# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 01:00:42 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 2-[[5-chloranyl-2-(oxan-4-ylamino)pyridin-4-yl]amino]-N-methyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1ccccc1Nc2cc(NC3CCOCC3)ncc2Cl
#
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
 CQ8  CQ8  2-[[5-chloranyl-2-(oxan-4-ylamino)pyridin-4-yl]amino]-N-methyl-benzamide  ligand  46  25  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CQ8
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
 CQ8  CL    CL  CL    0  -0.135  -4.2116  -1.5763   0.7046
 CQ8  C12   C   CR6   0  -0.255  -2.5232  -1.6814   0.3251
 CQ8  C8    C   CR6   0   0.576  -1.6606  -0.6050   0.5965
 CQ8  N1    N   NH1   0  -0.794  -2.1383   0.5341   1.1738
 CQ8  C7    C   CR6   0   0.317  -1.4871   1.7657   1.2523
 CQ8  C6    C   CR16  0  -0.321  -1.5264   2.4520   2.4650
 CQ8  C5    C   CR16  0  -0.250  -0.9272   3.6932   2.6008
 CQ8  C4    C   CR16  0  -0.255  -0.2481   4.2591   1.5315
 CQ8  C3    C   CR16  0  -0.280  -0.2010   3.5808   0.3238
 CQ8  C2    C   CR6   0  -0.074  -0.8278   2.3475   0.1587
 CQ8  C1    C   C     0   0.512  -0.8788   1.7359  -1.2085
 CQ8  O     O   O     0  -0.468  -1.9220   1.3339  -1.6990
 CQ8  N     N   NH1   0  -0.618   0.2968   1.6917  -1.8541
 CQ8  C     C   CH3   0  -0.519   0.4334   1.1159  -3.1706
 CQ8  C11   C   CR16  0  -0.050  -2.0136  -2.8187  -0.2615
 CQ8  N2    N   N     0  -0.484  -0.7467  -2.9656  -0.6147
 CQ8  C10   C   CR6   0   0.517   0.0946  -1.9555  -0.3609
 CQ8  C9    C   CR16  0  -0.495  -0.3185  -0.7823   0.2818
 CQ8  N3    N   NH1   0  -0.672   1.3708  -2.1363  -0.7873
 CQ8  C13   C   CH1   0  -0.073   2.4718  -1.2503  -0.5047
 CQ8  C17   C   CH2   0  -0.462   3.5808  -1.4361  -1.5332
 CQ8  C16   C   CH2   0  -0.183   4.7541  -0.5228  -1.2079
 CQ8  O1    O   O2    0  -0.481   5.2411  -0.7217   0.1002
 CQ8  C15   C   CH2   0  -0.185   4.2491  -0.4937   1.0775
 CQ8  C14   C   CH2   0  -0.457   3.0559  -1.4195   0.8986
 CQ8  H11   H   HCR6  0   0.273  -2.6761  -3.6526  -0.4695
 CQ8  H1    H   HNH1  0   0.397  -2.9962   0.4558   1.6977
 CQ8  H9    H   HCR6  0   0.278   0.3944  -0.0138   0.5404
 CQ8  H6    H   HCR6  0   0.273  -2.0280   1.9963   3.3098
 CQ8  H5    H   HCR6  0   0.266  -0.9762   4.2084   3.5511
 CQ8  H4    H   HCR6  0   0.263   0.2324   5.2226   1.6320
 CQ8  H3    H   HCR6  0   0.269   0.3018   4.0378  -0.5195
 CQ8  H     H   HNH1  0   0.404   1.1274   2.0109  -1.3851
 CQ8  HC1   H   HCH3  0   0.247  -0.2298   1.5970  -3.8887
 CQ8  HC2   H   HCH3  0   0.251   1.4576   1.2580  -3.5036
 CQ8  HC3   H   HCH3  0   0.241   0.2173   0.0463  -3.1634
 CQ8  HA    H   HNH1  0   0.377   1.5973  -3.0769  -1.0715
 CQ8  H13   H   HCH1  0   0.211   2.1042  -0.2222  -0.6029
 CQ8  H171  H   HCH2  0   0.236   3.9145  -2.4789  -1.5332
 CQ8  H172  H   HCH2  0   0.249   3.2144  -1.2102  -2.5374
 CQ8  H141  H   HCH2  0   0.245   2.3073  -1.1986   1.6637
 CQ8  H142  H   HCH2  0   0.232   3.3623  -2.4606   1.0399
 CQ8  H161  H   HCH2  0   0.243   5.5832  -0.7112  -1.8913
 CQ8  H162  H   HCH2  0   0.197   4.4482   0.5254  -1.3467
 CQ8  H151  H   HCH2  0   0.242   4.7165  -0.6479   2.0510
 CQ8  H152  H   HCH2  0   0.198   3.9071   0.5522   1.0387

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
 CQ8  CL   C12   single    1.734  0.020  1.734
 CQ8  C12  C8    aromatic  1.406  0.020  1.406
 CQ8  C12  C11   aromatic  1.377  0.020  1.377
 CQ8  C8   N1    single    1.363  0.020  1.363
 CQ8  C8   C9    aromatic  1.390  0.020  1.390
 CQ8  N1   C7    single    1.395  0.020  1.395
 CQ8  C7   C6    aromatic  1.394  0.020  1.394
 CQ8  C7   C2    aromatic  1.403  0.020  1.403
 CQ8  C6   C5    aromatic  1.385  0.020  1.385
 CQ8  C5   C4    aromatic  1.387  0.020  1.387
 CQ8  C4   C3    aromatic  1.386  0.020  1.386
 CQ8  C3   C2    aromatic  1.393  0.020  1.393
 CQ8  C2   C1    single    1.499  0.020  1.499
 CQ8  C1   O     double    1.221  0.020  1.221
 CQ8  C1   N     single    1.342  0.020  1.342
 CQ8  N    C     single    1.443  0.020  1.443
 CQ8  C11  N2    aromatic  1.323  0.020  1.323
 CQ8  N2   C10   aromatic  1.339  0.020  1.339
 CQ8  C10  C9    aromatic  1.400  0.020  1.400
 CQ8  C10  N3    single    1.358  0.020  1.358
 CQ8  N3   C13   single    1.441  0.020  1.441
 CQ8  C13  C17   single    1.524  0.020  1.524
 CQ8  C13  C14   single    1.529  0.020  1.529
 CQ8  C17  C16   single    1.522  0.020  1.522
 CQ8  C16  O1    single    1.410  0.020  1.410
 CQ8  O1   C15   single    1.411  0.020  1.411
 CQ8  C15  C14   single    1.521  0.020  1.521
 CQ8  C11  H11   single    0.930  0.020  1.080
 CQ8  N1   H1    single    0.860  0.020  1.020
 CQ8  C9   H9    single    0.930  0.020  1.080
 CQ8  C6   H6    single    0.930  0.020  1.080
 CQ8  C5   H5    single    0.930  0.020  1.080
 CQ8  C4   H4    single    0.930  0.020  1.080
 CQ8  C3   H3    single    0.930  0.020  1.080
 CQ8  N    H     single    0.860  0.020  1.020
 CQ8  C    HC1   single    0.970  0.020  1.090
 CQ8  C    HC2   single    0.970  0.020  1.090
 CQ8  C    HC3   single    0.970  0.020  1.090
 CQ8  N3   HA    single    0.860  0.020  1.020
 CQ8  C13  H13   single    0.970  0.020  1.090
 CQ8  C17  H171  single    0.970  0.020  1.090
 CQ8  C17  H172  single    0.970  0.020  1.090
 CQ8  C14  H141  single    0.970  0.020  1.090
 CQ8  C14  H142  single    0.970  0.020  1.090
 CQ8  C16  H161  single    0.970  0.020  1.090
 CQ8  C16  H162  single    0.970  0.020  1.090
 CQ8  C15  H151  single    0.970  0.020  1.090
 CQ8  C15  H152  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
 CQ8  C11   C12  C8    119.17  3.000
 CQ8  C11   C12  CL    120.24  3.000
 CQ8  C8    C12  CL    120.59  3.000
 CQ8  C9    C8   N1    122.74  3.000
 CQ8  C9    C8   C12   116.82  3.000
 CQ8  N1    C8   C12   120.43  3.000
 CQ8  H1    N1   C7    115.87  3.000
 CQ8  H1    N1   C8    116.95  3.000
 CQ8  C7    N1   C8    126.71  3.000
 CQ8  C2    C7   C6    119.16  3.000
 CQ8  C2    C7   N1    122.78  3.000
 CQ8  C6    C7   N1    118.05  3.000
 CQ8  H6    C6   C5    120.07  3.000
 CQ8  H6    C6   C7    118.98  3.000
 CQ8  C5    C6   C7    120.95  3.000
 CQ8  H5    C5   C4    120.32  3.000
 CQ8  H5    C5   C6    119.55  3.000
 CQ8  C4    C5   C6    120.12  3.000
 CQ8  H4    C4   C3    120.13  3.000
 CQ8  H4    C4   C5    120.62  3.000
 CQ8  C3    C4   C5    119.25  3.000
 CQ8  H3    C3   C2    119.35  3.000
 CQ8  H3    C3   C4    119.19  3.000
 CQ8  C2    C3   C4    121.41  3.000
 CQ8  C1    C2   C3    118.99  3.000
 CQ8  C1    C2   C7    121.72  3.000
 CQ8  C3    C2   C7    119.08  3.000
 CQ8  N     C1   O     122.99  3.000
 CQ8  N     C1   C2    114.99  3.000
 CQ8  O     C1   C2    122.00  3.000
 CQ8  H     N    C     118.28  3.000
 CQ8  H     N    C1    119.25  3.000
 CQ8  C     N    C1    122.33  3.000
 CQ8  HC3   C    HC2   108.48  3.000
 CQ8  HC3   C    HC1   108.47  3.000
 CQ8  HC2   C    HC1   108.31  3.000
 CQ8  HC3   C    N     111.48  3.000
 CQ8  HC2   C    N     108.46  3.000
 CQ8  HC1   C    N     111.55  3.000
 CQ8  H11   C11  N2    116.62  3.000
 CQ8  H11   C11  C12   119.36  3.000
 CQ8  N2    C11  C12   124.02  3.000
 CQ8  C10   N2   C11   117.85  3.000
 CQ8  N3    C10  C9    122.22  3.000
 CQ8  N3    C10  N2    115.51  3.000
 CQ8  C9    C10  N2    122.27  3.000
 CQ8  H9    C9   C10   120.77  3.000
 CQ8  H9    C9   C8    119.51  3.000
 CQ8  C10   C9   C8    119.72  3.000
 CQ8  HA    N3   C13   117.21  3.000
 CQ8  HA    N3   C10   115.08  3.000
 CQ8  C13   N3   C10   125.07  3.000
 CQ8  H13   C13  C14   108.31  3.000
 CQ8  H13   C13  C17   107.33  3.000
 CQ8  C14   C13  C17   109.14  3.000
 CQ8  H13   C13  N3    107.63  3.000
 CQ8  C14   C13  N3    113.81  3.000
 CQ8  C17   C13  N3    110.40  3.000
 CQ8  H172  C17  H171  107.41  3.000
 CQ8  H172  C17  C16   109.32  3.000
 CQ8  H171  C17  C16   109.67  3.000
 CQ8  H172  C17  C13   110.55  3.000
 CQ8  H171  C17  C13   109.75  3.000
 CQ8  C16   C17  C13   110.09  3.000
 CQ8  H162  C16  H161  107.26  3.000
 CQ8  H162  C16  O1    110.32  3.000
 CQ8  H161  C16  O1    107.11  3.000
 CQ8  H162  C16  C17   109.29  3.000
 CQ8  H161  C16  C17   110.39  3.000
 CQ8  O1    C16  C17   112.32  3.000
 CQ8  C15   O1   C16   112.14  3.000
 CQ8  H152  C15  H151  107.38  3.000
 CQ8  H152  C15  C14   109.30  3.000
 CQ8  H151  C15  C14   110.80  3.000
 CQ8  H152  C15  O1    110.33  3.000
 CQ8  H151  C15  O1    107.10  3.000
 CQ8  C14   C15  O1    111.82  3.000
 CQ8  H142  C14  H141  107.08  3.000
 CQ8  H142  C14  C15   110.14  3.000
 CQ8  H141  C14  C15   109.39  3.000
 CQ8  H142  C14  C13   109.31  3.000
 CQ8  H141  C14  C13   111.00  3.000
 CQ8  C15   C14  C13   109.89  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
 CQ8  CONST_01  C10  C9   C8   C12     0.00   0.0  0
 CQ8  CONST_02  C10  N2   C11  C12     0.00   0.0  0
 CQ8  CONST_03  N2   C11  C12  C8      0.00   0.0  0
 CQ8  CONST_04  N2   C10  C9   C8      0.00   0.0  0
 CQ8  CONST_05  C4   C5   C6   C7      0.00   0.0  0
 CQ8  CONST_06  C4   C3   C2   C7      0.00   0.0  0
 CQ8  CONST_07  C3   C2   C7   C6      0.00   0.0  0
 CQ8  CONST_08  C3   C4   C5   C6      0.00   0.0  0
 CQ8  CONST_09  C2   C7   C6   C5      0.00   0.0  0
 CQ8  CONST_10  C2   C3   C4   C5      0.00   0.0  0
 CQ8  CONST_11  C9   C8   C12  C11     0.00   0.0  0
 CQ8  CONST_12  C9   C10  N2   C11     0.00   0.0  0
 CQ8  CONST_13  C9   C8   C12  CL    180.00   0.0  0
 CQ8  CONST_14  N2   C11  C12  CL    180.00   0.0  0
 CQ8  CONST_15  N3   C10  C9   C8    180.00   0.0  0
 CQ8  CONST_16  C11  C12  C8   N1    180.00   0.0  0
 CQ8  CONST_17  C10  C9   C8   N1    180.00   0.0  0
 CQ8  CONST_18  C5   C6   C7   N1    180.00   0.0  0
 CQ8  CONST_19  C3   C2   C7   N1    180.00   0.0  0
 CQ8  CONST_20  C1   C2   C7   C6    180.00   0.0  0
 CQ8  CONST_21  C1   C2   C3   C4    180.00   0.0  0
 CQ8  CONST_22  N3   C10  N2   C11   180.00   0.0  0
 CQ8  CONST_23  C13  N3   C10  N2    180.00   0.0  0
 CQ8  CONST_24  C13  N3   C10  C9      0.00   0.0  0
 CQ8  CONST_25  H9   C9   C8   C12   180.00   0.0  0
 CQ8  CONST_26  H11  C11  C12  C8    180.00   0.0  0
 CQ8  CONST_27  H5   C5   C6   C7    180.00   0.0  0
 CQ8  CONST_28  H3   C3   C2   C7    180.00   0.0  0
 CQ8  CONST_29  H4   C4   C5   C6    180.00   0.0  0
 CQ8  CONST_30  H6   C6   C5   C4    180.00   0.0  0
 CQ8  CONST_31  HA   N3   C10  N2      0.00   0.0  0
 CQ8  CONST_32  C    N    C1   C2    180.00   0.0  0
 CQ8  CONST_33  H    N    C1   C2      0.00   0.0  0
 CQ8  CONST_34  C    N    C1   O       0.00   0.0  0
 CQ8  Var_01    O1   C16  C17  C13    55.82  30.0  1
 CQ8  Var_02    O1   C15  C14  C13   -56.99  30.0  1
 CQ8  Var_03    C14  C15  O1   C16    59.66  30.0  1
 CQ8  Var_04    C7   N1   C8   C12  -165.84  30.0  2
 CQ8  Var_05    C6   C7   N1   C8   -135.94  30.0  2
 CQ8  Var_06    O    C1   C2   C7     45.73  30.0  2
 CQ8  Var_07    HC1  C    N    C1     57.07  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
 CQ8  chir_01  C13  N3  C17  C14  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
 CQ8  plan-1  CL   0.020
 CQ8  plan-1  C12  0.020
 CQ8  plan-1  C8   0.020
 CQ8  plan-1  N1   0.020
 CQ8  plan-1  C11  0.020
 CQ8  plan-1  N2   0.020
 CQ8  plan-1  C10  0.020
 CQ8  plan-1  C9   0.020
 CQ8  plan-1  N3   0.020
 CQ8  plan-1  H11  0.020
 CQ8  plan-1  H9   0.020
 CQ8  plan-2  N1   0.020
 CQ8  plan-2  C7   0.020
 CQ8  plan-2  C6   0.020
 CQ8  plan-2  C5   0.020
 CQ8  plan-2  C4   0.020
 CQ8  plan-2  C3   0.020
 CQ8  plan-2  C2   0.020
 CQ8  plan-2  C1   0.020
 CQ8  plan-2  H6   0.020
 CQ8  plan-2  H5   0.020
 CQ8  plan-2  H4   0.020
 CQ8  plan-2  H3   0.020
 CQ8  plan-3  C2   0.020
 CQ8  plan-3  C1   0.020
 CQ8  plan-3  O    0.020
 CQ8  plan-3  N    0.020
 CQ8  plan-3  C    0.020
 CQ8  plan-3  H    0.020
 CQ8  plan-4  C10  0.020
 CQ8  plan-4  N3   0.020
 CQ8  plan-4  C13  0.020
 CQ8  plan-4  HA   0.020

