# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 12:59:20 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: ethyl 4-[(4-methylpyridin-2-yl)amino]piperidine-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)N1CCC(CC1)Nc2cc(C)ccn2
#
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
 AT2  AT2  'ethyl 4-[(4-methylpyridin-2-yl)amino]piperidine-1-carboxylate'  ligand  40  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AT2
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
 AT2  C1    C  CH3   0  -0.726  -4.6984   2.2427   1.3676
 AT2  C2    C  CR6   0   0.195  -4.2913   1.1948   0.3777
 AT2  C3    C  CR16  0  -0.405  -5.1292   0.8552  -0.6896
 AT2  C4    C  CR16  0  -0.061  -4.6918  -0.1068  -1.5773
 AT2  C6    C  CR6   0   0.501  -2.7210  -0.4256  -0.4689
 AT2  C7    C  CR16  0  -0.454  -3.0759   0.5456   0.4866
 AT2  C9    C  CH1   0  -0.077  -0.4429  -0.7992   0.4564
 AT2  C10   C  CH2   0  -0.438   0.3116   0.4590   0.0151
 AT2  C11   C  CH2   0  -0.324   1.5183   0.7067   0.9121
 AT2  N5    N  N     0  -0.476  -3.5256  -0.7362  -1.4873
 AT2  N8    N  NH1   0  -0.668  -1.5574  -1.1279  -0.4005
 AT2  N12   N  NT    0  -0.481   2.3855  -0.4603   0.9365
 AT2  C13   C  CH2   0  -0.323   1.7177  -1.6620   1.4023
 AT2  C14   C  CH2   0  -0.441   0.5123  -1.9866   0.5275
 AT2  C15   C  C     0   0.762   3.5620  -0.5564   0.2779
 AT2  O16   O  O     0  -0.531   4.2201  -1.5762   0.1852
 AT2  O17   O  O2    0  -0.481   3.9461   0.6068  -0.2496
 AT2  C18   C  CH2   0  -0.166   5.2125   0.6460  -0.9154
 AT2  C19   C  CH3   0  -0.688   5.3835   2.0314  -1.4909
 AT2  H11   H  HCH3  0   0.253  -4.8142   3.2109   0.8780
 AT2  H12   H  HCH3  0   0.252  -5.6599   1.9987   1.8207
 AT2  H13   H  HCH3  0   0.247  -3.9642   2.3534   2.1639
 AT2  H3    H  HCR6  0   0.249  -6.0922   1.3296  -0.8246
 AT2  H4    H  HCR6  0   0.251  -5.3180  -0.3921  -2.4169
 AT2  H7    H  HCR6  0   0.259  -2.4095   0.7901   1.3033
 AT2  H9    H  HCH1  0   0.237  -0.8290  -0.6337   1.4692
 AT2  H101  H  HCH2  0   0.231   0.6421   0.3390  -1.0214
 AT2  H102  H  HCH2  0   0.249  -0.3456   1.3316   0.0455
 AT2  H111  H  HCH2  0   0.243   1.1828   0.8977   1.9364
 AT2  H112  H  HCH2  0   0.273   2.0641   1.5885   0.5925
 AT2  HN8   H  HNH1  0   0.372  -1.3508  -1.6733  -1.2239
 AT2  H131  H  HCH2  0   0.270   2.4172  -2.4928   1.4156
 AT2  H132  H  HCH2  0   0.245   1.3921  -1.4983   2.4342
 AT2  H141  H  HCH2  0   0.233   0.8574  -2.2453  -0.4792
 AT2  H142  H  HCH2  0   0.254  -0.0049  -2.8593   0.9315
 AT2  H181  H  HCH2  0   0.229   5.2460  -0.1048  -1.7071
 AT2  H182  H  HCH2  0   0.228   6.0119   0.4217  -0.2056
 AT2  H191  H  HCH3  0   0.237   6.3484   2.0918  -1.9937
 AT2  H192  H  HCH3  0   0.234   4.6098   2.2583  -2.2247
 AT2  H193  H  HCH3  0   0.234   5.3620   2.7961  -0.7146

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
 AT2  C1   C2    single    1.498  0.020  1.498
 AT2  C1   H11   single    0.970  0.020  1.090
 AT2  C1   H12   single    0.970  0.020  1.090
 AT2  C1   H13   single    0.970  0.020  1.090
 AT2  C2   C3    aromatic  1.399  0.020  1.399
 AT2  C2   C7    aromatic  1.382  0.020  1.382
 AT2  C3   C4    aromatic  1.380  0.020  1.380
 AT2  C3   H3    single    0.930  0.020  1.080
 AT2  C4   N5    aromatic  1.328  0.020  1.328
 AT2  C4   H4    single    0.930  0.020  1.080
 AT2  C6   C7    aromatic  1.408  0.020  1.408
 AT2  C6   N5    aromatic  1.335  0.020  1.335
 AT2  C6   N8    single    1.361  0.020  1.361
 AT2  C7   H7    single    0.930  0.020  1.080
 AT2  C9   C10   single    1.532  0.020  1.532
 AT2  C9   N8    single    1.444  0.020  1.444
 AT2  C9   C14   single    1.526  0.020  1.526
 AT2  C9   H9    single    0.970  0.020  1.090
 AT2  C10  C11   single    1.524  0.020  1.524
 AT2  C10  H101  single    0.970  0.020  1.090
 AT2  C10  H102  single    0.970  0.020  1.090
 AT2  C11  N12   single    1.454  0.020  1.454
 AT2  C11  H111  single    0.970  0.020  1.090
 AT2  C11  H112  single    0.970  0.020  1.090
 AT2  N8   HN8   single    0.890  0.020  1.040
 AT2  N12  C13   single    1.452  0.020  1.452
 AT2  N12  C15   single    1.352  0.020  1.352
 AT2  C13  C14   single    1.524  0.020  1.524
 AT2  C13  H131  single    0.970  0.020  1.090
 AT2  C13  H132  single    0.970  0.020  1.090
 AT2  C14  H141  single    0.970  0.020  1.090
 AT2  C14  H142  single    0.970  0.020  1.090
 AT2  C15  O16   double    1.217  0.020  1.217
 AT2  C15  O17   single    1.334  0.020  1.334
 AT2  O17  C18   single    1.431  0.020  1.431
 AT2  C18  C19   single    1.510  0.020  1.510
 AT2  C18  H181  single    0.970  0.020  1.090
 AT2  C18  H182  single    0.970  0.020  1.090
 AT2  C19  H191  single    0.970  0.020  1.090
 AT2  C19  H192  single    0.970  0.020  1.090
 AT2  C19  H193  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
 AT2  H13   C1   H12   108.27  3.000
 AT2  H13   C1   H11   108.03  3.000
 AT2  H12   C1   H11   106.94  3.000
 AT2  H13   C1   C2    111.79  3.000
 AT2  H12   C1   C2    110.95  3.000
 AT2  H11   C1   C2    110.68  3.000
 AT2  C7    C2   C3    118.22  3.000
 AT2  C7    C2   C1    121.03  3.000
 AT2  C3    C2   C1    120.75  3.000
 AT2  H3    C3   C4    120.50  3.000
 AT2  H3    C3   C2    121.46  3.000
 AT2  C4    C3   C2    118.04  3.000
 AT2  H4    C4   N5    115.74  3.000
 AT2  H4    C4   C3    119.86  3.000
 AT2  N5    C4   C3    124.40  3.000
 AT2  N8    C6   N5    115.70  3.000
 AT2  N8    C6   C7    122.51  3.000
 AT2  N5    C6   C7    121.77  3.000
 AT2  H7    C7   C6    120.86  3.000
 AT2  H7    C7   C2    119.66  3.000
 AT2  C6    C7   C2    119.49  3.000
 AT2  H9    C9   C14   107.15  3.000
 AT2  H9    C9   N8    108.11  3.000
 AT2  C14   C9   N8    109.50  3.000
 AT2  H9    C9   C10   108.39  3.000
 AT2  C14   C9   C10   110.13  3.000
 AT2  N8    C9   C10   113.34  3.000
 AT2  H102  C10  H101  107.18  3.000
 AT2  H102  C10  C11   109.27  3.000
 AT2  H101  C10  C11   109.65  3.000
 AT2  H102  C10  C9    110.58  3.000
 AT2  H101  C10  C9    109.36  3.000
 AT2  C11   C10  C9    110.73  3.000
 AT2  H112  C11  H111  106.74  3.000
 AT2  H112  C11  N12   110.92  3.000
 AT2  H111  C11  N12   107.89  3.000
 AT2  H112  C11  C10   110.91  3.000
 AT2  H111  C11  C10   109.66  3.000
 AT2  N12   C11  C10   110.59  3.000
 AT2  C6    N5   C4    118.08  3.000
 AT2  HN8   N8   C9    116.70  3.000
 AT2  HN8   N8   C6    114.40  3.000
 AT2  C9    N8   C6    124.91  3.000
 AT2  C15   N12  C13   119.86  3.000
 AT2  C15   N12  C11   124.61  3.000
 AT2  C13   N12  C11   113.29  3.000
 AT2  H132  C13  H131  107.13  3.000
 AT2  H132  C13  C14   109.74  3.000
 AT2  H131  C13  C14   110.70  3.000
 AT2  H132  C13  N12   108.40  3.000
 AT2  H131  C13  N12   109.93  3.000
 AT2  C14   C13  N12   110.85  3.000
 AT2  H142  C14  H141  107.49  3.000
 AT2  H142  C14  C13   109.42  3.000
 AT2  H141  C14  C13   109.19  3.000
 AT2  H142  C14  C9    110.04  3.000
 AT2  H141  C14  C9    109.77  3.000
 AT2  C13   C14  C9    110.86  3.000
 AT2  O17   C15  O16   123.01  3.000
 AT2  O17   C15  N12   112.42  3.000
 AT2  O16   C15  N12   124.56  3.000
 AT2  C18   O17  C15   117.56  3.000
 AT2  H182  C18  H181  107.91  3.000
 AT2  H182  C18  C19   110.69  3.000
 AT2  H181  C18  C19   110.56  3.000
 AT2  H182  C18  O17   109.85  3.000
 AT2  H181  C18  O17   110.22  3.000
 AT2  C19   C18  O17   107.62  3.000
 AT2  H193  C19  H192  108.63  3.000
 AT2  H193  C19  H191  107.89  3.000
 AT2  H192  C19  H191  107.84  3.000
 AT2  H193  C19  C18   111.71  3.000
 AT2  H192  C19  C18   111.54  3.000
 AT2  H191  C19  C18   109.09  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
 AT2  CONST_01  N5    C4   C3   C2      0.00   0.0  0
 AT2  CONST_02  N5    C6   C7   C2      0.00   0.0  0
 AT2  CONST_03  C6    C7   C2   C3      0.00   0.0  0
 AT2  CONST_04  C6    N5   C4   C3      0.00   0.0  0
 AT2  CONST_05  C7    C2   C3   C4      0.00   0.0  0
 AT2  CONST_06  C7    C6   N5   C4      0.00   0.0  0
 AT2  CONST_07  C4    C3   C2   C1    180.00   0.0  0
 AT2  CONST_08  C6    C7   C2   C1    180.00   0.0  0
 AT2  CONST_09  N8    C6   C7   C2    180.00   0.0  0
 AT2  CONST_10  N8    C6   N5   C4    180.00   0.0  0
 AT2  CONST_11  C9    N8   C6   C7      0.00   0.0  0
 AT2  CONST_12  N5    C6   N8   C9    180.00   0.0  0
 AT2  CONST_13  H4    C4   C3   C2    180.00   0.0  0
 AT2  CONST_14  H7    C7   C2   C3    180.00   0.0  0
 AT2  CONST_15  H3    C3   C2   C7    180.00   0.0  0
 AT2  CONST_16  HN8   N8   C6   C7    180.00   0.0  0
 AT2  Var_01    N12   C11  C10  C9     55.60  30.0  1
 AT2  Var_02    N12   C13  C14  C9    -55.23  30.0  1
 AT2  Var_03    C13   N12  C11  C10   -58.52  30.0  1
 AT2  Var_04    C14   C13  N12  C11    58.30  30.0  1
 AT2  Var_05    O16   C15  N12  C11  -172.07  30.0  2
 AT2  Var_06    H11   C1   C2   C3    -62.51  30.0  2
 AT2  Var_07    C19   C18  O17  C15   176.72  30.0  3
 AT2  Var_08    H191  C19  C18  O17   179.28  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
 AT2  chir_01  C9  C10  N8  C14  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
 AT2  plan-1  C1   0.020
 AT2  plan-1  C2   0.020
 AT2  plan-1  C3   0.020
 AT2  plan-1  C4   0.020
 AT2  plan-1  C6   0.020
 AT2  plan-1  C7   0.020
 AT2  plan-1  N5   0.020
 AT2  plan-1  N8   0.020
 AT2  plan-1  H3   0.020
 AT2  plan-1  H4   0.020
 AT2  plan-1  H7   0.020
 AT2  plan-2  C6   0.020
 AT2  plan-2  C9   0.020
 AT2  plan-2  N8   0.020
 AT2  plan-2  HN8  0.020
 AT2  plan-3  N12  0.020
 AT2  plan-3  C15  0.020
 AT2  plan-3  O16  0.020
 AT2  plan-3  O17  0.020

