# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 23:33:05 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-[(2S)-1-methylpyrrolidin-2-yl]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC[C@H]1c2cccnc2
#
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
 NCT  NCT  3-[(2S)-1-methylpyrrolidin-2-yl]pyridine  ligand  26  12  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NCT
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
 NCT  N1    N  N     0  -0.403  -0.2935   1.2987  -2.4222
 NCT  C1    C  CR16  0  -0.087  -0.2549   0.9966  -1.1310
 NCT  C2    C  CR6   0   0.025   0.0602  -0.2665  -0.6355
 NCT  C3    C  CR16  0  -0.208   0.3533  -1.2567  -1.5629
 NCT  C4    C  CR16  0  -0.316   0.3101  -0.9568  -2.9166
 NCT  C5    C  CR16  0  -0.079  -0.0192   0.3348  -3.2956
 NCT  N2    N  NT    0  -0.423   0.5510   0.5384   1.6442
 NCT  C6    C  CH1   0  -0.106   0.0352  -0.5538   0.8387
 NCT  C7    C  CH2   0  -0.448  -1.3841  -0.7458   1.3934
 NCT  C8    C  CH2   0  -0.467  -1.2804  -0.3123   2.8671
 NCT  C9    C  CH2   0  -0.279   0.1463   0.2279   3.0039
 NCT  C10   C  CH3   0  -0.524   1.9702   0.7570   1.5084
 NCT  HC1   H  HCR6  0   0.253  -0.4747   1.7997  -0.4354
 NCT  HC3   H  HCR6  0   0.264   0.6172  -2.2536  -1.2292
 NCT  HC4   H  HCR6  0   0.269   0.5318  -1.7060  -3.6644
 NCT  HC5   H  HCR6  0   0.261  -0.0599   0.6038  -4.3453
 NCT  HC6   H  HCH1  0   0.217   0.6136  -1.4797   1.0161
 NCT  HC71  H  HCH2  0   0.243  -1.7203  -1.7744   1.2675
 NCT  HC72  H  HCH2  0   0.238  -2.0846  -0.1083   0.8518
 NCT  HC81  H  HCH2  0   0.237  -1.4526  -1.1394   3.5547
 NCT  HC82  H  HCH2  0   0.238  -2.0186   0.4561   3.0963
 NCT  HC91  H  HCH2  0   0.193   0.8002  -0.5417   3.4465
 NCT  HC92  H  HCH2  0   0.235   0.2142   1.1119   3.6414
 NCT  H101  H  HCH3  0   0.195   2.5678  -0.1202   1.8026
 NCT  H102  H  HCH3  0   0.235   2.2241   1.0063   0.4776
 NCT  H103  H  HCH3  0   0.236   2.2800   1.5953   2.1338

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
 NCT  N1   C1    aromatic  1.327  0.020  1.327
 NCT  N1   C5    aromatic  1.329  0.020  1.329
 NCT  C1   C2    aromatic  1.393  0.020  1.393
 NCT  C1   HC1   single    0.930  0.020  1.080
 NCT  C2   C3    aromatic  1.388  0.020  1.388
 NCT  C2   C6    single    1.502  0.020  1.502
 NCT  C3   C4    aromatic  1.387  0.020  1.387
 NCT  C3   HC3   single    0.930  0.020  1.080
 NCT  C4   C5    aromatic  1.386  0.020  1.386
 NCT  C4   HC4   single    0.930  0.020  1.080
 NCT  C5   HC5   single    0.930  0.020  1.080
 NCT  N2   C6    single    1.452  0.020  1.452
 NCT  N2   C9    single    1.452  0.020  1.452
 NCT  N2   C10   single    1.442  0.020  1.442
 NCT  C6   C7    single    1.536  0.020  1.536
 NCT  C6   HC6   single    0.970  0.020  1.090
 NCT  C7   C8    single    1.540  0.020  1.540
 NCT  C7   HC71  single    0.970  0.020  1.090
 NCT  C7   HC72  single    0.970  0.020  1.090
 NCT  C8   C9    single    1.532  0.020  1.532
 NCT  C8   HC81  single    0.970  0.020  1.090
 NCT  C8   HC82  single    0.970  0.020  1.090
 NCT  C9   HC91  single    0.970  0.020  1.090
 NCT  C9   HC92  single    0.970  0.020  1.090
 NCT  C10  H101  single    0.970  0.020  1.090
 NCT  C10  H102  single    0.970  0.020  1.090
 NCT  C10  H103  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
 NCT  C5    N1   C1    117.93  3.000
 NCT  HC1   C1   C2    119.28  3.000
 NCT  HC1   C1   N1    116.71  3.000
 NCT  C2    C1   N1    124.00  3.000
 NCT  C6    C2   C3    121.52  3.000
 NCT  C6    C2   C1    121.25  3.000
 NCT  C3    C2   C1    117.20  3.000
 NCT  HC3   C3   C4    120.46  3.000
 NCT  HC3   C3   C2    120.12  3.000
 NCT  C4    C3   C2    119.42  3.000
 NCT  HC4   C4   C5    120.35  3.000
 NCT  HC4   C4   C3    121.24  3.000
 NCT  C5    C4   C3    118.41  3.000
 NCT  HC5   C5   C4    120.32  3.000
 NCT  HC5   C5   N1    116.64  3.000
 NCT  C4    C5   N1    123.04  3.000
 NCT  C10   N2   C9    113.25  3.000
 NCT  C10   N2   C6    114.29  3.000
 NCT  C9    N2   C6    105.05  3.000
 NCT  HC6   C6   C7    108.71  3.000
 NCT  HC6   C6   N2    110.80  3.000
 NCT  C7    C6   N2    102.83  3.000
 NCT  HC6   C6   C2    107.98  3.000
 NCT  C7    C6   C2    113.19  3.000
 NCT  N2    C6   C2    113.25  3.000
 NCT  HC72  C7   HC71  107.23  3.000
 NCT  HC72  C7   C8    110.72  3.000
 NCT  HC71  C7   C8    113.40  3.000
 NCT  HC72  C7   C6    109.94  3.000
 NCT  HC71  C7   C6    111.19  3.000
 NCT  C8    C7   C6    104.37  3.000
 NCT  HC82  C8   HC81  107.19  3.000
 NCT  HC82  C8   C9    111.31  3.000
 NCT  HC81  C8   C9    111.01  3.000
 NCT  HC82  C8   C7    110.74  3.000
 NCT  HC81  C8   C7    112.32  3.000
 NCT  C9    C8   C7    104.33  3.000
 NCT  HC92  C9   HC91  107.10  3.000
 NCT  HC92  C9   C8    113.30  3.000
 NCT  HC91  C9   C8    110.01  3.000
 NCT  HC92  C9   N2    110.87  3.000
 NCT  HC91  C9   N2    111.09  3.000
 NCT  C8    C9   N2    104.55  3.000
 NCT  H103  C10  H102  107.47  3.000
 NCT  H103  C10  H101  107.75  3.000
 NCT  H102  C10  H101  107.95  3.000
 NCT  H103  C10  N2    110.00  3.000
 NCT  H102  C10  N2    110.66  3.000
 NCT  H101  C10  N2    112.83  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
 NCT  CONST_01  C3    C2   C1  N1    0.00   0.0  0
 NCT  CONST_02  C3    C4   C5  N1    0.00   0.0  0
 NCT  CONST_03  C4    C5   N1  C1    0.00   0.0  0
 NCT  CONST_04  C4    C3   C2  C1    0.00   0.0  0
 NCT  CONST_05  C5    N1   C1  C2    0.00   0.0  0
 NCT  CONST_06  C5    C4   C3  C2    0.00   0.0  0
 NCT  CONST_07  C6    C2   C1  N1  180.00   0.0  0
 NCT  CONST_08  C6    C2   C3  C4  180.00   0.0  0
 NCT  CONST_09  HC4   C4   C5  N1  180.00   0.0  0
 NCT  CONST_10  HC5   C5   N1  C1  180.00   0.0  0
 NCT  CONST_11  HC3   C3   C2  C1  180.00   0.0  0
 NCT  CONST_12  HC1   C1   C2  C3  180.00   0.0  0
 NCT  Var_01    C7    C8   C9  N2   20.32  30.0  1
 NCT  Var_02    C8    C9   N2  C6  -40.47  30.0  1
 NCT  Var_03    C9    C8   C7  C6    5.62  30.0  1
 NCT  Var_04    H101  C10  N2  C6  -60.17  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
 NCT  chir_01  C6  C2  N2  C7  negativ

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
 NCT  plan-1  N1   0.020
 NCT  plan-1  C1   0.020
 NCT  plan-1  C2   0.020
 NCT  plan-1  C3   0.020
 NCT  plan-1  C4   0.020
 NCT  plan-1  C5   0.020
 NCT  plan-1  C6   0.020
 NCT  plan-1  HC1  0.020
 NCT  plan-1  HC3  0.020
 NCT  plan-1  HC4  0.020
 NCT  plan-1  HC5  0.020

