# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 04:22:00 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 5-(6-morpholin-4-yl-2-pyrrolidin-1-yl-pyrimidin-4-yl)-4-(trifluoromethyl)pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(c(cn1)c2cc(nc(n2)N3CCCC3)N4CCOCC4)C(F)(F)F
#
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
 UGI  UGI  5-(6-morpholin-4-yl-2-pyrrolidin-1-yl-pyrimidin-4-yl)-4-(trifluoromethyl)pyridin-2-amine  ligand  49  28  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UGI
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
 UGI  C4   C  CR6   0   0.230   0.4608  -0.4717   0.4228
 UGI  C5   C  CR16  0  -0.466  -0.6759  -1.2456   0.2787
 UGI  C6   C  CR6   0   0.599  -1.9074  -0.5612   0.2916
 UGI  N1   N  N     0  -0.534  -1.9402   0.7602   0.4198
 UGI  N3   N  N     0  -0.500   0.4336   0.8485   0.5528
 UGI  FAZ  F  F     0  -0.306   3.8737   0.2747  -2.1509
 UGI  FBA  F  F     0  -0.304   3.0173   1.5955  -0.6991
 UGI  FBB  F  F     0  -0.304   1.7442   0.3905  -1.9637
 UGI  CAS  C  CR6   0  -0.120   2.9198  -0.7183  -0.2431
 UGI  CAR  C  CR16  0  -0.403   4.1138  -1.3761  -0.0552
 UGI  CAQ  C  CR6   0   0.507   4.1721  -2.4393   0.8611
 UGI  NAX  N  NH2   0  -0.818   5.3415  -3.0844   1.1094
 UGI  NAP  N  N     0  -0.421   3.1039  -2.8394   1.5380
 UGI  CAO  C  CR16  0  -0.068   1.9671  -2.1935   1.3453
 UGI  CAH  C  CR6   0  -0.031   1.7873  -1.1199   0.4825
 UGI  C2   C  CR6   0   0.623  -0.7786   1.4074   0.5225
 UGI  NAI  N  NT    0  -0.510  -0.8327   2.7475   0.6175
 UGI  CAT  C  CH2   0  -0.239  -2.0636   3.5088   0.5236
 UGI  CAU  C  CH2   0  -0.471  -1.5700   4.9367   0.3110
 UGI  CAV  C  CH2   0  -0.473  -0.2359   4.9593   1.0511
 UGI  CAW  C  CH2   0  -0.240   0.3488   3.5796   0.7652
 UGI  NAG  N  NT    0  -0.517  -3.1053  -1.1967   0.1559
 UGI  CAJ  C  CH2   0  -0.304  -3.2189  -2.6377   0.2451
 UGI  CAK  C  CH2   0  -0.162  -4.4314  -3.1192  -0.5349
 UGI  OAL  O  O2    0  -0.453  -5.6074  -2.4653  -0.1425
 UGI  CAM  C  CH2   0  -0.172  -5.4875  -1.0784  -0.3364
 UGI  CAN  C  CH2   0  -0.311  -4.3390  -0.4930   0.4615
 UGI  H1   H  HCR6  0   0.234  -0.5887  -2.3123   0.1553
 UGI  H2   H  HCR6  0   0.253   5.0010  -1.1004  -0.6073
 UGI  H3   H  HNH2  0   0.366   6.0995  -2.9956   0.4581
 UGI  H4   H  HNH2  0   0.370   5.2807  -3.9607   1.5968
 UGI  H5   H  HCR6  0   0.243   1.1249  -2.5384   1.9357
 UGI  H6   H  HCH2  0   0.233  -2.6890   3.1498  -0.2942
 UGI  H7   H  HCH2  0   0.216  -2.6551   3.4222   1.4417
 UGI  H8   H  HCH2  0   0.228  -1.4128   5.1234  -0.7537
 UGI  H9   H  HCH2  0   0.235  -2.2795   5.6794   0.6747
 UGI  H10  H  HCH2  0   0.237   0.4241   5.7631   0.7264
 UGI  H11  H  HCH2  0   0.227  -0.4021   5.0839   2.1236
 UGI  H12  H  HCH2  0   0.235   0.9908   3.2162   1.5676
 UGI  H13  H  HCH2  0   0.226   0.9482   3.5749  -0.1501
 UGI  H14  H  HCH2  0   0.238  -2.3416  -3.1185  -0.1827
 UGI  H15  H  HCH2  0   0.225  -3.2926  -2.9577   1.2931
 UGI  H16  H  HCH2  0   0.194  -4.2472  -2.9745  -1.6098
 UGI  H17  H  HCH2  0   0.229  -4.5749  -4.1869  -0.3619
 UGI  H18  H  HCH2  0   0.193  -5.3467  -0.8474  -1.4026
 UGI  H19  H  HCH2  0   0.226  -6.4259  -0.6228  -0.0173
 UGI  H20  H  HCH2  0   0.219  -4.5574  -0.5623   1.5356
 UGI  H21  H  HCH2  0   0.268  -4.2203   0.5600   0.2208
 UGI  CAY  C  CT    0   1.073   2.8777   0.3939  -1.2611

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
 UGI  NAX  CAQ  single    1.358  0.020  1.358
 UGI  CAQ  CAR  aromatic  1.405  0.020  1.405
 UGI  CAQ  NAP  aromatic  1.326  0.020  1.326
 UGI  CAR  CAS  aromatic  1.376  0.020  1.376
 UGI  NAP  CAO  aromatic  1.322  0.020  1.322
 UGI  FAZ  CAY  single    1.341  0.020  1.341
 UGI  CAS  CAY  single    1.508  0.020  1.508
 UGI  CAS  CAH  aromatic  1.404  0.020  1.404
 UGI  CAO  CAH  aromatic  1.389  0.020  1.389
 UGI  CAY  FBA  single    1.334  0.020  1.334
 UGI  CAY  FBB  single    1.334  0.020  1.334
 UGI  CAH  C4   single    1.478  0.020  1.478
 UGI  C4   C5   aromatic  1.383  0.020  1.383
 UGI  C4   N3   aromatic  1.327  0.020  1.327
 UGI  C5   C6   aromatic  1.409  0.020  1.409
 UGI  N3   C2   aromatic  1.335  0.020  1.335
 UGI  CAJ  CAK  single    1.520  0.020  1.520
 UGI  CAJ  NAG  single    1.448  0.020  1.448
 UGI  CAK  OAL  single    1.402  0.020  1.402
 UGI  C6   NAG  single    1.363  0.020  1.363
 UGI  C6   N1   aromatic  1.328  0.020  1.328
 UGI  NAG  CAN  single    1.453  0.020  1.453
 UGI  C2   N1   aromatic  1.334  0.020  1.334
 UGI  C2   NAI  single    1.344  0.020  1.344
 UGI  CAT  NAI  single    1.450  0.020  1.450
 UGI  CAT  CAU  single    1.526  0.020  1.526
 UGI  OAL  CAM  single    1.406  0.020  1.406
 UGI  NAI  CAW  single    1.453  0.020  1.453
 UGI  CAN  CAM  single    1.516  0.020  1.516
 UGI  CAU  CAV  single    1.526  0.020  1.526
 UGI  CAW  CAV  single    1.526  0.020  1.526
 UGI  C5   H1   single    0.930  0.020  1.080
 UGI  CAR  H2   single    0.930  0.020  1.080
 UGI  NAX  H3   single    0.890  0.020  1.040
 UGI  NAX  H4   single    0.890  0.020  1.040
 UGI  CAO  H5   single    0.930  0.020  1.080
 UGI  CAT  H6   single    0.970  0.020  1.090
 UGI  CAT  H7   single    0.970  0.020  1.090
 UGI  CAU  H8   single    0.970  0.020  1.090
 UGI  CAU  H9   single    0.970  0.020  1.090
 UGI  CAV  H10  single    0.970  0.020  1.090
 UGI  CAV  H11  single    0.970  0.020  1.090
 UGI  CAW  H12  single    0.970  0.020  1.090
 UGI  CAW  H13  single    0.970  0.020  1.090
 UGI  CAJ  H14  single    0.970  0.020  1.090
 UGI  CAJ  H15  single    0.970  0.020  1.090
 UGI  CAK  H16  single    0.970  0.020  1.090
 UGI  CAK  H17  single    0.970  0.020  1.090
 UGI  CAM  H18  single    0.970  0.020  1.090
 UGI  CAM  H19  single    0.970  0.020  1.090
 UGI  CAN  H20  single    0.970  0.020  1.090
 UGI  CAN  H21  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
 UGI  CAH  C4   N3   116.81  3.000
 UGI  N3   C4   C5   123.38  3.000
 UGI  CAH  C4   C5   119.78  3.000
 UGI  H1   C5   C6   123.56  3.000
 UGI  H1   C5   C4   119.97  3.000
 UGI  C6   C5   C4   116.47  3.000
 UGI  NAG  C6   N1   116.87  3.000
 UGI  N1   C6   C5   120.39  3.000
 UGI  NAG  C6   C5   122.74  3.000
 UGI  C2   N1   C6   117.96  3.000
 UGI  C2   N3   C4   115.65  3.000
 UGI  CAH  CAS  CAR  119.51  3.000
 UGI  CAH  CAS  CAY  122.51  3.000
 UGI  CAR  CAS  CAY  117.96  3.000
 UGI  H2   CAR  CAQ  119.49  3.000
 UGI  H2   CAR  CAS  121.37  3.000
 UGI  CAQ  CAR  CAS  119.14  3.000
 UGI  NAP  CAQ  NAX  117.18  3.000
 UGI  NAP  CAQ  CAR  121.85  3.000
 UGI  NAX  CAQ  CAR  120.95  3.000
 UGI  H4   NAX  H3   115.97  3.000
 UGI  H4   NAX  CAQ  116.79  3.000
 UGI  H3   NAX  CAQ  119.33  3.000
 UGI  CAO  NAP  CAQ  118.09  3.000
 UGI  H5   CAO  CAH  118.90  3.000
 UGI  H5   CAO  NAP  115.66  3.000
 UGI  CAH  CAO  NAP  125.43  3.000
 UGI  CAO  CAH  CAS  115.97  3.000
 UGI  CAO  CAH  C4   118.71  3.000
 UGI  CAS  CAH  C4   125.30  3.000
 UGI  NAI  C2   N3   116.88  3.000
 UGI  NAI  C2   N1   117.01  3.000
 UGI  N3   C2   N1   126.11  3.000
 UGI  CAW  NAI  CAT  113.34  3.000
 UGI  CAW  NAI  C2   123.05  3.000
 UGI  CAT  NAI  C2   123.55  3.000
 UGI  H7   CAT  H6   107.03  3.000
 UGI  H7   CAT  CAU  111.43  3.000
 UGI  H6   CAT  CAU  112.90  3.000
 UGI  H7   CAT  NAI  111.25  3.000
 UGI  H6   CAT  NAI  111.26  3.000
 UGI  CAU  CAT  NAI  103.05  3.000
 UGI  H9   CAU  H8   107.61  3.000
 UGI  H9   CAU  CAV  113.41  3.000
 UGI  H8   CAU  CAV  110.15  3.000
 UGI  H9   CAU  CAT  112.38  3.000
 UGI  H8   CAU  CAT  110.02  3.000
 UGI  CAV  CAU  CAT  103.25  3.000
 UGI  H11  CAV  H10  107.50  3.000
 UGI  H11  CAV  CAW  110.21  3.000
 UGI  H10  CAV  CAW  112.28  3.000
 UGI  H11  CAV  CAU  110.17  3.000
 UGI  H10  CAV  CAU  113.33  3.000
 UGI  CAW  CAV  CAU  103.35  3.000
 UGI  H13  CAW  H12  106.96  3.000
 UGI  H13  CAW  CAV  111.75  3.000
 UGI  H12  CAW  CAV  112.91  3.000
 UGI  H13  CAW  NAI  110.98  3.000
 UGI  H12  CAW  NAI  111.28  3.000
 UGI  CAV  CAW  NAI  103.03  3.000
 UGI  CAN  NAG  CAJ  113.73  3.000
 UGI  CAN  NAG  C6   119.97  3.000
 UGI  CAJ  NAG  C6   121.79  3.000
 UGI  H15  CAJ  H14  107.49  3.000
 UGI  H15  CAJ  CAK  110.11  3.000
 UGI  H14  CAJ  CAK  107.54  3.000
 UGI  H15  CAJ  NAG  110.73  3.000
 UGI  H14  CAJ  NAG  110.62  3.000
 UGI  CAK  CAJ  NAG  110.25  3.000
 UGI  H17  CAK  H16  107.80  3.000
 UGI  H17  CAK  OAL  107.57  3.000
 UGI  H16  CAK  OAL  110.65  3.000
 UGI  H17  CAK  CAJ  109.48  3.000
 UGI  H16  CAK  CAJ  109.03  3.000
 UGI  OAL  CAK  CAJ  112.20  3.000
 UGI  CAM  OAL  CAK  110.50  3.000
 UGI  H19  CAM  H18  107.81  3.000
 UGI  H19  CAM  CAN  109.66  3.000
 UGI  H18  CAM  CAN  109.40  3.000
 UGI  H19  CAM  OAL  107.36  3.000
 UGI  H18  CAM  OAL  110.60  3.000
 UGI  CAN  CAM  OAL  111.91  3.000
 UGI  H21  CAN  H20  107.43  3.000
 UGI  H21  CAN  CAM  109.90  3.000
 UGI  H20  CAN  CAM  109.86  3.000
 UGI  H21  CAN  NAG  109.27  3.000
 UGI  H20  CAN  NAG  110.12  3.000
 UGI  CAM  CAN  NAG  110.21  3.000
 UGI  CAS  CAY  FBB  112.18  3.000
 UGI  FBB  CAY  FBA  108.25  3.000
 UGI  CAS  CAY  FBA  112.15  3.000
 UGI  FBB  CAY  FAZ  106.35  3.000
 UGI  FBA  CAY  FAZ  106.37  3.000
 UGI  CAS  CAY  FAZ  111.20  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
 UGI  CONST_01  CAR  CAS  CAH  C4    180.00   0.0  0
 UGI  CONST_02  NAP  CAO  CAH  C4    180.00   0.0  0
 UGI  CONST_03  N1   C6   C5   C4      0.00   0.0  0
 UGI  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 UGI  CONST_07  C2   N3   C4   C5      0.00   0.0  0
 UGI  CONST_08  C2   N1   C6   C5      0.00   0.0  0
 UGI  CONST_09  CAH  C4   C5   C6    180.00   0.0  0
 UGI  CONST_10  N3   C4   C5   C6      0.00   0.0  0
 UGI  CONST_11  N3   C2   N1   C6      0.00   0.0  0
 UGI  CONST_14  NAP  CAQ  CAR  CAS     0.00   0.0  0
 UGI  CONST_15  NAP  CAO  CAH  CAS     0.00   0.0  0
 UGI  CONST_16  CAO  NAP  CAQ  CAR     0.00   0.0  0
 UGI  CONST_17  CAO  CAH  CAS  CAR     0.00   0.0  0
 UGI  CONST_18  CAH  CAS  CAR  CAQ     0.00   0.0  0
 UGI  CONST_19  CAH  CAO  NAP  CAQ     0.00   0.0  0
 UGI  CONST_20  C2   N3   C4   CAH   180.00   0.0  0
 UGI  CONST_21  NAG  C6   C5   C4    180.00   0.0  0
 UGI  CONST_22  NAI  C2   N3   C4    180.00   0.0  0
 UGI  CONST_23  NAI  C2   N1   C6    180.00   0.0  0
 UGI  CONST_24  NAG  C6   N1   C2    180.00   0.0  0
 UGI  CONST_25  CAY  CAS  CAH  C4      0.00   0.0  0
 UGI  CONST_26  CAQ  CAR  CAS  CAY   180.00   0.0  0
 UGI  CONST_27  CAO  CAH  CAS  CAY   180.00   0.0  0
 UGI  CONST_28  NAX  CAQ  CAR  CAS   180.00   0.0  0
 UGI  CONST_29  CAO  NAP  CAQ  NAX   180.00   0.0  0
 UGI  CONST_30  H5   CAO  CAH  C4      0.00   0.0  0
 UGI  CONST_31  H1   C5   C6   N1    180.00   0.0  0
 UGI  CONST_32  H2   CAR  CAQ  NAP   180.00   0.0  0
 UGI  CONST_34  H4   NAX  CAQ  CAR   180.00   0.0  0
 UGI  Var_01    CAJ  NAG  C6   C5     12.07  30.0  2
 UGI  Var_02    CAK  CAJ  NAG  C6   -154.15  30.0  1
 UGI  Var_03    CAM  CAN  NAG  C6    153.22  30.0  1
 UGI  Var_04    CAT  NAI  C2   N1     -4.27  30.0  2
 UGI  Var_05    CAU  CAT  NAI  C2   -165.28  30.0  1
 UGI  Var_06    CAV  CAW  NAI  C2   -171.27  30.0  1
 UGI  Var_07    CAV  CAU  CAT  NAI   -30.46  30.0  1
 UGI  Var_08    CAU  CAV  CAW  NAI   -30.00  30.0  1
 UGI  Var_09    CAW  CAV  CAU  CAT    37.72  30.0  1
 UGI  Var_10    OAL  CAK  CAJ  NAG   -53.89  30.0  1
 UGI  Var_11    OAL  CAM  CAN  NAG    54.52  30.0  1
 UGI  Var_12    CAN  CAM  OAL  CAK   -59.68  30.0  1
 UGI  Var_13    CAR  CAS  CAY  FAZ    21.55  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
 UGI  plan-1  C4   0.020
 UGI  plan-1  C5   0.020
 UGI  plan-1  C6   0.020
 UGI  plan-1  N1   0.020
 UGI  plan-1  N3   0.020
 UGI  plan-1  CAH  0.020
 UGI  plan-1  C2   0.020
 UGI  plan-1  NAI  0.020
 UGI  plan-1  NAG  0.020
 UGI  plan-1  H1   0.020
 UGI  plan-2  C4   0.020
 UGI  plan-2  CAS  0.020
 UGI  plan-2  CAR  0.020
 UGI  plan-2  CAQ  0.020
 UGI  plan-2  NAX  0.020
 UGI  plan-2  NAP  0.020
 UGI  plan-2  CAO  0.020
 UGI  plan-2  CAH  0.020
 UGI  plan-2  H2   0.020
 UGI  plan-2  H5   0.020
 UGI  plan-2  CAY  0.020
 UGI  plan-3  CAQ  0.020
 UGI  plan-3  NAX  0.020
 UGI  plan-3  H3   0.020
 UGI  plan-3  H4   0.020

