# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 00:39:29 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 2-chloro-4-(6-methoxy-3,4-dihydroquinolin-1(2H)-yl)pyrido[2,3-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2N(CCCc2c1)c3nc(Cl)nc4ncccc34
#
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
 E3Y  E3Y  2-chloro-4-(6-methoxy-3,4-dihydroquinolin-1(2H)-yl)pyrido[2,3-d]pyrimidine  ligand  38  23  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E3Y
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
 E3Y  C1   C   CR6   0   0.281   2.0035   0.9940   1.0860
 E3Y  C2   C   CR66  0   0.371   3.1325  -0.6648   0.1035
 E3Y  C3   C   CR16  0  -0.049   4.3101  -2.4335  -0.7098
 E3Y  C6   C   CR66  0  -0.126   1.9233  -1.1689  -0.4246
 E3Y  C7   C   CR6   0   0.498   0.7490  -0.3732  -0.1981
 E3Y  C8   C   CR6   0   0.295  -1.6563  -0.2491  -0.1803
 E3Y  C9   C   CR16  0  -0.261  -1.8616  -0.4330   1.1841
 E3Y  C11  C   CR6   0   0.389  -4.0664   0.4996   1.0244
 E3Y  C13  C   CR16  0  -0.400  -3.8741   0.6519  -0.3439
 E3Y  C14  C   CR6   0   0.064  -2.6838   0.2861  -0.9604
 E3Y  C16  C   CH2   0  -0.453  -1.1410   0.1704  -2.9442
 E3Y  C17  C   CH2   0  -0.357  -0.5207  -1.0016  -2.2021
 E3Y  C10  C   CR16  0  -0.396  -3.0444  -0.0567   1.7938
 E3Y  C12  C   CH3   0  -0.437  -5.5050   0.7346   2.8960
 E3Y  C15  C   CH2   0  -0.490  -2.5566   0.4218  -2.4540
 E3Y  C4   C   CR16  0  -0.326   3.1522  -3.0757  -1.1760
 E3Y  C5   C   CR16  0  -0.172   1.9498  -2.4373  -1.0295
 E3Y  N1   N   N     0  -0.404   3.1585   0.4554   0.8645
 E3Y  N2   N   N     0  -0.413   4.3092  -1.2845  -0.0783
 E3Y  N3   N   NT    0  -0.585  -0.4434  -0.6800  -0.7746
 E3Y  N4   N   N     0  -0.415   0.8131   0.6712   0.6078
 E3Y  CL1  CL  CL    0  -0.100   1.9991   2.3765   2.1348
 E3Y  H1   H   HCR6  0   0.282   5.2754  -2.9078  -0.8493
 E3Y  H2   H   HCR6  0   0.268  -1.0877  -0.8838   1.7909
 E3Y  H3   H   HCR6  0   0.257  -4.6750   1.0689  -0.9447
 E3Y  H4   H   HCH2  0   0.245  -0.5122   1.0519  -2.7968
 E3Y  H5   H   HCH2  0   0.257  -1.1431  -0.0436  -4.0138
 E3Y  H6   H   HCH2  0   0.264  -1.1111  -1.9105  -2.3402
 E3Y  H7   H   HCH2  0   0.282   0.4755  -1.1878  -2.5919
 E3Y  H8   H   HCR6  0   0.280  -3.1530  -0.2164   2.8576
 E3Y  H9   H   HCH3  0   0.228  -4.7954   1.2958   3.5097
 E3Y  H10  H   HCH3  0   0.260  -6.5053   1.1190   3.0784
 E3Y  H11  H   HCH3  0   0.228  -5.4731  -0.3166   3.1948
 E3Y  H12  H   HCH2  0   0.257  -3.2356  -0.2985  -2.9200
 E3Y  H13  H   HCH2  0   0.262  -2.9008   1.4090  -2.7680
 E3Y  H14  H   HCR6  0   0.285   3.2202  -4.0524  -1.6328
 E3Y  H15  H   HCR6  0   0.305   1.0372  -2.9181  -1.3536
 E3Y  O1   O   O2    0  -0.473  -5.2566   0.8991   1.5142

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
 E3Y  O1   C12  single    1.414  0.020  1.414
 E3Y  O1   C11  single    1.348  0.020  1.348
 E3Y  C13  C11  aromatic  1.390  0.020  1.390
 E3Y  C13  C14  aromatic  1.389  0.020  1.389
 E3Y  C11  C10  aromatic  1.395  0.020  1.395
 E3Y  C15  C14  single    1.505  0.020  1.505
 E3Y  C15  C16  single    1.519  0.020  1.519
 E3Y  C14  C8   aromatic  1.397  0.020  1.397
 E3Y  C10  C9   aromatic  1.383  0.020  1.383
 E3Y  C16  C17  single    1.520  0.020  1.520
 E3Y  C8   C9   aromatic  1.392  0.020  1.392
 E3Y  C8   N3   single    1.418  0.020  1.418
 E3Y  C5   C4   aromatic  1.369  0.020  1.369
 E3Y  C5   C6   aromatic  1.406  0.020  1.406
 E3Y  C4   C3   aromatic  1.404  0.020  1.404
 E3Y  C17  N3   single    1.465  0.020  1.465
 E3Y  N3   C7   single    1.360  0.020  1.360
 E3Y  C6   C7   aromatic  1.436  0.020  1.436
 E3Y  C6   C2   aromatic  1.412  0.020  1.412
 E3Y  C3   N2   aromatic  1.311  0.020  1.311
 E3Y  C7   N4   aromatic  1.321  0.020  1.321
 E3Y  C2   N2   aromatic  1.342  0.020  1.342
 E3Y  C2   N1   aromatic  1.355  0.020  1.355
 E3Y  N4   C1   aromatic  1.323  0.020  1.323
 E3Y  C1   N1   aromatic  1.293  0.020  1.293
 E3Y  C1   CL1  single    1.735  0.020  1.735
 E3Y  C3   H1   single    0.930  0.020  1.080
 E3Y  C9   H2   single    0.930  0.020  1.080
 E3Y  C13  H3   single    0.930  0.020  1.080
 E3Y  C16  H4   single    0.970  0.020  1.090
 E3Y  C16  H5   single    0.970  0.020  1.090
 E3Y  C17  H6   single    0.970  0.020  1.090
 E3Y  C17  H7   single    0.970  0.020  1.090
 E3Y  C10  H8   single    0.930  0.020  1.080
 E3Y  C12  H9   single    0.970  0.020  1.090
 E3Y  C12  H10  single    0.970  0.020  1.090
 E3Y  C12  H11  single    0.970  0.020  1.090
 E3Y  C15  H12  single    0.970  0.020  1.090
 E3Y  C15  H13  single    0.970  0.020  1.090
 E3Y  C4   H14  single    0.930  0.020  1.080
 E3Y  C5   H15  single    0.930  0.020  1.080

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
 E3Y  CL1  C1   N4   114.24  3.000
 E3Y  CL1  C1   N1   115.94  3.000
 E3Y  N4   C1   N1   129.79  3.000
 E3Y  N2   C2   N1   116.17  3.000
 E3Y  N1   C2   C6   121.44  3.000
 E3Y  N2   C2   C6   122.35  3.000
 E3Y  H1   C3   N2   116.48  3.000
 E3Y  H1   C3   C4   119.43  3.000
 E3Y  N2   C3   C4   124.08  3.000
 E3Y  C5   C6   C7   125.67  3.000
 E3Y  C7   C6   C2   116.31  3.000
 E3Y  C5   C6   C2   117.83  3.000
 E3Y  N4   C7   N3   118.67  3.000
 E3Y  N4   C7   C6   119.64  3.000
 E3Y  N3   C7   C6   121.68  3.000
 E3Y  N3   C8   C14  120.78  3.000
 E3Y  N3   C8   C9   119.80  3.000
 E3Y  C14  C8   C9   119.31  3.000
 E3Y  H2   C9   C10  118.55  3.000
 E3Y  H2   C9   C8   119.96  3.000
 E3Y  C10  C9   C8   121.49  3.000
 E3Y  O1   C11  C10  124.39  3.000
 E3Y  C10  C11  C13  119.03  3.000
 E3Y  O1   C11  C13  116.59  3.000
 E3Y  H3   C13  C14  119.21  3.000
 E3Y  H3   C13  C11  119.02  3.000
 E3Y  C14  C13  C11  121.76  3.000
 E3Y  C15  C14  C13  119.27  3.000
 E3Y  C15  C14  C8   121.78  3.000
 E3Y  C13  C14  C8   118.90  3.000
 E3Y  H5   C16  H4   106.96  3.000
 E3Y  H5   C16  C15  110.31  3.000
 E3Y  H4   C16  C15  111.05  3.000
 E3Y  H5   C16  C17  109.17  3.000
 E3Y  H4   C16  C17  108.74  3.000
 E3Y  C15  C16  C17  110.52  3.000
 E3Y  H7   C17  H6   107.92  3.000
 E3Y  H7   C17  N3   109.82  3.000
 E3Y  H6   C17  N3   109.53  3.000
 E3Y  H7   C17  C16  109.35  3.000
 E3Y  H6   C17  C16  111.05  3.000
 E3Y  N3   C17  C16  109.15  3.000
 E3Y  H8   C10  C11  121.87  3.000
 E3Y  H8   C10  C9   118.66  3.000
 E3Y  C11  C10  C9   119.47  3.000
 E3Y  H11  C12  H10  108.73  3.000
 E3Y  H11  C12  H9   108.74  3.000
 E3Y  H10  C12  H9   108.76  3.000
 E3Y  H11  C12  O1   111.96  3.000
 E3Y  H10  C12  O1   106.53  3.000
 E3Y  H9   C12  O1   112.02  3.000
 E3Y  H13  C15  H12  106.09  3.000
 E3Y  H13  C15  C16  110.53  3.000
 E3Y  H12  C15  C16  109.38  3.000
 E3Y  H13  C15  C14  109.89  3.000
 E3Y  H12  C15  C14  108.11  3.000
 E3Y  C16  C15  C14  112.59  3.000
 E3Y  H14  C4   C5   121.46  3.000
 E3Y  H14  C4   C3   120.14  3.000
 E3Y  C5   C4   C3   118.39  3.000
 E3Y  H15  C5   C4   120.12  3.000
 E3Y  H15  C5   C6   120.96  3.000
 E3Y  C4   C5   C6   118.90  3.000
 E3Y  C2   N1   C1   115.05  3.000
 E3Y  C3   N2   C2   118.06  3.000
 E3Y  C17  N3   C8   115.47  3.000
 E3Y  C17  N3   C7   120.59  3.000
 E3Y  C8   N3   C7   120.26  3.000
 E3Y  C7   N4   C1   117.21  3.000
 E3Y  C12  O1   C11  118.42  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
 E3Y  CONST_01  C6   C7   N4   C1      0.00   0.0  0
 E3Y  CONST_02  C6   C2   N1   C1      0.00   0.0  0
 E3Y  CONST_03  N2   C2   N1   C1    180.00   0.0  0
 E3Y  CONST_04  C4   C5   C6   C2      0.00   0.0  0
 E3Y  CONST_05  N4   C7   C6   C2      0.00   0.0  0
 E3Y  CONST_06  C4   C3   N2   C2      0.00   0.0  0
 E3Y  CONST_07  N4   C1   N1   C2      0.00   0.0  0
 E3Y  CONST_08  C6   C5   C4   C3      0.00   0.0  0
 E3Y  CONST_09  C6   C2   N2   C3      0.00   0.0  0
 E3Y  CONST_10  N1   C2   N2   C3    180.00   0.0  0
 E3Y  CONST_11  C4   C5   C6   C7    180.00   0.0  0
 E3Y  CONST_12  N2   C2   C6   C7    180.00   0.0  0
 E3Y  CONST_13  N1   C2   C6   C7      0.00   0.0  0
 E3Y  CONST_14  N1   C1   N4   C7      0.00   0.0  0
 E3Y  CONST_15  C11  C13  C14  C8      0.00   0.0  0
 E3Y  CONST_16  C11  C10  C9   C8      0.00   0.0  0
 E3Y  CONST_17  C13  C11  C10  C9      0.00   0.0  0
 E3Y  CONST_18  C13  C14  C8   C9      0.00   0.0  0
 E3Y  CONST_19  C10  C11  C13  C14     0.00   0.0  0
 E3Y  CONST_20  C10  C9   C8   C14     0.00   0.0  0
 E3Y  CONST_21  N2   C3   C4   C5      0.00   0.0  0
 E3Y  CONST_22  N4   C7   C6   C5    180.00   0.0  0
 E3Y  CONST_23  N2   C2   C6   C5      0.00   0.0  0
 E3Y  CONST_24  N1   C2   C6   C5    180.00   0.0  0
 E3Y  CONST_25  N3   C7   N4   C1    180.00   0.0  0
 E3Y  CONST_26  N3   C7   C6   C2    180.00   0.0  0
 E3Y  CONST_27  N3   C7   C6   C5      0.00   0.0  0
 E3Y  CONST_28  CL1  C1   N1   C2    180.00   0.0  0
 E3Y  CONST_29  CL1  C1   N4   C7    180.00   0.0  0
 E3Y  CONST_30  O1   C11  C10  C9    180.00   0.0  0
 E3Y  CONST_31  O1   C11  C13  C14   180.00   0.0  0
 E3Y  CONST_32  H15  C5   C6   C2    180.00   0.0  0
 E3Y  CONST_33  H1   C3   N2   C2    180.00   0.0  0
 E3Y  CONST_34  H14  C4   C5   C6    180.00   0.0  0
 E3Y  CONST_35  H3   C13  C14  C8    180.00   0.0  0
 E3Y  CONST_36  H8   C10  C9   C8    180.00   0.0  0
 E3Y  CONST_37  H2   C9   C10  C11   180.00   0.0  0
 E3Y  Var_01    C8   N3   C7   C6    155.56  30.0  2
 E3Y  Var_02    C14  C8   N3   C7    136.44  30.0  1
 E3Y  Var_03    C16  C17  N3   C7   -106.00  30.0  1
 E3Y  Var_04    C16  C15  C14  C8    -10.79  30.0  1
 E3Y  Var_05    C17  C16  C15  C14    40.83  30.0  1
 E3Y  Var_06    N3   C17  C16  C15   -61.91  30.0  1
 E3Y  Var_07    H9   C12  O1   C11    60.98  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
 E3Y  plan-1  C1   0.020
 E3Y  plan-1  C2   0.020
 E3Y  plan-1  C3   0.020
 E3Y  plan-1  C6   0.020
 E3Y  plan-1  C7   0.020
 E3Y  plan-1  C4   0.020
 E3Y  plan-1  C5   0.020
 E3Y  plan-1  N1   0.020
 E3Y  plan-1  N2   0.020
 E3Y  plan-1  N3   0.020
 E3Y  plan-1  N4   0.020
 E3Y  plan-1  CL1  0.020
 E3Y  plan-1  H1   0.020
 E3Y  plan-1  H14  0.020
 E3Y  plan-1  H15  0.020
 E3Y  plan-2  C8   0.020
 E3Y  plan-2  C9   0.020
 E3Y  plan-2  C11  0.020
 E3Y  plan-2  C13  0.020
 E3Y  plan-2  C14  0.020
 E3Y  plan-2  C10  0.020
 E3Y  plan-2  C15  0.020
 E3Y  plan-2  N3   0.020
 E3Y  plan-2  H2   0.020
 E3Y  plan-2  H3   0.020
 E3Y  plan-2  H8   0.020
 E3Y  plan-2  O1   0.020

