# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 10:24:53 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 1-[6-(2-carboxyethyl)-7-hydroxy-2,4-dioxo-3,4-dihydropteridin-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(=C(CCC(O)=O)N=C2C(=O)NC(=O)N=C12)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
 RLP  RLP  1-[6-(2-carboxyethyl)-7-hydroxy-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl]-1-deoxy-D-ribitol  ligand  44  27  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RLP
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
 RLP  O19   O  OC    -1  -0.623  -2.6818   1.5583  -6.1257
 RLP  C18   C  C      0   0.424  -2.5570   0.5482  -5.4054
 RLP  O18   O  O      0  -0.602  -3.1350  -0.5459  -5.5466
 RLP  C17   C  CH2    0  -0.580  -1.5850   0.6934  -4.2173
 RLP  C16   C  CH2    0  -0.559  -1.4064  -0.5723  -3.3793
 RLP  C7    C  CR6    0   0.095  -0.3982  -0.3842  -2.2851
 RLP  C8    C  CR6    0   0.611  -0.7441   0.2295  -1.0661
 RLP  O8    O  OH1    0  -0.568  -1.9557   0.6346  -0.7798
 RLP  N9    N  NR6    0  -0.515   0.1810   0.4598  -0.1241
 RLP  C10   C  CR66   0   0.565   1.4906   0.0710  -0.3226
 RLP  C5    C  CR66   0  -0.058   1.7652  -0.5392  -1.5636
 RLP  N6    N  N      0  -0.333   0.8490  -0.7465  -2.4873
 RLP  C4    C  CR6    0   0.538   3.1456  -0.9513  -1.8151
 RLP  O4    O  OC     0  -0.451   3.5340  -1.4827  -2.8369
 RLP  N3    N  NR16   0  -0.718   3.9815  -0.6724  -0.7675
 RLP  C2    C  CR6    0   0.562   3.6398  -0.0713   0.4442
 RLP  O2    O  OC     0  -0.490   4.5095   0.1002   1.2816
 RLP  N1    N  N      0  -0.548   2.3500   0.2961   0.6371
 RLP  C11   C  CH2    0  -0.360  -0.1776   1.0882   1.1546
 RLP  C12   C  CH1    0   0.001  -0.4591   0.0091   2.2118
 RLP  O12   O  OH1    0  -0.651  -1.3276  -0.9785   1.7154
 RLP  C13   C  CH1    0  -0.038  -1.0157   0.6602   3.4931
 RLP  O13   O  OH1    0  -0.654  -0.4852   1.9462   3.7201
 RLP  C14   C  CH1    0  -0.012  -0.8235  -0.2143   4.7491
 RLP  O14   O  OH1    0  -0.654  -0.9554  -1.5922   4.5107
 RLP  C15   C  CH2    0  -0.161  -1.7528   0.2642   5.8539
 RLP  O15   O  OH1    0  -0.671  -1.4306  -0.4059   7.0487
 RLP  H171  H  HCH2   0   0.230  -1.9358   1.5248  -3.5957
 RLP  H172  H  HCH2   0   0.244  -0.6101   1.0144  -4.5968
 RLP  H161  H  HCH2   0   0.275  -1.0500  -1.3857  -4.0101
 RLP  H162  H  HCH2   0   0.245  -2.3704  -0.9144  -2.9893
 RLP  HO8   H  HOH1   0   0.516  -2.5915   0.3922  -1.4674
 RLP  HN3   H  HNR6   0   0.415   4.9538  -0.9307  -0.8790
 RLP  H111  H  HCH2   0   0.299  -1.0325   1.7418   0.9959
 RLP  H112  H  HCH2   0   0.298   0.6674   1.7048   1.4421
 RLP  H121  H  HCH1   0   0.264   0.4828  -0.5015   2.4301
 RLP  H12O  H  HOH1   0   0.448  -2.2054  -0.5974   1.5972
 RLP  H131  H  HCH1   0   0.238  -2.0894   0.8226   3.3258
 RLP  H13O  H  HOH1   0   0.452   0.4340   1.8639   3.9978
 RLP  H141  H  HCH1   0   0.231   0.2153  -0.0817   5.0793
 RLP  H14O  H  HOH1   0   0.441  -1.8290  -1.7697   4.1462
 RLP  H151  H  HCH2   0   0.195  -2.7911   0.0680   5.5460
 RLP  H152  H  HCH2   0   0.204  -1.6533   1.3512   5.9581
 RLP  H15O  H  HOH1   0   0.455  -2.0227  -0.0899   7.7366

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
 RLP  O19  C18   deloc     1.247  0.020  1.247
 RLP  C18  O18   deloc     1.245  0.020  1.245
 RLP  C18  C17   single    1.542  0.020  1.542
 RLP  C17  C16   single    1.528  0.020  1.528
 RLP  C17  H171  single    0.970  0.020  1.090
 RLP  C17  H172  single    0.970  0.020  1.090
 RLP  C16  C7    single    1.500  0.020  1.500
 RLP  C16  H161  single    0.970  0.020  1.090
 RLP  C16  H162  single    0.970  0.020  1.090
 RLP  C7   C8    aromatic  1.408  0.020  1.408
 RLP  C7   N6    aromatic  1.314  0.020  1.314
 RLP  C8   O8    single    1.309  0.020  1.309
 RLP  C8   N9    aromatic  1.340  0.020  1.340
 RLP  O8   HO8   single    0.850  0.020  0.980
 RLP  N9   C10   aromatic  1.380  0.020  1.380
 RLP  N9   C11   single    1.469  0.020  1.469
 RLP  C10  C5    aromatic  1.410  0.020  1.410
 RLP  C10  N1    aromatic  1.308  0.020  1.308
 RLP  C5   N6    aromatic  1.317  0.020  1.317
 RLP  C5   C4    aromatic  1.462  0.020  1.462
 RLP  C4   O4    double    1.215  0.020  1.215
 RLP  C4   N3    aromatic  1.369  0.020  1.369
 RLP  N3   C2    aromatic  1.395  0.020  1.395
 RLP  N3   HN3   single    0.860  0.020  1.020
 RLP  C2   O2    double    1.219  0.020  1.219
 RLP  C2   N1    aromatic  1.355  0.020  1.355
 RLP  C11  C12   single    1.537  0.020  1.537
 RLP  C11  H111  single    0.970  0.020  1.090
 RLP  C11  H112  single    0.970  0.020  1.090
 RLP  C12  O12   single    1.406  0.020  1.406
 RLP  C12  C13   single    1.541  0.020  1.541
 RLP  C12  H121  single    0.970  0.020  1.090
 RLP  O12  H12O  single    0.850  0.020  0.980
 RLP  C13  O13   single    1.409  0.020  1.409
 RLP  C13  C14   single    1.543  0.020  1.543
 RLP  C13  H131  single    0.970  0.020  1.090
 RLP  O13  H13O  single    0.850  0.020  0.980
 RLP  C14  O14   single    1.405  0.020  1.405
 RLP  C14  C15   single    1.521  0.020  1.521
 RLP  C14  H141  single    0.970  0.020  1.090
 RLP  O14  H14O  single    0.850  0.020  0.980
 RLP  C15  O15   single    1.407  0.020  1.407
 RLP  C15  H151  single    0.970  0.020  1.090
 RLP  C15  H152  single    0.970  0.020  1.090
 RLP  O15  H15O  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
 RLP  C17   C18  O18   117.56  3.000
 RLP  C17   C18  O19   115.60  3.000
 RLP  O18   C18  O19   126.84  3.000
 RLP  H172  C17  H171  105.03  3.000
 RLP  H172  C17  C16   109.21  3.000
 RLP  H171  C17  C16   110.77  3.000
 RLP  H172  C17  C18   108.79  3.000
 RLP  H171  C17  C18   107.86  3.000
 RLP  C16   C17  C18   114.72  3.000
 RLP  H162  C16  H161  105.13  3.000
 RLP  H162  C16  C7    111.79  3.000
 RLP  H161  C16  C7    107.23  3.000
 RLP  H162  C16  C17   110.57  3.000
 RLP  H161  C16  C17   109.82  3.000
 RLP  C7    C16  C17   112.01  3.000
 RLP  N6    C7   C8    119.10  3.000
 RLP  N6    C7   C16   119.42  3.000
 RLP  C8    C7   C16   121.41  3.000
 RLP  N9    C8   O8    115.59  3.000
 RLP  N9    C8   C7    120.92  3.000
 RLP  O8    C8   C7    123.47  3.000
 RLP  HO8   O8   C8    112.04  3.000
 RLP  C11   N9   C10   118.50  3.000
 RLP  C11   N9   C8    121.11  3.000
 RLP  C10   N9   C8    120.36  3.000
 RLP  N1    C10  C5    126.33  3.000
 RLP  N1    C10  N9    118.00  3.000
 RLP  C5    C10  N9    115.67  3.000
 RLP  C4    C5   N6    119.44  3.000
 RLP  C4    C5   C10   117.21  3.000
 RLP  N6    C5   C10   123.35  3.000
 RLP  C5    N6   C7    120.58  3.000
 RLP  N3    C4   O4    122.50  3.000
 RLP  N3    C4   C5    112.79  3.000
 RLP  O4    C4   C5    124.71  3.000
 RLP  HN3   N3   C2    116.16  3.000
 RLP  HN3   N3   C4    116.76  3.000
 RLP  C2    N3   C4    127.08  3.000
 RLP  N1    C2   O2    122.89  3.000
 RLP  N1    C2   N3    118.27  3.000
 RLP  O2    C2   N3    118.84  3.000
 RLP  C2    N1   C10   118.32  3.000
 RLP  H112  C11  H111  108.02  3.000
 RLP  H112  C11  C12   111.07  3.000
 RLP  H111  C11  C12   112.23  3.000
 RLP  H112  C11  N9    106.48  3.000
 RLP  H111  C11  N9    108.77  3.000
 RLP  C12   C11  N9    110.07  3.000
 RLP  H121  C12  C13   110.02  3.000
 RLP  H121  C12  O12   105.94  3.000
 RLP  C13   C12  O12   111.55  3.000
 RLP  H121  C12  C11   107.90  3.000
 RLP  C13   C12  C11   109.97  3.000
 RLP  O12   C12  C11   111.32  3.000
 RLP  H12O  O12  C12   109.15  3.000
 RLP  H131  C13  C14   109.24  3.000
 RLP  H131  C13  O13   104.92  3.000
 RLP  C14   C13  O13   109.84  3.000
 RLP  H131  C13  C12   106.78  3.000
 RLP  C14   C13  C12   113.10  3.000
 RLP  O13   C13  C12   112.54  3.000
 RLP  H13O  O13  C13   109.11  3.000
 RLP  H141  C14  C15   108.76  3.000
 RLP  H141  C14  O14   104.97  3.000
 RLP  C15   C14  O14   112.00  3.000
 RLP  H141  C14  C13   107.11  3.000
 RLP  C15   C14  C13   109.69  3.000
 RLP  O14   C14  C13   113.97  3.000
 RLP  H14O  O14  C14   109.28  3.000
 RLP  H152  C15  H151  106.80  3.000
 RLP  H152  C15  O15   111.75  3.000
 RLP  H151  C15  O15   111.63  3.000
 RLP  H152  C15  C14   109.00  3.000
 RLP  H151  C15  C14   108.48  3.000
 RLP  O15   C15  C14   109.09  3.000
 RLP  H15O  O15  C15   108.06  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
 RLP  CONST_01  C10  N9   C8   C7      0.00   0.0  0
 RLP  CONST_02  C10  C5   N6   C7      0.00   0.0  0
 RLP  CONST_03  C4   C5   N6   C7    180.00   0.0  0
 RLP  CONST_04  C5   N6   C7   C8      0.00   0.0  0
 RLP  CONST_05  C5   C10  N9   C8      0.00   0.0  0
 RLP  CONST_06  N1   C10  N9   C8    180.00   0.0  0
 RLP  CONST_07  N6   C7   C8   N9      0.00   0.0  0
 RLP  CONST_08  N6   C5   C10  N9      0.00   0.0  0
 RLP  CONST_09  C4   C5   C10  N9    180.00   0.0  0
 RLP  CONST_10  C2   N1   C10  N9    180.00   0.0  0
 RLP  CONST_11  N3   C4   C5   C10     0.00   0.0  0
 RLP  CONST_12  N3   C2   N1   C10     0.00   0.0  0
 RLP  CONST_13  C2   N1   C10  C5      0.00   0.0  0
 RLP  CONST_14  C2   N3   C4   C5      0.00   0.0  0
 RLP  CONST_15  N1   C10  C5   N6    180.00   0.0  0
 RLP  CONST_16  N3   C4   C5   N6    180.00   0.0  0
 RLP  CONST_17  N1   C10  C5   C4      0.00   0.0  0
 RLP  CONST_18  N1   C2   N3   C4      0.00   0.0  0
 RLP  CONST_19  N9   C8   C7   C16   180.00   0.0  0
 RLP  CONST_20  C5   N6   C7   C16   180.00   0.0  0
 RLP  CONST_21  C11  N9   C8   C7    180.00   0.0  0
 RLP  CONST_22  N6   C7   C8   O8    180.00   0.0  0
 RLP  CONST_23  C10  N9   C8   O8    180.00   0.0  0
 RLP  CONST_24  O4   C4   C5   C10   180.00   0.0  0
 RLP  CONST_25  O2   C2   N1   C10   180.00   0.0  0
 RLP  CONST_26  C11  N9   C10  C5    180.00   0.0  0
 RLP  CONST_27  O4   C4   C5   N6      0.00   0.0  0
 RLP  CONST_28  O2   C2   N3   C4    180.00   0.0  0
 RLP  CONST_29  C2   N3   C4   O4    180.00   0.0  0
 RLP  CONST_30  C11  N9   C10  N1      0.00   0.0  0
 RLP  CONST_31  HN3  N3   C4   C5    180.00   0.0  0
 RLP  Var_01    C8   C7   C16  C17    81.99  30.0  2
 RLP  Var_02    C12  C11  N9   C8     94.21  30.0  2
 RLP  Var_03    C7   C16  C17  C18   177.09  30.0  3
 RLP  Var_04    C16  C17  C18  O19  -177.78  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
 RLP  chir_01  C12  C11  O12  C13  positiv
 RLP  chir_02  C13  O13  C12  C14  negativ
 RLP  chir_03  C14  O14  C13  C15  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
 RLP  plan-1  C16  0.020
 RLP  plan-1  C7   0.020
 RLP  plan-1  C8   0.020
 RLP  plan-1  O8   0.020
 RLP  plan-1  N9   0.020
 RLP  plan-1  C10  0.020
 RLP  plan-1  C5   0.020
 RLP  plan-1  N6   0.020
 RLP  plan-1  C4   0.020
 RLP  plan-1  O4   0.020
 RLP  plan-1  N3   0.020
 RLP  plan-1  C2   0.020
 RLP  plan-1  O2   0.020
 RLP  plan-1  N1   0.020
 RLP  plan-1  C11  0.020
 RLP  plan-1  HN3  0.020
 RLP  plan-2  O19  0.020
 RLP  plan-2  C18  0.020
 RLP  plan-2  O18  0.020
 RLP  plan-2  C17  0.020

