# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 11:32:52 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 3-methyl-N-(pyridin-4-ylmethyl)imidazo[1,2-a]pyrazin-8-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cnc2n1ccnc2NCc3ccncc3
#
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
 SCE  SCE  3-methyl-N-(pyridin-4-ylmethyl)imidazo[1,2-a]pyrazin-8-amine  ligand  31  18  .  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_SCE
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
 SCE  C01   C  CR5   0   0.276   3.7824   0.7906   0.2992
 SCE  N02   N  N     0  -0.508   2.7155  -0.0584   0.2288
 SCE  C03   C  CR56  0   0.401   1.7531   0.5594  -0.5215
 SCE  N04   N  N     0  -0.459   2.1423   1.7474  -0.9310
 SCE  C05   C  CR15  0  -0.247   3.3914   1.8933  -0.4275
 SCE  C06   C  CR16  0  -0.084   2.5096  -1.3145   0.7569
 SCE  C07   C  CR16  0  -0.162   1.3195  -1.8988   0.4933
 SCE  N08   N  N     0  -0.454   0.3249  -1.3352  -0.2451
 SCE  C09   C  CR6   0   0.452   0.5262  -0.1430  -0.7439
 SCE  N10   N  NH1   0  -0.669  -0.4177   0.4617  -1.4878
 SCE  C11   C  CH2   0  -0.334  -1.6887  -0.1431  -1.7613
 SCE  C12   C  CR6   0   0.180  -2.6349  -0.1774  -0.5862
 SCE  C13   C  CR16  0  -0.368  -3.6981  -1.0732  -0.5748
 SCE  C14   C  CR16  0  -0.062  -4.5818  -1.0602   0.4919
 SCE  N15   N  N     0  -0.412  -4.4730  -0.2336   1.5268
 SCE  C16   C  CR16  0  -0.062  -3.4550   0.6189   1.5143
 SCE  C17   C  CR16  0  -0.356  -2.5193   0.6882   0.4928
 SCE  C18   C  CH3   0  -0.744   5.0295   0.4704   1.0327
 SCE  H05   H  HCR5  0   0.260   3.9759   2.7846  -0.6020
 SCE  H06   H  HCR6  0   0.303   3.2961  -1.7594   1.3452
 SCE  H07   H  HCR6  0   0.265   1.1190  -2.8855   0.8895
 SCE  HN10  H  HNH1  0   0.407  -0.2280   1.3876  -1.8326
 SCE  H111  H  HCH2  0   0.290  -2.1536   0.4279  -2.5663
 SCE  H112  H  HCH2  0   0.261  -1.5516  -1.1587  -2.1395
 SCE  H13   H  HCR6  0   0.264  -3.8411  -1.7798  -1.3832
 SCE  H14   H  HCR6  0   0.262  -5.4148  -1.7544   0.5114
 SCE  H16   H  HCR6  0   0.261  -3.3733   1.2881   2.3639
 SCE  H17   H  HCR6  0   0.260  -1.7155   1.4100   0.5500
 SCE  H181  H  HCH3  0   0.256   5.5088  -0.4321   0.6479
 SCE  H182  H  HCH3  0   0.268   5.7365   1.2909   0.9312
 SCE  H183  H  HCH3  0   0.256   4.8477   0.3166   2.0983

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
 SCE  C16  N15   aromatic  1.328  0.020  1.328
 SCE  C16  C17   aromatic  1.387  0.020  1.387
 SCE  N15  C14   aromatic  1.329  0.020  1.329
 SCE  C17  C12   aromatic  1.388  0.020  1.388
 SCE  C14  C13   aromatic  1.385  0.020  1.385
 SCE  C12  C13   aromatic  1.390  0.020  1.390
 SCE  C12  C11   single    1.509  0.020  1.509
 SCE  N10  C11   single    1.434  0.020  1.434
 SCE  N10  C09   single    1.345  0.020  1.345
 SCE  N04  C05   aromatic  1.355  0.020  1.355
 SCE  N04  C03   aromatic  1.316  0.020  1.316
 SCE  C05  C01   aromatic  1.377  0.020  1.377
 SCE  C03  C09   aromatic  1.431  0.020  1.431
 SCE  C03  N02   aromatic  1.368  0.020  1.368
 SCE  C09  N08   aromatic  1.308  0.020  1.308
 SCE  C01  N02   aromatic  1.365  0.020  1.365
 SCE  C01  C18   single    1.482  0.020  1.482
 SCE  N02  C06   aromatic  1.378  0.020  1.378
 SCE  N08  C07   aromatic  1.361  0.020  1.361
 SCE  C07  C06   aromatic  1.352  0.020  1.352
 SCE  C05  H05   single    0.930  0.020  1.080
 SCE  C06  H06   single    0.930  0.020  1.080
 SCE  C07  H07   single    0.930  0.020  1.080
 SCE  N10  HN10  single    0.860  0.020  1.020
 SCE  C11  H111  single    0.970  0.020  1.090
 SCE  C11  H112  single    0.970  0.020  1.090
 SCE  C13  H13   single    0.930  0.020  1.080
 SCE  C14  H14   single    0.930  0.020  1.080
 SCE  C16  H16   single    0.930  0.020  1.080
 SCE  C17  H17   single    0.930  0.020  1.080
 SCE  C18  H181  single    0.970  0.020  1.090
 SCE  C18  H182  single    0.970  0.020  1.090
 SCE  C18  H183  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
 SCE  C18   C01  C05   132.31  3.000
 SCE  C18   C01  N02   123.29  3.000
 SCE  C05   C01  N02   104.40  3.000
 SCE  C06   N02  C03   121.12  3.000
 SCE  C06   N02  C01   131.59  3.000
 SCE  C03   N02  C01   107.30  3.000
 SCE  C09   C03  N04   130.43  3.000
 SCE  C09   C03  N02   117.82  3.000
 SCE  N04   C03  N02   111.75  3.000
 SCE  C05   N04  C03   104.74  3.000
 SCE  H05   C05  N04   121.86  3.000
 SCE  H05   C05  C01   126.32  3.000
 SCE  N04   C05  C01   111.82  3.000
 SCE  H06   C06  C07   124.76  3.000
 SCE  H06   C06  N02   118.44  3.000
 SCE  C07   C06  N02   116.80  3.000
 SCE  H07   C07  N08   116.16  3.000
 SCE  H07   C07  C06   119.07  3.000
 SCE  N08   C07  C06   124.77  3.000
 SCE  C09   N08  C07   118.16  3.000
 SCE  N10   C09  N08   120.83  3.000
 SCE  N08   C09  C03   121.34  3.000
 SCE  N10   C09  C03   117.83  3.000
 SCE  HN10  N10  C11   119.33  3.000
 SCE  HN10  N10  C09   118.09  3.000
 SCE  C11   N10  C09   122.54  3.000
 SCE  H112  C11  H111  106.54  3.000
 SCE  H112  C11  C12   109.10  3.000
 SCE  H111  C11  C12   108.62  3.000
 SCE  H112  C11  N10   110.30  3.000
 SCE  H111  C11  N10   107.32  3.000
 SCE  C12   C11  N10   114.64  3.000
 SCE  C17   C12  C13   117.33  3.000
 SCE  C13   C12  C11   120.04  3.000
 SCE  C17   C12  C11   122.61  3.000
 SCE  H13   C13  C14   119.78  3.000
 SCE  H13   C13  C12   121.01  3.000
 SCE  C14   C13  C12   119.22  3.000
 SCE  H14   C14  N15   116.55  3.000
 SCE  H14   C14  C13   119.86  3.000
 SCE  N15   C14  C13   123.59  3.000
 SCE  C16   N15  C14   117.05  3.000
 SCE  H16   C16  C17   119.69  3.000
 SCE  H16   C16  N15   116.52  3.000
 SCE  C17   C16  N15   123.79  3.000
 SCE  H17   C17  C16   119.71  3.000
 SCE  H17   C17  C12   121.27  3.000
 SCE  C16   C17  C12   119.02  3.000
 SCE  H183  C18  H182  107.79  3.000
 SCE  H183  C18  H181  107.50  3.000
 SCE  H182  C18  H181  107.78  3.000
 SCE  H183  C18  C01   111.92  3.000
 SCE  H182  C18  C01   109.74  3.000
 SCE  H181  C18  C01   111.94  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
 SCE  CONST_01  C03   N04  C05  C01    0.00   0.0  0
 SCE  CONST_02  N04   C03  N02  C01    0.00   0.0  0
 SCE  CONST_03  C09   C03  N02  C01  180.00   0.0  0
 SCE  CONST_04  C07   C06  N02  C01  180.00   0.0  0
 SCE  CONST_05  C05   N04  C03  N02    0.00   0.0  0
 SCE  CONST_06  N08   C09  C03  N02    0.00   0.0  0
 SCE  CONST_07  N04   C05  C01  N02    0.00   0.0  0
 SCE  CONST_08  N08   C07  C06  N02    0.00   0.0  0
 SCE  CONST_09  C07   N08  C09  C03    0.00   0.0  0
 SCE  CONST_10  C05   C01  N02  C03    0.00   0.0  0
 SCE  CONST_11  C07   C06  N02  C03    0.00   0.0  0
 SCE  CONST_12  N08   C09  C03  N04  180.00   0.0  0
 SCE  CONST_13  C06   N02  C03  N04  180.00   0.0  0
 SCE  CONST_14  C09   C03  N04  C05  180.00   0.0  0
 SCE  CONST_15  C06   N02  C01  C05  180.00   0.0  0
 SCE  CONST_16  C09   C03  N02  C06    0.00   0.0  0
 SCE  CONST_17  C09   N08  C07  C06    0.00   0.0  0
 SCE  CONST_18  N15   C16  C17  C12    0.00   0.0  0
 SCE  CONST_19  N15   C14  C13  C12    0.00   0.0  0
 SCE  CONST_20  C16   N15  C14  C13    0.00   0.0  0
 SCE  CONST_21  C16   C17  C12  C13    0.00   0.0  0
 SCE  CONST_22  C17   C16  N15  C14    0.00   0.0  0
 SCE  CONST_23  C17   C12  C13  C14    0.00   0.0  0
 SCE  CONST_24  N10   C09  C03  N02  180.00   0.0  0
 SCE  CONST_25  C18   C01  N02  C03  180.00   0.0  0
 SCE  CONST_26  C18   C01  C05  N04  180.00   0.0  0
 SCE  CONST_27  N10   C09  C03  N04    0.00   0.0  0
 SCE  CONST_28  C18   C01  N02  C06    0.00   0.0  0
 SCE  CONST_29  N10   C09  N08  C07  180.00   0.0  0
 SCE  CONST_30  C16   C17  C12  C11  180.00   0.0  0
 SCE  CONST_31  C14   C13  C12  C11  180.00   0.0  0
 SCE  CONST_32  H06   C06  N02  C01    0.00   0.0  0
 SCE  CONST_33  H05   C05  C01  N02  180.00   0.0  0
 SCE  CONST_34  H07   C07  C06  N02  180.00   0.0  0
 SCE  CONST_35  H16   C16  C17  C12  180.00   0.0  0
 SCE  CONST_36  H14   C14  C13  C12  180.00   0.0  0
 SCE  CONST_37  H17   C17  C12  C13  180.00   0.0  0
 SCE  CONST_38  H13   C13  C14  N15  180.00   0.0  0
 SCE  CONST_39  C11   N10  C09  C03  180.00   0.0  0
 SCE  CONST_40  C11   N10  C09  N08    0.00   0.0  0
 SCE  CONST_41  HN10  N10  C09  C03    0.00   0.0  0
 SCE  Var_01    C12   C11  N10  C09   72.92  30.0  3
 SCE  Var_02    C17   C12  C11  N10   22.05  30.0  2
 SCE  Var_03    H181  C18  C01  N02   59.45  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
 SCE  plan-1  C11   0.020
 SCE  plan-1  C12   0.020
 SCE  plan-1  C13   0.020
 SCE  plan-1  C14   0.020
 SCE  plan-1  N15   0.020
 SCE  plan-1  C16   0.020
 SCE  plan-1  C17   0.020
 SCE  plan-1  H13   0.020
 SCE  plan-1  H14   0.020
 SCE  plan-1  H16   0.020
 SCE  plan-1  H17   0.020
 SCE  plan-2  C01   0.020
 SCE  plan-2  N02   0.020
 SCE  plan-2  C03   0.020
 SCE  plan-2  N04   0.020
 SCE  plan-2  C05   0.020
 SCE  plan-2  C06   0.020
 SCE  plan-2  C07   0.020
 SCE  plan-2  N08   0.020
 SCE  plan-2  C09   0.020
 SCE  plan-2  N10   0.020
 SCE  plan-2  C18   0.020
 SCE  plan-2  H05   0.020
 SCE  plan-2  H06   0.020
 SCE  plan-2  H07   0.020
 SCE  plan-3  C09   0.020
 SCE  plan-3  N10   0.020
 SCE  plan-3  C11   0.020
 SCE  plan-3  HN10  0.020

