# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 22:51:11 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: [(2~{S})-3-(1~{H}-indol-3-yl)-1-[(2~{E})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylidene]hydrazinyl]-1-oxidanylidene-propan-2-yl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(\C=N\NC(=O)[C@@H]([NH3+])Cc2c[nH]c3ccccc23)c1O
#
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
 EWE  EWE  '[(2~{S})-3-(1~{H}-indol-3-yl)-1-[(2~{E})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylidene]hydrazinyl]-1-oxidanylidene-propan-2-yl]azanium'  ligand  54  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EWE
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
 EWE  C1    C  CR15  0  -0.048   -5.0051   2.3843   0.0723
 EWE  C10   C  CR5   0  -0.042   -4.9033   1.0520   0.3698
 EWE  C11   C  CR56  0   0.362   -7.1039   1.6522   0.2139
 EWE  C12   C  CR56  0   0.014   -6.2468   0.5584   0.4650
 EWE  C13   C  CR16  0  -0.381   -6.8051  -0.6952   0.7475
 EWE  C14   C  CR16  0  -0.260   -8.1793  -0.8230   0.7660
 EWE  C15   C  CR16  0  -0.283   -9.0139   0.2780   0.5097
 EWE  C16   C  CR16  0  -0.299   -8.4919   1.5264   0.2332
 EWE  C2    C  CR6   0   0.135    3.8978  -3.4727   0.4513
 EWE  C2A   C  CH3   0  -0.721    3.9056  -4.9590   0.6254
 EWE  C3    C  CR6   0   0.294    2.6870  -2.7963   0.2093
 EWE  C4    C  CR6   0  -0.005    2.7050  -1.4051   0.0449
 EWE  C4A   C  C1    0   0.031    1.4828  -0.6609  -0.2219
 EWE  C5    C  CR6   0  -0.074    3.9412  -0.7377   0.1342
 EWE  C5A   C  CH2   0  -0.216    4.0026   0.7558  -0.0316
 EWE  C6    C  CR16  0  -0.139    5.0687  -1.4952   0.3748
 EWE  C7    C  C     0   0.587   -1.9362  -1.1861  -0.6288
 EWE  C8    C  CH1   0  -0.256   -3.1063  -0.2372  -0.8325
 EWE  C9    C  CH2   0  -0.552   -3.6491   0.2575   0.5167
 EWE  N1    N  N     0  -0.399    5.0394  -2.8200   0.5267
 EWE  N11   N  NT3   1  -0.786   -4.1552  -0.9705  -1.5786
 EWE  N2    N  NR15  0  -0.679   -6.3148   2.7410  -0.0186
 EWE  N4A   N  N     0  -0.281    0.3629  -1.2670  -0.2848
 EWE  O1P   O  O     0  -0.707    4.7507   3.7378   0.3604
 EWE  O2P   O  OH1   0  -0.737    5.8775   2.8468  -1.6995
 EWE  O3P   O  OH1   0  -0.727    7.1621   2.6899   0.5304
 EWE  O4    O  O     0  -0.428   -2.0957  -2.3818  -0.5153
 EWE  O4P   O  O2    0  -0.592    5.3330   1.2001   0.1917
 EWE  P     P  P     0   1.464    5.7092   2.7251  -0.1169
 EWE  H1    H  HCR5  0   0.294   -4.2240   3.1134  -0.0767
 EWE  H13   H  HCR6  0   0.246   -6.1762  -1.5523   0.9595
 EWE  H14   H  HCR6  0   0.252   -8.6242  -1.7848   0.9855
 EWE  H15   H  HCR6  0   0.254  -10.0876   0.1453   0.5325
 EWE  H16   H  HCR6  0   0.264   -9.1373   2.3739   0.0407
 EWE  H2A1  H  HCH3  0   0.250    3.5545  -5.4703  -0.2729
 EWE  H2A2  H  HCH3  0   0.250    4.9163  -5.2993   0.8391
 EWE  H2A3  H  HCH3  0   0.249    3.2564  -5.2732   1.4443
 EWE  H4A   H  H     0   0.279    1.5424   0.4156  -0.3719
 EWE  H5A1  H  HCH2  0   0.262    3.6698   1.0282  -1.0393
 EWE  H5A2  H  HCH2  0   0.266    3.3318   1.2449   0.6803
 EWE  H6    H  HCR6  0   0.263    6.0439  -1.0336   0.4519
 EWE  H8    H  HCH1  0   0.353   -2.8287   0.6147  -1.4538
 EWE  H9    H  HCH2  0   0.304   -2.8631   0.8580   0.9771
 EWE  H91   H  HCH2  0   0.289   -3.8096  -0.5945   1.1829
 EWE  HN11  H  HNT3  0   0.466   -4.4095  -1.8515  -1.1275
 EWE  HN13  H  HNT3  0   0.484   -5.0017  -0.4027  -1.6633
 EWE  HN12  H  HNT3  0   0.489   -3.8629  -1.1986  -2.5302
 EWE  HN2   H  HNR5  0   0.415   -6.6432   3.6711  -0.2196
 EWE  HN3   H  HNH1  0   0.433   -0.6759   0.4461  -0.6864
 EWE  H2    H  HOH1  0   0.498    6.5371   2.2642  -2.0999
 EWE  HO3   H  HOH1  0   0.482    0.8059  -2.9503  -0.0139
 EWE  H3    H  HOH1  0   0.507    7.5898   3.5549   0.5914
 EWE  N3    N  NH1   0  -0.503   -0.7446  -0.5562  -0.5420
 EWE  O3    O  OH1   0  -0.621    1.5800  -3.5326   0.1472

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
 EWE  N1   C6    aromatic  1.334  0.020  1.334
 EWE  N1   C2    aromatic  1.317  0.020  1.317
 EWE  C6   C5    aromatic  1.379  0.020  1.379
 EWE  C2A  C2    single    1.497  0.020  1.497
 EWE  C2   C3    aromatic  1.408  0.020  1.408
 EWE  C5   C5A   single    1.504  0.020  1.504
 EWE  C5   C4    aromatic  1.408  0.020  1.408
 EWE  C5A  O4P   single    1.420  0.020  1.420
 EWE  C3   C4    aromatic  1.401  0.020  1.401
 EWE  C3   O3    single    1.331  0.020  1.331
 EWE  C4   C4A   single    1.456  0.020  1.456
 EWE  O4P  P     single    1.601  0.020  1.601
 EWE  O1P  P     double    1.474  0.020  1.474
 EWE  P    O3P   single    1.591  0.020  1.591
 EWE  P    O2P   single    1.596  0.020  1.596
 EWE  C4A  N4A   double    1.275  0.020  1.275
 EWE  N4A  N3    single    1.341  0.020  1.341
 EWE  N3   C7    single    1.351  0.020  1.351
 EWE  O4   C7    double    1.212  0.020  1.212
 EWE  N2   C1    aromatic  1.360  0.020  1.360
 EWE  N2   C11   aromatic  1.365  0.020  1.365
 EWE  C7   C8    single    1.520  0.020  1.520
 EWE  C1   C10   aromatic  1.369  0.020  1.369
 EWE  N11  C8    single    1.481  0.020  1.481
 EWE  C11  C16   aromatic  1.394  0.020  1.394
 EWE  C11  C12   aromatic  1.412  0.020  1.412
 EWE  C16  C15   aromatic  1.381  0.020  1.381
 EWE  C8   C9    single    1.536  0.020  1.536
 EWE  C10  C12   aromatic  1.434  0.020  1.434
 EWE  C10  C9    single    1.492  0.020  1.492
 EWE  C12  C13   aromatic  1.401  0.020  1.401
 EWE  C15  C14   aromatic  1.405  0.020  1.405
 EWE  C13  C14   aromatic  1.380  0.020  1.380
 EWE  C1   H1    single    0.930  0.020  1.080
 EWE  C13  H13   single    0.930  0.020  1.080
 EWE  C14  H14   single    0.930  0.020  1.080
 EWE  C15  H15   single    0.930  0.020  1.080
 EWE  C16  H16   single    0.930  0.020  1.080
 EWE  C2A  H2A1  single    0.970  0.020  1.090
 EWE  C2A  H2A2  single    0.970  0.020  1.090
 EWE  C2A  H2A3  single    0.970  0.020  1.090
 EWE  C4A  H4A   single    0.930  0.020  1.080
 EWE  C5A  H5A1  single    0.970  0.020  1.090
 EWE  C5A  H5A2  single    0.970  0.020  1.090
 EWE  C6   H6    single    0.930  0.020  1.080
 EWE  C8   H8    single    0.970  0.020  1.090
 EWE  C9   H9    single    0.970  0.020  1.090
 EWE  C9   H91   single    0.970  0.020  1.090
 EWE  N11  HN11  single    0.890  0.020  1.040
 EWE  N11  HN13  single    0.890  0.020  1.040
 EWE  N11  HN12  single    0.890  0.020  1.040
 EWE  N2   HN2   single    0.860  0.020  1.020
 EWE  N3   HN3   single    0.860  0.020  1.020
 EWE  O2P  H2    single    0.850  0.020  0.980
 EWE  O3   HO3   single    0.850  0.020  0.980
 EWE  O3P  H3    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
 EWE  H1    C1   N2    120.71  3.000
 EWE  H1    C1   C10   129.34  3.000
 EWE  N2    C1   C10   109.95  3.000
 EWE  C9    C10  C12   126.70  3.000
 EWE  C9    C10  C1    127.02  3.000
 EWE  C12   C10  C1    106.24  3.000
 EWE  N2    C11  C16   130.55  3.000
 EWE  C16   C11  C12   122.15  3.000
 EWE  N2    C11  C12   107.30  3.000
 EWE  C13   C12  C11   119.14  3.000
 EWE  C13   C12  C10   133.99  3.000
 EWE  C11   C12  C10   106.87  3.000
 EWE  H13   C13  C14   120.12  3.000
 EWE  H13   C13  C12   121.04  3.000
 EWE  C14   C13  C12   118.84  3.000
 EWE  H14   C14  C15   119.29  3.000
 EWE  H14   C14  C13   119.62  3.000
 EWE  C15   C14  C13   121.09  3.000
 EWE  H15   C15  C16   119.34  3.000
 EWE  H15   C15  C14   119.30  3.000
 EWE  C16   C15  C14   121.35  3.000
 EWE  H16   C16  C15   121.20  3.000
 EWE  H16   C16  C11   121.37  3.000
 EWE  C15   C16  C11   117.43  3.000
 EWE  N1    C2   C3    121.14  3.000
 EWE  C3    C2   C2A   120.11  3.000
 EWE  N1    C2   C2A   118.75  3.000
 EWE  H2A3  C2A  H2A2  108.38  3.000
 EWE  H2A3  C2A  H2A1  106.93  3.000
 EWE  H2A2  C2A  H2A1  108.30  3.000
 EWE  H2A3  C2A  C2    111.73  3.000
 EWE  H2A2  C2A  C2    109.78  3.000
 EWE  H2A1  C2A  C2    111.58  3.000
 EWE  O3    C3   C4    123.68  3.000
 EWE  O3    C3   C2    117.23  3.000
 EWE  C4    C3   C2    119.09  3.000
 EWE  C5    C4   C4A   120.43  3.000
 EWE  C4A   C4   C3    121.22  3.000
 EWE  C5    C4   C3    118.34  3.000
 EWE  H4A   C4A  N4A   120.76  3.000
 EWE  H4A   C4A  C4    119.01  3.000
 EWE  N4A   C4A  C4    120.23  3.000
 EWE  C6    C5   C5A   122.09  3.000
 EWE  C5A   C5   C4    119.98  3.000
 EWE  C6    C5   C4    117.93  3.000
 EWE  H5A2  C5A  H5A1  107.53  3.000
 EWE  H5A2  C5A  O4P   109.41  3.000
 EWE  H5A1  C5A  O4P   110.57  3.000
 EWE  H5A2  C5A  C5    110.33  3.000
 EWE  H5A1  C5A  C5    109.63  3.000
 EWE  O4P   C5A  C5    109.37  3.000
 EWE  H6    C6   N1    115.81  3.000
 EWE  H6    C6   C5    121.00  3.000
 EWE  N1    C6   C5    123.19  3.000
 EWE  O4    C7   N3    124.78  3.000
 EWE  O4    C7   C8    121.82  3.000
 EWE  N3    C7   C8    113.36  3.000
 EWE  H8    C8   N11   106.26  3.000
 EWE  H8    C8   C9    109.81  3.000
 EWE  N11   C8   C9    110.59  3.000
 EWE  H8    C8   C7    111.60  3.000
 EWE  C9    C8   C7    110.81  3.000
 EWE  N11   C8   C7    107.67  3.000
 EWE  H91   C9   H9    106.12  3.000
 EWE  H91   C9   C8    109.63  3.000
 EWE  H9    C9   C8    107.06  3.000
 EWE  H91   C9   C10   110.58  3.000
 EWE  H9    C9   C10   110.74  3.000
 EWE  C8    C9   C10   112.46  3.000
 EWE  C6    N1   C2    120.31  3.000
 EWE  HN12  N11  HN13  106.48  3.000
 EWE  HN12  N11  HN11  106.86  3.000
 EWE  HN13  N11  HN11  108.01  3.000
 EWE  HN12  N11  C8    112.16  3.000
 EWE  HN13  N11  C8    110.66  3.000
 EWE  HN11  N11  C8    112.37  3.000
 EWE  HN2   N2   C11   125.64  3.000
 EWE  HN2   N2   C1    124.72  3.000
 EWE  C11   N2   C1    109.64  3.000
 EWE  N3    N4A  C4A   118.88  3.000
 EWE  H2    O2P  P     115.89  3.000
 EWE  H3    O3P  P     114.19  3.000
 EWE  P     O4P  C5A   119.20  3.000
 EWE  O4P   P    O3P    96.61  3.000
 EWE  O3P   P    O2P   107.99  3.000
 EWE  O4P   P    O2P   106.77  3.000
 EWE  O2P   P    O1P   109.71  3.000
 EWE  O3P   P    O1P   118.51  3.000
 EWE  O4P   P    O1P   116.06  3.000
 EWE  HN3   N3   N4A   119.66  3.000
 EWE  HN3   N3   C7    120.74  3.000
 EWE  N4A   N3   C7    119.59  3.000
 EWE  HO3   O3   C3    109.59  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
 EWE  CONST_01  C16   C11  N2   C1   180.00   0.0  0
 EWE  CONST_02  C12   C11  N2   C1     0.00   0.0  0
 EWE  CONST_03  C11   C12  C10  C1     0.00   0.0  0
 EWE  CONST_04  C13   C12  C10  C1   180.00   0.0  0
 EWE  CONST_05  C11   N2   C1   C10    0.00   0.0  0
 EWE  CONST_06  N2    C11  C12  C10    0.00   0.0  0
 EWE  CONST_07  C16   C11  C12  C10  180.00   0.0  0
 EWE  CONST_08  C14   C13  C12  C10  180.00   0.0  0
 EWE  CONST_09  C14   C15  C16  C11    0.00   0.0  0
 EWE  CONST_10  C14   C13  C12  C11    0.00   0.0  0
 EWE  CONST_11  C15   C16  C11  C12    0.00   0.0  0
 EWE  CONST_12  N2    C1   C10  C12    0.00   0.0  0
 EWE  CONST_13  C15   C14  C13  C12    0.00   0.0  0
 EWE  CONST_14  N2    C11  C12  C13  180.00   0.0  0
 EWE  CONST_15  C16   C11  C12  C13    0.00   0.0  0
 EWE  CONST_16  C16   C15  C14  C13    0.00   0.0  0
 EWE  CONST_17  N2    C11  C16  C15  180.00   0.0  0
 EWE  CONST_18  C5    C6   N1   C2     0.00   0.0  0
 EWE  CONST_19  C5    C4   C3   C2     0.00   0.0  0
 EWE  CONST_20  C6    N1   C2   C3     0.00   0.0  0
 EWE  CONST_21  C6    C5   C4   C3     0.00   0.0  0
 EWE  CONST_22  N1    C6   C5   C4     0.00   0.0  0
 EWE  CONST_23  N1    C2   C3   C4     0.00   0.0  0
 EWE  CONST_24  C9    C10  C12  C11  180.00   0.0  0
 EWE  CONST_25  C9    C10  C12  C13    0.00   0.0  0
 EWE  CONST_26  C4A   C4   C3   C2   180.00   0.0  0
 EWE  CONST_27  C6    N1   C2   C2A  180.00   0.0  0
 EWE  CONST_28  C4    C3   C2   C2A  180.00   0.0  0
 EWE  CONST_29  C5A   C5   C4   C3   180.00   0.0  0
 EWE  CONST_30  C6    C5   C4   C4A  180.00   0.0  0
 EWE  CONST_31  O3    C3   C4   C5   180.00   0.0  0
 EWE  CONST_32  N1    C6   C5   C5A  180.00   0.0  0
 EWE  CONST_33  N2    C1   C10  C9   180.00   0.0  0
 EWE  CONST_34  O3    C3   C2   N1   180.00   0.0  0
 EWE  CONST_35  HN2   N2   C1   C10  180.00   0.0  0
 EWE  CONST_36  H13   C13  C12  C10    0.00   0.0  0
 EWE  CONST_37  H1    C1   N2   C11  180.00   0.0  0
 EWE  CONST_38  H15   C15  C16  C11  180.00   0.0  0
 EWE  CONST_39  H16   C16  C11  C12  180.00   0.0  0
 EWE  CONST_40  H14   C14  C13  C12  180.00   0.0  0
 EWE  CONST_41  H6    C6   N1   C2   180.00   0.0  0
 EWE  CONST_42  N4A   N3   C7   C8   180.00   0.0  0
 EWE  CONST_43  O4    C7   N3   N4A    0.00   0.0  0
 EWE  CONST_44  HN3   N3   C7   C8     0.00   0.0  0
 EWE  Var_01    C8    C9   C10  C1   -83.68  30.0  2
 EWE  Var_02    N4A   C4A  C4   C3     1.38  30.0  2
 EWE  Var_03    O4P   C5A  C5   C4   175.99  30.0  2
 EWE  Var_04    H2A1  C2A  C2   C3    62.00  30.0  2
 EWE  Var_05    C7    N3   N4A  C4A  179.16  30.0  3
 EWE  Var_06    O1P   P    O4P  C5A   44.67  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
 EWE  chir_01  C8  C7  N11  C9  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
 EWE  plan-1  C2   0.020
 EWE  plan-1  C2A  0.020
 EWE  plan-1  C3   0.020
 EWE  plan-1  C4   0.020
 EWE  plan-1  C4A  0.020
 EWE  plan-1  C5   0.020
 EWE  plan-1  C5A  0.020
 EWE  plan-1  C6   0.020
 EWE  plan-1  N1   0.020
 EWE  plan-1  H6   0.020
 EWE  plan-1  O3   0.020
 EWE  plan-2  C1   0.020
 EWE  plan-2  C10  0.020
 EWE  plan-2  C11  0.020
 EWE  plan-2  C12  0.020
 EWE  plan-2  C13  0.020
 EWE  plan-2  C14  0.020
 EWE  plan-2  C15  0.020
 EWE  plan-2  C16  0.020
 EWE  plan-2  C9   0.020
 EWE  plan-2  N2   0.020
 EWE  plan-2  H1   0.020
 EWE  plan-2  H13  0.020
 EWE  plan-2  H14  0.020
 EWE  plan-2  H15  0.020
 EWE  plan-2  H16  0.020
 EWE  plan-2  HN2  0.020
 EWE  plan-3  C7   0.020
 EWE  plan-3  C8   0.020
 EWE  plan-3  N4A  0.020
 EWE  plan-3  O4   0.020
 EWE  plan-3  HN3  0.020
 EWE  plan-3  N3   0.020
 EWE  plan-4  C4   0.020
 EWE  plan-4  C4A  0.020
 EWE  plan-4  N4A  0.020
 EWE  plan-4  H4A  0.020
 EWE  plan-4  N3   0.020

