
 KBF  H8   C12  N    109.29  3.000
 KBF  C13  C12  N    112.16  3.000
 KBF  H13  C15  H12  108.07  3.000
 KBF  H13  C15  C16  112.75  3.000
 KBF  H12  C15  C16  110.41  3.000
 KBF  H13  C15  C14  112.97  3.000
 KBF  H12  C15  C14  111.02  3.000
 KBF  C16  C15  C14  101.58  3.000
 KBF  H11  C14  H10  107.22  3.000
 KBF  H11  C14  C13  111.91  3.000
 KBF  H10  C14  C13  110.75  3.000
 KBF  H11  C14  C15  112.89  3.000
 KBF  H10  C14  C15  110.45  3.000
 KBF  C13  C14  C15  103.67  3.000
 KBF  H9   C13  O3   107.50  3.000
 KBF  H9   C13  C14  111.55  3.000
 KBF  O3   C13  C14  106.82  3.000
 KBF  H9   C13  C12  108.76  3.000
 KBF  O3   C13  C12  110.32  3.000
 KBF  C14  C13  C12  111.80  3.000
 KBF  C16  O3   C13  108.71  3.000
 KBF  H14  C16  H15  107.85  3.000
 KBF  H14  C16  O3   111.33  3.000
 KBF  H15  C16  O3   108.54  3.000
 KBF  H14  C16  C15  110.63  3.000
 KBF  H15  C16  C15  113.92  3.000
 KBF  O3   C16  C15  104.58  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
 KBF  CONST_01  C6   C5   C4   C3      0.00   0.0  0
 KBF  CONST_02  C10  C1   C2   C3      0.00   0.0  0
 KBF  CONST_03  C6   C7   C8   C3      0.00   0.0  0
 KBF  CONST_04  C10  C9   C8   C3      0.00   0.0  0
 KBF  CONST_05  C7   C6   C5   C4      0.00   0.0  0
 KBF  CONST_06  C1   C2   C3   C4    180.00   0.0  0
 KBF  CONST_07  C7   C8   C3   C4      0.00   0.0  0
 KBF  CONST_08  C9   C8   C3   C4    180.00   0.0  0
 KBF  CONST_09  C2   C3   C4   C5    180.00   0.0  0
 KBF  CONST_10  C8   C3   C4   C5      0.00   0.0  0
 KBF  CONST_11  C8   C7   C6   C5      0.00   0.0  0
 KBF  CONST_12  C9   C8   C7   C6    180.00   0.0  0
 KBF  CONST_13  C2   C3   C8   C7    180.00   0.0  0
 KBF  CONST_14  C10  C9   C8   C7    180.00   0.0  0
 KBF  CONST_15  C1   C2   C3   C8      0.00   0.0  0
 KBF  CONST_16  C1   C10  C9   C8      0.00   0.0  0
 KBF  CONST_17  C2   C3   C8   C9      0.00   0.0  0
 KBF  CONST_18  C2   C1   C10  C9      0.00   0.0  0
 KBF  CONST_19  O1   C1   C2   C3    180.00   0.0  0
 KBF  CONST_20  C11  C10  C9   C8    180.00   0.0  0
 KBF  CONST_21  O1   C1   C10  C9    180.00   0.0  0
 KBF  CONST_22  C11  C10  C1   C2    180.00   0.0  0
 KBF  CONST_23  H3   C5   C4   C3    180.00   0.0  0
 KBF  CONST_24  H5   C7   C8   C3    180.00   0.0  0
 KBF  CONST_25  H6   C9   C8   C3    180.00   0.0  0
 KBF  CONST_26  H4   C6   C5   C4    180.00   0.0  0
 KBF  CONST_27  H1   C2   C3   C4      0.00   0.0  0
 KBF  CONST_28  H2   C4   C5   C6    180.00   0.0  0
 KBF  CONST_29  C12  N    C11  C10   180.00   0.0  0
 KBF  CONST_30  H21  N    C11  C10     0.00   0.0  0
 KBF  CONST_31  O2   C11  N    C12     0.00   0.0  0
 KBF  Var_01    O3   C16  C15  C14    38.17  30.0  1
 KBF  Var_02    C16  C15  C14  C13   -27.22  30.0  1
 KBF  Var_03    N    C11  C10  C9    -19.39  30.0  2
 KBF  Var_04    C13  C12  N    C11  -105.09  30.0  3

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
 KBF  chir_01  C13  C14  O3  C12  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
 KBF  plan-1  C3   0.020
 KBF  plan-1  C4   0.020
 KBF  plan-1  C5   0.020
 KBF  plan-1  C6   0.020
 KBF  plan-1  C7   0.020
 KBF  plan-1  C8   0.020
 KBF  plan-1  C9   0.020
 KBF  plan-1  C10  0.020
 KBF  plan-1  C1   0.020
 KBF  plan-1  O1   0.020
 KBF  plan-1  C2   0.020
 KBF  plan-1  C11  0.020
 KBF  plan-1  H2   0.020
 KBF  plan-1  H3   0.020
 KBF  plan-1  H4   0.020
 KBF  plan-1  H5   0.020
 KBF  plan-1  H6   0.020
 KBF  plan-1  H1   0.020
 KBF  plan-2  C10  0.020
 KBF  plan-2  C11  0.020
 KBF  plan-2  N    0.020
 KBF  plan-2  C12  0.020
 KBF  plan-2  O2   0.020
 KBF  plan-2  H21  0.020

