# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 13:23:00 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 3-bromo-6-phenyl-N-(pyrimidin-5-ylmethyl)imidazo[1,2-a]pyridin-8-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1cnc2n1cc(cc2NCc3cncnc3)c4ccccc4
#
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
 SCW  SCW  3-bromo-6-phenyl-N-(pyrimidin-5-ylmethyl)imidazo[1,2-a]pyridin-8-amine  ligand  38  24  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SCW
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
 SCW  C01   C   CR5   0   0.076   1.9558   2.0920   0.1180
 SCW  N02   N   N     0  -0.533   1.3401   0.8667   0.0846
 SCW  C03   C   CR56  0   0.467  -0.0060   1.1314   0.0691
 SCW  N04   N   N     0  -0.468  -0.2552   2.4267   0.0918
 SCW  C05   C   CR15  0  -0.183   0.9541   3.0267   0.1223
 SCW  C06   C   CR16  0  -0.051   1.8538  -0.4040   0.0562
 SCW  C07   C   CR6   0  -0.031   0.9862  -1.4525   0.0382
 SCW  C08   C   CR16  0  -0.333  -0.4191  -1.2253   0.0462
 SCW  C09   C   CR6   0   0.292  -0.9322   0.0493   0.0463
 SCW  N10   N   NH1   0  -0.682  -2.2542   0.3713   0.0136
 SCW  C11   C   CR6   0   0.076   1.5106  -2.8324   0.0043
 SCW  C12   C   CH2   0  -0.346  -3.2730  -0.6317   0.2201
 SCW  C13   C   CR6   0  -0.046  -4.6280  -0.0180   0.0491
 SCW  C14   C   CR16  0  -0.024  -5.1124   0.3564  -1.1979
 SCW  N15   N   N     0  -0.390  -6.3005   0.9199  -1.3609
 SCW  C16   C   CR16  0   0.056  -7.0180   1.1149  -0.2629
 SCW  N17   N   N     0  -0.390  -6.6633   0.8005   0.9720
 SCW  C18   C   CR16  0  -0.040  -5.4695   0.2378   1.1198
 SCW  C19   C   CR16  0  -0.311   2.6432  -3.1883   0.7381
 SCW  C20   C   CR16  0  -0.239   3.1437  -4.4809   0.6863
 SCW  C21   C   CR16  0  -0.264   2.5158  -5.4434  -0.0933
 SCW  C22   C   CR16  0  -0.240   1.3835  -5.1021  -0.8211
 SCW  C23   C   CR16  0  -0.308   0.8847  -3.8087  -0.7721
 SCW  BR24  BR  BR    0   0.019   3.7891   2.3048   0.1644
 SCW  H05   H   HCR5  0   0.279   1.0700   4.0993   0.1474
 SCW  H06   H   HCR6  0   0.303   2.9276  -0.5040   0.0245
 SCW  H08   H   HCR6  0   0.279  -1.0807  -2.0799   0.0751
 SCW  HN10  H   HNH1  0   0.393  -2.4782   1.3049   0.3235
 SCW  H121  H   HCH2  0   0.265  -3.1426  -1.4292  -0.5161
 SCW  H122  H   HCH2  0   0.256  -3.1978  -1.0992   1.2100
 SCW  H14   H   HCR6  0   0.280  -4.5194   0.1903  -2.0918
 SCW  H16   H   HCR6  0   0.267  -7.9905   1.5771  -0.3910
 SCW  H18   H   HCR6  0   0.279  -5.1686  -0.0215   2.1301
 SCW  H19   H   HCR6  0   0.256   3.1275  -2.4564   1.3726
 SCW  H20   H   HCR6  0   0.259   4.0219  -4.7377   1.2643
 SCW  H21   H   HCR6  0   0.259   2.9036  -6.4529  -0.1307
 SCW  H22   H   HCR6  0   0.260   0.8894  -5.8424  -1.4367
 SCW  H23   H   HCR6  0   0.256   0.0107  -3.5553  -1.3594

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
 SCW  N17  C16   aromatic  1.323  0.020  1.323
 SCW  N17  C18   aromatic  1.328  0.020  1.328
 SCW  C16  N15   aromatic  1.326  0.020  1.326
 SCW  C18  C13   aromatic  1.386  0.020  1.386
 SCW  N15  C14   aromatic  1.325  0.020  1.325
 SCW  C13  C14   aromatic  1.389  0.020  1.389
 SCW  C13  C12   single    1.497  0.020  1.497
 SCW  N04  C05   aromatic  1.350  0.020  1.350
 SCW  N04  C03   aromatic  1.319  0.020  1.319
 SCW  N10  C12   single    1.444  0.020  1.444
 SCW  N10  C09   single    1.361  0.020  1.361
 SCW  C05  C01   aromatic  1.370  0.020  1.370
 SCW  C03  C09   aromatic  1.425  0.020  1.425
 SCW  C03  N02   aromatic  1.372  0.020  1.372
 SCW  C09  C08   aromatic  1.374  0.020  1.374
 SCW  C01  N02   aromatic  1.372  0.020  1.372
 SCW  C01  BR24  single    1.846  0.020  1.846
 SCW  N02  C06   aromatic  1.371  0.020  1.371
 SCW  C08  C07   aromatic  1.424  0.020  1.424
 SCW  C06  C07   aromatic  1.361  0.020  1.361
 SCW  C07  C11   single    1.477  0.020  1.477
 SCW  C23  C11   aromatic  1.396  0.020  1.396
 SCW  C23  C22   aromatic  1.387  0.020  1.387
 SCW  C11  C19   aromatic  1.396  0.020  1.396
 SCW  C22  C21   aromatic  1.389  0.020  1.389
 SCW  C19  C20   aromatic  1.387  0.020  1.387
 SCW  C21  C20   aromatic  1.389  0.020  1.389
 SCW  C05  H05   single    0.930  0.020  1.080
 SCW  C06  H06   single    0.930  0.020  1.080
 SCW  C08  H08   single    0.930  0.020  1.080
 SCW  N10  HN10  single    0.890  0.020  1.040
 SCW  C12  H121  single    0.970  0.020  1.090
 SCW  C12  H122  single    0.970  0.020  1.090
 SCW  C14  H14   single    0.930  0.020  1.080
 SCW  C16  H16   single    0.930  0.020  1.080
 SCW  C18  H18   single    0.930  0.020  1.080
 SCW  C19  H19   single    0.930  0.020  1.080
 SCW  C20  H20   single    0.930  0.020  1.080
 SCW  C21  H21   single    0.930  0.020  1.080
 SCW  C22  H22   single    0.930  0.020  1.080
 SCW  C23  H23   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
 SCW  BR24  C01  C05   130.34  3.000
 SCW  BR24  C01  N02   123.32  3.000
 SCW  C05   C01  N02   106.34  3.000
 SCW  C06   N02  C03   123.11  3.000
 SCW  C06   N02  C01   131.33  3.000
 SCW  C03   N02  C01   105.56  3.000
 SCW  C09   C03  N04   128.56  3.000
 SCW  C09   C03  N02   119.44  3.000
 SCW  N04   C03  N02   112.00  3.000
 SCW  C05   N04  C03   105.51  3.000
 SCW  H05   C05  N04   122.57  3.000
 SCW  H05   C05  C01   126.84  3.000
 SCW  N04   C05  C01   110.59  3.000
 SCW  H06   C06  C07   124.24  3.000
 SCW  H06   C06  N02   117.35  3.000
 SCW  C07   C06  N02   118.39  3.000
 SCW  C11   C07  C08   119.99  3.000
 SCW  C11   C07  C06   119.59  3.000
 SCW  C08   C07  C06   120.41  3.000
 SCW  H08   C08  C09   120.31  3.000
 SCW  H08   C08  C07   118.56  3.000
 SCW  C09   C08  C07   121.11  3.000
 SCW  N10   C09  C08   125.61  3.000
 SCW  C08   C09  C03   117.51  3.000
 SCW  N10   C09  C03   116.88  3.000
 SCW  HN10  N10  C12   116.24  3.000
 SCW  HN10  N10  C09   115.29  3.000
 SCW  C12   N10  C09   121.16  3.000
 SCW  C23   C11  C19   118.56  3.000
 SCW  C19   C11  C07   120.96  3.000
 SCW  C23   C11  C07   120.48  3.000
 SCW  H122  C12  H121  106.77  3.000
 SCW  H122  C12  C13   109.85  3.000
 SCW  H121  C12  C13   109.27  3.000
 SCW  H122  C12  N10   112.11  3.000
 SCW  H121  C12  N10   109.04  3.000
 SCW  C13   C12  N10   109.72  3.000
 SCW  C18   C13  C14   115.60  3.000
 SCW  C14   C13  C12   121.91  3.000
 SCW  C18   C13  C12   122.48  3.000
 SCW  H14   C14  N15   116.98  3.000
 SCW  H14   C14  C13   120.50  3.000
 SCW  N15   C14  C13   122.53  3.000
 SCW  C16   N15  C14   116.48  3.000
 SCW  H16   C16  N17   116.87  3.000
 SCW  H16   C16  N15   116.76  3.000
 SCW  N17   C16  N15   126.37  3.000
 SCW  C18   N17  C16   116.47  3.000
 SCW  H18   C18  N17   117.00  3.000
 SCW  H18   C18  C13   120.45  3.000
 SCW  N17   C18  C13   122.56  3.000
 SCW  H19   C19  C20   119.36  3.000
 SCW  H19   C19  C11   119.91  3.000
 SCW  C20   C19  C11   120.72  3.000
 SCW  H20   C20  C21   120.15  3.000
 SCW  H20   C20  C19   119.60  3.000
 SCW  C21   C20  C19   120.25  3.000
 SCW  H21   C21  C22   120.23  3.000
 SCW  H21   C21  C20   120.26  3.000
 SCW  C22   C21  C20   119.51  3.000
 SCW  H22   C22  C23   119.58  3.000
 SCW  H22   C22  C21   120.16  3.000
 SCW  C23   C22  C21   120.26  3.000
 SCW  H23   C23  C22   119.29  3.000
 SCW  H23   C23  C11   120.00  3.000
 SCW  C22   C23  C11   120.70  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
 SCW  CONST_01  C03   N04  C05  C01     0.00   0.0  0
 SCW  CONST_02  N04   C03  N02  C01     0.00   0.0  0
 SCW  CONST_03  C09   C03  N02  C01   180.00   0.0  0
 SCW  CONST_04  C07   C06  N02  C01   180.00   0.0  0
 SCW  CONST_05  C05   N04  C03  N02     0.00   0.0  0
 SCW  CONST_06  C08   C09  C03  N02     0.00   0.0  0
 SCW  CONST_07  N04   C05  C01  N02     0.00   0.0  0
 SCW  CONST_08  C08   C07  C06  N02     0.00   0.0  0
 SCW  CONST_09  C11   C07  C06  N02   180.00   0.0  0
 SCW  CONST_10  C07   C08  C09  C03     0.00   0.0  0
 SCW  CONST_11  C05   C01  N02  C03     0.00   0.0  0
 SCW  CONST_12  C07   C06  N02  C03     0.00   0.0  0
 SCW  CONST_13  C08   C09  C03  N04   180.00   0.0  0
 SCW  CONST_14  C06   N02  C03  N04   180.00   0.0  0
 SCW  CONST_15  C09   C03  N04  C05   180.00   0.0  0
 SCW  CONST_16  C06   N02  C01  C05   180.00   0.0  0
 SCW  CONST_17  C09   C03  N02  C06     0.00   0.0  0
 SCW  CONST_18  C09   C08  C07  C06     0.00   0.0  0
 SCW  CONST_21  C22   C23  C11  C07   180.00   0.0  0
 SCW  CONST_22  C20   C19  C11  C07   180.00   0.0  0
 SCW  CONST_25  C11   C07  C08  C09   180.00   0.0  0
 SCW  CONST_26  C21   C22  C23  C11     0.00   0.0  0
 SCW  CONST_27  C21   C20  C19  C11     0.00   0.0  0
 SCW  CONST_28  C16   N17  C18  C13     0.00   0.0  0
 SCW  CONST_29  C16   N15  C14  C13     0.00   0.0  0
 SCW  CONST_30  N17   C16  N15  C14     0.00   0.0  0
 SCW  CONST_31  N17   C18  C13  C14     0.00   0.0  0
 SCW  CONST_32  C18   N17  C16  N15     0.00   0.0  0
 SCW  CONST_33  C18   C13  C14  N15     0.00   0.0  0
 SCW  CONST_34  C22   C23  C11  C19     0.00   0.0  0
 SCW  CONST_35  C22   C21  C20  C19     0.00   0.0  0
 SCW  CONST_36  C23   C11  C19  C20     0.00   0.0  0
 SCW  CONST_37  C23   C22  C21  C20     0.00   0.0  0
 SCW  CONST_38  N10   C09  C03  N02   180.00   0.0  0
 SCW  CONST_39  BR24  C01  N02  C03   180.00   0.0  0
 SCW  CONST_40  BR24  C01  C05  N04   180.00   0.0  0
 SCW  CONST_41  N10   C09  C03  N04     0.00   0.0  0
 SCW  CONST_42  BR24  C01  N02  C06     0.00   0.0  0
 SCW  CONST_43  N10   C09  C08  C07   180.00   0.0  0
 SCW  CONST_44  N17   C18  C13  C12   180.00   0.0  0
 SCW  CONST_45  N15   C14  C13  C12   180.00   0.0  0
 SCW  CONST_46  H06   C06  N02  C01     0.00   0.0  0
 SCW  CONST_47  H05   C05  C01  N02   180.00   0.0  0
 SCW  CONST_48  H08   C08  C09  C03   180.00   0.0  0
 SCW  CONST_49  H23   C23  C11  C07     0.00   0.0  0
 SCW  CONST_50  H19   C19  C11  C07     0.00   0.0  0
 SCW  CONST_51  H22   C22  C23  C11   180.00   0.0  0
 SCW  CONST_52  H20   C20  C19  C11   180.00   0.0  0
 SCW  CONST_53  H16   C16  N15  C14   180.00   0.0  0
 SCW  CONST_54  H18   C18  C13  C14   180.00   0.0  0
 SCW  CONST_55  H14   C14  N15  C16   180.00   0.0  0
 SCW  CONST_56  H21   C21  C20  C19   180.00   0.0  0
 SCW  CONST_57  C12   N10  C09  C03   180.00   0.0  0
 SCW  CONST_58  C12   N10  C09  C08     0.00   0.0  0
 SCW  Var_01    C13   C12  N10  C09  -176.60  30.0  3
 SCW  Var_02    C18   C13  C12  N10  -106.79  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
 SCW  plan-1  C12   0.020
 SCW  plan-1  C13   0.020
 SCW  plan-1  C14   0.020
 SCW  plan-1  N15   0.020
 SCW  plan-1  C16   0.020
 SCW  plan-1  N17   0.020
 SCW  plan-1  C18   0.020
 SCW  plan-1  H14   0.020
 SCW  plan-1  H16   0.020
 SCW  plan-1  H18   0.020
 SCW  plan-2  C07   0.020
 SCW  plan-2  C11   0.020
 SCW  plan-2  C19   0.020
 SCW  plan-2  C20   0.020
 SCW  plan-2  C21   0.020
 SCW  plan-2  C22   0.020
 SCW  plan-2  C23   0.020
 SCW  plan-2  H19   0.020
 SCW  plan-2  H20   0.020
 SCW  plan-2  H21   0.020
 SCW  plan-2  H22   0.020
 SCW  plan-2  H23   0.020
 SCW  plan-3  C01   0.020
 SCW  plan-3  N02   0.020
 SCW  plan-3  C03   0.020
 SCW  plan-3  N04   0.020
 SCW  plan-3  C05   0.020
 SCW  plan-3  C06   0.020
 SCW  plan-3  C07   0.020
 SCW  plan-3  C08   0.020
 SCW  plan-3  C09   0.020
 SCW  plan-3  N10   0.020
 SCW  plan-3  C11   0.020
 SCW  plan-3  BR24  0.020
 SCW  plan-3  H05   0.020
 SCW  plan-3  H06   0.020
 SCW  plan-3  H08   0.020
 SCW  plan-4  C09   0.020
 SCW  plan-4  N10   0.020
 SCW  plan-4  C12   0.020
 SCW  plan-4  HN10  0.020

