# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 02:48:54 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: N-[6-(1,2,3,4-tetrahydroacridin-9-ylamino)hexyl]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCCCCCCNc1c2CCCCc2nc3ccccc13)c4cccnc4
#
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
 TNH  TNH  N-[6-(1,2,3,4-tetrahydroacridin-9-ylamino)hexyl]pyridine-3-carboxamide  ligand  60  30  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TNH
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
 TNH  C1   C  CH2   0  -0.500    6.5737   2.0789  -1.5645
 TNH  C2   C  CH2   0  -0.447    5.6093   3.2502  -1.6684
 TNH  C3   C  CH2   0  -0.441    4.8555   3.4110  -0.3586
 TNH  C4   C  CH2   0  -0.520    3.9858   2.1851  -0.1241
 TNH  C5   C  CR6   0   0.001    4.7497   0.8919  -0.2359
 TNH  C6   C  CR6   0   0.163    5.9939   0.8467  -0.9141
 TNH  N1   N  N     0  -0.480    6.7479  -0.2248  -0.9831
 TNH  C7   C  CR66  0   0.157    6.3313  -1.3562  -0.3807
 TNH  C8   C  CR16  0  -0.297    7.1615  -2.4995  -0.4621
 TNH  C9   C  CR16  0  -0.266    6.7824  -3.6823   0.1102
 TNH  C10  C  CR16  0  -0.255    5.5488  -3.7772   0.7835
 TNH  C11  C  CR16  0  -0.341    4.7276  -2.6856   0.8780
 TNH  C12  C  CR66  0   0.052    5.1000  -1.4430   0.3123
 TNH  C13  C  CR6   0   0.352    4.2936  -0.2657   0.3789
 TNH  N2   N  NH1   0  -0.681    3.0938  -0.2698   1.0782
 TNH  C14  C  CH2   0  -0.282    1.8420  -0.1227   0.3406
 TNH  C15  C  CH2   0  -0.448    0.6624  -0.0269   1.2921
 TNH  C16  C  CH2   0  -0.419   -0.6573   0.1194   0.5456
 TNH  C17  C  CH2   0  -0.423   -1.8638   0.1851   1.4733
 TNH  C18  C  CH2   0  -0.427   -3.1758   0.3483   0.7172
 TNH  C19  C  CH2   0  -0.283   -4.3732   0.4192   1.6576
 TNH  N3   N  NH1   0  -0.643   -5.6305   0.6015   0.9629
 TNH  C20  C  C     0   0.526   -6.3409  -0.4148   0.4555
 TNH  O1   O  O     0  -0.489   -6.0410  -1.5912   0.6118
 TNH  C21  C  CR6   0  -0.129   -7.5654  -0.0401  -0.3161
 TNH  C22  C  CR16  0  -0.152   -8.6409  -0.9218  -0.3488
 TNH  C23  C  CR16  0  -0.318   -9.7659  -0.5799  -1.0770
 TNH  C24  C  CR16  0  -0.055   -9.7663   0.6236  -1.7684
 TNH  N4   N  N     0  -0.399   -8.7376   1.4623  -1.7690
 TNH  C25  C  CR16  0  -0.079   -7.6680   1.1340  -1.0568
 TNH  H1   H  HCH2  0   0.254    6.9653   1.8007  -2.5453
 TNH  H2   H  HCH2  0   0.249    7.4434   2.3820  -0.9718
 TNH  H3   H  HCH2  0   0.239    6.1608   4.1571  -1.9227
 TNH  H4   H  HCH2  0   0.223    4.8923   3.0813  -2.4781
 TNH  H5   H  HCH2  0   0.223    5.5660   3.5355   0.4648
 TNH  H6   H  HCH2  0   0.239    4.2275   4.3036  -0.3737
 TNH  H7   H  HCH2  0   0.252    3.5008   2.2276   0.8550
 TNH  H8   H  HCH2  0   0.243    3.1734   2.2048  -0.8593
 TNH  H9   H  HCR6  0   0.254    8.1017  -2.4108  -0.9920
 TNH  H10  H  HCR6  0   0.259    7.4243  -4.5507   0.0399
 TNH  H11  H  HCR6  0   0.260    5.2446  -4.7193   1.2200
 TNH  H12  H  HCR6  0   0.243    3.7800  -2.8008   1.3880
 TNH  H13  H  HCH2  0   0.243    1.8818   0.7772  -0.2713
 TNH  H14  H  HCH2  0   0.221    0.6277  -0.9208   1.9250
 TNH  H15  H  HCH2  0   0.225    0.8083   0.8254   1.9626
 TNH  H16  H  HCH2  0   0.217   -0.6267   1.0233  -0.0724
 TNH  H17  H  HCH2  0   0.216   -0.7809  -0.7191  -0.1480
 TNH  H18  H  HCH2  0   0.217   -1.9026  -0.7238   2.0836
 TNH  H19  H  HCH2  0   0.215   -1.7387   1.0178   2.1738
 TNH  H20  H  HCH2  0   0.221   -3.1423   1.2576   0.1091
 TNH  H21  H  HCH2  0   0.225   -3.3091  -0.4876   0.0241
 TNH  H22  H  HCH2  0   0.241   -4.4303  -0.4856   2.2647
 TNH  H23  H  HCH2  0   0.249   -4.2582   1.2567   2.3464
 TNH  H24  H  HNH1  0   0.409   -5.9604   1.5449   0.8434
 TNH  H25  H  HCR6  0   0.277   -8.6003  -1.8558   0.1961
 TNH  H26  H  HCR6  0   0.278  -10.6275  -1.2316  -1.1144
 TNH  H27  H  HCR6  0   0.273  -10.6323   0.9182  -2.3501
 TNH  H28  H  HCR6  0   0.265   -6.8409   1.8351  -1.1010
 TNH  HNW  H  HNH1  0   0.370    3.0243  -1.0458   1.7200
 TNH  HAQ  H  HCH2  0   0.222    1.6924  -0.9625  -0.3509

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
 TNH  C2   C3   single    1.520  0.020  1.520
 TNH  C2   C1   single    1.521  0.020  1.521
 TNH  C3   C4   single    1.521  0.020  1.521
 TNH  C1   C6   single    1.509  0.020  1.509
 TNH  C4   C5   single    1.506  0.020  1.506
 TNH  C6   C5   aromatic  1.418  0.020  1.418
 TNH  C6   N1   aromatic  1.312  0.020  1.312
 TNH  C5   C13  aromatic  1.388  0.020  1.388
 TNH  N1   C7   aromatic  1.348  0.020  1.348
 TNH  C13  N2   single    1.389  0.020  1.389
 TNH  C13  C12  aromatic  1.428  0.020  1.428
 TNH  C7   C12  aromatic  1.416  0.020  1.416
 TNH  C7   C8   aromatic  1.415  0.020  1.415
 TNH  N2   C14  single    1.460  0.020  1.460
 TNH  C12  C11  aromatic  1.415  0.020  1.415
 TNH  C8   C9   aromatic  1.368  0.020  1.368
 TNH  C14  C15  single    1.519  0.020  1.519
 TNH  C15  C16  single    1.523  0.020  1.523
 TNH  C11  C10  aromatic  1.369  0.020  1.369
 TNH  C9   C10  aromatic  1.409  0.020  1.409
 TNH  C16  C17  single    1.523  0.020  1.523
 TNH  C17  C18  single    1.523  0.020  1.523
 TNH  C18  C19  single    1.524  0.020  1.524
 TNH  C19  N3   single    1.448  0.020  1.448
 TNH  N3   C20  single    1.340  0.020  1.340
 TNH  O1   C20  double    1.224  0.020  1.224
 TNH  C20  C21  single    1.495  0.020  1.495
 TNH  C21  C22  aromatic  1.391  0.020  1.391
 TNH  C21  C25  aromatic  1.392  0.020  1.392
 TNH  C22  C23  aromatic  1.383  0.020  1.383
 TNH  C25  N4   aromatic  1.326  0.020  1.326
 TNH  C23  C24  aromatic  1.388  0.020  1.388
 TNH  N4   C24  aromatic  1.327  0.020  1.327
 TNH  C1   H1   single    0.970  0.020  1.090
 TNH  C1   H2   single    0.970  0.020  1.090
 TNH  C2   H3   single    0.970  0.020  1.090
 TNH  C2   H4   single    0.970  0.020  1.090
 TNH  C3   H5   single    0.970  0.020  1.090
 TNH  C3   H6   single    0.970  0.020  1.090
 TNH  C4   H7   single    0.970  0.020  1.090
 TNH  C4   H8   single    0.970  0.020  1.090
 TNH  C8   H9   single    0.930  0.020  1.080
 TNH  C9   H10  single    0.930  0.020  1.080
 TNH  C10  H11  single    0.930  0.020  1.080
 TNH  C11  H12  single    0.930  0.020  1.080
 TNH  C14  H13  single    0.970  0.020  1.090
 TNH  C15  H14  single    0.970  0.020  1.090
 TNH  C15  H15  single    0.970  0.020  1.090
 TNH  C16  H16  single    0.970  0.020  1.090
 TNH  C16  H17  single    0.970  0.020  1.090
 TNH  C17  H18  single    0.970  0.020  1.090
 TNH  C17  H19  single    0.970  0.020  1.090
 TNH  C18  H20  single    0.970  0.020  1.090
 TNH  C18  H21  single    0.970  0.020  1.090
 TNH  C19  H22  single    0.970  0.020  1.090
 TNH  C19  H23  single    0.970  0.020  1.090
 TNH  N3   H24  single    0.860  0.020  1.020
 TNH  C22  H25  single    0.930  0.020  1.080
 TNH  C23  H26  single    0.930  0.020  1.080
 TNH  C24  H27  single    0.930  0.020  1.080
 TNH  C25  H28  single    0.930  0.020  1.080
 TNH  N2   HNW  single    0.890  0.020  1.040
 TNH  C14  HAQ  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
 TNH  H2   C1   H1   105.77  3.000
 TNH  H2   C1   C6   107.33  3.000
 TNH  H1   C1   C6   108.47  3.000
 TNH  H2   C1   C2   109.11  3.000
 TNH  H1   C1   C2   111.24  3.000
 TNH  C6   C1   C2   114.50  3.000
 TNH  H4   C2   H3   106.67  3.000
 TNH  H4   C2   C3   109.21  3.000
 TNH  H3   C2   C3   111.31  3.000
 TNH  H4   C2   C1   110.31  3.000
 TNH  H3   C2   C1   109.60  3.000
 TNH  C3   C2   C1   109.70  3.000
 TNH  H6   C3   H5   106.90  3.000
 TNH  H6   C3   C4   109.41  3.000
 TNH  H5   C3   C4   110.29  3.000
 TNH  H6   C3   C2   111.10  3.000
 TNH  H5   C3   C2   109.78  3.000
 TNH  C4   C3   C2   109.34  3.000
 TNH  H8   C4   H7   105.74  3.000
 TNH  H8   C4   C5   109.97  3.000
 TNH  H7   C4   C5   108.95  3.000
 TNH  H8   C4   C3   107.81  3.000
 TNH  H7   C4   C3   111.12  3.000
 TNH  C5   C4   C3   112.99  3.000
 TNH  C13  C5   C6   118.28  3.000
 TNH  C13  C5   C4   121.11  3.000
 TNH  C6   C5   C4   120.53  3.000
 TNH  N1   C6   C5   123.75  3.000
 TNH  N1   C6   C1   115.04  3.000
 TNH  C5   C6   C1   121.15  3.000
 TNH  C7   N1   C6   118.97  3.000
 TNH  C12  C7   C8   119.27  3.000
 TNH  C8   C7   N1   118.11  3.000
 TNH  C12  C7   N1   122.62  3.000
 TNH  H9   C8   C9   121.09  3.000
 TNH  H9   C8   C7   118.12  3.000
 TNH  C9   C8   C7   120.80  3.000
 TNH  H10  C9   C10  119.76  3.000
 TNH  H10  C9   C8   120.16  3.000
 TNH  C10  C9   C8   120.08  3.000
 TNH  H11  C10  C11  119.85  3.000
 TNH  H11  C10  C9   119.85  3.000
 TNH  C11  C10  C9   120.29  3.000
 TNH  H12  C11  C12  120.81  3.000
 TNH  H12  C11  C10  118.21  3.000
 TNH  C12  C11  C10  120.98  3.000
 TNH  C13  C12  C11  123.81  3.000
 TNH  C11  C12  C7   118.58  3.000
 TNH  C13  C12  C7   117.60  3.000
 TNH  N2   C13  C12  120.58  3.000
 TNH  C12  C13  C5   118.77  3.000
 TNH  N2   C13  C5   120.63  3.000
 TNH  HNW  N2   C14  109.85  3.000
 TNH  HNW  N2   C13  112.45  3.000
 TNH  C14  N2   C13  119.07  3.000
 TNH  HAQ  C14  H13  106.45  3.000
 TNH  HAQ  C14  C15  109.69  3.000
 TNH  H13  C14  C15  109.16  3.000
 TNH  HAQ  C14  N2   110.97  3.000
 TNH  H13  C14  N2   109.61  3.000
 TNH  C15  C14  N2   110.84  3.000
 TNH  H15  C15  H14  106.60  3.000
 TNH  H15  C15  C16  109.94  3.000
 TNH  H14  C15  C16  109.51  3.000
 TNH  H15  C15  C14  109.24  3.000
 TNH  H14  C15  C14  109.57  3.000
 TNH  C16  C15  C14  111.84  3.000
 TNH  H17  C16  H16  106.12  3.000
 TNH  H17  C16  C17  109.23  3.000
 TNH  H16  C16  C17  109.27  3.000
 TNH  H17  C16  C15  109.55  3.000
 TNH  H16  C16  C15  109.36  3.000
 TNH  C17  C16  C15  113.08  3.000
 TNH  H19  C17  H18  106.16  3.000
 TNH  H19  C17  C18  109.54  3.000
 TNH  H18  C17  C18  109.57  3.000
 TNH  H19  C17  C16  109.38  3.000
 TNH  H18  C17  C16  109.36  3.000
 TNH  C18  C17  C16  112.62  3.000
 TNH  H21  C18  H20  106.66  3.000
 TNH  H21  C18  C19  109.31  3.000
 TNH  H20  C18  C19  109.16  3.000
 TNH  H21  C18  C17  109.73  3.000
 TNH  H20  C18  C17  109.78  3.000
 TNH  C19  C18  C17  112.05  3.000
 TNH  H23  C19  H22  106.91  3.000
 TNH  H23  C19  N3   107.33  3.000
 TNH  H22  C19  N3   109.03  3.000
 TNH  H23  C19  C18  110.04  3.000
 TNH  H22  C19  C18  110.24  3.000
 TNH  N3   C19  C18  113.08  3.000
 TNH  H24  N3   C20  119.48  3.000
 TNH  H24  N3   C19  117.37  3.000
 TNH  C20  N3   C19  123.13  3.000
 TNH  C21  C20  O1   120.50  3.000
 TNH  C21  C20  N3   116.08  3.000
 TNH  O1   C20  N3   123.42  3.000
 TNH  C25  C21  C22  117.72  3.000
 TNH  C25  C21  C20  123.12  3.000
 TNH  C22  C21  C20  119.11  3.000
 TNH  H25  C22  C23  120.60  3.000
 TNH  H25  C22  C21  120.42  3.000
 TNH  C23  C22  C21  118.98  3.000
 TNH  H26  C23  C24  120.35  3.000
 TNH  H26  C23  C22  121.17  3.000
 TNH  C24  C23  C22  118.48  3.000
 TNH  H27  C24  N4   116.56  3.000
 TNH  H27  C24  C23  120.21  3.000
 TNH  N4   C24  C23  123.23  3.000
 TNH  C25  N4   C24  117.93  3.000
 TNH  H28  C25  N4   115.65  3.000
 TNH  H28  C25  C21  120.69  3.000
 TNH  N4   C25  C21  123.64  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
 TNH  CONST_01  C7   N1   C6   C5      0.00   0.0  0
 TNH  CONST_02  C7   C12  C13  C5      0.00   0.0  0
 TNH  CONST_03  C11  C12  C13  C5    180.00   0.0  0
 TNH  CONST_04  C12  C13  C5   C6      0.00   0.0  0
 TNH  CONST_05  C12  C7   N1   C6      0.00   0.0  0
 TNH  CONST_06  C8   C7   N1   C6    180.00   0.0  0
 TNH  CONST_07  C13  C5   C6   N1      0.00   0.0  0
 TNH  CONST_08  C13  C12  C7   N1      0.00   0.0  0
 TNH  CONST_09  C11  C12  C7   N1    180.00   0.0  0
 TNH  CONST_10  C9   C8   C7   N1    180.00   0.0  0
 TNH  CONST_11  C10  C11  C12  C7      0.00   0.0  0
 TNH  CONST_12  C10  C9   C8   C7      0.00   0.0  0
 TNH  CONST_13  C13  C12  C7   C8    180.00   0.0  0
 TNH  CONST_14  C11  C12  C7   C8      0.00   0.0  0
 TNH  CONST_15  C11  C10  C9   C8      0.00   0.0  0
 TNH  CONST_16  C12  C7   C8   C9      0.00   0.0  0
 TNH  CONST_17  C12  C11  C10  C9      0.00   0.0  0
 TNH  CONST_18  C13  C12  C11  C10   180.00   0.0  0
 TNH  CONST_19  C24  C23  C22  C21     0.00   0.0  0
 TNH  CONST_20  C24  N4   C25  C21     0.00   0.0  0
 TNH  CONST_21  N4   C25  C21  C22     0.00   0.0  0
 TNH  CONST_22  N4   C24  C23  C22     0.00   0.0  0
 TNH  CONST_23  C25  C21  C22  C23     0.00   0.0  0
 TNH  CONST_24  C25  N4   C24  C23     0.00   0.0  0
 TNH  CONST_25  N2   C13  C5   C4      0.00   0.0  0
 TNH  CONST_26  N2   C13  C5   C6    180.00   0.0  0
 TNH  CONST_27  N2   C13  C12  C7    180.00   0.0  0
 TNH  CONST_28  N2   C13  C12  C11     0.00   0.0  0
 TNH  CONST_29  C23  C22  C21  C20   180.00   0.0  0
 TNH  CONST_30  N4   C25  C21  C20   180.00   0.0  0
 TNH  CONST_31  H9   C8   C7   N1      0.00   0.0  0
 TNH  CONST_32  H12  C11  C12  C7    180.00   0.0  0
 TNH  CONST_33  H10  C9   C8   C7    180.00   0.0  0
 TNH  CONST_34  H11  C10  C9   C8    180.00   0.0  0
 TNH  CONST_35  H26  C23  C22  C21   180.00   0.0  0
 TNH  CONST_36  H28  C25  C21  C22   180.00   0.0  0
 TNH  CONST_37  H27  C24  C23  C22   180.00   0.0  0
 TNH  CONST_38  H25  C22  C23  C24   180.00   0.0  0
 TNH  CONST_42  C21  C20  N3   C19   180.00   0.0  0
 TNH  CONST_43  H24  N3   C20  C21     0.00   0.0  0
 TNH  CONST_44  O1   C20  N3   C19     0.00   0.0  0
 TNH  Var_01    C4   C3   C2   C1    -64.65  30.0  1
 TNH  Var_02    C5   C4   C3   C2     51.92  30.0  1
 TNH  Var_03    C5   C6   C1   C2    -11.59  30.0  1
 TNH  Var_04    C6   C1   C2   C3     44.08  30.0  1
 TNH  Var_05    C6   C5   C4   C3    -19.36  30.0  1
 TNH  Var_06    C22  C21  C20  N3   -150.91  30.0  2
 TNH  Var_07    C15  C14  N2   C13  -174.90  30.0  3
 TNH  Var_08    C16  C15  C14  N2   -179.68  30.0  3
 TNH  Var_09    C17  C16  C15  C14   178.65  30.0  3
 TNH  Var_10    C18  C17  C16  C15   179.30  30.0  3
 TNH  Var_11    C19  C18  C17  C16  -179.73  30.0  3
 TNH  Var_12    N3   C19  C18  C17   178.83  30.0  3
 TNH  Var_13    C20  N3   C19  C18    85.04  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
 TNH  plan-1  C20  0.020
 TNH  plan-1  C21  0.020
 TNH  plan-1  C22  0.020
 TNH  plan-1  C23  0.020
 TNH  plan-1  C24  0.020
 TNH  plan-1  N4   0.020
 TNH  plan-1  C25  0.020
 TNH  plan-1  H25  0.020
 TNH  plan-1  H26  0.020
 TNH  plan-1  H27  0.020
 TNH  plan-1  H28  0.020
 TNH  plan-2  C1   0.020
 TNH  plan-2  C4   0.020
 TNH  plan-2  C5   0.020
 TNH  plan-2  C6   0.020
 TNH  plan-2  N1   0.020
 TNH  plan-2  C7   0.020
 TNH  plan-2  C8   0.020
 TNH  plan-2  C9   0.020
 TNH  plan-2  C10  0.020
 TNH  plan-2  C11  0.020
 TNH  plan-2  C12  0.020
 TNH  plan-2  C13  0.020
 TNH  plan-2  N2   0.020
 TNH  plan-2  H9   0.020
 TNH  plan-2  H10  0.020
 TNH  plan-2  H11  0.020
 TNH  plan-2  H12  0.020
 TNH  plan-3  C19  0.020
 TNH  plan-3  N3   0.020
 TNH  plan-3  C20  0.020
 TNH  plan-3  O1   0.020
 TNH  plan-3  C21  0.020
 TNH  plan-3  H24  0.020
 TNH  plan-4  C13  0.020
 TNH  plan-4  N2   0.020
 TNH  plan-4  C14  0.020
 TNH  plan-4  HNW  0.020

