# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 00:03:36 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (1~{R},2~{S})-2-[(2,4-dimethylpyrimidin-5-yl)oxymethyl]-~{N}-(5-fluoranylpyridin-2-yl)-2-(3-fluorophenyl)cyclopropane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(OC[C@]2(C[C@H]2C(=O)Nc3ccc(F)cn3)c4cccc(F)c4)c(C)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
 NRK  NRK  (1~{R},2~{S})-2-[(2,4-dimethylpyrimidin-5-yl)oxymethyl]-~{N}-(5-fluoranylpyridin-2-yl)-2-(3-fluorophenyl)cyclopropane-1-carboxamide  ligand  50  30  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NRK
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
 NRK  C01   C  CH1   0  -0.438  -0.7443  -1.6646   1.1392
 NRK  C02   C  CH2   0  -0.450   0.3433  -1.3993   2.1342
 NRK  C03   C  CT    0  -0.094   0.5805  -1.0682   0.7015
 NRK  C04   C  CH2   0  -0.182   0.6568   0.3841   0.3075
 NRK  C05   C  C     0   0.595  -2.0048  -0.8629   1.1484
 NRK  C06   C  CR6   0   0.136   1.4599  -1.9501  -0.1277
 NRK  C07   C  CR16  0  -0.455   2.7280  -2.3015   0.3209
 NRK  C08   C  CR6   0   0.543   3.5289  -3.0853  -0.4870
 NRK  C09   C  CR16  0  -0.421   3.1225  -3.5308  -1.7294
 NRK  C10   C  CR16  0  -0.224   1.8559  -3.1707  -2.1702
 NRK  C11   C  CR16  0  -0.304   1.0299  -2.3872  -1.3777
 NRK  O12   O  O2    0  -0.456   1.9953   0.7850   0.5497
 NRK  C13   C  CR6   0   0.291   2.3618   2.0337   0.2295
 NRK  C14   C  CR6   0   0.182   3.7101   2.3738   0.4211
 NRK  N15   N  N     0  -0.414   4.1374   3.5905   0.1340
 NRK  C16   C  CR6   0   0.326   3.2694   4.4849  -0.3421
 NRK  N17   N  N     0  -0.402   1.9877   4.2426  -0.5521
 NRK  C18   C  CR16  0  -0.154   1.5336   3.0234  -0.2685
 NRK  O19   O  O     0  -0.446  -2.1370   0.1717   1.7696
 NRK  N20   N  NH1   0  -0.740  -2.9778  -1.4294   0.3754
 NRK  C21   C  CR6   0   0.519  -4.2700  -0.9835   0.1112
 NRK  C22   C  CR16  0  -0.379  -5.1267  -1.8576  -0.5688
 NRK  C23   C  CR16  0  -0.292  -6.4052  -1.4365  -0.8644
 NRK  C24   C  CR6   0   0.421  -6.7730  -0.1651  -0.4629
 NRK  C25   C  CR16  0  -0.202  -5.8722   0.6339   0.2057
 NRK  N26   N  N     0  -0.410  -4.6379   0.2280   0.4825
 NRK  C27   C  CH3   0  -0.726   3.8000   5.8418  -0.6841
 NRK  C28   C  CH3   0  -0.728   4.6837   1.3714   0.9487
 NRK  F29   F  F     0  -0.304  -8.0037   0.2931  -0.7267
 NRK  F30   F  F     0  -0.316   4.7510  -3.4263  -0.0446
 NRK  H011  H  HCH1  0   0.296  -0.8662  -2.7014   0.8438
 NRK  H021  H  HCH2  0   0.275   0.2023  -0.5733   2.8202
 NRK  H022  H  HCH2  0   0.276   0.8394  -2.2610   2.5612
 NRK  H041  H  HCH2  0   0.245   0.4078   0.5040  -0.7534
 NRK  H042  H  HCH2  0   0.246  -0.0362   0.9929   0.8923
 NRK  H071  H  HCR6  0   0.271   3.0872  -1.9727   1.2879
 NRK  H091  H  HCR6  0   0.281   3.7742  -4.1471  -2.3343
 NRK  H101  H  HCR6  0   0.269   1.5135  -3.5112  -3.1381
 NRK  H111  H  HCR6  0   0.257   0.0402  -2.1212  -1.7292
 NRK  H181  H  HCR6  0   0.286   0.4780   2.8525  -0.4472
 NRK  H201  H  HNH1  0   0.424  -2.7461  -2.3145  -0.0483
 NRK  H221  H  HCR6  0   0.295  -4.7974  -2.8463  -0.8598
 NRK  H231  H  HCR6  0   0.303  -7.0971  -2.0808  -1.3905
 NRK  H251  H  HCR6  0   0.284  -6.1493   1.6328   0.5241
 NRK  H271  H  HCH3  0   0.255   4.2673   5.8293  -1.6715
 NRK  H273  H  HCH3  0   0.246   3.0018   6.5801  -0.7040
 NRK  H272  H  HCH3  0   0.248   4.5603   6.1570   0.0286
 NRK  H282  H  HCH3  0   0.256   4.7498   0.5063   0.2871
 NRK  H281  H  HCH3  0   0.255   5.6708   1.8179   1.0403
 NRK  H283  H  HCH3  0   0.257   4.3757   0.9970   1.9263

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
 NRK  C02  C01   single    1.498  0.020  1.498
 NRK  C02  C03   single    1.490  0.020  1.490
 NRK  C01  C05   single    1.494  0.020  1.494
 NRK  C01  C03   single    1.517  0.020  1.517
 NRK  O19  C05   double    1.214  0.020  1.214
 NRK  C05  N20   single    1.366  0.020  1.366
 NRK  N20  C21   single    1.392  0.020  1.392
 NRK  C21  N26   aromatic  1.319  0.020  1.319
 NRK  C21  C22   aromatic  1.400  0.020  1.400
 NRK  N26  C25   aromatic  1.328  0.020  1.328
 NRK  C25  C24   aromatic  1.377  0.020  1.377
 NRK  C22  C23   aromatic  1.378  0.020  1.378
 NRK  C03  C06   single    1.496  0.020  1.496
 NRK  C03  C04   single    1.507  0.020  1.507
 NRK  C24  C23   aromatic  1.383  0.020  1.383
 NRK  C24  F29   single    1.340  0.020  1.340
 NRK  C06  C11   aromatic  1.392  0.020  1.392
 NRK  C06  C07   aromatic  1.390  0.020  1.390
 NRK  C11  C10   aromatic  1.387  0.020  1.387
 NRK  C04  O12   single    1.418  0.020  1.418
 NRK  C07  C08   aromatic  1.382  0.020  1.382
 NRK  C10  C09   aromatic  1.389  0.020  1.389
 NRK  C08  C09   aromatic  1.381  0.020  1.381
 NRK  C08  F30   single    1.344  0.020  1.344
 NRK  O12  C13   single    1.340  0.020  1.340
 NRK  C18  C13   aromatic  1.383  0.020  1.383
 NRK  C18  N17   aromatic  1.331  0.020  1.331
 NRK  C13  C14   aromatic  1.404  0.020  1.404
 NRK  N17  C16   aromatic  1.321  0.020  1.321
 NRK  C14  C28   single    1.494  0.020  1.494
 NRK  C14  N15   aromatic  1.321  0.020  1.321
 NRK  C16  N15   aromatic  1.334  0.020  1.334
 NRK  C16  C27   single    1.496  0.020  1.496
 NRK  C01  H011  single    0.970  0.020  1.090
 NRK  C02  H021  single    0.970  0.020  1.090
 NRK  C02  H022  single    0.970  0.020  1.090
 NRK  C04  H041  single    0.970  0.020  1.090
 NRK  C04  H042  single    0.970  0.020  1.090
 NRK  C07  H071  single    0.930  0.020  1.080
 NRK  C09  H091  single    0.930  0.020  1.080
 NRK  C10  H101  single    0.930  0.020  1.080
 NRK  C11  H111  single    0.930  0.020  1.080
 NRK  C18  H181  single    0.930  0.020  1.080
 NRK  N20  H201  single    0.860  0.020  1.020
 NRK  C22  H221  single    0.930  0.020  1.080
 NRK  C23  H231  single    0.930  0.020  1.080
 NRK  C25  H251  single    0.930  0.020  1.080
 NRK  C27  H271  single    0.970  0.020  1.090
 NRK  C27  H273  single    0.970  0.020  1.090
 NRK  C27  H272  single    0.970  0.020  1.090
 NRK  C28  H282  single    0.970  0.020  1.090
 NRK  C28  H281  single    0.970  0.020  1.090
 NRK  C28  H283  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
 NRK  H011  C01  C05   114.82  3.000
 NRK  H011  C01  C03   113.28  3.000
 NRK  C05   C01  C03   121.84  3.000
 NRK  H011  C01  C02   115.58  3.000
 NRK  C03   C01  C02    59.21  3.000
 NRK  C05   C01  C02   120.90  3.000
 NRK  H022  C02  H021  114.65  3.000
 NRK  H022  C02  C03   118.92  3.000
 NRK  H021  C02  C03   117.42  3.000
 NRK  H022  C02  C01   117.00  3.000
 NRK  H021  C02  C01   117.48  3.000
 NRK  C03   C02  C01    61.05  3.000
 NRK  C06   C03  C04   113.17  3.000
 NRK  C04   C03  C02   118.29  3.000
 NRK  C06   C03  C02   119.71  3.000
 NRK  C04   C03  C01   119.90  3.000
 NRK  C06   C03  C01   116.19  3.000
 NRK  C02   C03  C01    59.74  3.000
 NRK  H042  C04  H041  108.24  3.000
 NRK  H042  C04  O12   110.48  3.000
 NRK  H041  C04  O12   110.41  3.000
 NRK  H042  C04  C03   111.42  3.000
 NRK  H041  C04  C03   110.30  3.000
 NRK  O12   C04  C03   106.00  3.000
 NRK  N20   C05  O19   124.44  3.000
 NRK  N20   C05  C01   112.03  3.000
 NRK  O19   C05  C01   123.53  3.000
 NRK  C11   C06  C07   119.48  3.000
 NRK  C07   C06  C03   120.41  3.000
 NRK  C11   C06  C03   120.07  3.000
 NRK  H071  C07  C08   120.15  3.000
 NRK  H071  C07  C06   120.94  3.000
 NRK  C08   C07  C06   118.91  3.000
 NRK  F30   C08  C09   118.82  3.000
 NRK  F30   C08  C07   118.60  3.000
 NRK  C09   C08  C07   122.58  3.000
 NRK  H091  C09  C10   121.31  3.000
 NRK  H091  C09  C08   120.63  3.000
 NRK  C10   C09  C08   118.06  3.000
 NRK  H101  C10  C11   120.04  3.000
 NRK  H101  C10  C09   119.41  3.000
 NRK  C11   C10  C09   120.55  3.000
 NRK  H111  C11  C10   119.82  3.000
 NRK  H111  C11  C06   119.76  3.000
 NRK  C10   C11  C06   120.42  3.000
 NRK  C13   O12  C04   118.73  3.000
 NRK  C18   C13  C14   116.80  3.000
 NRK  C14   C13  O12   117.12  3.000
 NRK  C18   C13  O12   126.08  3.000
 NRK  C28   C14  N15   118.95  3.000
 NRK  N15   C14  C13   120.28  3.000
 NRK  C28   C14  C13   120.78  3.000
 NRK  C16   N15  C14   118.98  3.000
 NRK  C27   C16  N17   118.29  3.000
 NRK  C27   C16  N15   117.30  3.000
 NRK  N17   C16  N15   124.39  3.000
 NRK  C18   N17  C16   117.71  3.000
 NRK  H181  C18  N17   116.19  3.000
 NRK  H181  C18  C13   121.97  3.000
 NRK  N17   C18  C13   121.84  3.000
 NRK  H201  N20  C21   114.50  3.000
 NRK  H201  N20  C05   115.99  3.000
 NRK  C21   N20  C05   129.48  3.000
 NRK  N26   C21  C22   122.64  3.000
 NRK  C22   C21  N20   117.39  3.000
 NRK  N26   C21  N20   119.96  3.000
 NRK  H221  C22  C23   120.26  3.000
 NRK  H221  C22  C21   120.99  3.000
 NRK  C23   C22  C21   118.75  3.000
 NRK  H231  C23  C24   121.23  3.000
 NRK  H231  C23  C22   121.04  3.000
 NRK  C24   C23  C22   117.73  3.000
 NRK  F29   C24  C25   119.87  3.000
 NRK  F29   C24  C23   120.11  3.000
 NRK  C25   C24  C23   120.02  3.000
 NRK  H251  C25  N26   117.24  3.000
 NRK  H251  C25  C24   120.65  3.000
 NRK  N26   C25  C24   122.11  3.000
 NRK  C25   N26  C21   118.75  3.000
 NRK  H272  C27  H273  109.14  3.000
 NRK  H272  C27  H271  107.23  3.000
 NRK  H273  C27  H271  107.76  3.000
 NRK  H272  C27  C16   111.13  3.000
 NRK  H273  C27  C16   111.07  3.000
 NRK  H271  C27  C16   110.36  3.000
 NRK  H283  C28  H281  108.77  3.000
 NRK  H283  C28  H282  106.76  3.000
 NRK  H281  C28  H282  108.76  3.000
 NRK  H283  C28  C14   111.27  3.000
 NRK  H281  C28  C14   110.24  3.000
 NRK  H282  C28  C14   110.94  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
 NRK  CONST_01  C09   C10  C11  C06     0.00   0.0  0
 NRK  CONST_02  C09   C08  C07  C06     0.00   0.0  0
 NRK  CONST_03  C10   C11  C06  C07     0.00   0.0  0
 NRK  CONST_04  C10   C09  C08  C07     0.00   0.0  0
 NRK  CONST_05  C11   C06  C07  C08     0.00   0.0  0
 NRK  CONST_06  C11   C10  C09  C08     0.00   0.0  0
 NRK  CONST_07  C16   N17  C18  C13     0.00   0.0  0
 NRK  CONST_08  C16   N15  C14  C13     0.00   0.0  0
 NRK  CONST_09  N17   C18  C13  C14     0.00   0.0  0
 NRK  CONST_10  N17   C16  N15  C14     0.00   0.0  0
 NRK  CONST_11  C18   C13  C14  N15     0.00   0.0  0
 NRK  CONST_12  C18   N17  C16  N15     0.00   0.0  0
 NRK  CONST_13  C24   C25  N26  C21     0.00   0.0  0
 NRK  CONST_14  C24   C23  C22  C21     0.00   0.0  0
 NRK  CONST_15  C25   N26  C21  C22     0.00   0.0  0
 NRK  CONST_16  C25   C24  C23  C22     0.00   0.0  0
 NRK  CONST_17  N26   C21  C22  C23     0.00   0.0  0
 NRK  CONST_18  N26   C25  C24  C23     0.00   0.0  0
 NRK  CONST_19  C10   C11  C06  C03   180.00   0.0  0
 NRK  CONST_20  C08   C07  C06  C03   180.00   0.0  0
 NRK  CONST_21  F30   C08  C07  C06   180.00   0.0  0
 NRK  CONST_22  F30   C08  C09  C10   180.00   0.0  0
 NRK  CONST_23  N17   C18  C13  O12   180.00   0.0  0
 NRK  CONST_24  N15   C14  C13  O12   180.00   0.0  0
 NRK  CONST_25  C27   C16  N15  C14   180.00   0.0  0
 NRK  CONST_26  C28   C14  N15  C16   180.00   0.0  0
 NRK  CONST_27  C28   C14  C13  C18   180.00   0.0  0
 NRK  CONST_28  C27   C16  N17  C18   180.00   0.0  0
 NRK  CONST_29  C25   N26  C21  N20   180.00   0.0  0
 NRK  CONST_30  C23   C22  C21  N20   180.00   0.0  0
 NRK  CONST_31  F29   C24  C23  C22   180.00   0.0  0
 NRK  CONST_32  F29   C24  C25  N26   180.00   0.0  0
 NRK  CONST_33  H111  C11  C06  C03     0.00   0.0  0
 NRK  CONST_34  H071  C07  C06  C03     0.00   0.0  0
 NRK  CONST_35  H101  C10  C11  C06   180.00   0.0  0
 NRK  CONST_36  H091  C09  C08  C07   180.00   0.0  0
 NRK  CONST_37  H181  C18  C13  C14   180.00   0.0  0
 NRK  CONST_38  H251  C25  N26  C21   180.00   0.0  0
 NRK  CONST_39  H231  C23  C22  C21   180.00   0.0  0
 NRK  CONST_40  H221  C22  C23  C24   180.00   0.0  0
 NRK  CONST_41  C21   N20  C05  C01   180.00   0.0  0
 NRK  CONST_42  N26   C21  N20  C05     0.00   0.0  0
 NRK  CONST_43  C22   C21  N20  C05   180.00   0.0  0
 NRK  CONST_44  H201  N20  C21  C22     0.00   0.0  0
 NRK  CONST_45  C21   N20  C05  O19     0.00   0.0  0
 NRK  Var_01    C06   C03  C02  C01  -104.80  30.0  1
 NRK  Var_02    C11   C06  C03  C01    62.78  30.0  2
 NRK  Var_03    O12   C04  C03  C01   153.93  30.0  3
 NRK  Var_04    O19   C05  C01  C02    13.50  30.0  3
 NRK  Var_05    C18   C13  O12  C04     3.38  30.0  2
 NRK  Var_06    H282  C28  C14  C13    60.13  30.0  2
 NRK  Var_07    H271  C27  C16  N15    81.51  30.0  2

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
 NRK  chir_01  C01  C02  C05  C03  both
 NRK  chir_02  C03  C01  C06  C04  both

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
 NRK  plan-1  C03   0.020
 NRK  plan-1  C06   0.020
 NRK  plan-1  C07   0.020
 NRK  plan-1  C08   0.020
 NRK  plan-1  C09   0.020
 NRK  plan-1  C10   0.020
 NRK  plan-1  C11   0.020
 NRK  plan-1  F30   0.020
 NRK  plan-1  H071  0.020
 NRK  plan-1  H091  0.020
 NRK  plan-1  H101  0.020
 NRK  plan-1  H111  0.020
 NRK  plan-2  O12   0.020
 NRK  plan-2  C13   0.020
 NRK  plan-2  C14   0.020
 NRK  plan-2  N15   0.020
 NRK  plan-2  C16   0.020
 NRK  plan-2  N17   0.020
 NRK  plan-2  C18   0.020
 NRK  plan-2  C27   0.020
 NRK  plan-2  C28   0.020
 NRK  plan-2  H181  0.020
 NRK  plan-3  N20   0.020
 NRK  plan-3  C21   0.020
 NRK  plan-3  C22   0.020
 NRK  plan-3  C23   0.020
 NRK  plan-3  C24   0.020
 NRK  plan-3  C25   0.020
 NRK  plan-3  N26   0.020
 NRK  plan-3  F29   0.020
 NRK  plan-3  H221  0.020
 NRK  plan-3  H231  0.020
 NRK  plan-3  H251  0.020
 NRK  plan-4  C01   0.020
 NRK  plan-4  C05   0.020
 NRK  plan-4  O19   0.020
 NRK  plan-4  N20   0.020
 NRK  plan-4  C21   0.020
 NRK  plan-4  H201  0.020

