# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 18:38:50 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 3-amino-N-methyl-6-[3-(1H-tetrazol-5-yl)phenyl]pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1nc(cnc1N)c2cccc(c2)c3[nH]nnn3
#
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
 EM7  EM7  3-amino-N-methyl-6-[3-(1H-tetrazol-5-yl)phenyl]pyrazine-2-carboxamide  ligand  34  22  .  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_EM7
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
 EM7  C13   C  CH3   0  -0.513   5.3150   2.4554   0.4375
 EM7  N7    N  NH1   0  -0.629   4.1871   1.5740   0.2623
 EM7  C12   C  C     0   0.554   4.3213   0.2521   0.1546
 EM7  O1    O  O     0  -0.506   5.4120  -0.3162   0.2007
 EM7  C5    C  CR6   0   0.003   3.0464  -0.5033  -0.0282
 EM7  N6    N  N     0  -0.414   1.9321   0.1968  -0.0655
 EM7  C4    C  CR6   0   0.478   3.0096  -1.9196  -0.1571
 EM7  N8    N  NH2   0  -0.831   4.0898  -2.7004  -0.1062
 EM7  N5    N  N     0  -0.413   1.8277  -2.5225  -0.3466
 EM7  C3    C  CR16  0  -0.097   0.7399  -1.7874  -0.3833
 EM7  C2    C  CR6   0   0.170   0.7593  -0.3982  -0.2270
 EM7  C7    C  CR6   0   0.101  -0.4527   0.4372  -0.2579
 EM7  C8    C  CR16  0  -0.373  -1.7104  -0.1095  -0.0205
 EM7  C6    C  CR16  0  -0.289  -0.3583   1.8065  -0.5184
 EM7  C11   C  CR16  0  -0.222  -1.4926   2.5997  -0.5466
 EM7  C10   C  CR16  0  -0.297  -2.7435   2.0488  -0.3175
 EM7  C9    C  CR6   0   0.088  -2.8524   0.6868  -0.0508
 EM7  C1    C  CR5   0   0.505  -4.1452   0.0647   0.2038
 EM7  N2    N  N     0  -0.345  -4.3883  -1.2235   0.3081
 EM7  N3    N  N     0  -0.138  -5.6923  -1.3451   0.5382
 EM7  N4    N  N     0  -0.071  -6.2610  -0.2056   0.5798
 EM7  N1    N  NR15  0  -0.507  -5.3131   0.6911   0.3738
 EM7  H131  H  HCH3  0   0.240   5.8562   2.2400   1.3594
 EM7  H132  H  HCH3  0   0.240   6.0149   2.3831  -0.3952
 EM7  H133  H  HCH3  0   0.253   4.9461   3.4754   0.4879
 EM7  H7    H  HNH1  0   0.411   3.2565   1.9576   0.2172
 EM7  H81N  H  HNH2  0   0.417   5.0027  -2.2963   0.0184
 EM7  H82N  H  HNH2  0   0.399   3.9831  -3.6957  -0.1970
 EM7  H3    H  HCR6  0   0.275  -0.1878  -2.3195  -0.5616
 EM7  H8    H  HCR6  0   0.263  -1.8193  -1.1610   0.2090
 EM7  H6    H  HCR6  0   0.266   0.6091   2.2507  -0.7097
 EM7  H11   H  HCR6  0   0.272  -1.4035   3.6576  -0.7530
 EM7  H10   H  HCR6  0   0.260  -3.6160   2.6877  -0.3574
 EM7  H1    H  HNR5  0   0.451  -5.5369   1.6765   0.3763

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
 EM7  C13  N7    single    1.442  0.020  1.442
 EM7  N7   C12   single    1.333  0.020  1.333
 EM7  C12  O1    double    1.231  0.020  1.231
 EM7  C12  C5    single    1.493  0.020  1.493
 EM7  C5   N6    aromatic  1.316  0.020  1.316
 EM7  C5   C4    aromatic  1.423  0.020  1.423
 EM7  N6   C2    aromatic  1.325  0.020  1.325
 EM7  C4   N8    single    1.334  0.020  1.334
 EM7  C4   N5    aromatic  1.340  0.020  1.340
 EM7  N5   C3    aromatic  1.313  0.020  1.313
 EM7  C3   C2    aromatic  1.398  0.020  1.398
 EM7  C2   C7    single    1.472  0.020  1.472
 EM7  C7   C8    aromatic  1.392  0.020  1.392
 EM7  C7   C6    aromatic  1.397  0.020  1.397
 EM7  C8   C9    aromatic  1.393  0.020  1.393
 EM7  C6   C11   aromatic  1.384  0.020  1.384
 EM7  C11  C10   aromatic  1.386  0.020  1.386
 EM7  C10  C9    aromatic  1.392  0.020  1.392
 EM7  C9   C1    single    1.457  0.020  1.457
 EM7  C1   N2    aromatic  1.315  0.020  1.315
 EM7  C1   N1    aromatic  1.336  0.020  1.336
 EM7  N2   N3    aromatic  1.330  0.020  1.330
 EM7  N3   N4    aromatic  1.274  0.020  1.274
 EM7  N4   N1    aromatic  1.321  0.020  1.321
 EM7  C13  H131  single    0.970  0.020  1.090
 EM7  C13  H132  single    0.970  0.020  1.090
 EM7  C13  H133  single    0.970  0.020  1.090
 EM7  N7   H7    single    0.860  0.020  1.020
 EM7  N8   H81N  single    0.860  0.020  1.020
 EM7  N8   H82N  single    0.860  0.020  1.020
 EM7  C3   H3    single    0.930  0.020  1.080
 EM7  C8   H8    single    0.930  0.020  1.080
 EM7  C6   H6    single    0.930  0.020  1.080
 EM7  C11  H11   single    0.930  0.020  1.080
 EM7  C10  H10   single    0.930  0.020  1.080
 EM7  N1   H1    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
 EM7  H133  C13  H132  108.41  3.000
 EM7  H133  C13  H131  108.35  3.000
 EM7  H132  C13  H131  108.30  3.000
 EM7  H133  C13  N7    108.31  3.000
 EM7  H132  C13  N7    111.65  3.000
 EM7  H131  C13  N7    111.72  3.000
 EM7  H7    N7   C12   117.84  3.000
 EM7  H7    N7   C13   119.67  3.000
 EM7  C12   N7   C13   122.49  3.000
 EM7  C5    C12  O1    121.85  3.000
 EM7  C5    C12  N7    115.19  3.000
 EM7  O1    C12  N7    122.96  3.000
 EM7  C4    C5   N6    120.33  3.000
 EM7  C4    C5   C12   122.47  3.000
 EM7  N6    C5   C12   117.20  3.000
 EM7  C2    N6   C5    120.92  3.000
 EM7  N5    C4   N8    117.14  3.000
 EM7  N5    C4   C5    118.91  3.000
 EM7  N8    C4   C5    123.95  3.000
 EM7  H82N  N8   H81N  120.35  3.000
 EM7  H82N  N8   C4    119.36  3.000
 EM7  H81N  N8   C4    120.29  3.000
 EM7  C3    N5   C4    118.85  3.000
 EM7  H3    C3   C2    121.19  3.000
 EM7  H3    C3   N5    116.01  3.000
 EM7  C2    C3   N5    122.79  3.000
 EM7  C7    C2   C3    123.37  3.000
 EM7  C7    C2   N6    118.45  3.000
 EM7  C3    C2   N6    118.17  3.000
 EM7  C6    C7   C8    118.54  3.000
 EM7  C6    C7   C2    120.30  3.000
 EM7  C8    C7   C2    121.16  3.000
 EM7  H8    C8   C9    118.55  3.000
 EM7  H8    C8   C7    120.60  3.000
 EM7  C9    C8   C7    120.85  3.000
 EM7  H6    C6   C11   119.60  3.000
 EM7  H6    C6   C7    119.73  3.000
 EM7  C11   C6   C7    120.67  3.000
 EM7  H11   C11  C10   119.65  3.000
 EM7  H11   C11  C6    119.79  3.000
 EM7  C10   C11  C6    120.56  3.000
 EM7  H10   C10  C9    121.44  3.000
 EM7  H10   C10  C11   119.15  3.000
 EM7  C9    C10  C11   119.41  3.000
 EM7  C1    C9   C10   121.37  3.000
 EM7  C1    C9   C8    118.66  3.000
 EM7  C10   C9   C8    119.97  3.000
 EM7  N1    C1   N2    106.71  3.000
 EM7  N1    C1   C9    126.70  3.000
 EM7  N2    C1   C9    126.59  3.000
 EM7  N3    N2   C1    106.54  3.000
 EM7  N4    N3   N2    111.19  3.000
 EM7  N1    N4   N3    106.37  3.000
 EM7  H1    N1   N4    120.17  3.000
 EM7  H1    N1   C1    130.62  3.000
 EM7  N4    N1   C1    109.20  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
 EM7  CONST_01  C3    C2   N6   C5     0.00   0.0  0
 EM7  CONST_02  C7    C2   N6   C5   180.00   0.0  0
 EM7  CONST_03  C3    N5   C4   C5     0.00   0.0  0
 EM7  CONST_04  N5    C4   C5   N6     0.00   0.0  0
 EM7  CONST_05  N5    C3   C2   N6     0.00   0.0  0
 EM7  CONST_08  C2    N6   C5   C4     0.00   0.0  0
 EM7  CONST_09  C2    C3   N5   C4     0.00   0.0  0
 EM7  CONST_10  C7    C2   C3   N5   180.00   0.0  0
 EM7  CONST_13  C9    C8   C7   C2   180.00   0.0  0
 EM7  CONST_14  C11   C6   C7   C2   180.00   0.0  0
 EM7  CONST_15  C10   C9   C8   C7     0.00   0.0  0
 EM7  CONST_16  C1    C9   C8   C7   180.00   0.0  0
 EM7  CONST_17  C10   C11  C6   C7     0.00   0.0  0
 EM7  CONST_18  C11   C6   C7   C8     0.00   0.0  0
 EM7  CONST_19  C11   C10  C9   C8     0.00   0.0  0
 EM7  CONST_20  N2    C1   C9   C8     0.00   0.0  0
 EM7  CONST_21  N1    C1   C9   C8   180.00   0.0  0
 EM7  CONST_22  C9    C8   C7   C6     0.00   0.0  0
 EM7  CONST_23  C9    C10  C11  C6     0.00   0.0  0
 EM7  CONST_24  C1    C9   C10  C11  180.00   0.0  0
 EM7  CONST_25  N2    C1   C9   C10  180.00   0.0  0
 EM7  CONST_26  N1    C1   C9   C10    0.00   0.0  0
 EM7  CONST_27  N3    N2   C1   C9   180.00   0.0  0
 EM7  CONST_28  N4    N1   C1   C9   180.00   0.0  0
 EM7  CONST_29  N4    N3   N2   C1     0.00   0.0  0
 EM7  CONST_30  N3    N4   N1   C1     0.00   0.0  0
 EM7  CONST_31  N4    N1   C1   N2     0.00   0.0  0
 EM7  CONST_32  N1    N4   N3   N2     0.00   0.0  0
 EM7  CONST_33  N1    C1   N2   N3     0.00   0.0  0
 EM7  CONST_34  C2    N6   C5   C12  180.00   0.0  0
 EM7  CONST_35  N5    C4   C5   C12  180.00   0.0  0
 EM7  CONST_36  N8    C4   C5   N6   180.00   0.0  0
 EM7  CONST_37  C3    N5   C4   N8   180.00   0.0  0
 EM7  CONST_38  H3    C3   C2   N6   180.00   0.0  0
 EM7  CONST_39  H8    C8   C7   C2     0.00   0.0  0
 EM7  CONST_40  H6    C6   C7   C2     0.00   0.0  0
 EM7  CONST_41  H11   C11  C6   C7   180.00   0.0  0
 EM7  CONST_42  H10   C10  C9   C8   180.00   0.0  0
 EM7  CONST_43  H1    N1   C1   C9     0.00   0.0  0
 EM7  CONST_44  H81N  N8   C4   C5     0.00   0.0  0
 EM7  CONST_45  H82N  N8   C4   C5   180.00   0.0  0
 EM7  CONST_46  C5    C12  N7   C13  180.00   0.0  0
 EM7  CONST_47  H7    N7   C12  C5     0.00   0.0  0
 EM7  CONST_48  O1    C12  N7   C13    0.00   0.0  0
 EM7  Var_01    N6    C5   C12  N7     0.04  30.0  2
 EM7  Var_02    H131  C13  N7   C12  -61.30  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
 EM7  plan-1  C9    0.020
 EM7  plan-1  C1    0.020
 EM7  plan-1  N2    0.020
 EM7  plan-1  N3    0.020
 EM7  plan-1  N4    0.020
 EM7  plan-1  N1    0.020
 EM7  plan-1  H1    0.020
 EM7  plan-2  C12   0.020
 EM7  plan-2  C5    0.020
 EM7  plan-2  N6    0.020
 EM7  plan-2  C4    0.020
 EM7  plan-2  N8    0.020
 EM7  plan-2  N5    0.020
 EM7  plan-2  C3    0.020
 EM7  plan-2  C2    0.020
 EM7  plan-2  C7    0.020
 EM7  plan-2  H3    0.020
 EM7  plan-3  C2    0.020
 EM7  plan-3  C7    0.020
 EM7  plan-3  C8    0.020
 EM7  plan-3  C6    0.020
 EM7  plan-3  C11   0.020
 EM7  plan-3  C10   0.020
 EM7  plan-3  C9    0.020
 EM7  plan-3  C1    0.020
 EM7  plan-3  H8    0.020
 EM7  plan-3  H6    0.020
 EM7  plan-3  H11   0.020
 EM7  plan-3  H10   0.020
 EM7  plan-4  C13   0.020
 EM7  plan-4  N7    0.020
 EM7  plan-4  C12   0.020
 EM7  plan-4  O1    0.020
 EM7  plan-4  C5    0.020
 EM7  plan-4  H7    0.020
 EM7  plan-5  C4    0.020
 EM7  plan-5  N8    0.020
 EM7  plan-5  H81N  0.020
 EM7  plan-5  H82N  0.020

