# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:01:04 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: 5-(4,6-dimorpholin-4-yl-1,3,5-triazin-2-yl)-4-(trifluoromethyl)pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(c(cn1)c2nc(nc(n2)N3CCOCC3)N4CCOCC4)C(F)(F)F
#
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
 A3W  A3W  5-(4,6-dimorpholin-4-yl-1,3,5-triazin-2-yl)-4-(trifluoromethyl)pyridin-2-amine  ligand  49  29  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A3W
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
 A3W  CAD  C  CH2   0  -0.323  -3.4297   2.3424   0.1431
 A3W  CAA  C  CH2   0  -0.184  -4.4878   2.5049  -0.9347
 A3W  OAB  O  O2    0  -0.484  -5.6562   1.7737  -0.6361
 A3W  CAC  C  CH2   0  -0.183  -5.3761   0.3992  -0.4906
 A3W  CAF  C  CH2   0  -0.328  -4.3556   0.1470   0.6055
 A3W  NAE  N  NT    0  -0.507  -3.1635   0.9320   0.3507
 A3W  CAM  C  CR6   0   0.656  -1.9230   0.4168   0.4051
 A3W  NAR  N  N     0  -0.508  -0.8911   1.2533   0.2076
 A3W  NAL  N  N     0  -0.539  -1.7954  -0.8866   0.6379
 A3W  CAK  C  CR6   0   0.651  -0.5482  -1.3479   0.6908
 A3W  NAJ  N  NT    0  -0.502  -0.3700  -2.6606   0.9200
 A3W  CAI  C  CH2   0  -0.339   0.9288  -3.3048   0.8954
 A3W  CAH  C  CH2   0  -0.182   0.9643  -4.3199  -0.2348
 A3W  OAG  O  O2    0  -0.484  -0.0922  -5.2497  -0.1329
 A3W  CAN  C  CH2   0  -0.180  -1.3509  -4.6119  -0.1321
 A3W  CAO  C  CH2   0  -0.340  -1.4674  -3.6048   1.0004
 A3W  NAP  N  N     0  -0.504   0.5468  -0.5822   0.5546
 A3W  CAQ  C  CR6   0   0.312   0.3025   0.6900   0.3012
 A3W  CAU  C  CR6   0  -0.056   1.4592   1.5980   0.1702
 A3W  CAT  C  CR16  0  -0.066   1.3853   2.8311   0.8069
 A3W  NAY  N  N     0  -0.453   2.3563   3.7261   0.8597
 A3W  CAZ  C  CR6   0   0.514   3.5032   3.4472   0.2406
 A3W  NBC  N  NH2   0  -0.835   4.4834   4.3619   0.3010
 A3W  CBA  C  CR16  0  -0.437   3.6799   2.2454  -0.4777
 A3W  CAV  C  CR6   0  -0.108   2.6610   1.3242  -0.5065
 A3W  CAW  C  CT    0   1.073   2.8692   0.0761  -1.3274
 A3W  FBB  F  F     0  -0.308   3.2775  -0.9557  -0.5831
 A3W  FAS  F  F     0  -0.304   1.7653  -0.2905  -1.9803
 A3W  FAX  F  F     0  -0.305   3.8135   0.2588  -2.2609
 A3W  H1   H  HCH2  0   0.277  -2.5168   2.8520  -0.1521
 A3W  H2   H  HCH2  0   0.240  -3.7779   2.7901   1.0812
 A3W  H3   H  HCH2  0   0.243  -4.7711   3.5549  -1.0177
 A3W  H4   H  HCH2  0   0.207  -4.0715   2.1879  -1.9015
 A3W  H5   H  HCH2  0   0.243  -6.3132  -0.1012  -0.2425
 A3W  H6   H  HCH2  0   0.207  -5.0057  -0.0227  -1.4357
 A3W  H7   H  HCH2  0   0.241  -4.7742   0.4288   1.5786
 A3W  H8   H  HCH2  0   0.280  -4.1047  -0.9093   0.6417
 A3W  H9   H  HCH2  0   0.281   1.7112  -2.5650   0.7619
 A3W  H10  H  HCH2  0   0.245   1.0940  -3.8054   1.8550
 A3W  H11  H  HCH2  0   0.205   0.9211  -3.7887  -1.1967
 A3W  H12  H  HCH2  0   0.243   1.8981  -4.8833  -0.2031
 A3W  H13  H  HCH2  0   0.207  -1.5265  -4.1017  -1.0900
 A3W  H14  H  HCH2  0   0.243  -2.1096  -5.3874  -0.0197
 A3W  H15  H  HCH2  0   0.246  -1.4224  -4.1200   1.9655
 A3W  H16  H  HCH2  0   0.282  -2.4171  -3.0802   0.9425
 A3W  H17  H  HCR6  0   0.269   0.4697   3.0945   1.3243
 A3W  H18  H  HNH2  0   0.399   4.3563   5.1981   0.8437
 A3W  H19  H  HNH2  0   0.408   5.3864   4.1941  -0.1042
 A3W  H20  H  HCR6  0   0.288   4.6092   2.0838  -1.0056

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
 A3W  CAA  OAB  single    1.410  0.020  1.410
 A3W  CAA  CAD  single    1.519  0.020  1.519
 A3W  OAB  CAC  single    1.410  0.020  1.410
 A3W  CAC  CAF  single    1.519  0.020  1.519
 A3W  CAD  NAE  single    1.450  0.020  1.450
 A3W  NAE  CAF  single    1.450  0.020  1.450
 A3W  NAE  CAM  single    1.344  0.020  1.344
 A3W  CAM  NAR  aromatic  1.343  0.020  1.343
 A3W  CAM  NAL  aromatic  1.330  0.020  1.330
 A3W  NAR  CAQ  aromatic  1.323  0.020  1.323
 A3W  NAL  CAK  aromatic  1.331  0.020  1.331
 A3W  CAT  NAY  aromatic  1.322  0.020  1.322
 A3W  CAT  CAU  aromatic  1.390  0.020  1.390
 A3W  NAY  CAZ  aromatic  1.333  0.020  1.333
 A3W  CAN  CAO  single    1.520  0.020  1.520
 A3W  CAN  OAG  single    1.411  0.020  1.411
 A3W  CAQ  CAU  single    1.476  0.020  1.476
 A3W  CAQ  NAP  aromatic  1.320  0.020  1.320
 A3W  CAK  NAP  aromatic  1.343  0.020  1.343
 A3W  CAK  NAJ  single    1.344  0.020  1.344
 A3W  CAO  NAJ  single    1.450  0.020  1.450
 A3W  CAU  CAV  aromatic  1.406  0.020  1.406
 A3W  NAJ  CAI  single    1.450  0.020  1.450
 A3W  CAZ  NBC  single    1.342  0.020  1.342
 A3W  CAZ  CBA  aromatic  1.411  0.020  1.411
 A3W  OAG  CAH  single    1.411  0.020  1.411
 A3W  CAH  CAI  single    1.520  0.020  1.520
 A3W  CAV  CBA  aromatic  1.374  0.020  1.374
 A3W  CAV  CAW  single    1.508  0.020  1.508
 A3W  FBB  CAW  single    1.336  0.020  1.336
 A3W  CAW  FAX  single    1.340  0.020  1.340
 A3W  CAW  FAS  single    1.334  0.020  1.334
 A3W  CAD  H1   single    0.970  0.020  1.090
 A3W  CAD  H2   single    0.970  0.020  1.090
 A3W  CAA  H3   single    0.970  0.020  1.090
 A3W  CAA  H4   single    0.970  0.020  1.090
 A3W  CAC  H5   single    0.970  0.020  1.090
 A3W  CAC  H6   single    0.970  0.020  1.090
 A3W  CAF  H7   single    0.970  0.020  1.090
 A3W  CAF  H8   single    0.970  0.020  1.090
 A3W  CAI  H9   single    0.970  0.020  1.090
 A3W  CAI  H10  single    0.970  0.020  1.090
 A3W  CAH  H11  single    0.970  0.020  1.090
 A3W  CAH  H12  single    0.970  0.020  1.090
 A3W  CAN  H13  single    0.970  0.020  1.090
 A3W  CAN  H14  single    0.970  0.020  1.090
 A3W  CAO  H15  single    0.970  0.020  1.090
 A3W  CAO  H16  single    0.970  0.020  1.090
 A3W  CAT  H17  single    0.930  0.020  1.080
 A3W  NBC  H18  single    0.860  0.020  1.020
 A3W  NBC  H19  single    0.860  0.020  1.020
 A3W  CBA  H20  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
 A3W  H2   CAD  H1   107.93  3.000
 A3W  H2   CAD  NAE  109.45  3.000
 A3W  H1   CAD  NAE  109.93  3.000
 A3W  H2   CAD  CAA  110.02  3.000
 A3W  H1   CAD  CAA  110.01  3.000
 A3W  NAE  CAD  CAA  109.48  3.000
 A3W  H4   CAA  H3   108.00  3.000
 A3W  H4   CAA  OAB  110.52  3.000
 A3W  H3   CAA  OAB  107.46  3.000
 A3W  H4   CAA  CAD  109.23  3.000
 A3W  H3   CAA  CAD  109.75  3.000
 A3W  OAB  CAA  CAD  111.80  3.000
 A3W  CAC  OAB  CAA  111.26  3.000
 A3W  H6   CAC  H5   107.99  3.000
 A3W  H6   CAC  CAF  109.29  3.000
 A3W  H5   CAC  CAF  109.69  3.000
 A3W  H6   CAC  OAB  110.63  3.000
 A3W  H5   CAC  OAB  107.45  3.000
 A3W  CAF  CAC  OAB  111.70  3.000
 A3W  H8   CAF  H7   107.98  3.000
 A3W  H8   CAF  NAE  110.03  3.000
 A3W  H7   CAF  NAE  109.32  3.000
 A3W  H8   CAF  CAC  109.92  3.000
 A3W  H7   CAF  CAC  109.96  3.000
 A3W  NAE  CAF  CAC  109.61  3.000
 A3W  CAM  NAE  CAF  122.96  3.000
 A3W  CAM  NAE  CAD  123.22  3.000
 A3W  CAF  NAE  CAD  113.63  3.000
 A3W  NAL  CAM  NAR  124.22  3.000
 A3W  NAL  CAM  NAE  118.11  3.000
 A3W  NAR  CAM  NAE  117.67  3.000
 A3W  CAQ  NAR  CAM  114.68  3.000
 A3W  CAK  NAL  CAM  115.88  3.000
 A3W  NAP  CAK  NAJ  117.77  3.000
 A3W  NAJ  CAK  NAL  118.00  3.000
 A3W  NAP  CAK  NAL  124.22  3.000
 A3W  CAO  NAJ  CAI  112.93  3.000
 A3W  CAI  NAJ  CAK  123.34  3.000
 A3W  CAO  NAJ  CAK  123.02  3.000
 A3W  H10  CAI  H9   108.11  3.000
 A3W  H10  CAI  CAH  110.06  3.000
 A3W  H9   CAI  CAH  110.31  3.000
 A3W  H10  CAI  NAJ  108.87  3.000
 A3W  H9   CAI  NAJ  110.18  3.000
 A3W  CAH  CAI  NAJ  109.29  3.000
 A3W  H12  CAH  H11  107.97  3.000
 A3W  H12  CAH  OAG  107.36  3.000
 A3W  H11  CAH  OAG  110.62  3.000
 A3W  H12  CAH  CAI  110.08  3.000
 A3W  H11  CAH  CAI  109.09  3.000
 A3W  OAG  CAH  CAI  111.65  3.000
 A3W  CAN  OAG  CAH  111.72  3.000
 A3W  H14  CAN  H13  107.97  3.000
 A3W  H14  CAN  CAO  109.93  3.000
 A3W  H13  CAN  CAO  109.24  3.000
 A3W  H14  CAN  OAG  107.41  3.000
 A3W  H13  CAN  OAG  110.60  3.000
 A3W  CAO  CAN  OAG  111.61  3.000
 A3W  H16  CAO  H15  108.07  3.000
 A3W  H16  CAO  CAN  110.32  3.000
 A3W  H15  CAO  CAN  109.99  3.000
 A3W  H16  CAO  NAJ  110.13  3.000
 A3W  H15  CAO  NAJ  108.91  3.000
 A3W  CAN  CAO  NAJ  109.40  3.000
 A3W  CAQ  NAP  CAK  114.71  3.000
 A3W  CAU  CAQ  NAP  117.70  3.000
 A3W  NAP  CAQ  NAR  126.22  3.000
 A3W  CAU  CAQ  NAR  116.02  3.000
 A3W  CAV  CAU  CAT  116.02  3.000
 A3W  CAV  CAU  CAQ  126.34  3.000
 A3W  CAT  CAU  CAQ  117.61  3.000
 A3W  H17  CAT  NAY  115.90  3.000
 A3W  H17  CAT  CAU  118.62  3.000
 A3W  NAY  CAT  CAU  125.47  3.000
 A3W  CAZ  NAY  CAT  118.16  3.000
 A3W  CBA  CAZ  NBC  120.79  3.000
 A3W  CBA  CAZ  NAY  121.49  3.000
 A3W  NBC  CAZ  NAY  117.70  3.000
 A3W  H19  NBC  H18  118.09  3.000
 A3W  H19  NBC  CAZ  121.65  3.000
 A3W  H18  NBC  CAZ  119.94  3.000
 A3W  H20  CBA  CAV  121.81  3.000
 A3W  H20  CBA  CAZ  118.92  3.000
 A3W  CAV  CBA  CAZ  119.27  3.000
 A3W  CAW  CAV  CBA  117.64  3.000
 A3W  CAW  CAV  CAU  122.75  3.000
 A3W  CBA  CAV  CAU  119.55  3.000
 A3W  FAX  CAW  FAS  106.23  3.000
 A3W  FAS  CAW  FBB  108.26  3.000
 A3W  FAX  CAW  FBB  106.14  3.000
 A3W  FAS  CAW  CAV  112.31  3.000
 A3W  FAX  CAW  CAV  111.32  3.000
 A3W  FBB  CAW  CAV  112.21  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
 A3W  CONST_01  CAU  CAQ  NAR  CAM   180.00   0.0  0
 A3W  CONST_02  NAP  CAQ  NAR  CAM     0.00   0.0  0
 A3W  CONST_03  NAP  CAK  NAL  CAM     0.00   0.0  0
 A3W  CONST_04  CAK  NAL  CAM  NAR     0.00   0.0  0
 A3W  CONST_07  CAK  NAP  CAQ  NAR     0.00   0.0  0
 A3W  CONST_08  CAQ  NAR  CAM  NAL     0.00   0.0  0
 A3W  CONST_09  CAQ  NAP  CAK  NAL     0.00   0.0  0
 A3W  CONST_10  CAU  CAQ  NAP  CAK   180.00   0.0  0
 A3W  CONST_13  NAY  CAT  CAU  CAQ   180.00   0.0  0
 A3W  CONST_14  CBA  CAV  CAU  CAQ   180.00   0.0  0
 A3W  CONST_15  CAZ  NAY  CAT  CAU     0.00   0.0  0
 A3W  CONST_16  CAZ  CBA  CAV  CAU     0.00   0.0  0
 A3W  CONST_17  CBA  CAZ  NAY  CAT     0.00   0.0  0
 A3W  CONST_18  CBA  CAV  CAU  CAT     0.00   0.0  0
 A3W  CONST_19  CAV  CAU  CAT  NAY     0.00   0.0  0
 A3W  CONST_20  CAV  CBA  CAZ  NAY     0.00   0.0  0
 A3W  CONST_21  CAQ  NAR  CAM  NAE   180.00   0.0  0
 A3W  CONST_22  CAK  NAL  CAM  NAE   180.00   0.0  0
 A3W  CONST_23  NAJ  CAK  NAL  CAM   180.00   0.0  0
 A3W  CONST_24  CAQ  NAP  CAK  NAJ   180.00   0.0  0
 A3W  CONST_25  CAW  CAV  CAU  CAQ     0.00   0.0  0
 A3W  CONST_26  NBC  CAZ  NAY  CAT   180.00   0.0  0
 A3W  CONST_27  CAW  CAV  CAU  CAT   180.00   0.0  0
 A3W  CONST_28  CAW  CAV  CBA  CAZ   180.00   0.0  0
 A3W  CONST_29  CAV  CBA  CAZ  NBC   180.00   0.0  0
 A3W  CONST_30  H17  CAT  CAU  CAQ     0.00   0.0  0
 A3W  CONST_31  H20  CBA  CAV  CAU   180.00   0.0  0
 A3W  CONST_32  H18  NBC  CAZ  NAY     0.00   0.0  0
 A3W  CONST_33  H19  NBC  CAZ  NAY   180.00   0.0  0
 A3W  Var_01    CAC  CAF  NAE  CAD    52.72  30.0  1
 A3W  Var_02    NAR  CAM  NAE  CAD    -2.48  30.0  2
 A3W  Var_03    CAF  CAC  OAB  CAA    58.55  30.0  1
 A3W  Var_04    CAF  NAE  CAD  CAA   -52.68  30.0  1
 A3W  Var_05    NAE  CAD  CAA  OAB    54.67  30.0  1
 A3W  Var_06    NAE  CAF  CAC  OAB   -54.63  30.0  1
 A3W  Var_07    CAO  NAJ  CAK  NAL     5.26  30.0  2
 A3W  Var_08    CAN  CAO  NAJ  CAK   116.19  30.0  1
 A3W  Var_09    CAH  CAI  NAJ  CAK  -116.10  30.0  1
 A3W  Var_10    OAG  CAN  CAO  NAJ    54.99  30.0  1
 A3W  Var_11    OAG  CAH  CAI  NAJ   -55.18  30.0  1
 A3W  Var_12    CAO  CAN  OAG  CAH   -57.69  30.0  1
 A3W  Var_13    H3   CAA  OAB  CAC  -179.11  30.0  1
 A3W  Var_14    FBB  CAW  CAV  CAU   -85.50  30.0  2

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
 A3W  plan-1  NAE  0.020
 A3W  plan-1  CAM  0.020
 A3W  plan-1  NAR  0.020
 A3W  plan-1  NAL  0.020
 A3W  plan-1  CAK  0.020
 A3W  plan-1  NAJ  0.020
 A3W  plan-1  NAP  0.020
 A3W  plan-1  CAQ  0.020
 A3W  plan-1  CAU  0.020
 A3W  plan-2  CAZ  0.020
 A3W  plan-2  NBC  0.020
 A3W  plan-2  H18  0.020
 A3W  plan-2  H19  0.020
 A3W  plan-3  CAQ  0.020
 A3W  plan-3  CAU  0.020
 A3W  plan-3  CAT  0.020
 A3W  plan-3  NAY  0.020
 A3W  plan-3  CAZ  0.020
 A3W  plan-3  NBC  0.020
 A3W  plan-3  CBA  0.020
 A3W  plan-3  CAV  0.020
 A3W  plan-3  CAW  0.020
 A3W  plan-3  H17  0.020
 A3W  plan-3  H20  0.020

