# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 20:12:57 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 8-(pyrimidin-2-ylamino)naphthalene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc2cccc(Nc3ncccn3)c2c1
#
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
 UI2  UI2  8-(pyrimidin-2-ylamino)naphthalene-2-carboximidamide  ligand  33  20  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UI2
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
 UI2  C1    C  CR16  0  -0.258  -0.3938  -3.3068   0.2775
 UI2  C2    C  CR16  0  -0.327   0.9641  -3.2358   0.1374
 UI2  C3    C  CR66  0   0.096   1.6046  -1.9776   0.1200
 UI2  C4    C  CR66  0   0.081   0.8338  -0.7907   0.2371
 UI2  C5    C  CR6   0   0.319  -0.5787  -0.9010   0.4160
 UI2  C6    C  CR16  0  -0.292  -1.1673  -2.1423   0.4301
 UI2  C10   C  CR16  0  -0.300   3.0059  -1.8678  -0.0319
 UI2  C11   C  CR16  0  -0.283   3.6189  -0.6490  -0.0876
 UI2  C12   C  CR6   0   0.018   2.8559   0.5381   0.0034
 UI2  C13   C  CR16  0  -0.359   1.4943   0.4553   0.1603
 UI2  N17   N  NH1   0  -0.771  -1.3100   0.2717   0.6187
 UI2  C18   C  CR6   0   0.584  -2.5429   0.5930   0.1374
 UI2  N19   N  N     0  -0.456  -3.0354   1.7509   0.5883
 UI2  C20   C  CR16  0  -0.017  -4.2207   2.1072   0.1253
 UI2  C21   C  CR16  0  -0.380  -4.9360   1.3358  -0.7786
 UI2  C22   C  CR16  0  -0.007  -4.3255   0.1588  -1.1747
 UI2  N23   N  N     0  -0.446  -3.1371  -0.2217  -0.7285
 UI2  C28   C  C     0   0.333   3.5110   1.8753  -0.0659
 UI2  N29   N  N     0  -0.640   3.1315   2.9069   0.5864
 UI2  N30   N  NH2   0  -0.805   4.6139   1.9300  -0.8643
 UI2  H1    H  HCR6  0   0.263  -0.8899  -4.2684   0.2945
 UI2  H2    H  HCR6  0   0.258   1.5595  -4.1345   0.0358
 UI2  H6    H  HCR6  0   0.269  -2.2332  -2.2363   0.5754
 UI2  H10   H  HCR6  0   0.262   3.5951  -2.7735  -0.1049
 UI2  H11   H  HCR6  0   0.265   4.6944  -0.5939  -0.1918
 UI2  H13   H  HCR6  0   0.252   0.9141   1.3689   0.1834
 UI2  H17   H  HNH1  0   0.405  -0.9085   0.9723   1.2225
 UI2  H20   H  HCR6  0   0.276  -4.6184   3.0476   0.4903
 UI2  H21   H  HCR6  0   0.276  -5.9054   1.6328  -1.1482
 UI2  H22   H  HCR6  0   0.274  -4.8085  -0.5068  -1.8816
 UI2  H29   H  H     0   0.332   2.3716   2.6768   1.2159
 UI2  H301  H  HNH2  0   0.386   5.0058   2.8451  -1.0214
 UI2  H302  H  HNH2  0   0.394   4.6650   1.3146  -1.6590

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
 UI2  C1   C2    aromatic  1.367  0.020  1.367
 UI2  C1   C6    aromatic  1.406  0.020  1.406
 UI2  C1   H1    single    0.930  0.020  1.080
 UI2  C2   C3    aromatic  1.412  0.020  1.412
 UI2  C2   H2    single    0.930  0.020  1.080
 UI2  C3   C4    aromatic  1.420  0.020  1.420
 UI2  C3   C10   aromatic  1.414  0.020  1.414
 UI2  C4   C5    aromatic  1.428  0.020  1.428
 UI2  C4   C13   aromatic  1.412  0.020  1.412
 UI2  C5   C6    aromatic  1.374  0.020  1.374
 UI2  C5   N17   single    1.397  0.020  1.397
 UI2  C6   H6    single    0.930  0.020  1.080
 UI2  C10  C11   aromatic  1.365  0.020  1.365
 UI2  C10  H10   single    0.930  0.020  1.080
 UI2  C11  C12   aromatic  1.414  0.020  1.414
 UI2  C11  H11   single    0.930  0.020  1.080
 UI2  C12  C13   aromatic  1.373  0.020  1.373
 UI2  C12  C28   single    1.491  0.020  1.491
 UI2  C13  H13   single    0.930  0.020  1.080
 UI2  N17  C18   single    1.362  0.020  1.362
 UI2  N17  H17   single    0.860  0.020  1.020
 UI2  C18  N19   aromatic  1.337  0.020  1.337
 UI2  C18  N23   aromatic  1.329  0.020  1.329
 UI2  N19  C20   aromatic  1.321  0.020  1.321
 UI2  C20  C21   aromatic  1.387  0.020  1.387
 UI2  C20  H20   single    0.930  0.020  1.080
 UI2  C21  C22   aromatic  1.384  0.020  1.384
 UI2  C21  H21   single    0.930  0.020  1.080
 UI2  C22  N23   aromatic  1.325  0.020  1.325
 UI2  C22  H22   single    0.930  0.020  1.080
 UI2  C28  N29   double    1.278  0.020  1.278
 UI2  C28  N30   single    1.363  0.020  1.363
 UI2  N29  H29   single    0.890  0.020  1.040
 UI2  N30  H301  single    0.890  0.020  1.040
 UI2  N30  H302  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
 UI2  H1    C1   C6    118.82  3.000
 UI2  H1    C1   C2    120.21  3.000
 UI2  C6    C1   C2    120.96  3.000
 UI2  H2    C2   C3    119.27  3.000
 UI2  H2    C2   C1    120.84  3.000
 UI2  C3    C2   C1    119.88  3.000
 UI2  C10   C3   C4    118.81  3.000
 UI2  C10   C3   C2    121.34  3.000
 UI2  C4    C3   C2    119.84  3.000
 UI2  C13   C4   C5    122.52  3.000
 UI2  C13   C4   C3    118.62  3.000
 UI2  C5    C4   C3    118.86  3.000
 UI2  N17   C5   C6    122.19  3.000
 UI2  N17   C5   C4    118.11  3.000
 UI2  C6    C5   C4    119.66  3.000
 UI2  H6    C6   C5    120.20  3.000
 UI2  H6    C6   C1    119.04  3.000
 UI2  C5    C6   C1    120.76  3.000
 UI2  H10   C10  C11   119.97  3.000
 UI2  H10   C10  C3    118.79  3.000
 UI2  C11   C10  C3    121.25  3.000
 UI2  H11   C11  C12   119.98  3.000
 UI2  H11   C11  C10   119.72  3.000
 UI2  C12   C11  C10   120.30  3.000
 UI2  C28   C12  C13   119.69  3.000
 UI2  C28   C12  C11   120.86  3.000
 UI2  C13   C12  C11   119.45  3.000
 UI2  H13   C13  C12   118.88  3.000
 UI2  H13   C13  C4    119.52  3.000
 UI2  C12   C13  C4    121.55  3.000
 UI2  H17   N17  C18   114.09  3.000
 UI2  H17   N17  C5    117.50  3.000
 UI2  C18   N17  C5    128.37  3.000
 UI2  N23   C18  N19   125.87  3.000
 UI2  N23   C18  N17   119.36  3.000
 UI2  N19   C18  N17   114.76  3.000
 UI2  C20   N19  C18   116.48  3.000
 UI2  H20   C20  C21   120.84  3.000
 UI2  H20   C20  N19   116.42  3.000
 UI2  C21   C20  N19   122.75  3.000
 UI2  H21   C21  C22   122.17  3.000
 UI2  H21   C21  C20   122.23  3.000
 UI2  C22   C21  C20   115.60  3.000
 UI2  H22   C22  N23   116.28  3.000
 UI2  H22   C22  C21   120.80  3.000
 UI2  N23   C22  C21   122.92  3.000
 UI2  C22   N23  C18   116.38  3.000
 UI2  N30   C28  N29   120.46  3.000
 UI2  N30   C28  C12   114.77  3.000
 UI2  N29   C28  C12   124.73  3.000
 UI2  H29   N29  C28   110.89  3.000
 UI2  H302  N30  H301  114.36  3.000
 UI2  H302  N30  C28   118.63  3.000
 UI2  H301  N30  C28   116.27  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
 UI2  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 UI2  CONST_02  C10   C3   C2   C1    180.00   0.0  0
 UI2  CONST_03  C4    C5   C6   C1      0.00   0.0  0
 UI2  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 UI2  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 UI2  CONST_06  C13   C4   C3   C2    180.00   0.0  0
 UI2  CONST_07  C11   C10  C3   C2    180.00   0.0  0
 UI2  CONST_08  C6    C1   C2   C3      0.00   0.0  0
 UI2  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 UI2  CONST_10  C12   C13  C4   C3      0.00   0.0  0
 UI2  CONST_11  C12   C11  C10  C3      0.00   0.0  0
 UI2  CONST_12  C11   C10  C3   C4      0.00   0.0  0
 UI2  CONST_13  C11   C12  C13  C4      0.00   0.0  0
 UI2  CONST_14  C10   C3   C4   C5    180.00   0.0  0
 UI2  CONST_15  C12   C13  C4   C5    180.00   0.0  0
 UI2  CONST_16  C13   C4   C5   C6    180.00   0.0  0
 UI2  CONST_17  C13   C4   C3   C10     0.00   0.0  0
 UI2  CONST_18  C13   C12  C11  C10     0.00   0.0  0
 UI2  CONST_19  C21   C20  N19  C18     0.00   0.0  0
 UI2  CONST_20  C21   C22  N23  C18     0.00   0.0  0
 UI2  CONST_21  C22   N23  C18  N19     0.00   0.0  0
 UI2  CONST_22  C22   C21  C20  N19     0.00   0.0  0
 UI2  CONST_23  N23   C18  N19  C20     0.00   0.0  0
 UI2  CONST_24  N23   C22  C21  C20     0.00   0.0  0
 UI2  CONST_25  N17   C5   C6   C1    180.00   0.0  0
 UI2  CONST_26  N17   C5   C4   C3    180.00   0.0  0
 UI2  CONST_27  C28   C12  C13  C4    180.00   0.0  0
 UI2  CONST_28  C28   C12  C11  C10   180.00   0.0  0
 UI2  CONST_29  N17   C5   C4   C13     0.00   0.0  0
 UI2  CONST_30  C20   N19  C18  N17   180.00   0.0  0
 UI2  CONST_31  C22   N23  C18  N17   180.00   0.0  0
 UI2  CONST_32  H6    C6   C1   C2    180.00   0.0  0
 UI2  CONST_33  H10   C10  C3   C2      0.00   0.0  0
 UI2  CONST_34  H1    C1   C2   C3    180.00   0.0  0
 UI2  CONST_35  H13   C13  C4   C3    180.00   0.0  0
 UI2  CONST_36  H11   C11  C10  C3    180.00   0.0  0
 UI2  CONST_37  H2    C2   C3   C4    180.00   0.0  0
 UI2  CONST_38  H20   C20  N19  C18   180.00   0.0  0
 UI2  CONST_39  H22   C22  N23  C18   180.00   0.0  0
 UI2  CONST_40  H21   C21  C20  N19   180.00   0.0  0
 UI2  CONST_41  H29   N29  C28  C12     0.00   0.0  0
 UI2  CONST_42  H301  N30  C28  C12   180.00   0.0  0
 UI2  Var_01    C18   N17  C5   C4    141.39  30.0  2
 UI2  Var_02    N19   C18  N17  C5    174.96  30.0  2
 UI2  Var_03    N29   C28  C12  C11  -145.07  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
 UI2  plan-1  N17   0.020
 UI2  plan-1  C18   0.020
 UI2  plan-1  N19   0.020
 UI2  plan-1  C20   0.020
 UI2  plan-1  C21   0.020
 UI2  plan-1  C22   0.020
 UI2  plan-1  N23   0.020
 UI2  plan-1  H20   0.020
 UI2  plan-1  H21   0.020
 UI2  plan-1  H22   0.020
 UI2  plan-2  C1    0.020
 UI2  plan-2  C2    0.020
 UI2  plan-2  C3    0.020
 UI2  plan-2  C4    0.020
 UI2  plan-2  C5    0.020
 UI2  plan-2  C6    0.020
 UI2  plan-2  C10   0.020
 UI2  plan-2  C11   0.020
 UI2  plan-2  C12   0.020
 UI2  plan-2  C13   0.020
 UI2  plan-2  N17   0.020
 UI2  plan-2  C28   0.020
 UI2  plan-2  H1    0.020
 UI2  plan-2  H2    0.020
 UI2  plan-2  H6    0.020
 UI2  plan-2  H10   0.020
 UI2  plan-2  H11   0.020
 UI2  plan-2  H13   0.020
 UI2  plan-3  C12   0.020
 UI2  plan-3  C28   0.020
 UI2  plan-3  N29   0.020
 UI2  plan-3  N30   0.020
 UI2  plan-3  H29   0.020
 UI2  plan-3  H301  0.020
 UI2  plan-3  H302  0.020

