# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 20:16:38 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 5-chloranyl-~{N}-(4-chlorophenyl)-2-(3,5-dimethylpyrazol-1-yl)pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)n(n1)c2ncc(Cl)c(Nc3ccc(Cl)cc3)n2
#
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
 RC0  RC0  5-chloranyl-~{N}-(4-chlorophenyl)-2-(3,5-dimethylpyrazol-1-yl)pyrimidin-4-amine  ligand  35  22  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RC0
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
 RC0  N1   N   NR5   0  -0.451  -2.4428  -1.3858  -0.0678
 RC0  N3   N   N     0  -0.489  -0.8501   0.2699   0.0074
 RC0  C5   C   CR6   0   0.656  -0.4972   1.5438   0.0228
 RC0  C6   C   CR5   0   0.430  -3.6677  -2.0003   0.0367
 RC0  C7   C   CR15  0  -0.573  -3.4072  -3.3392  -0.0449
 RC0  C10  C   CR5   0   0.310  -2.0050  -3.4564  -0.1982
 RC0  C13  C   CR6   0   0.373   1.9489   1.0783   0.0923
 RC0  C15  C   CR6   0  -0.058   4.3588  -0.3188   0.1568
 RC0  C17  C   CH3   0  -0.708  -4.9878  -1.3421   0.2226
 RC0  C20  C   CR16  0  -0.203   3.1623  -1.0037   0.0430
 RC0  C21  C   CR16  0  -0.200   4.3674   1.0652   0.2379
 RC0  C22  C   CH3   0  -0.733  -1.2061  -4.7034  -0.3417
 RC0  C2   C   CR6   0   0.636  -2.1337  -0.0253  -0.0425
 RC0  N4   N   N     0  -0.290  -1.4394  -2.2765  -0.2076
 RC0  N8   N   N     0  -0.461  -3.1401   0.8225  -0.0748
 RC0  C9   C   CR6   0  -0.239  -1.5030   2.5374   0.0012
 RC0  C12  C   CR16  0   0.027  -2.8050   2.1112  -0.0454
 RC0  CL4  CL  CL    0  -0.097  -1.1161   4.2149   0.0328
 RC0  CL6  CL  CL    0  -0.134   5.8553  -1.1929   0.1989
 RC0  C18  C   CR16  0  -0.364   3.1688   1.7520   0.2055
 RC0  C19  C   CR16  0  -0.324   1.9568  -0.3165   0.0096
 RC0  H1   H   HCR5  0   0.268  -4.1334  -4.1346   0.0035
 RC0  H2   H   HCH3  0   0.257  -5.2599  -0.7182  -0.6267
 RC0  H3   H   HCH3  0   0.252  -5.7430  -2.1179   0.3356
 RC0  H4   H   HCH3  0   0.255  -5.0106  -0.7098   1.1088
 RC0  H5   H   HCR6  0   0.279   3.1536  -2.0834  -0.0212
 RC0  H6   H   HCR6  0   0.284   5.2967   1.6104   0.3292
 RC0  H7   H   HCH3  0   0.250  -1.3439  -5.3581   0.5195
 RC0  H8   H   HCH3  0   0.250  -1.5148  -5.2651  -1.2242
 RC0  H9   H   HCH3  0   0.248  -0.1450  -4.4786  -0.4334
 RC0  H10  H   HNH1  0   0.415   0.9965   2.8738   0.0903
 RC0  H11  H   HCR6  0   0.299  -3.6139   2.8321  -0.0653
 RC0  H12  H   HCR6  0   0.282   3.1872   2.8337   0.2670
 RC0  H13  H   HCR6  0   0.327   1.0387  -0.8752  -0.0802
 RC0  N11  N   NH1   0  -0.773   0.8078   1.8824   0.0635

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
 RC0  C22  C10  single    1.488  0.020  1.488
 RC0  C10  N4   aromatic  1.309  0.020  1.309
 RC0  C10  C7   aromatic  1.415  0.020  1.415
 RC0  N4   N1   aromatic  1.349  0.020  1.349
 RC0  C7   C6   aromatic  1.366  0.020  1.366
 RC0  N8   C12  aromatic  1.332  0.020  1.332
 RC0  N8   C2   aromatic  1.316  0.020  1.316
 RC0  N1   C6   aromatic  1.374  0.020  1.374
 RC0  N1   C2   single    1.395  0.020  1.395
 RC0  C6   C17  single    1.487  0.020  1.487
 RC0  C12  C9   aromatic  1.371  0.020  1.371
 RC0  C2   N3   aromatic  1.318  0.020  1.318
 RC0  N3   C5   aromatic  1.322  0.020  1.322
 RC0  C9   C5   aromatic  1.414  0.020  1.414
 RC0  C9   CL4  single    1.722  0.020  1.722
 RC0  C5   N11  single    1.349  0.020  1.349
 RC0  N11  C13  single    1.396  0.020  1.396
 RC0  C18  C13  aromatic  1.398  0.020  1.398
 RC0  C18  C21  aromatic  1.382  0.020  1.382
 RC0  C13  C19  aromatic  1.397  0.020  1.397
 RC0  C21  C15  aromatic  1.386  0.020  1.386
 RC0  C19  C20  aromatic  1.388  0.020  1.388
 RC0  C15  C20  aromatic  1.383  0.020  1.383
 RC0  C15  CL6  single    1.734  0.020  1.734
 RC0  C7   H1   single    0.930  0.020  1.080
 RC0  C17  H2   single    0.970  0.020  1.090
 RC0  C17  H3   single    0.970  0.020  1.090
 RC0  C17  H4   single    0.970  0.020  1.090
 RC0  C20  H5   single    0.930  0.020  1.080
 RC0  C21  H6   single    0.930  0.020  1.080
 RC0  C22  H7   single    0.970  0.020  1.090
 RC0  C22  H8   single    0.970  0.020  1.090
 RC0  C22  H9   single    0.970  0.020  1.090
 RC0  N11  H10  single    0.860  0.020  1.020
 RC0  C12  H11  single    0.930  0.020  1.080
 RC0  C18  H12  single    0.930  0.020  1.080
 RC0  C19  H13  single    0.930  0.020  1.080

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
 RC0  N4   N1   C2   118.74  3.000
 RC0  C2   N1   C6   129.19  3.000
 RC0  N4   N1   C6   112.06  3.000
 RC0  C2   N3   C5   118.44  3.000
 RC0  N11  C5   C9   120.81  3.000
 RC0  N11  C5   N3   120.04  3.000
 RC0  C9   C5   N3   119.15  3.000
 RC0  C17  C6   C7   127.63  3.000
 RC0  C17  C6   N1   127.08  3.000
 RC0  C7   C6   N1   105.28  3.000
 RC0  H1   C7   C10  127.66  3.000
 RC0  H1   C7   C6   126.28  3.000
 RC0  C10  C7   C6   106.05  3.000
 RC0  N4   C10  C22  121.53  3.000
 RC0  N4   C10  C7   110.75  3.000
 RC0  C22  C10  C7   127.72  3.000
 RC0  C19  C13  C18  118.74  3.000
 RC0  C19  C13  N11  125.33  3.000
 RC0  C18  C13  N11  115.93  3.000
 RC0  CL6  C15  C21  119.78  3.000
 RC0  CL6  C15  C20  119.94  3.000
 RC0  C21  C15  C20  120.29  3.000
 RC0  H4   C17  H3   108.35  3.000
 RC0  H4   C17  H2   107.27  3.000
 RC0  H3   C17  H2   108.43  3.000
 RC0  H4   C17  C6   112.17  3.000
 RC0  H3   C17  C6   108.27  3.000
 RC0  H2   C17  C6   112.23  3.000
 RC0  H5   C20  C19  119.06  3.000
 RC0  H5   C20  C15  120.40  3.000
 RC0  C19  C20  C15  120.54  3.000
 RC0  H6   C21  C18  119.79  3.000
 RC0  H6   C21  C15  120.91  3.000
 RC0  C18  C21  C15  119.31  3.000
 RC0  H9   C22  H8   108.30  3.000
 RC0  H9   C22  H7   108.28  3.000
 RC0  H8   C22  H7   107.10  3.000
 RC0  H9   C22  C10  111.01  3.000
 RC0  H8   C22  C10  110.96  3.000
 RC0  H7   C22  C10  111.05  3.000
 RC0  N8   C2   N3   126.96  3.000
 RC0  N3   C2   N1   115.77  3.000
 RC0  N8   C2   N1   117.27  3.000
 RC0  C10  N4   N1   105.85  3.000
 RC0  C12  N8   C2   115.49  3.000
 RC0  CL4  C9   C12  121.13  3.000
 RC0  CL4  C9   C5   121.63  3.000
 RC0  C12  C9   C5   117.24  3.000
 RC0  H11  C12  C9   120.19  3.000
 RC0  H11  C12  N8   117.10  3.000
 RC0  C9   C12  N8   122.72  3.000
 RC0  H12  C18  C21  118.70  3.000
 RC0  H12  C18  C13  120.02  3.000
 RC0  C21  C18  C13  121.28  3.000
 RC0  H13  C19  C20  119.00  3.000
 RC0  H13  C19  C13  121.15  3.000
 RC0  C20  C19  C13  119.85  3.000
 RC0  H10  N11  C13  114.35  3.000
 RC0  H10  N11  C5   115.35  3.000
 RC0  C13  N11  C5   130.30  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
 RC0  CONST_01  C7   C10  N4   N1      0.00   0.0  0
 RC0  CONST_02  C10  C7   C6   N1      0.00   0.0  0
 RC0  CONST_03  C12  N8   C2   N1    180.00   0.0  0
 RC0  CONST_04  C5   N3   C2   N1    180.00   0.0  0
 RC0  CONST_05  C12  N8   C2   N3      0.00   0.0  0
 RC0  CONST_06  N4   N1   C2   N3      0.00   0.0  0
 RC0  CONST_07  C6   N1   C2   N3    180.00   0.0  0
 RC0  CONST_08  C12  C9   C5   N3      0.00   0.0  0
 RC0  CONST_09  N8   C2   N3   C5      0.00   0.0  0
 RC0  CONST_10  N8   C12  C9   C5      0.00   0.0  0
 RC0  CONST_11  N4   C10  C7   C6      0.00   0.0  0
 RC0  CONST_12  C10  N4   N1   C6      0.00   0.0  0
 RC0  CONST_13  N8   C2   N1   C6      0.00   0.0  0
 RC0  CONST_14  N4   N1   C6   C7      0.00   0.0  0
 RC0  CONST_15  C2   N1   C6   C7    180.00   0.0  0
 RC0  CONST_16  C2   N1   N4   C10   180.00   0.0  0
 RC0  CONST_17  C15  C21  C18  C13     0.00   0.0  0
 RC0  CONST_18  C15  C20  C19  C13     0.00   0.0  0
 RC0  CONST_19  C18  C13  C19  C20     0.00   0.0  0
 RC0  CONST_20  C18  C21  C15  C20     0.00   0.0  0
 RC0  CONST_21  C19  C13  C18  C21     0.00   0.0  0
 RC0  CONST_22  C19  C20  C15  C21     0.00   0.0  0
 RC0  CONST_23  C9   C12  N8   C2      0.00   0.0  0
 RC0  CONST_24  C9   C5   N3   C2      0.00   0.0  0
 RC0  CONST_25  N8   C2   N1   N4    180.00   0.0  0
 RC0  CONST_26  C22  C10  N4   N1    180.00   0.0  0
 RC0  CONST_27  CL4  C9   C5   N3    180.00   0.0  0
 RC0  CONST_28  C22  C10  C7   C6    180.00   0.0  0
 RC0  CONST_29  C17  C6   C7   C10   180.00   0.0  0
 RC0  CONST_30  N4   N1   C6   C17   180.00   0.0  0
 RC0  CONST_31  C2   N1   C6   C17     0.00   0.0  0
 RC0  CONST_32  N11  C13  C19  C20   180.00   0.0  0
 RC0  CONST_33  N11  C13  C18  C21   180.00   0.0  0
 RC0  CONST_34  N11  C5   N3   C2    180.00   0.0  0
 RC0  CONST_35  CL4  C9   C12  N8    180.00   0.0  0
 RC0  CONST_36  C12  C9   C5   N11   180.00   0.0  0
 RC0  CONST_37  C18  C21  C15  CL6   180.00   0.0  0
 RC0  CONST_38  C19  C20  C15  CL6   180.00   0.0  0
 RC0  CONST_39  H1   C7   C6   N1    180.00   0.0  0
 RC0  CONST_40  H11  C12  C9   C5    180.00   0.0  0
 RC0  CONST_41  H6   C21  C18  C13   180.00   0.0  0
 RC0  CONST_42  H5   C20  C19  C13   180.00   0.0  0
 RC0  CONST_43  H12  C18  C21  C15   180.00   0.0  0
 RC0  CONST_44  H13  C19  C20  C15   180.00   0.0  0
 RC0  Var_01    C13  N11  C5   N3      0.15  30.0  2
 RC0  Var_02    C18  C13  N11  C5   -176.67  30.0  2
 RC0  Var_03    H2   C17  C6   N1     64.25  30.0  2
 RC0  Var_04    H7   C22  C10  C7    -58.96  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
 RC0  plan-1  N1   0.020
 RC0  plan-1  C6   0.020
 RC0  plan-1  C7   0.020
 RC0  plan-1  C10  0.020
 RC0  plan-1  C17  0.020
 RC0  plan-1  C22  0.020
 RC0  plan-1  C2   0.020
 RC0  plan-1  N4   0.020
 RC0  plan-1  H1   0.020
 RC0  plan-2  N1   0.020
 RC0  plan-2  N3   0.020
 RC0  plan-2  C5   0.020
 RC0  plan-2  C2   0.020
 RC0  plan-2  N8   0.020
 RC0  plan-2  C9   0.020
 RC0  plan-2  C12  0.020
 RC0  plan-2  CL4  0.020
 RC0  plan-2  H11  0.020
 RC0  plan-2  N11  0.020
 RC0  plan-3  C13  0.020
 RC0  plan-3  C15  0.020
 RC0  plan-3  C20  0.020
 RC0  plan-3  C21  0.020
 RC0  plan-3  CL6  0.020
 RC0  plan-3  C18  0.020
 RC0  plan-3  C19  0.020
 RC0  plan-3  H5   0.020
 RC0  plan-3  H6   0.020
 RC0  plan-3  H12  0.020
 RC0  plan-3  H13  0.020
 RC0  plan-3  N11  0.020

