# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 23:40:31 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 5-[(~{Z})-(1,3-dimethyl-5-oxidanylidene-pyrazol-4-ylidene)-oxidanyl-methyl]-2-(phenylmethyl)isoindole-1,3-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1N=C(C)C(=C(O)/c2ccc3C(=O)N(Cc4ccccc4)C(=O)c3c2)\C1=O
#
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
 CQC  CQC  5-[(~{Z})-(1,3-dimethyl-5-oxidanylidene-pyrazol-4-ylidene)-oxidanyl-methyl]-2-(phenylmethyl)isoindole-1,3-dione  ligand  45  28  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CQC
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
 CQC  C10  C  C     0   0.347  -3.1640  -1.0465  -0.2273
 CQC  C15  C  CH2   0  -0.432   4.2023  -0.8192  -1.1353
 CQC  C21  C  CH3   0  -0.510  -6.4971   2.5231   0.2802
 CQC  C22  C  CH3   0  -0.761  -1.8586   1.5953   1.1940
 CQC  C24  C  CR16  0  -0.295   4.7139   1.6416  -0.9882
 CQC  C26  C  CR16  0  -0.262   5.7733   2.5954   0.9506
 CQC  C28  C  CR16  0  -0.296   5.3441   0.2301   0.8470
 CQC  C01  C  CR6   0  -0.106  -1.7170  -1.2909  -0.0369
 CQC  C02  C  CR16  0  -0.237  -1.3007  -2.1820   0.9537
 CQC  C03  C  CR16  0  -0.288   0.0501  -2.4500   1.1543
 CQC  C04  C  CR56  0  -0.017   0.9478  -1.8190   0.3218
 CQC  C05  C  CR56  0  -0.019   0.5329  -0.9536  -0.6741
 CQC  C06  C  CR16  0  -0.285  -0.7965  -0.6656  -0.8793
 CQC  C07  C  CR5   0   0.593   2.4299  -1.8931   0.2736
 CQC  C09  C  CR5   0   0.592   1.7369  -0.4588  -1.3851
 CQC  C11  C  CR5   0  -0.307  -3.7638   0.1363   0.0530
 CQC  C16  C  CR5   0   0.600  -5.1823   0.4469  -0.1979
 CQC  C19  C  CR5   0   0.288  -3.2289   1.3312   0.6791
 CQC  C23  C  CR6   0   0.140   4.7715   0.3750  -0.4141
 CQC  C25  C  CR16  0  -0.242   5.2110   2.7466  -0.3100
 CQC  C27  C  CR16  0  -0.241   5.8416   1.3334   1.5266
 CQC  N08  N  NR5   0  -0.590   2.8182  -1.0686  -0.7699
 CQC  N17  N  NR5   0  -0.376  -5.3054   1.7222   0.2618
 CQC  N18  N  N     0  -0.271  -4.1513   2.2242   0.7932
 CQC  O12  O  OH1   0  -0.538  -3.8791  -2.0570  -0.6805
 CQC  O13  O  O     0  -0.391   1.7955   0.3101  -2.3092
 CQC  O14  O  O     0  -0.392   3.1685  -2.5301   0.9790
 CQC  O20  O  O     0  -0.483  -6.0698  -0.2264  -0.7012
 CQC  H1   H  HCH2  0   0.293   4.2443  -0.6800  -2.2150
 CQC  H2   H  HCH2  0   0.293   4.7709  -1.7194  -0.9051
 CQC  H3   H  HCH3  0   0.248  -6.8205   2.7241   1.3017
 CQC  H4   H  HCH3  0   0.250  -6.3304   3.4708  -0.2307
 CQC  H5   H  HCH3  0   0.254  -7.2870   1.9847  -0.2358
 CQC  H6   H  HCH3  0   0.256  -1.1325   1.6885   0.3855
 CQC  H7   H  HCH3  0   0.267  -1.8543   2.5281   1.7557
 CQC  H8   H  HCH3  0   0.253  -1.5123   0.7969   1.8513
 CQC  H10  H  HCR6  0   0.259   6.1606   3.4567   1.4794
 CQC  H11  H  HCR6  0   0.253   5.4084  -0.7514   1.3007
 CQC  H12  H  HCR6  0   0.298  -2.0349  -2.6562   1.5925
 CQC  H13  H  HCR6  0   0.286   0.3697  -3.1268   1.9348
 CQC  H14  H  HCR6  0   0.298  -1.1196   0.0090  -1.6615
 CQC  H16  H  HCR6  0   0.258   5.1595   3.7259  -0.7679
 CQC  H17  H  HCR6  0   0.258   6.2874   1.2053   2.5045
 CQC  H15  H  HOH1  0   0.500  -3.3196  -2.8138  -0.9021
 CQC  H9   H  HCR6  0   0.254   4.2817   1.7682  -1.9730

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
 CQC  O20  C16  double    1.222  0.020  1.222
 CQC  O12  C10  single    1.318  0.020  1.318
 CQC  C27  C26  aromatic  1.389  0.020  1.389
 CQC  C27  C28  aromatic  1.388  0.020  1.388
 CQC  C16  N17  single    1.361  0.020  1.361
 CQC  C16  C11  single    1.474  0.020  1.474
 CQC  C21  N17  single    1.436  0.020  1.436
 CQC  C26  C25  aromatic  1.389  0.020  1.389
 CQC  C10  C11  double    1.355  0.020  1.355
 CQC  C10  C01  single    1.480  0.020  1.480
 CQC  N17  N18  single    1.366  0.020  1.366
 CQC  C11  C19  single    1.451  0.020  1.451
 CQC  C28  C23  aromatic  1.393  0.020  1.393
 CQC  C06  C01  aromatic  1.396  0.020  1.396
 CQC  C06  C05  aromatic  1.376  0.020  1.376
 CQC  C01  C02  aromatic  1.396  0.020  1.396
 CQC  O13  C09  double    1.204  0.020  1.204
 CQC  C25  C24  aromatic  1.389  0.020  1.389
 CQC  C05  C09  single    1.483  0.020  1.483
 CQC  C05  C04  aromatic  1.383  0.020  1.383
 CQC  C09  N08  single    1.385  0.020  1.385
 CQC  N18  C19  double    1.289  0.020  1.289
 CQC  C19  C22  single    1.487  0.020  1.487
 CQC  C02  C03  aromatic  1.392  0.020  1.392
 CQC  C23  C24  aromatic  1.392  0.020  1.392
 CQC  C23  C15  single    1.507  0.020  1.507
 CQC  C04  C03  aromatic  1.377  0.020  1.377
 CQC  C04  C07  single    1.485  0.020  1.485
 CQC  N08  C15  single    1.453  0.020  1.453
 CQC  N08  C07  single    1.385  0.020  1.385
 CQC  C07  O14  double    1.204  0.020  1.204
 CQC  C15  H1   single    0.970  0.020  1.090
 CQC  C15  H2   single    0.970  0.020  1.090
 CQC  C21  H3   single    0.970  0.020  1.090
 CQC  C21  H4   single    0.970  0.020  1.090
 CQC  C21  H5   single    0.970  0.020  1.090
 CQC  C22  H6   single    0.970  0.020  1.090
 CQC  C22  H7   single    0.970  0.020  1.090
 CQC  C22  H8   single    0.970  0.020  1.090
 CQC  C24  H9   single    0.930  0.020  1.080
 CQC  C26  H10  single    0.930  0.020  1.080
 CQC  C28  H11  single    0.930  0.020  1.080
 CQC  C02  H12  single    0.930  0.020  1.080
 CQC  C03  H13  single    0.930  0.020  1.080
 CQC  C06  H14  single    0.930  0.020  1.080
 CQC  C25  H16  single    0.930  0.020  1.080
 CQC  C27  H17  single    0.930  0.020  1.080
 CQC  O12  H15  single    0.850  0.020  0.980

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
 CQC  O12  C10  C11  119.99  3.000
 CQC  C11  C10  C01  123.38  3.000
 CQC  O12  C10  C01  116.62  3.000
 CQC  H2   C15  H1   107.16  3.000
 CQC  H2   C15  N08  107.59  3.000
 CQC  H1   C15  N08  107.93  3.000
 CQC  H2   C15  C23  110.89  3.000
 CQC  H1   C15  C23  111.01  3.000
 CQC  N08  C15  C23  112.05  3.000
 CQC  H5   C21  H4   108.65  3.000
 CQC  H5   C21  H3   108.71  3.000
 CQC  H4   C21  H3   108.92  3.000
 CQC  H5   C21  N17  108.72  3.000
 CQC  H4   C21  N17  110.62  3.000
 CQC  H3   C21  N17  111.17  3.000
 CQC  H8   C22  H7   108.36  3.000
 CQC  H8   C22  H6   107.33  3.000
 CQC  H7   C22  H6   107.85  3.000
 CQC  H8   C22  C19  111.79  3.000
 CQC  H7   C22  C19  109.53  3.000
 CQC  H6   C22  C19  111.83  3.000
 CQC  H9   C24  C25  119.61  3.000
 CQC  H9   C24  C23  119.87  3.000
 CQC  C25  C24  C23  120.52  3.000
 CQC  H10  C26  C27  120.19  3.000
 CQC  H10  C26  C25  120.12  3.000
 CQC  C27  C26  C25  119.69  3.000
 CQC  H11  C28  C27  119.59  3.000
 CQC  H11  C28  C23  119.87  3.000
 CQC  C27  C28  C23  120.54  3.000
 CQC  C06  C01  C02  121.17  3.000
 CQC  C02  C01  C10  119.23  3.000
 CQC  C06  C01  C10  119.55  3.000
 CQC  H12  C02  C03  119.27  3.000
 CQC  H12  C02  C01  119.75  3.000
 CQC  C03  C02  C01  120.97  3.000
 CQC  H13  C03  C04  122.03  3.000
 CQC  H13  C03  C02  120.75  3.000
 CQC  C04  C03  C02  117.21  3.000
 CQC  C07  C04  C05  107.90  3.000
 CQC  C07  C04  C03  130.34  3.000
 CQC  C05  C04  C03  121.76  3.000
 CQC  C09  C05  C06  130.02  3.000
 CQC  C09  C05  C04  108.08  3.000
 CQC  C06  C05  C04  121.89  3.000
 CQC  H14  C06  C05  121.80  3.000
 CQC  H14  C06  C01  121.23  3.000
 CQC  C05  C06  C01  116.97  3.000
 CQC  O14  C07  N08  125.76  3.000
 CQC  O14  C07  C04  128.31  3.000
 CQC  N08  C07  C04  105.93  3.000
 CQC  O13  C09  N08  125.74  3.000
 CQC  N08  C09  C05  105.89  3.000
 CQC  O13  C09  C05  128.37  3.000
 CQC  C19  C11  C16  104.75  3.000
 CQC  C19  C11  C10  130.14  3.000
 CQC  C16  C11  C10  125.08  3.000
 CQC  O20  C16  N17  126.11  3.000
 CQC  N17  C16  C11  103.13  3.000
 CQC  O20  C16  C11  130.76  3.000
 CQC  N18  C19  C11  110.17  3.000
 CQC  N18  C19  C22  120.37  3.000
 CQC  C11  C19  C22  129.43  3.000
 CQC  C28  C23  C24  119.03  3.000
 CQC  C24  C23  C15  120.55  3.000
 CQC  C28  C23  C15  120.42  3.000
 CQC  H16  C25  C26  120.13  3.000
 CQC  H16  C25  C24  119.76  3.000
 CQC  C26  C25  C24  120.12  3.000
 CQC  H17  C27  C28  119.73  3.000
 CQC  H17  C27  C26  120.17  3.000
 CQC  C28  C27  C26  120.10  3.000
 CQC  C09  N08  C07  112.19  3.000
 CQC  C07  N08  C15  123.95  3.000
 CQC  C09  N08  C15  123.79  3.000
 CQC  N18  N17  C16  113.53  3.000
 CQC  N18  N17  C21  119.42  3.000
 CQC  C16  N17  C21  127.01  3.000
 CQC  N17  N18  C19  108.40  3.000
 CQC  H15  O12  C10  111.39  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
 CQC  CONST_01  C27  C26  C25  C24    0.00   0.0  0
 CQC  CONST_02  C27  C28  C23  C24    0.00   0.0  0
 CQC  CONST_03  C23  C28  C27  C26    0.00   0.0  0
 CQC  CONST_04  C23  C24  C25  C26    0.00   0.0  0
 CQC  CONST_05  C25  C26  C27  C28    0.00   0.0  0
 CQC  CONST_06  C25  C24  C23  C28    0.00   0.0  0
 CQC  CONST_07  C04  C05  C06  C01    0.00   0.0  0
 CQC  CONST_08  C04  C03  C02  C01    0.00   0.0  0
 CQC  CONST_09  C05  C06  C01  C02    0.00   0.0  0
 CQC  CONST_10  C05  C04  C03  C02    0.00   0.0  0
 CQC  CONST_11  C06  C01  C02  C03    0.00   0.0  0
 CQC  CONST_12  C06  C05  C04  C03    0.00   0.0  0
 CQC  CONST_13  C09  N08  C07  C04    0.00   0.0  0
 CQC  CONST_14  N18  N17  C16  C11    0.00   0.0  0
 CQC  CONST_15  C05  C06  C01  C10  180.00   0.0  0
 CQC  CONST_16  C03  C02  C01  C10  180.00   0.0  0
 CQC  CONST_17  C27  C28  C23  C15  180.00   0.0  0
 CQC  CONST_18  C25  C24  C23  C15  180.00   0.0  0
 CQC  CONST_19  C04  C07  N08  C15  180.00   0.0  0
 CQC  CONST_20  C11  C16  N17  C21  180.00   0.0  0
 CQC  CONST_21  O14  C07  N08  C09  180.00   0.0  0
 CQC  CONST_22  O20  C16  N17  N18  180.00   0.0  0
 CQC  CONST_23  H10  C26  C25  C24  180.00   0.0  0
 CQC  CONST_24  H11  C28  C23  C24  180.00   0.0  0
 CQC  CONST_25  H9   C24  C25  C26  180.00   0.0  0
 CQC  CONST_26  H13  C03  C02  C01  180.00   0.0  0
 CQC  CONST_27  H14  C06  C01  C02  180.00   0.0  0
 CQC  CONST_28  H12  C02  C03  C04  180.00   0.0  0
 CQC  CONST_29  H17  C27  C28  C23  180.00   0.0  0
 CQC  CONST_30  H16  C25  C24  C23  180.00   0.0  0
 CQC  CONST_31  O14  C07  N08  C15    0.00   0.0  0
 CQC  CONST_32  O20  C16  N17  C21    0.00   0.0  0
 CQC  Var_01    N08  C15  C23  C24  -92.13  30.0  2
 CQC  Var_02    C16  C11  C10  C01  176.10  30.0  2
 CQC  Var_03    C11  C10  C01  C02  112.05  30.0  2
 CQC  Var_04    C23  C15  N08  C07  -90.54  30.0  3
 CQC  Var_05    H6   C22  C19  C11   70.42  30.0  3
 CQC  Var_06    H3   C21  N17  C16  113.65  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
 CQC  plan-1  C10  0.020
 CQC  plan-1  C21  0.020
 CQC  plan-1  C22  0.020
 CQC  plan-1  C11  0.020
 CQC  plan-1  C16  0.020
 CQC  plan-1  C19  0.020
 CQC  plan-1  N17  0.020
 CQC  plan-1  N18  0.020
 CQC  plan-1  O20  0.020
 CQC  plan-2  C15  0.020
 CQC  plan-2  C24  0.020
 CQC  plan-2  C26  0.020
 CQC  plan-2  C28  0.020
 CQC  plan-2  C23  0.020
 CQC  plan-2  C25  0.020
 CQC  plan-2  C27  0.020
 CQC  plan-2  H10  0.020
 CQC  plan-2  H11  0.020
 CQC  plan-2  H16  0.020
 CQC  plan-2  H17  0.020
 CQC  plan-2  H9   0.020
 CQC  plan-3  C10  0.020
 CQC  plan-3  C15  0.020
 CQC  plan-3  C01  0.020
 CQC  plan-3  C02  0.020
 CQC  plan-3  C03  0.020
 CQC  plan-3  C04  0.020
 CQC  plan-3  C05  0.020
 CQC  plan-3  C06  0.020
 CQC  plan-3  C07  0.020
 CQC  plan-3  C09  0.020
 CQC  plan-3  N08  0.020
 CQC  plan-3  O13  0.020
 CQC  plan-3  O14  0.020
 CQC  plan-3  H12  0.020
 CQC  plan-3  H13  0.020
 CQC  plan-3  H14  0.020

