# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 07:09:15 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-carbamimidoyl-N-[3-(cyclopentyloxy)phenyl]naphthalene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc2cc(ccc2c1)C(=O)Nc3cccc(OC4CCCC4)c3
#
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
 426  426  6-carbamimidoyl-N-[3-(cyclopentyloxy)phenyl]naphthalene-2-carboxamide  ligand  51  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_426
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
 426  N18   N  N     0  -0.637  -0.0374   1.6661   8.0614
 426  C17   C  C     0   0.333   0.4589   0.6189   7.5233
 426  N19   N  NH2   0  -0.803   1.0316  -0.3532   8.2867
 426  C4    C  CR6   0   0.008   0.5132   0.3742   6.0536
 426  C5    C  CR16  0  -0.360  -0.5310   0.7738   5.2581
 426  C6    C  CR66  0   0.137  -0.4989   0.5726   3.8619
 426  C10   C  CR16  0  -0.298  -1.5692   0.9646   3.0254
 426  C11   C  CR16  0  -0.293  -1.5143   0.7565   1.6767
 426  C12   C  CR6   0  -0.042  -0.3765   0.1530   1.0871
 426  C13   C  CR16  0  -0.334   0.6813  -0.2182   1.8784
 426  C1    C  CR66  0   0.136   0.6401  -0.0347   3.2761
 426  C2    C  CR16  0  -0.296   1.7055  -0.4381   4.1141
 426  C3    C  CR16  0  -0.277   1.6409  -0.2492   5.4653
 426  C20   C  C     0   0.530  -0.2624  -0.0677  -0.3867
 426  O23   O  O     0  -0.457   0.8206  -0.0476  -0.9459
 426  N21   N  NH1   0  -0.762  -1.4419  -0.3021  -1.0144
 426  C22   C  CR6   0   0.412  -1.7009  -0.5160  -2.3723
 426  C28   C  CR16  0  -0.389  -3.0077  -0.8675  -2.7076
 426  C27   C  CR16  0  -0.226  -3.3388  -1.0746  -4.0369
 426  C26   C  CR16  0  -0.374  -2.3952  -0.9374  -5.0385
 426  C25   C  CR6   0   0.427  -1.0881  -0.5841  -4.7011
 426  O33   O  O2    0  -0.491  -0.2276  -0.4788  -5.7307
 426  C34   C  CH1   0   0.024   1.1275  -0.1157  -5.5173
 426  C38   C  CH2   0  -0.462   1.9241  -0.4149  -6.7879
 426  C37   C  CH2   0  -0.449   3.1076   0.5733  -6.7687
 426  C36   C  CH2   0  -0.459   2.8596   1.5048  -5.5653
 426  C35   C  CH2   0  -0.475   1.3676   1.3717  -5.2746
 426  C24   C  CR16  0  -0.471  -0.7348  -0.3729  -3.3701
 426  H18   H  H     0   0.334  -0.3214   2.3307   7.3514
 426  H191  H  HNH2  0   0.386   0.8948  -0.2751   9.2821
 426  H192  H  HNH2  0   0.395   1.0246  -1.2989   7.9421
 426  H5    H  HCR6  0   0.267  -1.4087   1.2345   5.6964
 426  H10   H  HCR6  0   0.266  -2.4365   1.4403   3.4654
 426  H11   H  HCR6  0   0.267  -2.3411   1.0923   1.0635
 426  H13   H  HCR6  0   0.265   1.5604  -0.6716   1.4374
 426  H2    H  HCR6  0   0.265   2.5797  -0.8980   3.6707
 426  H3    H  HCR6  0   0.268   2.4694  -0.5595   6.0882
 426  H21   H  HNH1  0   0.423  -2.2491  -0.4173  -0.4211
 426  H28   H  HCR6  0   0.268  -3.7599  -0.9732  -1.9355
 426  H27   H  HCR6  0   0.262  -4.3535  -1.3473  -4.2953
 426  H26   H  HCR6  0   0.260  -2.6581  -1.1019  -6.0755
 426  H34   H  HCH1  0   0.227   1.5421  -0.6981  -4.6846
 426  H381  H  HCH2  0   0.238   1.2856  -0.2352  -7.6558
 426  H382  H  HCH2  0   0.245   2.2412  -1.4569  -6.8325
 426  H371  H  HCH2  0   0.234   3.1381   1.1446  -7.6969
 426  H372  H  HCH2  0   0.235   4.0663   0.0616  -6.6842
 426  H361  H  HCH2  0   0.240   3.1585   2.5346  -5.7601
 426  H362  H  HCH2  0   0.229   3.4318   1.1638  -4.6992
 426  H351  H  HCH2  0   0.233   0.7810   1.9508  -5.9945
 426  H352  H  HCH2  0   0.244   1.0964   1.7122  -4.2743
 426  H24   H  HCR6  0   0.297   0.2703  -0.0999  -3.1010

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
 426  N18  C17   double    1.278  0.020  1.278
 426  N18  H18   single    0.890  0.020  1.040
 426  C17  N19   single    1.362  0.020  1.362
 426  C17  C4    single    1.491  0.020  1.491
 426  N19  H191  single    0.890  0.020  1.040
 426  N19  H192  single    0.890  0.020  1.040
 426  C4   C5    aromatic  1.372  0.020  1.372
 426  C4   C3    aromatic  1.417  0.020  1.417
 426  C5   C6    aromatic  1.411  0.020  1.411
 426  C5   H5    single    0.930  0.020  1.080
 426  C6   C10   aromatic  1.414  0.020  1.414
 426  C6   C1    aromatic  1.418  0.020  1.418
 426  C10  C11   aromatic  1.366  0.020  1.366
 426  C10  H10   single    0.930  0.020  1.080
 426  C11  C12   aromatic  1.416  0.020  1.416
 426  C11  H11   single    0.930  0.020  1.080
 426  C12  C13   aromatic  1.372  0.020  1.372
 426  C12  C20   single    1.495  0.020  1.495
 426  C13  C1    aromatic  1.410  0.020  1.410
 426  C13  H13   single    0.930  0.020  1.080
 426  C1   C2    aromatic  1.414  0.020  1.414
 426  C2   C3    aromatic  1.366  0.020  1.366
 426  C2   H2    single    0.930  0.020  1.080
 426  C3   H3    single    0.930  0.020  1.080
 426  C20  O23   double    1.219  0.020  1.219
 426  C20  N21   single    1.357  0.020  1.357
 426  N21  C22   single    1.399  0.020  1.399
 426  N21  H21   single    0.860  0.020  1.020
 426  C22  C28   aromatic  1.394  0.020  1.394
 426  C22  C24   aromatic  1.396  0.020  1.396
 426  C28  C27   aromatic  1.386  0.020  1.386
 426  C28  H28   single    0.930  0.020  1.080
 426  C27  C26   aromatic  1.383  0.020  1.383
 426  C27  H27   single    0.930  0.020  1.080
 426  C26  C25   aromatic  1.395  0.020  1.395
 426  C26  H26   single    0.930  0.020  1.080
 426  C25  O33   single    1.346  0.020  1.346
 426  C25  C24   aromatic  1.393  0.020  1.393
 426  O33  C34   single    1.419  0.020  1.419
 426  C34  C38   single    1.529  0.020  1.529
 426  C34  C35   single    1.526  0.020  1.526
 426  C34  H34   single    0.970  0.020  1.090
 426  C38  C37   single    1.542  0.020  1.542
 426  C38  H381  single    0.970  0.020  1.090
 426  C38  H382  single    0.970  0.020  1.090
 426  C37  C36   single    1.542  0.020  1.542
 426  C37  H371  single    0.970  0.020  1.090
 426  C37  H372  single    0.970  0.020  1.090
 426  C36  C35   single    1.526  0.020  1.526
 426  C36  H361  single    0.970  0.020  1.090
 426  C36  H362  single    0.970  0.020  1.090
 426  C35  H351  single    0.970  0.020  1.090
 426  C35  H352  single    0.970  0.020  1.090
 426  C24  H24   single    0.930  0.020  1.080

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
 426  H18   N18  C17   110.57  3.000
 426  C4    C17  N19   114.83  3.000
 426  C4    C17  N18   124.32  3.000
 426  N19   C17  N18   120.81  3.000
 426  H192  N19  H191  114.20  3.000
 426  H192  N19  C17   118.41  3.000
 426  H191  N19  C17   116.18  3.000
 426  C3    C4   C5    119.55  3.000
 426  C3    C4   C17   120.71  3.000
 426  C5    C4   C17   119.74  3.000
 426  H5    C5   C6    118.63  3.000
 426  H5    C5   C4    120.37  3.000
 426  C6    C5   C4    120.99  3.000
 426  C1    C6   C10   118.85  3.000
 426  C1    C6   C5    119.23  3.000
 426  C10   C6   C5    121.92  3.000
 426  H10   C10  C11   120.03  3.000
 426  H10   C10  C6    119.20  3.000
 426  C11   C10  C6    120.77  3.000
 426  H11   C11  C12   120.65  3.000
 426  H11   C11  C10   118.77  3.000
 426  C12   C11  C10   120.55  3.000
 426  C20   C12  C13   118.02  3.000
 426  C20   C12  C11   122.33  3.000
 426  C13   C12  C11   119.63  3.000
 426  H13   C13  C1    118.80  3.000
 426  H13   C13  C12   120.28  3.000
 426  C1    C13  C12   120.92  3.000
 426  C2    C1   C13   121.88  3.000
 426  C2    C1   C6    118.86  3.000
 426  C13   C1   C6    119.26  3.000
 426  H2    C2   C3    120.13  3.000
 426  H2    C2   C1    119.13  3.000
 426  C3    C2   C1    120.74  3.000
 426  H3    C3   C2    119.58  3.000
 426  H3    C3   C4    119.78  3.000
 426  C2    C3   C4    120.62  3.000
 426  N21   C20  O23   124.27  3.000
 426  N21   C20  C12   114.54  3.000
 426  O23   C20  C12   121.18  3.000
 426  H21   N21  C22   113.92  3.000
 426  H21   N21  C20   116.33  3.000
 426  C22   N21  C20   129.54  3.000
 426  C24   C22  C28   120.17  3.000
 426  C24   C22  N21   123.37  3.000
 426  C28   C22  N21   116.46  3.000
 426  H28   C28  C27   120.22  3.000
 426  H28   C28  C22   120.28  3.000
 426  C27   C28  C22   119.50  3.000
 426  H27   C27  C26   119.47  3.000
 426  H27   C27  C28   119.40  3.000
 426  C26   C27  C28   121.13  3.000
 426  H26   C26  C25   119.85  3.000
 426  H26   C26  C27   120.87  3.000
 426  C25   C26  C27   119.28  3.000
 426  C24   C25  O33   123.84  3.000
 426  C24   C25  C26   120.46  3.000
 426  O33   C25  C26   115.70  3.000
 426  C34   O33  C25   121.03  3.000
 426  H34   C34  C35   109.70  3.000
 426  H34   C34  C38   109.26  3.000
 426  C35   C34  C38   103.94  3.000
 426  H34   C34  O33   109.82  3.000
 426  C35   C34  O33   115.06  3.000
 426  C38   C34  O33   108.81  3.000
 426  H382  C38  H381  107.15  3.000
 426  H382  C38  C37   112.95  3.000
 426  H381  C38  C37   110.68  3.000
 426  H382  C38  C34   111.87  3.000
 426  H381  C38  C34   108.87  3.000
 426  C37   C38  C34   105.31  3.000
 426  H372  C37  H371  106.70  3.000
 426  H372  C37  C36   111.38  3.000
 426  H371  C37  C36   110.63  3.000
 426  H372  C37  C38   112.03  3.000
 426  H371  C37  C38   110.28  3.000
 426  C36   C37  C38   105.87  3.000
 426  H362  C36  H361  107.04  3.000
 426  H362  C36  C35   109.50  3.000
 426  H361  C36  C35   112.62  3.000
 426  H362  C36  C37   110.24  3.000
 426  H361  C36  C37   112.78  3.000
 426  C35   C36  C37   104.67  3.000
 426  H352  C35  H351  107.74  3.000
 426  H352  C35  C36   112.99  3.000
 426  H351  C35  C36   110.64  3.000
 426  H352  C35  C34   114.26  3.000
 426  H351  C35  C34   109.08  3.000
 426  C36   C35  C34   102.04  3.000
 426  H24   C24  C25   120.96  3.000
 426  H24   C24  C22   119.58  3.000
 426  C25   C24  C22   119.46  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
 426  CONST_01  C10   C6   C5   C4   180.00   0.0  0
 426  CONST_02  C1    C6   C5   C4     0.00   0.0  0
 426  CONST_03  C1    C2   C3   C4     0.00   0.0  0
 426  CONST_04  C2    C3   C4   C5     0.00   0.0  0
 426  CONST_05  C11   C10  C6   C5   180.00   0.0  0
 426  CONST_06  C13   C1   C6   C5   180.00   0.0  0
 426  CONST_07  C2    C1   C6   C5     0.00   0.0  0
 426  CONST_08  C3    C4   C5   C6     0.00   0.0  0
 426  CONST_09  C12   C11  C10  C6     0.00   0.0  0
 426  CONST_10  C12   C13  C1   C6     0.00   0.0  0
 426  CONST_11  C3    C2   C1   C6     0.00   0.0  0
 426  CONST_12  C13   C1   C6   C10    0.00   0.0  0
 426  CONST_13  C2    C1   C6   C10  180.00   0.0  0
 426  CONST_14  C13   C12  C11  C10    0.00   0.0  0
 426  CONST_15  C1    C6   C10  C11    0.00   0.0  0
 426  CONST_16  C1    C13  C12  C11    0.00   0.0  0
 426  CONST_17  C2    C1   C13  C12  180.00   0.0  0
 426  CONST_18  C3    C2   C1   C13  180.00   0.0  0
 426  CONST_19  C26   C27  C28  C22    0.00   0.0  0
 426  CONST_20  C26   C25  C24  C22    0.00   0.0  0
 426  CONST_21  C25   C24  C22  C28    0.00   0.0  0
 426  CONST_22  C25   C26  C27  C28    0.00   0.0  0
 426  CONST_23  C24   C22  C28  C27    0.00   0.0  0
 426  CONST_24  C24   C25  C26  C27    0.00   0.0  0
 426  CONST_25  C6    C5   C4   C17  180.00   0.0  0
 426  CONST_26  C2    C3   C4   C17  180.00   0.0  0
 426  CONST_27  C20   C12  C11  C10  180.00   0.0  0
 426  CONST_28  C20   C12  C13  C1   180.00   0.0  0
 426  CONST_29  C27   C28  C22  N21  180.00   0.0  0
 426  CONST_30  C25   C24  C22  N21  180.00   0.0  0
 426  CONST_31  O33   C25  C24  C22  180.00   0.0  0
 426  CONST_32  O33   C25  C26  C27  180.00   0.0  0
 426  CONST_33  H2    C2   C3   C4   180.00   0.0  0
 426  CONST_34  H3    C3   C4   C5   180.00   0.0  0
 426  CONST_35  H10   C10  C6   C5     0.00   0.0  0
 426  CONST_36  H11   C11  C10  C6   180.00   0.0  0
 426  CONST_37  H13   C13  C1   C6   180.00   0.0  0
 426  CONST_38  H5    C5   C6   C10    0.00   0.0  0
 426  CONST_39  H27   C27  C28  C22  180.00   0.0  0
 426  CONST_40  H24   C24  C22  C28  180.00   0.0  0
 426  CONST_41  H26   C26  C27  C28  180.00   0.0  0
 426  CONST_42  H28   C28  C27  C26  180.00   0.0  0
 426  CONST_43  C22   N21  C20  C12  180.00   0.0  0
 426  CONST_44  C28   C22  N21  C20  180.00   0.0  0
 426  CONST_45  C24   C22  N21  C20    0.00   0.0  0
 426  CONST_46  H21   N21  C22  C28    0.00   0.0  0
 426  CONST_47  C22   N21  C20  O23    0.00   0.0  0
 426  CONST_48  H18   N18  C17  C4     0.00   0.0  0
 426  CONST_49  H191  N19  C17  C4   180.00   0.0  0
 426  Var_01    C36   C37  C38  C34   -5.98  30.0  1
 426  Var_02    C37   C36  C35  C34   38.50  30.0  1
 426  Var_03    C35   C36  C37  C38  -20.20  30.0  1
 426  Var_04    C24   C25  O33  C34   -0.99  30.0  2
 426  Var_05    C5    C4   C17  N18  -37.39  30.0  2
 426  Var_06    O23   C20  C12  C11  149.15  30.0  2

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
 426  chir_01  C34  O33  C38  C35  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
 426  plan-1  N21   0.020
 426  plan-1  C22   0.020
 426  plan-1  C28   0.020
 426  plan-1  C27   0.020
 426  plan-1  C26   0.020
 426  plan-1  C25   0.020
 426  plan-1  O33   0.020
 426  plan-1  C24   0.020
 426  plan-1  H28   0.020
 426  plan-1  H27   0.020
 426  plan-1  H26   0.020
 426  plan-1  H24   0.020
 426  plan-2  C17   0.020
 426  plan-2  C4    0.020
 426  plan-2  C5    0.020
 426  plan-2  C6    0.020
 426  plan-2  C10   0.020
 426  plan-2  C11   0.020
 426  plan-2  C12   0.020
 426  plan-2  C13   0.020
 426  plan-2  C1    0.020
 426  plan-2  C2    0.020
 426  plan-2  C3    0.020
 426  plan-2  C20   0.020
 426  plan-2  H5    0.020
 426  plan-2  H10   0.020
 426  plan-2  H11   0.020
 426  plan-2  H13   0.020
 426  plan-2  H2    0.020
 426  plan-2  H3    0.020
 426  plan-3  C12   0.020
 426  plan-3  C20   0.020
 426  plan-3  O23   0.020
 426  plan-3  N21   0.020
 426  plan-3  C22   0.020
 426  plan-3  H21   0.020
 426  plan-4  N18   0.020
 426  plan-4  C17   0.020
 426  plan-4  N19   0.020
 426  plan-4  C4    0.020
 426  plan-4  H18   0.020
 426  plan-4  H191  0.020
 426  plan-4  H192  0.020

