# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 10:22:40 2022
#   Inital geometry file: a 97 line input string
#   Ligand name: 4-chloranyl-6-[1,5-dimethyl-4-(phenylmethyl)pyrazol-3-yl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(c(Cc2ccccc2)c1C)c3cc(Cl)nc(N)n3
#
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
 1S2  1S2  "4-chloranyl-6-[1,5-dimethyl-4-(phenylmethyl)pyrazol-3-yl]pyrimidin-2-amine"  ligand  38  22  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1S2
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
 1S2  C02  C   CR6   0   0.561  -26.0182   4.1355   0.5231
 1S2  C04  C   CR6   0   0.243  -28.2668   4.4306   0.7312
 1S2  C05  C   CR16  0  -0.324  -28.0680   5.7754   1.0599
 1S2  C06  C   CR6   0   0.196  -26.7496   6.1753   1.0872
 1S2  C08  C   CR5   0   0.409  -31.4297   2.6462   0.4372
 1S2  C09  C   CR5   0  -0.176  -30.0611   2.5953   0.2610
 1S2  C10  C   CR5   0   0.235  -29.6158   3.8716   0.6760
 1S2  C12  C   CR16  0  -0.333  -29.3662  -0.9907   0.4798
 1S2  C13  C   CR16  0  -0.238  -29.1284  -1.9956   1.4102
 1S2  C14  C   CR16  0  -0.273  -28.5830  -1.6834   2.6470
 1S2  C15  C   CR16  0  -0.238  -28.2784  -0.3600   2.9436
 1S2  C16  C   CR16  0  -0.285  -28.5179   0.6399   2.0121
 1S2  C17  C   CR6   0   0.137  -29.0633   0.3377   0.7649
 1S2  C19  C   CH3   0  -0.744  -32.4779   1.6220   0.2010
 1S2  C20  C   CH2   0  -0.612  -29.3045   1.4163  -0.2655
 1S2  N01  N   N     0  -0.448  -25.7218   5.4065   0.8311
 1S2  N03  N   N     0  -0.496  -27.2497   3.6221   0.4682
 1S2  N07  N   NR5   0  -0.303  -31.7109   3.8804   0.9114
 1S2  N11  N   N     0  -0.305  -30.6372   4.6283   1.0614
 1S2  N22  N   NH2   0  -0.824  -24.9955   3.3193   0.2414
 1S2  CL1  CL  CL    0  -0.103  -26.3853   7.8220   1.4887
 1S2  H1   H   HCR6  0   0.281  -28.8840   6.4458   1.2755
 1S2  H3   H   HCR6  0   0.250  -29.3743  -3.0217   1.1676
 1S2  H4   H   HCR6  0   0.250  -28.3985  -2.4624   3.3756
 1S2  H5   H   HCR6  0   0.250  -27.8525  -0.1052   3.9059
 1S2  H6   H   HCR6  0   0.248  -28.2785   1.6670   2.2585
 1S2  H10  H   HCH3  0   0.261  -32.9711   1.3292   1.1299
 1S2  H11  H   HCH3  0   0.260  -33.2511   1.9813  -0.4803
 1S2  H12  H   HCH3  0   0.266  -32.0412   0.7259  -0.2347
 1S2  H13  H   HCH2  0   0.259  -29.8529   0.9834  -1.1057
 1S2  H14  H   HCH2  0   0.275  -28.3471   1.7508  -0.6637
 1S2  H15  H   HNH2  0   0.404  -25.1607   2.3438   0.0671
 1S2  H16  H   HNH2  0   0.403  -24.0480   3.6407   0.3302
 1S2  C18  C   CH3   0  -0.526  -33.0180   4.3873   1.2574
 1S2  H2   H   HCR6  0   0.245  -29.7967  -1.2449  -0.4822
 1S2  H7   H   HCH3  0   0.275  -32.9217   5.4379   1.5115
 1S2  H8   H   HCH3  0   0.261  -33.7007   4.2850   0.4156
 1S2  H9   H   HCH3  0   0.261  -33.4276   3.8480   2.1106

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
 1S2  C20  C09  single    1.497  0.020  1.497
 1S2  C20  C17  single    1.511  0.020  1.511
 1S2  C19  C08  single    1.484  0.020  1.484
 1S2  C09  C08  aromatic  1.381  0.020  1.381
 1S2  C09  C10  aromatic  1.414  0.020  1.414
 1S2  C08  N07  aromatic  1.352  0.020  1.352
 1S2  N22  C02  single    1.338  0.020  1.338
 1S2  N03  C02  aromatic  1.335  0.020  1.335
 1S2  N03  C04  aromatic  1.326  0.020  1.326
 1S2  C17  C12  aromatic  1.392  0.020  1.392
 1S2  C17  C16  aromatic  1.394  0.020  1.394
 1S2  C10  C04  single    1.461  0.020  1.461
 1S2  C10  N11  aromatic  1.328  0.020  1.328
 1S2  C02  N01  aromatic  1.341  0.020  1.341
 1S2  N07  N11  aromatic  1.317  0.020  1.317
 1S2  N07  C18  single    1.444  0.020  1.444
 1S2  C04  C05  aromatic  1.399  0.020  1.399
 1S2  C12  C13  aromatic  1.390  0.020  1.390
 1S2  N01  C06  aromatic  1.309  0.020  1.309
 1S2  C05  C06  aromatic  1.378  0.020  1.378
 1S2  C06  CL1  single    1.734  0.020  1.734
 1S2  C16  C15  aromatic  1.387  0.020  1.387
 1S2  C13  C14  aromatic  1.387  0.020  1.387
 1S2  C15  C14  aromatic  1.390  0.020  1.390
 1S2  C05  H1   single    0.930  0.020  1.080
 1S2  C12  H2   single    0.930  0.020  1.080
 1S2  C13  H3   single    0.930  0.020  1.080
 1S2  C14  H4   single    0.930  0.020  1.080
 1S2  C15  H5   single    0.930  0.020  1.080
 1S2  C16  H6   single    0.930  0.020  1.080
 1S2  C18  H7   single    0.970  0.020  1.090
 1S2  C18  H8   single    0.970  0.020  1.090
 1S2  C18  H9   single    0.970  0.020  1.090
 1S2  C19  H10  single    0.970  0.020  1.090
 1S2  C19  H11  single    0.970  0.020  1.090
 1S2  C19  H12  single    0.970  0.020  1.090
 1S2  C20  H13  single    0.970  0.020  1.090
 1S2  C20  H14  single    0.970  0.020  1.090
 1S2  N22  H15  single    0.860  0.020  1.020
 1S2  N22  H16  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
 1S2  N22  C02  N03  117.49  3.000
 1S2  N03  C02  N01  125.29  3.000
 1S2  N22  C02  N01  117.22  3.000
 1S2  N03  C04  C10  117.88  3.000
 1S2  C10  C04  C05  120.53  3.000
 1S2  N03  C04  C05  121.60  3.000
 1S2  H1   C05  C06  122.67  3.000
 1S2  H1   C05  C04  122.51  3.000
 1S2  C06  C05  C04  114.82  3.000
 1S2  CL1  C06  N01  115.99  3.000
 1S2  CL1  C06  C05  118.77  3.000
 1S2  N01  C06  C05  125.24  3.000
 1S2  N07  C08  C19  122.60  3.000
 1S2  N07  C08  C09  106.54  3.000
 1S2  C19  C08  C09  130.86  3.000
 1S2  C20  C09  C10  130.93  3.000
 1S2  C10  C09  C08  103.97  3.000
 1S2  C20  C09  C08  125.10  3.000
 1S2  N11  C10  C09  110.93  3.000
 1S2  N11  C10  C04  118.75  3.000
 1S2  C09  C10  C04  130.32  3.000
 1S2  H2   C12  C17  119.47  3.000
 1S2  H2   C12  C13  119.50  3.000
 1S2  C17  C12  C13  121.04  3.000
 1S2  H3   C13  C14  120.15  3.000
 1S2  H3   C13  C12  119.76  3.000
 1S2  C14  C13  C12  120.09  3.000
 1S2  H4   C14  C15  120.28  3.000
 1S2  H4   C14  C13  120.34  3.000
 1S2  C15  C14  C13  119.38  3.000
 1S2  H5   C15  C16  119.68  3.000
 1S2  H5   C15  C14  119.99  3.000
 1S2  C16  C15  C14  120.34  3.000
 1S2  H6   C16  C17  119.70  3.000
 1S2  H6   C16  C15  119.51  3.000
 1S2  C17  C16  C15  120.79  3.000
 1S2  C20  C17  C16  121.17  3.000
 1S2  C16  C17  C12  118.37  3.000
 1S2  C20  C17  C12  120.45  3.000
 1S2  H12  C19  H11  107.79  3.000
 1S2  H12  C19  H10  107.52  3.000
 1S2  H11  C19  H10  107.43  3.000
 1S2  H12  C19  C08  110.40  3.000
 1S2  H11  C19  C08  111.87  3.000
 1S2  H10  C19  C08  111.63  3.000
 1S2  H14  C20  H13  106.36  3.000
 1S2  H14  C20  C17  109.16  3.000
 1S2  H13  C20  C17  108.76  3.000
 1S2  H14  C20  C09  109.33  3.000
 1S2  H13  C20  C09  109.20  3.000
 1S2  C17  C20  C09  113.78  3.000
 1S2  C06  N01  C02  115.35  3.000
 1S2  C04  N03  C02  117.71  3.000
 1S2  N11  N07  C18  120.75  3.000
 1S2  C18  N07  C08  126.36  3.000
 1S2  N11  N07  C08  112.88  3.000
 1S2  N07  N11  C10  105.68  3.000
 1S2  H16  N22  H15  118.76  3.000
 1S2  H16  N22  C02  120.47  3.000
 1S2  H15  N22  C02  120.20  3.000
 1S2  H9   C18  H8   108.86  3.000
 1S2  H9   C18  H7   109.22  3.000
 1S2  H8   C18  H7   109.12  3.000
 1S2  H9   C18  N07  110.75  3.000
 1S2  H8   C18  N07  110.46  3.000
 1S2  H7   C18  N07  108.40  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
 1S2  CONST_01  C10  C04  N03  C02   180.00   0.0  0
 1S2  CONST_02  C05  C04  N03  C02     0.00   0.0  0
 1S2  CONST_03  C05  C06  N01  C02     0.00   0.0  0
 1S2  CONST_04  N01  C02  N03  C04     0.00   0.0  0
 1S2  CONST_05  C08  C09  C10  C04   180.00   0.0  0
 1S2  CONST_06  N07  N11  C10  C04   180.00   0.0  0
 1S2  CONST_07  N01  C06  C05  C04     0.00   0.0  0
 1S2  CONST_08  C09  C10  C04  C05   180.00   0.0  0
 1S2  CONST_09  N11  C10  C04  C05     0.00   0.0  0
 1S2  CONST_10  N03  C02  N01  C06     0.00   0.0  0
 1S2  CONST_11  N03  C04  C05  C06     0.00   0.0  0
 1S2  CONST_12  C10  C04  C05  C06   180.00   0.0  0
 1S2  CONST_13  N11  C10  C09  C08     0.00   0.0  0
 1S2  CONST_14  C10  N11  N07  C08     0.00   0.0  0
 1S2  CONST_15  N11  N07  C08  C09     0.00   0.0  0
 1S2  CONST_16  N03  C04  C10  C09     0.00   0.0  0
 1S2  CONST_17  N07  N11  C10  C09     0.00   0.0  0
 1S2  CONST_18  N07  C08  C09  C10     0.00   0.0  0
 1S2  CONST_19  C15  C16  C17  C12     0.00   0.0  0
 1S2  CONST_20  C15  C14  C13  C12     0.00   0.0  0
 1S2  CONST_21  C16  C17  C12  C13     0.00   0.0  0
 1S2  CONST_22  C16  C15  C14  C13     0.00   0.0  0
 1S2  CONST_23  C17  C12  C13  C14     0.00   0.0  0
 1S2  CONST_24  C17  C16  C15  C14     0.00   0.0  0
 1S2  CONST_25  N11  C10  C04  N03   180.00   0.0  0
 1S2  CONST_26  CL1  C06  N01  C02   180.00   0.0  0
 1S2  CONST_27  N22  C02  N03  C04   180.00   0.0  0
 1S2  CONST_28  C20  C09  C10  C04     0.00   0.0  0
 1S2  CONST_29  CL1  C06  C05  C04   180.00   0.0  0
 1S2  CONST_30  N22  C02  N01  C06   180.00   0.0  0
 1S2  CONST_31  C18  N07  C08  C09   180.00   0.0  0
 1S2  CONST_32  C19  C08  C09  C10   180.00   0.0  0
 1S2  CONST_33  C18  N07  N11  C10   180.00   0.0  0
 1S2  CONST_34  C20  C17  C12  C13   180.00   0.0  0
 1S2  CONST_35  C20  C17  C16  C15   180.00   0.0  0
 1S2  CONST_36  N11  N07  C08  C19   180.00   0.0  0
 1S2  CONST_37  N07  C08  C09  C20   180.00   0.0  0
 1S2  CONST_38  N11  C10  C09  C20   180.00   0.0  0
 1S2  CONST_39  H1   C05  C04  C10     0.00   0.0  0
 1S2  CONST_40  H6   C16  C17  C12   180.00   0.0  0
 1S2  CONST_41  H4   C14  C13  C12   180.00   0.0  0
 1S2  CONST_42  H5   C15  C14  C13   180.00   0.0  0
 1S2  CONST_43  H2   C12  C13  C14   180.00   0.0  0
 1S2  CONST_44  H6   C16  C15  C14   180.00   0.0  0
 1S2  CONST_45  H3   C13  C14  C15   180.00   0.0  0
 1S2  CONST_46  H2   C12  C17  C16   180.00   0.0  0
 1S2  CONST_47  H4   C14  C15  C16   180.00   0.0  0
 1S2  CONST_48  H3   C13  C12  C17   180.00   0.0  0
 1S2  CONST_49  H5   C15  C16  C17   180.00   0.0  0
 1S2  CONST_50  H1   C05  C06  N01   180.00   0.0  0
 1S2  CONST_51  H1   C05  C04  N03   180.00   0.0  0
 1S2  CONST_52  H15  N22  C02  N01   180.00   0.0  0
 1S2  CONST_53  H16  N22  C02  N01     0.00   0.0  0
 1S2  CONST_54  H15  N22  C02  N03     0.00   0.0  0
 1S2  CONST_55  H16  N22  C02  N03   180.00   0.0  0
 1S2  Var_01    C17  C20  C09  C08   -79.66  30.0  2
 1S2  Var_02    C12  C17  C20  C09   130.23  30.0  2
 1S2  Var_03    C16  C17  C20  C09   -50.66  30.0  2
 1S2  Var_04    C17  C20  C09  C10   100.82  30.0  2
 1S2  Var_05    H13  C20  C09  C08    42.05  30.0  2
 1S2  Var_06    H14  C20  C09  C08   158.03  30.0  2
 1S2  Var_07    H7   C18  N07  C08  -174.42  30.0  2
 1S2  Var_08    H8   C18  N07  C08   -54.92  30.0  2
 1S2  Var_09    H9   C18  N07  C08    65.77  30.0  2
 1S2  Var_10    H10  C19  C08  C09   115.73  30.0  2
 1S2  Var_11    H11  C19  C08  C09  -123.84  30.0  2
 1S2  Var_12    H12  C19  C08  C09    -3.81  30.0  2
 1S2  Var_13    H13  C20  C09  C10  -137.47  30.0  2
 1S2  Var_14    H14  C20  C09  C10   -21.49  30.0  2
 1S2  Var_15    H13  C20  C17  C12     8.28  30.0  1
 1S2  Var_16    H14  C20  C17  C12  -107.37  30.0  1
 1S2  Var_17    H13  C20  C17  C16  -172.61  30.0  1
 1S2  Var_18    H14  C20  C17  C16    71.74  30.0  1
 1S2  Var_19    H10  C19  C08  N07   -63.77  30.0  2
 1S2  Var_20    H11  C19  C08  N07    56.66  30.0  2
 1S2  Var_21    H12  C19  C08  N07   176.69  30.0  2
 1S2  Var_22    H7   C18  N07  N11     6.55  30.0  2
 1S2  Var_23    H8   C18  N07  N11   126.06  30.0  2
 1S2  Var_24    H9   C18  N07  N11  -113.25  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
 1S2  plan-1  C04  0.020
 1S2  plan-1  C08  0.020
 1S2  plan-1  C09  0.020
 1S2  plan-1  C10  0.020
 1S2  plan-1  C19  0.020
 1S2  plan-1  C20  0.020
 1S2  plan-1  N07  0.020
 1S2  plan-1  N11  0.020
 1S2  plan-1  C18  0.020
 1S2  plan-2  C12  0.020
 1S2  plan-2  C13  0.020
 1S2  plan-2  C14  0.020
 1S2  plan-2  C15  0.020
 1S2  plan-2  C16  0.020
 1S2  plan-2  C17  0.020
 1S2  plan-2  C20  0.020
 1S2  plan-2  H3   0.020
 1S2  plan-2  H4   0.020
 1S2  plan-2  H5   0.020
 1S2  plan-2  H6   0.020
 1S2  plan-2  H2   0.020
 1S2  plan-3  C02  0.020
 1S2  plan-3  C04  0.020
 1S2  plan-3  C05  0.020
 1S2  plan-3  C06  0.020
 1S2  plan-3  C10  0.020
 1S2  plan-3  N01  0.020
 1S2  plan-3  N03  0.020
 1S2  plan-3  N22  0.020
 1S2  plan-3  CL1  0.020
 1S2  plan-3  H1   0.020
 1S2  plan-4  C02  0.020
 1S2  plan-4  N22  0.020
 1S2  plan-4  H15  0.020
 1S2  plan-4  H16  0.020

