# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 13:26:52 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 5-(1-methyl-1H-pyrazol-4-yl)-4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2c[nH]c3ncnc(N4CCOCC4)c23
#
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
 3JA  3JA  5-(1-methyl-1H-pyrazol-4-yl)-4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidine  ligand  37  21  .  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_3JA
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
 3JA  N3   N  NR15  0  -0.658   2.2383   2.7653   0.2771
 3JA  C4   C  CR15  0  -0.103  -1.8652   0.7169  -0.9044
 3JA  N2   N  N     0  -0.281  -3.1678   0.7976  -0.7063
 3JA  C7   C  CR56  0   0.484   2.5597   1.4853  -0.0119
 3JA  C6   C  CR15  0  -0.067   0.8789   2.8789   0.3602
 3JA  C9   C  CR6   0   0.425   1.5574  -0.6434  -0.3032
 3JA  C13  C  CH2   0  -0.191  -0.4841  -3.6468  -0.9378
 3JA  C8   C  CR56  0  -0.081   1.3692   0.7346  -0.0581
 3JA  N5   N  N     0  -0.439   3.7875   1.0345  -0.2639
 3JA  N1   N  NR5   0  -0.265  -3.3158   1.5704   0.3639
 3JA  C2   C  CR15  0   0.007  -2.1385   1.9852   0.8616
 3JA  C3   C  CR5   0  -0.225  -1.1485   1.4501   0.0612
 3JA  C5   C  CR5   0  -0.007   0.2887   1.6609   0.1547
 3JA  N4   N  N     0  -0.474   2.7740  -1.0820  -0.6156
 3JA  C10  C  CR16  0   0.034   3.8036  -0.2381  -0.5955
 3JA  N6   N  NT    0  -0.498   0.5411  -1.5640  -0.2484
 3JA  C11  C  CH2   0  -0.337  -0.2790  -1.6037   0.9611
 3JA  C12  C  CH2   0  -0.189  -1.5368  -2.4143   0.7179
 3JA  O1   O  O2    0  -0.483  -1.2393  -3.7108   0.2509
 3JA  C14  C  CH2   0  -0.313   0.8235  -2.9043  -0.7392
 3JA  H1   H  HNR5  0   0.415   2.8951   3.5251   0.3550
 3JA  H2   H  HCR5  0   0.251  -1.4670   0.1374  -1.7238
 3JA  H3   H  HCR5  0   0.291   0.4156   3.8376   0.5288
 3JA  H4   H  HCH2  0   0.242  -0.2779  -4.6713  -1.2508
 3JA  H5   H  HCH2  0   0.204  -1.0627  -3.1589  -1.7355
 3JA  H6   H  HCH3  0   0.259  -5.1195   0.9531   1.2234
 3JA  H7   H  HCH3  0   0.258  -4.5457   2.5568   1.7032
 3JA  H8   H  HCH3  0   0.260  -5.2450   2.3173   0.0964
 3JA  H9   H  HCR5  0   0.287  -2.0773   2.6138   1.7357
 3JA  H10  H  HCR6  0   0.248   4.7663  -0.6607  -0.8628
 3JA  H11  H  HCH2  0   0.239   0.2956  -2.0558   1.7816
 3JA  H12  H  HCH2  0   0.277  -0.5609  -0.6013   1.2727
 3JA  H13  H  HCH2  0   0.242  -2.0841  -2.5192   1.6558
 3JA  H14  H  HCH2  0   0.211  -2.1823  -1.8863   0.0038
 3JA  H15  H  HCH2  0   0.224   1.4696  -3.4593  -0.0463
 3JA  H16  H  HCH2  0   0.257   1.3441  -2.8458  -1.6939
 3JA  C1   C  CH3   0  -0.507  -4.6339   1.8622   0.8731

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
 3JA  N2   C4   aromatic  1.320  0.020  1.320
 3JA  N2   N1   aromatic  1.328  0.020  1.328
 3JA  C4   C3   aromatic  1.408  0.020  1.408
 3JA  C1   N1   single    1.443  0.020  1.443
 3JA  N1   C2   aromatic  1.344  0.020  1.344
 3JA  C13  O1   single    1.410  0.020  1.410
 3JA  C13  C14  single    1.517  0.020  1.517
 3JA  C3   C2   aromatic  1.381  0.020  1.381
 3JA  C3   C5   single    1.456  0.020  1.456
 3JA  O1   C12  single    1.410  0.020  1.410
 3JA  C14  N6   single    1.455  0.020  1.455
 3JA  C5   C6   aromatic  1.369  0.020  1.369
 3JA  C5   C8   aromatic  1.439  0.020  1.439
 3JA  C6   N3   aromatic  1.367  0.020  1.367
 3JA  C12  C11  single    1.516  0.020  1.516
 3JA  N6   C11  single    1.462  0.020  1.462
 3JA  N6   C9   single    1.372  0.020  1.372
 3JA  C8   C9   aromatic  1.412  0.020  1.412
 3JA  C8   C7   aromatic  1.408  0.020  1.408
 3JA  N3   C7   aromatic  1.351  0.020  1.351
 3JA  C9   N4   aromatic  1.330  0.020  1.330
 3JA  C7   N5   aromatic  1.332  0.020  1.332
 3JA  N4   C10  aromatic  1.331  0.020  1.331
 3JA  N5   C10  aromatic  1.315  0.020  1.315
 3JA  N3   H1   single    0.860  0.020  1.020
 3JA  C4   H2   single    0.930  0.020  1.080
 3JA  C6   H3   single    0.930  0.020  1.080
 3JA  C13  H4   single    0.970  0.020  1.090
 3JA  C13  H5   single    0.970  0.020  1.090
 3JA  C1   H6   single    0.970  0.020  1.090
 3JA  C1   H7   single    0.970  0.020  1.090
 3JA  C1   H8   single    0.970  0.020  1.090
 3JA  C2   H9   single    0.930  0.020  1.080
 3JA  C10  H10  single    0.930  0.020  1.080
 3JA  C11  H11  single    0.970  0.020  1.090
 3JA  C11  H12  single    0.970  0.020  1.090
 3JA  C12  H13  single    0.970  0.020  1.090
 3JA  C12  H14  single    0.970  0.020  1.090
 3JA  C14  H15  single    0.970  0.020  1.090
 3JA  C14  H16  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
 3JA  H1   N3   C6   125.53  3.000
 3JA  H1   N3   C7   125.18  3.000
 3JA  C6   N3   C7   109.17  3.000
 3JA  H2   C4   C3   127.74  3.000
 3JA  H2   C4   N2   120.70  3.000
 3JA  C3   C4   N2   111.56  3.000
 3JA  N1   N2   C4   105.45  3.000
 3JA  N5   C7   C8   126.35  3.000
 3JA  N5   C7   N3   125.48  3.000
 3JA  C8   C7   N3   108.12  3.000
 3JA  H3   C6   C5   129.01  3.000
 3JA  H3   C6   N3   120.72  3.000
 3JA  C5   C6   N3   110.23  3.000
 3JA  N6   C9   N4   117.74  3.000
 3JA  N4   C9   C8   118.97  3.000
 3JA  N6   C9   C8   123.29  3.000
 3JA  H5   C13  H4   107.94  3.000
 3JA  H5   C13  C14  109.35  3.000
 3JA  H4   C13  C14  109.53  3.000
 3JA  H5   C13  O1   110.48  3.000
 3JA  H4   C13  O1   107.49  3.000
 3JA  C14  C13  O1   111.95  3.000
 3JA  C5   C8   C9   138.93  3.000
 3JA  C9   C8   C7   114.40  3.000
 3JA  C5   C8   C7   106.66  3.000
 3JA  C10  N5   C7   112.73  3.000
 3JA  C2   N1   C1   127.39  3.000
 3JA  C2   N1   N2   112.36  3.000
 3JA  C1   N1   N2   120.25  3.000
 3JA  H9   C2   C3   130.92  3.000
 3JA  H9   C2   N1   121.99  3.000
 3JA  C3   C2   N1   107.09  3.000
 3JA  C5   C3   C2   127.92  3.000
 3JA  C5   C3   C4   128.45  3.000
 3JA  C2   C3   C4   103.55  3.000
 3JA  C3   C5   C8   129.69  3.000
 3JA  C8   C5   C6   105.74  3.000
 3JA  C3   C5   C6   124.35  3.000
 3JA  C10  N4   C9   119.64  3.000
 3JA  H10  C10  N4   115.83  3.000
 3JA  H10  C10  N5   116.73  3.000
 3JA  N4   C10  N5   127.43  3.000
 3JA  C14  N6   C11  111.29  3.000
 3JA  C11  N6   C9   117.82  3.000
 3JA  C14  N6   C9   117.43  3.000
 3JA  H12  C11  H11  107.52  3.000
 3JA  H12  C11  C12  108.90  3.000
 3JA  H11  C11  C12  109.49  3.000
 3JA  H12  C11  N6   110.96  3.000
 3JA  H11  C11  N6   109.60  3.000
 3JA  C12  C11  N6   110.32  3.000
 3JA  H14  C12  H13  108.09  3.000
 3JA  H14  C12  O1   110.54  3.000
 3JA  H13  C12  O1   107.59  3.000
 3JA  H14  C12  C11  109.57  3.000
 3JA  H13  C12  C11  109.25  3.000
 3JA  O1   C12  C11  111.70  3.000
 3JA  C12  O1   C13  110.52  3.000
 3JA  H16  C14  H15  107.40  3.000
 3JA  H16  C14  N6   109.82  3.000
 3JA  H15  C14  N6   111.52  3.000
 3JA  H16  C14  C13  108.89  3.000
 3JA  H15  C14  C13  110.03  3.000
 3JA  N6   C14  C13  109.14  3.000
 3JA  H8   C1   H7   108.89  3.000
 3JA  H8   C1   H6   109.17  3.000
 3JA  H7   C1   H6   108.92  3.000
 3JA  H8   C1   N1   110.23  3.000
 3JA  H7   C1   N1   108.97  3.000
 3JA  H6   C1   N1   110.62  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
 3JA  CONST_01  C3   C5   C6   N3    180.00   0.0  0
 3JA  CONST_02  C8   C5   C6   N3      0.00   0.0  0
 3JA  CONST_03  C5   C8   C7   N3      0.00   0.0  0
 3JA  CONST_04  C9   C8   C7   N3    180.00   0.0  0
 3JA  CONST_05  C10  N5   C7   N3    180.00   0.0  0
 3JA  CONST_06  C2   N1   N2   C4      0.00   0.0  0
 3JA  CONST_07  N1   C2   C3   C4      0.00   0.0  0
 3JA  CONST_10  C2   C3   C4   N2      0.00   0.0  0
 3JA  CONST_11  C5   C3   C4   N2    180.00   0.0  0
 3JA  CONST_12  C3   C2   N1   N2      0.00   0.0  0
 3JA  CONST_13  C3   C5   C8   C7    180.00   0.0  0
 3JA  CONST_14  C6   C5   C8   C7      0.00   0.0  0
 3JA  CONST_15  N4   C9   C8   C7      0.00   0.0  0
 3JA  CONST_16  C5   C6   N3   C7      0.00   0.0  0
 3JA  CONST_17  N4   C10  N5   C7      0.00   0.0  0
 3JA  CONST_19  C9   C8   C5   C6    180.00   0.0  0
 3JA  CONST_20  C8   C7   N3   C6      0.00   0.0  0
 3JA  CONST_21  N5   C7   N3   C6    180.00   0.0  0
 3JA  CONST_22  C3   C5   C8   C9      0.00   0.0  0
 3JA  CONST_23  N5   C7   C8   C9      0.00   0.0  0
 3JA  CONST_24  N5   C10  N4   C9      0.00   0.0  0
 3JA  CONST_26  C10  N4   C9   C8      0.00   0.0  0
 3JA  CONST_27  C10  N5   C7   C8      0.00   0.0  0
 3JA  CONST_28  C5   C8   C7   N5    180.00   0.0  0
 3JA  CONST_29  C3   C4   N2   N1      0.00   0.0  0
 3JA  CONST_30  C5   C3   C2   N1    180.00   0.0  0
 3JA  CONST_31  N4   C9   C8   C5    180.00   0.0  0
 3JA  CONST_32  N6   C9   C8   C7    180.00   0.0  0
 3JA  CONST_33  N6   C9   C8   C5      0.00   0.0  0
 3JA  CONST_34  N6   C9   N4   C10   180.00   0.0  0
 3JA  CONST_35  C1   N1   N2   C4    180.00   0.0  0
 3JA  CONST_36  C3   C2   N1   C1    180.00   0.0  0
 3JA  CONST_37  H9   C2   C3   C4    180.00   0.0  0
 3JA  CONST_38  H3   C6   N3   C7    180.00   0.0  0
 3JA  CONST_39  H10  C10  N5   C7    180.00   0.0  0
 3JA  CONST_40  H1   N3   C7   C8    180.00   0.0  0
 3JA  CONST_41  H2   C4   N2   N1    180.00   0.0  0
 3JA  Var_01    C13  C14  N6   C9   -165.17  30.0  1
 3JA  Var_02    C12  C11  N6   C9    165.97  30.0  1
 3JA  Var_03    C11  C12  O1   C13   -57.84  30.0  1
 3JA  Var_04    C14  N6   C9   C8    169.89  30.0  2
 3JA  Var_05    O1   C13  C14  N6    -57.63  30.0  1
 3JA  Var_06    O1   C12  C11  N6     55.31  30.0  1
 3JA  Var_07    C14  C13  O1   C12    59.36  30.0  1
 3JA  Var_08    H6   C1   N1   N2     64.00  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
 3JA  plan-1  C4   0.020
 3JA  plan-1  N2   0.020
 3JA  plan-1  N1   0.020
 3JA  plan-1  C2   0.020
 3JA  plan-1  C3   0.020
 3JA  plan-1  C5   0.020
 3JA  plan-1  H2   0.020
 3JA  plan-1  H9   0.020
 3JA  plan-1  C1   0.020
 3JA  plan-2  N3   0.020
 3JA  plan-2  C7   0.020
 3JA  plan-2  C6   0.020
 3JA  plan-2  C9   0.020
 3JA  plan-2  C8   0.020
 3JA  plan-2  N5   0.020
 3JA  plan-2  C3   0.020
 3JA  plan-2  C5   0.020
 3JA  plan-2  N4   0.020
 3JA  plan-2  C10  0.020
 3JA  plan-2  N6   0.020
 3JA  plan-2  H1   0.020
 3JA  plan-2  H3   0.020
 3JA  plan-2  H10  0.020

