# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 20:48:19 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 7-(2,4-diamino-6-ethylpyrimidin-5-yl)-1-(3-methoxypropyl)quinolinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1c2ccc3ccc[n+](CCCOC)c3c2
#
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
 L1B  L1B  7-(2,4-diamino-6-ethylpyrimidin-5-yl)-1-(3-methoxypropyl)quinolinium  ligand  49  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L1B
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
 L1B  C1    C  CR6   0   0.485   2.0215  -1.0248   0.9572
 L1B  N1    N  N     0  -0.507   3.0848  -1.8139   0.8790
 L1B  C2    C  CR6   0   0.546   4.1153  -1.3768   0.1555
 L1B  N2    N  N     0  -0.502   4.1768  -0.2176  -0.5048
 L1B  C3    C  CR6   0   0.280   3.1112   0.5741  -0.4281
 L1B  C4    C  CR6   0  -0.146   1.9791   0.2321   0.3026
 L1B  N3    N  NH2   0  -0.825   0.9776  -1.4853   1.6761
 L1B  N4    N  NH2   0  -0.824   5.1930  -2.1736   0.0909
 L1B  C5    C  CH2   0  -0.516   3.1713   1.8145  -1.2723
 L1B  C6    C  CH3   0  -0.661   2.6826   1.5176  -2.6903
 L1B  C7    C  CR16  0  -0.270   0.8399   2.3398   1.0537
 L1B  C8    C  CR16  0  -0.285  -0.2747   3.1167   1.1730
 L1B  C9    C  CR66  0   0.031  -1.5152   2.6764   0.6632
 L1B  C10   C  CR66  0   0.449  -1.5773   1.4213   0.0152
 L1B  C11   C  CR16  0  -0.352  -0.4155   0.6483  -0.1235
 L1B  C12   C  CR6   0   0.022   0.7834   1.0877   0.3962
 L1B  C13   C  CR16  0  -0.112  -2.6843   3.4447   0.7911
 L1B  C14   C  CR16  0  -0.349  -3.8691   2.9735   0.2906
 L1B  C15   C  CR16  0   0.072  -3.8850   1.7327  -0.3307
 L1B  N5    N  NR6   1  -0.502  -2.7935   0.9926  -0.4638
 L1B  C16   C  CH2   0  -0.369  -2.9248  -0.3345  -1.0888
 L1B  C17   C  CH2   0  -0.487  -2.9462  -1.4503  -0.0536
 L1B  C18   C  CH2   0  -0.122  -3.0833  -2.7940  -0.7467
 L1B  O1    O  O2    0  -0.483  -3.0942  -3.8019   0.2281
 L1B  C19   C  CH3   0  -0.399  -3.2168  -5.0866  -0.3288
 L1B  HN31  H  HNH2  0   0.396   1.1261  -2.3045   2.2414
 L1B  HN32  H  HNH2  0   0.403   0.2570  -0.8593   1.9912
 L1B  HN41  H  HNH2  0   0.397   5.9864  -1.9112  -0.4654
 L1B  HN42  H  HNH2  0   0.397   5.1948  -3.0667   0.5490
 L1B  H51   H  HCH2  0   0.252   4.2059   2.1582  -1.3066
 L1B  H52   H  HCH2  0   0.247   2.5796   2.6230  -0.8443
 L1B  H61   H  HCH3  0   0.232   3.2710   0.7203  -3.1445
 L1B  H62   H  HCH3  0   0.227   1.6372   1.2074  -2.6928
 L1B  H63   H  HCH3  0   0.240   2.7705   2.4025  -3.3199
 L1B  H8    H  HCR6  0   0.287  -0.2286   4.0740   1.6753
 L1B  H11   H  HCR6  0   0.302  -0.4365  -0.3008  -0.6390
 L1B  H13   H  HCR6  0   0.310  -2.6389   4.4046   1.2889
 L1B  H14   H  HCR6  0   0.314  -4.7892   3.5316   0.3685
 L1B  H15   H  HCR6  0   0.350  -4.7988   1.3185  -0.7303
 L1B  H161  H  HCH2  0   0.311  -3.8514  -0.3233  -1.6587
 L1B  H162  H  HCH2  0   0.303  -2.1187  -0.4568  -1.8103
 L1B  H171  H  HCH2  0   0.250  -2.0319  -1.4434   0.5451
 L1B  H172  H  HCH2  0   0.267  -3.7848  -1.2950   0.6290
 L1B  H181  H  HCH2  0   0.208  -4.0067  -2.8157  -1.3444
 L1B  H182  H  HCH2  0   0.206  -2.2496  -2.9385  -1.4497
 L1B  H191  H  HCH3  0   0.206  -4.1512  -5.2028  -0.8906
 L1B  H192  H  HCH3  0   0.206  -2.3869  -5.3215  -1.0059
 L1B  H193  H  HCH3  0   0.235  -3.2122  -5.8086   0.4866
 L1B  H7    H  HCR6  0   0.283   1.7796   2.6733   1.4732

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
 L1B  C1   N1    aromatic  1.326  0.020  1.326
 L1B  C1   C4    aromatic  1.418  0.020  1.418
 L1B  C1   N3    single    1.348  0.020  1.348
 L1B  N1   C2    aromatic  1.333  0.020  1.333
 L1B  C2   N2    aromatic  1.336  0.020  1.336
 L1B  C2   N4    single    1.342  0.020  1.342
 L1B  N2   C3    aromatic  1.330  0.020  1.330
 L1B  C3   C4    aromatic  1.390  0.020  1.390
 L1B  C3   C5    single    1.502  0.020  1.502
 L1B  C4   C12   single    1.473  0.020  1.473
 L1B  N3   HN31  single    0.890  0.020  1.040
 L1B  N3   HN32  single    0.890  0.020  1.040
 L1B  N4   HN41  single    0.860  0.020  1.020
 L1B  N4   HN42  single    0.860  0.020  1.020
 L1B  C5   C6    single    1.529  0.020  1.529
 L1B  C5   H51   single    0.970  0.020  1.090
 L1B  C5   H52   single    0.970  0.020  1.090
 L1B  C6   H61   single    0.970  0.020  1.090
 L1B  C6   H62   single    0.970  0.020  1.090
 L1B  C6   H63   single    0.970  0.020  1.090
 L1B  C7   C8    aromatic  1.364  0.020  1.364
 L1B  C7   C12   aromatic  1.415  0.020  1.415
 L1B  C7   H7    single    0.930  0.020  1.080
 L1B  C8   C9    aromatic  1.412  0.020  1.412
 L1B  C8   H8    single    0.930  0.020  1.080
 L1B  C9   C10   aromatic  1.414  0.020  1.414
 L1B  C9   C13   aromatic  1.405  0.020  1.405
 L1B  C10  C11   aromatic  1.402  0.020  1.402
 L1B  C10  N5    aromatic  1.376  0.020  1.376
 L1B  C11  C12   aromatic  1.379  0.020  1.379
 L1B  C11  H11   single    0.930  0.020  1.080
 L1B  C13  C14   aromatic  1.370  0.020  1.370
 L1B  C13  H13   single    0.930  0.020  1.080
 L1B  C14  C15   aromatic  1.388  0.020  1.388
 L1B  C14  H14   single    0.930  0.020  1.080
 L1B  C15  N5    aromatic  1.325  0.020  1.325
 L1B  C15  H15   single    0.930  0.020  1.080
 L1B  N5   C16   single    1.473  0.020  1.473
 L1B  C16  C17   single    1.522  0.020  1.522
 L1B  C16  H161  single    0.970  0.020  1.090
 L1B  C16  H162  single    0.970  0.020  1.090
 L1B  C17  C18   single    1.518  0.020  1.518
 L1B  C17  H171  single    0.970  0.020  1.090
 L1B  C17  H172  single    0.970  0.020  1.090
 L1B  C18  O1    single    1.402  0.020  1.402
 L1B  C18  H181  single    0.970  0.020  1.090
 L1B  C18  H182  single    0.970  0.020  1.090
 L1B  O1   C19   single    1.405  0.020  1.405
 L1B  C19  H191  single    0.970  0.020  1.090
 L1B  C19  H192  single    0.970  0.020  1.090
 L1B  C19  H193  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
 L1B  N3    C1   C4    121.72  3.000
 L1B  N3    C1   N1    116.67  3.000
 L1B  C4    C1   N1    121.61  3.000
 L1B  C2    N1   C1    117.18  3.000
 L1B  N4    C2   N2    117.04  3.000
 L1B  N4    C2   N1    116.90  3.000
 L1B  N2    C2   N1    126.06  3.000
 L1B  C3    N2   C2    116.83  3.000
 L1B  C5    C3   C4    122.10  3.000
 L1B  C5    C3   N2    115.29  3.000
 L1B  C4    C3   N2    122.44  3.000
 L1B  C12   C4   C3    123.47  3.000
 L1B  C12   C4   C1    120.64  3.000
 L1B  C3    C4   C1    115.88  3.000
 L1B  HN32  N3   HN31  115.89  3.000
 L1B  HN32  N3   C1    120.62  3.000
 L1B  HN31  N3   C1    117.60  3.000
 L1B  HN42  N4   HN41  118.95  3.000
 L1B  HN42  N4   C2    120.52  3.000
 L1B  HN41  N4   C2    120.41  3.000
 L1B  H52   C5   H51   107.07  3.000
 L1B  H52   C5   C6    109.56  3.000
 L1B  H51   C5   C6    109.58  3.000
 L1B  H52   C5   C3    111.74  3.000
 L1B  H51   C5   C3    108.42  3.000
 L1B  C6    C5   C3    110.38  3.000
 L1B  H63   C6   H62   107.88  3.000
 L1B  H63   C6   H61   108.04  3.000
 L1B  H62   C6   H61   107.97  3.000
 L1B  H63   C6   C5    110.64  3.000
 L1B  H62   C6   C5    111.33  3.000
 L1B  H61   C6   C5    110.85  3.000
 L1B  H7    C7   C12   119.19  3.000
 L1B  H7    C7   C8    120.02  3.000
 L1B  C12   C7   C8    120.79  3.000
 L1B  H8    C8   C9    118.75  3.000
 L1B  H8    C8   C7    120.65  3.000
 L1B  C9    C8   C7    120.59  3.000
 L1B  C13   C9   C10   119.39  3.000
 L1B  C13   C9   C8    121.86  3.000
 L1B  C10   C9   C8    118.75  3.000
 L1B  N5    C10  C11   121.75  3.000
 L1B  N5    C10  C9    118.36  3.000
 L1B  C11   C10  C9    119.89  3.000
 L1B  H11   C11  C12   118.48  3.000
 L1B  H11   C11  C10   121.02  3.000
 L1B  C12   C11  C10   120.49  3.000
 L1B  C11   C12  C7    119.47  3.000
 L1B  C11   C12  C4    119.78  3.000
 L1B  C7    C12  C4    120.72  3.000
 L1B  H13   C13  C14   120.63  3.000
 L1B  H13   C13  C9    119.48  3.000
 L1B  C14   C13  C9    119.89  3.000
 L1B  H14   C14  C15   119.02  3.000
 L1B  H14   C14  C13   122.22  3.000
 L1B  C15   C14  C13   118.75  3.000
 L1B  H15   C15  N5    116.45  3.000
 L1B  H15   C15  C14   121.22  3.000
 L1B  N5    C15  C14   122.33  3.000
 L1B  C16   N5   C15   118.19  3.000
 L1B  C16   N5   C10   120.49  3.000
 L1B  C15   N5   C10   121.27  3.000
 L1B  H162  C16  H161  106.53  3.000
 L1B  H162  C16  C17   112.26  3.000
 L1B  H161  C16  C17   110.60  3.000
 L1B  H162  C16  N5    108.45  3.000
 L1B  H161  C16  N5    106.79  3.000
 L1B  C17   C16  N5    111.91  3.000
 L1B  H172  C17  H171  107.40  3.000
 L1B  H172  C17  C18   109.98  3.000
 L1B  H171  C17  C18   109.34  3.000
 L1B  H172  C17  C16   109.37  3.000
 L1B  H171  C17  C16   110.86  3.000
 L1B  C18   C17  C16   109.85  3.000
 L1B  H182  C18  H181  106.63  3.000
 L1B  H182  C18  O1    110.84  3.000
 L1B  H181  C18  O1    110.92  3.000
 L1B  H182  C18  C17   109.85  3.000
 L1B  H181  C18  C17   109.95  3.000
 L1B  O1    C18  C17   108.64  3.000
 L1B  C19   O1   C18   112.47  3.000
 L1B  H193  C19  H192  108.48  3.000
 L1B  H193  C19  H191  108.48  3.000
 L1B  H192  C19  H191  107.81  3.000
 L1B  H193  C19  O1    107.99  3.000
 L1B  H192  C19  O1    111.99  3.000
 L1B  H191  C19  O1    111.98  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
 L1B  CONST_01  N2    C2   N1   C1     0.00   0.0  0
 L1B  CONST_02  N2    C3   C4   C1     0.00   0.0  0
 L1B  CONST_05  C3    C4   C1   N1     0.00   0.0  0
 L1B  CONST_06  C12   C4   C1   N1   180.00   0.0  0
 L1B  CONST_07  C3    N2   C2   N1     0.00   0.0  0
 L1B  CONST_08  C4    C1   N1   C2     0.00   0.0  0
 L1B  CONST_09  C4    C3   N2   C2     0.00   0.0  0
 L1B  CONST_10  C12   C4   C3   N2   180.00   0.0  0
 L1B  CONST_13  C8    C7   C12  C4   180.00   0.0  0
 L1B  CONST_14  C10   C11  C12  C4   180.00   0.0  0
 L1B  CONST_15  C10   C9   C8   C7     0.00   0.0  0
 L1B  CONST_16  C13   C9   C8   C7   180.00   0.0  0
 L1B  CONST_17  C10   C11  C12  C7     0.00   0.0  0
 L1B  CONST_18  C11   C12  C7   C8     0.00   0.0  0
 L1B  CONST_19  C11   C10  C9   C8     0.00   0.0  0
 L1B  CONST_20  N5    C10  C9   C8   180.00   0.0  0
 L1B  CONST_21  C14   C13  C9   C8   180.00   0.0  0
 L1B  CONST_22  C12   C7   C8   C9     0.00   0.0  0
 L1B  CONST_23  C12   C11  C10  C9     0.00   0.0  0
 L1B  CONST_24  C15   N5   C10  C9     0.00   0.0  0
 L1B  CONST_25  C15   C14  C13  C9     0.00   0.0  0
 L1B  CONST_26  C14   C13  C9   C10    0.00   0.0  0
 L1B  CONST_27  C14   C15  N5   C10    0.00   0.0  0
 L1B  CONST_28  C13   C9   C10  C11  180.00   0.0  0
 L1B  CONST_29  C15   N5   C10  C11  180.00   0.0  0
 L1B  CONST_30  N5    C10  C11  C12  180.00   0.0  0
 L1B  CONST_31  N5    C10  C9   C13    0.00   0.0  0
 L1B  CONST_32  N5    C15  C14  C13    0.00   0.0  0
 L1B  CONST_33  N4    C2   N1   C1   180.00   0.0  0
 L1B  CONST_34  C5    C3   C4   C1   180.00   0.0  0
 L1B  CONST_35  N3    C1   N1   C2   180.00   0.0  0
 L1B  CONST_36  C5    C3   N2   C2   180.00   0.0  0
 L1B  CONST_37  N4    C2   N2   C3   180.00   0.0  0
 L1B  CONST_38  N3    C1   C4   C3   180.00   0.0  0
 L1B  CONST_39  C12   C4   C1   N3     0.00   0.0  0
 L1B  CONST_40  C12   C4   C3   C5     0.00   0.0  0
 L1B  CONST_41  C16   N5   C10  C9   180.00   0.0  0
 L1B  CONST_42  C16   N5   C10  C11    0.00   0.0  0
 L1B  CONST_43  C16   N5   C15  C14  180.00   0.0  0
 L1B  CONST_44  H7    C7   C12  C4     0.00   0.0  0
 L1B  CONST_45  H11   C11  C12  C4     0.00   0.0  0
 L1B  CONST_46  H13   C13  C9   C8     0.00   0.0  0
 L1B  CONST_47  H14   C14  C13  C9   180.00   0.0  0
 L1B  CONST_48  H8    C8   C9   C10  180.00   0.0  0
 L1B  CONST_49  H15   C15  N5   C10  180.00   0.0  0
 L1B  CONST_50  HN31  N3   C1   N1     0.00   0.0  0
 L1B  CONST_52  HN41  N4   C2   N1   180.00   0.0  0
 L1B  CONST_53  HN42  N4   C2   N1     0.00   0.0  0
 L1B  Var_01    C6    C5   C3   N2    85.83  30.0  2
 L1B  Var_02    C17   C16  N5   C10   76.60  30.0  2
 L1B  Var_03    C18   C17  C16  N5   179.97  30.0  3
 L1B  Var_04    H61   C6   C5   C3   -57.38  30.0  3
 L1B  Var_05    O1    C18  C17  C16  179.73  30.0  3
 L1B  Var_06    H191  C19  O1   C18  -60.92  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
 L1B  plan-1  C1    0.020
 L1B  plan-1  N1    0.020
 L1B  plan-1  C2    0.020
 L1B  plan-1  N2    0.020
 L1B  plan-1  C3    0.020
 L1B  plan-1  C4    0.020
 L1B  plan-1  N3    0.020
 L1B  plan-1  N4    0.020
 L1B  plan-1  C5    0.020
 L1B  plan-1  C12   0.020
 L1B  plan-2  C4    0.020
 L1B  plan-2  C7    0.020
 L1B  plan-2  C8    0.020
 L1B  plan-2  C9    0.020
 L1B  plan-2  C10   0.020
 L1B  plan-2  C11   0.020
 L1B  plan-2  C12   0.020
 L1B  plan-2  C13   0.020
 L1B  plan-2  C14   0.020
 L1B  plan-2  C15   0.020
 L1B  plan-2  N5    0.020
 L1B  plan-2  C16   0.020
 L1B  plan-2  H8    0.020
 L1B  plan-2  H11   0.020
 L1B  plan-2  H13   0.020
 L1B  plan-2  H14   0.020
 L1B  plan-2  H15   0.020
 L1B  plan-2  H7    0.020
 L1B  plan-3  C1    0.020
 L1B  plan-3  N3    0.020
 L1B  plan-3  HN31  0.020
 L1B  plan-3  HN32  0.020
 L1B  plan-4  C2    0.020
 L1B  plan-4  N4    0.020
 L1B  plan-4  HN41  0.020
 L1B  plan-4  HN42  0.020

