# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 11:20:58 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 8-ethyl-5-methyl-2-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-[1,2,4]triazolo[1,5-c]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1cnc(C)n2nc(CCc3nc(nn3C)N4CCCC4)nc12
#
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
 5MF  5MF  8-ethyl-5-methyl-2-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-[1,2,4]triazolo[1,5-c]pyrimidine  ligand  49  25  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5MF
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
 5MF  C10  C  CR5   0   0.350   1.7650   0.1610  -0.7148
 5MF  C13  C  CH2   0  -0.558  -0.4048  -0.5316   0.3029
 5MF  C17  C  CR5   0   0.565  -3.9333  -0.3791  -0.0562
 5MF  C20  C  CH3   0  -0.521  -1.8409  -2.9687  -1.0007
 5MF  C21  C  CH2   0  -0.257  -6.3523  -0.3548  -0.4765
 5MF  C22  C  CH2   0  -0.482  -7.3429   0.8058  -0.4039
 5MF  C23  C  CH2   0  -0.477  -6.8312   1.6370   0.7703
 5MF  C24  C  CH2   0  -0.254  -5.3154   1.5375   0.6352
 5MF  C25  C  CH3   0  -0.664   4.6557  -2.5993   1.7971
 5MF  N1   N  N     0  -0.429   5.8364   1.5017  -0.1239
 5MF  C2   C  CR16  0  -0.127   6.0170   0.1841   0.1454
 5MF  C3   C  CR6   0  -0.048   5.0323  -0.7632   0.1182
 5MF  C4   C  CR6   0   0.476   4.6587   1.9380  -0.4399
 5MF  C5   C  CH3   0  -0.736   4.3835   3.3625  -0.7517
 5MF  C6   C  CH2   0  -0.504   5.2480  -2.2068   0.4444
 5MF  N7   N  N     0  -0.393   3.6221   1.0582  -0.4945
 5MF  C8   C  CR56  0   0.554   3.7536  -0.2773  -0.2253
 5MF  N9   N  N     0  -0.484   2.5767  -0.8574  -0.3640
 5MF  N11  N  N     0  -0.286   2.3480   1.3392  -0.8065
 5MF  C12  C  CH2   0  -0.538   0.3108  -0.0282  -0.9602
 5MF  C14  C  CR5   0   0.488  -1.8654  -0.7004   0.0767
 5MF  N15  N  NR5   0  -0.304  -2.4352  -1.7598  -0.4945
 5MF  N16  N  N     0  -0.359  -3.7729  -1.5764  -0.5916
 5MF  N18  N  N     0  -0.527  -2.7854   0.2010   0.3702
 5MF  N19  N  NR5   0  -0.537  -5.1363   0.2168   0.0662
 5MF  H1   H  HCH2  0   0.277   0.0487  -1.4648   0.6404
 5MF  H2   H  HCH2  0   0.286  -0.2760   0.1928   1.1071
 5MF  H3   H  HCH3  0   0.264  -2.3080  -3.8361  -0.5383
 5MF  H4   H  HCH3  0   0.260  -1.9628  -3.0309  -2.0810
 5MF  H5   H  HCH3  0   0.258  -0.7801  -2.9821  -0.7684
 5MF  H6   H  HCH2  0   0.221  -6.6900  -1.2098   0.1202
 5MF  H7   H  HCH2  0   0.231  -6.2074  -0.7122  -1.4994
 5MF  H8   H  HCH2  0   0.236  -7.3027   1.3913  -1.3252
 5MF  H9   H  HCH2  0   0.247  -8.3691   0.4641  -0.2734
 5MF  H10  H  HCH2  0   0.246  -7.1811   2.6687   0.7536
 5MF  H11  H  HCH2  0   0.235  -7.1500   1.1908   1.7148
 5MF  H12  H  HCH2  0   0.216  -4.9226   2.3204  -0.0246
 5MF  H13  H  HCH2  0   0.235  -4.8029   1.6349   1.5940
 5MF  H14  H  HCH3  0   0.229   5.1122  -2.0280   2.6055
 5MF  H15  H  HCH3  0   0.232   3.5801  -2.4267   1.8263
 5MF  H16  H  HCH3  0   0.238   4.8285  -3.6573   1.9939
 5MF  H17  H  HCR6  0   0.275   7.0318  -0.1028   0.3956
 5MF  H18  H  HCH3  0   0.271   5.2912   3.9442  -0.6218
 5MF  H19  H  HCH3  0   0.273   4.0341   3.4749  -1.7789
 5MF  H20  H  HCH3  0   0.271   3.6056   3.7626  -0.1008
 5MF  H21  H  HCH2  0   0.251   6.3197  -2.4132   0.4393
 5MF  H22  H  HCH2  0   0.249   4.8062  -2.8246  -0.3409
 5MF  H23  H  HCH2  0   0.276  -0.1279   0.9152  -1.2848
 5MF  H24  H  HCH2  0   0.273   0.1812  -0.7457  -1.7748

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
 5MF  C23  C22  single    1.527  0.020  1.527
 5MF  C23  C24  single    1.525  0.020  1.525
 5MF  C22  C21  single    1.528  0.020  1.528
 5MF  C24  N19  single    1.449  0.020  1.449
 5MF  C21  N19  single    1.449  0.020  1.449
 5MF  N19  C17  single    1.348  0.020  1.348
 5MF  C17  N16  aromatic  1.321  0.020  1.321
 5MF  C17  N18  aromatic  1.355  0.020  1.355
 5MF  N16  N15  aromatic  1.354  0.020  1.354
 5MF  N18  C14  aromatic  1.321  0.020  1.321
 5MF  N15  C14  aromatic  1.332  0.020  1.332
 5MF  N15  C20  single    1.439  0.020  1.439
 5MF  C14  C13  single    1.488  0.020  1.488
 5MF  C12  C13  single    1.537  0.020  1.537
 5MF  C12  C10  single    1.487  0.020  1.487
 5MF  C10  N9   aromatic  1.349  0.020  1.349
 5MF  C10  N11  aromatic  1.318  0.020  1.318
 5MF  N9   C8   aromatic  1.319  0.020  1.319
 5MF  N11  N7   aromatic  1.342  0.020  1.342
 5MF  C8   N7   aromatic  1.369  0.020  1.369
 5MF  C8   C3   aromatic  1.410  0.020  1.410
 5MF  N7   C4   aromatic  1.361  0.020  1.361
 5MF  C6   C25  single    1.528  0.020  1.528
 5MF  C6   C3   single    1.496  0.020  1.496
 5MF  C3   C2   aromatic  1.367  0.020  1.367
 5MF  C4   C5   single    1.484  0.020  1.484
 5MF  C4   N1   aromatic  1.295  0.020  1.295
 5MF  C2   N1   aromatic  1.357  0.020  1.357
 5MF  C13  H1   single    0.970  0.020  1.090
 5MF  C13  H2   single    0.970  0.020  1.090
 5MF  C20  H3   single    0.970  0.020  1.090
 5MF  C20  H4   single    0.970  0.020  1.090
 5MF  C20  H5   single    0.970  0.020  1.090
 5MF  C21  H6   single    0.970  0.020  1.090
 5MF  C21  H7   single    0.970  0.020  1.090
 5MF  C22  H8   single    0.970  0.020  1.090
 5MF  C22  H9   single    0.970  0.020  1.090
 5MF  C23  H10  single    0.970  0.020  1.090
 5MF  C23  H11  single    0.970  0.020  1.090
 5MF  C24  H12  single    0.970  0.020  1.090
 5MF  C24  H13  single    0.970  0.020  1.090
 5MF  C25  H14  single    0.970  0.020  1.090
 5MF  C25  H15  single    0.970  0.020  1.090
 5MF  C25  H16  single    0.970  0.020  1.090
 5MF  C2   H17  single    0.930  0.020  1.080
 5MF  C5   H18  single    0.970  0.020  1.090
 5MF  C5   H19  single    0.970  0.020  1.090
 5MF  C5   H20  single    0.970  0.020  1.090
 5MF  C6   H21  single    0.970  0.020  1.090
 5MF  C6   H22  single    0.970  0.020  1.090
 5MF  C12  H23  single    0.970  0.020  1.090
 5MF  C12  H24  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
 5MF  C12  C10  N11  122.34  3.000
 5MF  N11  C10  N9   115.28  3.000
 5MF  C12  C10  N9   122.38  3.000
 5MF  H2   C13  H1   106.92  3.000
 5MF  H2   C13  C14  107.68  3.000
 5MF  H1   C13  C14  110.99  3.000
 5MF  H2   C13  C12  109.49  3.000
 5MF  H1   C13  C12  109.93  3.000
 5MF  C14  C13  C12  111.68  3.000
 5MF  N19  C17  N18  122.56  3.000
 5MF  N18  C17  N16  114.37  3.000
 5MF  N19  C17  N16  123.07  3.000
 5MF  H5   C20  H4   108.71  3.000
 5MF  H5   C20  H3   108.58  3.000
 5MF  H4   C20  H3   109.14  3.000
 5MF  H5   C20  N15  109.78  3.000
 5MF  H4   C20  N15  110.53  3.000
 5MF  H3   C20  N15  110.05  3.000
 5MF  H7   C21  H6   107.17  3.000
 5MF  H7   C21  N19  111.60  3.000
 5MF  H6   C21  N19  111.24  3.000
 5MF  H7   C21  C22  112.27  3.000
 5MF  H6   C21  C22  111.53  3.000
 5MF  N19  C21  C22  103.10  3.000
 5MF  H9   C22  H8   107.68  3.000
 5MF  H9   C22  C23  113.23  3.000
 5MF  H8   C22  C23  110.15  3.000
 5MF  H9   C22  C21  112.22  3.000
 5MF  H8   C22  C21  110.07  3.000
 5MF  C23  C22  C21  103.47  3.000
 5MF  H11  C23  H10  107.84  3.000
 5MF  H11  C23  C24  109.88  3.000
 5MF  H10  C23  C24  112.31  3.000
 5MF  H11  C23  C22  110.16  3.000
 5MF  H10  C23  C22  113.33  3.000
 5MF  C24  C23  C22  103.26  3.000
 5MF  H13  C24  H12  107.25  3.000
 5MF  H13  C24  N19  111.60  3.000
 5MF  H12  C24  N19  111.73  3.000
 5MF  H13  C24  C23  112.52  3.000
 5MF  H12  C24  C23  111.27  3.000
 5MF  N19  C24  C23  102.54  3.000
 5MF  H16  C25  H15  107.78  3.000
 5MF  H16  C25  H14  107.96  3.000
 5MF  H15  C25  H14  108.08  3.000
 5MF  H16  C25  C6   110.35  3.000
 5MF  H15  C25  C6   111.45  3.000
 5MF  H14  C25  C6   111.07  3.000
 5MF  C4   N1   C2   119.77  3.000
 5MF  H17  C2   C3   119.72  3.000
 5MF  H17  C2   N1   115.30  3.000
 5MF  C3   C2   N1   124.98  3.000
 5MF  C8   C3   C6   121.09  3.000
 5MF  C6   C3   C2   124.11  3.000
 5MF  C8   C3   C2   114.79  3.000
 5MF  N7   C4   C5   118.10  3.000
 5MF  C5   C4   N1   122.91  3.000
 5MF  N7   C4   N1   118.99  3.000
 5MF  H20  C5   H19  107.20  3.000
 5MF  H20  C5   H18  109.18  3.000
 5MF  H19  C5   H18  108.98  3.000
 5MF  H20  C5   C4   111.04  3.000
 5MF  H19  C5   C4   110.87  3.000
 5MF  H18  C5   C4   109.52  3.000
 5MF  H22  C6   H21  106.66  3.000
 5MF  H22  C6   C3   109.31  3.000
 5MF  H21  C6   C3   108.85  3.000
 5MF  H22  C6   C25  109.53  3.000
 5MF  H21  C6   C25  109.65  3.000
 5MF  C3   C6   C25  112.65  3.000
 5MF  N11  N7   C8   109.96  3.000
 5MF  C8   N7   C4   123.36  3.000
 5MF  N11  N7   C4   126.68  3.000
 5MF  N9   C8   N7   108.82  3.000
 5MF  N7   C8   C3   118.11  3.000
 5MF  N9   C8   C3   133.07  3.000
 5MF  C8   N9   C10  103.43  3.000
 5MF  N7   N11  C10  102.51  3.000
 5MF  H24  C12  H23  107.37  3.000
 5MF  H24  C12  C13  110.02  3.000
 5MF  H23  C12  C13  109.93  3.000
 5MF  H24  C12  C10  108.81  3.000
 5MF  H23  C12  C10  109.43  3.000
 5MF  C13  C12  C10  111.20  3.000
 5MF  N18  C14  N15  109.88  3.000
 5MF  N15  C14  C13  125.14  3.000
 5MF  N18  C14  C13  124.93  3.000
 5MF  N16  N15  C14  110.23  3.000
 5MF  C14  N15  C20  129.98  3.000
 5MF  N16  N15  C20  119.78  3.000
 5MF  N15  N16  C17  102.34  3.000
 5MF  C14  N18  C17  103.18  3.000
 5MF  C24  N19  C21  113.75  3.000
 5MF  C21  N19  C17  122.72  3.000
 5MF  C24  N19  C17  123.28  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
 5MF  CONST_01  N7   C8   N9   C10     0.00   0.0  0
 5MF  CONST_02  C3   C8   N9   C10   180.00   0.0  0
 5MF  CONST_03  C8   N7   N11  C10     0.00   0.0  0
 5MF  CONST_04  C4   N7   N11  C10   180.00   0.0  0
 5MF  CONST_05  C14  N15  N16  C17     0.00   0.0  0
 5MF  CONST_06  N15  C14  N18  C17     0.00   0.0  0
 5MF  CONST_07  N11  N7   C4   N1    180.00   0.0  0
 5MF  CONST_08  C8   N7   C4   N1      0.00   0.0  0
 5MF  CONST_09  C8   C3   C2   N1      0.00   0.0  0
 5MF  CONST_10  N9   C8   C3   C2    180.00   0.0  0
 5MF  CONST_11  N7   C8   C3   C2      0.00   0.0  0
 5MF  CONST_12  N7   C4   N1   C2      0.00   0.0  0
 5MF  CONST_13  N11  N7   C8   C3    180.00   0.0  0
 5MF  CONST_14  C4   N7   C8   C3      0.00   0.0  0
 5MF  CONST_15  C4   N1   C2   C3      0.00   0.0  0
 5MF  CONST_16  N9   C8   N7   C4    180.00   0.0  0
 5MF  CONST_17  N9   C10  N11  N7      0.00   0.0  0
 5MF  CONST_18  N11  C10  N9   C8      0.00   0.0  0
 5MF  CONST_19  N11  N7   C8   N9      0.00   0.0  0
 5MF  CONST_20  N16  C17  N18  C14     0.00   0.0  0
 5MF  CONST_21  N18  C17  N16  N15     0.00   0.0  0
 5MF  CONST_22  N18  C14  N15  N16     0.00   0.0  0
 5MF  CONST_23  N19  C17  N18  C14   180.00   0.0  0
 5MF  CONST_24  N19  C17  N16  N15   180.00   0.0  0
 5MF  CONST_25  C17  N18  C14  C13   180.00   0.0  0
 5MF  CONST_26  N16  N15  C14  C13   180.00   0.0  0
 5MF  CONST_27  C20  N15  N16  C17   180.00   0.0  0
 5MF  CONST_28  N18  C14  N15  C20   180.00   0.0  0
 5MF  CONST_29  C6   C3   C2   N1    180.00   0.0  0
 5MF  CONST_30  C5   C4   N1   C2    180.00   0.0  0
 5MF  CONST_31  N11  N7   C4   C5      0.00   0.0  0
 5MF  CONST_32  C8   N7   C4   C5    180.00   0.0  0
 5MF  CONST_33  N9   C8   C3   C6      0.00   0.0  0
 5MF  CONST_34  N7   C8   C3   C6    180.00   0.0  0
 5MF  CONST_35  C12  C10  N11  N7    180.00   0.0  0
 5MF  CONST_36  C12  C10  N9   C8    180.00   0.0  0
 5MF  CONST_37  H17  C2   N1   C4    180.00   0.0  0
 5MF  Var_01    C23  C24  N19  C17  -170.45  30.0  1
 5MF  Var_02    C22  C21  N19  C17  -166.36  30.0  1
 5MF  Var_03    C24  C23  C22  C21    37.42  30.0  1
 5MF  Var_04    N16  C17  N19  C21    -5.15  30.0  2
 5MF  Var_05    N19  C24  C23  C22   -31.92  30.0  1
 5MF  Var_06    N19  C21  C22  C23   -27.95  30.0  1
 5MF  Var_07    C14  C13  C12  C10   178.93  30.0  3
 5MF  Var_08    N9   C10  C12  C13    61.60  30.0  2
 5MF  Var_09    C8   C3   C6   C25   -71.84  30.0  2
 5MF  Var_10    N18  C14  C13  C12   -95.41  30.0  2
 5MF  Var_11    H18  C5   C4   N1     -2.78  30.0  2
 5MF  Var_12    H3   C20  N15  C14   125.22  30.0  2
 5MF  Var_13    H14  C25  C6   C3    -60.64  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
 5MF  plan-1  C13  0.020
 5MF  plan-1  C17  0.020
 5MF  plan-1  C20  0.020
 5MF  plan-1  C14  0.020
 5MF  plan-1  N15  0.020
 5MF  plan-1  N16  0.020
 5MF  plan-1  N18  0.020
 5MF  plan-1  N19  0.020
 5MF  plan-2  C10  0.020
 5MF  plan-2  N1   0.020
 5MF  plan-2  C2   0.020
 5MF  plan-2  C3   0.020
 5MF  plan-2  C4   0.020
 5MF  plan-2  C5   0.020
 5MF  plan-2  C6   0.020
 5MF  plan-2  N7   0.020
 5MF  plan-2  C8   0.020
 5MF  plan-2  N9   0.020
 5MF  plan-2  N11  0.020
 5MF  plan-2  C12  0.020
 5MF  plan-2  H17  0.020

