# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 23:40:06 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: N-methyl-2-(tetrahydro-2H-pyran-4-yloxy)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1ccccc1OC2CCOCC2
#
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
 2LX  2LX  N-methyl-2-(tetrahydro-2H-pyran-4-yloxy)benzamide  ligand  34  17  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2LX
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
 2LX  C01  C  CH3   0  -0.514   3.8748   2.5908  -0.0900
 2LX  N02  N  NH1   0  -0.611   3.2795   1.2867  -0.2608
 2LX  C03  C  C     0   0.502   2.3022   0.8329   0.5358
 2LX  C04  C  CR6   0  -0.174   1.8597  -0.5678   0.2434
 2LX  C05  C  CR16  0  -0.249   2.7787  -1.6079   0.2942
 2LX  C06  C  CR16  0  -0.276   2.3832  -2.9240   0.0972
 2LX  C07  C  CR16  0  -0.242   1.0507  -3.1901  -0.1703
 2LX  C08  C  CR16  0  -0.376   0.1173  -2.1635  -0.2409
 2LX  C09  C  CR6   0   0.398   0.5123  -0.8434  -0.0320
 2LX  O10  O  O2    0  -0.475  -0.3008   0.2216  -0.1179
 2LX  C11  C  CH1   0   0.020  -1.6998   0.0591  -0.3181
 2LX  C12  C  CH2   0  -0.494  -2.4193  -0.3745   0.9523
 2LX  C13  C  CH2   0  -0.187  -3.9233  -0.3666   0.7079
 2LX  O14  O  O2    0  -0.480  -4.3816   0.8954   0.2786
 2LX  C15  C  CH2   0  -0.193  -3.7619   1.3032  -0.9209
 2LX  C16  C  CH2   0  -0.472  -2.2487   1.3984  -0.7775
 2LX  O17  O  O     0  -0.484   1.8275   1.4929   1.4484
 2LX  H1   H  HCH3  0   0.239   3.1381   3.3871  -0.2008
 2LX  H2   H  HCH3  0   0.239   4.3445   2.6925   0.8888
 2LX  H3   H  HCH3  0   0.251   4.6381   2.7222  -0.8514
 2LX  H4   H  HNH1  0   0.409   3.6023   0.7076  -1.0176
 2LX  H5   H  HCR6  0   0.264   3.8174  -1.3876   0.5084
 2LX  H6   H  HCR6  0   0.257   3.1066  -3.7257   0.1531
 2LX  H7   H  HCR6  0   0.264   0.7203  -4.2081  -0.3305
 2LX  H8   H  HCR6  0   0.278  -0.9095  -2.4147  -0.4661
 2LX  H9   H  HCH1  0   0.228  -1.8808  -0.6752  -1.1137
 2LX  H10  H  HCH2  0   0.252  -2.1217  -1.3759   1.2712
 2LX  H11  H  HCH2  0   0.242  -2.1697   0.3169   1.7624
 2LX  H12  H  HCH2  0   0.203  -4.1782  -1.1394  -0.0327
 2LX  H13  H  HCH2  0   0.244  -4.4576  -0.6079   1.6277
 2LX  H14  H  HCH2  0   0.203  -4.0100   0.6068  -1.7354
 2LX  H15  H  HCH2  0   0.245  -4.1792   2.2756  -1.1845
 2LX  H16  H  HCH2  0   0.239  -1.9932   2.1728  -0.0484
 2LX  H17  H  HCH2  0   0.251  -1.8131   1.6851  -1.7373

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
 2LX  C13  C12  single    1.524  0.020  1.524
 2LX  C13  O14  single    1.410  0.020  1.410
 2LX  C12  C11  single    1.523  0.020  1.523
 2LX  C11  O10  single    1.423  0.020  1.423
 2LX  C11  C16  single    1.519  0.020  1.519
 2LX  O14  C15  single    1.410  0.020  1.410
 2LX  O10  C09  single    1.343  0.020  1.343
 2LX  C01  N02  single    1.444  0.020  1.444
 2LX  N02  C03  single    1.340  0.020  1.340
 2LX  C09  C08  aromatic  1.394  0.020  1.394
 2LX  C09  C04  aromatic  1.403  0.020  1.403
 2LX  C08  C07  aromatic  1.389  0.020  1.389
 2LX  C03  C04  single    1.498  0.020  1.498
 2LX  C03  O17  double    1.222  0.020  1.222
 2LX  C04  C05  aromatic  1.389  0.020  1.389
 2LX  C15  C16  single    1.523  0.020  1.523
 2LX  C07  C06  aromatic  1.385  0.020  1.385
 2LX  C05  C06  aromatic  1.388  0.020  1.388
 2LX  C01  H1   single    0.970  0.020  1.090
 2LX  C01  H2   single    0.970  0.020  1.090
 2LX  C01  H3   single    0.970  0.020  1.090
 2LX  N02  H4   single    0.860  0.020  1.020
 2LX  C05  H5   single    0.930  0.020  1.080
 2LX  C06  H6   single    0.930  0.020  1.080
 2LX  C07  H7   single    0.930  0.020  1.080
 2LX  C08  H8   single    0.930  0.020  1.080
 2LX  C11  H9   single    0.970  0.020  1.090
 2LX  C12  H10  single    0.970  0.020  1.090
 2LX  C12  H11  single    0.970  0.020  1.090
 2LX  C13  H12  single    0.970  0.020  1.090
 2LX  C13  H13  single    0.970  0.020  1.090
 2LX  C15  H14  single    0.970  0.020  1.090
 2LX  C15  H15  single    0.970  0.020  1.090
 2LX  C16  H16  single    0.970  0.020  1.090
 2LX  C16  H17  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
 2LX  H3   C01  H2   108.38  3.000
 2LX  H3   C01  H1   108.38  3.000
 2LX  H2   C01  H1   108.31  3.000
 2LX  H3   C01  N02  108.43  3.000
 2LX  H2   C01  N02  111.59  3.000
 2LX  H1   C01  N02  111.65  3.000
 2LX  H4   N02  C03  119.09  3.000
 2LX  H4   N02  C01  118.46  3.000
 2LX  C03  N02  C01  122.43  3.000
 2LX  O17  C03  C04  122.42  3.000
 2LX  O17  C03  N02  122.97  3.000
 2LX  C04  C03  N02  114.59  3.000
 2LX  C09  C04  C05  119.71  3.000
 2LX  C05  C04  C03  119.85  3.000
 2LX  C09  C04  C03  120.39  3.000
 2LX  H5   C05  C06  119.61  3.000
 2LX  H5   C05  C04  119.30  3.000
 2LX  C06  C05  C04  121.08  3.000
 2LX  H6   C06  C07  120.75  3.000
 2LX  H6   C06  C05  120.33  3.000
 2LX  C07  C06  C05  118.92  3.000
 2LX  H7   C07  C08  118.84  3.000
 2LX  H7   C07  C06  120.21  3.000
 2LX  C08  C07  C06  120.95  3.000
 2LX  H8   C08  C09  121.37  3.000
 2LX  H8   C08  C07  118.50  3.000
 2LX  C09  C08  C07  120.12  3.000
 2LX  O10  C09  C08  124.76  3.000
 2LX  C08  C09  C04  119.20  3.000
 2LX  O10  C09  C04  116.00  3.000
 2LX  C11  O10  C09  120.92  3.000
 2LX  H9   C11  C16  108.12  3.000
 2LX  H9   C11  C12  109.65  3.000
 2LX  C16  C11  C12  109.43  3.000
 2LX  H9   C11  O10  109.91  3.000
 2LX  C16  C11  O10  107.29  3.000
 2LX  C12  C11  O10  112.32  3.000
 2LX  H11  C12  H10  107.52  3.000
 2LX  H11  C12  C13  109.92  3.000
 2LX  H10  C12  C13  108.69  3.000
 2LX  H11  C12  C11  109.27  3.000
 2LX  H10  C12  C11  112.07  3.000
 2LX  C13  C12  C11  109.33  3.000
 2LX  H13  C13  H12  107.38  3.000
 2LX  H13  C13  O14  107.19  3.000
 2LX  H12  C13  O14  110.39  3.000
 2LX  H13  C13  C12  110.31  3.000
 2LX  H12  C13  C12  109.45  3.000
 2LX  O14  C13  C12  111.99  3.000
 2LX  C15  O14  C13  112.03  3.000
 2LX  H15  C15  H14  107.41  3.000
 2LX  H15  C15  C16  110.32  3.000
 2LX  H14  C15  C16  109.48  3.000
 2LX  H15  C15  O14  107.18  3.000
 2LX  H14  C15  O14  110.34  3.000
 2LX  C16  C15  O14  112.00  3.000
 2LX  H17  C16  H16  107.86  3.000
 2LX  H17  C16  C15  109.26  3.000
 2LX  H16  C16  C15  109.82  3.000
 2LX  H17  C16  C11  110.69  3.000
 2LX  H16  C16  C11  109.78  3.000
 2LX  C15  C16  C11  109.42  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
 2LX  CONST_01  C07  C08  C09  C04     0.00   0.0  0
 2LX  CONST_02  C07  C06  C05  C04     0.00   0.0  0
 2LX  CONST_03  C08  C09  C04  C05     0.00   0.0  0
 2LX  CONST_04  C08  C07  C06  C05     0.00   0.0  0
 2LX  CONST_05  C09  C08  C07  C06     0.00   0.0  0
 2LX  CONST_06  C09  C04  C05  C06     0.00   0.0  0
 2LX  CONST_07  C08  C09  C04  C03   180.00   0.0  0
 2LX  CONST_08  C06  C05  C04  C03   180.00   0.0  0
 2LX  CONST_09  O10  C09  C04  C05   180.00   0.0  0
 2LX  CONST_10  O10  C09  C08  C07   180.00   0.0  0
 2LX  CONST_11  H8   C08  C09  C04   180.00   0.0  0
 2LX  CONST_12  H6   C06  C05  C04   180.00   0.0  0
 2LX  CONST_13  H7   C07  C06  C05   180.00   0.0  0
 2LX  CONST_14  H5   C05  C06  C07   180.00   0.0  0
 2LX  CONST_15  C04  C03  N02  C01   180.00   0.0  0
 2LX  CONST_16  H4   N02  C03  C04     0.00   0.0  0
 2LX  CONST_17  O17  C03  N02  C01     0.00   0.0  0
 2LX  Var_01    O14  C13  C12  C11   -56.79  30.0  1
 2LX  Var_02    O14  C15  C16  C11    56.85  30.0  1
 2LX  Var_03    C16  C15  O14  C13   -59.49  30.0  1
 2LX  Var_04    C09  C04  C03  N02  -124.11  30.0  2
 2LX  Var_05    H1   C01  N02  C03   -60.78  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
 2LX  chir_01  C11  C12  O10  C16  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
 2LX  plan-1  C03  0.020
 2LX  plan-1  C04  0.020
 2LX  plan-1  C05  0.020
 2LX  plan-1  C06  0.020
 2LX  plan-1  C07  0.020
 2LX  plan-1  C08  0.020
 2LX  plan-1  C09  0.020
 2LX  plan-1  O10  0.020
 2LX  plan-1  H5   0.020
 2LX  plan-1  H6   0.020
 2LX  plan-1  H7   0.020
 2LX  plan-1  H8   0.020
 2LX  plan-2  C01  0.020
 2LX  plan-2  N02  0.020
 2LX  plan-2  C03  0.020
 2LX  plan-2  C04  0.020
 2LX  plan-2  O17  0.020
 2LX  plan-2  H4   0.020

