# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:40:25 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (1S)-N,2,2-trimethyl-N-(pyridin-3-yl)cyclopropane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C(=O)[C@H]1CC1(C)C)c2cccnc2
#
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
 NXJ  NXJ  (1S)-N,2,2-trimethyl-N-(pyridin-3-yl)cyclopropane-1-carboxamide  ligand  31  15  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NXJ
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
 NXJ  N1   N  N     0  -0.403  -3.6765   0.6124   0.9350
 NXJ  C4   C  CT    0  -0.002   3.1549  -0.1470   0.2116
 NXJ  C5   C  CH3   0  -0.657   4.1977   0.5060  -0.6635
 NXJ  C6   C  CH3   0  -0.669   2.8418  -1.5745  -0.1675
 NXJ  C7   C  CR6   0   0.230  -1.5656   0.2048  -0.1083
 NXJ  C8   C  CR16  0  -0.166  -2.1253  -0.7909  -0.8941
 NXJ  C10  C  CR16  0  -0.068  -4.2062  -0.3435   0.1788
 NXJ  N    N  NT    0  -0.567  -0.1979   0.5522  -0.2228
 NXJ  C    C  CH3   0  -0.541   0.1975   1.2982  -1.4061
 NXJ  O    O  O     0  -0.482   0.2568  -0.4824   1.7223
 NXJ  C1   C  C     0   0.558   0.6394   0.2193   0.7981
 NXJ  C11  C  CR16  0  -0.074  -2.3878   0.8800   0.7868
 NXJ  C2   C  CH1   0  -0.432   2.0289   0.7474   0.7001
 NXJ  C3   C  CH2   0  -0.461   3.0791   0.2526   1.6477
 NXJ  C9   C  CR16  0  -0.328  -3.4759  -1.0681  -0.7508
 NXJ  H1   H  HCH3  0   0.233   5.1350  -0.0531  -0.6298
 NXJ  H2   H  HCH3  0   0.230   3.8708   0.5377  -1.7050
 NXJ  H3   H  HCH3  0   0.230   4.4077   1.5287  -0.3478
 NXJ  H4   H  HCH3  0   0.233   2.0954  -2.0269   0.4843
 NXJ  H5   H  HCH3  0   0.228   2.4740  -1.6353  -1.1940
 NXJ  H6   H  HCH3  0   0.237   3.7434  -2.1865  -0.1055
 NXJ  H7   H  HCR6  0   0.281  -1.5155  -1.3394  -1.6011
 NXJ  H8   H  HCR6  0   0.269  -5.2630  -0.5410   0.3170
 NXJ  H9   H  HCH3  0   0.250  -0.0171   2.3640  -1.3052
 NXJ  H10  H  HCH3  0   0.265   1.2569   1.1704  -1.6085
 NXJ  H11  H  HCH3  0   0.262  -0.3458   0.9201  -2.2699
 NXJ  H12  H  HCR6  0   0.270  -1.9733   1.6697   1.4056
 NXJ  H13  H  HCH1  0   0.288   2.1031   1.7865   0.3963
 NXJ  H14  H  HCH2  0   0.254   2.7872  -0.4937   2.3763
 NXJ  H15  H  HCH2  0   0.257   3.7883   0.9832   2.0173
 NXJ  H16  H  HCR6  0   0.277  -3.9544  -1.8371  -1.3409

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
 NXJ  C6   C4   single    1.510  0.020  1.510
 NXJ  C5   C4   single    1.510  0.020  1.510
 NXJ  C4   C3   single    1.493  0.020  1.493
 NXJ  C4   C2   single    1.519  0.020  1.519
 NXJ  C3   C2   single    1.499  0.020  1.499
 NXJ  C11  N1   aromatic  1.325  0.020  1.325
 NXJ  C11  C7   aromatic  1.390  0.020  1.390
 NXJ  N1   C10  aromatic  1.329  0.020  1.329
 NXJ  C2   C1   single    1.490  0.020  1.490
 NXJ  O    C1   double    1.222  0.020  1.222
 NXJ  C1   N    single    1.362  0.020  1.362
 NXJ  N    C7   single    1.416  0.020  1.416
 NXJ  N    C    single    1.454  0.020  1.454
 NXJ  C7   C8   aromatic  1.386  0.020  1.386
 NXJ  C10  C9   aromatic  1.386  0.020  1.386
 NXJ  C8   C9   aromatic  1.386  0.020  1.386
 NXJ  C5   H1   single    0.970  0.020  1.090
 NXJ  C5   H2   single    0.970  0.020  1.090
 NXJ  C5   H3   single    0.970  0.020  1.090
 NXJ  C6   H4   single    0.970  0.020  1.090
 NXJ  C6   H5   single    0.970  0.020  1.090
 NXJ  C6   H6   single    0.970  0.020  1.090
 NXJ  C8   H7   single    0.930  0.020  1.080
 NXJ  C10  H8   single    0.930  0.020  1.080
 NXJ  C    H9   single    0.970  0.020  1.090
 NXJ  C    H10  single    0.970  0.020  1.090
 NXJ  C    H11  single    0.970  0.020  1.090
 NXJ  C11  H12  single    0.930  0.020  1.080
 NXJ  C2   H13  single    0.970  0.020  1.090
 NXJ  C3   H14  single    0.970  0.020  1.090
 NXJ  C3   H15  single    0.970  0.020  1.090
 NXJ  C9   H16  single    0.930  0.020  1.080

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
 NXJ  C11  N1   C10  118.00  3.000
 NXJ  C3   C4   C2    59.68  3.000
 NXJ  C2   C4   C6   118.94  3.000
 NXJ  C3   C4   C6   118.96  3.000
 NXJ  C2   C4   C5   116.34  3.000
 NXJ  C3   C4   C5   118.48  3.000
 NXJ  C6   C4   C5   114.00  3.000
 NXJ  H3   C5   H2   107.85  3.000
 NXJ  H3   C5   H1   107.81  3.000
 NXJ  H2   C5   H1   107.53  3.000
 NXJ  H3   C5   C4   111.77  3.000
 NXJ  H2   C5   C4   111.01  3.000
 NXJ  H1   C5   C4   110.70  3.000
 NXJ  H6   C6   H5   107.47  3.000
 NXJ  H6   C6   H4   107.41  3.000
 NXJ  H5   C6   H4   107.97  3.000
 NXJ  H6   C6   C4   110.16  3.000
 NXJ  H5   C6   C4   111.01  3.000
 NXJ  H4   C6   C4   112.62  3.000
 NXJ  C11  C7   N    120.28  3.000
 NXJ  N    C7   C8   121.36  3.000
 NXJ  C11  C7   C8   118.36  3.000
 NXJ  H7   C8   C9   120.99  3.000
 NXJ  H7   C8   C7   120.43  3.000
 NXJ  C9   C8   C7   118.58  3.000
 NXJ  H8   C10  C9   120.25  3.000
 NXJ  H8   C10  N1   116.56  3.000
 NXJ  C9   C10  N1   123.19  3.000
 NXJ  C1   N    C    124.64  3.000
 NXJ  C    N    C7   117.04  3.000
 NXJ  C1   N    C7   118.26  3.000
 NXJ  H11  C    H10  107.35  3.000
 NXJ  H11  C    H9   108.33  3.000
 NXJ  H10  C    H9   108.89  3.000
 NXJ  H11  C    N    109.39  3.000
 NXJ  H10  C    N    110.89  3.000
 NXJ  H9   C    N    111.86  3.000
 NXJ  C2   C1   O    123.05  3.000
 NXJ  O    C1   N    121.00  3.000
 NXJ  C2   C1   N    115.95  3.000
 NXJ  H12  C11  C7   119.64  3.000
 NXJ  H12  C11  N1   117.05  3.000
 NXJ  C7   C11  N1   123.31  3.000
 NXJ  H13  C2   C3   116.44  3.000
 NXJ  H13  C2   C1   114.94  3.000
 NXJ  C3   C2   C1   119.67  3.000
 NXJ  H13  C2   C4   115.03  3.000
 NXJ  C1   C2   C4   120.26  3.000
 NXJ  C3   C2   C4    59.29  3.000
 NXJ  H15  C3   H14  114.31  3.000
 NXJ  H15  C3   C2   116.87  3.000
 NXJ  H14  C3   C2   117.65  3.000
 NXJ  H15  C3   C4   118.40  3.000
 NXJ  H14  C3   C4   118.45  3.000
 NXJ  C2   C3   C4    61.02  3.000
 NXJ  H16  C9   C10  120.31  3.000
 NXJ  H16  C9   C8   121.14  3.000
 NXJ  C10  C9   C8   118.56  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
 NXJ  CONST_01  C8   C7   C11  N1     0.00   0.0  0
 NXJ  CONST_02  C8   C9   C10  N1     0.00   0.0  0
 NXJ  CONST_03  C10  N1   C11  C7     0.00   0.0  0
 NXJ  CONST_04  C10  C9   C8   C7     0.00   0.0  0
 NXJ  CONST_05  C9   C10  N1   C11    0.00   0.0  0
 NXJ  CONST_06  C9   C8   C7   C11    0.00   0.0  0
 NXJ  CONST_07  N    C7   C11  N1   180.00   0.0  0
 NXJ  CONST_08  C9   C8   C7   N    180.00   0.0  0
 NXJ  CONST_09  H16  C9   C10  N1   180.00   0.0  0
 NXJ  CONST_10  H12  C11  C7   C8   180.00   0.0  0
 NXJ  CONST_11  H8   C10  C9   C8   180.00   0.0  0
 NXJ  CONST_12  H7   C8   C9   C10  180.00   0.0  0
 NXJ  CONST_13  C2   C1   N    C7   180.00   0.0  0
 NXJ  CONST_18  O    C1   N    C7     0.00   0.0  0
 NXJ  CONST_19  C2   C1   N    C      0.00   0.0  0
 NXJ  CONST_20  O    C1   N    C    180.00   0.0  0
 NXJ  Var_01    C1   C2   C3   C4   109.64  30.0  1
 NXJ  Var_02    C2   C3   C4   C5   105.52  30.0  1
 NXJ  Var_03    O    C1   C2   C4    79.05  30.0  3
 NXJ  Var_04    H4   C6   C4   C2   -37.38  30.0  3
 NXJ  Var_05    H1   C5   C4   C2   156.92  30.0  3
 NXJ  Var_06    H9   C    N    C7    81.16  30.0  3

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
 NXJ  chir_01  C2  C4  C3  C1  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
 NXJ  plan-1  N1   0.020
 NXJ  plan-1  C7   0.020
 NXJ  plan-1  C8   0.020
 NXJ  plan-1  C10  0.020
 NXJ  plan-1  N    0.020
 NXJ  plan-1  C11  0.020
 NXJ  plan-1  C9   0.020
 NXJ  plan-1  H7   0.020
 NXJ  plan-1  H8   0.020
 NXJ  plan-1  H12  0.020
 NXJ  plan-1  H16  0.020
 NXJ  plan-2  C7   0.020
 NXJ  plan-2  N    0.020
 NXJ  plan-2  C    0.020
 NXJ  plan-2  O    0.020
 NXJ  plan-2  C1   0.020
 NXJ  plan-2  C2   0.020

