# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:41:05 2022
#   Inital geometry file: a 97 line input string
#   Ligand name: 4-(4-methyl-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc2C(=O)N(C(=O)c12)c3ccc(cc3)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
 7C1  7C1  4-(4-methyl-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzenecarboximidamide  ligand  34  21  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7C1
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
 7C1  C1    C  CR6   0   0.087  -3.9517  -0.9591  -0.3531
 7C1  C2    C  CR16  0  -0.301  -5.0683  -0.2337   0.0777
 7C1  C3    C  CR16  0  -0.226  -4.9568   0.9883   0.7303
 7C1  C4    C  CR16  0  -0.323  -3.7113   1.5538   0.9916
 7C1  C5    C  CR56  0  -0.018  -2.6102   0.8428   0.5701
 7C1  C6    C  CR56  0  -0.058  -2.7222  -0.3769  -0.0819
 7C1  C7    C  CR5   0   0.559  -1.3554  -0.8561  -0.3856
 7C1  C8    C  CR5   0   0.570  -1.1751   1.1756   0.7018
 7C1  N9    N  NR5   0  -0.726  -0.4888   0.1197   0.1112
 7C1  N20   N  NH2   0  -0.802   5.8103  -0.6033   0.9059
 7C1  O10   O  O     0  -0.389  -1.0021  -1.8617  -0.9429
 7C1  C21   C  CH3   0  -0.730  -4.1023  -2.2682  -1.0626
 7C1  O11   O  O     0  -0.390  -0.6658   2.1408   1.2083
 7C1  C12   C  CR6   0   0.332   0.9199   0.0391   0.0302
 7C1  C13   C  CR16  0  -0.259   1.6209   0.9598  -0.7367
 7C1  C14   C  CR16  0  -0.293   3.0015   0.8821  -0.8083
 7C1  C15   C  CR6   0   0.008   3.6929  -0.1126  -0.1210
 7C1  C16   C  CR16  0  -0.283   2.9764  -1.0301   0.6442
 7C1  C17   C  CR16  0  -0.256   1.5950  -0.9567   0.7214
 7C1  C18   C  C     0   0.333   5.1779  -0.1925  -0.2279
 7C1  N19   N  N     0  -0.638   5.8397   0.0537  -1.2925
 7C1  H2    H  HCR6  0   0.272  -6.0551  -0.6404  -0.1051
 7C1  H3    H  HCR6  0   0.278  -5.8559   1.5052   1.0378
 7C1  H4    H  HCR6  0   0.275  -3.6183   2.5036   1.5006
 7C1  HN20  H  HNH2  0   0.395   5.3844  -0.4009   1.7949
 7C1  HN2A  H  HNH2  0   0.386   6.8163  -0.5446   0.9031
 7C1  H21   H  HCH3  0   0.258  -3.7229  -2.2074  -2.0830
 7C1  H21A  H  HCH3  0   0.257  -3.5492  -3.0619  -0.5617
 7C1  H21B  H  HCH3  0   0.252  -5.1494  -2.5604  -1.1106
 7C1  H13   H  HCR6  0   0.277   1.0930   1.7344  -1.2768
 7C1  H14   H  HCR6  0   0.272   3.5411   1.6155  -1.3939
 7C1  H16   H  HCR6  0   0.273   3.4933  -1.8171   1.1774
 7C1  H17   H  HCR6  0   0.277   1.0477  -1.6703   1.3230
 7C1  HN19  H  H     0   0.334   5.2167   0.2406  -2.0692

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
 7C1  C6   C1    aromatic  1.387  0.020  1.387
 7C1  C21  C1    single    1.497  0.020  1.497
 7C1  C1   C2    aromatic  1.400  0.020  1.400
 7C1  C2   C3    aromatic  1.390  0.020  1.390
 7C1  C2   H2    single    0.930  0.020  1.080
 7C1  C4   C3    aromatic  1.393  0.020  1.393
 7C1  C3   H3    single    0.930  0.020  1.080
 7C1  C5   C4    aromatic  1.377  0.020  1.377
 7C1  C4   H4    single    0.930  0.020  1.080
 7C1  C8   C5    single    1.479  0.020  1.479
 7C1  C6   C5    aromatic  1.388  0.020  1.388
 7C1  C7   C6    single    1.480  0.020  1.480
 7C1  O10  C7    double    1.203  0.020  1.203
 7C1  N9   C7    single    1.397  0.020  1.397
 7C1  N9   C8    single    1.391  0.020  1.391
 7C1  O11  C8    double    1.203  0.020  1.203
 7C1  C12  N9    single    1.413  0.020  1.413
 7C1  N20  C18   single    1.362  0.020  1.362
 7C1  N20  HN20  single    0.890  0.020  1.040
 7C1  N20  HN2A  single    0.890  0.020  1.040
 7C1  C21  H21   single    0.970  0.020  1.090
 7C1  C21  H21A  single    0.970  0.020  1.090
 7C1  C21  H21B  single    0.970  0.020  1.090
 7C1  C17  C12   aromatic  1.388  0.020  1.388
 7C1  C13  C12   aromatic  1.388  0.020  1.388
 7C1  C14  C13   aromatic  1.385  0.020  1.385
 7C1  C13  H13   single    0.930  0.020  1.080
 7C1  C15  C14   aromatic  1.393  0.020  1.393
 7C1  C14  H14   single    0.930  0.020  1.080
 7C1  C18  C15   single    1.491  0.020  1.491
 7C1  C15  C16   aromatic  1.393  0.020  1.393
 7C1  C16  C17   aromatic  1.385  0.020  1.385
 7C1  C16  H16   single    0.930  0.020  1.080
 7C1  C17  H17   single    0.930  0.020  1.080
 7C1  N19  C18   double    1.278  0.020  1.278
 7C1  N19  HN19  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
 7C1  C21   C1   C6    123.30  3.000
 7C1  C21   C1   C2    121.26  3.000
 7C1  C6    C1   C2    115.43  3.000
 7C1  H2    C2   C3    118.86  3.000
 7C1  H2    C2   C1    118.72  3.000
 7C1  C3    C2   C1    122.43  3.000
 7C1  H3    C3   C4    119.73  3.000
 7C1  H3    C3   C2    119.15  3.000
 7C1  C4    C3   C2    121.12  3.000
 7C1  H4    C4   C5    121.93  3.000
 7C1  H4    C4   C3    121.45  3.000
 7C1  C5    C4   C3    116.62  3.000
 7C1  C8    C5   C6    108.54  3.000
 7C1  C6    C5   C4    122.22  3.000
 7C1  C8    C5   C4    129.24  3.000
 7C1  C7    C6   C5    107.85  3.000
 7C1  C7    C6   C1    129.98  3.000
 7C1  C5    C6   C1    122.17  3.000
 7C1  O10   C7   N9    124.53  3.000
 7C1  N9    C7   C6    105.90  3.000
 7C1  O10   C7   C6    129.58  3.000
 7C1  O11   C8   N9    125.37  3.000
 7C1  O11   C8   C5    128.95  3.000
 7C1  N9    C8   C5    105.67  3.000
 7C1  C12   N9   C8    124.02  3.000
 7C1  C12   N9   C7    123.94  3.000
 7C1  C8    N9   C7    112.04  3.000
 7C1  HN2A  N20  HN20  114.41  3.000
 7C1  HN2A  N20  C18   116.35  3.000
 7C1  HN20  N20  C18   118.57  3.000
 7C1  H21B  C21  H21A  108.25  3.000
 7C1  H21B  C21  H21   107.97  3.000
 7C1  H21A  C21  H21   107.11  3.000
 7C1  H21B  C21  C1    110.65  3.000
 7C1  H21A  C21  C1    111.60  3.000
 7C1  H21   C21  C1    111.10  3.000
 7C1  C17   C12  C13   120.36  3.000
 7C1  C13   C12  N9    119.82  3.000
 7C1  C17   C12  N9    119.83  3.000
 7C1  H13   C13  C14   120.06  3.000
 7C1  H13   C13  C12   120.28  3.000
 7C1  C14   C13  C12   119.66  3.000
 7C1  H14   C14  C15   120.22  3.000
 7C1  H14   C14  C13   119.14  3.000
 7C1  C15   C14  C13   120.63  3.000
 7C1  C18   C15  C16   121.08  3.000
 7C1  C16   C15  C14   119.09  3.000
 7C1  C18   C15  C14   119.82  3.000
 7C1  H16   C16  C17   119.17  3.000
 7C1  H16   C16  C15   120.27  3.000
 7C1  C17   C16  C15   120.56  3.000
 7C1  H17   C17  C16   120.02  3.000
 7C1  H17   C17  C12   120.28  3.000
 7C1  C16   C17  C12   119.70  3.000
 7C1  N19   C18  C15   124.43  3.000
 7C1  N19   C18  N20   120.76  3.000
 7C1  C15   C18  N20   114.77  3.000
 7C1  HN19  N19  C18   110.85  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
 7C1  CONST_01  C4    C5   C6   C1     0.00   0.0  0
 7C1  CONST_02  C4    C3   C2   C1     0.00   0.0  0
 7C1  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 7C1  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 7C1  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 7C1  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 7C1  CONST_07  C15   C16  C17  C12    0.00   0.0  0
 7C1  CONST_08  C15   C14  C13  C12    0.00   0.0  0
 7C1  CONST_09  C16   C17  C12  C13    0.00   0.0  0
 7C1  CONST_10  C16   C15  C14  C13    0.00   0.0  0
 7C1  CONST_11  C17   C12  C13  C14    0.00   0.0  0
 7C1  CONST_12  C17   C16  C15  C14    0.00   0.0  0
 7C1  CONST_13  C16   C17  C12  N9   180.00   0.0  0
 7C1  CONST_14  C14   C13  C12  N9   180.00   0.0  0
 7C1  CONST_15  C8    N9   C7   C6     0.00   0.0  0
 7C1  CONST_16  C12   N9   C7   C6   180.00   0.0  0
 7C1  CONST_17  C21   C1   C2   C3   180.00   0.0  0
 7C1  CONST_18  C21   C1   C6   C5   180.00   0.0  0
 7C1  CONST_19  C21   C1   C6   C7     0.00   0.0  0
 7C1  CONST_20  C18   C15  C14  C13  180.00   0.0  0
 7C1  CONST_21  C18   C15  C16  C17  180.00   0.0  0
 7C1  CONST_22  O10   C7   N9   C8   180.00   0.0  0
 7C1  CONST_23  C12   N9   C7   O10    0.00   0.0  0
 7C1  CONST_24  H3    C3   C2   C1   180.00   0.0  0
 7C1  CONST_25  H4    C4   C3   C2   180.00   0.0  0
 7C1  CONST_26  H2    C2   C3   C4   180.00   0.0  0
 7C1  CONST_27  H17   C17  C12  N9     0.00   0.0  0
 7C1  CONST_28  H13   C13  C12  N9     0.00   0.0  0
 7C1  CONST_29  H16   C16  C17  C12  180.00   0.0  0
 7C1  CONST_30  H14   C14  C13  C12  180.00   0.0  0
 7C1  CONST_32  HN2A  N20  C18  C15  180.00   0.0  0
 7C1  CONST_33  HN19  N19  C18  C15    0.00   0.0  0
 7C1  Var_01    C17   C12  N9   C7   -65.37  30.0  2
 7C1  Var_02    C14   C15  C18  N20  145.41  30.0  2
 7C1  Var_03    H21   C21  C1   C2   116.04  30.0  2

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
 7C1  plan-1  N9    0.020
 7C1  plan-1  C12   0.020
 7C1  plan-1  C13   0.020
 7C1  plan-1  C14   0.020
 7C1  plan-1  C15   0.020
 7C1  plan-1  C16   0.020
 7C1  plan-1  C17   0.020
 7C1  plan-1  C18   0.020
 7C1  plan-1  H13   0.020
 7C1  plan-1  H14   0.020
 7C1  plan-1  H16   0.020
 7C1  plan-1  H17   0.020
 7C1  plan-2  C1    0.020
 7C1  plan-2  C2    0.020
 7C1  plan-2  C3    0.020
 7C1  plan-2  C4    0.020
 7C1  plan-2  C5    0.020
 7C1  plan-2  C6    0.020
 7C1  plan-2  C7    0.020
 7C1  plan-2  C8    0.020
 7C1  plan-2  N9    0.020
 7C1  plan-2  O10   0.020
 7C1  plan-2  C21   0.020
 7C1  plan-2  O11   0.020
 7C1  plan-2  C12   0.020
 7C1  plan-2  H2    0.020
 7C1  plan-2  H3    0.020
 7C1  plan-2  H4    0.020
 7C1  plan-3  N20   0.020
 7C1  plan-3  C15   0.020
 7C1  plan-3  C18   0.020
 7C1  plan-3  N19   0.020
 7C1  plan-3  HN20  0.020
 7C1  plan-3  HN2A  0.020
 7C1  plan-3  HN19  0.020

