# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 04:11:34 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (2R)-6-[[methyl-(3,4,5-trimethoxyphenyl)amino]methyl]-1,2,5,6,7,8-hexahydroquinazoline-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1OC)N(C)C[C@H]2CCC3=C(C2)C(=N[C@H](N)N3)N
#
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
 TQD  TQD  (2R)-6-[[methyl-(3,4,5-trimethoxyphenyl)amino]methyl]-1,2,5,6,7,8-hexahydroquinazoline-2,4-diamine  ligand  56  27  .  2021-08-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TQD
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
 TQD  C2D   C  CH1   0   0.156   4.8125   1.1400   1.6096
 TQD  C4D   C  C     0   0.406   2.5126   0.8679   1.7283
 TQD  C4A   C  C     0  -0.148   2.5391  -0.1662   0.7061
 TQD  C5D   C  CH2   0  -0.476   1.2863  -0.6896   0.0572
 TQD  C6D   C  CH1   0  -0.248   1.4776  -2.0752  -0.5557
 TQD  C7'   C  CH2   0  -0.430   2.7694  -2.1154  -1.3613
 TQD  C8    C  CH2   0  -0.526   3.9698  -1.8711  -0.4604
 TQD  C8A   C  C     0   0.389   3.7647  -0.6945   0.4453
 TQD  C8'   C  CH2   0  -0.324   0.2881  -2.4862  -1.4272
 TQD  C1'   C  CR6   0   0.426  -1.7645  -1.3520  -0.6550
 TQD  C2'   C  CR16  0  -0.553  -2.4918  -1.0643   0.5054
 TQD  C3'   C  CR6   0   0.374  -3.3029   0.0674   0.5669
 TQD  C3B   C  CH3   0  -0.437  -3.9241  -0.3875   2.8124
 TQD  C4'   C  CR6   0   0.130  -3.4065   0.9316  -0.5203
 TQD  C4B   C  CH3   0  -0.406  -3.5778   3.1896   0.0437
 TQD  C5'   C  CR6   0   0.356  -2.6716   0.6478  -1.6752
 TQD  C5B   C  CH3   0  -0.437  -2.1204   1.3059  -3.8875
 TQD  C6'   C  CR16  0  -0.520  -1.8678  -0.4817  -1.7504
 TQD  N1'   N  NH1   0  -0.679   4.8594  -0.1995   1.0665
 TQD  N2'   N  NH2   0  -0.791   5.0181   2.1170   0.5434
 TQD  N3'   N  N     0  -0.495   3.5642   1.4064   2.2531
 TQD  N4'   N  NH2   0  -0.829   1.2901   1.2892   2.1794
 TQD  N9'   N  NT    0  -0.501  -0.9902  -2.4993  -0.7373
 TQD  O3'   O  O2    0  -0.468  -4.0248   0.4094   1.6509
 TQD  O4'   O  O2    0  -0.484  -4.2146   2.0289  -0.4666
 TQD  O5'   O  O2    0  -0.467  -2.8240   1.5276  -2.6832
 TQD  C9'   C  CH3   0  -0.561  -1.0719  -3.4691   0.3295
 TQD  H2'   H  HCH1  0   0.206   5.6089   1.1938   2.3618
 TQD  H5'1  H  HCH2  0   0.226   0.4673  -0.7518   0.7797
 TQD  H5'2  H  HCH2  0   0.228   0.9339   0.0019  -0.7187
 TQD  H6'   H  HCH1  0   0.233   1.5769  -2.7982   0.2643
 TQD  H7'1  H  HCH2  0   0.239   2.8810  -3.0801  -1.8624
 TQD  H7'2  H  HCH2  0   0.227   2.7341  -1.3547  -2.1485
 TQD  H81   H  HCH2  0   0.260   4.1583  -2.7558   0.1572
 TQD  H82   H  HCH2  0   0.257   4.8728  -1.7191  -1.0577
 TQD  H8'1  H  HCH2  0   0.246   0.2413  -1.8295  -2.2961
 TQD  H8'2  H  HCH2  0   0.244   0.4686  -3.4915  -1.8204
 TQD  H2'1  H  HCR6  0   0.284  -2.4037  -1.7042   1.3694
 TQD  H3B1  H  HCH3  0   0.260  -4.5686   0.0716   3.5583
 TQD  H3B2  H  HCH3  0   0.226  -4.2641  -1.4121   2.6395
 TQD  H3B3  H  HCH3  0   0.225  -2.9030  -0.4167   3.2019
 TQD  H4B1  H  HCH3  0   0.216  -2.7143   3.4792  -0.5611
 TQD  H4B2  H  HCH3  0   0.231  -4.3064   3.9988   0.0165
 TQD  H4B3  H  HCH3  0   0.216  -3.2483   3.0532   1.0769
 TQD  H5B1  H  HCH3  0   0.260  -2.3907   2.1191  -4.5569
 TQD  H5B2  H  HCH3  0   0.225  -1.0374   1.3193  -3.7385
 TQD  H5B3  H  HCH3  0   0.226  -2.3979   0.3583  -4.3566
 TQD  H6'1  H  HCR6  0   0.276  -1.3406  -0.7075  -2.6651
 TQD  H1D   H  HNH1  0   0.384   5.7616  -0.5648   0.8062
 TQD  H2A1  H  HNH2  0   0.339   4.8445   3.0396   0.9268
 TQD  H2A2  H  HNH2  0   0.336   5.9929   2.1131   0.2618
 TQD  H4'1  H  HNH2  0   0.376   0.5219   0.6406   2.1538
 TQD  H4'2  H  HNH2  0   0.373   1.3164   1.8421   3.0217
 TQD  H9'1  H  HCH3  0   0.218  -0.6250  -3.1379   1.2753
 TQD  H9'2  H  HCH3  0   0.249  -2.1093  -3.7407   0.5268
 TQD  H9'3  H  HCH3  0   0.256  -0.5507  -4.3739   0.0187

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
 TQD  C2D  N1'   single    1.446  0.020  1.446
 TQD  C2D  N2'   single    1.461  0.020  1.461
 TQD  C2D  N3'   single    1.429  0.020  1.429
 TQD  C2D  H2'   single    0.970  0.020  1.090
 TQD  C4D  C4A   single    1.454  0.020  1.454
 TQD  C4D  N3'   double    1.293  0.020  1.293
 TQD  C4D  N4'   single    1.369  0.020  1.369
 TQD  C4A  C5D   single    1.505  0.020  1.505
 TQD  C4A  C8A   double    1.360  0.020  1.360
 TQD  C5D  C6D   single    1.527  0.020  1.527
 TQD  C5D  H5'1  single    0.970  0.020  1.090
 TQD  C5D  H5'2  single    0.970  0.020  1.090
 TQD  C6D  C7'   single    1.523  0.020  1.523
 TQD  C6D  C8'   single    1.531  0.020  1.531
 TQD  C6D  H6'   single    0.970  0.020  1.090
 TQD  C7'  C8    single    1.521  0.020  1.521
 TQD  C7'  H7'1  single    0.970  0.020  1.090
 TQD  C7'  H7'2  single    0.970  0.020  1.090
 TQD  C8   C8A   single    1.499  0.020  1.499
 TQD  C8   H81   single    0.970  0.020  1.090
 TQD  C8   H82   single    0.970  0.020  1.090
 TQD  C8A  N1'   single    1.353  0.020  1.353
 TQD  C8'  N9'   single    1.453  0.020  1.453
 TQD  C8'  H8'1  single    0.970  0.020  1.090
 TQD  C8'  H8'2  single    0.970  0.020  1.090
 TQD  C1'  C2'   aromatic  1.399  0.020  1.399
 TQD  C1'  C6'   aromatic  1.403  0.020  1.403
 TQD  C1'  N9'   single    1.387  0.020  1.387
 TQD  C2'  C3'   aromatic  1.394  0.020  1.394
 TQD  C2'  H2'1  single    0.930  0.020  1.080
 TQD  C3'  C4'   aromatic  1.393  0.020  1.393
 TQD  C3'  O3'   single    1.347  0.020  1.347
 TQD  C3B  O3'   single    1.412  0.020  1.412
 TQD  C3B  H3B1  single    0.970  0.020  1.090
 TQD  C3B  H3B2  single    0.970  0.020  1.090
 TQD  C3B  H3B3  single    0.970  0.020  1.090
 TQD  C4'  C5'   aromatic  1.398  0.020  1.398
 TQD  C4'  O4'   single    1.364  0.020  1.364
 TQD  C4B  O4'   single    1.419  0.020  1.419
 TQD  C4B  H4B1  single    0.970  0.020  1.090
 TQD  C4B  H4B2  single    0.970  0.020  1.090
 TQD  C4B  H4B3  single    0.970  0.020  1.090
 TQD  C5'  C6'   aromatic  1.388  0.020  1.388
 TQD  C5'  O5'   single    1.347  0.020  1.347
 TQD  C5B  O5'   single    1.412  0.020  1.412
 TQD  C5B  H5B1  single    0.970  0.020  1.090
 TQD  C5B  H5B2  single    0.970  0.020  1.090
 TQD  C5B  H5B3  single    0.970  0.020  1.090
 TQD  C6'  H6'1  single    0.930  0.020  1.080
 TQD  N1'  H1D   single    0.890  0.020  1.040
 TQD  N2'  H2A1  single    0.890  0.020  1.040
 TQD  N2'  H2A2  single    0.890  0.020  1.040
 TQD  N4'  H4'1  single    0.890  0.020  1.040
 TQD  N4'  H4'2  single    0.890  0.020  1.040
 TQD  N9'  C9'   single    1.444  0.020  1.444
 TQD  C9'  H9'1  single    0.970  0.020  1.090
 TQD  C9'  H9'2  single    0.970  0.020  1.090
 TQD  C9'  H9'3  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
 TQD  H2'   C2D  N3'   108.44  3.000
 TQD  H2'   C2D  N2'   111.44  3.000
 TQD  N3'   C2D  N2'   109.08  3.000
 TQD  H2'   C2D  N1'   106.23  3.000
 TQD  N3'   C2D  N1'   111.72  3.000
 TQD  N2'   C2D  N1'   109.93  3.000
 TQD  N4'   C4D  N3'   117.66  3.000
 TQD  N4'   C4D  C4A   117.81  3.000
 TQD  N3'   C4D  C4A   124.52  3.000
 TQD  C8A   C4A  C5D   122.18  3.000
 TQD  C8A   C4A  C4D   115.31  3.000
 TQD  C5D   C4A  C4D   122.36  3.000
 TQD  H5'2  C5D  H5'1  105.21  3.000
 TQD  H5'2  C5D  C6D   109.16  3.000
 TQD  H5'1  C5D  C6D   107.90  3.000
 TQD  H5'2  C5D  C4A   110.67  3.000
 TQD  H5'1  C5D  C4A   111.00  3.000
 TQD  C6D   C5D  C4A   112.60  3.000
 TQD  H6'   C6D  C8'   108.59  3.000
 TQD  H6'   C6D  C7'   107.52  3.000
 TQD  C8'   C6D  C7'   110.54  3.000
 TQD  H6'   C6D  C5D   108.01  3.000
 TQD  C8'   C6D  C5D   112.01  3.000
 TQD  C7'   C6D  C5D   110.03  3.000
 TQD  H7'2  C7'  H7'1  106.67  3.000
 TQD  H7'2  C7'  C8    109.85  3.000
 TQD  H7'1  C7'  C8    109.44  3.000
 TQD  H7'2  C7'  C6D   109.55  3.000
 TQD  H7'1  C7'  C6D   110.64  3.000
 TQD  C8    C7'  C6D   110.61  3.000
 TQD  H82   C8   H81   106.15  3.000
 TQD  H82   C8   C8A   109.51  3.000
 TQD  H81   C8   C8A   108.47  3.000
 TQD  H82   C8   C7'   110.53  3.000
 TQD  H81   C8   C7'   109.88  3.000
 TQD  C8A   C8   C7'   112.09  3.000
 TQD  N1'   C8A  C8    117.00  3.000
 TQD  N1'   C8A  C4A   119.95  3.000
 TQD  C8    C8A  C4A   122.97  3.000
 TQD  H8'2  C8'  H8'1  105.90  3.000
 TQD  H8'2  C8'  N9'   107.91  3.000
 TQD  H8'1  C8'  N9'   110.26  3.000
 TQD  H8'2  C8'  C6D   108.85  3.000
 TQD  H8'1  C8'  C6D   108.99  3.000
 TQD  N9'   C8'  C6D   114.57  3.000
 TQD  N9'   C1'  C6'   120.54  3.000
 TQD  N9'   C1'  C2'   120.63  3.000
 TQD  C6'   C1'  C2'   118.80  3.000
 TQD  H2'1  C2'  C3'   119.60  3.000
 TQD  H2'1  C2'  C1'   119.98  3.000
 TQD  C3'   C2'  C1'   120.40  3.000
 TQD  O3'   C3'  C4'   115.53  3.000
 TQD  O3'   C3'  C2'   123.62  3.000
 TQD  C4'   C3'  C2'   120.85  3.000
 TQD  H3B3  C3B  H3B2  108.77  3.000
 TQD  H3B3  C3B  H3B1  108.69  3.000
 TQD  H3B2  C3B  H3B1  108.65  3.000
 TQD  H3B3  C3B  O3'   112.01  3.000
 TQD  H3B2  C3B  O3'   112.12  3.000
 TQD  H3B1  C3B  O3'   106.48  3.000
 TQD  O4'   C4'  C5'   120.49  3.000
 TQD  O4'   C4'  C3'   120.84  3.000
 TQD  C5'   C4'  C3'   118.67  3.000
 TQD  H4B3  C4B  H4B2  108.54  3.000
 TQD  H4B3  C4B  H4B1  108.53  3.000
 TQD  H4B2  C4B  H4B1  108.53  3.000
 TQD  H4B3  C4B  O4'   111.91  3.000
 TQD  H4B2  C4B  O4'   107.37  3.000
 TQD  H4B1  C4B  O4'   111.86  3.000
 TQD  O5'   C5'  C6'   123.82  3.000
 TQD  O5'   C5'  C4'   115.23  3.000
 TQD  C6'   C5'  C4'   120.95  3.000
 TQD  H5B3  C5B  H5B2  108.70  3.000
 TQD  H5B3  C5B  H5B1  108.72  3.000
 TQD  H5B2  C5B  H5B1  108.71  3.000
 TQD  H5B3  C5B  O5'   112.06  3.000
 TQD  H5B2  C5B  O5'   112.05  3.000
 TQD  H5B1  C5B  O5'   106.48  3.000
 TQD  H6'1  C6'  C5'   119.92  3.000
 TQD  H6'1  C6'  C1'   119.73  3.000
 TQD  C5'   C6'  C1'   120.33  3.000
 TQD  H1D   N1'  C8A   118.26  3.000
 TQD  H1D   N1'  C2D   117.51  3.000
 TQD  C8A   N1'  C2D   119.03  3.000
 TQD  H2A2  N2'  H2A1  105.84  3.000
 TQD  H2A2  N2'  C2D   109.58  3.000
 TQD  H2A1  N2'  C2D   107.97  3.000
 TQD  C4D   N3'  C2D   116.74  3.000
 TQD  H4'2  N4'  H4'1  113.26  3.000
 TQD  H4'2  N4'  C4D   114.89  3.000
 TQD  H4'1  N4'  C4D   118.36  3.000
 TQD  C9'   N9'  C1'   118.70  3.000
 TQD  C9'   N9'  C8'   113.99  3.000
 TQD  C1'   N9'  C8'   120.81  3.000
 TQD  C3B   O3'  C3'   118.72  3.000
 TQD  C4B   O4'  C4'   113.98  3.000
 TQD  C5B   O5'  C5'   118.64  3.000
 TQD  H9'3  C9'  H9'2  107.44  3.000
 TQD  H9'3  C9'  H9'1  107.56  3.000
 TQD  H9'2  C9'  H9'1  107.86  3.000
 TQD  H9'3  C9'  N9'   108.67  3.000
 TQD  H9'2  C9'  N9'   110.78  3.000
 TQD  H9'1  C9'  N9'   114.27  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
 TQD  CONST_01  C4'   C3'  C2'  C1'     0.00   0.0  0
 TQD  CONST_02  C4'   C5'  C6'  C1'     0.00   0.0  0
 TQD  CONST_03  C5'   C6'  C1'  C2'     0.00   0.0  0
 TQD  CONST_04  C5'   C4'  C3'  C2'     0.00   0.0  0
 TQD  CONST_05  C6'   C1'  C2'  C3'     0.00   0.0  0
 TQD  CONST_06  C6'   C5'  C4'  C3'     0.00   0.0  0
 TQD  CONST_07  C4A   C4D  N3'  C2D     0.00   0.0  0
 TQD  CONST_08  O3'   C3'  C2'  C1'   180.00   0.0  0
 TQD  CONST_09  O5'   C5'  C6'  C1'   180.00   0.0  0
 TQD  CONST_10  O4'   C4'  C3'  C2'   180.00   0.0  0
 TQD  CONST_11  N9'   C1'  C2'  C3'   180.00   0.0  0
 TQD  CONST_12  O5'   C5'  C4'  C3'   180.00   0.0  0
 TQD  CONST_13  O3'   C3'  C4'  C5'   180.00   0.0  0
 TQD  CONST_14  N9'   C1'  C6'  C5'   180.00   0.0  0
 TQD  CONST_15  O4'   C4'  C5'  C6'   180.00   0.0  0
 TQD  CONST_16  N4'   C4D  N3'  C2D   180.00   0.0  0
 TQD  CONST_17  H6'1  C6'  C1'  C2'   180.00   0.0  0
 TQD  CONST_18  H2'1  C2'  C3'  C4'   180.00   0.0  0
 TQD  CONST_21  C9'   N9'  C1'  C2'     0.00   0.0  0
 TQD  CONST_22  C9'   N9'  C1'  C6'   180.00   0.0  0
 TQD  CONST_24  H4'2  N4'  C4D  C4A   180.00   0.0  0
 TQD  Var_01    C4A   C8A  N1'  C2D   -21.83  30.0  1
 TQD  Var_02    C6D   C5D  C4A  C4D  -158.16  30.0  1
 TQD  Var_03    C7'   C8   C8A  C4A    17.82  30.0  1
 TQD  Var_04    N3'   C4D  C4A  C5D  -175.50  30.0  1
 TQD  Var_05    C8A   C8   C7'  C6D   -47.24  30.0  1
 TQD  Var_06    C1'   N9'  C8'  C6D    87.43  30.0  3
 TQD  Var_07    C4'   C3'  O3'  C3B  -177.26  30.0  1
 TQD  Var_08    C5'   C4'  O4'  C4B   -91.53  30.0  2
 TQD  Var_09    C6'   C5'  O5'  C5B    -0.63  30.0  1
 TQD  Var_10    H9'1  C9'  N9'  C1'   -70.20  30.0  3
 TQD  Var_11    H3B1  C3B  O3'  C3'   179.15  30.0  3
 TQD  Var_12    H4B1  C4B  O4'  C4'    59.69  30.0  3
 TQD  Var_13    H5B1  C5B  O5'  C5'   179.59  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 TQD  chir_01  C2D  N1'  N2'  N3'  negativ
 TQD  chir_02  C6D  C5D  C7'  C8'  positiv

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
 TQD  plan-1  C1'   0.020
 TQD  plan-1  C2'   0.020
 TQD  plan-1  C3'   0.020
 TQD  plan-1  C4'   0.020
 TQD  plan-1  C5'   0.020
 TQD  plan-1  C6'   0.020
 TQD  plan-1  N9'   0.020
 TQD  plan-1  O3'   0.020
 TQD  plan-1  O4'   0.020
 TQD  plan-1  O5'   0.020
 TQD  plan-1  H2'1  0.020
 TQD  plan-1  H6'1  0.020
 TQD  plan-2  C8'   0.020
 TQD  plan-2  C1'   0.020
 TQD  plan-2  N9'   0.020
 TQD  plan-2  C9'   0.020
 TQD  plan-3  C2D   0.020
 TQD  plan-3  C4D   0.020
 TQD  plan-3  C4A   0.020
 TQD  plan-3  N3'   0.020
 TQD  plan-3  N4'   0.020
 TQD  plan-3  H4'1  0.020
 TQD  plan-3  H4'2  0.020
 TQD  plan-4  C2D   0.020
 TQD  plan-4  C8A   0.020
 TQD  plan-4  N1'   0.020
 TQD  plan-4  H1D   0.020

