# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:30:13 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: N-[(6-methylpyridin-3-yl)methyl]cyclobutanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(CNC(=O)C2CCC2)cn1
#
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
 NWY  NWY  N-[(6-methylpyridin-3-yl)methyl]cyclobutanecarboxamide  ligand  31  15  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NWY
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
 NWY  N1   N  N     0  -0.423  -3.7075   0.5709  -0.8964
 NWY  C4   C  CR6   0   0.031  -1.4807   0.8350  -0.0387
 NWY  C5   C  CH2   0  -0.391  -0.1734   1.5793  -0.0776
 NWY  C6   C  C     0   0.580   1.8430   0.2138   0.3275
 NWY  C7   C  C     0  -0.398   2.9426  -0.5652  -0.3461
 NWY  C8   C  C     0  -0.422   3.5153  -1.7923   0.3884
 NWY  C10  C  C     0  -0.424   4.3602   0.0580  -0.2935
 NWY  N    N  NH1   0  -0.627   0.9314   0.7505  -0.5036
 NWY  C    C  CH3   0  -0.714  -5.2442  -1.1311  -0.1383
 NWY  O    O  O     0  -0.504   1.8142   0.3728   1.5416
 NWY  C1   C  CR6   0   0.234  -3.9077  -0.4569  -0.0753
 NWY  C11  C  CR16  0  -0.121  -2.5328   1.1876  -0.8727
 NWY  C2   C  CR16  0  -0.332  -2.9142  -0.8891   0.8020
 NWY  C3   C  CR16  0  -0.172  -1.6939  -0.2384   0.8196
 NWY  C9   C  C     0  -0.459   4.9251  -1.3523  -0.0467
 NWY  H1   H  HCH2  0   0.271  -0.2535   2.4272  -0.7600
 NWY  H2   H  HCH2  0   0.269   0.0613   1.9845   0.9061
 NWY  H3   H  H     0   0.264   2.6803  -0.8174  -1.3763
 NWY  H4   H  H     0   0.232   3.3807  -1.7026   1.4665
 NWY  H5   H  H     0   0.237   3.1599  -2.7709   0.0669
 NWY  H6   H  H     0   0.240   4.6949   0.6007  -1.1771
 NWY  H7   H  H     0   0.234   4.4792   0.6986   0.5812
 NWY  H8   H  HNH1  0   0.401   0.9947   0.5376  -1.4858
 NWY  H9   H  HCH3  0   0.251  -5.4185  -1.5485  -1.1312
 NWY  H10  H  HCH3  0   0.243  -5.3224  -1.9395   0.5865
 NWY  H11  H  HCH3  0   0.251  -6.0473  -0.4191   0.0566
 NWY  H12  H  HCR6  0   0.256  -2.4150   2.0190  -1.5624
 NWY  H13  H  HCR6  0   0.264  -3.0992  -1.7258   1.4627
 NWY  H14  H  HCR6  0   0.265  -0.9154  -0.5598   1.5009
 NWY  H15  H  H     0   0.232   5.7317  -1.4512   0.6793
 NWY  H16  H  H     0   0.230   5.2327  -1.8324  -0.9763

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
 NWY  C8   C9   single    1.540  0.020  1.540
 NWY  C8   C7   single    1.540  0.020  1.540
 NWY  C9   C10  single    1.539  0.020  1.539
 NWY  C7   C10  single    1.549  0.020  1.549
 NWY  C7   C6   single    1.507  0.020  1.507
 NWY  C    C1   single    1.498  0.020  1.498
 NWY  C6   O    double    1.225  0.020  1.225
 NWY  C6   N    single    1.345  0.020  1.345
 NWY  N1   C1   aromatic  1.331  0.020  1.331
 NWY  N1   C11  aromatic  1.327  0.020  1.327
 NWY  C1   C2   aromatic  1.394  0.020  1.394
 NWY  C11  C4   aromatic  1.388  0.020  1.388
 NWY  N    C5   single    1.445  0.020  1.445
 NWY  C2   C3   aromatic  1.383  0.020  1.383
 NWY  C4   C3   aromatic  1.391  0.020  1.391
 NWY  C4   C5   single    1.505  0.020  1.505
 NWY  C5   H1   single    0.970  0.020  1.090
 NWY  C5   H2   single    0.970  0.020  1.090
 NWY  C7   H3   single    0.970  0.020  1.090
 NWY  C8   H4   single    0.970  0.020  1.090
 NWY  C8   H5   single    0.970  0.020  1.090
 NWY  C10  H6   single    0.970  0.020  1.090
 NWY  C10  H7   single    0.970  0.020  1.090
 NWY  N    H8   single    0.860  0.020  1.020
 NWY  C    H9   single    0.970  0.020  1.090
 NWY  C    H10  single    0.970  0.020  1.090
 NWY  C    H11  single    0.970  0.020  1.090
 NWY  C11  H12  single    0.930  0.020  1.080
 NWY  C2   H13  single    0.930  0.020  1.080
 NWY  C3   H14  single    0.930  0.020  1.080
 NWY  C9   H15  single    0.970  0.020  1.090
 NWY  C9   H16  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
 NWY  C11  N1   C1   118.76  3.000
 NWY  C3   C4   C11  116.79  3.000
 NWY  C3   C4   C5   122.06  3.000
 NWY  C11  C4   C5   121.15  3.000
 NWY  H2   C5   H1   106.95  3.000
 NWY  H2   C5   N    108.34  3.000
 NWY  H1   C5   N    108.50  3.000
 NWY  H2   C5   C4   110.35  3.000
 NWY  H1   C5   C4   109.67  3.000
 NWY  N    C5   C4   112.83  3.000
 NWY  O    C6   N    123.00  3.000
 NWY  N    C6   C7   115.13  3.000
 NWY  O    C6   C7   121.84  3.000
 NWY  H3   C7   C10  110.15  3.000
 NWY  H3   C7   C8   110.79  3.000
 NWY  C10  C7   C8    87.94  3.000
 NWY  H3   C7   C6   111.45  3.000
 NWY  C10  C7   C6   116.40  3.000
 NWY  C8   C7   C6   118.03  3.000
 NWY  H5   C8   H4   108.99  3.000
 NWY  H5   C8   C9   118.16  3.000
 NWY  H4   C8   C9   111.65  3.000
 NWY  H5   C8   C7   116.97  3.000
 NWY  H4   C8   C7   111.11  3.000
 NWY  C9   C8   C7    88.74  3.000
 NWY  H7   C10  H6   108.92  3.000
 NWY  H7   C10  C9   111.68  3.000
 NWY  H6   C10  C9   118.27  3.000
 NWY  H7   C10  C7   111.30  3.000
 NWY  H6   C10  C7   116.99  3.000
 NWY  C9   C10  C7    88.44  3.000
 NWY  H8   N    C6   118.40  3.000
 NWY  H8   N    C5   117.18  3.000
 NWY  C6   N    C5   124.38  3.000
 NWY  H11  C    H10  108.24  3.000
 NWY  H11  C    H9   107.14  3.000
 NWY  H10  C    H9   108.08  3.000
 NWY  H11  C    C1   110.82  3.000
 NWY  H10  C    C1   111.73  3.000
 NWY  H9   C    C1   110.67  3.000
 NWY  C2   C1   C    121.51  3.000
 NWY  C2   C1   N1   121.37  3.000
 NWY  C    C1   N1   117.12  3.000
 NWY  H12  C11  C4   119.58  3.000
 NWY  H12  C11  N1   116.12  3.000
 NWY  C4   C11  N1   124.31  3.000
 NWY  H13  C2   C3   120.46  3.000
 NWY  H13  C2   C1   120.14  3.000
 NWY  C3   C2   C1   119.40  3.000
 NWY  H14  C3   C2   120.17  3.000
 NWY  H14  C3   C4   120.46  3.000
 NWY  C2   C3   C4   119.37  3.000
 NWY  H16  C9   H15  108.61  3.000
 NWY  H16  C9   C10  111.73  3.000
 NWY  H15  C9   C10  117.50  3.000
 NWY  H16  C9   C8   111.93  3.000
 NWY  H15  C9   C8   117.62  3.000
 NWY  C10  C9   C8    88.34  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
 NWY  CONST_01  C3   C2   C1   N1      0.00   0.0  0
 NWY  CONST_02  C3   C4   C11  N1      0.00   0.0  0
 NWY  CONST_03  C1   N1   C11  C4      0.00   0.0  0
 NWY  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 NWY  CONST_05  C2   C1   N1   C11     0.00   0.0  0
 NWY  CONST_06  C2   C3   C4   C11     0.00   0.0  0
 NWY  CONST_07  C5   C4   C11  N1    180.00   0.0  0
 NWY  CONST_08  C2   C3   C4   C5    180.00   0.0  0
 NWY  CONST_09  C11  N1   C1   C     180.00   0.0  0
 NWY  CONST_10  C3   C2   C1   C     180.00   0.0  0
 NWY  CONST_11  H13  C2   C1   N1    180.00   0.0  0
 NWY  CONST_12  H12  C11  N1   C1    180.00   0.0  0
 NWY  CONST_13  H14  C3   C2   C1    180.00   0.0  0
 NWY  CONST_14  C7   C6   N    C5    180.00   0.0  0
 NWY  CONST_15  H8   N    C6   C7      0.00   0.0  0
 NWY  CONST_16  O    C6   N    C5      0.00   0.0  0
 NWY  Var_01    C10  C9   C8   C7     19.26  30.0  1
 NWY  Var_02    C11  C4   C5   N    -116.12  30.0  3
 NWY  Var_03    H9   C    C1   N1     61.06  30.0  2
 NWY  Var_04    C6   N    C5   C4   -101.86  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
 NWY  chir_01  C7  C8  C10  C6  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
 NWY  plan-1  N1   0.020
 NWY  plan-1  C4   0.020
 NWY  plan-1  C5   0.020
 NWY  plan-1  C    0.020
 NWY  plan-1  C1   0.020
 NWY  plan-1  C11  0.020
 NWY  plan-1  C2   0.020
 NWY  plan-1  C3   0.020
 NWY  plan-1  H12  0.020
 NWY  plan-1  H13  0.020
 NWY  plan-1  H14  0.020
 NWY  plan-2  C5   0.020
 NWY  plan-2  C6   0.020
 NWY  plan-2  C7   0.020
 NWY  plan-2  N    0.020
 NWY  plan-2  O    0.020
 NWY  plan-2  H8   0.020

