# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 04:04:21 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 2-[(7-carbamimidoyl-2-methoxynaphthalen-1-yl)oxy]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2ccc(cc2c1OCC(N)=O)C(N)=N
#
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
 1UP  1UP  2-[(7-carbamimidoyl-2-methoxynaphthalen-1-yl)oxy]acetamide  ligand  35  20  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1UP
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
 1UP  O3   O  O     0  -0.475   0.6334  -3.1944  -0.3655
 1UP  C13  C  C     0   0.491   1.5678  -2.8490   0.3379
 1UP  N1   N  NH2   0  -0.798   2.2623  -3.6857   1.1184
 1UP  C12  C  CH2   0  -0.283   2.0401  -1.4031   0.4299
 1UP  O2   O  O2    0  -0.476   1.4229  -0.6436  -0.5842
 1UP  C11  C  CR6   0   0.211   0.9612   0.5857  -0.2339
 1UP  C2   C  CR6   0   0.326   1.8372   1.6385  -0.0500
 1UP  O1   O  O2    0  -0.463   3.1439   1.3633  -0.1924
 1UP  C1   C  CH3   0  -0.440   4.0829   2.4153  -0.0655
 1UP  C10  C  CR66  0   0.074  -0.4322   0.7739  -0.0913
 1UP  C5   C  CR66  0   0.078  -0.9302   2.0634   0.2239
 1UP  C4   C  CR16  0  -0.316  -0.0175   3.1214   0.4011
 1UP  C3   C  CR16  0  -0.382   1.3296   2.9176   0.2701
 1UP  C9   C  CR16  0  -0.386  -1.3430  -0.2923  -0.2603
 1UP  C8   C  CR6   0   0.058  -2.6965  -0.1155  -0.1178
 1UP  C14  C  C     0   0.333  -3.6163  -1.2889  -0.2872
 1UP  N3   N  NH2   0  -0.822  -4.9519  -1.0043  -0.2958
 1UP  N2   N  N     0  -0.648  -3.2462  -2.4988  -0.4681
 1UP  C7   C  CR16  0  -0.309  -3.1843   1.1829   0.1834
 1UP  C6   C  CR16  0  -0.292  -2.3267   2.2320   0.3524
 1UP  H1   H  HNH2  0   0.407   2.0124  -4.6596   1.1725
 1UP  H2   H  HNH2  0   0.411   3.0448  -3.3783   1.6709
 1UP  H3   H  HCH2  0   0.264   1.7903  -1.0274   1.4285
 1UP  H4   H  HCH2  0   0.266   3.1292  -1.3620   0.3327
 1UP  H5   H  HCH3  0   0.264   5.0601   1.9751  -0.2460
 1UP  H6   H  HCH3  0   0.233   3.9103   3.2053  -0.8001
 1UP  H7   H  HCH3  0   0.232   4.0749   2.8527   0.9357
 1UP  H8   H  HCR6  0   0.265  -0.3879   4.1090   0.6445
 1UP  H9   H  HCR6  0   0.291   2.0028   3.7522   0.4105
 1UP  H10  H  HCR6  0   0.265  -0.9341  -1.2594  -0.5172
 1UP  H11  H  HNH2  0   0.395  -5.2961  -0.2198   0.2286
 1UP  H12  H  HNH2  0   0.383  -5.5575  -1.8078  -0.2447
 1UP  H13  H  H     0   0.333  -2.2393  -2.5933  -0.4978
 1UP  H14  H  HCR6  0   0.246  -4.2421   1.3787   0.2877
 1UP  H15  H  HCR6  0   0.262  -2.7169   3.2143   0.5882

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
 1UP  O2   C12  single    1.409  0.020  1.409
 1UP  O2   C11  single    1.359  0.020  1.359
 1UP  N1   C13  single    1.339  0.020  1.339
 1UP  O3   C13  double    1.220  0.020  1.220
 1UP  C13  C12  single    1.524  0.020  1.524
 1UP  O1   C2   single    1.343  0.020  1.343
 1UP  O1   C1   single    1.416  0.020  1.416
 1UP  N2   C14  double    1.278  0.020  1.278
 1UP  C11  C2   aromatic  1.382  0.020  1.382
 1UP  C11  C10  aromatic  1.413  0.020  1.413
 1UP  C9   C10  aromatic  1.412  0.020  1.412
 1UP  C9   C8   aromatic  1.372  0.020  1.372
 1UP  C14  N3   single    1.366  0.020  1.366
 1UP  C14  C8   single    1.501  0.020  1.501
 1UP  C2   C3   aromatic  1.413  0.020  1.413
 1UP  C10  C5   aromatic  1.418  0.020  1.418
 1UP  C8   C7   aromatic  1.419  0.020  1.419
 1UP  C3   C4   aromatic  1.369  0.020  1.369
 1UP  C5   C4   aromatic  1.409  0.020  1.409
 1UP  C5   C6   aromatic  1.412  0.020  1.412
 1UP  C7   C6   aromatic  1.366  0.020  1.366
 1UP  N1   H1   single    0.860  0.020  1.020
 1UP  N1   H2   single    0.860  0.020  1.020
 1UP  C12  H3   single    0.970  0.020  1.090
 1UP  C12  H4   single    0.970  0.020  1.090
 1UP  C1   H5   single    0.970  0.020  1.090
 1UP  C1   H6   single    0.970  0.020  1.090
 1UP  C1   H7   single    0.970  0.020  1.090
 1UP  C4   H8   single    0.930  0.020  1.080
 1UP  C3   H9   single    0.930  0.020  1.080
 1UP  C9   H10  single    0.930  0.020  1.080
 1UP  N3   H11  single    0.890  0.020  1.040
 1UP  N3   H12  single    0.890  0.020  1.040
 1UP  N2   H13  single    0.890  0.020  1.040
 1UP  C7   H14  single    0.930  0.020  1.080
 1UP  C6   H15  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
 1UP  C12  C13  N1   113.40  3.000
 1UP  C12  C13  O3   122.75  3.000
 1UP  N1   C13  O3   123.84  3.000
 1UP  H2   N1   H1   117.33  3.000
 1UP  H2   N1   C13  122.19  3.000
 1UP  H1   N1   C13  120.48  3.000
 1UP  H4   C12  H3   107.15  3.000
 1UP  H4   C12  O2   110.60  3.000
 1UP  H3   C12  O2   111.78  3.000
 1UP  H4   C12  C13  109.80  3.000
 1UP  H3   C12  C13  108.04  3.000
 1UP  O2   C12  C13  109.40  3.000
 1UP  C11  O2   C12  116.80  3.000
 1UP  C10  C11  C2   120.67  3.000
 1UP  C10  C11  O2   118.78  3.000
 1UP  C2   C11  O2   120.54  3.000
 1UP  C3   C2   O1   123.99  3.000
 1UP  C3   C2   C11  119.48  3.000
 1UP  O1   C2   C11  116.53  3.000
 1UP  C1   O1   C2   118.92  3.000
 1UP  H7   C1   H6   109.00  3.000
 1UP  H7   C1   H5   108.72  3.000
 1UP  H6   C1   H5   108.86  3.000
 1UP  H7   C1   O1   112.00  3.000
 1UP  H6   C1   O1   111.85  3.000
 1UP  H5   C1   O1   106.29  3.000
 1UP  C9   C10  C5   119.12  3.000
 1UP  C5   C10  C11  119.34  3.000
 1UP  C9   C10  C11  121.54  3.000
 1UP  C6   C5   C4   122.65  3.000
 1UP  C6   C5   C10  118.43  3.000
 1UP  C4   C5   C10  118.91  3.000
 1UP  H8   C4   C3   119.61  3.000
 1UP  H8   C4   C5   119.46  3.000
 1UP  C3   C4   C5   120.93  3.000
 1UP  H9   C3   C4   119.04  3.000
 1UP  H9   C3   C2   120.30  3.000
 1UP  C4   C3   C2   120.67  3.000
 1UP  H10  C9   C8   120.86  3.000
 1UP  H10  C9   C10  117.38  3.000
 1UP  C8   C9   C10  121.76  3.000
 1UP  C7   C8   C14  121.91  3.000
 1UP  C7   C8   C9   118.61  3.000
 1UP  C14  C8   C9   119.48  3.000
 1UP  N2   C14  N3   118.66  3.000
 1UP  N3   C14  C8   115.93  3.000
 1UP  N2   C14  C8   125.36  3.000
 1UP  H12  N3   H11  112.98  3.000
 1UP  H12  N3   C14  114.92  3.000
 1UP  H11  N3   C14  119.64  3.000
 1UP  H13  N2   C14  112.39  3.000
 1UP  H14  C7   C6   117.61  3.000
 1UP  H14  C7   C8   121.51  3.000
 1UP  C6   C7   C8   120.88  3.000
 1UP  H15  C6   C7   119.84  3.000
 1UP  H15  C6   C5   118.97  3.000
 1UP  C7   C6   C5   121.19  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
 1UP  CONST_01  C4   C3   C2   C11     0.00   0.0  0
 1UP  CONST_02  C8   C9   C10  C11   180.00   0.0  0
 1UP  CONST_03  C4   C5   C10  C11     0.00   0.0  0
 1UP  CONST_04  C6   C5   C10  C11   180.00   0.0  0
 1UP  CONST_05  C9   C10  C11  C2    180.00   0.0  0
 1UP  CONST_06  C5   C10  C11  C2      0.00   0.0  0
 1UP  CONST_07  C5   C4   C3   C2      0.00   0.0  0
 1UP  CONST_08  C3   C2   C11  C10     0.00   0.0  0
 1UP  CONST_09  C7   C8   C9   C10     0.00   0.0  0
 1UP  CONST_10  C3   C4   C5   C10     0.00   0.0  0
 1UP  CONST_11  C7   C6   C5   C10     0.00   0.0  0
 1UP  CONST_12  C8   C9   C10  C5      0.00   0.0  0
 1UP  CONST_13  C8   C7   C6   C5      0.00   0.0  0
 1UP  CONST_14  C9   C10  C5   C4    180.00   0.0  0
 1UP  CONST_15  C7   C6   C5   C4    180.00   0.0  0
 1UP  CONST_16  C6   C5   C4   C3    180.00   0.0  0
 1UP  CONST_17  C6   C5   C10  C9      0.00   0.0  0
 1UP  CONST_18  C6   C7   C8   C9      0.00   0.0  0
 1UP  CONST_19  C3   C2   C11  O2    180.00   0.0  0
 1UP  CONST_20  C9   C10  C11  O2      0.00   0.0  0
 1UP  CONST_21  C5   C10  C11  O2    180.00   0.0  0
 1UP  CONST_22  C10  C11  C2   O1    180.00   0.0  0
 1UP  CONST_23  C4   C3   C2   O1    180.00   0.0  0
 1UP  CONST_24  C14  C8   C9   C10   180.00   0.0  0
 1UP  CONST_25  C6   C7   C8   C14   180.00   0.0  0
 1UP  CONST_26  H9   C3   C2   C11   180.00   0.0  0
 1UP  CONST_27  H10  C9   C10  C11     0.00   0.0  0
 1UP  CONST_28  H8   C4   C3   C2    180.00   0.0  0
 1UP  CONST_29  H15  C6   C5   C10   180.00   0.0  0
 1UP  CONST_30  H14  C7   C6   C5    180.00   0.0  0
 1UP  CONST_31  H13  N2   C14  C8      0.00   0.0  0
 1UP  CONST_33  H12  N3   C14  C8    180.00   0.0  0
 1UP  CONST_34  H1   N1   C13  O3      0.00   0.0  0
 1UP  CONST_35  H2   N1   C13  O3    180.00   0.0  0
 1UP  Var_01    C2   C11  O2   C12    75.55  30.0  2
 1UP  Var_02    C3   C2   O1   C1     -2.39  30.0  2
 1UP  Var_03    N2   C14  C8   C9      5.23  30.0  3
 1UP  Var_04    H3   C12  O2   C11    17.68  30.0  3
 1UP  Var_05    H5   C1   O1   C2   -178.33  30.0  3
 1UP  Var_06    O2   C12  C13  O3    -11.36  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
 1UP  plan-1  O2   0.020
 1UP  plan-1  C11  0.020
 1UP  plan-1  C2   0.020
 1UP  plan-1  O1   0.020
 1UP  plan-1  C10  0.020
 1UP  plan-1  C5   0.020
 1UP  plan-1  C4   0.020
 1UP  plan-1  C3   0.020
 1UP  plan-1  C9   0.020
 1UP  plan-1  C8   0.020
 1UP  plan-1  C14  0.020
 1UP  plan-1  C7   0.020
 1UP  plan-1  C6   0.020
 1UP  plan-1  H8   0.020
 1UP  plan-1  H9   0.020
 1UP  plan-1  H10  0.020
 1UP  plan-1  H14  0.020
 1UP  plan-1  H15  0.020
 1UP  plan-2  O3   0.020
 1UP  plan-2  C13  0.020
 1UP  plan-2  N1   0.020
 1UP  plan-2  C12  0.020
 1UP  plan-2  H1   0.020
 1UP  plan-2  H2   0.020
 1UP  plan-3  C8   0.020
 1UP  plan-3  C14  0.020
 1UP  plan-3  N3   0.020
 1UP  plan-3  N2   0.020
 1UP  plan-3  H11  0.020
 1UP  plan-3  H12  0.020
 1UP  plan-3  H13  0.020

