# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 11:23:02 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 6-chloranyl-5,8-dimethyl-2-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-[1,2,4]triazolo[1,5-a]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(nc1CCc2nn3c(C)c(Cl)cc(C)c3n2)N4CCCC4
#
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
 5M9  5M9  6-chloranyl-5,8-dimethyl-2-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-[1,2,4]triazolo[1,5-a]pyridine  ligand  47  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_5M9
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
 5M9  C01  C   CR6   0  -0.235  -5.5533   0.0629  -0.1140
 5M9  C02  C   CR16  0  -0.104  -5.2947   1.3953   0.2840
 5M9  C04  C   CR6   0   0.443  -4.5527  -0.8039  -0.4546
 5M9  C06  C   CR56  0   0.546  -2.9871   0.9974  -0.0023
 5M9  N09  N   N     0  -0.292  -2.1719  -0.9505  -0.6654
 5M9  C11  C   CH2   0  -0.558   1.0031  -0.1342   0.6650
 5M9  C18  C   CH2   0  -0.259   6.9262  -0.5016  -0.2343
 5M9  C19  C   CH2   0  -0.477   8.0194   0.5598  -0.2852
 5M9  C20  C   CH2   0  -0.482   7.3304   1.7308  -0.9827
 5M9  C21  C   CH2   0  -0.253   5.9077   1.6923  -0.4266
 5M9  C22  C   CH3   0  -0.521   2.3821  -2.9186   0.7342
 5M9  C23  C   CH3   0  -0.706  -4.6783  -2.2187  -0.8872
 5M9  C03  C   CR6   0  -0.107  -4.0221   1.8883   0.3489
 5M9  N05  N   N     0  -0.428  -3.2952  -0.2796  -0.3804
 5M9  N07  N   N     0  -0.487  -1.6723   1.1518  -0.0463
 5M9  C08  C   CR5   0   0.352  -1.2301  -0.0493  -0.4511
 5M9  C12  C   CR5   0   0.489   2.4524  -0.4204   0.4902
 5M9  N13  N   N     0  -0.527   3.3837   0.4835   0.2446
 5M9  C14  C   CR5   0   0.564   4.5119  -0.2585   0.1314
 5M9  N15  N   N     0  -0.358   4.3285  -1.5573   0.2882
 5M9  N16  N   NR5   0  -0.304   2.9977  -1.6352   0.5225
 5M9  N17  N   NT    0  -0.537   5.7212   0.2903  -0.1035
 5M9  CL1  CL  CL    0  -0.112  -7.2027  -0.4522  -0.1592
 5M9  H1   H   HCR6  0   0.287  -6.1305   2.0329   0.5410
 5M9  H2   H   HCH2  0   0.276   0.6248   0.2782  -1.4190
 5M9  H3   H   HCH2  0   0.267   0.3151  -1.3904  -0.9730
 5M9  H4   H   HCH2  0   0.283   0.8993   0.9038   0.9789
 5M9  H5   H   HCH2  0   0.277   0.5855  -0.7503   1.4641
 5M9  H6   H   HCH2  0   0.217   6.9151  -1.1079  -1.1488
 5M9  H7   H   HCH2  0   0.234   7.0437  -1.1886   0.6070
 5M9  H8   H   HCH2  0   0.235   8.3128   0.8427   0.7283
 5M9  H9   H   HCH2  0   0.246   8.9112   0.2134  -0.8061
 5M9  H10  H   HCH2  0   0.247   7.8172   2.6881  -0.7994
 5M9  H11  H   HCH2  0   0.235   7.3164   1.5669  -2.0625
 5M9  H12  H   HCH2  0   0.220   5.8132   2.3228   0.4642
 5M9  H13  H   HCH2  0   0.232   5.1714   2.0435  -1.1528
 5M9  H14  H   HCH3  0   0.264   2.8826  -3.4420   1.5467
 5M9  H15  H   HCH3  0   0.259   1.3371  -2.7857   1.0001
 5M9  H16  H   HCH3  0   0.260   2.4401  -3.5253  -0.1682
 5M9  H17  H   HCH3  0   0.262  -5.7146  -2.5404  -0.8838
 5M9  H18  H   HCH3  0   0.273  -4.2810  -2.3498  -1.8945
 5M9  H19  H   HCH3  0   0.272  -4.1108  -2.8748  -0.2266
 5M9  H20  H   HCH3  0   0.256  -3.1827   3.8191  -0.0419
 5M9  H21  H   HCH3  0   0.255  -4.5897   3.8374   1.0244
 5M9  H22  H   HCH3  0   0.255  -3.0220   3.2885   1.6233
 5M9  C10  C   CH2   0  -0.539   0.2137  -0.3592  -0.6325
 5M9  C24  C   CH3   0  -0.721  -3.6905   3.2839   0.7615

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
 5M9  C19  C20  single    1.527  0.020  1.527
 5M9  C19  C18  single    1.525  0.020  1.525
 5M9  C20  C21  single    1.528  0.020  1.528
 5M9  C18  N17  single    1.448  0.020  1.448
 5M9  C21  N17  single    1.451  0.020  1.451
 5M9  N17  C14  single    1.349  0.020  1.349
 5M9  C14  N15  aromatic  1.321  0.020  1.321
 5M9  C14  N13  aromatic  1.355  0.020  1.355
 5M9  N15  N16  aromatic  1.353  0.020  1.353
 5M9  N13  C12  aromatic  1.321  0.020  1.321
 5M9  N16  C12  aromatic  1.332  0.020  1.332
 5M9  N16  C22  single    1.439  0.020  1.439
 5M9  C12  C11  single    1.488  0.020  1.488
 5M9  C10  C11  single    1.535  0.020  1.535
 5M9  C10  C08  single    1.488  0.020  1.488
 5M9  C08  N07  aromatic  1.342  0.020  1.342
 5M9  C08  N09  aromatic  1.321  0.020  1.321
 5M9  N07  C06  aromatic  1.325  0.020  1.325
 5M9  N09  N05  aromatic  1.339  0.020  1.339
 5M9  C06  N05  aromatic  1.367  0.020  1.367
 5M9  C06  C03  aromatic  1.410  0.020  1.410
 5M9  N05  C04  aromatic  1.364  0.020  1.364
 5M9  C24  C03  single    1.493  0.020  1.493
 5M9  C03  C02  aromatic  1.366  0.020  1.366
 5M9  C04  C23  single    1.485  0.020  1.485
 5M9  C04  C01  aromatic  1.367  0.020  1.367
 5M9  C02  C01  aromatic  1.414  0.020  1.414
 5M9  C01  CL1  single    1.728  0.020  1.728
 5M9  C02  H1   single    0.930  0.020  1.080
 5M9  C10  H2   single    0.970  0.020  1.090
 5M9  C10  H3   single    0.970  0.020  1.090
 5M9  C11  H4   single    0.970  0.020  1.090
 5M9  C11  H5   single    0.970  0.020  1.090
 5M9  C18  H6   single    0.970  0.020  1.090
 5M9  C18  H7   single    0.970  0.020  1.090
 5M9  C19  H8   single    0.970  0.020  1.090
 5M9  C19  H9   single    0.970  0.020  1.090
 5M9  C20  H10  single    0.970  0.020  1.090
 5M9  C20  H11  single    0.970  0.020  1.090
 5M9  C21  H12  single    0.970  0.020  1.090
 5M9  C21  H13  single    0.970  0.020  1.090
 5M9  C22  H14  single    0.970  0.020  1.090
 5M9  C22  H15  single    0.970  0.020  1.090
 5M9  C22  H16  single    0.970  0.020  1.090
 5M9  C23  H17  single    0.970  0.020  1.090
 5M9  C23  H18  single    0.970  0.020  1.090
 5M9  C23  H19  single    0.970  0.020  1.090
 5M9  C24  H20  single    0.970  0.020  1.090
 5M9  C24  H21  single    0.970  0.020  1.090
 5M9  C24  H22  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
 5M9  CL1  C01  C04  120.20  3.000
 5M9  CL1  C01  C02  117.55  3.000
 5M9  C04  C01  C02  122.25  3.000
 5M9  H1   C02  C03  119.70  3.000
 5M9  H1   C02  C01  118.72  3.000
 5M9  C03  C02  C01  121.58  3.000
 5M9  N05  C04  C23  117.39  3.000
 5M9  C23  C04  C01  127.94  3.000
 5M9  N05  C04  C01  114.67  3.000
 5M9  N07  C06  N05  108.87  3.000
 5M9  N05  C06  C03  119.58  3.000
 5M9  N07  C06  C03  131.55  3.000
 5M9  C08  N09  N05  102.81  3.000
 5M9  H5   C11  H4   106.87  3.000
 5M9  H5   C11  C12  110.48  3.000
 5M9  H4   C11  C12  108.06  3.000
 5M9  H5   C11  C10  109.83  3.000
 5M9  H4   C11  C10  109.52  3.000
 5M9  C12  C11  C10  111.93  3.000
 5M9  H7   C18  H6   107.18  3.000
 5M9  H7   C18  N17  111.34  3.000
 5M9  H6   C18  N17  111.66  3.000
 5M9  H7   C18  C19  112.73  3.000
 5M9  H6   C18  C19  111.35  3.000
 5M9  N17  C18  C19  102.65  3.000
 5M9  H9   C19  H8   107.83  3.000
 5M9  H9   C19  C20  113.25  3.000
 5M9  H8   C19  C20  110.27  3.000
 5M9  H9   C19  C18  112.43  3.000
 5M9  H8   C19  C18  109.99  3.000
 5M9  C20  C19  C18  103.03  3.000
 5M9  H11  C20  H10  107.69  3.000
 5M9  H11  C20  C21  110.13  3.000
 5M9  H10  C20  C21  112.15  3.000
 5M9  H11  C20  C19  110.02  3.000
 5M9  H10  C20  C19  113.28  3.000
 5M9  C21  C20  C19  103.56  3.000
 5M9  H13  C21  H12  107.30  3.000
 5M9  H13  C21  N17  111.85  3.000
 5M9  H12  C21  N17  111.35  3.000
 5M9  H13  C21  C20  112.19  3.000
 5M9  H12  C21  C20  111.21  3.000
 5M9  N17  C21  C20  103.01  3.000
 5M9  H16  C22  H15  108.80  3.000
 5M9  H16  C22  H14  109.04  3.000
 5M9  H15  C22  H14  108.57  3.000
 5M9  H16  C22  N16  110.62  3.000
 5M9  H15  C22  N16  109.78  3.000
 5M9  H14  C22  N16  110.00  3.000
 5M9  H19  C23  H18  107.32  3.000
 5M9  H19  C23  H17  108.47  3.000
 5M9  H18  C23  H17  108.37  3.000
 5M9  H19  C23  C04  110.66  3.000
 5M9  H18  C23  C04  110.66  3.000
 5M9  H17  C23  C04  111.25  3.000
 5M9  C24  C03  C06  119.77  3.000
 5M9  C24  C03  C02  123.88  3.000
 5M9  C06  C03  C02  116.35  3.000
 5M9  N09  N05  C06  109.74  3.000
 5M9  C06  N05  C04  125.58  3.000
 5M9  N09  N05  C04  124.68  3.000
 5M9  C08  N07  C06  103.46  3.000
 5M9  N07  C08  C10  122.88  3.000
 5M9  N07  C08  N09  115.11  3.000
 5M9  C10  C08  N09  122.00  3.000
 5M9  N16  C12  N13  109.88  3.000
 5M9  N16  C12  C11  124.86  3.000
 5M9  N13  C12  C11  125.25  3.000
 5M9  C14  N13  C12  103.17  3.000
 5M9  N17  C14  N15  123.04  3.000
 5M9  N15  C14  N13  114.38  3.000
 5M9  N17  C14  N13  122.57  3.000
 5M9  N16  N15  C14  102.34  3.000
 5M9  N15  N16  C12  110.23  3.000
 5M9  C12  N16  C22  129.93  3.000
 5M9  N15  N16  C22  119.83  3.000
 5M9  C14  N17  C21  123.18  3.000
 5M9  C14  N17  C18  122.65  3.000
 5M9  C21  N17  C18  113.67  3.000
 5M9  H3   C10  H2   106.97  3.000
 5M9  H3   C10  C08  108.97  3.000
 5M9  H2   C10  C08  109.35  3.000
 5M9  H3   C10  C11  110.77  3.000
 5M9  H2   C10  C11  109.23  3.000
 5M9  C08  C10  C11  111.43  3.000
 5M9  H22  C24  H21  108.27  3.000
 5M9  H22  C24  H20  107.13  3.000
 5M9  H21  C24  H20  108.25  3.000
 5M9  H22  C24  C03  111.01  3.000
 5M9  H21  C24  C03  111.02  3.000
 5M9  H20  C24  C03  111.01  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
 5M9  CONST_01  N09  N05  C04  C01   180.00   0.0  0
 5M9  CONST_02  C06  N05  C04  C01     0.00   0.0  0
 5M9  CONST_03  C06  C03  C02  C01     0.00   0.0  0
 5M9  CONST_04  N07  C06  C03  C02   180.00   0.0  0
 5M9  CONST_05  N05  C06  C03  C02     0.00   0.0  0
 5M9  CONST_06  N05  C04  C01  C02     0.00   0.0  0
 5M9  CONST_07  C08  N09  N05  C04   180.00   0.0  0
 5M9  CONST_08  N07  C06  N05  C04   180.00   0.0  0
 5M9  CONST_09  C03  C06  N05  C04     0.00   0.0  0
 5M9  CONST_10  C03  C02  C01  C04     0.00   0.0  0
 5M9  CONST_11  N09  C08  N07  C06     0.00   0.0  0
 5M9  CONST_12  C08  N09  N05  C06     0.00   0.0  0
 5M9  CONST_13  N07  C06  N05  N09     0.00   0.0  0
 5M9  CONST_14  C03  C06  N05  N09   180.00   0.0  0
 5M9  CONST_15  C08  N07  C06  C03   180.00   0.0  0
 5M9  CONST_16  N07  C08  N09  N05     0.00   0.0  0
 5M9  CONST_17  C08  N07  C06  N05     0.00   0.0  0
 5M9  CONST_18  N15  C14  N13  C12     0.00   0.0  0
 5M9  CONST_19  C14  N15  N16  C12     0.00   0.0  0
 5M9  CONST_20  N16  N15  C14  N13     0.00   0.0  0
 5M9  CONST_21  N15  N16  C12  N13     0.00   0.0  0
 5M9  CONST_22  N16  C12  N13  C14     0.00   0.0  0
 5M9  CONST_23  N17  C14  N13  C12   180.00   0.0  0
 5M9  CONST_24  N17  C14  N15  N16   180.00   0.0  0
 5M9  CONST_25  C24  C03  C02  C01   180.00   0.0  0
 5M9  CONST_26  C23  C04  C01  C02   180.00   0.0  0
 5M9  CONST_27  C10  C08  N07  C06   180.00   0.0  0
 5M9  CONST_28  C23  C04  N05  C06   180.00   0.0  0
 5M9  CONST_29  C23  C04  N05  N09     0.00   0.0  0
 5M9  CONST_30  N05  N09  C08  C10   180.00   0.0  0
 5M9  CONST_31  C14  N13  C12  C11   180.00   0.0  0
 5M9  CONST_32  N15  N16  C12  C11   180.00   0.0  0
 5M9  CONST_33  C14  N15  N16  C22   180.00   0.0  0
 5M9  CONST_34  N13  C12  N16  C22   180.00   0.0  0
 5M9  CONST_35  N07  C06  C03  C24     0.00   0.0  0
 5M9  CONST_36  N05  C06  C03  C24   180.00   0.0  0
 5M9  CONST_37  CL1  C01  C02  C03   180.00   0.0  0
 5M9  CONST_38  CL1  C01  C04  N05   180.00   0.0  0
 5M9  CONST_39  H1   C02  C01  C04   180.00   0.0  0
 5M9  Var_01    C21  C20  C19  C18    37.61  30.0  1
 5M9  Var_02    C20  C21  N17  C18     7.68  30.0  1
 5M9  Var_03    N15  C14  N17  C18     1.39  30.0  2
 5M9  Var_04    N17  C21  C20  C19   -27.85  30.0  1
 5M9  Var_05    C21  N17  C18  C19    15.69  30.0  1
 5M9  Var_06    N17  C18  C19  C20   -32.36  30.0  1
 5M9  Var_07    C11  C10  C08  N09  -121.29  30.0  3
 5M9  Var_08    N13  C12  C11  C10    96.84  30.0  1
 5M9  Var_09    C12  C11  C10  C08  -179.10  30.0  3
 5M9  Var_10    H17  C23  C04  C01    -1.68  30.0  2
 5M9  Var_11    H20  C24  C03  C02  -119.01  30.0  2
 5M9  Var_12    H14  C22  N16  C12  -126.19  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
 5M9  plan-1  C11  0.020
 5M9  plan-1  C22  0.020
 5M9  plan-1  C12  0.020
 5M9  plan-1  N13  0.020
 5M9  plan-1  C14  0.020
 5M9  plan-1  N15  0.020
 5M9  plan-1  N16  0.020
 5M9  plan-1  N17  0.020
 5M9  plan-2  C01  0.020
 5M9  plan-2  C02  0.020
 5M9  plan-2  C04  0.020
 5M9  plan-2  C06  0.020
 5M9  plan-2  N09  0.020
 5M9  plan-2  C23  0.020
 5M9  plan-2  C03  0.020
 5M9  plan-2  N05  0.020
 5M9  plan-2  N07  0.020
 5M9  plan-2  C08  0.020
 5M9  plan-2  CL1  0.020
 5M9  plan-2  H1   0.020
 5M9  plan-2  C10  0.020
 5M9  plan-2  C24  0.020

