# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 10:05:17 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 8-hydroxy-4-methyl-9-nitro-2H-benzo[g]chromen-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=O)Oc2cc3c(ccc(O)c3[N+]([O-])=O)cc12
#
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
 CZ0  CZ0  8-hydroxy-4-methyl-9-nitro-2H-benzo[g]chromen-2-one  ligand  29  20  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CZ0
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
 CZ0  C1    C  CR16   0  -0.400  -2.8348   2.1127  -0.1365
 CZ0  N1    N  N      1   0.336  -2.7407  -1.6090  -0.0304
 CZ0  C2    C  CR6    0   0.392  -3.2464   0.7589  -0.1319
 CZ0  O2    O  O     -1  -0.364  -3.5130  -1.9756  -0.8821
 CZ0  C3    C  CR6    0   0.087  -2.2878  -0.2332  -0.0687
 CZ0  O3    O  O      0  -0.375  -2.3223  -2.3162   0.8582
 CZ0  C4    C  CR16   0  -0.271  -1.5137   2.4283  -0.1002
 CZ0  C5    C  CR66   0   0.093  -0.5153   1.4251  -0.0519
 CZ0  C6    C  CR66   0   0.143  -0.8975   0.0551  -0.0243
 CZ0  C7    C  CR16   0  -0.406   0.1156  -0.9223   0.0034
 CZ0  C8    C  CR16   0  -0.402   0.8430   1.7719  -0.0373
 CZ0  C9    C  CR66   0  -0.027   1.8313   0.8136  -0.0064
 CZ0  C10   C  CR66   0   0.418   1.4308  -0.5399   0.0077
 CZ0  O11   O  O      0  -0.470   2.3529  -1.5310   0.0275
 CZ0  C12   C  CR6    0   0.556   3.6906  -1.2975   0.0370
 CZ0  C13   C  CR16   0  -0.548   4.1198   0.0843   0.0256
 CZ0  C14   C  CR6    0   0.280   3.2492   1.1123   0.0047
 CZ0  O15   O  OH1    0  -0.593  -4.5328   0.4291  -0.1470
 CZ0  O16   O  O      0  -0.426   4.4168  -2.2584   0.0543
 CZ0  C17   C  CH3    0  -0.753   3.7099   2.5293  -0.0085
 CZ0  H1    H  HCR6   0   0.301  -3.5850   2.8929  -0.1690
 CZ0  H4    H  HCR6   0   0.284  -1.2117   3.4676  -0.1090
 CZ0  H7    H  HCR6   0   0.276  -0.1058  -1.9794   0.0139
 CZ0  H8    H  HCR6   0   0.282   1.1036   2.8226  -0.0567
 CZ0  H13   H  HCR6   0   0.286   5.1881   0.2515   0.0340
 CZ0  HO15  H  HOH1   0   0.495  -5.0911   1.2164  -0.1314
 CZ0  H17   H  HCH3   0   0.268   3.3289   3.0696   0.8595
 CZ0  H17A  H  HCH3   0   0.272   4.7958   2.5896   0.0007
 CZ0  H17B  H  HCH3   0   0.267   3.3448   3.0474  -0.8967

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
 CZ0  C1   C2    aromatic  1.415  0.020  1.415
 CZ0  C1   C4    aromatic  1.359  0.020  1.359
 CZ0  N1   O2    single    1.207  0.020  1.207
 CZ0  N1   C3    single    1.449  0.020  1.449
 CZ0  N1   O3    double    1.210  0.020  1.210
 CZ0  C2   C3    aromatic  1.381  0.020  1.381
 CZ0  C2   O15   single    1.328  0.020  1.328
 CZ0  C3   C6    aromatic  1.421  0.020  1.421
 CZ0  C4   C5    aromatic  1.416  0.020  1.416
 CZ0  C5   C6    aromatic  1.422  0.020  1.422
 CZ0  C5   C8    aromatic  1.402  0.020  1.402
 CZ0  C6   C7    aromatic  1.408  0.020  1.408
 CZ0  C7   C10   aromatic  1.370  0.020  1.370
 CZ0  C8   C9    aromatic  1.377  0.020  1.377
 CZ0  C9   C10   aromatic  1.412  0.020  1.412
 CZ0  C9   C14   single    1.449  0.020  1.449
 CZ0  C10  O11   single    1.354  0.020  1.354
 CZ0  O11  C12   single    1.358  0.020  1.358
 CZ0  C12  C13   single    1.447  0.020  1.447
 CZ0  C12  O16   double    1.205  0.020  1.205
 CZ0  C13  C14   double    1.347  0.020  1.347
 CZ0  C14  C17   single    1.490  0.020  1.490
 CZ0  C1   H1    single    0.930  0.020  1.080
 CZ0  C4   H4    single    0.930  0.020  1.080
 CZ0  C7   H7    single    0.930  0.020  1.080
 CZ0  C8   H8    single    0.930  0.020  1.080
 CZ0  C13  H13   single    0.930  0.020  1.080
 CZ0  O15  HO15  single    0.850  0.020  0.980
 CZ0  C17  H17   single    0.970  0.020  1.090
 CZ0  C17  H17A  single    0.970  0.020  1.090
 CZ0  C17  H17B  single    0.970  0.020  1.090

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
 CZ0  H1    C1   C4    120.47  3.000
 CZ0  H1    C1   C2    119.20  3.000
 CZ0  C4    C1   C2    120.33  3.000
 CZ0  O3    N1   C3    117.79  3.000
 CZ0  O3    N1   O2    124.19  3.000
 CZ0  C3    N1   O2    118.02  3.000
 CZ0  O15   C2   C3    119.63  3.000
 CZ0  O15   C2   C1    121.29  3.000
 CZ0  C3    C2   C1    119.05  3.000
 CZ0  C6    C3   C2    122.34  3.000
 CZ0  C6    C3   N1    119.85  3.000
 CZ0  C2    C3   N1    117.80  3.000
 CZ0  H4    C4   C5    118.94  3.000
 CZ0  H4    C4   C1    119.61  3.000
 CZ0  C5    C4   C1    121.46  3.000
 CZ0  C8    C5   C6    119.89  3.000
 CZ0  C8    C5   C4    120.54  3.000
 CZ0  C6    C5   C4    119.57  3.000
 CZ0  C7    C6   C5    118.40  3.000
 CZ0  C7    C6   C3    124.32  3.000
 CZ0  C5    C6   C3    117.24  3.000
 CZ0  H7    C7   C10   118.03  3.000
 CZ0  H7    C7   C6    122.15  3.000
 CZ0  C10   C7   C6    119.81  3.000
 CZ0  H8    C8   C9    120.20  3.000
 CZ0  H8    C8   C5    118.24  3.000
 CZ0  C9    C8   C5    121.56  3.000
 CZ0  C14   C9   C10   118.37  3.000
 CZ0  C14   C9   C8    123.98  3.000
 CZ0  C10   C9   C8    117.64  3.000
 CZ0  O11   C10  C9    120.59  3.000
 CZ0  O11   C10  C7    116.72  3.000
 CZ0  C9    C10  C7    122.69  3.000
 CZ0  C12   O11  C10   123.04  3.000
 CZ0  O16   C12  C13   125.66  3.000
 CZ0  O16   C12  O11   117.19  3.000
 CZ0  C13   C12  O11   117.15  3.000
 CZ0  H13   C13  C14   121.37  3.000
 CZ0  H13   C13  C12   116.14  3.000
 CZ0  C14   C13  C12   122.49  3.000
 CZ0  C17   C14  C13   121.73  3.000
 CZ0  C17   C14  C9    119.90  3.000
 CZ0  C13   C14  C9    118.36  3.000
 CZ0  HO15  O15  C2    110.95  3.000
 CZ0  H17B  C17  H17A  108.34  3.000
 CZ0  H17B  C17  H17   107.19  3.000
 CZ0  H17A  C17  H17   108.34  3.000
 CZ0  H17B  C17  C14   110.80  3.000
 CZ0  H17A  C17  C14   111.18  3.000
 CZ0  H17   C17  C14   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
 CZ0  CONST_01  C6   C3   C2   C1      0.00   0.0  0
 CZ0  CONST_02  C6   C5   C4   C1      0.00   0.0  0
 CZ0  CONST_03  C8   C5   C4   C1    180.00   0.0  0
 CZ0  CONST_04  C5   C4   C1   C2      0.00   0.0  0
 CZ0  CONST_05  C5   C6   C3   C2      0.00   0.0  0
 CZ0  CONST_06  C7   C6   C3   C2    180.00   0.0  0
 CZ0  CONST_07  C4   C1   C2   C3      0.00   0.0  0
 CZ0  CONST_08  C4   C5   C6   C3      0.00   0.0  0
 CZ0  CONST_09  C8   C5   C6   C3    180.00   0.0  0
 CZ0  CONST_10  C10  C7   C6   C3    180.00   0.0  0
 CZ0  CONST_11  C7   C6   C5   C4    180.00   0.0  0
 CZ0  CONST_12  C9   C8   C5   C4    180.00   0.0  0
 CZ0  CONST_13  C10  C7   C6   C5      0.00   0.0  0
 CZ0  CONST_14  C10  C9   C8   C5      0.00   0.0  0
 CZ0  CONST_15  C9   C8   C5   C6      0.00   0.0  0
 CZ0  CONST_16  C9   C10  C7   C6      0.00   0.0  0
 CZ0  CONST_17  C8   C5   C6   C7      0.00   0.0  0
 CZ0  CONST_18  C8   C9   C10  C7      0.00   0.0  0
 CZ0  CONST_19  N1   C3   C2   C1    180.00   0.0  0
 CZ0  CONST_20  C5   C6   C3   N1    180.00   0.0  0
 CZ0  CONST_21  C7   C6   C3   N1      0.00   0.0  0
 CZ0  CONST_22  O15  C2   C1   C4    180.00   0.0  0
 CZ0  CONST_23  O15  C2   C3   C6    180.00   0.0  0
 CZ0  CONST_24  H4   C4   C1   C2    180.00   0.0  0
 CZ0  CONST_25  H1   C1   C2   C3    180.00   0.0  0
 CZ0  CONST_26  H7   C7   C6   C3      0.00   0.0  0
 CZ0  CONST_27  H8   C8   C5   C4      0.00   0.0  0
 CZ0  Var_01    C13  C14  C9   C8   -179.52  30.0  1
 CZ0  Var_02    C12  C13  C14  C9      0.01  30.0  1
 CZ0  Var_03    C13  C12  O11  C10     0.03  30.0  1
 CZ0  Var_04    C14  C13  C12  O11    -0.08  30.0  1
 CZ0  Var_05    H17  C17  C14  C9     59.51  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
 CZ0  plan-1  C1   0.020
 CZ0  plan-1  N1   0.020
 CZ0  plan-1  C2   0.020
 CZ0  plan-1  C3   0.020
 CZ0  plan-1  C4   0.020
 CZ0  plan-1  C5   0.020
 CZ0  plan-1  C6   0.020
 CZ0  plan-1  C7   0.020
 CZ0  plan-1  C8   0.020
 CZ0  plan-1  C9   0.020
 CZ0  plan-1  C10  0.020
 CZ0  plan-1  O11  0.020
 CZ0  plan-1  C14  0.020
 CZ0  plan-1  O15  0.020
 CZ0  plan-1  H1   0.020
 CZ0  plan-1  H4   0.020
 CZ0  plan-1  H7   0.020
 CZ0  plan-1  H8   0.020
 CZ0  plan-2  N1   0.020
 CZ0  plan-2  O2   0.020
 CZ0  plan-2  C3   0.020
 CZ0  plan-2  O3   0.020
 CZ0  plan-3  O11  0.020
 CZ0  plan-3  C12  0.020
 CZ0  plan-3  C13  0.020
 CZ0  plan-3  O16  0.020

