# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 17:52:13 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 6-ethyl-5-methyl-7-oxidanylidene-1H-pyrazolo[1,5-a]pyrimidine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC1=C(C)N=C2N(NC=C2C#N)C1=O
#
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
 EM6  EM6  6-ethyl-5-methyl-7-oxidanylidene-1H-pyrazolo[1,5-a]pyrimidine-3-carbonitrile  ligand  25  15  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EM6
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
 EM6  C01   C  CH3   0  -0.654  -3.8790   0.0370   1.0287
 EM6  C02   C  CH2   0  -0.502  -3.2181  -0.1434  -0.3373
 EM6  C03   C  CR6   0  -0.147  -1.7184  -0.1654  -0.2571
 EM6  C04   C  CR6   0   0.212  -0.9816  -1.3390  -0.2002
 EM6  C05   C  CH3   0  -0.758  -1.6633  -2.6731  -0.2528
 EM6  N06   N  N     0  -0.485   0.3641  -1.3912  -0.1027
 EM6  C07   C  CR56  0   0.671   0.9811  -0.2435  -0.0562
 EM6  C08   C  CR5   0  -0.331   2.3636   0.0911   0.0481
 EM6  C09   C  CSP   0   0.017   3.4283  -0.8237   0.1265
 EM6  N10   N  NS    0  -0.244   4.2902  -1.5860   0.1996
 EM6  C11   C  CR15  0   0.193   2.4342   1.4684   0.0584
 EM6  N12   N  NR15  0  -0.412   1.2061   1.9601  -0.0315
 EM6  N13   N  N     0  -0.402   0.3251   0.9459  -0.1019
 EM6  C14   C  CR6   0   0.565  -1.0616   1.0991  -0.2000
 EM6  O15   O  O     0  -0.481  -1.5341   2.2272  -0.2273
 EM6  H01   H  HCH3  0   0.228  -3.5680   0.9711   1.4970
 EM6  H01A  H  HCH3  0   0.231  -4.9653   0.0581   0.9336
 EM6  H01B  H  HCH3  0   0.223  -3.6208  -0.7784   1.7056
 EM6  H02   H  HCH2  0   0.247  -3.5826  -1.0614  -0.7996
 EM6  H02A  H  HCH2  0   0.245  -3.5330   0.6672  -0.9979
 EM6  H05   H  HCH3  0   0.261  -2.1692  -2.8173  -1.2091
 EM6  H05A  H  HCH3  0   0.262  -0.9365  -3.4721  -0.1285
 EM6  H05B  H  HCH3  0   0.256  -2.4192  -2.7702   0.5270
 EM6  H11   H  HCR5  0   0.350   3.2904   2.1186   0.1261
 EM6  HN12  H  HNR5  0   0.459   0.8931   2.9214  -0.0471

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
 EM6  C01  C02   single  1.528  0.020  1.528
 EM6  C02  C03   single  1.502  0.020  1.502
 EM6  C03  C04   double  1.387  0.020  1.387
 EM6  C03  C14   single  1.426  0.020  1.426
 EM6  C04  C05   single  1.499  0.020  1.499
 EM6  C04  N06   single  1.350  0.020  1.350
 EM6  N06  C07   double  1.304  0.020  1.304
 EM6  C07  C08   single  1.426  0.020  1.426
 EM6  C07  N13   single  1.359  0.020  1.359
 EM6  C08  C09   single  1.406  0.020  1.406
 EM6  C08  C11   double  1.379  0.020  1.379
 EM6  C09  N10   triple  1.153  0.020  1.153
 EM6  C11  N12   single  1.326  0.020  1.326
 EM6  N12  N13   single  1.345  0.020  1.345
 EM6  N13  C14   single  1.399  0.020  1.399
 EM6  C14  O15   double  1.223  0.020  1.223
 EM6  C01  H01   single  0.970  0.020  1.090
 EM6  C01  H01A  single  0.970  0.020  1.090
 EM6  C01  H01B  single  0.970  0.020  1.090
 EM6  C02  H02   single  0.970  0.020  1.090
 EM6  C02  H02A  single  0.970  0.020  1.090
 EM6  C05  H05   single  0.970  0.020  1.090
 EM6  C05  H05A  single  0.970  0.020  1.090
 EM6  C05  H05B  single  0.970  0.020  1.090
 EM6  C11  H11   single  0.930  0.020  1.080
 EM6  N12  HN12  single  0.860  0.020  1.020

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
 EM6  H01B  C01  H01A  107.72  3.000
 EM6  H01B  C01  H01   107.84  3.000
 EM6  H01A  C01  H01   107.75  3.000
 EM6  H01B  C01  C02   111.36  3.000
 EM6  H01A  C01  C02   110.80  3.000
 EM6  H01   C01  C02   111.21  3.000
 EM6  H02A  C02  H02   105.79  3.000
 EM6  H02A  C02  C03   109.34  3.000
 EM6  H02   C02  C03   110.13  3.000
 EM6  H02A  C02  C01   109.17  3.000
 EM6  H02   C02  C01   109.49  3.000
 EM6  C03   C02  C01   112.69  3.000
 EM6  C14   C03  C04   120.27  3.000
 EM6  C14   C03  C02   116.68  3.000
 EM6  C04   C03  C02   123.03  3.000
 EM6  N06   C04  C05   114.92  3.000
 EM6  N06   C04  C03   124.41  3.000
 EM6  C05   C04  C03   120.67  3.000
 EM6  H05B  C05  H05A  108.44  3.000
 EM6  H05B  C05  H05   107.07  3.000
 EM6  H05A  C05  H05   108.23  3.000
 EM6  H05B  C05  C04   111.68  3.000
 EM6  H05A  C05  C04   110.24  3.000
 EM6  H05   C05  C04   111.04  3.000
 EM6  C07   N06  C04   116.12  3.000
 EM6  N13   C07  C08   105.37  3.000
 EM6  N13   C07  N06   122.73  3.000
 EM6  C08   C07  N06   131.90  3.000
 EM6  C11   C08  C09   127.63  3.000
 EM6  C11   C08  C07   106.53  3.000
 EM6  C09   C08  C07   125.84  3.000
 EM6  N10   C09  C08   180.00  3.000
 EM6  H11   C11  N12   121.10  3.000
 EM6  H11   C11  C08   130.09  3.000
 EM6  N12   C11  C08   108.81  3.000
 EM6  HN12  N12  N13   120.88  3.000
 EM6  HN12  N12  C11   129.82  3.000
 EM6  N13   N12  C11   109.30  3.000
 EM6  C14   N13  N12   124.78  3.000
 EM6  C14   N13  C07   125.22  3.000
 EM6  N12   N13  C07   109.99  3.000
 EM6  O15   C14  N13   119.05  3.000
 EM6  O15   C14  C03   129.71  3.000
 EM6  N13   C14  C03   111.24  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
 EM6  CONST_01  C07  N13  C14  C03    0.00   0.0  0
 EM6  CONST_02  N12  N13  C14  C03  180.00   0.0  0
 EM6  CONST_03  C08  C07  N06  C04  180.00   0.0  0
 EM6  CONST_04  N13  C07  N06  C04    0.00   0.0  0
 EM6  CONST_05  N12  N13  C07  N06  180.00   0.0  0
 EM6  CONST_06  C14  N13  C07  N06    0.00   0.0  0
 EM6  CONST_07  N12  N13  C07  C08    0.00   0.0  0
 EM6  CONST_08  C14  N13  C07  C08  180.00   0.0  0
 EM6  CONST_09  O15  C14  N13  C07  180.00   0.0  0
 EM6  CONST_10  O15  C14  N13  N12    0.00   0.0  0
 EM6  Var_01    C04  C03  C02  C01   96.14  30.0  3
 EM6  Var_02    H05  C05  C04  C03   63.88  30.0  3
 EM6  Var_03    H01  C01  C02  C03   59.64  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
 EM6  plan-1  C02   0.020
 EM6  plan-1  C03   0.020
 EM6  plan-1  C04   0.020
 EM6  plan-1  C05   0.020
 EM6  plan-1  N06   0.020
 EM6  plan-1  C07   0.020
 EM6  plan-1  C08   0.020
 EM6  plan-1  C09   0.020
 EM6  plan-1  N10   0.020
 EM6  plan-1  C11   0.020
 EM6  plan-1  N12   0.020
 EM6  plan-1  N13   0.020
 EM6  plan-1  C14   0.020
 EM6  plan-1  O15   0.020
 EM6  plan-1  H11   0.020
 EM6  plan-1  HN12  0.020

