# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:26:52 2022
#   Inital geometry file: a 143 line input string
#   Ligand name: 2-[6-(dimethylamino)-3-(dimethyliminio)-3H-xanthen-9-yl]-5-formylbenzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1ccc2c(OC3=CC(C=CC3=C2c4ccc(C=O)cc4C([O-])=O)=[N+](C)C)c1
#
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
 323  323  2-[6-(dimethylamino)-3-(dimethyliminio)-3H-xanthen-9-yl]-5-formylbenzoate  ligand  53  31  .  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_323
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
 323  C1    C  C      0   0.320   0.0114  -0.1502   0.1207
 323  O1    O  O2     0  -0.470  -0.0765   2.6271   0.0612
 323  N1    N  N      1  -0.491  -4.7890   2.7026   0.1149
 323  C10   C  CR16   0  -0.306  -2.4742  -0.1168   0.1601
 323  C11   C  CR16   0  -0.334  -3.6403   0.5842   0.1547
 323  C12   C  CR6    0   0.432  -3.6376   2.0130   0.1162
 323  C13   C  CR16   0  -0.485  -2.3920   2.6705   0.0833
 323  C14   C  CH3    0  -0.546   5.9324   2.3920   0.3184
 323  C15   C  CH3    0  -0.547   4.5106   4.4461   0.1820
 323  C16   C  CH3    0  -0.546  -6.0635   2.0111   0.1625
 323  C17   C  CH3    0  -0.547  -4.7696   4.1515   0.0919
 323  C18   C  CR6    0  -0.048   0.0585  -1.6134   0.3563
 323  C19   C  CR16   0  -0.259   0.0786  -2.0457   1.6788
 323  O2    O  OC    -1  -0.554   0.0366  -0.7804  -2.2292
 323  N2    N  NT     0  -0.491   4.6195   3.0014   0.2185
 323  C2    C  CR6    0  -0.028  -1.2169   0.5272   0.1319
 323  C20   C  CR16   0  -0.268   0.1280  -3.4006   1.9583
 323  C21   C  CR6    0   0.002   0.1552  -4.3254   0.9184
 323  C22   C  CR16   0  -0.314   0.1321  -3.8849  -0.4017
 323  C23   C  CR6    0  -0.082   0.0853  -2.5317  -0.6937
 323  C24   C  C      0   0.425   0.0658  -2.0237  -2.1230
 323  C25   C  C1     0   0.119   0.2102  -5.7602   1.2451
 323  O3    O  O      0  -0.565   0.0799  -2.8651  -3.0328
 323  C3    C  CR6    0   0.424  -1.2291   1.9358   0.0896
 323  O4    O  O      0  -0.378   0.2337  -6.6481   0.4258
 323  C4    C  CR6    0   0.425   1.1171   2.0110   0.1120
 323  C5    C  CR6    0  -0.031   1.1936   0.6043   0.1554
 323  C6    C  CR16   0  -0.485   2.2306   2.8184   0.1287
 323  C7    C  CR6    0   0.432   3.5142   2.2409   0.1923
 323  C8    C  CR16   0  -0.335   3.6068   0.8150   0.2324
 323  C9    C  CR16   0  -0.306   2.4883   0.0411   0.2115
 323  H10   H  HCR6   0   0.272  -2.5121  -1.1977   0.1862
 323  H11   H  HCR6   0   0.291  -4.5709   0.0375   0.1787
 323  H13   H  HCR6   0   0.298  -2.3201   3.7480   0.0572
 323  H114  H  HCH3   0   0.270   6.6864   3.1716   0.3344
 323  H214  H  HCH3   0   0.253   6.0358   1.8063   1.2336
 323  H314  H  HCH3   0   0.253   6.1416   1.7419  -0.5329
 323  H115  H  HCH3   0   0.253   4.0050   4.7860  -0.7240
 323  H215  H  HCH3   0   0.252   3.9627   4.8307   1.0452
 323  H315  H  HCH3   0   0.272   5.5042   4.8817   0.1936
 323  H116  H  HCH3   0   0.252  -6.1705   1.4243   1.0766
 323  H216  H  HCH3   0   0.270  -6.8658   2.7407   0.1383
 323  H316  H  HCH3   0   0.253  -6.1923   1.3452  -0.6922
 323  H117  H  HCH3   0   0.252  -4.2554   4.5602   0.9645
 323  H217  H  HCH3   0   0.252  -4.2775   4.5318  -0.8057
 323  H317  H  HCH3   0   0.271  -5.7888   4.5237   0.0987
 323  H19   H  HCR6   0   0.271   0.0581  -1.3255   2.4865
 323  H20   H  HCR6   0   0.276   0.1464  -3.7378   2.9877
 323  H22   H  HCR6   0   0.265   0.1523  -4.6002  -1.2138
 323  H25   H  H      0   0.201   0.2303  -5.9838   2.3263
 323  H6    H  HCR6   0   0.298   2.0928   3.8896   0.1019
 323  H8    H  HCR6   0   0.291   4.5705   0.3309   0.2791
 323  H9    H  HCR6   0   0.272   2.5920  -1.0354   0.2385

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
 323  O4   C25   double    1.208  0.020  1.208
 323  C25  C21   single    1.473  0.020  1.473
 323  C21  C22   aromatic  1.392  0.020  1.392
 323  C21  C20   aromatic  1.392  0.020  1.392
 323  C22  C23   aromatic  1.385  0.020  1.385
 323  C20  C19   aromatic  1.384  0.020  1.384
 323  O3   C24   deloc     1.239  0.020  1.239
 323  C23  C24   single    1.517  0.020  1.517
 323  C23  C18   aromatic  1.395  0.020  1.395
 323  C19  C18   aromatic  1.392  0.020  1.392
 323  C24  O2    deloc     1.248  0.020  1.248
 323  C18  C1    single    1.483  0.020  1.483
 323  C10  C11   aromatic  1.361  0.020  1.361
 323  C10  C2    aromatic  1.413  0.020  1.413
 323  C1   C2    double    1.403  0.020  1.403
 323  C1   C5    single    1.403  0.020  1.403
 323  C11  C12   aromatic  1.429  0.020  1.429
 323  C2   C3    aromatic  1.409  0.020  1.409
 323  C9   C5    aromatic  1.413  0.020  1.413
 323  C9   C8    aromatic  1.360  0.020  1.360
 323  C5   C4    aromatic  1.409  0.020  1.409
 323  C17  N1    single    1.449  0.020  1.449
 323  C12  N1    double    1.342  0.020  1.342
 323  C12  C13   aromatic  1.409  0.020  1.409
 323  C8   C7    aromatic  1.429  0.020  1.429
 323  C3   C13   aromatic  1.376  0.020  1.376
 323  C3   O1    single    1.344  0.020  1.344
 323  N1   C16   single    1.451  0.020  1.451
 323  C4   O1    single    1.344  0.020  1.344
 323  C4   C6    aromatic  1.376  0.020  1.376
 323  C7   C6    aromatic  1.409  0.020  1.409
 323  C7   N2    single    1.342  0.020  1.342
 323  C15  N2    single    1.449  0.020  1.449
 323  N2   C14   single    1.451  0.020  1.451
 323  C10  H10   single    0.930  0.020  1.080
 323  C11  H11   single    0.930  0.020  1.080
 323  C13  H13   single    0.930  0.020  1.080
 323  C14  H114  single    0.970  0.020  1.090
 323  C14  H214  single    0.970  0.020  1.090
 323  C14  H314  single    0.970  0.020  1.090
 323  C15  H115  single    0.970  0.020  1.090
 323  C15  H215  single    0.970  0.020  1.090
 323  C15  H315  single    0.970  0.020  1.090
 323  C16  H116  single    0.970  0.020  1.090
 323  C16  H216  single    0.970  0.020  1.090
 323  C16  H316  single    0.970  0.020  1.090
 323  C17  H117  single    0.970  0.020  1.090
 323  C17  H217  single    0.970  0.020  1.090
 323  C17  H317  single    0.970  0.020  1.090
 323  C19  H19   single    0.930  0.020  1.080
 323  C20  H20   single    0.930  0.020  1.080
 323  C22  H22   single    0.930  0.020  1.080
 323  C25  H25   single    0.930  0.020  1.080
 323  C6   H6    single    0.930  0.020  1.080
 323  C8   H8    single    0.930  0.020  1.080
 323  C9   H9    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
 323  C5    C1   C2    118.55  3.000
 323  C5    C1   C18   120.00  3.000
 323  C2    C1   C18   120.20  3.000
 323  C4    O1   C3    121.65  3.000
 323  C17   N1   C16   119.26  3.000
 323  C16   N1   C12   120.58  3.000
 323  C17   N1   C12   120.15  3.000
 323  H10   C10  C2    119.14  3.000
 323  H10   C10  C11   119.00  3.000
 323  C2    C10  C11   121.86  3.000
 323  H11   C11  C12   120.56  3.000
 323  H11   C11  C10   118.55  3.000
 323  C12   C11  C10   120.89  3.000
 323  C13   C12  C11   117.96  3.000
 323  C13   C12  N1    121.24  3.000
 323  C11   C12  N1    120.80  3.000
 323  H13   C13  C3    118.47  3.000
 323  H13   C13  C12   121.66  3.000
 323  C3    C13  C12   119.87  3.000
 323  H314  C14  H214  108.44  3.000
 323  H314  C14  H114  107.84  3.000
 323  H214  C14  H114  107.90  3.000
 323  H314  C14  N2    111.72  3.000
 323  H214  C14  N2    111.64  3.000
 323  H114  C14  N2    109.15  3.000
 323  H315  C15  H215  108.03  3.000
 323  H315  C15  H115  107.93  3.000
 323  H215  C15  H115  108.30  3.000
 323  H315  C15  N2    109.34  3.000
 323  H215  C15  N2    111.64  3.000
 323  H115  C15  N2    111.47  3.000
 323  H316  C16  H216  107.80  3.000
 323  H316  C16  H116  108.44  3.000
 323  H216  C16  H116  107.93  3.000
 323  H316  C16  N1    111.65  3.000
 323  H216  C16  N1    109.18  3.000
 323  H116  C16  N1    111.70  3.000
 323  H317  C17  H217  108.00  3.000
 323  H317  C17  H117  107.99  3.000
 323  H217  C17  H117  108.32  3.000
 323  H317  C17  N1    109.29  3.000
 323  H217  C17  N1    111.55  3.000
 323  H117  C17  N1    111.57  3.000
 323  C23   C18  C19   120.70  3.000
 323  C19   C18  C1    117.26  3.000
 323  C23   C18  C1    122.04  3.000
 323  H19   C19  C20   120.09  3.000
 323  H19   C19  C18   120.15  3.000
 323  C20   C19  C18   119.77  3.000
 323  C7    N2   C15   120.17  3.000
 323  C15   N2   C14   119.24  3.000
 323  C7    N2   C14   120.57  3.000
 323  C3    C2   C10   116.65  3.000
 323  C3    C2   C1    119.34  3.000
 323  C10   C2   C1    124.00  3.000
 323  H20   C20  C21   120.18  3.000
 323  H20   C20  C19   119.81  3.000
 323  C21   C20  C19   120.01  3.000
 323  C25   C21  C22   121.29  3.000
 323  C22   C21  C20   119.87  3.000
 323  C25   C21  C20   118.84  3.000
 323  H22   C22  C23   119.21  3.000
 323  H22   C22  C21   120.14  3.000
 323  C23   C22  C21   120.64  3.000
 323  C24   C23  C22   121.75  3.000
 323  C24   C23  C18   119.23  3.000
 323  C22   C23  C18   119.02  3.000
 323  O3    C24  C23   117.65  3.000
 323  C23   C24  O2    114.46  3.000
 323  O3    C24  O2    127.89  3.000
 323  H25   C25  O4    120.98  3.000
 323  H25   C25  C21   114.53  3.000
 323  O4    C25  C21   124.49  3.000
 323  C2    C3   C13   122.77  3.000
 323  C13   C3   O1    116.75  3.000
 323  C2    C3   O1    120.48  3.000
 323  C6    C4   C5    122.79  3.000
 323  C6    C4   O1    116.76  3.000
 323  C5    C4   O1    120.45  3.000
 323  C9    C5   C4    116.66  3.000
 323  C4    C5   C1    119.36  3.000
 323  C9    C5   C1    123.97  3.000
 323  H6    C6   C7    121.59  3.000
 323  H6    C6   C4    118.58  3.000
 323  C7    C6   C4    119.83  3.000
 323  C8    C7   C6    117.98  3.000
 323  C6    C7   N2    121.26  3.000
 323  C8    C7   N2    120.76  3.000
 323  H8    C8   C9    118.66  3.000
 323  H8    C8   C7    120.43  3.000
 323  C9    C8   C7    120.92  3.000
 323  H9    C9   C8    119.14  3.000
 323  H9    C9   C5    119.04  3.000
 323  C8    C9   C5    121.82  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
 323  CONST_01  C13   C12  C11  C10     0.00   0.0  0
 323  CONST_02  C13   C3   C2   C10     0.00   0.0  0
 323  CONST_03  C3    C2   C10  C11     0.00   0.0  0
 323  CONST_04  C3    C13  C12  C11     0.00   0.0  0
 323  CONST_05  C2    C10  C11  C12     0.00   0.0  0
 323  CONST_06  C2    C3   C13  C12     0.00   0.0  0
 323  CONST_07  C21   C22  C23  C18     0.00   0.0  0
 323  CONST_08  C21   C20  C19  C18     0.00   0.0  0
 323  CONST_09  C22   C21  C20  C19     0.00   0.0  0
 323  CONST_10  C22   C23  C18  C19     0.00   0.0  0
 323  CONST_11  C23   C22  C21  C20     0.00   0.0  0
 323  CONST_12  C23   C18  C19  C20     0.00   0.0  0
 323  CONST_13  C8    C9   C5   C4      0.00   0.0  0
 323  CONST_14  C8    C7   C6   C4      0.00   0.0  0
 323  CONST_15  C7    C8   C9   C5      0.00   0.0  0
 323  CONST_16  C7    C6   C4   C5      0.00   0.0  0
 323  CONST_17  C9    C5   C4   C6      0.00   0.0  0
 323  CONST_18  C9    C8   C7   C6      0.00   0.0  0
 323  CONST_19  C22   C23  C18  C1    180.00   0.0  0
 323  CONST_20  C20   C19  C18  C1    180.00   0.0  0
 323  CONST_21  C24   C23  C18  C1      0.00   0.0  0
 323  CONST_22  C10   C11  C12  N1    180.00   0.0  0
 323  CONST_23  C3    C13  C12  N1    180.00   0.0  0
 323  CONST_24  C25   C21  C20  C19   180.00   0.0  0
 323  CONST_25  C24   C23  C18  C19   180.00   0.0  0
 323  CONST_26  C9    C8   C7   N2    180.00   0.0  0
 323  CONST_27  C4    C6   C7   N2    180.00   0.0  0
 323  CONST_28  C24   C23  C22  C21   180.00   0.0  0
 323  CONST_29  C25   C21  C22  C23   180.00   0.0  0
 323  CONST_30  H19   C19  C18  C1      0.00   0.0  0
 323  CONST_31  H10   C10  C2   C1      0.00   0.0  0
 323  CONST_32  H9    C9   C5   C1      0.00   0.0  0
 323  CONST_33  H13   C13  C3   O1      0.00   0.0  0
 323  CONST_34  H6    C6   C4   O1      0.00   0.0  0
 323  CONST_35  H11   C11  C12  C13   180.00   0.0  0
 323  CONST_36  H22   C22  C23  C18   180.00   0.0  0
 323  CONST_37  H20   C20  C19  C18   180.00   0.0  0
 323  CONST_38  H8    C8   C9   C5    180.00   0.0  0
 323  CONST_39  C17   N1   C12  C11   180.00   0.0  0
 323  CONST_40  C16   N1   C12  C11     0.00   0.0  0
 323  CONST_41  C17   N1   C12  C13     0.00   0.0  0
 323  CONST_42  C16   N1   C12  C13   180.00   0.0  0
 323  CONST_43  C8    C7   N2   C14     0.00   0.0  0
 323  CONST_44  C6    C7   N2   C14   180.00   0.0  0
 323  CONST_45  C8    C7   N2   C15   180.00   0.0  0
 323  CONST_46  C6    C7   N2   C15     0.00   0.0  0
 323  Var_01    C18   C1   C2   C10    -9.79   0.0  0
 323  Var_02    C3    C2   C1   C18   171.36   0.0  0
 323  Var_03    C2    C1   C18  C19   -84.38  30.0  2
 323  Var_04    O3    C24  C23  C18  -179.44  30.0  2
 323  Var_05    O4    C25  C21  C20   179.78  30.0  2
 323  Var_06    H117  C17  N1   C12   -60.41  30.0  3
 323  Var_07    H116  C16  N1   C12    61.54  30.0  3
 323  Var_08    H115  C15  N2   C7    -59.76  30.0  3
 323  Var_09    H114  C14  N2   C7   -179.44  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
 323  plan-1  C1   0.020
 323  plan-1  C18  0.020
 323  plan-1  C19  0.020
 323  plan-1  C20  0.020
 323  plan-1  C21  0.020
 323  plan-1  C22  0.020
 323  plan-1  C23  0.020
 323  plan-1  C24  0.020
 323  plan-1  C25  0.020
 323  plan-1  H19  0.020
 323  plan-1  H20  0.020
 323  plan-1  H22  0.020
 323  plan-2  C14  0.020
 323  plan-2  C15  0.020
 323  plan-2  N2   0.020
 323  plan-2  C7   0.020
 323  plan-3  O2   0.020
 323  plan-3  C23  0.020
 323  plan-3  C24  0.020
 323  plan-3  O3   0.020
 323  plan-4  C21  0.020
 323  plan-4  C25  0.020
 323  plan-4  O4   0.020
 323  plan-4  H25  0.020
 323  plan-5  C1   0.020
 323  plan-5  O1   0.020
 323  plan-5  N1   0.020
 323  plan-5  C10  0.020
 323  plan-5  C11  0.020
 323  plan-5  C12  0.020
 323  plan-5  C13  0.020
 323  plan-5  C16  0.020
 323  plan-5  C17  0.020
 323  plan-5  C18  0.020
 323  plan-5  N2   0.020
 323  plan-5  C2   0.020
 323  plan-5  C3   0.020
 323  plan-5  C4   0.020
 323  plan-5  C5   0.020
 323  plan-5  C6   0.020
 323  plan-5  C7   0.020
 323  plan-5  C8   0.020
 323  plan-5  C9   0.020
 323  plan-5  H10  0.020
 323  plan-5  H11  0.020
 323  plan-5  H13  0.020
 323  plan-5  H6   0.020
 323  plan-5  H8   0.020
 323  plan-5  H9   0.020

