# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 13:44:57 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: N-[2-(6-amino-4-methylpyridin-2-yl)ethyl]-4-cyanobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCNC(=O)c2ccc(cc2)C#N)c1
#
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
 AT6  AT6  N-[2-(6-amino-4-methylpyridin-2-yl)ethyl]-4-cyanobenzamide  ligand  37  21  .  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_AT6
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
 AT6  C2    C  CR6   0   0.205   5.3714   1.1149  -0.3901
 AT6  C1    C  CR16  0  -0.445   5.8583  -0.0606   0.1417
 AT6  C6    C  CR6   0   0.443   4.9684  -0.9436   0.7789
 AT6  N5    N  N     0  -0.486   3.6712  -0.6816   0.8946
 AT6  C4    C  CR6   0   0.277   3.2003   0.4586   0.3855
 AT6  C3    C  CR16  0  -0.431   4.0023   1.3793  -0.2622
 AT6  C10   C  CH2   0  -0.534   1.7239   0.6897   0.5440
 AT6  C11   C  CH2   0  -0.246   0.9106  -0.3443  -0.2286
 AT6  N12   N  NH1   0  -0.652  -0.5042  -0.1456   0.0052
 AT6  C24   C  C     0   0.531  -1.4542  -0.4874  -0.8766
 AT6  O25   O  O     0  -0.481  -1.2213  -1.0019  -1.9610
 AT6  C26   C  CR6   0  -0.020  -2.8639  -0.1989  -0.4557
 AT6  C27   C  CR16  0  -0.276  -3.1897   0.8757   0.3681
 AT6  C28   C  CR16  0  -0.223  -4.5073   1.1204   0.7131
 AT6  C29   C  CR6   0   0.004  -5.5084   0.2785   0.2339
 AT6  C30   C  CR16  0  -0.227  -5.1934  -0.7947  -0.5992
 AT6  C31   C  CR16  0  -0.257  -3.8753  -1.0198  -0.9483
 AT6  C32   C  CSP   0   0.062  -6.8688   0.5188   0.5953
 AT6  N33   N  NS    0  -0.245  -7.9661   0.7088   0.8898
 AT6  N7    N  NH2   0  -0.838   5.4229  -2.0953   1.3527
 AT6  C9    C  CH3   0  -0.726   6.2701   2.0785  -1.1025
 AT6  H1    H  HCR6  0   0.256   6.9111  -0.3069   0.0737
 AT6  H3    H  HCR6  0   0.246   3.5771   2.2903  -0.6639
 AT6  H101  H  HCH2  0   0.254   1.4684   0.6332   1.6069
 AT6  H102  H  HCH2  0   0.255   1.4600   1.6911   0.1998
 AT6  H111  H  HCH2  0   0.252   1.1043  -0.2484  -1.2966
 AT6  H112  H  HCH2  0   0.245   1.2134  -1.3512   0.0704
 AT6  HN12  H  HNH1  0   0.408  -0.7798   0.1148   0.9392
 AT6  H27   H  HCR6  0   0.276  -2.4256   1.5505   0.7306
 AT6  H28   H  HCR6  0   0.289  -4.7569   1.9615   1.3451
 AT6  H30   H  HCR6  0   0.288  -5.9748  -1.4438  -0.9698
 AT6  H31   H  HCR6  0   0.277  -3.6318  -1.8472  -1.6003
 AT6  HN71  H  HNH2  0   0.388   6.3024  -2.4635   1.0312
 AT6  HN72  H  HNH2  0   0.380   4.7290  -2.7974   1.5507
 AT6  H91   H  HCH3  0   0.255   6.1232   2.0103  -2.1822
 AT6  H92   H  HCH3  0   0.249   6.0526   3.1069  -0.8145
 AT6  H93   H  HCH3  0   0.248   7.3206   1.8794  -0.8970

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
 AT6  C2   C1    aromatic  1.379  0.020  1.379
 AT6  C2   C3    aromatic  1.400  0.020  1.400
 AT6  C2   C9    single    1.498  0.020  1.498
 AT6  C1   C6    aromatic  1.406  0.020  1.406
 AT6  C1   H1    single    0.930  0.020  1.080
 AT6  C6   N5    aromatic  1.328  0.020  1.328
 AT6  C6   N7    single    1.365  0.020  1.365
 AT6  N5   C4    aromatic  1.335  0.020  1.335
 AT6  C4   C3    aromatic  1.382  0.020  1.382
 AT6  C4   C10   single    1.503  0.020  1.503
 AT6  C3   H3    single    0.930  0.020  1.080
 AT6  C10  C11   single    1.526  0.020  1.526
 AT6  C10  H101  single    0.970  0.020  1.090
 AT6  C10  H102  single    0.970  0.020  1.090
 AT6  C11  N12   single    1.448  0.020  1.448
 AT6  C11  H111  single    0.970  0.020  1.090
 AT6  C11  H112  single    0.970  0.020  1.090
 AT6  N12  C24   single    1.341  0.020  1.341
 AT6  N12  HN12  single    0.860  0.020  1.020
 AT6  C24  O25   double    1.223  0.020  1.223
 AT6  C24  C26   single    1.499  0.020  1.499
 AT6  C26  C27   aromatic  1.393  0.020  1.393
 AT6  C26  C31   aromatic  1.393  0.020  1.393
 AT6  C27  C28   aromatic  1.384  0.020  1.384
 AT6  C27  H27   single    0.930  0.020  1.080
 AT6  C28  C29   aromatic  1.393  0.020  1.393
 AT6  C28  H28   single    0.930  0.020  1.080
 AT6  C29  C30   aromatic  1.395  0.020  1.395
 AT6  C29  C32   single    1.428  0.020  1.428
 AT6  C30  C31   aromatic  1.382  0.020  1.382
 AT6  C30  H30   single    0.930  0.020  1.080
 AT6  C31  H31   single    0.930  0.020  1.080
 AT6  C32  N33   triple    1.152  0.020  1.152
 AT6  N7   HN71  single    0.890  0.020  1.040
 AT6  N7   HN72  single    0.890  0.020  1.040
 AT6  C9   H91   single    0.970  0.020  1.090
 AT6  C9   H92   single    0.970  0.020  1.090
 AT6  C9   H93   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
 AT6  C9    C2   C3    120.57  3.000
 AT6  C9    C2   C1    121.33  3.000
 AT6  C3    C2   C1    118.10  3.000
 AT6  H1    C1   C6    120.05  3.000
 AT6  H1    C1   C2    120.84  3.000
 AT6  C6    C1   C2    119.11  3.000
 AT6  N7    C6   N5    117.07  3.000
 AT6  N7    C6   C1    120.64  3.000
 AT6  N5    C6   C1    122.25  3.000
 AT6  C4    N5   C6    118.67  3.000
 AT6  C10   C4   C3    121.14  3.000
 AT6  C10   C4   N5    115.96  3.000
 AT6  C3    C4   N5    122.90  3.000
 AT6  H3    C3   C4    120.43  3.000
 AT6  H3    C3   C2    120.60  3.000
 AT6  C4    C3   C2    118.97  3.000
 AT6  H102  C10  H101  107.29  3.000
 AT6  H102  C10  C11   109.47  3.000
 AT6  H101  C10  C11   109.41  3.000
 AT6  H102  C10  C4    110.21  3.000
 AT6  H101  C10  C4    108.89  3.000
 AT6  C11   C10  C4    111.47  3.000
 AT6  H112  C11  H111  107.45  3.000
 AT6  H112  C11  N12   110.67  3.000
 AT6  H111  C11  N12   108.65  3.000
 AT6  H112  C11  C10   109.76  3.000
 AT6  H111  C11  C10   110.00  3.000
 AT6  N12   C11  C10   110.25  3.000
 AT6  HN12  N12  C24   118.78  3.000
 AT6  HN12  N12  C11   116.89  3.000
 AT6  C24   N12  C11   123.46  3.000
 AT6  C26   C24  O25   120.61  3.000
 AT6  C26   C24  N12   115.64  3.000
 AT6  O25   C24  N12   123.76  3.000
 AT6  C31   C26  C27   119.61  3.000
 AT6  C31   C26  C24   118.04  3.000
 AT6  C27   C26  C24   122.31  3.000
 AT6  H27   C27  C28   118.59  3.000
 AT6  H27   C27  C26   120.95  3.000
 AT6  C28   C27  C26   120.44  3.000
 AT6  H28   C28  C29   120.35  3.000
 AT6  H28   C28  C27   120.20  3.000
 AT6  C29   C28  C27   119.44  3.000
 AT6  C32   C29  C30   119.73  3.000
 AT6  C32   C29  C28   119.73  3.000
 AT6  C30   C29  C28   120.54  3.000
 AT6  H30   C30  C31   120.32  3.000
 AT6  H30   C30  C29   120.23  3.000
 AT6  C31   C30  C29   119.45  3.000
 AT6  H31   C31  C30   119.46  3.000
 AT6  H31   C31  C26   120.05  3.000
 AT6  C30   C31  C26   120.48  3.000
 AT6  N33   C32  C29   180.00  3.000
 AT6  HN72  N7   HN71  114.21  3.000
 AT6  HN72  N7   C6    116.21  3.000
 AT6  HN71  N7   C6    117.75  3.000
 AT6  H93   C9   H92   108.37  3.000
 AT6  H93   C9   H91   107.76  3.000
 AT6  H92   C9   H91   107.06  3.000
 AT6  H93   C9   C2    111.81  3.000
 AT6  H92   C9   C2    111.20  3.000
 AT6  H91   C9   C2    110.46  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
 AT6  CONST_01  N5    C6   C1   C2     0.00   0.0  0
 AT6  CONST_02  N5    C4   C3   C2     0.00   0.0  0
 AT6  CONST_03  C4    C3   C2   C1     0.00   0.0  0
 AT6  CONST_04  C4    N5   C6   C1     0.00   0.0  0
 AT6  CONST_05  C3    C2   C1   C6     0.00   0.0  0
 AT6  CONST_06  C3    C4   N5   C6     0.00   0.0  0
 AT6  CONST_07  C29   C28  C27  C26    0.00   0.0  0
 AT6  CONST_08  C29   C30  C31  C26    0.00   0.0  0
 AT6  CONST_09  C30   C31  C26  C27    0.00   0.0  0
 AT6  CONST_10  C30   C29  C28  C27    0.00   0.0  0
 AT6  CONST_11  C31   C26  C27  C28    0.00   0.0  0
 AT6  CONST_12  C31   C30  C29  C28    0.00   0.0  0
 AT6  CONST_13  N7    C6   C1   C2   180.00   0.0  0
 AT6  CONST_14  C10   C4   C3   C2   180.00   0.0  0
 AT6  CONST_15  C9    C2   C1   C6   180.00   0.0  0
 AT6  CONST_16  C10   C4   N5   C6   180.00   0.0  0
 AT6  CONST_17  N7    C6   N5   C4   180.00   0.0  0
 AT6  CONST_18  C9    C2   C3   C4   180.00   0.0  0
 AT6  CONST_19  C28   C27  C26  C24  180.00   0.0  0
 AT6  CONST_20  C30   C31  C26  C24  180.00   0.0  0
 AT6  CONST_21  C32   C29  C28  C27  180.00   0.0  0
 AT6  CONST_22  C32   C29  C30  C31  180.00   0.0  0
 AT6  CONST_23  H3    C3   C2   C1   180.00   0.0  0
 AT6  CONST_24  H1    C1   C6   N5   180.00   0.0  0
 AT6  CONST_25  H28   C28  C27  C26  180.00   0.0  0
 AT6  CONST_26  H30   C30  C31  C26  180.00   0.0  0
 AT6  CONST_27  H31   C31  C26  C27  180.00   0.0  0
 AT6  CONST_28  H27   C27  C28  C29  180.00   0.0  0
 AT6  CONST_31  C26   C24  N12  C11  180.00   0.0  0
 AT6  CONST_32  HN12  N12  C24  C26    0.00   0.0  0
 AT6  CONST_33  O25   C24  N12  C11    0.00   0.0  0
 AT6  Var_01    C11   C10  C4   N5   -64.66  30.0  2
 AT6  Var_02    C27   C26  C24  N12   31.26  30.0  2
 AT6  Var_03    H91   C9   C2   C1   104.02  30.0  2
 AT6  Var_04    N12   C11  C10  C4   176.65  30.0  3
 AT6  Var_05    C24   N12  C11  C10  152.28  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
 AT6  plan-1  C2    0.020
 AT6  plan-1  C1    0.020
 AT6  plan-1  C6    0.020
 AT6  plan-1  N5    0.020
 AT6  plan-1  C4    0.020
 AT6  plan-1  C3    0.020
 AT6  plan-1  C10   0.020
 AT6  plan-1  N7    0.020
 AT6  plan-1  C9    0.020
 AT6  plan-1  H1    0.020
 AT6  plan-1  H3    0.020
 AT6  plan-2  C24   0.020
 AT6  plan-2  C26   0.020
 AT6  plan-2  C27   0.020
 AT6  plan-2  C28   0.020
 AT6  plan-2  C29   0.020
 AT6  plan-2  C30   0.020
 AT6  plan-2  C31   0.020
 AT6  plan-2  C32   0.020
 AT6  plan-2  N33   0.020
 AT6  plan-2  H27   0.020
 AT6  plan-2  H28   0.020
 AT6  plan-2  H30   0.020
 AT6  plan-2  H31   0.020
 AT6  plan-3  C11   0.020
 AT6  plan-3  N12   0.020
 AT6  plan-3  C24   0.020
 AT6  plan-3  O25   0.020
 AT6  plan-3  C26   0.020
 AT6  plan-3  HN12  0.020
 AT6  plan-4  C6    0.020
 AT6  plan-4  N7    0.020
 AT6  plan-4  HN71  0.020
 AT6  plan-4  HN72  0.020

