# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 20:46:41 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 6-(3-amino-2H-indazol-6-yl)-N~4~-ethylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNc1cc(nc(N)n1)c2ccc3c(N)[nH]nc3c2
#
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
 3Q0  3Q0  6-(3-amino-2H-indazol-6-yl)-N~4~-ethylpyrimidine-2,4-diamine  ligand  35  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3Q0
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
 3Q0  C13   C  CR16  0  -0.279  -2.2902  -1.6484  -0.3572
 3Q0  C12   C  CR16  0  -0.346  -0.9760  -1.2763  -0.3818
 3Q0  C20   C  CR16  0  -0.349  -1.5008   1.0144   0.2588
 3Q0  C5    C  CR16  0  -0.494   1.8576  -0.5308   0.0212
 3Q0  C14   C  CR56  0  -0.140  -3.2528  -0.6828  -0.0071
 3Q0  C11   C  CR6   0   0.041  -0.5702   0.0595  -0.0679
 3Q0  C19   C  CR56  0   0.280  -2.8662   0.6514   0.3009
 3Q0  C6    C  CR6   0   0.289   0.8660   0.4272  -0.0819
 3Q0  C4    C  CR6   0   0.543   3.1880  -0.0677   0.0038
 3Q0  C15   C  CR5   0   0.510  -4.6473  -0.6768   0.1331
 3Q0  C8    C  CR6   0   0.522   2.4346   2.0648  -0.1715
 3Q0  C1    C  CH3   0  -0.694   5.5185  -2.9636   0.2436
 3Q0  C2    C  CH2   0  -0.273   4.1374  -2.3467   0.1343
 3Q0  N7    N  N     0  -0.517   1.1451   1.7294  -0.1774
 3Q0  N10   N  N     0  -0.515   3.4695   1.2326  -0.0968
 3Q0  N17   N  NR15  0  -0.475  -4.9555   0.5737   0.4907
 3Q0  N18   N  N     0  -0.352  -3.9100   1.4159   0.6063
 3Q0  N16   N  NH2   0  -0.845  -5.5560  -1.6897   0.0305
 3Q0  N9    N  NH2   0  -0.826   2.7185   3.3892  -0.2188
 3Q0  N3    N  NH1   0  -0.651   4.2333  -0.9043   0.0919
 3Q0  H13   H  HCR6  0   0.252  -2.5760  -2.6622  -0.6093
 3Q0  H12   H  HCR6  0   0.244  -0.2322  -2.0066  -0.6689
 3Q0  H20   H  HCR6  0   0.250  -1.1933   2.0247   0.4931
 3Q0  H5    H  HCR6  0   0.266   1.6336  -1.5804   0.1280
 3Q0  H1    H  HCH3  0   0.236   6.0258  -2.6345   1.1509
 3Q0  H1A   H  HCH3  0   0.247   5.4393  -4.0489   0.2774
 3Q0  H1B   H  HCH3  0   0.235   6.1403  -2.6996  -0.6126
 3Q0  H2    H  HCH2  0   0.232   3.6325  -2.7223  -0.7619
 3Q0  H2A   H  HCH2  0   0.234   3.5325  -2.6568   0.9915
 3Q0  HN16  H  HNH2  0   0.398  -5.2710  -2.4494  -0.5677
 3Q0  HN1A  H  HNH2  0   0.396  -6.5084  -1.4145  -0.1549
 3Q0  HN9   H  HNH2  0   0.387   1.9876   4.0103  -0.5207
 3Q0  HN9A  H  HNH2  0   0.387   3.6560   3.6609  -0.4600
 3Q0  HN3   H  HNH1  0   0.387   5.1473  -0.4861   0.0186
 3Q0  HN17  H  HNR5  0   0.422  -5.8842   0.9225   0.6751

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
 3Q0  C12  C13   aromatic  1.366  0.020  1.366
 3Q0  C14  C13   aromatic  1.408  0.020  1.408
 3Q0  C13  H13   single    0.930  0.020  1.080
 3Q0  C11  C12   aromatic  1.431  0.020  1.431
 3Q0  C12  H12   single    0.930  0.020  1.080
 3Q0  C20  C11   aromatic  1.373  0.020  1.373
 3Q0  C20  C19   aromatic  1.413  0.020  1.413
 3Q0  C20  H20   single    0.930  0.020  1.080
 3Q0  C6   C5    aromatic  1.383  0.020  1.383
 3Q0  C4   C5    aromatic  1.409  0.020  1.409
 3Q0  C5   H5    single    0.930  0.020  1.080
 3Q0  C19  C14   aromatic  1.423  0.020  1.423
 3Q0  C14  C15   aromatic  1.402  0.020  1.402
 3Q0  C6   C11   single    1.483  0.020  1.483
 3Q0  N18  C19   aromatic  1.329  0.020  1.329
 3Q0  N7   C6    aromatic  1.335  0.020  1.335
 3Q0  N10  C4    aromatic  1.334  0.020  1.334
 3Q0  C4   N3    single    1.342  0.020  1.342
 3Q0  N17  C15   aromatic  1.337  0.020  1.337
 3Q0  C15  N16   single    1.365  0.020  1.365
 3Q0  N9   C8    single    1.355  0.020  1.355
 3Q0  C8   N7    aromatic  1.332  0.020  1.332
 3Q0  C8   N10   aromatic  1.330  0.020  1.330
 3Q0  C2   C1    single    1.517  0.020  1.517
 3Q0  C1   H1    single    0.970  0.020  1.090
 3Q0  C1   H1A   single    0.970  0.020  1.090
 3Q0  C1   H1B   single    0.970  0.020  1.090
 3Q0  N3   C2    single    1.446  0.020  1.446
 3Q0  C2   H2    single    0.970  0.020  1.090
 3Q0  C2   H2A   single    0.970  0.020  1.090
 3Q0  N18  N17   aromatic  1.348  0.020  1.348
 3Q0  N16  HN16  single    0.890  0.020  1.040
 3Q0  N16  HN1A  single    0.890  0.020  1.040
 3Q0  N9   HN9   single    0.890  0.020  1.040
 3Q0  N9   HN9A  single    0.890  0.020  1.040
 3Q0  N3   HN3   single    0.860  0.020  1.020
 3Q0  N17  HN17  single    0.860  0.020  1.020

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
 3Q0  H13   C13  C14   121.30  3.000
 3Q0  H13   C13  C12   120.31  3.000
 3Q0  C14   C13  C12   118.39  3.000
 3Q0  H12   C12  C11   119.58  3.000
 3Q0  H12   C12  C13   118.86  3.000
 3Q0  C11   C12  C13   121.54  3.000
 3Q0  H20   C20  C19   120.53  3.000
 3Q0  H20   C20  C11   120.56  3.000
 3Q0  C19   C20  C11   118.90  3.000
 3Q0  H5    C5   C4    121.14  3.000
 3Q0  H5    C5   C6    122.19  3.000
 3Q0  C4    C5   C6    116.65  3.000
 3Q0  C15   C14  C19   104.17  3.000
 3Q0  C15   C14  C13   135.08  3.000
 3Q0  C19   C14  C13   120.75  3.000
 3Q0  C6    C11  C20   119.11  3.000
 3Q0  C6    C11  C12   120.27  3.000
 3Q0  C20   C11  C12   120.61  3.000
 3Q0  N18   C19  C14   112.07  3.000
 3Q0  N18   C19  C20   128.14  3.000
 3Q0  C14   C19  C20   119.79  3.000
 3Q0  N7    C6   C11   116.42  3.000
 3Q0  N7    C6   C5    122.09  3.000
 3Q0  C11   C6   C5    121.48  3.000
 3Q0  N3    C4   N10   116.64  3.000
 3Q0  N3    C4   C5    122.00  3.000
 3Q0  N10   C4   C5    121.36  3.000
 3Q0  N16   C15  N17   124.12  3.000
 3Q0  N16   C15  C14   130.68  3.000
 3Q0  N17   C15  C14   105.08  3.000
 3Q0  N9    C8   N10   116.77  3.000
 3Q0  N10   C8   N7    126.57  3.000
 3Q0  N9    C8   N7    116.65  3.000
 3Q0  H1B   C1   H1A   107.89  3.000
 3Q0  H1B   C1   H1    108.35  3.000
 3Q0  H1A   C1   H1    107.99  3.000
 3Q0  H1B   C1   C2    111.36  3.000
 3Q0  H1A   C1   C2    109.97  3.000
 3Q0  H1    C1   C2    111.15  3.000
 3Q0  H2A   C2   H2    106.80  3.000
 3Q0  H2A   C2   N3    110.02  3.000
 3Q0  H2    C2   N3    110.40  3.000
 3Q0  H2A   C2   C1    109.38  3.000
 3Q0  H2    C2   C1    109.84  3.000
 3Q0  N3    C2   C1    110.33  3.000
 3Q0  C8    N7   C6    116.58  3.000
 3Q0  C8    N10  C4    116.74  3.000
 3Q0  HN17  N17  N18   118.84  3.000
 3Q0  HN17  N17  C15   125.77  3.000
 3Q0  N18   N17  C15   115.39  3.000
 3Q0  N17   N18  C19   103.30  3.000
 3Q0  HN1A  N16  HN16  111.31  3.000
 3Q0  HN1A  N16  C15   116.11  3.000
 3Q0  HN16  N16  C15   114.57  3.000
 3Q0  HN9A  N9   HN9   116.03  3.000
 3Q0  HN9A  N9   C8    117.88  3.000
 3Q0  HN9   N9   C8    117.51  3.000
 3Q0  HN3   N3   C2    118.43  3.000
 3Q0  HN3   N3   C4    116.30  3.000
 3Q0  C2    N3   C4    124.90  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
 3Q0  CONST_01  C20   C11  C12  C13     0.00   0.0  0
 3Q0  CONST_02  C6    C11  C12  C13   180.00   0.0  0
 3Q0  CONST_03  C20   C19  C14  C13     0.00   0.0  0
 3Q0  CONST_04  N18   C19  C14  C13   180.00   0.0  0
 3Q0  CONST_05  N17   C15  C14  C13   180.00   0.0  0
 3Q0  CONST_06  C19   C14  C13  C12     0.00   0.0  0
 3Q0  CONST_07  C15   C14  C13  C12   180.00   0.0  0
 3Q0  CONST_08  C19   C20  C11  C12     0.00   0.0  0
 3Q0  CONST_13  C15   C14  C19  C20   180.00   0.0  0
 3Q0  CONST_14  N17   N18  C19  C20   180.00   0.0  0
 3Q0  CONST_15  C8    N7   C6   C5      0.00   0.0  0
 3Q0  CONST_16  C8    N10  C4   C5      0.00   0.0  0
 3Q0  CONST_17  C11   C12  C13  C14     0.00   0.0  0
 3Q0  CONST_18  C11   C20  C19  C14     0.00   0.0  0
 3Q0  CONST_19  N17   N18  C19  C14     0.00   0.0  0
 3Q0  CONST_20  N18   N17  C15  C14     0.00   0.0  0
 3Q0  CONST_21  N18   C19  C20  C11   180.00   0.0  0
 3Q0  CONST_22  C4    C5   C6   C11   180.00   0.0  0
 3Q0  CONST_23  C8    N7   C6   C11   180.00   0.0  0
 3Q0  CONST_24  C6    C11  C20  C19   180.00   0.0  0
 3Q0  CONST_25  N17   C15  C14  C19     0.00   0.0  0
 3Q0  CONST_26  C15   N17  N18  C19     0.00   0.0  0
 3Q0  CONST_27  N10   C4   C5   C6      0.00   0.0  0
 3Q0  CONST_28  N10   C8   N7   C6      0.00   0.0  0
 3Q0  CONST_29  N7    C6   C5   C4      0.00   0.0  0
 3Q0  CONST_30  N7    C8   N10  C4      0.00   0.0  0
 3Q0  CONST_31  N18   C19  C14  C15     0.00   0.0  0
 3Q0  CONST_32  N16   C15  C14  C13     0.00   0.0  0
 3Q0  CONST_33  N16   C15  C14  C19   180.00   0.0  0
 3Q0  CONST_34  N3    C4   C5   C6    180.00   0.0  0
 3Q0  CONST_35  N9    C8   N7   C6    180.00   0.0  0
 3Q0  CONST_36  N9    C8   N10  C4    180.00   0.0  0
 3Q0  CONST_37  N3    C4   N10  C8    180.00   0.0  0
 3Q0  CONST_38  N16   C15  N17  N18   180.00   0.0  0
 3Q0  CONST_39  H20   C20  C11  C12   180.00   0.0  0
 3Q0  CONST_40  H12   C12  C11  C20   180.00   0.0  0
 3Q0  CONST_41  HN17  N17  C15  C14   180.00   0.0  0
 3Q0  CONST_42  H13   C13  C12  C11   180.00   0.0  0
 3Q0  CONST_43  H5    C5   C6   C11     0.00   0.0  0
 3Q0  CONST_44  C2    N3   C4   C5      0.00   0.0  0
 3Q0  CONST_45  N10   C4   N3   C2    180.00   0.0  0
 3Q0  CONST_46  HN3   N3   C4   C5    180.00   0.0  0
 3Q0  Var_01    C1    C2   N3   C4   -179.63  30.0  3
 3Q0  Var_02    H1    C1   C2   N3     60.33  30.0  3

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
 3Q0  plan-1  C5    0.020
 3Q0  plan-1  C11   0.020
 3Q0  plan-1  C6    0.020
 3Q0  plan-1  C4    0.020
 3Q0  plan-1  C8    0.020
 3Q0  plan-1  N7    0.020
 3Q0  plan-1  N10   0.020
 3Q0  plan-1  N9    0.020
 3Q0  plan-1  N3    0.020
 3Q0  plan-1  H5    0.020
 3Q0  plan-2  C13   0.020
 3Q0  plan-2  C12   0.020
 3Q0  plan-2  C20   0.020
 3Q0  plan-2  C14   0.020
 3Q0  plan-2  C11   0.020
 3Q0  plan-2  C19   0.020
 3Q0  plan-2  C6    0.020
 3Q0  plan-2  C15   0.020
 3Q0  plan-2  N17   0.020
 3Q0  plan-2  N18   0.020
 3Q0  plan-2  N16   0.020
 3Q0  plan-2  H13   0.020
 3Q0  plan-2  H12   0.020
 3Q0  plan-2  H20   0.020
 3Q0  plan-2  HN17  0.020
 3Q0  plan-3  C15   0.020
 3Q0  plan-3  N16   0.020
 3Q0  plan-3  HN16  0.020
 3Q0  plan-3  HN1A  0.020
 3Q0  plan-4  C8    0.020
 3Q0  plan-4  N9    0.020
 3Q0  plan-4  HN9   0.020
 3Q0  plan-4  HN9A  0.020
 3Q0  plan-5  C4    0.020
 3Q0  plan-5  C2    0.020
 3Q0  plan-5  N3    0.020
 3Q0  plan-5  HN3   0.020

