# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 09:29:10 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: N~6~-(2,6-dichlorophenyl)-N~6~-(pent-2-yn-1-yl)quinoline-4,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC#CCN(c1ccc2nccc(N)c2c1)c3c(Cl)cccc3Cl
#
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
 5JJ  5JJ  N~6~-(2,6-dichlorophenyl)-N~6~-(pent-2-yn-1-yl)quinoline-4,6-diamine  ligand  42  25  .  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_5JJ
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
 5JJ  C1   C   CR16  0  -0.099   5.3015   0.7445  -0.9389
 5JJ  C2   C   CR16  0  -0.418   5.1921  -0.4367  -0.1991
 5JJ  C3   C   CR6   0   0.377   3.9592  -0.8330   0.2898
 5JJ  C12  C   CR6   0   0.388  -1.9146   0.9355   0.0547
 5JJ  C13  C   CR6   0  -0.094  -2.6612   1.8923   0.7461
 5JJ  C14  C   CR16  0  -0.216  -3.7840   2.4877   0.1954
 5JJ  C15  C   CR16  0  -0.270  -4.1666   2.1419  -1.0907
 5JJ  C16  C   CR16  0  -0.215  -3.4415   1.2105  -1.8168
 5JJ  C17  C   CR6   0  -0.078  -2.3337   0.6118  -1.2387
 5JJ  C20  C   CH2   0  -0.529  -1.0582  -0.7311   1.6101
 5JJ  C21  C   CSP   0   0.077  -1.0900  -2.0705   1.0181
 5JJ  C22  C   CSP   0   0.071  -1.1143  -3.1662   0.5212
 5JJ  C23  C   CH2   0  -0.607  -1.1457  -4.4960  -0.0764
 5JJ  C25  C   CH3   0  -0.663  -1.1330  -5.6123   0.9674
 5JJ  C4   C   CR66  0   0.068   2.8406   0.0178   0.0094
 5JJ  C5   C   CR66  0   0.145   3.0824   1.1798  -0.7599
 5JJ  N6   N   N     0  -0.462   4.3014   1.5395  -1.2287
 5JJ  C7   C   CR16  0  -0.428   1.5358  -0.2671   0.4662
 5JJ  C8   C   CR6   0   0.404   0.4771   0.5689   0.1782
 5JJ  C9   C   CR16  0  -0.315   0.7251   1.7307  -0.5984
 5JJ  C10  C   CR16  0  -0.290   1.9796   2.0164  -1.0485
 5JJ  N11  N   NT    0  -0.576  -0.8016   0.3313   0.6567
 5JJ  CL1  CL  CL    0  -0.084  -1.4395  -0.5468  -2.1479
 5JJ  CL2  CL  CL    0  -0.090  -2.1545   2.3543   2.3304
 5JJ  N24  N   NH2   0  -0.852   3.8237  -1.9530   1.0473
 5JJ  H1   H   HCR6  0   0.250   6.2785   1.0338  -1.3140
 5JJ  H2   H   HCR6  0   0.263   6.0740  -1.0382  -0.0188
 5JJ  H3   H   HCR6  0   0.289  -4.3434   3.2205   0.7596
 5JJ  H4   H   HCR6  0   0.282  -5.0370   2.6059  -1.5336
 5JJ  H5   H   HCR6  0   0.289  -3.7388   0.9442  -2.8213
 5JJ  H6   H   HCH2  0   0.299  -2.0138  -0.5292   2.0964
 5JJ  H7   H   HCH2  0   0.286  -0.3081  -0.6900   2.4050
 5JJ  H8   H   HCH2  0   0.262  -2.0359  -4.5847  -0.7039
 5JJ  H9   H   HCH2  0   0.263  -0.2896  -4.6048  -0.7467
 5JJ  H10  H   HCH3  0   0.232  -0.2340  -5.5656   1.5809
 5JJ  H11  H   HCH3  0   0.232  -1.9980  -5.5435   1.6258
 5JJ  H12  H   HCH3  0   0.239  -1.1574  -6.5848   0.4771
 5JJ  H13  H   HCR6  0   0.247   1.3616  -1.1626   1.0447
 5JJ  H14  H   HCR6  0   0.272  -0.0837   2.4120  -0.8298
 5JJ  H15  H   HCR6  0   0.257   2.1555   2.9099  -1.6342
 5JJ  H16  H   HNH2  0   0.395   4.6013  -2.5922   1.0599
 5JJ  H17  H   HNH2  0   0.394   2.9325  -2.4163   1.0901

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
 5JJ  CL1  C17  single    1.723  0.020  1.723
 5JJ  C16  C17  aromatic  1.386  0.020  1.386
 5JJ  C16  C15  aromatic  1.386  0.020  1.386
 5JJ  C17  C12  aromatic  1.398  0.020  1.398
 5JJ  C15  C14  aromatic  1.386  0.020  1.386
 5JJ  C12  N11  single    1.402  0.020  1.402
 5JJ  C12  C13  aromatic  1.397  0.020  1.397
 5JJ  C20  N11  single    1.450  0.020  1.450
 5JJ  C20  C21  single    1.465  0.020  1.465
 5JJ  N11  C8   single    1.386  0.020  1.386
 5JJ  C14  C13  aromatic  1.385  0.020  1.385
 5JJ  C9   C8   aromatic  1.419  0.020  1.419
 5JJ  C9   C10  aromatic  1.363  0.020  1.363
 5JJ  C13  CL2  single    1.726  0.020  1.726
 5JJ  C8   C7   aromatic  1.379  0.020  1.379
 5JJ  C10  C5   aromatic  1.414  0.020  1.414
 5JJ  C7   C4   aromatic  1.411  0.020  1.411
 5JJ  C21  C22  triple    1.203  0.020  1.203
 5JJ  C5   C4   aromatic  1.414  0.020  1.414
 5JJ  C5   N6   aromatic  1.355  0.020  1.355
 5JJ  C4   C3   aromatic  1.433  0.020  1.433
 5JJ  N6   C1   aromatic  1.310  0.020  1.310
 5JJ  C22  C23  single    1.458  0.020  1.458
 5JJ  C3   N24  single    1.359  0.020  1.359
 5JJ  C3   C2   aromatic  1.384  0.020  1.384
 5JJ  C1   C2   aromatic  1.398  0.020  1.398
 5JJ  C23  C25  single    1.528  0.020  1.528
 5JJ  C1   H1   single    0.930  0.020  1.080
 5JJ  C2   H2   single    0.930  0.020  1.080
 5JJ  C14  H3   single    0.930  0.020  1.080
 5JJ  C15  H4   single    0.930  0.020  1.080
 5JJ  C16  H5   single    0.930  0.020  1.080
 5JJ  C20  H6   single    0.970  0.020  1.090
 5JJ  C20  H7   single    0.970  0.020  1.090
 5JJ  C23  H8   single    0.970  0.020  1.090
 5JJ  C23  H9   single    0.970  0.020  1.090
 5JJ  C25  H10  single    0.970  0.020  1.090
 5JJ  C25  H11  single    0.970  0.020  1.090
 5JJ  C25  H12  single    0.970  0.020  1.090
 5JJ  C7   H13  single    0.930  0.020  1.080
 5JJ  C9   H14  single    0.930  0.020  1.080
 5JJ  C10  H15  single    0.930  0.020  1.080
 5JJ  N24  H16  single    0.890  0.020  1.040
 5JJ  N24  H17  single    0.890  0.020  1.040

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
 5JJ  H1   C1   N6   116.67  3.000
 5JJ  H1   C1   C2   118.58  3.000
 5JJ  N6   C1   C2   124.75  3.000
 5JJ  H2   C2   C3   120.51  3.000
 5JJ  H2   C2   C1   119.59  3.000
 5JJ  C3   C2   C1   119.90  3.000
 5JJ  N24  C3   C4   121.37  3.000
 5JJ  N24  C3   C2   121.44  3.000
 5JJ  C4   C3   C2   117.14  3.000
 5JJ  N11  C12  C17  122.38  3.000
 5JJ  N11  C12  C13  120.46  3.000
 5JJ  C17  C12  C13  117.15  3.000
 5JJ  CL2  C13  C14  119.19  3.000
 5JJ  CL2  C13  C12  118.73  3.000
 5JJ  C14  C13  C12  122.08  3.000
 5JJ  H3   C14  C15  120.71  3.000
 5JJ  H3   C14  C13  120.23  3.000
 5JJ  C15  C14  C13  119.05  3.000
 5JJ  H4   C15  C16  119.67  3.000
 5JJ  H4   C15  C14  119.70  3.000
 5JJ  C16  C15  C14  120.63  3.000
 5JJ  H5   C16  C17  120.08  3.000
 5JJ  H5   C16  C15  120.57  3.000
 5JJ  C17  C16  C15  119.35  3.000
 5JJ  CL1  C17  C16  119.04  3.000
 5JJ  C16  C17  C12  121.72  3.000
 5JJ  CL1  C17  C12  119.24  3.000
 5JJ  H7   C20  H6   105.65  3.000
 5JJ  H7   C20  N11  109.21  3.000
 5JJ  H6   C20  N11  108.20  3.000
 5JJ  H7   C20  C21  110.06  3.000
 5JJ  H6   C20  C21  109.29  3.000
 5JJ  N11  C20  C21  114.08  3.000
 5JJ  C22  C21  C20  180.00  3.000
 5JJ  C23  C22  C21  180.00  3.000
 5JJ  H9   C23  H8   106.14  3.000
 5JJ  H9   C23  C25  109.86  3.000
 5JJ  H8   C23  C25  109.86  3.000
 5JJ  H9   C23  C22  108.98  3.000
 5JJ  H8   C23  C22  109.08  3.000
 5JJ  C25  C23  C22  112.70  3.000
 5JJ  H12  C25  H11  108.09  3.000
 5JJ  H12  C25  H10  108.07  3.000
 5JJ  H11  C25  H10  108.19  3.000
 5JJ  H12  C25  C23  110.15  3.000
 5JJ  H11  C25  C23  111.11  3.000
 5JJ  H10  C25  C23  111.11  3.000
 5JJ  C7   C4   C5   119.99  3.000
 5JJ  C5   C4   C3   117.43  3.000
 5JJ  C7   C4   C3   122.58  3.000
 5JJ  C10  C5   N6   118.30  3.000
 5JJ  N6   C5   C4   124.07  3.000
 5JJ  C10  C5   C4   117.63  3.000
 5JJ  C5   N6   C1   116.70  3.000
 5JJ  H13  C7   C8   119.37  3.000
 5JJ  H13  C7   C4   119.32  3.000
 5JJ  C8   C7   C4   121.31  3.000
 5JJ  N11  C8   C9   119.38  3.000
 5JJ  C9   C8   C7   118.44  3.000
 5JJ  N11  C8   C7   122.15  3.000
 5JJ  H14  C9   C10  119.02  3.000
 5JJ  H14  C9   C8   120.10  3.000
 5JJ  C10  C9   C8   120.87  3.000
 5JJ  H15  C10  C9   120.08  3.000
 5JJ  H15  C10  C5   118.16  3.000
 5JJ  C9   C10  C5   121.76  3.000
 5JJ  C8   N11  C20  121.05  3.000
 5JJ  C8   N11  C12  120.68  3.000
 5JJ  C20  N11  C12  117.22  3.000
 5JJ  H17  N24  H16  113.06  3.000
 5JJ  H17  N24  C3   119.47  3.000
 5JJ  H16  N24  C3   116.96  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
 5JJ  CONST_01  C10  C5   N6   C1    180.00   0.0  0
 5JJ  CONST_02  C4   C5   N6   C1      0.00   0.0  0
 5JJ  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 5JJ  CONST_04  C7   C4   C3   C2    180.00   0.0  0
 5JJ  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 5JJ  CONST_06  C5   N6   C1   C2      0.00   0.0  0
 5JJ  CONST_07  C8   C7   C4   C3    180.00   0.0  0
 5JJ  CONST_08  C10  C5   C4   C3    180.00   0.0  0
 5JJ  CONST_09  N6   C5   C4   C3      0.00   0.0  0
 5JJ  CONST_10  N6   C1   C2   C3      0.00   0.0  0
 5JJ  CONST_11  C15  C16  C17  C12     0.00   0.0  0
 5JJ  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 5JJ  CONST_13  C16  C17  C12  C13     0.00   0.0  0
 5JJ  CONST_14  C16  C15  C14  C13     0.00   0.0  0
 5JJ  CONST_15  C17  C16  C15  C14     0.00   0.0  0
 5JJ  CONST_16  C17  C12  C13  C14     0.00   0.0  0
 5JJ  CONST_17  C9   C8   C7   C4      0.00   0.0  0
 5JJ  CONST_18  C9   C10  C5   C4      0.00   0.0  0
 5JJ  CONST_19  C8   C9   C10  C5      0.00   0.0  0
 5JJ  CONST_20  C8   C7   C4   C5      0.00   0.0  0
 5JJ  CONST_21  C9   C10  C5   N6    180.00   0.0  0
 5JJ  CONST_22  C7   C4   C5   N6    180.00   0.0  0
 5JJ  CONST_23  C10  C9   C8   C7      0.00   0.0  0
 5JJ  CONST_24  C10  C5   C4   C7      0.00   0.0  0
 5JJ  CONST_25  N24  C3   C2   C1    180.00   0.0  0
 5JJ  CONST_26  CL1  C17  C12  C13   180.00   0.0  0
 5JJ  CONST_27  N11  C12  C13  C14   180.00   0.0  0
 5JJ  CONST_28  CL1  C17  C16  C15   180.00   0.0  0
 5JJ  CONST_29  CL2  C13  C14  C15   180.00   0.0  0
 5JJ  CONST_30  N11  C12  C17  C16   180.00   0.0  0
 5JJ  CONST_31  CL2  C13  C12  C17   180.00   0.0  0
 5JJ  CONST_32  N11  C8   C7   C4    180.00   0.0  0
 5JJ  CONST_33  N24  C3   C4   C5    180.00   0.0  0
 5JJ  CONST_34  N24  C3   C4   C7      0.00   0.0  0
 5JJ  CONST_35  N11  C8   C9   C10   180.00   0.0  0
 5JJ  CONST_36  H13  C7   C4   C3      0.00   0.0  0
 5JJ  CONST_37  H1   C1   C2   C3    180.00   0.0  0
 5JJ  CONST_38  H5   C16  C17  C12   180.00   0.0  0
 5JJ  CONST_39  H3   C14  C13  C12   180.00   0.0  0
 5JJ  CONST_40  H4   C15  C14  C13   180.00   0.0  0
 5JJ  CONST_41  H15  C10  C5   C4    180.00   0.0  0
 5JJ  CONST_42  H2   C2   C3   C4    180.00   0.0  0
 5JJ  CONST_43  H14  C9   C10  C5    180.00   0.0  0
 5JJ  CONST_44  H16  N24  C3   C2      0.00   0.0  0
 5JJ  Var_01    C9   C8   N11  C12    21.09  30.0  2
 5JJ  Var_02    C8   N11  C12  C13  -112.85  30.0  2
 5JJ  Var_03    C21  C20  N11  C12    91.18  30.0  2
 5JJ  Var_04    C25  C23  C22  C21   -22.17  30.0  3
 5JJ  Var_05    N11  C20  C21  C22    -1.84  30.0  1
 5JJ  Var_06    H10  C25  C23  C22   -60.28  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
 5JJ  plan-1  C12  0.020
 5JJ  plan-1  C13  0.020
 5JJ  plan-1  C14  0.020
 5JJ  plan-1  C15  0.020
 5JJ  plan-1  C16  0.020
 5JJ  plan-1  C17  0.020
 5JJ  plan-1  N11  0.020
 5JJ  plan-1  CL1  0.020
 5JJ  plan-1  CL2  0.020
 5JJ  plan-1  H3   0.020
 5JJ  plan-1  H4   0.020
 5JJ  plan-1  H5   0.020
 5JJ  plan-2  C1   0.020
 5JJ  plan-2  C2   0.020
 5JJ  plan-2  C3   0.020
 5JJ  plan-2  C4   0.020
 5JJ  plan-2  C5   0.020
 5JJ  plan-2  N6   0.020
 5JJ  plan-2  C7   0.020
 5JJ  plan-2  C8   0.020
 5JJ  plan-2  C9   0.020
 5JJ  plan-2  C10  0.020
 5JJ  plan-2  N11  0.020
 5JJ  plan-2  N24  0.020
 5JJ  plan-2  H1   0.020
 5JJ  plan-2  H2   0.020
 5JJ  plan-2  H13  0.020
 5JJ  plan-2  H14  0.020
 5JJ  plan-2  H15  0.020
 5JJ  plan-3  C3   0.020
 5JJ  plan-3  N24  0.020
 5JJ  plan-3  H16  0.020
 5JJ  plan-3  H17  0.020

