# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 08:22:53 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: (2~{S})-2-[2-[2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]ethylamino]-2-oxidanylidene-ethyl]-2-oxidanyl-butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CNCCNC(=O)C[C@](O)(CC(O)=O)C(O)=O)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
 DN9  DN9  '(2~{S})-2-[2-[2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]ethylamino]-2-oxidanylidene-ethyl]-2-oxidanyl-butanedioic acid'  ligand  55  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_DN9
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
 DN9  C1   C  CH2   0  -0.264   0.0474   0.7600  -0.9022
 DN9  C2   C  CH2   0  -0.310  -0.8584   0.0937   0.1272
 DN9  N3   N  NH1   0  -0.590   1.3086   1.1112  -0.2831
 DN9  N4   N  NH1   0  -0.629  -2.1197  -0.3329  -0.4322
 DN9  C5   C  C     0   0.562  -3.1930   0.4621  -0.5365
 DN9  C6   C  CH2   0  -0.588  -4.4106  -0.1671  -1.1758
 DN9  O7   O  O     0  -0.494  -3.2163   1.6194  -0.1390
 DN9  C8   C  CT    0   0.093  -5.5830  -0.2593  -0.1804
 DN9  C9   C  CH2   0  -0.592  -6.7361  -0.9840  -0.8857
 DN9  O10  O  OH1   0  -0.653  -5.2006  -0.9350   0.9837
 DN9  C11  C  C     0   0.568  -5.9991   1.1398   0.2788
 DN9  O12  O  OH1   0  -0.597  -6.4865   1.8455  -0.7325
 DN9  O13  O  O     0  -0.433  -5.8936   1.5514   1.4003
 DN9  C14  C  C     0   0.561  -7.9670  -1.1151  -0.0313
 DN9  O15  O  O     0  -0.433  -8.3142  -0.3063   0.7927
 DN9  O16  O  OH1   0  -0.588  -8.6544  -2.2117  -0.3139
 DN9  P17  P  P     0   1.465   4.5897  -3.1641  -0.2472
 DN9  O18  O  OH1   0  -0.729   6.0019  -3.6781   0.2785
 DN9  O19  O  O     0  -0.710   4.1441  -3.5980  -1.5838
 DN9  O20  O  OH1   0  -0.740   3.4847  -3.5535   0.8380
 DN9  O21  O  O2    0  -0.594   4.8895  -1.6051  -0.0715
 DN9  C23  C  CR6   0  -0.066   4.3970   0.7328  -0.1678
 DN9  C24  C  CR16  0  -0.139   5.5818   0.9683   0.5103
 DN9  N25  N  N     0  -0.407   5.9990   2.1862   0.8399
 DN9  C26  C  CR6   0   0.126   5.2680   3.2393   0.5174
 DN9  C27  C  CR6   0   0.252   4.0546   3.0954  -0.1727
 DN9  C28  C  CR6   0   0.079   3.6063   1.8286  -0.5291
 DN9  C29  C  CH2   0  -0.359   2.2865   1.6283  -1.2269
 DN9  C31  C  CH3   0  -0.786   5.7643   4.5972   0.9174
 DN9  H1   H  HCH2  0   0.228   0.2453   0.0524  -1.7122
 DN9  H2   H  HCH2  0   0.208  -0.4704   1.6197  -1.3523
 DN9  H3   H  HCH2  0   0.254  -0.3564  -0.7836   0.5347
 DN9  H4   H  HCH2  0   0.244  -1.0479   0.7745   0.9587
 DN9  H5   H  HNH1  0   0.350   1.1477   1.8094   0.4335
 DN9  H7   H  HNH1  0   0.406  -2.1687  -1.2635  -0.8121
 DN9  H8   H  HCH2  0   0.291  -4.6940   0.4304  -2.0436
 DN9  H9   H  HCH2  0   0.277  -4.1966  -1.1715  -1.5487
 DN9  H10  H  HCH2  0   0.310  -7.0218  -0.4610  -1.8027
 DN9  H11  H  HCH2  0   0.294  -6.3930  -1.9718  -1.2007
 DN9  H12  H  HOH1  0   0.457  -4.9037  -1.8199   0.7441
 DN9  H13  H  HOH1  0   0.485  -6.7397   2.7295  -0.4283
 DN9  H14  H  HOH1  0   0.483  -9.4640  -2.2431   0.2186
 DN9  H15  H  HOH1  0   0.505   6.1265  -4.6344   0.2146
 DN9  H16  H  HOH1  0   0.497   3.7065  -3.3523   1.7571
 DN9  H17  H  HCH2  0   0.256   3.8461  -0.7298  -1.6263
 DN9  H18  H  HCH2  0   0.258   2.9543  -0.8324  -0.1080
 DN9  H19  H  HCR6  0   0.256   6.2272   0.1514   0.8063
 DN9  H20  H  HCH2  0   0.246   2.4059   0.8883  -2.0235
 DN9  H21  H  HCH2  0   0.242   1.9622   2.5499  -1.7233
 DN9  H22  H  HOH1  0   0.486   3.7198   4.9838  -0.2496
 DN9  H23  H  HCH3  0   0.256   5.9185   5.2527   0.0561
 DN9  H24  H  HCH3  0   0.258   5.0715   5.1032   1.5950
 DN9  H25  H  HCH3  0   0.271   6.7183   4.5042   1.4311
 DN9  O30  O  OH1   0  -0.622   3.2920   4.1576  -0.4986
 DN9  C22  C  CH2   0  -0.202   3.9433  -0.6490  -0.5388

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
 DN9  O15  C14  double    1.206  0.020  1.206
 DN9  O16  C14  single    1.325  0.020  1.325
 DN9  C14  C9   single    1.504  0.020  1.504
 DN9  C9   C8   single    1.534  0.020  1.534
 DN9  O10  C8   single    1.399  0.020  1.399
 DN9  C8   C6   single    1.541  0.020  1.541
 DN9  C8   C11  single    1.530  0.020  1.530
 DN9  C6   C5   single    1.512  0.020  1.512
 DN9  C11  O13  double    1.199  0.020  1.199
 DN9  C11  O12  single    1.326  0.020  1.326
 DN9  C5   N4   single    1.340  0.020  1.340
 DN9  C5   O7   double    1.224  0.020  1.224
 DN9  N4   C2   single    1.444  0.020  1.444
 DN9  C1   C2   single    1.524  0.020  1.524
 DN9  C1   N3   single    1.448  0.020  1.448
 DN9  N3   C29  single    1.454  0.020  1.454
 DN9  O19  P17  double    1.474  0.020  1.474
 DN9  C29  C28  single    1.506  0.020  1.506
 DN9  C22  O21  single    1.424  0.020  1.424
 DN9  C22  C23  single    1.501  0.020  1.501
 DN9  C28  C23  aromatic  1.399  0.020  1.399
 DN9  C28  C27  aromatic  1.390  0.020  1.390
 DN9  O18  P17  single    1.592  0.020  1.592
 DN9  P17  O21  single    1.597  0.020  1.597
 DN9  P17  O20  single    1.597  0.020  1.597
 DN9  O30  C27  single    1.348  0.020  1.348
 DN9  C23  C24  aromatic  1.385  0.020  1.385
 DN9  C27  C26  aromatic  1.403  0.020  1.403
 DN9  C24  N25  aromatic  1.329  0.020  1.329
 DN9  C26  N25  aromatic  1.322  0.020  1.322
 DN9  C26  C31  single    1.500  0.020  1.500
 DN9  C1   H1   single    0.970  0.020  1.090
 DN9  C1   H2   single    0.970  0.020  1.090
 DN9  C2   H3   single    0.970  0.020  1.090
 DN9  C2   H4   single    0.970  0.020  1.090
 DN9  N3   H5   single    0.890  0.020  1.040
 DN9  N4   H7   single    0.860  0.020  1.020
 DN9  C6   H8   single    0.970  0.020  1.090
 DN9  C6   H9   single    0.970  0.020  1.090
 DN9  C9   H10  single    0.970  0.020  1.090
 DN9  C9   H11  single    0.970  0.020  1.090
 DN9  O10  H12  single    0.850  0.020  0.980
 DN9  O12  H13  single    0.850  0.020  0.980
 DN9  O16  H14  single    0.850  0.020  0.980
 DN9  O18  H15  single    0.850  0.020  0.980
 DN9  O20  H16  single    0.850  0.020  0.980
 DN9  C22  H17  single    0.970  0.020  1.090
 DN9  C22  H18  single    0.970  0.020  1.090
 DN9  C24  H19  single    0.930  0.020  1.080
 DN9  C29  H20  single    0.970  0.020  1.090
 DN9  C29  H21  single    0.970  0.020  1.090
 DN9  O30  H22  single    0.850  0.020  0.980
 DN9  C31  H23  single    0.970  0.020  1.090
 DN9  C31  H24  single    0.970  0.020  1.090
 DN9  C31  H25  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
 DN9  H2   C1   H1   106.73  3.000
 DN9  H2   C1   N3   113.29  3.000
 DN9  H1   C1   N3   108.42  3.000
 DN9  H2   C1   C2   109.77  3.000
 DN9  H1   C1   C2   108.96  3.000
 DN9  N3   C1   C2   109.56  3.000
 DN9  H4   C2   H3   107.29  3.000
 DN9  H4   C2   N4   109.13  3.000
 DN9  H3   C2   N4   108.02  3.000
 DN9  H4   C2   C1   110.18  3.000
 DN9  H3   C2   C1   109.31  3.000
 DN9  N4   C2   C1   112.74  3.000
 DN9  H5   N3   C29  108.71  3.000
 DN9  H5   N3   C1   109.34  3.000
 DN9  C29  N3   C1   113.23  3.000
 DN9  H7   N4   C5   118.70  3.000
 DN9  H7   N4   C2   117.51  3.000
 DN9  C5   N4   C2   123.68  3.000
 DN9  O7   C5   C6   121.02  3.000
 DN9  O7   C5   N4   123.44  3.000
 DN9  C6   C5   N4   115.54  3.000
 DN9  H9   C6   H8   106.43  3.000
 DN9  H9   C6   C8   108.33  3.000
 DN9  H8   C6   C8   110.42  3.000
 DN9  H9   C6   C5   111.66  3.000
 DN9  H8   C6   C5   108.51  3.000
 DN9  C8   C6   C5   111.38  3.000
 DN9  C11  C8   O10  105.44  3.000
 DN9  C11  C8   C9   111.44  3.000
 DN9  O10  C8   C9   111.09  3.000
 DN9  C11  C8   C6   110.25  3.000
 DN9  O10  C8   C6   111.00  3.000
 DN9  C9   C8   C6   107.66  3.000
 DN9  H11  C9   H10  105.83  3.000
 DN9  H11  C9   C14  110.01  3.000
 DN9  H10  C9   C14  107.71  3.000
 DN9  H11  C9   C8   108.89  3.000
 DN9  H10  C9   C8   110.85  3.000
 DN9  C14  C9   C8   113.28  3.000
 DN9  H12  O10  C8   108.71  3.000
 DN9  O13  C11  O12  124.25  3.000
 DN9  O12  C11  C8   110.96  3.000
 DN9  O13  C11  C8   124.79  3.000
 DN9  H13  O12  C11  110.02  3.000
 DN9  O16  C14  O15  123.48  3.000
 DN9  O16  C14  C9   112.06  3.000
 DN9  O15  C14  C9   124.43  3.000
 DN9  H14  O16  C14  110.05  3.000
 DN9  O21  P17  O20  107.04  3.000
 DN9  O20  P17  O19  109.58  3.000
 DN9  O21  P17  O19  116.34  3.000
 DN9  O20  P17  O18  108.10  3.000
 DN9  O21  P17  O18   96.45  3.000
 DN9  O19  P17  O18  118.20  3.000
 DN9  H15  O18  P17  114.33  3.000
 DN9  H16  O20  P17  115.88  3.000
 DN9  C22  O21  P17  119.64  3.000
 DN9  C28  C23  C24  118.47  3.000
 DN9  C24  C23  C22  122.41  3.000
 DN9  C28  C23  C22  119.11  3.000
 DN9  H19  C24  N25  115.89  3.000
 DN9  H19  C24  C23  121.04  3.000
 DN9  N25  C24  C23  123.07  3.000
 DN9  C26  N25  C24  119.74  3.000
 DN9  C31  C26  C27  120.67  3.000
 DN9  C31  C26  N25  118.24  3.000
 DN9  C27  C26  N25  121.09  3.000
 DN9  O30  C27  C28  118.28  3.000
 DN9  O30  C27  C26  121.83  3.000
 DN9  C28  C27  C26  119.89  3.000
 DN9  C29  C28  C27  121.50  3.000
 DN9  C27  C28  C23  117.73  3.000
 DN9  C29  C28  C23  120.72  3.000
 DN9  H21  C29  H20  105.75  3.000
 DN9  H21  C29  C28  110.93  3.000
 DN9  H20  C29  C28  109.37  3.000
 DN9  H21  C29  N3   113.21  3.000
 DN9  H20  C29  N3   107.79  3.000
 DN9  C28  C29  N3   109.62  3.000
 DN9  H25  C31  H24  107.62  3.000
 DN9  H25  C31  H23  107.44  3.000
 DN9  H24  C31  H23  107.47  3.000
 DN9  H25  C31  C26  109.80  3.000
 DN9  H24  C31  C26  112.00  3.000
 DN9  H23  C31  C26  112.29  3.000
 DN9  H22  O30  C27  111.24  3.000
 DN9  H18  C22  H17  107.37  3.000
 DN9  H18  C22  C23  109.27  3.000
 DN9  H17  C22  C23  109.90  3.000
 DN9  H18  C22  O21  111.03  3.000
 DN9  H17  C22  O21  109.60  3.000
 DN9  C23  C22  O21  109.65  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
 DN9  CONST_01  C26  C27  C28  C23     0.00   0.0  0
 DN9  CONST_02  C26  N25  C24  C23     0.00   0.0  0
 DN9  CONST_03  C27  C28  C23  C24     0.00   0.0  0
 DN9  CONST_04  C27  C26  N25  C24     0.00   0.0  0
 DN9  CONST_05  C28  C23  C24  N25     0.00   0.0  0
 DN9  CONST_06  C28  C27  C26  N25     0.00   0.0  0
 DN9  CONST_07  C27  C28  C23  C22   180.00   0.0  0
 DN9  CONST_08  N25  C24  C23  C22   180.00   0.0  0
 DN9  CONST_09  O30  C27  C28  C23   180.00   0.0  0
 DN9  CONST_10  C29  C28  C23  C24   180.00   0.0  0
 DN9  CONST_11  C31  C26  N25  C24   180.00   0.0  0
 DN9  CONST_12  O30  C27  C26  N25   180.00   0.0  0
 DN9  CONST_13  C29  C28  C27  C26   180.00   0.0  0
 DN9  CONST_14  C31  C26  C27  C28   180.00   0.0  0
 DN9  CONST_15  H19  C24  N25  C26   180.00   0.0  0
 DN9  CONST_16  C6   C5   N4   C2    180.00   0.0  0
 DN9  CONST_17  O7   C5   N4   C2      0.00   0.0  0
 DN9  CONST_18  H7   N4   C5   C6      0.00   0.0  0
 DN9  CONST_19  H13  O12  C11  C8    180.00   0.0  0
 DN9  CONST_20  H14  O16  C14  C9    180.00   0.0  0
 DN9  Var_01    C23  C28  C29  N3     72.93  30.0  2
 DN9  Var_02    C28  C23  C22  O21  -179.78  30.0  2
 DN9  Var_03    H23  C31  C26  N25   120.39  30.0  2
 DN9  Var_04    C28  C29  N3   C1   -174.04  30.0  3
 DN9  Var_05    C23  C22  O21  P17   175.67  30.0  1
 DN9  Var_06    C5   N4   C2   C1    -86.24  30.0  1
 DN9  Var_07    C29  N3   C1   C2    174.04  30.0  3
 DN9  Var_08    N4   C2   C1   N3   -177.75  30.0  3
 DN9  Var_09    C8   C6   C5   N4    115.87  30.0  1
 DN9  Var_10    O15  C14  C9   C8     32.61  30.0  1

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
 DN9  chir_01  C8  O10  C6  C11  positiv

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
 DN9  plan-1  C23  0.020
 DN9  plan-1  C24  0.020
 DN9  plan-1  N25  0.020
 DN9  plan-1  C26  0.020
 DN9  plan-1  C27  0.020
 DN9  plan-1  C28  0.020
 DN9  plan-1  C29  0.020
 DN9  plan-1  C31  0.020
 DN9  plan-1  H19  0.020
 DN9  plan-1  O30  0.020
 DN9  plan-1  C22  0.020
 DN9  plan-2  C2   0.020
 DN9  plan-2  N4   0.020
 DN9  plan-2  C5   0.020
 DN9  plan-2  C6   0.020
 DN9  plan-2  O7   0.020
 DN9  plan-2  H7   0.020
 DN9  plan-3  C8   0.020
 DN9  plan-3  C11  0.020
 DN9  plan-3  O12  0.020
 DN9  plan-3  O13  0.020
 DN9  plan-3  H13  0.020
 DN9  plan-4  C9   0.020
 DN9  plan-4  C14  0.020
 DN9  plan-4  O15  0.020
 DN9  plan-4  O16  0.020
 DN9  plan-4  H14  0.020

