# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 08:05:53 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 7-[[4-chloranyl-3-(methylaminomethyl)phenoxy]methyl]quinolin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1cc(OCc2ccc3ccc(N)nc3c2)ccc1Cl
#
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
 XEB  XEB  7-[[4-chloranyl-3-(methylaminomethyl)phenoxy]methyl]quinolin-2-amine  ligand  41  23  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XEB
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
 XEB  N01   N   N     0  -0.507  -5.0451  -0.6754  -1.2336
 XEB  C02   C   CR6   0   0.441  -6.2477  -0.9766  -0.8002
 XEB  N02   N   NH2   0  -0.835  -7.1151  -1.5579  -1.6630
 XEB  C03   C   CR16  0  -0.375  -6.6853  -0.6794   0.5296
 XEB  C04   C   CR16  0  -0.178  -5.8271  -0.0591   1.3769
 XEB  C05   C   CR66  0   0.047  -4.5229   0.2848   0.9370
 XEB  C06   C   CR16  0  -0.306  -3.5772   0.9333   1.7552
 XEB  C07   C   CR16  0  -0.295  -2.3327   1.2412   1.2738
 XEB  C08   C   CR6   0   0.097  -1.9838   0.9071  -0.0530
 XEB  C09   C   CR16  0  -0.368  -2.8928   0.2720  -0.8619
 XEB  C10   C   CR66  0   0.235  -4.1861  -0.0522  -0.3942
 XEB  C11   C   CH2   0  -0.269  -0.6176   1.2481  -0.5655
 XEB  O12   O   O2    0  -0.469   0.3201   0.4733   0.1681
 XEB  C21   C   CR6   0   0.417   1.6295   0.6097  -0.1160
 XEB  C22   C   CR16  0  -0.403   2.1428   1.4588  -1.0900
 XEB  C23   C   CR16  0  -0.183   3.5156   1.5073  -1.3000
 XEB  C24   C   CR6   0  -0.129   4.3670   0.7151  -0.5541
 XEB  C25   C   CR6   0   0.199   3.8754  -0.1394   0.4342
 XEB  C26   C   CR16  0  -0.418   2.5051  -0.1763   0.6352
 XEB  CL    CL  CL    0  -0.140   6.0750   0.8195  -0.8494
 XEB  C28   C   CH2   0  -0.337   4.7701  -1.0431   1.2347
 XEB  N29   N   NH1   0  -0.574   5.1952  -2.1710   0.4289
 XEB  C30   C   CH3   0  -0.522   6.1234  -3.0304   1.1344
 XEB  HN02  H   HNH2  0   0.388  -6.7434  -1.9417  -2.5156
 XEB  HN0A  H   HNH2  0   0.398  -7.9338  -2.0155  -1.3018
 XEB  H03   H   HCR6  0   0.275  -7.6856  -0.9506   0.8411
 XEB  H04   H   HCR6  0   0.269  -6.1296   0.1774   2.3899
 XEB  H06   H   HCR6  0   0.258  -3.8490   1.1913   2.7718
 XEB  H07   H   HCR6  0   0.253  -1.6161   1.7492   1.9071
 XEB  H09   H   HCR6  0   0.252  -2.6343   0.0040  -1.8797
 XEB  H11   H   HCH2  0   0.248  -0.5452   1.0300  -1.6359
 XEB  H11A  H   HCH2  0   0.244  -0.4150   2.3164  -0.4278
 XEB  H22   H   HCR6  0   0.290   1.5045   2.0888  -1.6933
 XEB  H23   H   HCR6  0   0.280   3.9124   2.1707  -2.0567
 XEB  H26   H   HCR6  0   0.265   2.0998  -0.8331   1.3966
 XEB  H28   H   HCH2  0   0.238   5.6619  -0.4969   1.5543
 XEB  H28A  H   HCH2  0   0.220   4.2456  -1.3426   2.1544
 XEB  HN29  H   HNH1  0   0.345   4.3778  -2.7085   0.1675
 XEB  H30   H   HCH3  0   0.234   6.3536  -3.9032   0.5239
 XEB  H30A  H   HCH3  0   0.223   7.0589  -2.4961   1.3113
 XEB  H30B  H   HCH3  0   0.195   5.7591  -3.3869   2.1082

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
 XEB  N01  C02   aromatic  1.313  0.020  1.313
 XEB  N01  C10   aromatic  1.353  0.020  1.353
 XEB  C02  N02   single    1.355  0.020  1.355
 XEB  C02  C03   aromatic  1.431  0.020  1.431
 XEB  C03  C04   aromatic  1.356  0.020  1.356
 XEB  C04  C05   aromatic  1.419  0.020  1.419
 XEB  C05  C06   aromatic  1.409  0.020  1.409
 XEB  C05  C10   aromatic  1.414  0.020  1.414
 XEB  C06  C07   aromatic  1.369  0.020  1.369
 XEB  C07  C08   aromatic  1.412  0.020  1.412
 XEB  C08  C09   aromatic  1.373  0.020  1.373
 XEB  C08  C11   single    1.498  0.020  1.498
 XEB  C09  C10   aromatic  1.413  0.020  1.413
 XEB  C11  O12   single    1.420  0.020  1.420
 XEB  O12  C21   single    1.347  0.020  1.347
 XEB  C21  C22   aromatic  1.390  0.020  1.390
 XEB  C21  C26   aromatic  1.396  0.020  1.396
 XEB  C22  C23   aromatic  1.390  0.020  1.390
 XEB  C23  C24   aromatic  1.382  0.020  1.382
 XEB  C24  C25   aromatic  1.396  0.020  1.396
 XEB  C24  CL    single    1.736  0.020  1.736
 XEB  C25  C26   aromatic  1.385  0.020  1.385
 XEB  C25  C28   single    1.503  0.020  1.503
 XEB  C28  N29   single    1.450  0.020  1.450
 XEB  N29  C30   single    1.448  0.020  1.448
 XEB  N02  HN02  single    0.890  0.020  1.040
 XEB  N02  HN0A  single    0.890  0.020  1.040
 XEB  C03  H03   single    0.930  0.020  1.080
 XEB  C04  H04   single    0.930  0.020  1.080
 XEB  C06  H06   single    0.930  0.020  1.080
 XEB  C07  H07   single    0.930  0.020  1.080
 XEB  C09  H09   single    0.930  0.020  1.080
 XEB  C11  H11   single    0.970  0.020  1.090
 XEB  C11  H11A  single    0.970  0.020  1.090
 XEB  C22  H22   single    0.930  0.020  1.080
 XEB  C23  H23   single    0.930  0.020  1.080
 XEB  C26  H26   single    0.930  0.020  1.080
 XEB  C28  H28   single    0.970  0.020  1.090
 XEB  C28  H28A  single    0.970  0.020  1.090
 XEB  N29  HN29  single    0.890  0.020  1.040
 XEB  C30  H30   single    0.970  0.020  1.090
 XEB  C30  H30A  single    0.970  0.020  1.090
 XEB  C30  H30B  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
 XEB  C10   N01  C02   118.83  3.000
 XEB  C03   C02  N02   119.02  3.000
 XEB  C03   C02  N01   122.62  3.000
 XEB  N02   C02  N01   118.33  3.000
 XEB  HN0A  N02  HN02  115.58  3.000
 XEB  HN0A  N02  C02   119.21  3.000
 XEB  HN02  N02  C02   117.83  3.000
 XEB  H03   C03  C04   121.31  3.000
 XEB  H03   C03  C02   119.87  3.000
 XEB  C04   C03  C02   118.82  3.000
 XEB  H04   C04  C05   119.59  3.000
 XEB  H04   C04  C03   120.49  3.000
 XEB  C05   C04  C03   119.93  3.000
 XEB  C10   C05  C06   119.78  3.000
 XEB  C10   C05  C04   116.95  3.000
 XEB  C06   C05  C04   123.28  3.000
 XEB  H06   C06  C07   120.28  3.000
 XEB  H06   C06  C05   119.09  3.000
 XEB  C07   C06  C05   120.63  3.000
 XEB  H07   C07  C08   119.80  3.000
 XEB  H07   C07  C06   120.08  3.000
 XEB  C08   C07  C06   120.11  3.000
 XEB  C11   C08  C09   120.50  3.000
 XEB  C11   C08  C07   119.53  3.000
 XEB  C09   C08  C07   119.97  3.000
 XEB  H09   C09  C10   118.19  3.000
 XEB  H09   C09  C08   120.66  3.000
 XEB  C10   C09  C08   121.15  3.000
 XEB  C09   C10  C05   118.36  3.000
 XEB  C09   C10  N01   118.77  3.000
 XEB  C05   C10  N01   122.87  3.000
 XEB  H11A  C11  H11   107.74  3.000
 XEB  H11A  C11  O12   110.17  3.000
 XEB  H11   C11  O12   110.65  3.000
 XEB  H11A  C11  C08   110.32  3.000
 XEB  H11   C11  C08   110.45  3.000
 XEB  O12   C11  C08   107.52  3.000
 XEB  C21   O12  C11   118.53  3.000
 XEB  C26   C21  C22   119.29  3.000
 XEB  C26   C21  O12   116.06  3.000
 XEB  C22   C21  O12   124.65  3.000
 XEB  H22   C22  C23   118.60  3.000
 XEB  H22   C22  C21   121.94  3.000
 XEB  C23   C22  C21   119.46  3.000
 XEB  H23   C23  C24   120.21  3.000
 XEB  H23   C23  C22   119.31  3.000
 XEB  C24   C23  C22   120.48  3.000
 XEB  CL    C24  C25   120.24  3.000
 XEB  CL    C24  C23   118.68  3.000
 XEB  C25   C24  C23   121.07  3.000
 XEB  C28   C25  C26   119.71  3.000
 XEB  C28   C25  C24   122.38  3.000
 XEB  C26   C25  C24   117.86  3.000
 XEB  H26   C26  C25   119.19  3.000
 XEB  H26   C26  C21   118.98  3.000
 XEB  C25   C26  C21   121.82  3.000
 XEB  H28A  C28  H28   106.29  3.000
 XEB  H28A  C28  N29   113.11  3.000
 XEB  H28   C28  N29   108.17  3.000
 XEB  H28A  C28  C25   108.97  3.000
 XEB  H28   C28  C25   109.93  3.000
 XEB  N29   C28  C25   110.26  3.000
 XEB  HN29  N29  C30   109.15  3.000
 XEB  HN29  N29  C28   108.65  3.000
 XEB  C30   N29  C28   112.25  3.000
 XEB  H30B  C30  H30A  107.41  3.000
 XEB  H30B  C30  H30   107.85  3.000
 XEB  H30A  C30  H30   107.56  3.000
 XEB  H30B  C30  N29   114.31  3.000
 XEB  H30A  C30  N29   109.73  3.000
 XEB  H30   C30  N29   109.74  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
 XEB  CONST_01  C04   C03  C02  N01    0.00   0.0  0
 XEB  CONST_02  C04   C05  C10  N01    0.00   0.0  0
 XEB  CONST_03  C06   C05  C10  N01  180.00   0.0  0
 XEB  CONST_04  C08   C09  C10  N01  180.00   0.0  0
 XEB  CONST_05  C05   C10  N01  C02    0.00   0.0  0
 XEB  CONST_06  C09   C10  N01  C02  180.00   0.0  0
 XEB  CONST_07  C05   C04  C03  C02    0.00   0.0  0
 XEB  CONST_08  C10   N01  C02  C03    0.00   0.0  0
 XEB  CONST_09  C06   C05  C04  C03  180.00   0.0  0
 XEB  CONST_10  C10   C05  C04  C03    0.00   0.0  0
 XEB  CONST_11  C07   C06  C05  C04  180.00   0.0  0
 XEB  CONST_12  C09   C10  C05  C04  180.00   0.0  0
 XEB  CONST_13  C08   C07  C06  C05    0.00   0.0  0
 XEB  CONST_14  C08   C09  C10  C05    0.00   0.0  0
 XEB  CONST_15  C09   C10  C05  C06    0.00   0.0  0
 XEB  CONST_16  C09   C08  C07  C06    0.00   0.0  0
 XEB  CONST_17  C10   C05  C06  C07    0.00   0.0  0
 XEB  CONST_18  C10   C09  C08  C07    0.00   0.0  0
 XEB  CONST_19  C24   C23  C22  C21    0.00   0.0  0
 XEB  CONST_20  C24   C25  C26  C21    0.00   0.0  0
 XEB  CONST_21  C25   C26  C21  C22    0.00   0.0  0
 XEB  CONST_22  C25   C24  C23  C22    0.00   0.0  0
 XEB  CONST_23  C26   C21  C22  C23    0.00   0.0  0
 XEB  CONST_24  C26   C25  C24  C23    0.00   0.0  0
 XEB  CONST_25  C10   N01  C02  N02  180.00   0.0  0
 XEB  CONST_26  C04   C03  C02  N02  180.00   0.0  0
 XEB  CONST_27  C11   C08  C07  C06  180.00   0.0  0
 XEB  CONST_28  C11   C08  C09  C10  180.00   0.0  0
 XEB  CONST_29  C23   C22  C21  O12  180.00   0.0  0
 XEB  CONST_30  C25   C26  C21  O12  180.00   0.0  0
 XEB  CONST_31  C28   C25  C26  C21  180.00   0.0  0
 XEB  CONST_32  CL    C24  C23  C22  180.00   0.0  0
 XEB  CONST_33  C28   C25  C24  C23  180.00   0.0  0
 XEB  CONST_34  CL    C24  C25  C26  180.00   0.0  0
 XEB  CONST_35  H03   C03  C02  N01  180.00   0.0  0
 XEB  CONST_36  H09   C09  C10  N01    0.00   0.0  0
 XEB  CONST_37  H04   C04  C03  C02  180.00   0.0  0
 XEB  CONST_38  H06   C06  C05  C04    0.00   0.0  0
 XEB  CONST_39  H07   C07  C06  C05  180.00   0.0  0
 XEB  CONST_40  H23   C23  C22  C21  180.00   0.0  0
 XEB  CONST_41  H26   C26  C21  C22  180.00   0.0  0
 XEB  CONST_42  H22   C22  C23  C24  180.00   0.0  0
 XEB  CONST_43  HN02  N02  C02  N01    0.00   0.0  0
 XEB  Var_01    O12   C11  C08  C07   65.69  30.0  2
 XEB  Var_02    C22   C21  O12  C11   -0.27  30.0  2
 XEB  Var_03    N29   C28  C25  C24  -74.92  30.0  2
 XEB  Var_04    C30   N29  C28  C25  176.63  30.0  3
 XEB  Var_05    H30   C30  N29  C28  175.51  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
 XEB  plan-1  O12   0.020
 XEB  plan-1  C21   0.020
 XEB  plan-1  C22   0.020
 XEB  plan-1  C23   0.020
 XEB  plan-1  C24   0.020
 XEB  plan-1  C25   0.020
 XEB  plan-1  C26   0.020
 XEB  plan-1  CL    0.020
 XEB  plan-1  C28   0.020
 XEB  plan-1  H22   0.020
 XEB  plan-1  H23   0.020
 XEB  plan-1  H26   0.020
 XEB  plan-2  N01   0.020
 XEB  plan-2  C02   0.020
 XEB  plan-2  N02   0.020
 XEB  plan-2  C03   0.020
 XEB  plan-2  C04   0.020
 XEB  plan-2  C05   0.020
 XEB  plan-2  C06   0.020
 XEB  plan-2  C07   0.020
 XEB  plan-2  C08   0.020
 XEB  plan-2  C09   0.020
 XEB  plan-2  C10   0.020
 XEB  plan-2  C11   0.020
 XEB  plan-2  H03   0.020
 XEB  plan-2  H04   0.020
 XEB  plan-2  H06   0.020
 XEB  plan-2  H07   0.020
 XEB  plan-2  H09   0.020
 XEB  plan-3  C02   0.020
 XEB  plan-3  N02   0.020
 XEB  plan-3  HN02  0.020
 XEB  plan-3  HN0A  0.020

