# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:12:55 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 4-[(3-cyclopropyl-1,2,4-oxadiazol-5-yl)methyl]piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CC(CCN1)Cc2onc(n2)C3CC3
#
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
 NXM  NXM  4-[(3-cyclopropyl-1,2,4-oxadiazol-5-yl)methyl]piperidine  ligand  32  15  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NXM
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
 NXM  N1   N  N     0  -0.460   1.3736  -0.0637   1.0446
 NXM  C4   C  CH2   0  -0.318  -4.4616  -0.3068  -0.3165
 NXM  C5   C  CH2   0  -0.430  -3.3268  -1.0189   0.4160
 NXM  C6   C  CR5   0   0.512   0.5088  -0.7402   0.3632
 NXM  C7   C  CR5   0   0.350   2.4174   0.0674   0.1702
 NXM  C8   C  CH1   0  -0.378   3.6616   0.7538   0.5295
 NXM  C10  C  CH2   0  -0.468   4.9790   0.0393   0.3440
 NXM  N    N  NH1   0  -0.575  -4.4099   1.1427  -0.2163
 NXM  C    C  CH2   0  -0.538  -0.8488  -1.1794   0.7623
 NXM  O    O  O     0  -0.330   0.9449  -1.0297  -0.8549
 NXM  C1   C  CH1   0  -0.251  -1.9652  -0.4970  -0.0390
 NXM  C2   C  CH2   0  -0.433  -1.9280   1.0247   0.0895
 NXM  C3   C  CH2   0  -0.314  -3.1163   1.6610  -0.6304
 NXM  C9   C  CH2   0  -0.470   4.6280   1.1871  -0.5353
 NXM  N2   N  N     0  -0.174   2.1999  -0.4901  -0.9819
 NXM  H2   H  HCH2  0   0.236  -5.4265  -0.6515   0.0603
 NXM  H3   H  HCH2  0   0.216  -3.4325  -0.8581   1.4955
 NXM  H4   H  HCH2  0   0.232  -3.3945  -2.0982   0.2510
 NXM  H5   H  HCH1  0   0.285   3.5682   1.3843   1.4045
 NXM  H6   H  HCH2  0   0.267   5.7285   0.1795   1.1111
 NXM  H7   H  HCH2  0   0.261   4.9422  -0.9571  -0.0770
 NXM  H8   H  HNH1  0   0.337  -4.5780   1.4107   0.7471
 NXM  H10  H  HCH2  0   0.285  -0.9237  -2.2639   0.6413
 NXM  H11  H  HCH2  0   0.272  -0.9645  -0.9639   1.8256
 NXM  H12  H  HCH1  0   0.236  -1.8384  -0.7578  -1.0970
 NXM  H13  H  HCH2  0   0.218  -1.9542   1.3002   1.1506
 NXM  H14  H  HCH2  0   0.233  -0.9980   1.4334  -0.3172
 NXM  H15  H  HCH2  0   0.215  -3.0140   1.4933  -1.7084
 NXM  H16  H  HCH2  0   0.237  -3.1077   2.7429  -0.4835
 NXM  H17  H  HCH2  0   0.262   4.3636   0.9825  -1.5646
 NXM  H18  H  HCH2  0   0.268   5.1339   2.1304  -0.3782
 NXM  H1   H  HCH2  0   0.215  -4.4285  -0.5739  -1.3786

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
 NXM  C9   C8   single    1.502  0.020  1.502
 NXM  C9   C10  single    1.488  0.020  1.488
 NXM  C8   C10  single    1.510  0.020  1.510
 NXM  C8   C7   single    1.466  0.020  1.466
 NXM  N2   C7   aromatic  1.298  0.020  1.298
 NXM  N2   O    aromatic  1.372  0.020  1.372
 NXM  C7   N1   aromatic  1.368  0.020  1.368
 NXM  C3   C2   single    1.528  0.020  1.528
 NXM  C3   N    single    1.454  0.020  1.454
 NXM  O    C6   aromatic  1.326  0.020  1.326
 NXM  C2   C1   single    1.528  0.020  1.528
 NXM  N1   C6   aromatic  1.292  0.020  1.292
 NXM  N    C4   single    1.454  0.020  1.454
 NXM  C6   C    single    1.482  0.020  1.482
 NXM  C1   C    single    1.534  0.020  1.534
 NXM  C1   C5   single    1.527  0.020  1.527
 NXM  C4   C5   single    1.527  0.020  1.527
 NXM  C4   H1   single    0.970  0.020  1.090
 NXM  C4   H2   single    0.970  0.020  1.090
 NXM  C5   H3   single    0.970  0.020  1.090
 NXM  C5   H4   single    0.970  0.020  1.090
 NXM  C8   H5   single    0.970  0.020  1.090
 NXM  C10  H6   single    0.970  0.020  1.090
 NXM  C10  H7   single    0.970  0.020  1.090
 NXM  N    H8   single    0.890  0.020  1.040
 NXM  C    H10  single    0.970  0.020  1.090
 NXM  C    H11  single    0.970  0.020  1.090
 NXM  C1   H12  single    0.970  0.020  1.090
 NXM  C2   H13  single    0.970  0.020  1.090
 NXM  C2   H14  single    0.970  0.020  1.090
 NXM  C3   H15  single    0.970  0.020  1.090
 NXM  C3   H16  single    0.970  0.020  1.090
 NXM  C9   H17  single    0.970  0.020  1.090
 NXM  C9   H18  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
 NXM  C7   N1   C6   102.93  3.000
 NXM  H2   C4   H1   106.52  3.000
 NXM  H2   C4   N    108.81  3.000
 NXM  H1   C4   N    107.98  3.000
 NXM  H2   C4   C5   110.12  3.000
 NXM  H1   C4   C5   109.20  3.000
 NXM  N    C4   C5   113.92  3.000
 NXM  H4   C5   H3   106.70  3.000
 NXM  H4   C5   C1   110.33  3.000
 NXM  H3   C5   C1   109.21  3.000
 NXM  H4   C5   C4   109.98  3.000
 NXM  H3   C5   C4   109.40  3.000
 NXM  C1   C5   C4   111.12  3.000
 NXM  O    C6   C    118.96  3.000
 NXM  C    C6   N1   128.78  3.000
 NXM  O    C6   N1   112.25  3.000
 NXM  N2   C7   C8   124.12  3.000
 NXM  N2   C7   N1   113.47  3.000
 NXM  C8   C7   N1   122.41  3.000
 NXM  H5   C8   C9   117.42  3.000
 NXM  H5   C8   C10  116.75  3.000
 NXM  C9   C8   C10   59.20  3.000
 NXM  H5   C8   C7   113.43  3.000
 NXM  C10  C8   C7   119.26  3.000
 NXM  C9   C8   C7   120.50  3.000
 NXM  H7   C10  H6   114.76  3.000
 NXM  H7   C10  C9   118.18  3.000
 NXM  H6   C10  C9   118.86  3.000
 NXM  H7   C10  C8   116.98  3.000
 NXM  H6   C10  C8   117.13  3.000
 NXM  C9   C10  C8    60.12  3.000
 NXM  H8   N    C3   108.90  3.000
 NXM  H8   N    C4   108.85  3.000
 NXM  C3   N    C4   111.56  3.000
 NXM  H11  C    H10  107.24  3.000
 NXM  H11  C    C1   110.12  3.000
 NXM  H10  C    C1   109.47  3.000
 NXM  H11  C    C6   107.52  3.000
 NXM  H10  C    C6   109.08  3.000
 NXM  C1   C    C6   113.22  3.000
 NXM  N2   O    C6   107.46  3.000
 NXM  H12  C1   C2   108.36  3.000
 NXM  H12  C1   C    108.29  3.000
 NXM  C2   C1   C    112.42  3.000
 NXM  H12  C1   C5   108.00  3.000
 NXM  C    C1   C5   109.94  3.000
 NXM  C2   C1   C5   109.70  3.000
 NXM  H14  C2   H13  106.63  3.000
 NXM  H14  C2   C3   109.29  3.000
 NXM  H13  C2   C3   109.43  3.000
 NXM  H14  C2   C1   111.19  3.000
 NXM  H13  C2   C1   109.33  3.000
 NXM  C3   C2   C1   110.87  3.000
 NXM  H16  C3   H15  106.45  3.000
 NXM  H16  C3   C2   110.06  3.000
 NXM  H15  C3   C2   109.10  3.000
 NXM  H16  C3   N    108.78  3.000
 NXM  H15  C3   N    107.99  3.000
 NXM  C2   C3   N    114.16  3.000
 NXM  H18  C9   H17  114.66  3.000
 NXM  H18  C9   C10  118.46  3.000
 NXM  H17  C9   C10  118.28  3.000
 NXM  H18  C9   C8   116.71  3.000
 NXM  H17  C9   C8   117.55  3.000
 NXM  C10  C9   C8    60.68  3.000
 NXM  O    N2   C7   103.89  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
 NXM  CONST_01  O    N2  C7  N1     0.00   0.0  0
 NXM  CONST_02  N2   O   C6  N1     0.00   0.0  0
 NXM  CONST_03  C7   N2  O   C6     0.00   0.0  0
 NXM  CONST_04  N2   C7  N1  C6     0.00   0.0  0
 NXM  CONST_05  O    C6  N1  C7     0.00   0.0  0
 NXM  CONST_06  C8   C7  N1  C6   180.00   0.0  0
 NXM  CONST_07  O    N2  C7  C8   180.00   0.0  0
 NXM  CONST_08  C    C6  N1  C7   180.00   0.0  0
 NXM  CONST_09  N2   O   C6  C    180.00   0.0  0
 NXM  Var_01    C9   C8  C7  N1  -164.17  30.0  2
 NXM  Var_02    C2   C3  N   C4   -53.45  30.0  1
 NXM  Var_03    C3   N   C4  C5    53.36  30.0  1
 NXM  Var_04    C10  C9  C8  C7  -108.02  30.0  1
 NXM  Var_05    C1   C2  C3  N     54.20  30.0  1
 NXM  Var_06    C1   C5  C4  N    -54.28  30.0  1
 NXM  Var_07    C1   C   C6  N1   113.23  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
 NXM  chir_02  C1  C2  C    C5  negativ
 NXM  chir_03  C8  C9  C10  C7  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
 NXM  plan-1  N1  0.020
 NXM  plan-1  C6  0.020
 NXM  plan-1  C7  0.020
 NXM  plan-1  C8  0.020
 NXM  plan-1  C   0.020
 NXM  plan-1  O   0.020
 NXM  plan-1  N2  0.020

