# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:19:14 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: 1-[6-(2-carboxyethyl)-2,4,7-trioxo-1,3,4,7-tetrahydropteridin-8(2H)-yl]-1-deoxy-D-ribitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@@H](O)CN1C(=O)C(=NC2=C1NC(=O)NC2=O)CCC(O)=O
#
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
 CRM  CRM  1-[6-(2-carboxyethyl)-2,4,7-trioxo-1,3,4,7-tetrahydropteridin-8(2H)-yl]-1-deoxy-D-ribitol  ligand  44  27  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CRM
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
 CRM  C2    C  CR6    0   0.678   3.2341  -0.0213   0.7584
 CRM  O15   O  OC     0  -0.460   3.9679  -0.0248   1.7210
 CRM  N3    N  NR16   0  -0.781   1.9271   0.4020   0.8455
 CRM  C4    C  CR66   0   0.738   1.0706   0.4026  -0.2100
 CRM  N10   N  NR6    0  -0.568  -0.2012   0.8410  -0.0363
 CRM  C17   C  CH2    0  -0.411  -0.6532   1.3084   1.2732
 CRM  C18   C  CH1    0   0.052  -1.0371   0.1615   2.2224
 CRM  C20   C  CH1    0  -0.037  -0.5974   0.5166   3.6583
 CRM  C22   C  CH1    0  -0.050  -1.0074  -0.5342   4.7065
 CRM  C25   C  CH2    0  -0.159  -0.5711  -0.1225   6.1049
 CRM  O26   O  OH1    0  -0.666  -0.9030  -1.1587   6.9949
 CRM  O23   O  OH1    0  -0.661  -2.3955  -0.8049   4.6641
 CRM  O21   O  OH1    0  -0.663   0.8132   0.6825   3.6633
 CRM  O19   O  OH1    0  -0.674  -2.4143  -0.0495   2.0808
 CRM  C9    C  CR6    0   0.562  -1.1059   0.8402  -1.0988
 CRM  O16   O  OC     0  -0.438  -2.2459   1.2314  -0.9524
 CRM  C8    C  CR6    0   0.076  -0.5769   0.3494  -2.3813
 CRM  C11   C  CH2    0  -0.480  -1.5315   0.3357  -3.5334
 CRM  C12   C  CH2    0  -0.587  -0.9478  -0.2087  -4.8223
 CRM  C13   C  C      0   0.418  -1.9272  -0.2342  -6.0102
 CRM  O28   O  OC    -1  -0.630  -1.4407  -0.5931  -7.1029
 CRM  O27   O  O      0  -0.607  -3.1129   0.0892  -5.8007
 CRM  N7    N  N      0  -0.365   0.6375  -0.0478  -2.5103
 CRM  C5    C  CR66   0  -0.085   1.4788  -0.0309  -1.4488
 CRM  C6    C  CR6    0   0.542   2.8444  -0.4819  -1.6353
 CRM  O14   O  OC     0  -0.441   3.3125  -0.8779  -2.6818
 CRM  N1    N  NR16   0  -0.724   3.6205  -0.4287  -0.4874
 CRM  H3    H  HNR6   0   0.446   1.6241   0.6776   1.7772
 CRM  H171  H  HCH2   0   0.313  -1.5231   1.9407   1.1173
 CRM  H172  H  HCH2   0   0.301   0.1155   1.9587   1.6889
 CRM  H18   H  HCH1   0   0.217  -0.4749  -0.7454   1.9406
 CRM  H20   H  HCH1   0   0.257  -1.0289   1.4866   3.9343
 CRM  H22   H  HCH1   0   0.250  -0.5210  -1.4826   4.4436
 CRM  H251  H  HCH2   0   0.203  -1.0768   0.8192   6.3668
 CRM  H252  H  HCH2   0   0.214   0.5040   0.0858   6.1094
 CRM  H26   H  HOH1   0   0.459  -0.6079  -0.9017   7.8729
 CRM  H23   H  HOH1   0   0.462  -2.8744  -0.0744   5.0750
 CRM  H21   H  HOH1   0   0.464   1.2327  -0.1658   3.8514
 CRM  H19   H  HOH1   0   0.453  -2.7085  -0.5649   2.8473
 CRM  H111  H  HCH2   0   0.247  -2.4142  -0.2412  -3.2430
 CRM  H112  H  HCH2   0   0.247  -1.9036   1.3539  -3.6852
 CRM  H121  H  HCH2   0   0.226  -0.0648   0.3671  -5.1138
 CRM  H122  H  HCH2   0   0.229  -0.5783  -1.2274  -4.6658
 CRM  H1    H  HNR6   0   0.433   4.5810  -0.7383  -0.5720

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
 CRM  C2   O15   double    1.210  0.020  1.210
 CRM  C2   N3    aromatic  1.377  0.020  1.377
 CRM  C2   N1    aromatic  1.366  0.020  1.366
 CRM  N3   C4    aromatic  1.359  0.020  1.359
 CRM  N3   H3    single    0.860  0.020  1.020
 CRM  C4   N10   aromatic  1.356  0.020  1.356
 CRM  C4   C5    aromatic  1.374  0.020  1.374
 CRM  N10  C17   single    1.462  0.020  1.462
 CRM  N10  C9    aromatic  1.396  0.020  1.396
 CRM  C17  C18   single    1.537  0.020  1.537
 CRM  C17  H171  single    0.970  0.020  1.090
 CRM  C17  H172  single    0.970  0.020  1.090
 CRM  C18  C20   single    1.543  0.020  1.543
 CRM  C18  O19   single    1.401  0.020  1.401
 CRM  C18  H18   single    0.970  0.020  1.090
 CRM  C20  C22   single    1.540  0.020  1.540
 CRM  C20  O21   single    1.420  0.020  1.420
 CRM  C20  H20   single    0.970  0.020  1.090
 CRM  C22  C25   single    1.522  0.020  1.522
 CRM  C22  O23   single    1.415  0.020  1.415
 CRM  C22  H22   single    0.970  0.020  1.090
 CRM  C25  O26   single    1.406  0.020  1.406
 CRM  C25  H251  single    0.970  0.020  1.090
 CRM  C25  H252  single    0.970  0.020  1.090
 CRM  O26  H26   single    0.850  0.020  0.980
 CRM  O23  H23   single    0.850  0.020  0.980
 CRM  O21  H21   single    0.850  0.020  0.980
 CRM  O19  H19   single    0.850  0.020  0.980
 CRM  C9   O16   double    1.214  0.020  1.214
 CRM  C9   C8    aromatic  1.472  0.020  1.472
 CRM  C8   C11   single    1.496  0.020  1.496
 CRM  C8   N7    aromatic  1.284  0.020  1.284
 CRM  C11  C12   single    1.516  0.020  1.516
 CRM  C11  H111  single    0.970  0.020  1.090
 CRM  C11  H112  single    0.970  0.020  1.090
 CRM  C12  C13   single    1.540  0.020  1.540
 CRM  C12  H121  single    0.970  0.020  1.090
 CRM  C12  H122  single    0.970  0.020  1.090
 CRM  C13  O28   deloc     1.249  0.020  1.249
 CRM  C13  O27   deloc     1.247  0.020  1.247
 CRM  N7   C5    aromatic  1.355  0.020  1.355
 CRM  C5   C6    aromatic  1.450  0.020  1.450
 CRM  C6   O14   double    1.213  0.020  1.213
 CRM  C6   N1    aromatic  1.387  0.020  1.387
 CRM  N1   H1    single    0.860  0.020  1.020

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
 CRM  N1    C2   N3    114.70  3.000
 CRM  N1    C2   O15   123.55  3.000
 CRM  N3    C2   O15   121.75  3.000
 CRM  H3    N3   C4    121.54  3.000
 CRM  H3    N3   C2    115.08  3.000
 CRM  C4    N3   C2    123.31  3.000
 CRM  C5    C4   N10   119.73  3.000
 CRM  C5    C4   N3    120.84  3.000
 CRM  N10   C4   N3    119.44  3.000
 CRM  C9    N10  C17   118.79  3.000
 CRM  C9    N10  C4    120.68  3.000
 CRM  C17   N10  C4    120.53  3.000
 CRM  H172  C17  H171  105.80  3.000
 CRM  H172  C17  C18   112.70  3.000
 CRM  H171  C17  C18   108.83  3.000
 CRM  H172  C17  N10   108.33  3.000
 CRM  H171  C17  N10   107.76  3.000
 CRM  C18   C17  N10   113.06  3.000
 CRM  H18   C18  O19   110.56  3.000
 CRM  H18   C18  C20   106.36  3.000
 CRM  O19   C18  C20   114.14  3.000
 CRM  H18   C18  C17   109.16  3.000
 CRM  O19   C18  C17   107.19  3.000
 CRM  C20   C18  C17   109.38  3.000
 CRM  H20   C20  O21   106.65  3.000
 CRM  H20   C20  C22   109.11  3.000
 CRM  O21   C20  C22   109.98  3.000
 CRM  H20   C20  C18   109.00  3.000
 CRM  O21   C20  C18   108.25  3.000
 CRM  C22   C20  C18   113.61  3.000
 CRM  H22   C22  O23   105.20  3.000
 CRM  H22   C22  C25   109.08  3.000
 CRM  O23   C22  C25   111.14  3.000
 CRM  H22   C22  C20   107.97  3.000
 CRM  O23   C22  C20   111.80  3.000
 CRM  C25   C22  C20   111.38  3.000
 CRM  H252  C25  H251  106.70  3.000
 CRM  H252  C25  O26   111.68  3.000
 CRM  H251  C25  O26   111.81  3.000
 CRM  H252  C25  C22   109.68  3.000
 CRM  H251  C25  C22   108.57  3.000
 CRM  O26   C25  C22   108.34  3.000
 CRM  H26   O26  C25   107.98  3.000
 CRM  H23   O23  C22   109.22  3.000
 CRM  H21   O21  C20   109.25  3.000
 CRM  H19   O19  C18   107.37  3.000
 CRM  C8    C9   O16   123.38  3.000
 CRM  C8    C9   N10   115.51  3.000
 CRM  O16   C9   N10   121.11  3.000
 CRM  N7    C8   C11   121.54  3.000
 CRM  N7    C8   C9    122.05  3.000
 CRM  C11   C8   C9    116.41  3.000
 CRM  H112  C11  H111  104.66  3.000
 CRM  H112  C11  C12   110.31  3.000
 CRM  H111  C11  C12   110.31  3.000
 CRM  H112  C11  C8    108.37  3.000
 CRM  H111  C11  C8    108.37  3.000
 CRM  C12   C11  C8    114.35  3.000
 CRM  H122  C12  H121  104.80  3.000
 CRM  H122  C12  C13   108.03  3.000
 CRM  H121  C12  C13   108.46  3.000
 CRM  H122  C12  C11   110.03  3.000
 CRM  H121  C12  C11   110.39  3.000
 CRM  C13   C12  C11   114.64  3.000
 CRM  O27   C13  O28   126.30  3.000
 CRM  O27   C13  C12   118.10  3.000
 CRM  O28   C13  C12   115.60  3.000
 CRM  C5    N7   C8    120.31  3.000
 CRM  C6    C5   N7    118.70  3.000
 CRM  C6    C5   C4    119.58  3.000
 CRM  N7    C5   C4    121.72  3.000
 CRM  N1    C6   O14   120.72  3.000
 CRM  N1    C6   C5    114.12  3.000
 CRM  O14   C6   C5    125.16  3.000
 CRM  H1    N1   C6    116.74  3.000
 CRM  H1    N1   C2    115.82  3.000
 CRM  C6    N1   C2    127.43  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
 CRM  CONST_01  N10  C4   N3   C2    180.00   0.0  0
 CRM  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 CRM  CONST_03  C5   C6   N1   C2      0.00   0.0  0
 CRM  CONST_04  C6   N1   C2   N3      0.00   0.0  0
 CRM  CONST_05  C9   N10  C4   N3    180.00   0.0  0
 CRM  CONST_06  N7   C5   C4   N3    180.00   0.0  0
 CRM  CONST_07  C6   C5   C4   N3      0.00   0.0  0
 CRM  CONST_08  N1   C2   N3   C4      0.00   0.0  0
 CRM  CONST_09  C8   C9   N10  C4      0.00   0.0  0
 CRM  CONST_10  C8   N7   C5   C4      0.00   0.0  0
 CRM  CONST_11  N1   C6   C5   C4      0.00   0.0  0
 CRM  CONST_12  N7   C5   C4   N10     0.00   0.0  0
 CRM  CONST_13  C6   C5   C4   N10   180.00   0.0  0
 CRM  CONST_14  N7   C8   C9   N10     0.00   0.0  0
 CRM  CONST_15  C5   C4   N10  C9      0.00   0.0  0
 CRM  CONST_16  C5   N7   C8   C9      0.00   0.0  0
 CRM  CONST_17  C6   C5   N7   C8    180.00   0.0  0
 CRM  CONST_18  N1   C6   C5   N7    180.00   0.0  0
 CRM  CONST_19  O14  C6   N1   C2    180.00   0.0  0
 CRM  CONST_20  C4   N3   C2   O15   180.00   0.0  0
 CRM  CONST_21  C6   N1   C2   O15   180.00   0.0  0
 CRM  CONST_22  C17  N10  C4   N3      0.00   0.0  0
 CRM  CONST_23  O16  C9   N10  C4    180.00   0.0  0
 CRM  CONST_24  O14  C6   C5   C4    180.00   0.0  0
 CRM  CONST_25  C11  C8   C9   N10   180.00   0.0  0
 CRM  CONST_26  C5   C4   N10  C17   180.00   0.0  0
 CRM  CONST_27  C8   C9   N10  C17   180.00   0.0  0
 CRM  CONST_28  N7   C8   C9   O16   180.00   0.0  0
 CRM  CONST_29  C5   N7   C8   C11   180.00   0.0  0
 CRM  CONST_30  O14  C6   C5   N7      0.00   0.0  0
 CRM  CONST_31  H1   N1   C2   N3    180.00   0.0  0
 CRM  CONST_32  H3   N3   C4   N10     0.00   0.0  0
 CRM  CONST_33  O16  C9   N10  C17     0.00   0.0  0
 CRM  Var_01    C18  C17  N10  C4    -80.78  30.0  2
 CRM  Var_02    C12  C11  C8   C9   -178.62  30.0  2
 CRM  Var_03    C13  C12  C11  C8    179.63  30.0  3
 CRM  Var_04    O28  C13  C12  C11   175.30  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
 CRM  chir_01  C18  C17  C20  O19  negativ
 CRM  chir_02  C20  O21  C18  C22  negativ
 CRM  chir_03  C22  O23  C20  C25  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
 CRM  plan-1  C2   0.020
 CRM  plan-1  O15  0.020
 CRM  plan-1  N3   0.020
 CRM  plan-1  C4   0.020
 CRM  plan-1  N10  0.020
 CRM  plan-1  C17  0.020
 CRM  plan-1  C9   0.020
 CRM  plan-1  O16  0.020
 CRM  plan-1  C8   0.020
 CRM  plan-1  C11  0.020
 CRM  plan-1  N7   0.020
 CRM  plan-1  C5   0.020
 CRM  plan-1  C6   0.020
 CRM  plan-1  O14  0.020
 CRM  plan-1  N1   0.020
 CRM  plan-1  H3   0.020
 CRM  plan-1  H1   0.020
 CRM  plan-2  C12  0.020
 CRM  plan-2  C13  0.020
 CRM  plan-2  O28  0.020
 CRM  plan-2  O27  0.020

