# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 01:32:24 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: {5-hydroxy-4-[(1E)-4-(1H-indol-3-yl)-3-oxobut-1-en-1-yl]-6-methylpyridin-3-yl}methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(\C=C\C(=O)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
 3SO  3SO  '{5-hydroxy-4-[(1E)-4-(1H-indol-3-yl)-3-oxobut-1-en-1-yl]-6-methylpyridin-3-yl}methyl dihydrogen phosphate'  ligand  47  28  .  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_3SO
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
 3SO  O01  O  OH1   0  -0.610   1.1346  -3.9214  -0.0876
 3SO  C02  C  CR6   0   0.250   2.1324  -3.0281  -0.1401
 3SO  C03  C  CR6   0   0.129   3.4489  -3.4141  -0.4400
 3SO  N04  N  N     0  -0.401   4.4297  -2.5315  -0.4820
 3SO  C05  C  CR16  0  -0.134   4.1786  -1.2507  -0.2285
 3SO  C06  C  CR6   0  -0.062   2.9188  -0.7767   0.0871
 3SO  C07  C  CH2   0  -0.213   2.6578   0.6763   0.3656
 3SO  O08  O  O2    0  -0.591   3.8590   1.4173   0.1947
 3SO  P09  P  P     0   1.464   3.8002   3.0162   0.2143
 3SO  O10  O  O     0  -0.707   3.0902   3.6320   1.3494
 3SO  O11  O  OH1   0  -0.728   5.3677   3.2603   0.0864
 3SO  O12  O  OH1   0  -0.740   3.1154   3.4640  -1.1566
 3SO  C13  C  CR6   0   0.099   1.8495  -1.6873   0.1282
 3SO  C14  C  C1    0  -0.242   0.5103  -1.2081   0.4729
 3SO  C15  C  C1    0  -0.330  -0.6597  -1.6554   0.0055
 3SO  C16  C  C     0   0.386  -1.9397  -1.0399   0.4295
 3SO  C17  C  CH2   0  -0.720  -3.1662  -1.6083  -0.2487
 3SO  C18  C  CR5   0   0.057  -4.4413  -0.9372   0.1092
 3SO  C19  C  CR15  0  -0.088  -5.4435  -1.4328   0.8931
 3SO  N20  N  NR15  0  -0.687  -6.4586  -0.5232   0.9895
 3SO  C21  C  CR56  0   0.352  -6.1395   0.5875   0.2644
 3SO  C22  C  CR56  0   0.040  -4.8671   0.3647  -0.3068
 3SO  C23  C  CR16  0  -0.376  -4.2972   1.3587  -1.1099
 3SO  C24  C  CR16  0  -0.271  -4.9985   2.5293  -1.3239
 3SO  C25  C  CR16  0  -0.284  -6.2632   2.7312  -0.7457
 3SO  C26  C  CR16  0  -0.306  -6.8500   1.7685   0.0532
 3SO  O27  O  O     0  -0.395  -1.9979  -0.1562   1.2565
 3SO  C28  C  CH3   0  -0.790   3.7710  -4.8504  -0.7263
 3SO  H1   H  HOH1  0   0.491   1.4613  -4.8179  -0.2249
 3SO  H2   H  HCR6  0   0.263   5.0273  -0.5824  -0.2851
 3SO  H3   H  HCH2  0   0.260   1.8783   1.0460  -0.3088
 3SO  H4   H  HCH2  0   0.267   2.2905   0.8060   1.3885
 3SO  H5   H  HOH1  0   0.506   5.6347   4.1781   0.2333
 3SO  H6   H  HOH1  0   0.498   3.5521   3.1640  -1.9653
 3SO  H7   H  H     0   0.276   0.4730  -0.3750   1.1693
 3SO  H8   H  H     0   0.273  -0.7217  -2.4554  -0.7196
 3SO  H9   H  HCH2  0   0.286  -2.9874  -1.5765  -1.3306
 3SO  H10  H  HCH2  0   0.300  -3.2024  -2.6766  -0.0068
 3SO  H11  H  HCR5  0   0.282  -5.5105  -2.3851   1.3963
 3SO  H12  H  HNR5  0   0.409  -7.3105  -0.6635   1.5060
 3SO  H13  H  HCR6  0   0.238  -3.3226   1.2138  -1.5607
 3SO  H14  H  HCR6  0   0.246  -4.5703   3.3057  -1.9446
 3SO  H15  H  HCR6  0   0.249  -6.7881   3.6599  -0.9300
 3SO  H16  H  HCR6  0   0.258  -7.8255   1.9279   0.4951
 3SO  H17  H  HCH3  0   0.261   3.1963  -5.2392  -1.5706
 3SO  H18  H  HCH3  0   0.275   4.8255  -4.9488  -0.9714
 3SO  H19  H  HCH3  0   0.260   3.5721  -5.4971   0.1326

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
 3SO  O10  P09  double    1.474  0.020  1.474
 3SO  O12  P09  single    1.596  0.020  1.596
 3SO  P09  O11  single    1.592  0.020  1.592
 3SO  P09  O08  single    1.600  0.020  1.600
 3SO  C05  N04  aromatic  1.330  0.020  1.330
 3SO  C05  C06  aromatic  1.383  0.020  1.383
 3SO  C07  O08  single    1.422  0.020  1.422
 3SO  C07  C06  single    1.502  0.020  1.502
 3SO  N04  C03  aromatic  1.320  0.020  1.320
 3SO  C06  C13  aromatic  1.405  0.020  1.405
 3SO  C03  C28  single    1.499  0.020  1.499
 3SO  C03  C02  aromatic  1.404  0.020  1.404
 3SO  C13  C02  aromatic  1.396  0.020  1.396
 3SO  C13  C14  single    1.463  0.020  1.463
 3SO  C02  O01  single    1.340  0.020  1.340
 3SO  C14  C15  double    1.337  0.020  1.337
 3SO  C15  C16  single    1.482  0.020  1.482
 3SO  C17  C16  single    1.512  0.020  1.512
 3SO  C17  C18  single    1.485  0.020  1.485
 3SO  C19  C18  aromatic  1.365  0.020  1.365
 3SO  C19  N20  aromatic  1.366  0.020  1.366
 3SO  C16  O27  double    1.212  0.020  1.212
 3SO  C18  C22  aromatic  1.432  0.020  1.432
 3SO  N20  C21  aromatic  1.364  0.020  1.364
 3SO  C22  C21  aromatic  1.412  0.020  1.412
 3SO  C22  C23  aromatic  1.399  0.020  1.399
 3SO  C21  C26  aromatic  1.394  0.020  1.394
 3SO  C23  C24  aromatic  1.381  0.020  1.381
 3SO  C26  C25  aromatic  1.382  0.020  1.382
 3SO  C24  C25  aromatic  1.405  0.020  1.405
 3SO  O01  H1   single    0.850  0.020  0.980
 3SO  C05  H2   single    0.930  0.020  1.080
 3SO  C07  H3   single    0.970  0.020  1.090
 3SO  C07  H4   single    0.970  0.020  1.090
 3SO  O11  H5   single    0.850  0.020  0.980
 3SO  O12  H6   single    0.850  0.020  0.980
 3SO  C14  H7   single    0.930  0.020  1.080
 3SO  C15  H8   single    0.930  0.020  1.080
 3SO  C17  H9   single    0.970  0.020  1.090
 3SO  C17  H10  single    0.970  0.020  1.090
 3SO  C19  H11  single    0.930  0.020  1.080
 3SO  N20  H12  single    0.860  0.020  1.020
 3SO  C23  H13  single    0.930  0.020  1.080
 3SO  C24  H14  single    0.930  0.020  1.080
 3SO  C25  H15  single    0.930  0.020  1.080
 3SO  C26  H16  single    0.930  0.020  1.080
 3SO  C28  H17  single    0.970  0.020  1.090
 3SO  C28  H18  single    0.970  0.020  1.090
 3SO  C28  H19  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
 3SO  H1   O01  C02  111.23  3.000
 3SO  C13  C02  C03  119.66  3.000
 3SO  C13  C02  O01  118.80  3.000
 3SO  C03  C02  O01  121.54  3.000
 3SO  C28  C03  N04  118.34  3.000
 3SO  C28  C03  C02  120.36  3.000
 3SO  N04  C03  C02  121.30  3.000
 3SO  C05  N04  C03  119.85  3.000
 3SO  H2   C05  C06  121.00  3.000
 3SO  H2   C05  N04  115.92  3.000
 3SO  C06  C05  N04  123.09  3.000
 3SO  C13  C06  C07  119.29  3.000
 3SO  C13  C06  C05  118.55  3.000
 3SO  C07  C06  C05  122.16  3.000
 3SO  H4   C07  H3   107.26  3.000
 3SO  H4   C07  O08  109.52  3.000
 3SO  H3   C07  O08  110.57  3.000
 3SO  H4   C07  C06  110.25  3.000
 3SO  H3   C07  C06  109.63  3.000
 3SO  O08  C07  C06  109.57  3.000
 3SO  P09  O08  C07  119.23  3.000
 3SO  O12  P09  O11  108.09  3.000
 3SO  O11  P09  O10  118.18  3.000
 3SO  O12  P09  O10  109.73  3.000
 3SO  O11  P09  O08   96.67  3.000
 3SO  O12  P09  O08  106.59  3.000
 3SO  O10  P09  O08  116.40  3.000
 3SO  H5   O11  P09  113.90  3.000
 3SO  H6   O12  P09  115.94  3.000
 3SO  C14  C13  C06  119.41  3.000
 3SO  C14  C13  C02  123.03  3.000
 3SO  C06  C13  C02  117.55  3.000
 3SO  H7   C14  C15  116.78  3.000
 3SO  H7   C14  C13  115.69  3.000
 3SO  C15  C14  C13  127.51  3.000
 3SO  H8   C15  C16  116.71  3.000
 3SO  H8   C15  C14  122.15  3.000
 3SO  C16  C15  C14  121.12  3.000
 3SO  O27  C16  C17  122.76  3.000
 3SO  O27  C16  C15  122.66  3.000
 3SO  C17  C16  C15  114.58  3.000
 3SO  H10  C17  H9   104.55  3.000
 3SO  H10  C17  C18  111.04  3.000
 3SO  H9   C17  C18  111.38  3.000
 3SO  H10  C17  C16  107.11  3.000
 3SO  H9   C17  C16  107.41  3.000
 3SO  C18  C17  C16  114.74  3.000
 3SO  C22  C18  C19  106.18  3.000
 3SO  C22  C18  C17  126.62  3.000
 3SO  C19  C18  C17  127.21  3.000
 3SO  H11  C19  N20  120.55  3.000
 3SO  H11  C19  C18  129.32  3.000
 3SO  N20  C19  C18  110.13  3.000
 3SO  H12  N20  C21  125.76  3.000
 3SO  H12  N20  C19  124.92  3.000
 3SO  C21  N20  C19  109.31  3.000
 3SO  C26  C21  C22  122.10  3.000
 3SO  C26  C21  N20  130.61  3.000
 3SO  C22  C21  N20  107.29  3.000
 3SO  C23  C22  C21  119.15  3.000
 3SO  C23  C22  C18  133.76  3.000
 3SO  C21  C22  C18  107.09  3.000
 3SO  H13  C23  C24  120.37  3.000
 3SO  H13  C23  C22  120.67  3.000
 3SO  C24  C23  C22  118.95  3.000
 3SO  H14  C24  C25  119.27  3.000
 3SO  H14  C24  C23  119.73  3.000
 3SO  C25  C24  C23  121.00  3.000
 3SO  H15  C25  C26  119.35  3.000
 3SO  H15  C25  C24  119.32  3.000
 3SO  C26  C25  C24  121.33  3.000
 3SO  H16  C26  C25  121.07  3.000
 3SO  H16  C26  C21  121.46  3.000
 3SO  C25  C26  C21  117.47  3.000
 3SO  H19  C28  H18  107.45  3.000
 3SO  H19  C28  H17  107.50  3.000
 3SO  H18  C28  H17  107.68  3.000
 3SO  H19  C28  C03  112.18  3.000
 3SO  H18  C28  C03  109.76  3.000
 3SO  H17  C28  C03  112.05  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
 3SO  CONST_01  C05  N04  C03  C02     0.00   0.0  0
 3SO  CONST_02  C05  C06  C13  C02     0.00   0.0  0
 3SO  CONST_03  C06  C05  N04  C03     0.00   0.0  0
 3SO  CONST_04  C06  C13  C02  C03     0.00   0.0  0
 3SO  CONST_05  C13  C06  C05  N04     0.00   0.0  0
 3SO  CONST_06  C13  C02  C03  N04     0.00   0.0  0
 3SO  CONST_07  C21  N20  C19  C18     0.00   0.0  0
 3SO  CONST_08  N20  C21  C22  C18     0.00   0.0  0
 3SO  CONST_09  C26  C21  C22  C18   180.00   0.0  0
 3SO  CONST_10  C24  C23  C22  C18   180.00   0.0  0
 3SO  CONST_11  C21  C22  C18  C19     0.00   0.0  0
 3SO  CONST_12  C23  C22  C18  C19   180.00   0.0  0
 3SO  CONST_13  C22  C21  N20  C19     0.00   0.0  0
 3SO  CONST_14  C26  C21  N20  C19   180.00   0.0  0
 3SO  CONST_15  C22  C18  C19  N20     0.00   0.0  0
 3SO  CONST_16  C23  C22  C21  N20   180.00   0.0  0
 3SO  CONST_17  C25  C26  C21  N20   180.00   0.0  0
 3SO  CONST_18  C24  C23  C22  C21     0.00   0.0  0
 3SO  CONST_19  C24  C25  C26  C21     0.00   0.0  0
 3SO  CONST_20  C25  C26  C21  C22     0.00   0.0  0
 3SO  CONST_21  C25  C24  C23  C22     0.00   0.0  0
 3SO  CONST_22  C26  C21  C22  C23     0.00   0.0  0
 3SO  CONST_23  C26  C25  C24  C23     0.00   0.0  0
 3SO  CONST_24  N04  C03  C02  O01   180.00   0.0  0
 3SO  CONST_25  C06  C13  C02  O01   180.00   0.0  0
 3SO  CONST_26  C07  C06  C13  C02   180.00   0.0  0
 3SO  CONST_27  C14  C13  C02  C03   180.00   0.0  0
 3SO  CONST_28  C07  C06  C05  N04   180.00   0.0  0
 3SO  CONST_29  C28  C03  N04  C05   180.00   0.0  0
 3SO  CONST_30  C14  C13  C06  C05   180.00   0.0  0
 3SO  CONST_31  C28  C03  C02  C13   180.00   0.0  0
 3SO  CONST_32  N20  C19  C18  C17   180.00   0.0  0
 3SO  CONST_33  C21  C22  C18  C17   180.00   0.0  0
 3SO  CONST_34  C23  C22  C18  C17     0.00   0.0  0
 3SO  CONST_35  H2   C05  N04  C03   180.00   0.0  0
 3SO  CONST_36  H12  N20  C19  C18   180.00   0.0  0
 3SO  CONST_37  H13  C23  C22  C18     0.00   0.0  0
 3SO  CONST_38  H16  C26  C21  N20     0.00   0.0  0
 3SO  CONST_39  H11  C19  N20  C21   180.00   0.0  0
 3SO  CONST_40  H15  C25  C26  C21   180.00   0.0  0
 3SO  CONST_41  H14  C24  C23  C22   180.00   0.0  0
 3SO  Var_01    C15  C14  C13  C02   -35.26  30.0  2
 3SO  Var_02    O08  C07  C06  C05     2.39  30.0  1
 3SO  Var_03    C19  C18  C17  C16  -107.80  30.0  2
 3SO  Var_04    H17  C28  C03  C02    58.33  30.0  2
 3SO  Var_05    C16  C15  C14  C13  -178.48   0.0  2
 3SO  Var_06    C18  C17  C16  C15  -176.33  30.0  1
 3SO  Var_07    O10  P09  O08  C07    50.33  30.0  1
 3SO  Var_08    C17  C16  C15  C14   176.70  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
 3SO  plan-1  O01  0.020
 3SO  plan-1  C02  0.020
 3SO  plan-1  C03  0.020
 3SO  plan-1  N04  0.020
 3SO  plan-1  C05  0.020
 3SO  plan-1  C06  0.020
 3SO  plan-1  C07  0.020
 3SO  plan-1  C13  0.020
 3SO  plan-1  C14  0.020
 3SO  plan-1  C28  0.020
 3SO  plan-1  H2   0.020
 3SO  plan-2  C17  0.020
 3SO  plan-2  C18  0.020
 3SO  plan-2  C19  0.020
 3SO  plan-2  N20  0.020
 3SO  plan-2  C21  0.020
 3SO  plan-2  C22  0.020
 3SO  plan-2  C23  0.020
 3SO  plan-2  C24  0.020
 3SO  plan-2  C25  0.020
 3SO  plan-2  C26  0.020
 3SO  plan-2  H11  0.020
 3SO  plan-2  H12  0.020
 3SO  plan-2  H13  0.020
 3SO  plan-2  H14  0.020
 3SO  plan-2  H15  0.020
 3SO  plan-2  H16  0.020
 3SO  plan-3  C15  0.020
 3SO  plan-3  C16  0.020
 3SO  plan-3  C17  0.020
 3SO  plan-3  O27  0.020
 3SO  plan-4  C13  0.020
 3SO  plan-4  C14  0.020
 3SO  plan-4  C15  0.020
 3SO  plan-4  C16  0.020
 3SO  plan-4  H7   0.020
 3SO  plan-4  H8   0.020

