# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 15:34:01 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (2R)-2-cyclopropyl-5-methyl-2-{3-[5-(prop-1-yn-1-yl)pyridin-3-yl]phenyl}-2H-imidazol-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC#Cc1cncc(c1)c2cccc(c2)[C@@]3(N=C(C)C(=N3)N)C4CC4
#
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
 1B1  1B1  (2R)-2-cyclopropyl-5-methyl-2-{3-[5-(prop-1-yn-1-yl)pyridin-3-yl]phenyl}-2H-imidazol-4-amine  ligand  45  25  .  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_1B1
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
 1B1  C1    C  CR5   0   0.051  -2.8429   0.2555  -0.2657
 1B1  N1    N  N     0  -0.431  -2.7555  -0.9926   0.4529
 1B1  C2    C  CR5   0   0.377  -3.5510  -0.8740   1.4516
 1B1  C4    C  CH1   0  -0.195  -3.3994   0.0595  -1.6717
 1B1  C5    C  CR6   0   0.189  -1.4814   0.9209  -0.3803
 1B1  C6    C  CR16  0  -0.369  -0.3305   0.1437  -0.4351
 1B1  C7    C  CR6   0   0.108   0.9261   0.7238  -0.6046
 1B1  C8    C  CR16  0  -0.323   1.0215   2.1109  -0.7124
 1B1  C9    C  CR16  0  -0.225  -0.1218   2.8910  -0.6574
 1B1  C10   C  CR16  0  -0.317  -1.3689   2.3032  -0.4970
 1B1  N3    N  NH2   0  -0.839  -3.8286  -1.8105   2.3718
 1B1  C13   C  CH2   0  -0.477  -3.0405  -1.1529  -2.4644
 1B1  C12   C  CH2   0  -0.488  -4.4421  -0.9716  -1.9558
 1B1  C14   C  CR6   0   0.005   2.1336  -0.1194  -0.6706
 1B1  C15   C  CR16  0  -0.237   3.3340   0.2763  -0.0925
 1B1  C16   C  CR6   0  -0.161   4.4519  -0.5502  -0.1852
 1B1  C17   C  CR16  0  -0.100   4.3089  -1.7632  -0.8643
 1B1  C19   C  CR16  0  -0.098   2.1196  -1.3497  -1.3290
 1B1  C21   C  CSP   0   0.199   5.7001  -0.1850   0.3945
 1B1  N17   N  N     0  -0.348  -3.7655   1.1315   0.4510
 1B1  N5    N  N     0  -0.388   3.1730  -2.1490  -1.4212
 1B1  C18   C  CR5   0   0.197  -4.1930   0.4692   1.4458
 1B1  C22   C  CSP   0  -0.044   6.7610   0.1186   0.8792
 1B1  C23   C  CH3   0  -0.821   8.0407   0.4902   1.4566
 1B1  H4    H  HCH1  0   0.258  -3.4785   0.9896  -2.2249
 1B1  H31N  H  HNH2  0   0.400  -3.2692  -2.6460   2.4079
 1B1  H32N  H  HNH2  0   0.408  -4.2998  -1.5574   3.2228
 1B1  H121  H  HCH2  0   0.246  -4.7679  -1.6118  -1.1462
 1B1  H122  H  HCH2  0   0.250  -5.2204  -0.7183  -2.6643
 1B1  H131  H  HCH2  0   0.248  -2.8540  -1.0311  -3.5237
 1B1  H132  H  HCH2  0   0.246  -2.4303  -1.9051  -1.9814
 1B1  H6    H  HCR6  0   0.252  -0.4177  -0.9285  -0.3210
 1B1  H10   H  HCR6  0   0.255  -2.2533   2.9244  -0.4583
 1B1  H8    H  HCR6  0   0.256   1.9854   2.5820  -0.8613
 1B1  H9    H  HCR6  0   0.258  -0.0422   3.9667  -0.7456
 1B1  H111  H  HCH3  0   0.264  -4.7244   0.9574   3.4489
 1B1  H112  H  HCH3  0   0.269  -5.5264   1.9434   2.2185
 1B1  H113  H  HCH3  0   0.263  -6.0328   0.2702   2.5006
 1B1  H15   H  HCR6  0   0.271   3.4043   1.2155   0.4420
 1B1  H19   H  HCR6  0   0.263   1.2140  -1.6928  -1.8182
 1B1  H17   H  HCR6  0   0.267   5.1553  -2.4348  -0.9532
 1B1  H231  H  HCH3  0   0.272   8.7148  -0.3653   1.4930
 1B1  H232  H  HCH3  0   0.272   8.5211   1.2717   0.8672
 1B1  H233  H  HCH3  0   0.272   7.9175   0.8655   2.4727
 1B1  C11   C  CH3   0  -0.755  -5.1742   0.9422   2.4541

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
 1B1  C1   N1    single    1.443  0.020  1.443
 1B1  C1   C4    single    1.525  0.020  1.525
 1B1  C1   C5    single    1.520  0.020  1.520
 1B1  C1   N17   single    1.460  0.020  1.460
 1B1  N1   C2    double    1.282  0.020  1.282
 1B1  C2   N3    single    1.342  0.020  1.342
 1B1  C2   C18   single    1.489  0.020  1.489
 1B1  C4   C12   single    1.494  0.020  1.494
 1B1  C4   C13   single    1.492  0.020  1.492
 1B1  C5   C6    aromatic  1.390  0.020  1.390
 1B1  C5   C10   aromatic  1.392  0.020  1.392
 1B1  C6   C7    aromatic  1.394  0.020  1.394
 1B1  C7   C8    aromatic  1.395  0.020  1.395
 1B1  C7   C14   single    1.474  0.020  1.474
 1B1  C8   C9    aromatic  1.385  0.020  1.385
 1B1  C9   C10   aromatic  1.388  0.020  1.388
 1B1  C11  C18   single    1.484  0.020  1.484
 1B1  C12  C13   single    1.502  0.020  1.502
 1B1  C14  C15   aromatic  1.390  0.020  1.390
 1B1  C14  C19   aromatic  1.396  0.020  1.396
 1B1  C15  C16   aromatic  1.393  0.020  1.393
 1B1  C16  C17   aromatic  1.397  0.020  1.397
 1B1  C16  C21   single    1.424  0.020  1.424
 1B1  C17  N5    aromatic  1.323  0.020  1.323
 1B1  C19  N5    aromatic  1.325  0.020  1.325
 1B1  C21  C22   triple    1.205  0.020  1.205
 1B1  C22  C23   single    1.452  0.020  1.452
 1B1  N17  C18   double    1.269  0.020  1.269
 1B1  C4   H4    single    0.970  0.020  1.090
 1B1  N3   H31N  single    0.890  0.020  1.040
 1B1  N3   H32N  single    0.890  0.020  1.040
 1B1  C12  H121  single    0.970  0.020  1.090
 1B1  C12  H122  single    0.970  0.020  1.090
 1B1  C13  H131  single    0.970  0.020  1.090
 1B1  C13  H132  single    0.970  0.020  1.090
 1B1  C6   H6    single    0.930  0.020  1.080
 1B1  C10  H10   single    0.930  0.020  1.080
 1B1  C8   H8    single    0.930  0.020  1.080
 1B1  C9   H9    single    0.930  0.020  1.080
 1B1  C11  H111  single    0.970  0.020  1.090
 1B1  C11  H112  single    0.970  0.020  1.090
 1B1  C11  H113  single    0.970  0.020  1.090
 1B1  C15  H15   single    0.930  0.020  1.080
 1B1  C19  H19   single    0.930  0.020  1.080
 1B1  C17  H17   single    0.930  0.020  1.080
 1B1  C23  H231  single    0.970  0.020  1.090
 1B1  C23  H232  single    0.970  0.020  1.090
 1B1  C23  H233  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
 1B1  N17   C1   C5    109.90  3.000
 1B1  N17   C1   C4    107.41  3.000
 1B1  C5    C1   C4    108.28  3.000
 1B1  N17   C1   N1    108.22  3.000
 1B1  C5    C1   N1    111.22  3.000
 1B1  C4    C1   N1    111.73  3.000
 1B1  C2    N1   C1    105.68  3.000
 1B1  C18   C2   N3    122.89  3.000
 1B1  C18   C2   N1    110.36  3.000
 1B1  N3    C2   N1    126.72  3.000
 1B1  H4    C4   C12   116.35  3.000
 1B1  H4    C4   C13   116.30  3.000
 1B1  C12   C4   C13    60.40  3.000
 1B1  H4    C4   C1    112.74  3.000
 1B1  C13   C4   C1    120.43  3.000
 1B1  C12   C4   C1    121.26  3.000
 1B1  C10   C5   C6    119.03  3.000
 1B1  C10   C5   C1    120.90  3.000
 1B1  C6    C5   C1    120.00  3.000
 1B1  H6    C6   C7    119.85  3.000
 1B1  H6    C6   C5    118.90  3.000
 1B1  C7    C6   C5    121.23  3.000
 1B1  C14   C7   C8    120.62  3.000
 1B1  C14   C7   C6    120.37  3.000
 1B1  C8    C7   C6    119.00  3.000
 1B1  H8    C8   C9    119.67  3.000
 1B1  H8    C8   C7    120.28  3.000
 1B1  C9    C8   C7    120.04  3.000
 1B1  H9    C9   C10   119.76  3.000
 1B1  H9    C9   C8    119.73  3.000
 1B1  C10   C9   C8    120.51  3.000
 1B1  H10   C10  C9    119.71  3.000
 1B1  H10   C10  C5    120.10  3.000
 1B1  C9    C10  C5    120.19  3.000
 1B1  H32N  N3   H31N  116.07  3.000
 1B1  H32N  N3   C2    120.12  3.000
 1B1  H31N  N3   C2    119.28  3.000
 1B1  H132  C13  H131  114.69  3.000
 1B1  H132  C13  C12   117.31  3.000
 1B1  H131  C13  C12   118.59  3.000
 1B1  H132  C13  C4    117.59  3.000
 1B1  H131  C13  C4    118.02  3.000
 1B1  C12   C13  C4     59.85  3.000
 1B1  H122  C12  H121  114.30  3.000
 1B1  H122  C12  C13   118.52  3.000
 1B1  H121  C12  C13   117.57  3.000
 1B1  H122  C12  C4    117.69  3.000
 1B1  H121  C12  C4    118.43  3.000
 1B1  C13   C12  C4     59.76  3.000
 1B1  C19   C14  C15   117.12  3.000
 1B1  C19   C14  C7    121.15  3.000
 1B1  C15   C14  C7    121.73  3.000
 1B1  H15   C15  C16   119.68  3.000
 1B1  H15   C15  C14   120.55  3.000
 1B1  C16   C15  C14   119.76  3.000
 1B1  C21   C16  C17   120.68  3.000
 1B1  C21   C16  C15   121.61  3.000
 1B1  C17   C16  C15   117.72  3.000
 1B1  H17   C17  N5    117.09  3.000
 1B1  H17   C17  C16   119.84  3.000
 1B1  N5    C17  C16   123.07  3.000
 1B1  H19   C19  N5    116.19  3.000
 1B1  H19   C19  C14   119.99  3.000
 1B1  N5    C19  C14   123.81  3.000
 1B1  C22   C21  C16   180.00  3.000
 1B1  C18   N17  C1    106.53  3.000
 1B1  C19   N5   C17   118.51  3.000
 1B1  N17   C18  C11   126.07  3.000
 1B1  N17   C18  C2    109.18  3.000
 1B1  C11   C18  C2    124.75  3.000
 1B1  C23   C22  C21   180.00  3.000
 1B1  H233  C23  H232  107.87  3.000
 1B1  H233  C23  H231  108.00  3.000
 1B1  H232  C23  H231  107.95  3.000
 1B1  H233  C23  C22   111.05  3.000
 1B1  H232  C23  C22   110.90  3.000
 1B1  H231  C23  C22   110.95  3.000
 1B1  H113  C11  H112  108.75  3.000
 1B1  H113  C11  H111  107.09  3.000
 1B1  H112  C11  H111  108.54  3.000
 1B1  H113  C11  C18   110.66  3.000
 1B1  H112  C11  C18   111.13  3.000
 1B1  H111  C11  C18   110.55  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
 1B1  CONST_01  C8    C7   C6   C5      0.00   0.0  0
 1B1  CONST_02  C14   C7   C6   C5    180.00   0.0  0
 1B1  CONST_03  C8    C9   C10  C5      0.00   0.0  0
 1B1  CONST_04  C9    C10  C5   C6      0.00   0.0  0
 1B1  CONST_05  C9    C8   C7   C6      0.00   0.0  0
 1B1  CONST_08  C10   C5   C6   C7      0.00   0.0  0
 1B1  CONST_09  C10   C9   C8   C7      0.00   0.0  0
 1B1  CONST_10  C16   C15  C14  C7    180.00   0.0  0
 1B1  CONST_11  N5    C19  C14  C7    180.00   0.0  0
 1B1  CONST_14  C14   C7   C8   C9    180.00   0.0  0
 1B1  CONST_15  C17   C16  C15  C14     0.00   0.0  0
 1B1  CONST_16  C17   N5   C19  C14     0.00   0.0  0
 1B1  CONST_17  N5    C19  C14  C15     0.00   0.0  0
 1B1  CONST_18  N5    C17  C16  C15     0.00   0.0  0
 1B1  CONST_19  C19   C14  C15  C16     0.00   0.0  0
 1B1  CONST_20  C19   N5   C17  C16     0.00   0.0  0
 1B1  CONST_21  C7    C6   C5   C1    180.00   0.0  0
 1B1  CONST_22  C9    C10  C5   C1    180.00   0.0  0
 1B1  CONST_23  C18   C2   N1   C1      0.00   0.0  0
 1B1  CONST_24  C21   C16  C15  C14   180.00   0.0  0
 1B1  CONST_25  N5    C17  C16  C21   180.00   0.0  0
 1B1  CONST_26  N3    C2   N1   C1    180.00   0.0  0
 1B1  CONST_27  H6    C6   C5   C1      0.00   0.0  0
 1B1  CONST_28  H10   C10  C5   C1      0.00   0.0  0
 1B1  CONST_29  H9    C9   C10  C5    180.00   0.0  0
 1B1  CONST_30  H8    C8   C7   C6    180.00   0.0  0
 1B1  CONST_31  H15   C15  C14  C7      0.00   0.0  0
 1B1  CONST_32  H19   C19  C14  C7      0.00   0.0  0
 1B1  CONST_33  H17   C17  C16  C15   180.00   0.0  0
 1B1  CONST_34  H31N  N3   C2   N1      0.00   0.0  0
 1B1  CONST_35  H32N  N3   C2   N1    180.00   0.0  0
 1B1  Var_01    C13   C12  C4   C1   -109.66  30.0  1
 1B1  Var_02    C2    C18  N17  C1      1.12  30.0  1
 1B1  Var_03    N17   C18  C2   N1     -0.38  30.0  1
 1B1  Var_04    H111  C11  C18  C2     61.36  30.0  3
 1B1  Var_05    H231  C23  C22  C21  -117.99  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 1B1  chir_01  C1  C4  C5   N17  negativ
 1B1  chir_02  C4  C1  C12  C13  both

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
 1B1  plan-1  C1    0.020
 1B1  plan-1  N1    0.020
 1B1  plan-1  C2    0.020
 1B1  plan-1  N3    0.020
 1B1  plan-1  C18   0.020
 1B1  plan-1  H31N  0.020
 1B1  plan-1  H32N  0.020
 1B1  plan-2  C1    0.020
 1B1  plan-2  C5    0.020
 1B1  plan-2  C6    0.020
 1B1  plan-2  C7    0.020
 1B1  plan-2  C8    0.020
 1B1  plan-2  C9    0.020
 1B1  plan-2  C10   0.020
 1B1  plan-2  C14   0.020
 1B1  plan-2  H6    0.020
 1B1  plan-2  H10   0.020
 1B1  plan-2  H8    0.020
 1B1  plan-2  H9    0.020
 1B1  plan-3  C7    0.020
 1B1  plan-3  C14   0.020
 1B1  plan-3  C15   0.020
 1B1  plan-3  C16   0.020
 1B1  plan-3  C17   0.020
 1B1  plan-3  C19   0.020
 1B1  plan-3  C21   0.020
 1B1  plan-3  N5    0.020
 1B1  plan-3  C22   0.020
 1B1  plan-3  H15   0.020
 1B1  plan-3  H19   0.020
 1B1  plan-3  H17   0.020

