# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 14:07:35 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 4-{(E)-[4-(hydroxymethyl)phenyl]diazenyl}benzyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1ccc(cc1)N=Nc2ccc(CO[P](O)(O)=O)cc2
#
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
 AZW  AZW  '4-{(E)-[4-(hydroxymethyl)phenyl]diazenyl}benzyl dihydrogen phosphate'  ligand  37  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AZW
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
 AZW  P     P  P     0   1.459  -5.9777  -0.5060   0.2598
 AZW  OP1   O  O     0  -0.710  -6.9882   0.4655  -0.1969
 AZW  OP2   O  OH1   0  -0.740  -5.9911  -1.7844  -0.7006
 AZW  O5'   O  O2    0  -0.584  -4.4664   0.0077   0.3217
 AZW  C5'   C  CH2   0  -0.255  -3.9101   0.7054  -0.8046
 AZW  C1A   C  CR6   0   0.083  -2.4206   0.6916  -0.6542
 AZW  C2A   C  CR16  0  -0.285  -1.7348   1.8448  -0.2989
 AZW  C6A   C  CR16  0  -0.268  -1.7049  -0.4923  -0.8488
 AZW  C3A   C  CR16  0  -0.271  -0.3564   1.8221  -0.1440
 AZW  C5A   C  CR16  0  -0.258  -0.3336  -0.5241  -0.6976
 AZW  C4A   C  CR6   0   0.221   0.3513   0.6420  -0.3412
 AZW  N5A   N  N     0  -0.266   1.7425   0.7325  -0.1577
 AZW  C1B   C  CR6   0   0.045   6.5448  -0.2813   0.1063
 AZW  C2B   C  CR16  0  -0.282   5.8568  -1.4084  -0.3337
 AZW  C6B   C  CR16  0  -0.283   5.8193   0.8738   0.4053
 AZW  C3B   C  CR16  0  -0.268   4.4805  -1.3835  -0.4815
 AZW  C5B   C  CR16  0  -0.253   4.4446   0.9051   0.2626
 AZW  C4B   C  CR6   0   0.210   3.7628  -0.2274  -0.1874
 AZW  N5B   N  N     0  -0.260   2.3736  -0.3113  -0.3721
 AZW  O3'   O  OH1   0  -0.665   8.4946   0.6282   1.1386
 AZW  H2    H  HOH1  0   0.495  -5.4053  -2.5101  -0.4462
 AZW  H5'   H  HCH2  0   0.257  -4.2006   0.2202  -1.7403
 AZW  H5''  H  HCH2  0   0.264  -4.2854   1.7297  -0.8236
 AZW  H2A   H  HCR6  0   0.266  -2.2771   2.7688  -0.1400
 AZW  H6A   H  HCR6  0   0.262  -2.2280  -1.3982  -1.1306
 AZW  H3A   H  HCR6  0   0.269   0.1813   2.7193   0.1338
 AZW  H5A   H  HCR6  0   0.271   0.2100  -1.4453  -0.8572
 AZW  H2B   H  HCR6  0   0.258   6.4010  -2.3172  -0.5616
 AZW  H6B   H  HCR6  0   0.261   6.3304   1.7600   0.7554
 AZW  H3B   H  HCR6  0   0.266   3.9483  -2.2623  -0.8225
 AZW  H5B   H  HCR6  0   0.267   3.8982   1.8074   0.5019
 AZW  H3'   H  HCH2  0   0.217   8.3549  -1.3388   0.4771
 AZW  H3''  H  HCH2  0   0.230   8.4572  -0.1292  -0.7921
 AZW  H3    H  HOH1  0   0.462   9.4405   0.7447   1.0140
 AZW  OP3   O  OH1   0  -0.730  -6.0576  -1.0253   1.7636
 AZW  HOP3  H  HOH1  0   0.505  -6.9457  -1.2777   2.0499
 AZW  C3'   C  CH2   0  -0.187   8.0437  -0.3214   0.2069

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
 AZW  OP1  P     double    1.474  0.020  1.474
 AZW  P    OP2   single    1.599  0.020  1.599
 AZW  P    O5'   single    1.597  0.020  1.597
 AZW  C5'  O5'   single    1.437  0.020  1.437
 AZW  C5'  C1A   single    1.497  0.020  1.497
 AZW  C2A  C1A   aromatic  1.388  0.020  1.388
 AZW  C2A  C3A   aromatic  1.387  0.020  1.387
 AZW  C1A  C6A   aromatic  1.397  0.020  1.397
 AZW  C3A  C4A   aromatic  1.390  0.020  1.390
 AZW  C6A  C5A   aromatic  1.380  0.020  1.380
 AZW  C4A  C5A   aromatic  1.399  0.020  1.399
 AZW  C4A  N5A   single    1.406  0.020  1.406
 AZW  N5B  N5A   double    1.238  0.020  1.238
 AZW  N5B  C4B   single    1.404  0.020  1.404
 AZW  C3B  C4B   aromatic  1.392  0.020  1.392
 AZW  C3B  C2B   aromatic  1.384  0.020  1.384
 AZW  C4B  C5B   aromatic  1.396  0.020  1.396
 AZW  C2B  C1B   aromatic  1.392  0.020  1.392
 AZW  C5B  C6B   aromatic  1.382  0.020  1.382
 AZW  C1B  C6B   aromatic  1.396  0.020  1.396
 AZW  C1B  C3'   single    1.503  0.020  1.503
 AZW  O3'  C3'   single    1.405  0.020  1.405
 AZW  OP2  H2    single    0.850  0.020  0.980
 AZW  C5'  H5'   single    0.970  0.020  1.090
 AZW  C5'  H5''  single    0.970  0.020  1.090
 AZW  C2A  H2A   single    0.930  0.020  1.080
 AZW  C6A  H6A   single    0.930  0.020  1.080
 AZW  C3A  H3A   single    0.930  0.020  1.080
 AZW  C5A  H5A   single    0.930  0.020  1.080
 AZW  C2B  H2B   single    0.930  0.020  1.080
 AZW  C6B  H6B   single    0.930  0.020  1.080
 AZW  C3B  H3B   single    0.930  0.020  1.080
 AZW  C5B  H5B   single    0.930  0.020  1.080
 AZW  C3'  H3'   single    0.970  0.020  1.090
 AZW  C3'  H3''  single    0.970  0.020  1.090
 AZW  O3'  H3    single    0.850  0.020  0.980
 AZW  P    OP3   single    1.593  0.020  1.593
 AZW  OP3  HOP3  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
 AZW  OP3   P    O5'   96.64  3.000
 AZW  OP3   P    OP2  107.82  3.000
 AZW  O5'   P    OP2  106.76  3.000
 AZW  OP3   P    OP1  118.22  3.000
 AZW  O5'   P    OP1  116.65  3.000
 AZW  OP2   P    OP1  109.58  3.000
 AZW  H2    OP2  P    115.92  3.000
 AZW  C5'   O5'  P    119.47  3.000
 AZW  H5''  C5'  H5'  108.08  3.000
 AZW  H5''  C5'  C1A  110.64  3.000
 AZW  H5'   C5'  C1A  110.26  3.000
 AZW  H5''  C5'  O5'  109.65  3.000
 AZW  H5'   C5'  O5'  110.64  3.000
 AZW  C1A   C5'  O5'  107.57  3.000
 AZW  C6A   C1A  C2A  119.12  3.000
 AZW  C6A   C1A  C5'  120.23  3.000
 AZW  C2A   C1A  C5'  120.64  3.000
 AZW  H2A   C2A  C3A  119.68  3.000
 AZW  H2A   C2A  C1A  119.94  3.000
 AZW  C3A   C2A  C1A  120.39  3.000
 AZW  H6A   C6A  C5A  119.28  3.000
 AZW  H6A   C6A  C1A  119.83  3.000
 AZW  C5A   C6A  C1A  120.89  3.000
 AZW  H3A   C3A  C4A  119.16  3.000
 AZW  H3A   C3A  C2A  120.58  3.000
 AZW  C4A   C3A  C2A  120.26  3.000
 AZW  H5A   C5A  C4A  120.12  3.000
 AZW  H5A   C5A  C6A  120.20  3.000
 AZW  C4A   C5A  C6A  119.69  3.000
 AZW  N5A   C4A  C5A  124.85  3.000
 AZW  N5A   C4A  C3A  115.50  3.000
 AZW  C5A   C4A  C3A  119.65  3.000
 AZW  N5B   N5A  C4A  115.30  3.000
 AZW  C3'   C1B  C6B  121.73  3.000
 AZW  C3'   C1B  C2B  119.51  3.000
 AZW  C6B   C1B  C2B  118.73  3.000
 AZW  H2B   C2B  C3B  119.46  3.000
 AZW  H2B   C2B  C1B  119.84  3.000
 AZW  C3B   C2B  C1B  120.70  3.000
 AZW  H6B   C6B  C5B  119.00  3.000
 AZW  H6B   C6B  C1B  120.11  3.000
 AZW  C5B   C6B  C1B  120.88  3.000
 AZW  H3B   C3B  C4B  119.16  3.000
 AZW  H3B   C3B  C2B  120.52  3.000
 AZW  C4B   C3B  C2B  120.32  3.000
 AZW  H5B   C5B  C4B  120.08  3.000
 AZW  H5B   C5B  C6B  119.89  3.000
 AZW  C4B   C5B  C6B  120.03  3.000
 AZW  N5B   C4B  C5B  125.03  3.000
 AZW  C5B   C4B  C3B  119.33  3.000
 AZW  N5B   C4B  C3B  115.64  3.000
 AZW  C4B   N5B  N5A  115.54  3.000
 AZW  H3    O3'  C3'  108.17  3.000
 AZW  HOP3  OP3  P    114.26  3.000
 AZW  H3''  C3'  H3'  106.22  3.000
 AZW  H3''  C3'  O3'  111.36  3.000
 AZW  H3'   C3'  O3'  111.86  3.000
 AZW  H3''  C3'  C1B  108.05  3.000
 AZW  H3'   C3'  C1B  108.90  3.000
 AZW  O3'   C3'  C1B  110.28  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
 AZW  CONST_01  C4A  C3A  C2A  C1A     0.00   0.0  0
 AZW  CONST_02  C4A  C5A  C6A  C1A     0.00   0.0  0
 AZW  CONST_03  C5A  C6A  C1A  C2A     0.00   0.0  0
 AZW  CONST_04  C5A  C4A  C3A  C2A     0.00   0.0  0
 AZW  CONST_05  C3A  C2A  C1A  C6A     0.00   0.0  0
 AZW  CONST_06  C3A  C4A  C5A  C6A     0.00   0.0  0
 AZW  CONST_07  C4B  C3B  C2B  C1B     0.00   0.0  0
 AZW  CONST_08  C4B  C5B  C6B  C1B     0.00   0.0  0
 AZW  CONST_09  C5B  C4B  C3B  C2B     0.00   0.0  0
 AZW  CONST_10  C5B  C6B  C1B  C2B     0.00   0.0  0
 AZW  CONST_11  C3B  C4B  C5B  C6B     0.00   0.0  0
 AZW  CONST_12  C3B  C2B  C1B  C6B     0.00   0.0  0
 AZW  CONST_13  C3A  C2A  C1A  C5'   180.00   0.0  0
 AZW  CONST_14  C5A  C6A  C1A  C5'   180.00   0.0  0
 AZW  CONST_15  N5A  C4A  C3A  C2A   180.00   0.0  0
 AZW  CONST_16  N5A  C4A  C5A  C6A   180.00   0.0  0
 AZW  CONST_17  N5B  C4B  C3B  C2B   180.00   0.0  0
 AZW  CONST_18  N5B  C4B  C5B  C6B   180.00   0.0  0
 AZW  CONST_19  C3'  C1B  C2B  C3B   180.00   0.0  0
 AZW  CONST_20  C3'  C1B  C6B  C5B   180.00   0.0  0
 AZW  CONST_21  H3A  C3A  C2A  C1A   180.00   0.0  0
 AZW  CONST_22  H5A  C5A  C6A  C1A   180.00   0.0  0
 AZW  CONST_23  H6A  C6A  C1A  C2A   180.00   0.0  0
 AZW  CONST_24  H2A  C2A  C1A  C6A   180.00   0.0  0
 AZW  CONST_25  H3B  C3B  C2B  C1B   180.00   0.0  0
 AZW  CONST_26  H5B  C5B  C6B  C1B   180.00   0.0  0
 AZW  CONST_27  H6B  C6B  C1B  C2B   180.00   0.0  0
 AZW  CONST_28  H2B  C2B  C1B  C6B   180.00   0.0  0
 AZW  CONST_29  N5B  N5A  C4A  C3A   180.00   0.0  0
 AZW  CONST_30  N5B  N5A  C4A  C5A     0.00   0.0  0
 AZW  CONST_31  C3B  C4B  N5B  N5A   180.00   0.0  0
 AZW  CONST_32  C5B  C4B  N5B  N5A     0.00   0.0  0
 AZW  Var_01    C2A  C1A  C5'  O5'  -107.03  30.0  2
 AZW  Var_02    O3'  C3'  C1B  C2B  -155.89  30.0  2
 AZW  Var_03    C1A  C5'  O5'  P    -162.99  30.0  1
 AZW  Var_04    OP3  P    O5'  C5'  -174.49  30.0  1

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
 AZW  plan-1  C5'  0.020
 AZW  plan-1  C1A  0.020
 AZW  plan-1  C2A  0.020
 AZW  plan-1  C6A  0.020
 AZW  plan-1  C3A  0.020
 AZW  plan-1  C5A  0.020
 AZW  plan-1  C4A  0.020
 AZW  plan-1  N5A  0.020
 AZW  plan-1  C4B  0.020
 AZW  plan-1  N5B  0.020
 AZW  plan-1  H2A  0.020
 AZW  plan-1  H6A  0.020
 AZW  plan-1  H3A  0.020
 AZW  plan-1  H5A  0.020
 AZW  plan-2  N5A  0.020
 AZW  plan-2  C1B  0.020
 AZW  plan-2  C2B  0.020
 AZW  plan-2  C6B  0.020
 AZW  plan-2  C3B  0.020
 AZW  plan-2  C5B  0.020
 AZW  plan-2  C4B  0.020
 AZW  plan-2  N5B  0.020
 AZW  plan-2  H2B  0.020
 AZW  plan-2  H6B  0.020
 AZW  plan-2  H3B  0.020
 AZW  plan-2  H5B  0.020
 AZW  plan-2  C3'  0.020

