# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 22:21:46 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: N-[4-(aminomethyl)phenyl]-6-carbamimidoylnaphthalene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(NC(=O)c2ccc3cc(ccc3c2)C(N)=N)cc1
#
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
 239  239  N-[4-(aminomethyl)phenyl]-6-carbamimidoylnaphthalene-2-carboxamide  ligand  42  24  .  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_239
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
 239  N18   N  N     0  -0.650  -1.5782  -0.6195  -7.0897
 239  C17   C  C     0   0.339  -0.3817  -0.2724  -6.8075
 239  N19   N  NH2   0  -0.822   0.6100   0.0067  -7.7021
 239  C12   C  CR6   0   0.050   0.0224  -0.2053  -5.3744
 239  C13   C  CR16  0  -0.345  -0.9259   0.0576  -4.4179
 239  C3    C  CR66  0   0.140  -0.5799   0.1379  -3.0531
 239  C4    C  CR16  0  -0.297  -1.5385   0.4264  -2.0540
 239  C5    C  CR16  0  -0.298  -1.1797   0.4941  -0.7381
 239  C6    C  CR6   0  -0.045   0.1656   0.2838  -0.3456
 239  C1    C  CR16  0  -0.334   1.1154   0.0226  -1.3014
 239  C2    C  CR66  0   0.136   0.7682  -0.0673  -2.6656
 239  C10   C  CR16  0  -0.296   1.7275  -0.3516  -3.6639
 239  C11   C  CR16  0  -0.289   1.3668  -0.4156  -4.9802
 239  C23   C  C     0   0.533   0.6144   0.3712   1.0782
 239  O35   O  O     0  -0.462   1.7599   0.6813   1.3595
 239  N24   N  NH1   0  -0.760  -0.3350   0.0659   1.9956
 239  C25   C  CR6   0   0.364  -0.2521   0.0799   3.3934
 239  C30   C  CR16  0  -0.343  -1.3662  -0.3896   4.0899
 239  C29   C  CR16  0  -0.298  -1.3801  -0.4062   5.4741
 239  C28   C  CR6   0   0.082  -0.2920   0.0468   6.2124
 239  C27   C  CR16  0  -0.275   0.8152   0.5089   5.5084
 239  C26   C  CR16  0  -0.301   0.8495   0.5335   4.1218
 239  C37   C  CH2   0  -0.343  -0.3219   0.0563   7.7187
 239  N38   N  NH2   0  -0.792   0.9401  -0.3929   8.2825
 239  H18   H  H     0   0.325  -1.7414  -0.5935  -8.0928
 239  H191  H  HNH2  0   0.393   0.3461   0.1109  -8.6691
 239  H192  H  HNH2  0   0.397   1.3583   0.6181  -7.4199
 239  H13   H  HCR6  0   0.258  -1.9552   0.2188  -4.7132
 239  H4    H  HCR6  0   0.265  -2.5662   0.6049  -2.3441
 239  H5    H  HCR6  0   0.264  -1.9371   0.7454  -0.0067
 239  H1    H  HCR6  0   0.263   2.1488  -0.1294  -1.0146
 239  H10   H  HCR6  0   0.263   2.7566  -0.5238  -3.3745
 239  H11   H  HCR6  0   0.264   2.1195  -0.6510  -5.7212
 239  H24   H  HNH1  0   0.422  -1.2100  -0.2874   1.6401
 239  H30   H  HCR6  0   0.268  -2.2298  -0.7523   3.5443
 239  H29   H  HCR6  0   0.252  -2.2577  -0.7854   5.9842
 239  H27   H  HCR6  0   0.248   1.6822   0.8580   6.0545
 239  H26   H  HCR6  0   0.277   1.7302   0.9047   3.6255
 239  H371  H  HCH2  0   0.238  -0.4936   1.0811   8.0616
 239  H372  H  HCH2  0   0.213  -1.1932  -0.5212   8.0564
 239  H381  H  HNH2  0   0.352   0.9174  -0.2808   9.2877
 239  H382  H  HNH2  0   0.343   1.0504  -1.3849   8.1133

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
 239  N18  C17   double    1.277  0.020  1.277
 239  N18  H18   single    0.890  0.020  1.040
 239  C17  N19   single    1.364  0.020  1.364
 239  C17  C12   single    1.490  0.020  1.490
 239  N19  H191  single    0.890  0.020  1.040
 239  N19  H192  single    0.890  0.020  1.040
 239  C12  C13   aromatic  1.372  0.020  1.372
 239  C12  C11   aromatic  1.417  0.020  1.417
 239  C13  C3    aromatic  1.410  0.020  1.410
 239  C13  H13   single    0.930  0.020  1.080
 239  C3   C4    aromatic  1.414  0.020  1.414
 239  C3   C2    aromatic  1.418  0.020  1.418
 239  C4   C5    aromatic  1.366  0.020  1.366
 239  C4   H4    single    0.930  0.020  1.080
 239  C5   C6    aromatic  1.417  0.020  1.417
 239  C5   H5    single    0.930  0.020  1.080
 239  C6   C1    aromatic  1.373  0.020  1.373
 239  C6   C23   single    1.495  0.020  1.495
 239  C1   C2    aromatic  1.411  0.020  1.411
 239  C1   H1    single    0.930  0.020  1.080
 239  C2   C10   aromatic  1.413  0.020  1.413
 239  C10  C11   aromatic  1.366  0.020  1.366
 239  C10  H10   single    0.930  0.020  1.080
 239  C11  H11   single    0.930  0.020  1.080
 239  C23  O35   double    1.220  0.020  1.220
 239  C23  N24   single    1.355  0.020  1.355
 239  N24  C25   single    1.400  0.020  1.400
 239  N24  H24   single    0.860  0.020  1.020
 239  C25  C30   aromatic  1.395  0.020  1.395
 239  C25  C26   aromatic  1.396  0.020  1.396
 239  C30  C29   aromatic  1.384  0.020  1.384
 239  C30  H30   single    0.930  0.020  1.080
 239  C29  C28   aromatic  1.391  0.020  1.391
 239  C29  H29   single    0.930  0.020  1.080
 239  C28  C27   aromatic  1.391  0.020  1.391
 239  C28  C37   single    1.507  0.020  1.507
 239  C27  C26   aromatic  1.387  0.020  1.387
 239  C27  H27   single    0.930  0.020  1.080
 239  C26  H26   single    0.930  0.020  1.080
 239  C37  N38   single    1.453  0.020  1.453
 239  C37  H371  single    0.970  0.020  1.090
 239  C37  H372  single    0.970  0.020  1.090
 239  N38  H381  single    0.890  0.020  1.040
 239  N38  H382  single    0.890  0.020  1.040

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
 239  H18   N18  C17   111.18  3.000
 239  C12   C17  N19   115.09  3.000
 239  C12   C17  N18   118.59  3.000
 239  N19   C17  N18   126.27  3.000
 239  H192  N19  H191  113.63  3.000
 239  H192  N19  C17   118.73  3.000
 239  H191  N19  C17   117.39  3.000
 239  C11   C12  C13   119.36  3.000
 239  C11   C12  C17   121.21  3.000
 239  C13   C12  C17   119.43  3.000
 239  H13   C13  C3    119.25  3.000
 239  H13   C13  C12   119.69  3.000
 239  C3    C13  C12   121.06  3.000
 239  C2    C3   C4    118.75  3.000
 239  C2    C3   C13   119.31  3.000
 239  C4    C3   C13   121.94  3.000
 239  H4    C4   C5    119.96  3.000
 239  H4    C4   C3    119.19  3.000
 239  C5    C4   C3    120.85  3.000
 239  H5    C5   C6    120.77  3.000
 239  H5    C5   C4    118.60  3.000
 239  C6    C5   C4    120.60  3.000
 239  C23   C6   C1    117.80  3.000
 239  C23   C6   C5    122.68  3.000
 239  C1    C6   C5    119.49  3.000
 239  H1    C1   C2    118.81  3.000
 239  H1    C1   C6    120.17  3.000
 239  C2    C1   C6    121.02  3.000
 239  C10   C2   C1    121.93  3.000
 239  C10   C2   C3    118.78  3.000
 239  C1    C2   C3    119.29  3.000
 239  H10   C10  C11   120.06  3.000
 239  H10   C10  C2    119.22  3.000
 239  C11   C10  C2    120.71  3.000
 239  H11   C11  C10   119.09  3.000
 239  H11   C11  C12   120.12  3.000
 239  C10   C11  C12   120.77  3.000
 239  N24   C23  O35   124.00  3.000
 239  N24   C23  C6    114.91  3.000
 239  O35   C23  C6    121.09  3.000
 239  H24   N24  C25   114.00  3.000
 239  H24   N24  C23   116.63  3.000
 239  C25   N24  C23   129.20  3.000
 239  C26   C25  C30   118.61  3.000
 239  C26   C25  N24   124.79  3.000
 239  C30   C25  N24   116.59  3.000
 239  H30   C30  C29   119.42  3.000
 239  H30   C30  C25   119.84  3.000
 239  C29   C30  C25   120.74  3.000
 239  H29   C29  C28   119.85  3.000
 239  H29   C29  C30   118.88  3.000
 239  C28   C29  C30   121.27  3.000
 239  C37   C28  C27   121.31  3.000
 239  C37   C28  C29   121.15  3.000
 239  C27   C28  C29   117.53  3.000
 239  H27   C27  C26   118.60  3.000
 239  H27   C27  C28   119.29  3.000
 239  C26   C27  C28   122.10  3.000
 239  H26   C26  C27   119.14  3.000
 239  H26   C26  C25   121.12  3.000
 239  C27   C26  C25   119.74  3.000
 239  H372  C37  H371  105.76  3.000
 239  H372  C37  N38   114.01  3.000
 239  H371  C37  N38   107.71  3.000
 239  H372  C37  C28   108.64  3.000
 239  H371  C37  C28   108.80  3.000
 239  N38   C37  C28   111.63  3.000
 239  H382  N38  H381  106.09  3.000
 239  H382  N38  C37   109.43  3.000
 239  H381  N38  C37   109.37  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
 239  CONST_01  C4    C3   C13  C12   180.00   0.0  0
 239  CONST_02  C2    C3   C13  C12     0.00   0.0  0
 239  CONST_03  C2    C10  C11  C12     0.00   0.0  0
 239  CONST_04  C10   C11  C12  C13     0.00   0.0  0
 239  CONST_05  C5    C4   C3   C13   180.00   0.0  0
 239  CONST_06  C1    C2   C3   C13   180.00   0.0  0
 239  CONST_07  C10   C2   C3   C13     0.00   0.0  0
 239  CONST_08  C11   C12  C13  C3      0.00   0.0  0
 239  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 239  CONST_10  C6    C1   C2   C3      0.00   0.0  0
 239  CONST_11  C11   C10  C2   C3      0.00   0.0  0
 239  CONST_12  C1    C2   C3   C4      0.00   0.0  0
 239  CONST_13  C10   C2   C3   C4    180.00   0.0  0
 239  CONST_14  C1    C6   C5   C4      0.00   0.0  0
 239  CONST_15  C2    C3   C4   C5      0.00   0.0  0
 239  CONST_16  C2    C1   C6   C5      0.00   0.0  0
 239  CONST_17  C10   C2   C1   C6    180.00   0.0  0
 239  CONST_18  C11   C10  C2   C1    180.00   0.0  0
 239  CONST_19  C28   C29  C30  C25     0.00   0.0  0
 239  CONST_20  C28   C27  C26  C25     0.00   0.0  0
 239  CONST_21  C27   C26  C25  C30     0.00   0.0  0
 239  CONST_22  C27   C28  C29  C30     0.00   0.0  0
 239  CONST_23  C26   C25  C30  C29     0.00   0.0  0
 239  CONST_24  C26   C27  C28  C29     0.00   0.0  0
 239  CONST_25  C3    C13  C12  C17   180.00   0.0  0
 239  CONST_26  C10   C11  C12  C17   180.00   0.0  0
 239  CONST_27  C23   C6   C5   C4    180.00   0.0  0
 239  CONST_28  C23   C6   C1   C2    180.00   0.0  0
 239  CONST_29  C29   C30  C25  N24   180.00   0.0  0
 239  CONST_30  C27   C26  C25  N24   180.00   0.0  0
 239  CONST_31  C37   C28  C29  C30   180.00   0.0  0
 239  CONST_32  C37   C28  C27  C26   180.00   0.0  0
 239  CONST_33  H10   C10  C11  C12   180.00   0.0  0
 239  CONST_34  H11   C11  C12  C13   180.00   0.0  0
 239  CONST_35  H4    C4   C3   C13     0.00   0.0  0
 239  CONST_36  H5    C5   C4   C3    180.00   0.0  0
 239  CONST_37  H1    C1   C2   C3    180.00   0.0  0
 239  CONST_38  H13   C13  C3   C4      0.00   0.0  0
 239  CONST_39  H29   C29  C30  C25   180.00   0.0  0
 239  CONST_40  H27   C27  C26  C25   180.00   0.0  0
 239  CONST_41  H26   C26  C25  C30   180.00   0.0  0
 239  CONST_42  H30   C30  C29  C28   180.00   0.0  0
 239  CONST_43  C25   N24  C23  C6    180.00   0.0  0
 239  CONST_44  C30   C25  N24  C23   180.00   0.0  0
 239  CONST_45  C26   C25  N24  C23     0.00   0.0  0
 239  CONST_46  H24   N24  C25  C30     0.00   0.0  0
 239  CONST_47  C25   N24  C23  O35     0.00   0.0  0
 239  CONST_48  H18   N18  C17  C12   180.00   0.0  0
 239  CONST_49  H191  N19  C17  C12   180.00   0.0  0
 239  Var_01    C13   C12  C17  N18   -27.81  30.0  2
 239  Var_02    O35   C23  C6   C5   -152.44  30.0  2
 239  Var_03    N38   C37  C28  C29   138.29  30.0  2
 239  Var_04    H381  N38  C37  C28   174.06  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
 239  plan-1  N24   0.020
 239  plan-1  C25   0.020
 239  plan-1  C30   0.020
 239  plan-1  C29   0.020
 239  plan-1  C28   0.020
 239  plan-1  C27   0.020
 239  plan-1  C26   0.020
 239  plan-1  C37   0.020
 239  plan-1  H30   0.020
 239  plan-1  H29   0.020
 239  plan-1  H27   0.020
 239  plan-1  H26   0.020
 239  plan-2  C17   0.020
 239  plan-2  C12   0.020
 239  plan-2  C13   0.020
 239  plan-2  C3    0.020
 239  plan-2  C4    0.020
 239  plan-2  C5    0.020
 239  plan-2  C6    0.020
 239  plan-2  C1    0.020
 239  plan-2  C2    0.020
 239  plan-2  C10   0.020
 239  plan-2  C11   0.020
 239  plan-2  C23   0.020
 239  plan-2  H13   0.020
 239  plan-2  H4    0.020
 239  plan-2  H5    0.020
 239  plan-2  H1    0.020
 239  plan-2  H10   0.020
 239  plan-2  H11   0.020
 239  plan-3  C6    0.020
 239  plan-3  C23   0.020
 239  plan-3  O35   0.020
 239  plan-3  N24   0.020
 239  plan-3  C25   0.020
 239  plan-3  H24   0.020
 239  plan-4  N18   0.020
 239  plan-4  C17   0.020
 239  plan-4  N19   0.020
 239  plan-4  C12   0.020
 239  plan-4  H18   0.020
 239  plan-4  H191  0.020
 239  plan-4  H192  0.020

