# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 03:31:32 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 5-(4-fluorophenyl)-1H-pyrrolo[2,3-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]c2ncc(c3ccc(F)cc3)c2c(N)n1
#
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
 4NR  4NR  5-(4-fluorophenyl)-1H-pyrrolo[2,3-d]pyrimidine-2,4-diamine  ligand  28  18  .  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_4NR
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
 4NR  CAF   C  CR16  0  -0.300  -2.4116   1.0984  -0.8575
 4NR  CAD   C  CR16  0  -0.396  -3.7492   0.7351  -0.8091
 4NR  CAL   C  CR6   0   0.505  -4.1412  -0.2357   0.0921
 4NR  FAC   F  F     0  -0.318  -5.4332  -0.6060   0.1346
 4NR  CAE   C  CR16  0  -0.391  -3.2420  -0.8377   0.9498
 4NR  CAG   C  CR16  0  -0.347  -1.9108  -0.4493   0.8984
 4NR  CAO   C  CR6   0   0.025  -1.4642   0.5170  -0.0091
 4NR  CAP   C  CR5   0   0.006  -0.0646   0.9421  -0.0500
 4NR  C5    C  CR56  0  -0.149   1.1320   0.1535  -0.0167
 4NR  C6    C  CR6   0   0.418   1.5088  -1.1999  -0.0862
 4NR  NAB   N  NH2   0  -0.818   0.6316  -2.1996  -0.1893
 4NR  N1    N  N     0  -0.519   2.8047  -1.5550  -0.0518
 4NR  C2    C  CR6   0   0.669   3.7444  -0.6313  -0.0102
 4NR  NAA   N  NH2   0  -0.826   5.0303  -1.0166  -0.0138
 4NR  N3    N  NR16  0  -0.710   3.4761   0.6869  -0.0107
 4NR  C4    C  CR56  0   0.449   2.1676   1.1045  -0.0229
 4NR  NAK   N  N     0  -0.491   1.7555   2.3543  -0.0572
 4NR  CAH   C  CR15  0  -0.182   0.3910   2.2463  -0.0770
 4NR  HAF   H  HCR6  0   0.255  -2.0962   1.8394  -1.5810
 4NR  HAD   H  HCR6  0   0.278  -4.4698   1.1908  -1.4758
 4NR  HAE   H  HCR6  0   0.278  -3.5731  -1.5869   1.6574
 4NR  HAG   H  HCR6  0   0.270  -1.2152  -0.8928   1.6006
 4NR  HAH   H  HCR5  0   0.231  -0.2259   3.1362  -0.0786
 4NR  HAB1  H  HNH2  0   0.415  -0.3500  -2.0279  -0.3149
 4NR  HAB2  H  HNH2  0   0.403   0.9605  -3.1444  -0.2918
 4NR  HAA1  H  HNH2  0   0.410   5.2205  -1.9913   0.1450
 4NR  HAA2  H  HNH2  0   0.412   5.7593  -0.3720   0.2410
 4NR  H3    H  HNR6  0   0.422   4.2202   1.3702  -0.0148

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
 4NR  CAF  CAD   aromatic  1.387  0.020  1.387
 4NR  CAF  CAO   aromatic  1.398  0.020  1.398
 4NR  CAD  CAL   aromatic  1.381  0.020  1.381
 4NR  CAL  FAC   single    1.345  0.020  1.345
 4NR  CAL  CAE   aromatic  1.381  0.020  1.381
 4NR  CAE  CAG   aromatic  1.388  0.020  1.388
 4NR  CAG  CAO   aromatic  1.399  0.020  1.399
 4NR  CAO  CAP   single    1.463  0.020  1.463
 4NR  CAP  C5    aromatic  1.433  0.020  1.433
 4NR  CAP  CAH   aromatic  1.382  0.020  1.382
 4NR  C5   C6    aromatic  1.407  0.020  1.407
 4NR  C5   C4    aromatic  1.406  0.020  1.406
 4NR  C6   NAB   single    1.334  0.020  1.334
 4NR  C6   N1    aromatic  1.344  0.020  1.344
 4NR  N1   C2    aromatic  1.318  0.020  1.318
 4NR  C2   NAA   single    1.342  0.020  1.342
 4NR  C2   N3    aromatic  1.345  0.020  1.345
 4NR  N3   C4    aromatic  1.374  0.020  1.374
 4NR  C4   NAK   aromatic  1.316  0.020  1.316
 4NR  NAK  CAH   aromatic  1.369  0.020  1.369
 4NR  CAF  HAF   single    0.930  0.020  1.080
 4NR  CAD  HAD   single    0.930  0.020  1.080
 4NR  CAE  HAE   single    0.930  0.020  1.080
 4NR  CAG  HAG   single    0.930  0.020  1.080
 4NR  CAH  HAH   single    0.930  0.020  1.080
 4NR  NAB  HAB1  single    0.860  0.020  1.020
 4NR  NAB  HAB2  single    0.860  0.020  1.020
 4NR  NAA  HAA1  single    0.890  0.020  1.040
 4NR  NAA  HAA2  single    0.890  0.020  1.040
 4NR  N3   H3    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
 4NR  HAF   CAF  CAO   119.51  3.000
 4NR  HAF   CAF  CAD   118.92  3.000
 4NR  CAO   CAF  CAD   121.56  3.000
 4NR  HAD   CAD  CAL   120.59  3.000
 4NR  HAD   CAD  CAF   120.68  3.000
 4NR  CAL   CAD  CAF   118.72  3.000
 4NR  CAE   CAL  FAC   119.08  3.000
 4NR  CAE   CAL  CAD   121.79  3.000
 4NR  FAC   CAL  CAD   119.13  3.000
 4NR  HAE   CAE  CAG   120.76  3.000
 4NR  HAE   CAE  CAL   120.57  3.000
 4NR  CAG   CAE  CAL   118.67  3.000
 4NR  HAG   CAG  CAO   119.89  3.000
 4NR  HAG   CAG  CAE   118.52  3.000
 4NR  CAO   CAG  CAE   121.58  3.000
 4NR  CAP   CAO  CAG   121.61  3.000
 4NR  CAP   CAO  CAF   120.69  3.000
 4NR  CAG   CAO  CAF   117.68  3.000
 4NR  CAH   CAP  C5    104.15  3.000
 4NR  CAH   CAP  CAO   126.16  3.000
 4NR  C5    CAP  CAO   129.64  3.000
 4NR  C4    C5   C6    116.95  3.000
 4NR  C4    C5   CAP   104.04  3.000
 4NR  C6    C5   CAP   138.75  3.000
 4NR  N1    C6   NAB   115.97  3.000
 4NR  N1    C6   C5    120.75  3.000
 4NR  NAB   C6   C5    123.28  3.000
 4NR  HAB2  NAB  HAB1  117.87  3.000
 4NR  HAB2  NAB  C6    119.79  3.000
 4NR  HAB1  NAB  C6    121.62  3.000
 4NR  C2    N1   C6    120.19  3.000
 4NR  N3    C2   NAA   118.19  3.000
 4NR  N3    C2   N1    122.99  3.000
 4NR  NAA   C2   N1    118.78  3.000
 4NR  HAA2  NAA  HAA1  116.36  3.000
 4NR  HAA2  NAA  C2    120.63  3.000
 4NR  HAA1  NAA  C2    117.32  3.000
 4NR  H3    N3   C4    119.73  3.000
 4NR  H3    N3   C2    121.06  3.000
 4NR  C4    N3   C2    119.20  3.000
 4NR  NAK   C4   N3    125.95  3.000
 4NR  NAK   C4   C5    114.31  3.000
 4NR  N3    C4   C5    119.73  3.000
 4NR  CAH   NAK  C4    103.74  3.000
 4NR  HAH   CAH  NAK   120.20  3.000
 4NR  HAH   CAH  CAP   126.01  3.000
 4NR  NAK   CAH  CAP   113.76  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
 4NR  CONST_01  CAE   CAL  CAD  CAF    0.00  0.0  0
 4NR  CONST_02  CAE   CAG  CAO  CAF    0.00  0.0  0
 4NR  CONST_05  CAG   CAO  CAF  CAD    0.00  0.0  0
 4NR  CONST_06  CAP   CAO  CAF  CAD  180.00  0.0  0
 4NR  CONST_07  CAG   CAE  CAL  CAD    0.00  0.0  0
 4NR  CONST_08  CAO   CAF  CAD  CAL    0.00  0.0  0
 4NR  CONST_09  CAO   CAG  CAE  CAL    0.00  0.0  0
 4NR  CONST_10  CAP   CAO  CAG  CAE  180.00  0.0  0
 4NR  CONST_13  C6    C5   CAP  CAO    0.00  0.0  0
 4NR  CONST_14  C4    C5   CAP  CAO  180.00  0.0  0
 4NR  CONST_15  NAK   CAH  CAP  CAO  180.00  0.0  0
 4NR  CONST_16  N1    C6   C5   CAP  180.00  0.0  0
 4NR  CONST_17  N3    C4   C5   CAP  180.00  0.0  0
 4NR  CONST_18  NAK   C4   C5   CAP    0.00  0.0  0
 4NR  CONST_19  C4    NAK  CAH  CAP    0.00  0.0  0
 4NR  CONST_20  NAK   CAH  CAP  C5     0.00  0.0  0
 4NR  CONST_21  C2    N1   C6   C5     0.00  0.0  0
 4NR  CONST_22  C2    N3   C4   C5     0.00  0.0  0
 4NR  CONST_23  CAH   NAK  C4   C5     0.00  0.0  0
 4NR  CONST_24  CAH   CAP  C5   C6   180.00  0.0  0
 4NR  CONST_25  N3    C4   C5   C6     0.00  0.0  0
 4NR  CONST_26  NAK   C4   C5   C6   180.00  0.0  0
 4NR  CONST_27  N3    C2   N1   C6     0.00  0.0  0
 4NR  CONST_28  C4    C5   C6   N1     0.00  0.0  0
 4NR  CONST_29  C4    N3   C2   N1     0.00  0.0  0
 4NR  CONST_30  NAK   C4   N3   C2   180.00  0.0  0
 4NR  CONST_31  CAH   NAK  C4   N3   180.00  0.0  0
 4NR  CONST_32  CAH   CAP  C5   C4     0.00  0.0  0
 4NR  CONST_33  FAC   CAL  CAD  CAF  180.00  0.0  0
 4NR  CONST_34  CAG   CAE  CAL  FAC  180.00  0.0  0
 4NR  CONST_35  NAB   C6   C5   CAP    0.00  0.0  0
 4NR  CONST_36  NAA   C2   N1   C6   180.00  0.0  0
 4NR  CONST_37  C4    C5   C6   NAB  180.00  0.0  0
 4NR  CONST_38  C2    N1   C6   NAB  180.00  0.0  0
 4NR  CONST_39  C4    N3   C2   NAA  180.00  0.0  0
 4NR  CONST_40  HAG   CAG  CAO  CAF  180.00  0.0  0
 4NR  CONST_41  HAE   CAE  CAL  CAD  180.00  0.0  0
 4NR  CONST_42  HAF   CAF  CAD  CAL  180.00  0.0  0
 4NR  CONST_43  HAD   CAD  CAL  CAE  180.00  0.0  0
 4NR  CONST_44  HAH   CAH  CAP  CAO    0.00  0.0  0
 4NR  CONST_45  H3    N3   C4   C5   180.00  0.0  0
 4NR  CONST_46  HAB1  NAB  C6   C5     0.00  0.0  0
 4NR  CONST_47  HAB2  NAB  C6   C5   180.00  0.0  0
 4NR  CONST_48  HAA1  NAA  C2   N1     0.00  0.0  0

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
 4NR  plan-1  CAF   0.020
 4NR  plan-1  CAD   0.020
 4NR  plan-1  CAL   0.020
 4NR  plan-1  FAC   0.020
 4NR  plan-1  CAE   0.020
 4NR  plan-1  CAG   0.020
 4NR  plan-1  CAO   0.020
 4NR  plan-1  CAP   0.020
 4NR  plan-1  HAF   0.020
 4NR  plan-1  HAD   0.020
 4NR  plan-1  HAE   0.020
 4NR  plan-1  HAG   0.020
 4NR  plan-2  CAO   0.020
 4NR  plan-2  CAP   0.020
 4NR  plan-2  C5    0.020
 4NR  plan-2  C6    0.020
 4NR  plan-2  NAB   0.020
 4NR  plan-2  N1    0.020
 4NR  plan-2  C2    0.020
 4NR  plan-2  NAA   0.020
 4NR  plan-2  N3    0.020
 4NR  plan-2  C4    0.020
 4NR  plan-2  NAK   0.020
 4NR  plan-2  CAH   0.020
 4NR  plan-2  HAH   0.020
 4NR  plan-2  H3    0.020
 4NR  plan-3  C6    0.020
 4NR  plan-3  NAB   0.020
 4NR  plan-3  HAB1  0.020
 4NR  plan-3  HAB2  0.020
 4NR  plan-4  C2    0.020
 4NR  plan-4  NAA   0.020
 4NR  plan-4  HAA1  0.020
 4NR  plan-4  HAA2  0.020

