# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 21:55:02 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 4-[1-(2,6-dichlorobenzyl)-2-methyl-1H-imidazol-4-yl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(cn1Cc2c(Cl)cccc2Cl)c3ccnc(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
 L23  L23  4-[1-(2,6-dichlorobenzyl)-2-methyl-1H-imidazol-4-yl]pyrimidin-2-amine  ligand  35  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L23
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
 L23  CL21  CL  CL    0  -0.098  -2.4120   1.0915   2.1839
 L23  C17   C   CR6   0  -0.106  -2.7393  -0.2318   1.1168
 L23  C20   C   CR16  0  -0.188  -3.2821  -1.3839   1.6584
 L23  C22   C   CR16  0  -0.282  -3.5454  -2.4587   0.8248
 L23  C18   C   CR16  0  -0.185  -3.2591  -2.3836  -0.5269
 L23  C16   C   CR6   0  -0.126  -2.7113  -1.2176  -1.0399
 L23  CL19  CL  CL    0  -0.103  -2.3292  -1.1900  -2.7304
 L23  C15   C   CR6   0   0.257  -2.4477  -0.1041  -0.2423
 L23  C11   C   CH2   0  -0.387  -1.8679   1.1687  -0.7921
 L23  N7    N   NR5   0  -0.441  -0.4693   1.3155  -0.4301
 L23  C3    C   CR15  0  -0.048   0.4797   0.3441  -0.5213
 L23  C8    C   CR5   0   0.441   0.1417   2.4490   0.0180
 L23  C12   C   CH3   0  -0.766  -0.5694   3.7352   0.2315
 L23  N4    N   N     0  -0.471   1.4152   2.2406   0.2188
 L23  C1    C   CR5   0   0.074   1.6453   0.9329  -0.1114
 L23  C2    C   CR6   0   0.215   2.9602   0.3199  -0.0183
 L23  C6    C   CR16  0  -0.381   4.0719   1.0428   0.4128
 L23  C10   C   CR16  0  -0.025   5.2675   0.3505   0.4491
 L23  N13   N   N     0  -0.460   5.3862  -0.9235   0.1074
 L23  C9    C   CR6   0   0.530   4.2587  -1.5286  -0.2866
 L23  N5    N   N     0  -0.495   3.0556  -0.9597  -0.3662
 L23  N14   N   NH2   0  -0.826   4.3425  -2.8393  -0.6014
 L23  H20   H   HCR6  0   0.291  -3.4962  -1.4416   2.7163
 L23  H22   H   HCR6  0   0.285  -3.9724  -3.3640   1.2336
 L23  H18   H   HCR6  0   0.290  -3.4562  -3.2241  -1.1773
 L23  H111  H   HCH2  0   0.299  -1.9670   1.2068  -1.8753
 L23  H112  H   HCH2  0   0.305  -2.4137   2.0253  -0.3993
 L23  H3    H   HCR5  0   0.300   0.2653  -0.6574  -0.8543
 L23  H121  H   HCH3  0   0.253  -1.3666   3.6403   0.9699
 L23  H122  H   HCH3  0   0.274   0.1383   4.4773   0.5925
 L23  H123  H   HCH3  0   0.264  -1.0159   4.1115  -0.6898
 L23  H6    H   HCR6  0   0.260   4.0046   2.0822   0.6950
 L23  H10   H   HCR6  0   0.266   6.1772   0.8487   0.7680
 L23  H141  H   HNH2  0   0.393   5.2525  -3.2344  -0.7633
 L23  H142  H   HNH2  0   0.392   3.5733  -3.2637  -1.0902

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
 L23  CL21  C17   single    1.731  0.020  1.731
 L23  C17   C20   aromatic  1.384  0.020  1.384
 L23  C17   C15   aromatic  1.396  0.020  1.396
 L23  C20   C22   aromatic  1.385  0.020  1.385
 L23  C22   C18   aromatic  1.384  0.020  1.384
 L23  C18   C16   aromatic  1.387  0.020  1.387
 L23  C16   CL19  single    1.733  0.020  1.733
 L23  C16   C15   aromatic  1.395  0.020  1.395
 L23  C15   C11   single    1.503  0.020  1.503
 L23  C11   N7    single    1.452  0.020  1.452
 L23  N7    C3    aromatic  1.361  0.020  1.361
 L23  N7    C8    aromatic  1.363  0.020  1.363
 L23  C3    C1    aromatic  1.369  0.020  1.369
 L23  C8    C12   single    1.485  0.020  1.485
 L23  C8    N4    aromatic  1.306  0.020  1.306
 L23  N4    C1    aromatic  1.368  0.020  1.368
 L23  C1    C2    single    1.454  0.020  1.454
 L23  C2    C6    aromatic  1.394  0.020  1.394
 L23  C2    N5    aromatic  1.329  0.020  1.329
 L23  C6    C10   aromatic  1.382  0.020  1.382
 L23  C10   N13   aromatic  1.324  0.020  1.324
 L23  N13   C9    aromatic  1.339  0.020  1.339
 L23  C9    N5    aromatic  1.333  0.020  1.333
 L23  C9    N14   single    1.351  0.020  1.351
 L23  C20   H20   single    0.930  0.020  1.080
 L23  C22   H22   single    0.930  0.020  1.080
 L23  C18   H18   single    0.930  0.020  1.080
 L23  C11   H111  single    0.970  0.020  1.090
 L23  C11   H112  single    0.970  0.020  1.090
 L23  C3    H3    single    0.930  0.020  1.080
 L23  C12   H121  single    0.970  0.020  1.090
 L23  C12   H122  single    0.970  0.020  1.090
 L23  C12   H123  single    0.970  0.020  1.090
 L23  C6    H6    single    0.930  0.020  1.080
 L23  C10   H10   single    0.930  0.020  1.080
 L23  N14   H141  single    0.890  0.020  1.040
 L23  N14   H142  single    0.890  0.020  1.040

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
 L23  C15   C17  C20   122.63  3.000
 L23  C15   C17  CL21  119.39  3.000
 L23  C20   C17  CL21  117.98  3.000
 L23  H20   C20  C22   120.65  3.000
 L23  H20   C20  C17   120.34  3.000
 L23  C22   C20  C17   119.00  3.000
 L23  H22   C22  C18   119.77  3.000
 L23  H22   C22  C20   119.81  3.000
 L23  C18   C22  C20   120.42  3.000
 L23  H18   C18  C16   120.22  3.000
 L23  H18   C18  C22   120.52  3.000
 L23  C16   C18  C22   119.26  3.000
 L23  C15   C16  CL19  120.22  3.000
 L23  C15   C16  C18   122.30  3.000
 L23  CL19  C16  C18   117.47  3.000
 L23  C11   C15  C16   122.67  3.000
 L23  C11   C15  C17   120.95  3.000
 L23  C16   C15  C17   116.38  3.000
 L23  H112  C11  H111  106.61  3.000
 L23  H112  C11  N7    108.26  3.000
 L23  H111  C11  N7    109.41  3.000
 L23  H112  C11  C15   109.93  3.000
 L23  H111  C11  C15   111.01  3.000
 L23  N7    C11  C15   111.47  3.000
 L23  C8    N7   C3    107.63  3.000
 L23  C8    N7   C11   126.70  3.000
 L23  C3    N7   C11   125.64  3.000
 L23  H3    C3   C1    131.47  3.000
 L23  H3    C3   N7    123.07  3.000
 L23  C1    C3   N7    105.47  3.000
 L23  N4    C8   C12   125.66  3.000
 L23  N4    C8   N7    110.79  3.000
 L23  C12   C8   N7    123.55  3.000
 L23  H123  C12  H122  108.15  3.000
 L23  H123  C12  H121  107.61  3.000
 L23  H122  C12  H121  108.08  3.000
 L23  H123  C12  C8    111.92  3.000
 L23  H122  C12  C8    109.10  3.000
 L23  H121  C12  C8    111.83  3.000
 L23  C1    N4   C8    106.22  3.000
 L23  C2    C1   N4    122.66  3.000
 L23  C2    C1   C3    127.45  3.000
 L23  N4    C1   C3    109.89  3.000
 L23  N5    C2   C6    121.51  3.000
 L23  N5    C2   C1    117.00  3.000
 L23  C6    C2   C1    121.49  3.000
 L23  H6    C6   C10   121.98  3.000
 L23  H6    C6   C2    122.03  3.000
 L23  C10   C6   C2    115.98  3.000
 L23  H10   C10  N13   116.25  3.000
 L23  H10   C10  C6    120.20  3.000
 L23  N13   C10  C6    123.55  3.000
 L23  C9    N13  C10   115.80  3.000
 L23  N14   C9   N5    117.14  3.000
 L23  N14   C9   N13   117.07  3.000
 L23  N5    C9   N13   125.77  3.000
 L23  C9    N5   C2    117.38  3.000
 L23  H142  N14  H141  116.64  3.000
 L23  H142  N14  C9    118.40  3.000
 L23  H141  N14  C9    118.37  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
 L23  CONST_01  C18   C22  C20  C17     0.00   0.0  0
 L23  CONST_02  C18   C16  C15  C17     0.00   0.0  0
 L23  CONST_03  C16   C15  C17  C20     0.00   0.0  0
 L23  CONST_04  C16   C18  C22  C20     0.00   0.0  0
 L23  CONST_05  C15   C17  C20  C22     0.00   0.0  0
 L23  CONST_06  C15   C16  C18  C22     0.00   0.0  0
 L23  CONST_07  N4    C1   C3   N7      0.00   0.0  0
 L23  CONST_08  C2    C1   C3   N7    180.00   0.0  0
 L23  CONST_09  C1    N4   C8   N7      0.00   0.0  0
 L23  CONST_10  N4    C8   N7   C3      0.00   0.0  0
 L23  CONST_11  C8    N4   C1   C3      0.00   0.0  0
 L23  CONST_12  C6    C2   C1   C3    180.00   0.0  0
 L23  CONST_13  N5    C2   C1   C3      0.00   0.0  0
 L23  CONST_14  C1    C3   N7   C8      0.00   0.0  0
 L23  CONST_15  C2    C1   N4   C8    180.00   0.0  0
 L23  CONST_16  C6    C2   C1   N4      0.00   0.0  0
 L23  CONST_17  N5    C2   C1   N4    180.00   0.0  0
 L23  CONST_18  C10   C6   C2   C1    180.00   0.0  0
 L23  CONST_19  C9    N5   C2   C1    180.00   0.0  0
 L23  CONST_20  N13   C10  C6   C2      0.00   0.0  0
 L23  CONST_21  N13   C9   N5   C2      0.00   0.0  0
 L23  CONST_22  C9    N5   C2   C6      0.00   0.0  0
 L23  CONST_23  C9    N13  C10  C6      0.00   0.0  0
 L23  CONST_24  N5    C2   C6   C10     0.00   0.0  0
 L23  CONST_25  N5    C9   N13  C10     0.00   0.0  0
 L23  CONST_26  C22   C20  C17  CL21  180.00   0.0  0
 L23  CONST_27  C16   C15  C17  CL21  180.00   0.0  0
 L23  CONST_28  CL19  C16  C15  C17   180.00   0.0  0
 L23  CONST_29  C11   C15  C17  C20   180.00   0.0  0
 L23  CONST_30  CL19  C16  C18  C22   180.00   0.0  0
 L23  CONST_31  C11   C15  C16  C18   180.00   0.0  0
 L23  CONST_32  C1    C3   N7   C11   180.00   0.0  0
 L23  CONST_33  N4    C8   N7   C11   180.00   0.0  0
 L23  CONST_34  C12   C8   N7   C3    180.00   0.0  0
 L23  CONST_35  C1    N4   C8   C12   180.00   0.0  0
 L23  CONST_36  N14   C9   N5   C2    180.00   0.0  0
 L23  CONST_37  N14   C9   N13  C10   180.00   0.0  0
 L23  CONST_38  H22   C22  C20  C17   180.00   0.0  0
 L23  CONST_39  H18   C18  C22  C20   180.00   0.0  0
 L23  CONST_40  H20   C20  C22  C18   180.00   0.0  0
 L23  CONST_41  H3    C3   N7   C8    180.00   0.0  0
 L23  CONST_42  H6    C6   C2   C1      0.00   0.0  0
 L23  CONST_43  H10   C10  C6   C2    180.00   0.0  0
 L23  CONST_45  H142  N14  C9   N13   180.00   0.0  0
 L23  Var_01    N7    C11  C15  C17    73.96  30.0  2
 L23  Var_02    C3    N7   C11  C15    46.12  30.0  2
 L23  Var_03    H121  C12  C8   N7     60.34  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
 L23  plan-1  C11   0.020
 L23  plan-1  N7    0.020
 L23  plan-1  C3    0.020
 L23  plan-1  C8    0.020
 L23  plan-1  C12   0.020
 L23  plan-1  N4    0.020
 L23  plan-1  C1    0.020
 L23  plan-1  C2    0.020
 L23  plan-1  H3    0.020
 L23  plan-2  CL21  0.020
 L23  plan-2  C17   0.020
 L23  plan-2  C20   0.020
 L23  plan-2  C22   0.020
 L23  plan-2  C18   0.020
 L23  plan-2  C16   0.020
 L23  plan-2  CL19  0.020
 L23  plan-2  C15   0.020
 L23  plan-2  C11   0.020
 L23  plan-2  H20   0.020
 L23  plan-2  H22   0.020
 L23  plan-2  H18   0.020
 L23  plan-3  C1    0.020
 L23  plan-3  C2    0.020
 L23  plan-3  C6    0.020
 L23  plan-3  C10   0.020
 L23  plan-3  N13   0.020
 L23  plan-3  C9    0.020
 L23  plan-3  N5    0.020
 L23  plan-3  N14   0.020
 L23  plan-3  H6    0.020
 L23  plan-3  H10   0.020
 L23  plan-4  C9    0.020
 L23  plan-4  N14   0.020
 L23  plan-4  H141  0.020
 L23  plan-4  H142  0.020

