# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 07:36:57 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 5-chloro-N-[(2,4-dimethyl-1,3-thiazol-5-yl)methyl]pyrazolo[1,5-a]pyrimidin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(CNc2cc(Cl)nc3ccnn23)c(C)n1
#
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
 5AV  5AV  5-chloro-N-[(2,4-dimethyl-1,3-thiazol-5-yl)methyl]pyrazolo[1,5-a]pyrimidin-7-amine  ligand  31  19  .  2021-08-04  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5AV
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
 5AV  C2   C   CR6   0   0.726   1.2435   0.0708  -0.0295
 5AV  C3   C   CR56  0   0.586   3.3072   1.2449   0.3759
 5AV  N4   N   N     0  -0.451   3.9942   0.1138   0.6077
 5AV  C7   C   CR15  0  -0.571   3.6611   2.5833   0.3724
 5AV  C9   C   CH2   0  -0.351  -0.9208  -0.9606  -0.5158
 5AV  C10  C   CR5   0  -0.295  -2.3469  -0.5459  -0.4191
 5AV  C11  C   CR5   0   0.065  -4.5369   0.2328   0.3041
 5AV  C13  C   CR5   0   0.329  -3.2970  -0.4674  -1.3920
 5AV  C15  C   CH3   0  -0.726  -5.7177   0.7394   1.0541
 5AV  C    C   CR6   0   0.152   3.3085  -0.9834   0.5094
 5AV  N    N   N     0  -0.439   1.9625   1.2253   0.0653
 5AV  S    S   S2    0   0.218  -3.0222  -0.0411   1.0892
 5AV  CL   CL  CL    0  -0.101   4.1766  -2.4574   0.7948
 5AV  C1   C   CR16  0  -0.431   1.9512  -1.1006   0.1931
 5AV  N5   N   N     0  -0.323   1.4505   2.4443  -0.1314
 5AV  C6   C   CR15  0  -0.001   2.4780   3.2574   0.0540
 5AV  N8   N   NH1   0  -0.666  -0.0502   0.1819  -0.3123
 5AV  N12  N   N     0  -0.396  -4.5247  -0.0321  -0.9609
 5AV  C14  C   CH3   0  -0.731  -3.1293  -0.8018  -2.8355
 5AV  H1   H   HCR5  0   0.274   4.6335   2.9992   0.5729
 5AV  H2   H   HCH2  0   0.284  -0.6971  -1.7145   0.2417
 5AV  H3   H   HCH2  0   0.280  -0.7343  -1.4231  -1.4881
 5AV  H4   H   HCH3  0   0.266  -5.9599   0.0942   1.8986
 5AV  H5   H   HCH3  0   0.267  -5.5336   1.7392   1.4485
 5AV  H6   H   HCH3  0   0.266  -6.5793   0.7819   0.3917
 5AV  H7   H   HCR6  0   0.311   1.4751  -2.0646   0.1143
 5AV  H8   H   HCR5  0   0.278   2.3360   4.3226  -0.0473
 5AV  H9   H   HNH1  0   0.422  -0.3900   1.0968  -0.5734
 5AV  H10  H   HCH3  0   0.255  -3.7784  -1.6320  -3.1173
 5AV  H11  H   HCH3  0   0.255  -3.4041   0.0506  -3.4577
 5AV  H12  H   HCH3  0   0.248  -2.1067  -1.0782  -3.0807

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
 5AV  C6   C7   aromatic  1.398  0.020  1.398
 5AV  C6   N5   aromatic  1.323  0.020  1.323
 5AV  C7   C3   aromatic  1.384  0.020  1.384
 5AV  N5   N    aromatic  1.337  0.020  1.337
 5AV  C3   N    aromatic  1.380  0.020  1.380
 5AV  C3   N4   aromatic  1.344  0.020  1.344
 5AV  N    C2   aromatic  1.363  0.020  1.363
 5AV  N4   C    aromatic  1.298  0.020  1.298
 5AV  N8   C2   single    1.329  0.020  1.329
 5AV  N8   C9   single    1.451  0.020  1.451
 5AV  C2   C1   aromatic  1.387  0.020  1.387
 5AV  S    C10  aromatic  1.728  0.020  1.728
 5AV  S    C11  aromatic  1.728  0.020  1.728
 5AV  C    C1   aromatic  1.399  0.020  1.399
 5AV  C    CL   single    1.734  0.020  1.734
 5AV  C9   C10  single    1.488  0.020  1.488
 5AV  C15  C11  single    1.488  0.020  1.488
 5AV  C10  C13  aromatic  1.362  0.020  1.362
 5AV  C11  N12  aromatic  1.292  0.020  1.292
 5AV  C13  N12  aromatic  1.372  0.020  1.372
 5AV  C13  C14  single    1.491  0.020  1.491
 5AV  C7   H1   single    0.930  0.020  1.080
 5AV  C9   H2   single    0.970  0.020  1.090
 5AV  C9   H3   single    0.970  0.020  1.090
 5AV  C15  H4   single    0.970  0.020  1.090
 5AV  C15  H5   single    0.970  0.020  1.090
 5AV  C15  H6   single    0.970  0.020  1.090
 5AV  C1   H7   single    0.930  0.020  1.080
 5AV  C6   H8   single    0.930  0.020  1.080
 5AV  N8   H9   single    0.860  0.020  1.020
 5AV  C14  H10  single    0.970  0.020  1.090
 5AV  C14  H11  single    0.970  0.020  1.090
 5AV  C14  H12  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
 5AV  N8   C2   C1   126.99  3.000
 5AV  C1   C2   N    115.79  3.000
 5AV  N8   C2   N    117.22  3.000
 5AV  N    C3   C7   105.20  3.000
 5AV  N    C3   N4   121.67  3.000
 5AV  C7   C3   N4   133.13  3.000
 5AV  C    N4   C3   115.38  3.000
 5AV  H1   C7   C6   128.35  3.000
 5AV  H1   C7   C3   127.15  3.000
 5AV  C6   C7   C3   104.50  3.000
 5AV  H3   C9   H2   106.87  3.000
 5AV  H3   C9   N8   110.83  3.000
 5AV  H2   C9   N8   108.87  3.000
 5AV  H3   C9   C10  109.84  3.000
 5AV  H2   C9   C10  110.10  3.000
 5AV  N8   C9   C10  110.27  3.000
 5AV  S    C10  C13  109.51  3.000
 5AV  C13  C10  C9   129.64  3.000
 5AV  S    C10  C9   120.84  3.000
 5AV  N12  C11  S    113.83  3.000
 5AV  N12  C11  C15  124.79  3.000
 5AV  S    C11  C15  121.38  3.000
 5AV  C14  C13  N12  118.42  3.000
 5AV  C14  C13  C10  126.87  3.000
 5AV  N12  C13  C10  114.71  3.000
 5AV  H6   C15  H5   108.56  3.000
 5AV  H6   C15  H4   108.60  3.000
 5AV  H5   C15  H4   107.45  3.000
 5AV  H6   C15  C11  109.57  3.000
 5AV  H5   C15  C11  111.14  3.000
 5AV  H4   C15  C11  111.43  3.000
 5AV  C1   C    CL   116.86  3.000
 5AV  CL   C    N4   116.21  3.000
 5AV  C1   C    N4   126.93  3.000
 5AV  N5   N    C3   113.16  3.000
 5AV  C3   N    C2   122.78  3.000
 5AV  N5   N    C2   124.06  3.000
 5AV  C11  S    C10   89.56  3.000
 5AV  H7   C1   C    121.34  3.000
 5AV  H7   C1   C2   121.22  3.000
 5AV  C    C1   C2   117.44  3.000
 5AV  C6   N5   N    104.03  3.000
 5AV  H8   C6   N5   119.41  3.000
 5AV  H8   C6   C7   127.47  3.000
 5AV  N5   C6   C7   113.12  3.000
 5AV  H9   N8   C9   118.37  3.000
 5AV  H9   N8   C2   117.26  3.000
 5AV  C9   N8   C2   123.25  3.000
 5AV  C13  N12  C11  112.39  3.000
 5AV  H12  C14  H11  107.89  3.000
 5AV  H12  C14  H10  107.93  3.000
 5AV  H11  C14  H10  107.31  3.000
 5AV  H12  C14  C13  112.40  3.000
 5AV  H11  C14  C13  110.41  3.000
 5AV  H10  C14  C13  110.72  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
 5AV  CONST_01  C6   N5   N    C2   180.00   0.0  0
 5AV  CONST_02  C7   C3   N    C2   180.00   0.0  0
 5AV  CONST_03  N4   C3   N    C2     0.00   0.0  0
 5AV  CONST_04  N4   C    C1   C2     0.00   0.0  0
 5AV  CONST_05  N5   C6   C7   C3     0.00   0.0  0
 5AV  CONST_06  C6   N5   N    C3     0.00   0.0  0
 5AV  CONST_07  C1   C2   N    C3     0.00   0.0  0
 5AV  CONST_08  C1   C    N4   C3     0.00   0.0  0
 5AV  CONST_09  C6   C7   C3   N4   180.00   0.0  0
 5AV  CONST_10  N5   N    C3   N4   180.00   0.0  0
 5AV  CONST_11  N    N5   C6   C7     0.00   0.0  0
 5AV  CONST_12  N5   N    C3   C7     0.00   0.0  0
 5AV  CONST_13  C    N4   C3   C7   180.00   0.0  0
 5AV  CONST_14  N12  C11  S    C10    0.00   0.0  0
 5AV  CONST_15  C11  N12  C13  C10    0.00   0.0  0
 5AV  CONST_16  C13  C10  S    C11    0.00   0.0  0
 5AV  CONST_17  S    C11  N12  C13    0.00   0.0  0
 5AV  CONST_18  N    C3   N4   C      0.00   0.0  0
 5AV  CONST_19  N    C2   C1   C      0.00   0.0  0
 5AV  CONST_20  C6   C7   C3   N      0.00   0.0  0
 5AV  CONST_21  N12  C13  C10  S      0.00   0.0  0
 5AV  CONST_22  N5   N    C2   C1   180.00   0.0  0
 5AV  CONST_23  CL   C    C1   C2   180.00   0.0  0
 5AV  CONST_24  N8   C2   N    C3   180.00   0.0  0
 5AV  CONST_25  CL   C    N4   C3   180.00   0.0  0
 5AV  CONST_26  C11  S    C10  C9   180.00   0.0  0
 5AV  CONST_27  N12  C13  C10  C9   180.00   0.0  0
 5AV  CONST_28  C15  C11  S    C10  180.00   0.0  0
 5AV  CONST_29  C14  C13  N12  C11  180.00   0.0  0
 5AV  CONST_30  C15  C11  N12  C13  180.00   0.0  0
 5AV  CONST_31  N8   C2   C1   C    180.00   0.0  0
 5AV  CONST_32  C14  C13  C10  S    180.00   0.0  0
 5AV  CONST_33  N8   C2   N    N5     0.00   0.0  0
 5AV  CONST_34  H8   C6   C7   C3   180.00   0.0  0
 5AV  CONST_35  H1   C7   C3   N4     0.00   0.0  0
 5AV  CONST_36  H7   C1   C    N4   180.00   0.0  0
 5AV  CONST_37  N    C2   N8   C9   180.00   0.0  0
 5AV  CONST_38  C1   C2   N8   C9     0.00   0.0  0
 5AV  CONST_39  H9   N8   C2   N      0.00   0.0  0
 5AV  Var_01    C10  C9   N8   C2   163.53  30.0  3
 5AV  Var_02    N8   C9   C10  C13  110.45  30.0  2
 5AV  Var_03    H10  C14  C13  C10  117.32  30.0  2
 5AV  Var_04    H4   C15  C11  S    -56.27  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
 5AV  plan-1  C9   0.020
 5AV  plan-1  C10  0.020
 5AV  plan-1  C11  0.020
 5AV  plan-1  C13  0.020
 5AV  plan-1  C15  0.020
 5AV  plan-1  S    0.020
 5AV  plan-1  N12  0.020
 5AV  plan-1  C14  0.020
 5AV  plan-2  C2   0.020
 5AV  plan-2  C3   0.020
 5AV  plan-2  N4   0.020
 5AV  plan-2  C7   0.020
 5AV  plan-2  C    0.020
 5AV  plan-2  N    0.020
 5AV  plan-2  CL   0.020
 5AV  plan-2  C1   0.020
 5AV  plan-2  N5   0.020
 5AV  plan-2  C6   0.020
 5AV  plan-2  N8   0.020
 5AV  plan-2  H1   0.020
 5AV  plan-2  H7   0.020
 5AV  plan-2  H8   0.020
 5AV  plan-3  C2   0.020
 5AV  plan-3  C9   0.020
 5AV  plan-3  N8   0.020
 5AV  plan-3  H9   0.020

