# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 06:26:44 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: (3R)-3-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#CC[C@H](C1CCCC1)n2cc(cn2)c3ncnc4[nH]ccc34
#
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
 RXT  RXT  (3R)-3-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile  ligand  41  23  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RXT
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
 RXT  CAK  C  CH2   0  -0.448  -4.9531  -0.2881   0.6433
 RXT  CAH  C  CH2   0  -0.443  -5.4571  -1.5374   1.3861
 RXT  CAI  C  CH2   0  -0.451  -4.2996  -2.5600   1.3328
 RXT  CAL  C  CH2   0  -0.423  -3.2431  -1.9419   0.4132
 RXT  CAU  C  CH1   0  -0.253  -3.4293  -0.4384   0.6125
 RXT  CAV  C  CH1   0  -0.099  -2.7721   0.4105  -0.4672
 RXT  CAJ  C  CH2   0  -0.539  -2.9824   1.9087  -0.2106
 RXT  CAB  C  CSP   0   0.134  -2.3243   2.7281  -1.2153
 RXT  NAA  N  NS    0  -0.257  -1.7995   3.3678  -2.0141
 RXT  NAW  N  NR5   0  -0.284  -1.3560   0.1152  -0.6006
 RXT  CAG  C  CR15  0   0.089  -0.3971   0.2666   0.3211
 RXT  NAO  N  N     0  -0.257  -0.8882  -0.3784  -1.7483
 RXT  CAF  C  CR15  0  -0.097   0.4022  -0.5451  -1.5591
 RXT  CAQ  C  CR5   0  -0.189   0.7870  -0.1524  -0.2594
 RXT  CAR  C  CR6   0   0.235   2.0894  -0.1588   0.3819
 RXT  NAM  N  N     0  -0.455   2.1219   0.1862   1.6707
 RXT  CAE  C  CR16  0   0.039   3.2868   0.2019   2.3097
 RXT  NAP  N  N     0  -0.423   4.4769  -0.0918   1.8176
 RXT  CAT  C  CR56  0   0.498   4.4421  -0.4315   0.5370
 RXT  CAS  C  CR56  0   0.007   3.2823  -0.4936  -0.2683
 RXT  CAD  C  CR15  0  -0.474   3.7110  -0.8931  -1.5721
 RXT  CAC  C  CR15  0   0.043   5.0625  -1.0510  -1.4998
 RXT  NAN  N  NR15  0  -0.652   5.5004  -0.7736  -0.2316
 RXT  H1   H  HCH2  0   0.230  -5.3268  -0.2792  -0.3852
 RXT  H2   H  HCH2  0   0.247  -5.2831   0.6396   1.1126
 RXT  H3   H  HCH2  0   0.233  -5.7111  -1.2969   2.4190
 RXT  H4   H  HCH2  0   0.234  -6.3655  -1.9235   0.9239
 RXT  H5   H  HCH2  0   0.230  -3.8798  -2.7067   2.3296
 RXT  H6   H  HCH2  0   0.235  -4.6229  -3.5397   0.9806
 RXT  H7   H  HCH2  0   0.243  -2.2335  -2.2854   0.6432
 RXT  H8   H  HCH2  0   0.224  -3.4457  -2.1982  -0.6317
 RXT  H9   H  HCH1  0   0.244  -3.0214  -0.1556   1.5915
 RXT  H10  H  HCH1  0   0.297  -3.2060   0.1565  -1.4344
 RXT  H11  H  HCH2  0   0.331  -4.0488   2.1385  -0.2259
 RXT  H12  H  HCH2  0   0.298  -2.6076   2.1987   0.7736
 RXT  H18  H  HCR5  0   0.287  -0.5932   0.6511   1.3090
 RXT  H19  H  HCR5  0   0.241   1.0066  -0.9482  -2.3551
 RXT  H20  H  HCR6  0   0.236   3.2533   0.4891   3.3550
 RXT  H21  H  HCR5  0   0.229   3.1194  -1.0505  -2.4576
 RXT  H22  H  HCR5  0   0.270   5.7609  -1.3437  -2.2662
 RXT  H23  H  HNR5  0   0.391   6.4574  -0.8144   0.0789

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
 RXT  CAE  NAM  aromatic  1.329  0.020  1.329
 RXT  CAE  NAP  aromatic  1.321  0.020  1.321
 RXT  NAM  CAR  aromatic  1.335  0.020  1.335
 RXT  NAP  CAT  aromatic  1.325  0.020  1.325
 RXT  CAF  CAQ  aromatic  1.411  0.020  1.411
 RXT  CAF  NAO  aromatic  1.315  0.020  1.315
 RXT  CAR  CAQ  single    1.452  0.020  1.452
 RXT  CAR  CAS  aromatic  1.399  0.020  1.399
 RXT  CAQ  CAG  aromatic  1.384  0.020  1.384
 RXT  NAO  NAW  aromatic  1.334  0.020  1.334
 RXT  CAT  CAS  aromatic  1.413  0.020  1.413
 RXT  CAT  NAN  aromatic  1.352  0.020  1.352
 RXT  CAS  CAD  aromatic  1.429  0.020  1.429
 RXT  NAN  CAC  aromatic  1.370  0.020  1.370
 RXT  NAW  CAG  aromatic  1.339  0.020  1.339
 RXT  NAW  CAV  single    1.453  0.020  1.453
 RXT  CAJ  CAB  single    1.454  0.020  1.454
 RXT  CAJ  CAV  single    1.535  0.020  1.535
 RXT  CAD  CAC  aromatic  1.363  0.020  1.363
 RXT  CAB  NAA  triple    1.150  0.020  1.150
 RXT  CAV  CAU  single    1.523  0.020  1.523
 RXT  CAL  CAI  single    1.531  0.020  1.531
 RXT  CAL  CAU  single    1.528  0.020  1.528
 RXT  CAI  CAH  single    1.545  0.020  1.545
 RXT  CAU  CAK  single    1.532  0.020  1.532
 RXT  CAH  CAK  single    1.538  0.020  1.538
 RXT  CAK  H1   single    0.970  0.020  1.090
 RXT  CAK  H2   single    0.970  0.020  1.090
 RXT  CAH  H3   single    0.970  0.020  1.090
 RXT  CAH  H4   single    0.970  0.020  1.090
 RXT  CAI  H5   single    0.970  0.020  1.090
 RXT  CAI  H6   single    0.970  0.020  1.090
 RXT  CAL  H7   single    0.970  0.020  1.090
 RXT  CAL  H8   single    0.970  0.020  1.090
 RXT  CAU  H9   single    0.970  0.020  1.090
 RXT  CAV  H10  single    0.970  0.020  1.090
 RXT  CAJ  H11  single    0.970  0.020  1.090
 RXT  CAJ  H12  single    0.970  0.020  1.090
 RXT  CAG  H18  single    0.930  0.020  1.080
 RXT  CAF  H19  single    0.930  0.020  1.080
 RXT  CAE  H20  single    0.930  0.020  1.080
 RXT  CAD  H21  single    0.930  0.020  1.080
 RXT  CAC  H22  single    0.930  0.020  1.080
 RXT  NAN  H23  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
 RXT  H2   CAK  H1   107.10  3.000
 RXT  H2   CAK  CAU  113.15  3.000
 RXT  H1   CAK  CAU  108.77  3.000
 RXT  H2   CAK  CAH  112.57  3.000
 RXT  H1   CAK  CAH  110.39  3.000
 RXT  CAU  CAK  CAH  104.83  3.000
 RXT  H4   CAH  H3   106.60  3.000
 RXT  H4   CAH  CAI  112.04  3.000
 RXT  H3   CAH  CAI  110.68  3.000
 RXT  H4   CAH  CAK  110.85  3.000
 RXT  H3   CAH  CAK  110.76  3.000
 RXT  CAI  CAH  CAK  105.98  3.000
 RXT  H6   CAI  H5   106.76  3.000
 RXT  H6   CAI  CAL  111.93  3.000
 RXT  H5   CAI  CAL  109.72  3.000
 RXT  H6   CAI  CAH  112.56  3.000
 RXT  H5   CAI  CAH  110.21  3.000
 RXT  CAL  CAI  CAH  105.69  3.000
 RXT  H8   CAL  H7   107.38  3.000
 RXT  H8   CAL  CAU  109.41  3.000
 RXT  H7   CAL  CAU  113.27  3.000
 RXT  H8   CAL  CAI  110.55  3.000
 RXT  H7   CAL  CAI  112.64  3.000
 RXT  CAU  CAL  CAI  103.58  3.000
 RXT  H9   CAU  CAV  109.17  3.000
 RXT  H9   CAU  CAL  108.94  3.000
 RXT  CAV  CAU  CAL  113.80  3.000
 RXT  H9   CAU  CAK  109.06  3.000
 RXT  CAL  CAU  CAK  102.74  3.000
 RXT  CAV  CAU  CAK  112.89  3.000
 RXT  H10  CAV  NAW  105.02  3.000
 RXT  H10  CAV  CAJ  108.74  3.000
 RXT  NAW  CAV  CAJ  110.33  3.000
 RXT  H10  CAV  CAU  109.12  3.000
 RXT  CAJ  CAV  CAU  111.51  3.000
 RXT  NAW  CAV  CAU  111.87  3.000
 RXT  H12  CAJ  H11  106.98  3.000
 RXT  H12  CAJ  CAB  108.53  3.000
 RXT  H11  CAJ  CAB  108.30  3.000
 RXT  H12  CAJ  CAV  111.27  3.000
 RXT  H11  CAJ  CAV  109.71  3.000
 RXT  CAB  CAJ  CAV  111.88  3.000
 RXT  NAA  CAB  CAJ  180.00  3.000
 RXT  NAO  NAW  CAG  112.52  3.000
 RXT  CAG  NAW  CAV  127.74  3.000
 RXT  NAO  NAW  CAV  119.74  3.000
 RXT  H18  CAG  CAQ  130.40  3.000
 RXT  H18  CAG  NAW  122.75  3.000
 RXT  CAQ  CAG  NAW  106.85  3.000
 RXT  CAF  NAO  NAW  105.50  3.000
 RXT  H19  CAF  CAQ  129.15  3.000
 RXT  H19  CAF  NAO  119.45  3.000
 RXT  CAQ  CAF  NAO  111.40  3.000
 RXT  CAR  CAQ  CAF  130.56  3.000
 RXT  CAR  CAQ  CAG  125.71  3.000
 RXT  CAF  CAQ  CAG  103.73  3.000
 RXT  CAS  CAR  NAM  119.33  3.000
 RXT  CAS  CAR  CAQ  124.10  3.000
 RXT  NAM  CAR  CAQ  116.57  3.000
 RXT  CAE  NAM  CAR  119.26  3.000
 RXT  H20  CAE  NAP  116.47  3.000
 RXT  H20  CAE  NAM  116.08  3.000
 RXT  NAP  CAE  NAM  127.45  3.000
 RXT  CAT  NAP  CAE  113.16  3.000
 RXT  NAN  CAT  CAS  107.90  3.000
 RXT  NAN  CAT  NAP  126.41  3.000
 RXT  CAS  CAT  NAP  125.69  3.000
 RXT  CAD  CAS  CAT  106.61  3.000
 RXT  CAD  CAS  CAR  138.28  3.000
 RXT  CAT  CAS  CAR  115.11  3.000
 RXT  H21  CAD  CAC  124.88  3.000
 RXT  H21  CAD  CAS  128.78  3.000
 RXT  CAC  CAD  CAS  106.35  3.000
 RXT  H22  CAC  NAN  120.41  3.000
 RXT  H22  CAC  CAD  129.55  3.000
 RXT  NAN  CAC  CAD  110.04  3.000
 RXT  H23  NAN  CAC  125.52  3.000
 RXT  H23  NAN  CAT  125.38  3.000
 RXT  CAC  NAN  CAT  109.11  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
 RXT  CONST_01  CAQ  CAF  NAO  NAW     0.00   0.0  0
 RXT  CONST_02  CAF  CAQ  CAG  NAW     0.00   0.0  0
 RXT  CONST_03  CAR  CAQ  CAG  NAW   180.00   0.0  0
 RXT  CONST_04  NAO  CAF  CAQ  CAG     0.00   0.0  0
 RXT  CONST_05  NAM  CAR  CAQ  CAG     0.00   0.0  0
 RXT  CONST_06  CAS  CAR  CAQ  CAG   180.00   0.0  0
 RXT  CONST_07  CAF  NAO  NAW  CAG     0.00   0.0  0
 RXT  CONST_08  CAR  CAQ  CAF  NAO   180.00   0.0  0
 RXT  CONST_09  CAQ  CAG  NAW  NAO     0.00   0.0  0
 RXT  CONST_10  NAM  CAR  CAQ  CAF   180.00   0.0  0
 RXT  CONST_11  CAS  CAR  CAQ  CAF     0.00   0.0  0
 RXT  CONST_12  CAE  NAM  CAR  CAQ   180.00   0.0  0
 RXT  CONST_13  CAT  CAS  CAR  CAQ   180.00   0.0  0
 RXT  CONST_14  CAD  CAS  CAR  CAQ     0.00   0.0  0
 RXT  CONST_15  NAP  CAE  NAM  CAR     0.00   0.0  0
 RXT  CONST_16  NAP  CAT  CAS  CAR     0.00   0.0  0
 RXT  CONST_17  NAN  CAT  CAS  CAR   180.00   0.0  0
 RXT  CONST_18  CAC  CAD  CAS  CAR   180.00   0.0  0
 RXT  CONST_19  CAT  NAP  CAE  NAM     0.00   0.0  0
 RXT  CONST_20  CAT  CAS  CAR  NAM     0.00   0.0  0
 RXT  CONST_21  CAD  CAS  CAR  NAM   180.00   0.0  0
 RXT  CONST_22  CAS  CAR  NAM  CAE     0.00   0.0  0
 RXT  CONST_23  CAS  CAT  NAP  CAE     0.00   0.0  0
 RXT  CONST_24  NAN  CAT  NAP  CAE   180.00   0.0  0
 RXT  CONST_25  CAD  CAS  CAT  NAP   180.00   0.0  0
 RXT  CONST_26  CAC  NAN  CAT  NAP   180.00   0.0  0
 RXT  CONST_27  CAC  CAD  CAS  CAT     0.00   0.0  0
 RXT  CONST_28  CAD  CAC  NAN  CAT     0.00   0.0  0
 RXT  CONST_29  CAC  NAN  CAT  CAS     0.00   0.0  0
 RXT  CONST_30  NAN  CAC  CAD  CAS     0.00   0.0  0
 RXT  CONST_31  NAN  CAT  CAS  CAD     0.00   0.0  0
 RXT  CONST_32  CAF  NAO  NAW  CAV   180.00   0.0  0
 RXT  CONST_33  CAQ  CAG  NAW  CAV   180.00   0.0  0
 RXT  CONST_34  H19  CAF  NAO  NAW   180.00   0.0  0
 RXT  CONST_35  H18  CAG  NAW  NAO   180.00   0.0  0
 RXT  CONST_36  H20  CAE  NAM  CAR   180.00   0.0  0
 RXT  CONST_37  H21  CAD  CAS  CAR     0.00   0.0  0
 RXT  CONST_38  H23  NAN  CAT  NAP     0.00   0.0  0
 RXT  CONST_39  H22  CAC  NAN  CAT   180.00   0.0  0
 RXT  Var_01    CAL  CAI  CAH  CAK    -7.10  30.0  1
 RXT  Var_02    CAU  CAL  CAI  CAH    30.02  30.0  1
 RXT  Var_03    CAU  CAK  CAH  CAI   -18.49  30.0  1
 RXT  Var_04    H11  CAJ  CAB  NAA  -126.79  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 RXT  chir_01  CAU  CAV  CAL  CAK  positiv
 RXT  chir_02  CAV  NAW  CAJ  CAU  positiv

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
 RXT  plan-1  CAV  0.020
 RXT  plan-1  NAW  0.020
 RXT  plan-1  CAG  0.020
 RXT  plan-1  NAO  0.020
 RXT  plan-1  CAF  0.020
 RXT  plan-1  CAQ  0.020
 RXT  plan-1  CAR  0.020
 RXT  plan-1  H18  0.020
 RXT  plan-1  H19  0.020
 RXT  plan-2  CAQ  0.020
 RXT  plan-2  CAR  0.020
 RXT  plan-2  NAM  0.020
 RXT  plan-2  CAE  0.020
 RXT  plan-2  NAP  0.020
 RXT  plan-2  CAT  0.020
 RXT  plan-2  CAS  0.020
 RXT  plan-2  CAD  0.020
 RXT  plan-2  CAC  0.020
 RXT  plan-2  NAN  0.020
 RXT  plan-2  H20  0.020
 RXT  plan-2  H21  0.020
 RXT  plan-2  H22  0.020
 RXT  plan-2  H23  0.020

