# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 06:37:55 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: ~{N}2-(1,3-benzodioxol-5-yl)benzene-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccccc1Nc2ccc3OCOc3c2
#
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
 WCU  WCU  ~{N}2-(1,3-benzodioxol-5-yl)benzene-1,2-diamine  ligand  29  17  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WCU
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
 WCU  C10  C  CR16  0  -0.343  -0.5289   0.6602   0.8117
 WCU  C13  C  CR56  0   0.318  -2.6958  -0.5886  -0.2922
 WCU  C01  C  CR16  0  -0.261   4.4798   1.3219  -0.2775
 WCU  C02  C  CR16  0  -0.289   3.3299   1.9062  -0.7940
 WCU  C03  C  CR16  0  -0.277   2.1551   1.1695  -0.8280
 WCU  C04  C  CR6   0   0.237   2.1048  -0.1294  -0.3336
 WCU  C05  C  CR6   0   0.236   3.2678  -0.7230   0.1920
 WCU  C06  C  CR16  0  -0.331   4.4503   0.0236   0.2045
 WCU  N07  N  NH2   0  -0.848   3.2425  -2.0304   0.6301
 WCU  N08  N  NH1   0  -0.795   0.9262  -0.9008  -0.3540
 WCU  C09  C  CR6   0   0.359  -0.3367  -0.4076  -0.0673
 WCU  C11  C  CR16  0  -0.334  -1.8100   1.1205   1.1353
 WCU  C12  C  CR56  0   0.264  -2.8810   0.4767   0.5714
 WCU  C14  C  CR16  0  -0.455  -1.4523  -1.0504  -0.6409
 WCU  O15  O  O     0  -0.489  -3.9013  -1.0282  -0.7285
 WCU  C16  C  CH2   0   0.067  -4.8692  -0.3617   0.0750
 WCU  O17  O  O     0  -0.493  -4.2160   0.7377   0.6856
 WCU  H1   H  HCR6  0   0.266   0.3247   1.1453   1.2644
 WCU  H3   H  HCR6  0   0.246   3.3490   2.9170  -1.1792
 WCU  H4   H  HCR6  0   0.260   1.2546   1.6096  -1.2392
 WCU  H5   H  HCR6  0   0.254   5.3514  -0.4233   0.6082
 WCU  H6   H  HNH2  0   0.374   2.3371  -2.3564   0.9339
 WCU  H7   H  HNH2  0   0.378   3.9678  -2.2749   1.2854
 WCU  H8   H  HNH1  0   0.392   0.9438  -1.7010  -0.9697
 WCU  H9   H  HCR6  0   0.270  -1.9365   1.9554   1.8114
 WCU  H10  H  HCR6  0   0.275  -1.3289  -1.8759  -1.3310
 WCU  H11  H  HCH2  0   0.244  -5.6861  -0.0074  -0.5533
 WCU  H13  H  HCH2  0   0.227  -5.2461  -1.0493   0.8415
 WCU  H2   H  HCR6  0   0.249   5.4076   1.8791  -0.2480

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
 WCU  O15  C13  single    1.355  0.020  1.355
 WCU  O15  C16  single    1.424  0.020  1.424
 WCU  C14  C13  aromatic  1.372  0.020  1.372
 WCU  C14  C09  aromatic  1.409  0.020  1.409
 WCU  C13  C12  aromatic  1.384  0.020  1.384
 WCU  N08  C09  single    1.386  0.020  1.386
 WCU  N08  C04  single    1.409  0.020  1.409
 WCU  C09  C10  aromatic  1.396  0.020  1.396
 WCU  C04  C03  aromatic  1.391  0.020  1.391
 WCU  C04  C05  aromatic  1.407  0.020  1.407
 WCU  C03  C02  aromatic  1.387  0.020  1.387
 WCU  C12  O17  single    1.365  0.020  1.365
 WCU  C12  C11  aromatic  1.371  0.020  1.371
 WCU  N07  C05  single    1.379  0.020  1.379
 WCU  C05  C06  aromatic  1.399  0.020  1.399
 WCU  C10  C11  aromatic  1.399  0.020  1.399
 WCU  C02  C01  aromatic  1.389  0.020  1.389
 WCU  C06  C01  aromatic  1.385  0.020  1.385
 WCU  C10  H1   single    0.930  0.020  1.080
 WCU  C01  H2   single    0.930  0.020  1.080
 WCU  C02  H3   single    0.930  0.020  1.080
 WCU  C03  H4   single    0.930  0.020  1.080
 WCU  C06  H5   single    0.930  0.020  1.080
 WCU  N07  H6   single    0.890  0.020  1.040
 WCU  N07  H7   single    0.890  0.020  1.040
 WCU  N08  H8   single    0.890  0.020  1.040
 WCU  C11  H9   single    0.930  0.020  1.080
 WCU  C14  H10  single    0.930  0.020  1.080
 WCU  C16  H11  single    0.970  0.020  1.090
 WCU  O17  C16  single    1.417  0.020  1.417
 WCU  C16  H13  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
 WCU  H1   C10  C11  118.58  3.000
 WCU  H1   C10  C09  119.87  3.000
 WCU  C11  C10  C09  121.54  3.000
 WCU  O15  C13  C14  127.98  3.000
 WCU  C14  C13  C12  122.63  3.000
 WCU  O15  C13  C12  109.36  3.000
 WCU  H2   C01  C06  119.42  3.000
 WCU  H2   C01  C02  120.19  3.000
 WCU  C06  C01  C02  120.39  3.000
 WCU  H3   C02  C03  120.16  3.000
 WCU  H3   C02  C01  120.71  3.000
 WCU  C03  C02  C01  119.12  3.000
 WCU  H4   C03  C04  118.97  3.000
 WCU  H4   C03  C02  119.84  3.000
 WCU  C04  C03  C02  121.19  3.000
 WCU  N08  C04  C05  117.76  3.000
 WCU  C05  C04  C03  119.79  3.000
 WCU  N08  C04  C03  122.44  3.000
 WCU  N07  C05  C06  121.25  3.000
 WCU  C06  C05  C04  118.48  3.000
 WCU  N07  C05  C04  120.21  3.000
 WCU  H5   C06  C05  119.09  3.000
 WCU  H5   C06  C01  119.89  3.000
 WCU  C05  C06  C01  121.01  3.000
 WCU  H7   N07  H6   111.82  3.000
 WCU  H7   N07  C05  115.05  3.000
 WCU  H6   N07  C05  114.74  3.000
 WCU  H8   N08  C09  115.09  3.000
 WCU  H8   N08  C04  115.35  3.000
 WCU  C09  N08  C04  124.37  3.000
 WCU  C14  C09  N08  118.35  3.000
 WCU  N08  C09  C10  121.86  3.000
 WCU  C14  C09  C10  119.74  3.000
 WCU  H9   C11  C12  121.88  3.000
 WCU  H9   C11  C10  120.36  3.000
 WCU  C12  C11  C10  117.75  3.000
 WCU  O17  C12  C11  129.78  3.000
 WCU  C11  C12  C13  120.91  3.000
 WCU  O17  C12  C13  109.29  3.000
 WCU  H10  C14  C09  121.11  3.000
 WCU  H10  C14  C13  121.46  3.000
 WCU  C09  C14  C13  117.43  3.000
 WCU  C16  O15  C13  105.73  3.000
 WCU  H13  C16  H11  110.44  3.000
 WCU  H13  C16  O17  110.10  3.000
 WCU  H11  C16  O17  109.98  3.000
 WCU  H13  C16  O15  109.55  3.000
 WCU  O17  C16  O15  107.04  3.000
 WCU  H11  C16  O15  109.66  3.000
 WCU  C16  O17  C12  105.45  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
 WCU  CONST_01  C13  C14  C09  C10    0.00   0.0  0
 WCU  CONST_02  C13  C12  C11  C10    0.00   0.0  0
 WCU  CONST_03  C04  C03  C02  C01    0.00   0.0  0
 WCU  CONST_04  C04  C05  C06  C01    0.00   0.0  0
 WCU  CONST_05  C05  C04  C03  C02    0.00   0.0  0
 WCU  CONST_06  C05  C06  C01  C02    0.00   0.0  0
 WCU  CONST_07  C06  C05  C04  C03    0.00   0.0  0
 WCU  CONST_08  C06  C01  C02  C03    0.00   0.0  0
 WCU  CONST_09  C12  C13  C14  C09    0.00   0.0  0
 WCU  CONST_10  C12  C11  C10  C09    0.00   0.0  0
 WCU  CONST_11  C14  C13  C12  C11    0.00   0.0  0
 WCU  CONST_12  C14  C09  C10  C11    0.00   0.0  0
 WCU  CONST_13  N08  C09  C14  C13  180.00   0.0  0
 WCU  CONST_14  N07  C05  C06  C01  180.00   0.0  0
 WCU  CONST_15  N08  C04  C03  C02  180.00   0.0  0
 WCU  CONST_16  N07  C05  C04  C03  180.00   0.0  0
 WCU  CONST_17  N08  C04  C05  C06  180.00   0.0  0
 WCU  CONST_18  C11  C10  C09  N08  180.00   0.0  0
 WCU  CONST_19  H10  C14  C09  C10  180.00   0.0  0
 WCU  CONST_20  H9   C11  C12  C13  180.00   0.0  0
 WCU  CONST_21  H4   C03  C02  C01  180.00   0.0  0
 WCU  CONST_22  H5   C06  C01  C02  180.00   0.0  0
 WCU  CONST_23  H2   C01  C02  C03  180.00   0.0  0
 WCU  CONST_24  H3   C02  C03  C04  180.00   0.0  0
 WCU  CONST_25  H1   C10  C11  C12  180.00   0.0  0
 WCU  Var_01    O17  C16  O15  C13   17.06  30.0  1
 WCU  Var_02    O15  C16  O17  C12  -17.34  30.0  1
 WCU  Var_03    C04  N08  C09  C10  -29.41  30.0  2
 WCU  Var_04    C09  N08  C04  C03  -40.61  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
 WCU  plan-1  C01  0.020
 WCU  plan-1  C02  0.020
 WCU  plan-1  C03  0.020
 WCU  plan-1  C04  0.020
 WCU  plan-1  C05  0.020
 WCU  plan-1  C06  0.020
 WCU  plan-1  N07  0.020
 WCU  plan-1  N08  0.020
 WCU  plan-1  H3   0.020
 WCU  plan-1  H4   0.020
 WCU  plan-1  H5   0.020
 WCU  plan-1  H2   0.020
 WCU  plan-2  C10  0.020
 WCU  plan-2  C13  0.020
 WCU  plan-2  N08  0.020
 WCU  plan-2  C09  0.020
 WCU  plan-2  C11  0.020
 WCU  plan-2  C12  0.020
 WCU  plan-2  C14  0.020
 WCU  plan-2  O15  0.020
 WCU  plan-2  O17  0.020
 WCU  plan-2  H1   0.020
 WCU  plan-2  H9   0.020
 WCU  plan-2  H10  0.020
 WCU  plan-3  C05  0.020
 WCU  plan-3  N07  0.020
 WCU  plan-3  H6   0.020
 WCU  plan-3  H7   0.020

