# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 03:23:28 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: tert-butyl {6-oxo-6-[(pyridin-3-ylmethyl)amino]hexyl}carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)OC(=O)NCCCCCC(=O)NCc1cccnc1
#
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
 PK9  PK9  'tert-butyl {6-oxo-6-[(pyridin-3-ylmethyl)amino]hexyl}carbamate'  ligand  50  23  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PK9
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
 PK9  O15   O  O     0  -0.509   3.3624  -1.0231  -1.4882
 PK9  C14   C  C     0   0.559   3.2353  -0.4423  -0.4175
 PK9  N16   N  NH1   0  -0.622   4.1258  -0.5535   0.5844
 PK9  C17   C  CH2   0  -0.388   5.3214  -1.3620   0.5157
 PK9  C18   C  CR6   0   0.034   6.5618  -0.5520   0.2461
 PK9  C23   C  CR16  0  -0.106   7.6043  -0.5172   1.1634
 PK9  N22   N  N     0  -0.400   8.7247   0.1765   0.9928
 PK9  C21   C  CR16  0  -0.070   8.8514   0.8811  -0.1235
 PK9  C20   C  CR16  0  -0.317   7.8743   0.9207  -1.1097
 PK9  C19   C  CR16  0  -0.180   6.7129   0.1921  -0.9203
 PK9  C13   C  CH2   0  -0.562   2.0428   0.4435  -0.1337
 PK9  C12   C  CH2   0  -0.419   0.7266  -0.3131  -0.2970
 PK9  C11   C  CH2   0  -0.421  -0.4849   0.5887  -0.1058
 PK9  C10   C  CH2   0  -0.469  -1.7993  -0.1728  -0.2103
 PK9  C09   C  CH2   0  -0.232  -3.0007   0.7469  -0.0642
 PK9  N08   N  NH1   0  -0.667  -4.2293  -0.0175  -0.0901
 PK9  C06   C  C     0   0.759  -5.4379   0.5757  -0.1181
 PK9  O07   O  O     0  -0.524  -5.6022   1.7738  -0.2438
 PK9  O05   O  O2    0  -0.506  -6.4068  -0.3349  -0.0023
 PK9  C02   C  CT    0   0.192  -7.8139   0.0172   0.0078
 PK9  C04   C  CH3   0  -0.668  -8.2380   0.5880  -1.3398
 PK9  C03   C  CH3   0  -0.658  -8.5024  -1.3231   0.2385
 PK9  C01   C  CH3   0  -0.674  -8.1441   0.9637   1.1572
 PK9  H16   H  HNH1  0   0.403   3.9735  -0.0240   1.4271
 PK9  H131  H  HCH2  0   0.247   2.0995   0.8805   0.8661
 PK9  H132  H  HCH2  0   0.260   2.0757   1.2758  -0.8433
 PK9  H171  H  HCH2  0   0.272   5.4310  -1.9021   1.4572
 PK9  H172  H  HCH2  0   0.271   5.1824  -2.1084  -0.2657
 PK9  H23   H  HCR6  0   0.259   7.5261  -1.0836   2.0868
 PK9  H19   H  HCR6  0   0.270   5.9360   0.1971  -1.6749
 PK9  H21   H  HCR6  0   0.264   9.7716   1.4419  -0.2438
 PK9  H20   H  HCR6  0   0.271   8.0271   1.5086  -2.0044
 PK9  H121  H  HCH2  0   0.229   0.6892  -0.7696  -1.2888
 PK9  H122  H  HCH2  0   0.228   0.6894  -1.1339   0.4261
 PK9  H111  H  HCH2  0   0.220  -0.4284   1.0807   0.8708
 PK9  H112  H  HCH2  0   0.221  -0.4628   1.3889  -0.8533
 PK9  H101  H  HCH2  0   0.231  -1.8525  -0.6927  -1.1719
 PK9  H102  H  HCH2  0   0.228  -1.8322  -0.9448   0.5659
 PK9  H091  H  HCH2  0   0.223  -2.9176   1.3156   0.8687
 PK9  H092  H  HCH2  0   0.232  -3.0050   1.4740  -0.8789
 PK9  H08   H  HNH1  0   0.394  -4.1796  -1.0016   0.1200
 PK9  H041  H  HCH3  0   0.233  -7.9932  -0.1022  -2.1492
 PK9  H042  H  HCH3  0   0.232  -9.3193   0.7317  -1.3470
 PK9  H043  H  HCH3  0   0.245  -7.7739   1.5491  -1.5494
 PK9  H031  H  HCH3  0   0.236  -8.2033  -1.7655   1.1902
 PK9  H032  H  HCH3  0   0.229  -9.5830  -1.1833   0.2601
 PK9  H033  H  HCH3  0   0.236  -8.2734  -2.0317  -0.5589
 PK9  H011  H  HCH3  0   0.246  -7.7690   1.9712   0.9942
 PK9  H012  H  HCH3  0   0.233  -9.2276   1.0242   1.2670
 PK9  H013  H  HCH3  0   0.234  -7.7410   0.5889   2.0996

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
 PK9  O15  C14   double    1.225  0.020  1.225
 PK9  C14  N16   single    1.345  0.020  1.345
 PK9  C14  C13   single    1.512  0.020  1.512
 PK9  N16  C17   single    1.445  0.020  1.445
 PK9  C17  C18   single    1.506  0.020  1.506
 PK9  C18  C23   aromatic  1.389  0.020  1.389
 PK9  C18  C19   aromatic  1.392  0.020  1.392
 PK9  C23  N22   aromatic  1.329  0.020  1.329
 PK9  N22  C21   aromatic  1.326  0.020  1.326
 PK9  C21  C20   aromatic  1.389  0.020  1.389
 PK9  C20  C19   aromatic  1.384  0.020  1.384
 PK9  C13  C12   single    1.527  0.020  1.527
 PK9  C12  C11   single    1.522  0.020  1.522
 PK9  C11  C10   single    1.523  0.020  1.523
 PK9  C10  C09   single    1.520  0.020  1.520
 PK9  C09  N08   single    1.447  0.020  1.447
 PK9  N08  C06   single    1.347  0.020  1.347
 PK9  C06  O07   double    1.216  0.020  1.216
 PK9  C06  O05   single    1.335  0.020  1.335
 PK9  O05  C02   single    1.451  0.020  1.451
 PK9  C02  C04   single    1.524  0.020  1.524
 PK9  C02  C03   single    1.524  0.020  1.524
 PK9  C02  C01   single    1.525  0.020  1.525
 PK9  N16  H16   single    0.860  0.020  1.020
 PK9  C13  H131  single    0.970  0.020  1.090
 PK9  C13  H132  single    0.970  0.020  1.090
 PK9  C17  H171  single    0.970  0.020  1.090
 PK9  C17  H172  single    0.970  0.020  1.090
 PK9  C23  H23   single    0.930  0.020  1.080
 PK9  C19  H19   single    0.930  0.020  1.080
 PK9  C21  H21   single    0.930  0.020  1.080
 PK9  C20  H20   single    0.930  0.020  1.080
 PK9  C12  H121  single    0.970  0.020  1.090
 PK9  C12  H122  single    0.970  0.020  1.090
 PK9  C11  H111  single    0.970  0.020  1.090
 PK9  C11  H112  single    0.970  0.020  1.090
 PK9  C10  H101  single    0.970  0.020  1.090
 PK9  C10  H102  single    0.970  0.020  1.090
 PK9  C09  H091  single    0.970  0.020  1.090
 PK9  C09  H092  single    0.970  0.020  1.090
 PK9  N08  H08   single    0.860  0.020  1.020
 PK9  C04  H041  single    0.970  0.020  1.090
 PK9  C04  H042  single    0.970  0.020  1.090
 PK9  C04  H043  single    0.970  0.020  1.090
 PK9  C03  H031  single    0.970  0.020  1.090
 PK9  C03  H032  single    0.970  0.020  1.090
 PK9  C03  H033  single    0.970  0.020  1.090
 PK9  C01  H011  single    0.970  0.020  1.090
 PK9  C01  H012  single    0.970  0.020  1.090
 PK9  C01  H013  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
 PK9  C13   C14  N16   115.51  3.000
 PK9  C13   C14  O15   121.58  3.000
 PK9  N16   C14  O15   122.91  3.000
 PK9  H16   N16  C17   117.34  3.000
 PK9  H16   N16  C14   118.67  3.000
 PK9  C17   N16  C14   123.96  3.000
 PK9  H172  C17  H171  107.01  3.000
 PK9  H172  C17  C18   110.19  3.000
 PK9  H171  C17  C18   109.76  3.000
 PK9  H172  C17  N16   108.17  3.000
 PK9  H171  C17  N16   108.61  3.000
 PK9  C18   C17  N16   112.90  3.000
 PK9  C19   C18  C23   117.29  3.000
 PK9  C19   C18  C17   121.81  3.000
 PK9  C23   C18  C17   120.90  3.000
 PK9  H23   C23  N22   116.24  3.000
 PK9  H23   C23  C18   119.63  3.000
 PK9  N22   C23  C18   124.13  3.000
 PK9  C21   N22  C23   117.77  3.000
 PK9  H21   C21  C20   120.23  3.000
 PK9  H21   C21  N22   116.70  3.000
 PK9  C20   C21  N22   123.07  3.000
 PK9  H20   C20  C19   121.19  3.000
 PK9  H20   C20  C21   120.24  3.000
 PK9  C19   C20  C21   118.57  3.000
 PK9  H19   C19  C20   120.28  3.000
 PK9  H19   C19  C18   120.56  3.000
 PK9  C20   C19  C18   119.16  3.000
 PK9  H132  C13  H131  106.71  3.000
 PK9  H132  C13  C12   109.48  3.000
 PK9  H131  C13  C12   109.92  3.000
 PK9  H132  C13  C14   107.47  3.000
 PK9  H131  C13  C14   111.42  3.000
 PK9  C12   C13  C14   111.68  3.000
 PK9  H122  C12  H121  106.58  3.000
 PK9  H122  C12  C11   109.53  3.000
 PK9  H121  C12  C11   109.53  3.000
 PK9  H122  C12  C13   109.28  3.000
 PK9  H121  C12  C13   109.49  3.000
 PK9  C11   C12  C13   112.27  3.000
 PK9  H112  C11  H111  106.23  3.000
 PK9  H112  C11  C10   109.63  3.000
 PK9  H111  C11  C10   109.30  3.000
 PK9  H112  C11  C12   109.34  3.000
 PK9  H111  C11  C12   109.70  3.000
 PK9  C10   C11  C12   112.46  3.000
 PK9  H102  C10  H101  106.64  3.000
 PK9  H102  C10  C09   109.55  3.000
 PK9  H101  C10  C09   109.48  3.000
 PK9  H102  C10  C11   109.26  3.000
 PK9  H101  C10  C11   109.87  3.000
 PK9  C09   C10  C11   111.90  3.000
 PK9  H092  C09  H091  106.86  3.000
 PK9  H092  C09  N08   109.57  3.000
 PK9  H091  C09  N08   110.71  3.000
 PK9  H092  C09  C10   109.53  3.000
 PK9  H091  C09  C10   109.63  3.000
 PK9  N08   C09  C10   110.47  3.000
 PK9  H08   N08  C06   118.61  3.000
 PK9  H08   N08  C09   118.05  3.000
 PK9  C06   N08  C09   121.98  3.000
 PK9  O05   C06  O07   125.68  3.000
 PK9  O05   C06  N08   110.43  3.000
 PK9  O07   C06  N08   123.88  3.000
 PK9  C02   O05  C06   122.62  3.000
 PK9  C01   C02  C03   109.50  3.000
 PK9  C01   C02  C04   111.95  3.000
 PK9  C03   C02  C04   109.72  3.000
 PK9  C01   C02  O05   111.46  3.000
 PK9  C03   C02  O05   103.05  3.000
 PK9  C04   C02  O05   110.78  3.000
 PK9  H043  C04  H042  107.77  3.000
 PK9  H043  C04  H041  108.67  3.000
 PK9  H042  C04  H041  107.50  3.000
 PK9  H043  C04  C02   112.50  3.000
 PK9  H042  C04  C02   109.34  3.000
 PK9  H041  C04  C02   110.89  3.000
 PK9  H033  C03  H032  107.81  3.000
 PK9  H033  C03  H031  108.45  3.000
 PK9  H032  C03  H031  107.85  3.000
 PK9  H033  C03  C02   111.44  3.000
 PK9  H032  C03  C02   109.77  3.000
 PK9  H031  C03  C02   111.39  3.000
 PK9  H013  C01  H012  107.40  3.000
 PK9  H013  C01  H011  108.68  3.000
 PK9  H012  C01  H011  107.83  3.000
 PK9  H013  C01  C02   110.96  3.000
 PK9  H012  C01  C02   108.99  3.000
 PK9  H011  C01  C02   112.79  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
 PK9  CONST_01  C21   N22  C23  C18     0.00   0.0  0
 PK9  CONST_02  C21   C20  C19  C18     0.00   0.0  0
 PK9  CONST_03  C20   C19  C18  C23     0.00   0.0  0
 PK9  CONST_04  C20   C21  N22  C23     0.00   0.0  0
 PK9  CONST_05  C19   C18  C23  N22     0.00   0.0  0
 PK9  CONST_06  C19   C20  C21  N22     0.00   0.0  0
 PK9  CONST_07  N22   C23  C18  C17   180.00   0.0  0
 PK9  CONST_08  C20   C19  C18  C17   180.00   0.0  0
 PK9  CONST_09  H20   C20  C19  C18   180.00   0.0  0
 PK9  CONST_10  H19   C19  C18  C23   180.00   0.0  0
 PK9  CONST_11  H21   C21  N22  C23   180.00   0.0  0
 PK9  CONST_12  H23   C23  N22  C21   180.00   0.0  0
 PK9  CONST_13  C17   N16  C14  O15     0.00   0.0  0
 PK9  CONST_14  C13   C14  N16  C17   180.00   0.0  0
 PK9  CONST_15  H16   N16  C14  O15   180.00   0.0  0
 PK9  Var_01    C23   C18  C17  N16   118.39  30.0  2
 PK9  Var_02    C18   C17  N16  C14   101.33  30.0  3
 PK9  Var_03    C12   C13  C14  O15    56.89  30.0  3
 PK9  Var_04    C11   C12  C13  C14  -176.17  30.0  3
 PK9  Var_05    C10   C11  C12  C13  -177.62  30.0  3
 PK9  Var_06    C09   C10  C11  C12  -178.08  30.0  3
 PK9  Var_07    N08   C09  C10  C11  -176.67  30.0  3
 PK9  Var_08    C06   N08  C09  C10  -172.96  30.0  3
 PK9  Var_09    O07   C06  N08  C09     6.82  30.0  2
 PK9  Var_10    C04   C02  O05  C06    65.90  30.0  3
 PK9  Var_11    H041  C04  C02  O05    54.86  30.0  3
 PK9  Var_12    H031  C03  C02  O05    60.94  30.0  3
 PK9  Var_13    H011  C01  C02  O05    72.89  30.0  3

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
 PK9  plan-1  C17  0.020
 PK9  plan-1  C18  0.020
 PK9  plan-1  C23  0.020
 PK9  plan-1  N22  0.020
 PK9  plan-1  C21  0.020
 PK9  plan-1  C20  0.020
 PK9  plan-1  C19  0.020
 PK9  plan-1  H23  0.020
 PK9  plan-1  H19  0.020
 PK9  plan-1  H21  0.020
 PK9  plan-1  H20  0.020
 PK9  plan-2  O15  0.020
 PK9  plan-2  C14  0.020
 PK9  plan-2  N16  0.020
 PK9  plan-2  C17  0.020
 PK9  plan-2  C13  0.020
 PK9  plan-2  H16  0.020
 PK9  plan-3  N08  0.020
 PK9  plan-3  C06  0.020
 PK9  plan-3  O07  0.020
 PK9  plan-3  O05  0.020

