# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 17:46:51 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 3-methyl-8-(piperidin-4-ylamino)-1H-1,7-naphthyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=Cc2ccnc(NC3CCNCC3)c2NC1=O
#
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
 6XC  6XC  3-methyl-8-(piperidin-4-ylamino)-1H-1,7-naphthyridin-2-one  ligand  37  19  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6XC
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
 6XC  C01   C  CH3   0  -0.711   5.3868  -0.8012  -0.2315
 6XC  C05   C  CR6   0  -0.112   3.9576  -0.3923  -0.1072
 6XC  C06   C  CR16  0  -0.194   3.5514   0.8945  -0.1253
 6XC  C08   C  CR66  0   0.128   2.1714   1.2631  -0.0044
 6XC  C09   C  CR16  0  -0.427   1.7256   2.5969   0.0205
 6XC  C11   C  CR16  0  -0.081   0.3840   2.8216   0.1712
 6XC  N13   N  N     0  -0.462  -0.5287   1.8423   0.2418
 6XC  C14   C  CR6   0   0.496  -0.1453   0.5835   0.1950
 6XC  N15   N  NH1   0  -0.694  -1.0821  -0.4085   0.2783
 6XC  C17   C  CH1   0  -0.061  -2.5063  -0.1239   0.3123
 6XC  C19   C  CH2   0  -0.447  -3.2481  -1.3427   0.8530
 6XC  C22   C  CH2   0  -0.321  -4.7560  -1.0925   0.8632
 6XC  N25   N  NH1   0  -0.574  -5.2999  -0.6771  -0.4190
 6XC  C27   C  CH2   0  -0.321  -4.5903   0.4749  -0.9521
 6XC  C30   C  CH2   0  -0.446  -3.0776   0.2788  -1.0467
 6XC  C33   C  CR66  0   0.220   1.2365   0.2455   0.1161
 6XC  N34   N  NR16  0  -0.749   1.6714  -1.0559   0.1636
 6XC  C36   C  CR6   0   0.516   2.9747  -1.4625   0.0695
 6XC  O37   O  O     0  -0.479   3.2725  -2.6484   0.1402
 6XC  H011  H  HCH3  0   0.251   5.7256  -1.3265   0.6631
 6XC  H012  H  HCH3  0   0.251   5.5317  -1.4820  -1.0716
 6XC  H013  H  HCH3  0   0.248   6.0282   0.0654  -0.3787
 6XC  H06   H  HCR6  0   0.271   4.2820   1.6882  -0.2324
 6XC  H09   H  HCR6  0   0.262   2.4285   3.4143  -0.0634
 6XC  H11   H  HCR6  0   0.256  -0.0031   3.8326   0.2245
 6XC  H15   H  HNH1  0   0.380  -0.8606  -1.2686  -0.2011
 6XC  H17   H  HCH1  0   0.237  -2.6529   0.7061   1.0087
 6XC  H191  H  HCH2  0   0.218  -3.0274  -2.2157   0.2267
 6XC  H192  H  HCH2  0   0.237  -2.9009  -1.5761   1.8627
 6XC  H301  H  HCH2  0   0.238  -2.5971   1.1931  -1.4000
 6XC  H302  H  HCH2  0   0.213  -2.8600  -0.5081  -1.7785
 6XC  H221  H  HCH2  0   0.239  -5.2814  -1.9902   1.1944
 6XC  H222  H  HCH2  0   0.218  -4.9827  -0.3109   1.5970
 6XC  H25   H  HNH1  0   0.338  -5.2129  -1.4455  -1.0748
 6XC  H271  H  HCH2  0   0.237  -5.0001   0.7177  -1.9345
 6XC  H272  H  HCH2  0   0.216  -4.8042   1.3337  -0.3059
 6XC  H34   H  HNR6  0   0.408   1.0070  -1.7943   0.3502

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
 6XC  C01  C05   single    1.492  0.020  1.492
 6XC  C05  C06   double    1.349  0.020  1.349
 6XC  C05  C36   single    1.464  0.020  1.464
 6XC  C06  C08   single    1.433  0.020  1.433
 6XC  C08  C09   aromatic  1.407  0.020  1.407
 6XC  C08  C33   aromatic  1.387  0.020  1.387
 6XC  C09  C11   aromatic  1.369  0.020  1.369
 6XC  C11  N13   aromatic  1.341  0.020  1.341
 6XC  N13  C14   aromatic  1.317  0.020  1.317
 6XC  C14  N15   single    1.367  0.020  1.367
 6XC  C14  C33   aromatic  1.425  0.020  1.425
 6XC  N15  C17   single    1.453  0.020  1.453
 6XC  C17  C19   single    1.526  0.020  1.526
 6XC  C17  C30   single    1.528  0.020  1.528
 6XC  C19  C22   single    1.529  0.020  1.529
 6XC  C22  N25   single    1.453  0.020  1.453
 6XC  N25  C27   single    1.454  0.020  1.454
 6XC  C27  C30   single    1.528  0.020  1.528
 6XC  C33  N34   single    1.373  0.020  1.373
 6XC  N34  C36   single    1.369  0.020  1.369
 6XC  C36  O37   double    1.225  0.020  1.225
 6XC  C01  H011  single    0.970  0.020  1.090
 6XC  C01  H012  single    0.970  0.020  1.090
 6XC  C01  H013  single    0.970  0.020  1.090
 6XC  C06  H06   single    0.930  0.020  1.080
 6XC  C09  H09   single    0.930  0.020  1.080
 6XC  C11  H11   single    0.930  0.020  1.080
 6XC  N15  H15   single    0.890  0.020  1.040
 6XC  C17  H17   single    0.970  0.020  1.090
 6XC  C19  H191  single    0.970  0.020  1.090
 6XC  C19  H192  single    0.970  0.020  1.090
 6XC  C30  H301  single    0.970  0.020  1.090
 6XC  C30  H302  single    0.970  0.020  1.090
 6XC  C22  H221  single    0.970  0.020  1.090
 6XC  C22  H222  single    0.970  0.020  1.090
 6XC  N25  H25   single    0.890  0.020  1.040
 6XC  C27  H271  single    0.970  0.020  1.090
 6XC  C27  H272  single    0.970  0.020  1.090
 6XC  N34  H34   single    0.860  0.020  1.020

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
 6XC  H013  C01  H012  108.34  3.000
 6XC  H013  C01  H011  108.13  3.000
 6XC  H012  C01  H011  106.84  3.000
 6XC  H013  C01  C05   110.96  3.000
 6XC  H012  C01  C05   111.25  3.000
 6XC  H011  C01  C05   111.16  3.000
 6XC  C36   C05  C06   119.78  3.000
 6XC  C36   C05  C01   116.93  3.000
 6XC  C06   C05  C01   123.28  3.000
 6XC  H06   C06  C08   117.96  3.000
 6XC  H06   C06  C05   119.78  3.000
 6XC  C08   C06  C05   122.26  3.000
 6XC  C33   C08  C09   118.72  3.000
 6XC  C33   C08  C06   117.88  3.000
 6XC  C09   C08  C06   123.40  3.000
 6XC  H09   C09  C11   121.44  3.000
 6XC  H09   C09  C08   120.63  3.000
 6XC  C11   C09  C08   117.93  3.000
 6XC  H11   C11  N13   115.83  3.000
 6XC  H11   C11  C09   120.58  3.000
 6XC  N13   C11  C09   123.59  3.000
 6XC  C14   N13  C11   119.89  3.000
 6XC  C33   C14  N15   119.72  3.000
 6XC  C33   C14  N13   120.74  3.000
 6XC  N15   C14  N13   119.48  3.000
 6XC  H15   N15  C17   113.15  3.000
 6XC  H15   N15  C14   116.04  3.000
 6XC  C17   N15  C14   122.08  3.000
 6XC  H17   C17  C30   108.44  3.000
 6XC  H17   C17  C19   108.39  3.000
 6XC  C30   C17  C19   110.11  3.000
 6XC  H17   C17  N15   107.16  3.000
 6XC  C30   C17  N15   113.41  3.000
 6XC  C19   C17  N15   109.18  3.000
 6XC  H192  C19  H191  107.07  3.000
 6XC  H192  C19  C22   110.01  3.000
 6XC  H191  C19  C22   109.42  3.000
 6XC  H192  C19  C17   110.09  3.000
 6XC  H191  C19  C17   109.61  3.000
 6XC  C22   C19  C17   110.56  3.000
 6XC  H222  C22  H221  106.48  3.000
 6XC  H222  C22  N25   108.04  3.000
 6XC  H221  C22  N25   108.82  3.000
 6XC  H222  C22  C19   108.98  3.000
 6XC  H221  C22  C19   110.01  3.000
 6XC  N25   C22  C19   114.21  3.000
 6XC  H25   N25  C27   108.74  3.000
 6XC  H25   N25  C22   108.78  3.000
 6XC  C27   N25  C22   111.54  3.000
 6XC  H272  C27  H271  106.44  3.000
 6XC  H272  C27  C30   109.28  3.000
 6XC  H271  C27  C30   110.14  3.000
 6XC  H272  C27  N25   108.02  3.000
 6XC  H271  C27  N25   108.84  3.000
 6XC  C30   C27  N25   113.83  3.000
 6XC  H302  C30  H301  107.33  3.000
 6XC  H302  C30  C27   109.26  3.000
 6XC  H301  C30  C27   110.38  3.000
 6XC  H302  C30  C17   109.28  3.000
 6XC  H301  C30  C17   110.12  3.000
 6XC  C27   C30  C17   110.41  3.000
 6XC  N34   C33  C14   122.02  3.000
 6XC  N34   C33  C08   119.00  3.000
 6XC  C14   C33  C08   118.97  3.000
 6XC  H34   N34  C36   114.94  3.000
 6XC  H34   N34  C33   119.39  3.000
 6XC  C36   N34  C33   125.52  3.000
 6XC  O37   C36  N34   121.02  3.000
 6XC  O37   C36  C05   123.48  3.000
 6XC  N34   C36  C05   115.50  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
 6XC  CONST_01  N13   C11  C09  C08    0.00   0.0  0
 6XC  CONST_02  N13   C14  C33  C08    0.00   0.0  0
 6XC  CONST_03  C14   C33  C08  C09    0.00   0.0  0
 6XC  CONST_04  C14   N13  C11  C09    0.00   0.0  0
 6XC  CONST_05  C33   C08  C09  C11    0.00   0.0  0
 6XC  CONST_06  C33   C14  N13  C11    0.00   0.0  0
 6XC  CONST_07  C33   N34  C36  C05    0.00   0.0  0
 6XC  CONST_08  N15   C14  C33  C08  180.00   0.0  0
 6XC  CONST_09  N15   C14  N13  C11  180.00   0.0  0
 6XC  CONST_10  N34   C33  C14  N15    0.00   0.0  0
 6XC  CONST_11  C17   N15  C14  N13    0.00   0.0  0
 6XC  CONST_12  C33   C14  N15  C17  180.00   0.0  0
 6XC  CONST_13  O37   C36  N34  C33  180.00   0.0  0
 6XC  CONST_14  H09   C09  C08  C06    0.00   0.0  0
 6XC  CONST_15  H11   C11  C09  C08  180.00   0.0  0
 6XC  CONST_16  H34   N34  C36  C05  180.00   0.0  0
 6XC  Var_01    N25   C22  C19  C17   53.91  30.0  1
 6XC  Var_02    N25   C27  C30  C17  -54.88  30.0  1
 6XC  Var_03    C27   N25  C22  C19  -53.49  30.0  1
 6XC  Var_04    C30   C27  N25  C22   53.94  30.0  1
 6XC  Var_05    H011  C01  C05  C06  117.93  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
 6XC  chir_01  C17  N15  C19  C30  positiv

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
 6XC  plan-1  C01  0.020
 6XC  plan-1  C05  0.020
 6XC  plan-1  C06  0.020
 6XC  plan-1  C08  0.020
 6XC  plan-1  C09  0.020
 6XC  plan-1  C11  0.020
 6XC  plan-1  N13  0.020
 6XC  plan-1  C14  0.020
 6XC  plan-1  N15  0.020
 6XC  plan-1  C33  0.020
 6XC  plan-1  N34  0.020
 6XC  plan-1  C36  0.020
 6XC  plan-1  O37  0.020
 6XC  plan-1  H06  0.020
 6XC  plan-1  H09  0.020
 6XC  plan-1  H11  0.020
 6XC  plan-1  H34  0.020
 6XC  plan-2  C14  0.020
 6XC  plan-2  N15  0.020
 6XC  plan-2  C17  0.020
 6XC  plan-2  H15  0.020

