# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 05:03:46 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: ~{N}4-(1,3-benzodioxol-5-ylmethyl)-6-(3-methoxyphenyl)pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2cc(NCc3ccc4OCOc4c3)nc(N)n2
#
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
 FW9  FW9  ~{N}4-(1,3-benzodioxol-5-ylmethyl)-6-(3-methoxyphenyl)pyrimidine-2,4-diamine  ligand  44  26  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FW9
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
 FW9  N12   N  NH2   0  -0.825  18.4501  62.8483  39.0261
 FW9  C17   C  CR6   0   0.101  15.1542  65.9759  41.1709
 FW9  C20   C  CR56  0   0.287  16.6771  67.5744  42.8211
 FW9  C22   C  CH2   0   0.071  17.0637  69.7632  42.7854
 FW9  C24   C  CR56  0   0.310  15.9119  68.1319  41.8075
 FW9  C26   C  CR16  0  -0.491  15.9374  65.1592  36.9109
 FW9  C01   C  CH3   0  -0.435  20.2423  63.8255  31.2060
 FW9  C03   C  CR6   0   0.413  18.8523  64.4393  33.0281
 FW9  C04   C  CR16  0  -0.391  18.4652  64.1947  34.3455
 FW9  C05   C  CR6   0   0.075  17.4936  64.9723  34.9631
 FW9  C06   C  CR16  0  -0.345  16.9087  66.0218  34.2483
 FW9  C07   C  CR16  0  -0.221  17.2966  66.2633  32.9434
 FW9  C08   C  CR16  0  -0.387  18.2626  65.4825  32.3187
 FW9  C09   C  CR6   0   0.294  17.1086  64.6801  36.3651
 FW9  C11   C  CR6   0   0.528  17.6207  63.6547  38.3245
 FW9  C14   C  CR6   0   0.582  15.6879  64.8346  38.2609
 FW9  C16   C  CH2   0  -0.371  14.3104  65.0924  40.2811
 FW9  C18   C  CR16  0  -0.319  15.9237  65.4280  42.1852
 FW9  C19   C  CR16  0  -0.332  16.7040  66.2208  43.0384
 FW9  C25   C  CR16  0  -0.380  15.1420  67.3667  40.9702
 FW9  N10   N  N     0  -0.521  17.9581  63.9207  37.0664
 FW9  N13   N  N     0  -0.511  16.5302  64.0857  38.9620
 FW9  N15   N  NH1   0  -0.667  14.5675  65.2657  38.8711
 FW9  O21   O  O     0  -0.484  17.3163  68.5606  43.4976
 FW9  O23   O  O     0  -0.485  16.0506  69.4802  41.8299
 FW9  H121  H  HNH2  0   0.388  19.3733  62.6874  38.6622
 FW9  H122  H  HNH2  0   0.388  18.3489  62.8165  40.0259
 FW9  H221  H  HCH2  0   0.230  17.9753  70.0917  42.2745
 FW9  H222  H  HCH2  0   0.241  16.7164  70.5347  43.4739
 FW9  H261  H  HCR6  0   0.262  15.2269  65.7509  36.3523
 FW9  H011  H  HCH3  0   0.258  21.0054  63.0748  31.0161
 FW9  H013  H  HCH3  0   0.227  19.4371  63.6965  30.4777
 FW9  H012  H  HCH3  0   0.227  20.6842  64.8163  31.0711
 FW9  H041  H  HCR6  0   0.256  18.9290  63.3834  34.8913
 FW9  H061  H  HCR6  0   0.248  16.1677  66.6640  34.7040
 FW9  H071  H  HCR6  0   0.259  16.8474  67.0804  32.3940
 FW9  H081  H  HCR6  0   0.280  18.5386  65.7020  31.2963
 FW9  H161  H  HCH2  0   0.270  13.2532  65.3145  40.4335
 FW9  H162  H  HCH2  0   0.258  14.4556  64.0474  40.5577
 FW9  H181  H  HCR6  0   0.250  15.9318  64.3538  42.3216
 FW9  H191  H  HCR6  0   0.268  17.3009  65.7797  43.8254
 FW9  H251  H  HCR6  0   0.265  14.5474  67.8170  40.1846
 FW9  H151  H  HNH1  0   0.401  13.9664  65.8881  38.3575
 FW9  O02   O  O2    0  -0.469  19.7979  63.6197  32.5311

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
 FW9  C01  O02   single    1.413  0.020  1.413
 FW9  O02  C03   single    1.346  0.020  1.346
 FW9  C08  C03   aromatic  1.393  0.020  1.393
 FW9  C08  C07   aromatic  1.390  0.020  1.390
 FW9  C03  C04   aromatic  1.395  0.020  1.395
 FW9  C07  C06   aromatic  1.383  0.020  1.383
 FW9  C04  C05   aromatic  1.389  0.020  1.389
 FW9  C06  C05   aromatic  1.398  0.020  1.398
 FW9  C05  C09   single    1.483  0.020  1.483
 FW9  C09  C26   aromatic  1.378  0.020  1.378
 FW9  C09  N10   aromatic  1.338  0.020  1.338
 FW9  C26  C14   aromatic  1.411  0.020  1.411
 FW9  N10  C11   aromatic  1.329  0.020  1.329
 FW9  C14  N15   single    1.347  0.020  1.347
 FW9  C14  N13   aromatic  1.327  0.020  1.327
 FW9  C11  N13   aromatic  1.335  0.020  1.335
 FW9  C11  N12   single    1.353  0.020  1.353
 FW9  N15  C16   single    1.444  0.020  1.444
 FW9  C16  C17   single    1.511  0.020  1.511
 FW9  C17  C25   aromatic  1.405  0.020  1.405
 FW9  C17  C18   aromatic  1.386  0.020  1.386
 FW9  C25  C24   aromatic  1.371  0.020  1.371
 FW9  C24  O23   single    1.356  0.020  1.356
 FW9  C24  C20   aromatic  1.387  0.020  1.387
 FW9  C18  C19   aromatic  1.402  0.020  1.402
 FW9  O23  C22   single    1.421  0.020  1.421
 FW9  C20  C19   aromatic  1.371  0.020  1.371
 FW9  C20  O21   single    1.356  0.020  1.356
 FW9  C22  O21   single    1.420  0.020  1.420
 FW9  N12  H121  single    0.890  0.020  1.040
 FW9  N12  H122  single    0.890  0.020  1.040
 FW9  C22  H221  single    0.970  0.020  1.090
 FW9  C22  H222  single    0.970  0.020  1.090
 FW9  C26  H261  single    0.930  0.020  1.080
 FW9  C01  H011  single    0.970  0.020  1.090
 FW9  C01  H013  single    0.970  0.020  1.090
 FW9  C01  H012  single    0.970  0.020  1.090
 FW9  C04  H041  single    0.930  0.020  1.080
 FW9  C06  H061  single    0.930  0.020  1.080
 FW9  C07  H071  single    0.930  0.020  1.080
 FW9  C08  H081  single    0.930  0.020  1.080
 FW9  C16  H161  single    0.970  0.020  1.090
 FW9  C16  H162  single    0.970  0.020  1.090
 FW9  C18  H181  single    0.930  0.020  1.080
 FW9  C19  H191  single    0.930  0.020  1.080
 FW9  C25  H251  single    0.930  0.020  1.080
 FW9  N15  H151  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
 FW9  H122  N12  H121  116.57  3.000
 FW9  H122  N12  C11   118.22  3.000
 FW9  H121  N12  C11   118.08  3.000
 FW9  C25   C17  C18   120.03  3.000
 FW9  C18   C17  C16   120.65  3.000
 FW9  C25   C17  C16   119.32  3.000
 FW9  O21   C20  C19   129.02  3.000
 FW9  O21   C20  C24   109.41  3.000
 FW9  C19   C20  C24   121.56  3.000
 FW9  H222  C22  H221  110.32  3.000
 FW9  H222  C22  O23   109.77  3.000
 FW9  H221  C22  O23   109.84  3.000
 FW9  H222  C22  O21   109.81  3.000
 FW9  H221  C22  O21   109.87  3.000
 FW9  O23   C22  O21   107.18  3.000
 FW9  O23   C24  C25   128.52  3.000
 FW9  O23   C24  C20   109.34  3.000
 FW9  C25   C24  C20   122.13  3.000
 FW9  H261  C26  C14   120.30  3.000
 FW9  H261  C26  C09   123.00  3.000
 FW9  C14   C26  C09   116.70  3.000
 FW9  H012  C01  H013  108.81  3.000
 FW9  H012  C01  H011  108.70  3.000
 FW9  H013  C01  H011  108.61  3.000
 FW9  H012  C01  O02   112.02  3.000
 FW9  H013  C01  O02   112.08  3.000
 FW9  H011  C01  O02   106.50  3.000
 FW9  O02   C03  C08   124.43  3.000
 FW9  C08   C03  C04   119.67  3.000
 FW9  O02   C03  C04   115.90  3.000
 FW9  H041  C04  C05   119.68  3.000
 FW9  H041  C04  C03   119.27  3.000
 FW9  C05   C04  C03   121.05  3.000
 FW9  C09   C05  C06   121.51  3.000
 FW9  C09   C05  C04   119.44  3.000
 FW9  C06   C05  C04   119.05  3.000
 FW9  H061  C06  C07   119.10  3.000
 FW9  H061  C06  C05   121.14  3.000
 FW9  C07   C06  C05   119.76  3.000
 FW9  H071  C07  C08   118.97  3.000
 FW9  H071  C07  C06   119.64  3.000
 FW9  C08   C07  C06   121.39  3.000
 FW9  H081  C08  C07   119.21  3.000
 FW9  H081  C08  C03   121.71  3.000
 FW9  C07   C08  C03   119.08  3.000
 FW9  N10   C09  C05   116.26  3.000
 FW9  N10   C09  C26   121.96  3.000
 FW9  C05   C09  C26   121.77  3.000
 FW9  N13   C11  N10   126.49  3.000
 FW9  N13   C11  N12   116.47  3.000
 FW9  N10   C11  N12   117.03  3.000
 FW9  N15   C14  N13   117.99  3.000
 FW9  N13   C14  C26   121.53  3.000
 FW9  N15   C14  C26   120.47  3.000
 FW9  H162  C16  H161  106.78  3.000
 FW9  H162  C16  N15   109.81  3.000
 FW9  H161  C16  N15   106.54  3.000
 FW9  H162  C16  C17   109.66  3.000
 FW9  H161  C16  C17   109.86  3.000
 FW9  N15   C16  C17   113.92  3.000
 FW9  H181  C18  C19   118.69  3.000
 FW9  H181  C18  C17   119.24  3.000
 FW9  C19   C18  C17   122.07  3.000
 FW9  H191  C19  C18   121.29  3.000
 FW9  H191  C19  C20   121.91  3.000
 FW9  C18   C19  C20   116.80  3.000
 FW9  H251  C25  C24   121.27  3.000
 FW9  H251  C25  C17   121.32  3.000
 FW9  C24   C25  C17   117.41  3.000
 FW9  C11   N10  C09   116.65  3.000
 FW9  C14   N13  C11   116.64  3.000
 FW9  H151  N15  C16   117.80  3.000
 FW9  H151  N15  C14   117.63  3.000
 FW9  C16   N15  C14   123.52  3.000
 FW9  C22   O21  C20   106.37  3.000
 FW9  C24   O23  C22   106.39  3.000
 FW9  C03   O02  C01   118.58  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
 FW9  CONST_01  C20   C24  C25  C17     0.00   0.0  0
 FW9  CONST_02  C20   C19  C18  C17     0.00   0.0  0
 FW9  CONST_03  C18   C17  C25  C24     0.00   0.0  0
 FW9  CONST_04  C18   C19  C20  C24     0.00   0.0  0
 FW9  CONST_07  C11   N10  C09  C26     0.00   0.0  0
 FW9  CONST_08  C11   N13  C14  C26     0.00   0.0  0
 FW9  CONST_09  C06   C07  C08  C03     0.00   0.0  0
 FW9  CONST_10  C06   C05  C04  C03     0.00   0.0  0
 FW9  CONST_11  C09   C05  C04  C03   180.00   0.0  0
 FW9  CONST_12  C07   C08  C03  C04     0.00   0.0  0
 FW9  CONST_13  C07   C06  C05  C04     0.00   0.0  0
 FW9  CONST_15  C08   C03  C04  C05     0.00   0.0  0
 FW9  CONST_16  C08   C07  C06  C05     0.00   0.0  0
 FW9  CONST_17  C14   C26  C09  C05   180.00   0.0  0
 FW9  CONST_18  C11   N10  C09  C05   180.00   0.0  0
 FW9  CONST_20  C09   C05  C06  C07   180.00   0.0  0
 FW9  CONST_21  N13   C14  C26  C09     0.00   0.0  0
 FW9  CONST_22  N13   C11  N10  C09     0.00   0.0  0
 FW9  CONST_23  N10   C09  C26  C14     0.00   0.0  0
 FW9  CONST_24  N10   C11  N13  C14     0.00   0.0  0
 FW9  CONST_25  C25   C17  C18  C19     0.00   0.0  0
 FW9  CONST_26  C25   C24  C20  C19     0.00   0.0  0
 FW9  CONST_27  C09   N10  C11  N12   180.00   0.0  0
 FW9  CONST_28  C14   N13  C11  N12   180.00   0.0  0
 FW9  CONST_29  C16   C17  C25  C24   180.00   0.0  0
 FW9  CONST_30  O02   C03  C04  C05   180.00   0.0  0
 FW9  CONST_31  O02   C03  C08  C07   180.00   0.0  0
 FW9  CONST_32  N15   C14  C26  C09   180.00   0.0  0
 FW9  CONST_33  N15   C14  N13  C11   180.00   0.0  0
 FW9  CONST_34  C19   C18  C17  C16   180.00   0.0  0
 FW9  CONST_35  H191  C19  C18  C17   180.00   0.0  0
 FW9  CONST_36  H251  C25  C24  C20   180.00   0.0  0
 FW9  CONST_37  H181  C18  C19  C20   180.00   0.0  0
 FW9  CONST_38  H071  C07  C08  C03   180.00   0.0  0
 FW9  CONST_39  H081  C08  C03  C04   180.00   0.0  0
 FW9  CONST_40  H061  C06  C05  C04   180.00   0.0  0
 FW9  CONST_41  H261  C26  C09  C05     0.00   0.0  0
 FW9  CONST_42  H041  C04  C05  C06   180.00   0.0  0
 FW9  CONST_43  C16   N15  C14  C26   180.00   0.0  0
 FW9  CONST_44  N13   C14  N15  C16     0.00   0.0  0
 FW9  CONST_45  H151  N15  C14  C26     0.00   0.0  0
 FW9  Var_01    O23   C22  O21  C20    11.10  30.0  1
 FW9  Var_02    C25   C24  O23  C22  -173.98  30.0  1
 FW9  Var_03    C24   C20  O21  C22    -6.81  30.0  1
 FW9  Var_04    O21   C22  O23  C24   -11.25  30.0  1
 FW9  Var_05    C14   N15  C16  C17    72.07  30.0  1
 FW9  Var_06    C08   C03  O02  C01     0.60  30.0  2
 FW9  Var_07    N15   C16  C17  C18  -125.49  30.0  2
 FW9  Var_08    H011  C01  O02  C03   179.15  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
 FW9  plan-1  C03   0.020
 FW9  plan-1  C04   0.020
 FW9  plan-1  C05   0.020
 FW9  plan-1  C06   0.020
 FW9  plan-1  C07   0.020
 FW9  plan-1  C08   0.020
 FW9  plan-1  C09   0.020
 FW9  plan-1  H041  0.020
 FW9  plan-1  H061  0.020
 FW9  plan-1  H071  0.020
 FW9  plan-1  H081  0.020
 FW9  plan-1  O02   0.020
 FW9  plan-2  N12   0.020
 FW9  plan-2  C26   0.020
 FW9  plan-2  C05   0.020
 FW9  plan-2  C09   0.020
 FW9  plan-2  C11   0.020
 FW9  plan-2  C14   0.020
 FW9  plan-2  N10   0.020
 FW9  plan-2  N13   0.020
 FW9  plan-2  N15   0.020
 FW9  plan-2  H261  0.020
 FW9  plan-3  C17   0.020
 FW9  plan-3  C20   0.020
 FW9  plan-3  C24   0.020
 FW9  plan-3  C16   0.020
 FW9  plan-3  C18   0.020
 FW9  plan-3  C19   0.020
 FW9  plan-3  C25   0.020
 FW9  plan-3  O21   0.020
 FW9  plan-3  O23   0.020
 FW9  plan-3  H181  0.020
 FW9  plan-3  H191  0.020
 FW9  plan-3  H251  0.020
 FW9  plan-4  N12   0.020
 FW9  plan-4  C11   0.020
 FW9  plan-4  H121  0.020
 FW9  plan-4  H122  0.020
 FW9  plan-5  C14   0.020
 FW9  plan-5  C16   0.020
 FW9  plan-5  N15   0.020
 FW9  plan-5  H151  0.020

