# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 09:22:09 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: (4~{R})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]-4-methyl-4,5-dihydro-1~{H}-pyridazin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)c1ccc(cc1[N](O)=O)C2=NNC(=O)C[C@H]2C
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 X5M  X5M  (4~{R})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]-4-methyl-4,5-dihydro-1~{H}-pyridazin-6-one  ligand  42  22  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X5M
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
 X5M  C01  C  CH3   0  -0.647  -17.3518  -21.7193  38.3239
 X5M  C02  C  CH2   0  -0.301  -18.8454  -21.4539  38.2293
 X5M  N03  N  NT    0  -0.499  -19.5973  -22.3101  39.1407
 X5M  C04  C  CH2   0  -0.321  -20.7884  -22.9455  38.5862
 X5M  C05  C  CH3   0  -0.673  -21.9274  -22.0003  38.2239
 X5M  C06  C  CR6   0   0.308  -19.7102  -21.8501  40.4616
 X5M  C07  C  CR16  0  -0.264  -20.1950  -20.5814  40.7755
 X5M  C08  C  CR16  0  -0.310  -20.2916  -20.1306  42.0804
 X5M  C09  C  CR6   0   0.053  -19.8819  -20.9244  43.1511
 X5M  C10  C  CR16  0  -0.315  -19.3528  -22.1792  42.8602
 X5M  C11  C  CR6   0   0.233  -19.2859  -22.6220  41.5534
 X5M  N12  N  N     0   0.330  -18.6798  -23.9276  41.3453
 X5M  O13  O  O     0  -0.357  -19.2150  -24.7038  40.5945
 X5M  O14  O  O     0  -0.379  -17.6612  -24.1618  41.9555
 X5M  C15  C  C     0   0.270  -19.9606  -20.4510  44.5457
 X5M  N16  N  N     0  -0.243  -19.4404  -21.1990  45.4402
 X5M  N17  N  NH1   0  -0.494  -19.4563  -20.7868  46.7295
 X5M  C18  C  C     0   0.531  -20.2700  -19.8361  47.2697
 X5M  O19  O  O     0  -0.451  -20.2606  -19.5966  48.4614
 X5M  C20  C  CH2   0  -0.566  -21.1840  -19.1896  46.2701
 X5M  C21  C  CH1   0  -0.389  -20.5540  -19.1105  44.8843
 X5M  C22  C  CH3   0  -0.644  -19.4684  -18.0326  44.8067
 X5M  H1   H  HCH3  0   0.224  -16.8053  -21.1048  37.6075
 X5M  H2   H  HCH3  0   0.221  -16.9693  -21.4860  39.3192
 X5M  H3   H  HCH3  0   0.223  -17.1317  -22.7662  38.1148
 X5M  H4   H  HCH2  0   0.220  -19.0381  -20.3888  38.3993
 X5M  H5   H  HCH2  0   0.237  -19.1931  -21.6587  37.2154
 X5M  H6   H  HCH2  0   0.244  -21.1459  -23.6888  39.2985
 X5M  H7   H  HCH2  0   0.233  -20.4754  -23.4990  37.6979
 X5M  H8   H  HCH3  0   0.233  -22.7470  -22.5618  37.7728
 X5M  H9   H  HCH3  0   0.224  -22.3243  -21.4898  39.1023
 X5M  H10  H  HCH3  0   0.226  -21.6134  -21.2413  37.5056
 X5M  H11  H  HCR6  0   0.279  -20.5106  -19.9274  39.9736
 X5M  H12  H  HCR6  0   0.268  -20.6969  -19.1417  42.2459
 X5M  H13  H  HCR6  0   0.285  -19.0012  -22.8102  43.6648
 X5M  H15  H  HCH2  0   0.287  -21.4722  -18.2011  46.6273
 X5M  H16  H  HCH2  0   0.299  -22.0972  -19.7944  46.2343
 X5M  H17  H  HCH1  0   0.283  -21.3456  -18.8586  44.1781
 X5M  H18  H  HCH3  0   0.247  -19.8934  -17.0575  45.0459
 X5M  H19  H  HCH3  0   0.236  -18.6563  -18.2277  45.5084
 X5M  H20  H  HCH3  0   0.247  -19.0364  -17.9740  43.8080
 X5M  H14  H  HNH1  0   0.412  -18.9218  -21.3741  47.3533

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
 X5M  C05  C04  single    1.524  0.020  1.524
 X5M  C01  C02  single    1.520  0.020  1.520
 X5M  C02  N03  single    1.459  0.020  1.459
 X5M  C04  N03  single    1.459  0.020  1.459
 X5M  N03  C06  single    1.403  0.020  1.403
 X5M  O13  N12  single    1.205  0.020  1.205
 X5M  C06  C07  aromatic  1.394  0.020  1.394
 X5M  C06  C11  aromatic  1.403  0.020  1.403
 X5M  C07  C08  aromatic  1.384  0.020  1.384
 X5M  N12  C11  single    1.454  0.020  1.454
 X5M  N12  O14  double    1.210  0.020  1.210
 X5M  C11  C10  aromatic  1.381  0.020  1.381
 X5M  C08  C09  aromatic  1.394  0.020  1.394
 X5M  C10  C09  aromatic  1.392  0.020  1.392
 X5M  C09  C15  single    1.475  0.020  1.475
 X5M  C22  C21  single    1.532  0.020  1.532
 X5M  C15  C21  single    1.505  0.020  1.505
 X5M  C15  N16  double    1.277  0.020  1.277
 X5M  C21  C20  single    1.524  0.020  1.524
 X5M  N16  N17  single    1.354  0.020  1.354
 X5M  C20  C18  single    1.501  0.020  1.501
 X5M  N17  C18  single    1.363  0.020  1.363
 X5M  C18  O19  double    1.216  0.020  1.216
 X5M  C01  H1   single    0.970  0.020  1.090
 X5M  C01  H2   single    0.970  0.020  1.090
 X5M  C01  H3   single    0.970  0.020  1.090
 X5M  C02  H4   single    0.970  0.020  1.090
 X5M  C02  H5   single    0.970  0.020  1.090
 X5M  C04  H6   single    0.970  0.020  1.090
 X5M  C04  H7   single    0.970  0.020  1.090
 X5M  C05  H8   single    0.970  0.020  1.090
 X5M  C05  H9   single    0.970  0.020  1.090
 X5M  C05  H10  single    0.970  0.020  1.090
 X5M  C07  H11  single    0.930  0.020  1.080
 X5M  C08  H12  single    0.930  0.020  1.080
 X5M  C10  H13  single    0.930  0.020  1.080
 X5M  C20  H15  single    0.970  0.020  1.090
 X5M  C20  H16  single    0.970  0.020  1.090
 X5M  C21  H17  single    0.970  0.020  1.090
 X5M  C22  H18  single    0.970  0.020  1.090
 X5M  C22  H19  single    0.970  0.020  1.090
 X5M  C22  H20  single    0.970  0.020  1.090
 X5M  N17  H14  single    0.860  0.020  1.020

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
 X5M  H3   C01  H2   108.02  3.000
 X5M  H3   C01  H1   108.30  3.000
 X5M  H2   C01  H1   107.63  3.000
 X5M  H3   C01  C02  110.75  3.000
 X5M  H2   C01  C02  111.34  3.000
 X5M  H1   C01  C02  110.68  3.000
 X5M  H5   C02  H4   105.69  3.000
 X5M  H5   C02  N03  107.82  3.000
 X5M  H4   C02  N03  112.51  3.000
 X5M  H5   C02  C01  109.77  3.000
 X5M  H4   C02  C01  109.44  3.000
 X5M  N03  C02  C01  111.41  3.000
 X5M  C06  N03  C04  115.77  3.000
 X5M  C06  N03  C02  115.92  3.000
 X5M  C04  N03  C02  116.02  3.000
 X5M  H7   C04  H6   106.26  3.000
 X5M  H7   C04  C05  109.58  3.000
 X5M  H6   C04  C05  109.46  3.000
 X5M  H7   C04  N03  107.20  3.000
 X5M  H6   C04  N03  108.44  3.000
 X5M  C05  C04  N03  115.49  3.000
 X5M  H10  C05  H9   108.01  3.000
 X5M  H10  C05  H8   107.57  3.000
 X5M  H9   C05  H8   107.49  3.000
 X5M  H10  C05  C04  111.89  3.000
 X5M  H9   C05  C04  111.77  3.000
 X5M  H8   C05  C04  109.92  3.000
 X5M  C11  C06  C07  115.51  3.000
 X5M  C11  C06  N03  121.86  3.000
 X5M  C07  C06  N03  122.57  3.000
 X5M  H11  C07  C08  118.78  3.000
 X5M  H11  C07  C06  119.00  3.000
 X5M  C08  C07  C06  122.22  3.000
 X5M  H12  C08  C09  120.88  3.000
 X5M  H12  C08  C07  117.93  3.000
 X5M  C09  C08  C07  121.20  3.000
 X5M  C15  C09  C10  120.47  3.000
 X5M  C15  C09  C08  121.84  3.000
 X5M  C10  C09  C08  117.66  3.000
 X5M  H13  C10  C11  120.07  3.000
 X5M  H13  C10  C09  119.61  3.000
 X5M  C11  C10  C09  120.32  3.000
 X5M  N12  C11  C10  116.31  3.000
 X5M  C10  C11  C06  123.04  3.000
 X5M  N12  C11  C06  120.57  3.000
 X5M  O14  N12  O13  124.28  3.000
 X5M  O14  N12  C11  116.89  3.000
 X5M  O13  N12  C11  118.83  3.000
 X5M  C21  C15  N16  121.67  3.000
 X5M  N16  C15  C09  116.91  3.000
 X5M  C21  C15  C09  121.32  3.000
 X5M  N17  N16  C15  118.95  3.000
 X5M  H14  N17  C18  118.48  3.000
 X5M  H14  N17  N16  113.89  3.000
 X5M  C18  N17  N16  126.64  3.000
 X5M  C20  C18  O19  124.95  3.000
 X5M  O19  C18  N17  121.42  3.000
 X5M  C20  C18  N17  113.58  3.000
 X5M  H16  C20  H15  106.91  3.000
 X5M  H16  C20  C21  110.08  3.000
 X5M  H15  C20  C21  111.11  3.000
 X5M  H16  C20  C18  106.95  3.000
 X5M  H15  C20  C18  109.48  3.000
 X5M  C21  C20  C18  112.10  3.000
 X5M  H17  C21  C22  108.61  3.000
 X5M  H17  C21  C20  107.50  3.000
 X5M  C22  C21  C20  112.05  3.000
 X5M  H17  C21  C15  110.27  3.000
 X5M  C20  C21  C15  108.75  3.000
 X5M  C22  C21  C15  109.63  3.000
 X5M  H20  C22  H19  107.70  3.000
 X5M  H20  C22  H18  107.90  3.000
 X5M  H19  C22  H18  108.00  3.000
 X5M  H20  C22  C21  111.42  3.000
 X5M  H19  C22  C21  111.67  3.000
 X5M  H18  C22  C21  110.00  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
 X5M  CONST_01  C09  C08  C07  C06    0.00   0.0  0
 X5M  CONST_02  C09  C10  C11  C06    0.00   0.0  0
 X5M  CONST_03  C10  C11  C06  C07    0.00   0.0  0
 X5M  CONST_04  C10  C09  C08  C07    0.00   0.0  0
 X5M  CONST_05  C11  C06  C07  C08    0.00   0.0  0
 X5M  CONST_06  C11  C10  C09  C08    0.00   0.0  0
 X5M  CONST_07  C15  C09  C08  C07  180.00   0.0  0
 X5M  CONST_08  C15  C09  C10  C11  180.00   0.0  0
 X5M  CONST_09  C20  C18  N17  N16    0.00   0.0  0
 X5M  CONST_10  C08  C07  C06  N03  180.00   0.0  0
 X5M  CONST_11  C10  C11  C06  N03  180.00   0.0  0
 X5M  CONST_12  N12  C11  C06  C07  180.00   0.0  0
 X5M  CONST_13  N12  C11  C10  C09  180.00   0.0  0
 X5M  CONST_14  O19  C18  N17  N16  180.00   0.0  0
 X5M  CONST_15  H12  C08  C07  C06  180.00   0.0  0
 X5M  CONST_16  H13  C10  C11  C06  180.00   0.0  0
 X5M  CONST_17  H11  C07  C08  C09  180.00   0.0  0
 X5M  CONST_18  H14  N17  C18  C20  180.00   0.0  0
 X5M  Var_01    C21  C15  C09  C08    3.15  30.0  2
 X5M  Var_02    C18  N17  N16  C15   19.17  30.0  1
 X5M  Var_03    C21  C20  C18  N17  -31.85  30.0  1
 X5M  Var_04    C06  N03  C02  C01   84.39  30.0  3
 X5M  Var_05    H1   C01  C02  N03  177.53  30.0  3
 X5M  Var_06    H8   C05  C04  N03  177.11  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 X5M  chir_01  C21  C22  C15  C20  negativ

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
 X5M  plan-1  N03  0.020
 X5M  plan-1  C06  0.020
 X5M  plan-1  C07  0.020
 X5M  plan-1  C08  0.020
 X5M  plan-1  C09  0.020
 X5M  plan-1  C10  0.020
 X5M  plan-1  C11  0.020
 X5M  plan-1  N12  0.020
 X5M  plan-1  C15  0.020
 X5M  plan-1  H11  0.020
 X5M  plan-1  H12  0.020
 X5M  plan-1  H13  0.020
 X5M  plan-2  C02  0.020
 X5M  plan-2  N03  0.020
 X5M  plan-2  C04  0.020
 X5M  plan-2  C06  0.020
 X5M  plan-3  C11  0.020
 X5M  plan-3  N12  0.020
 X5M  plan-3  O13  0.020
 X5M  plan-3  O14  0.020
 X5M  plan-4  N16  0.020
 X5M  plan-4  N17  0.020
 X5M  plan-4  C18  0.020
 X5M  plan-4  O19  0.020
 X5M  plan-4  C20  0.020
 X5M  plan-4  H14  0.020

