# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 04:06:25 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 2-amino-6-[(1R,2R)-1,2,3-trihydroxypropyl]pteridin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2ncc(nc2C(=O)N1)[C@@H](O)[C@H](O)CO
#
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
 NEO  NEO  2-amino-6-[(1R,2R)-1,2,3-trihydroxypropyl]pteridin-4(3H)-one  ligand  29  18  .  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_NEO
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
 NEO  N2    N  NR16  0  -0.714  -1.2129   0.0017   3.3653
 NEO  C1    C  CR6   0   0.536  -1.4623   0.2836   2.0399
 NEO  C10   C  CR66  0  -0.044  -0.2460   0.2784   1.2255
 NEO  N9    N  N     0  -0.368  -0.3518   0.5297  -0.0724
 NEO  C8    C  CR6   0   0.160   0.7454   0.5116  -0.7972
 NEO  C7    C  CR16  0  -0.106   1.9816   0.2447  -0.1841
 NEO  N6    N  N     0  -0.385   2.1012  -0.0033   1.1006
 NEO  C5    C  CR66  0   0.391   0.9855   0.0049   1.8437
 NEO  N4    N  N     0  -0.505   1.1168  -0.2538   3.1640
 NEO  C3    C  CR6   0   0.696   0.0293  -0.2483   3.8837
 NEO  N13   N  NH2   0  -0.822   0.0911  -0.4764   5.1951
 NEO  C16   C  CH1   0  -0.033   0.6101   0.8074  -2.2772
 NEO  O21   O  OH1   0  -0.656   1.8547   0.8364  -2.9228
 NEO  C26   C  CH1   0  -0.014  -0.3514  -0.1833  -2.9351
 NEO  O22   O  OH1   0  -0.678   0.2760  -1.4456  -2.8888
 NEO  C28   C  CH2   0  -0.174  -0.6883   0.2255  -4.3585
 NEO  O24   O  OH1   0  -0.676  -1.5621  -0.7528  -4.8820
 NEO  O11   O  OC    0  -0.436  -2.5838   0.5030   1.6347
 NEO  HN2   H  HNR6  0   0.432  -2.0152  -0.0137   3.9829
 NEO  H7    H  HCR6  0   0.275   2.8958   0.2409  -0.7651
 NEO  H131  H  HNH2  0   0.418   0.9746  -0.7368   5.5986
 NEO  H132  H  HNH2  0   0.421  -0.7323  -0.5972   5.7592
 NEO  H16   H  HCH1  0   0.271   0.1777   1.8096  -2.3732
 NEO  H21   H  HOH1  0   0.449   2.1175  -0.0747  -3.1046
 NEO  H26   H  HCH1  0   0.228  -1.2812  -0.1828  -2.3494
 NEO  H22   H  HOH1  0   0.455  -0.1671  -2.0234  -3.5205
 NEO  H281  H  HCH2  0   0.204  -1.1538   1.2194  -4.3414
 NEO  H282  H  HCH2  0   0.210   0.2274   0.3002  -4.9549
 NEO  H24   H  HOH1  0   0.462  -1.5451  -0.6965  -5.8411

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
 NEO  N2   C1    aromatic  1.378  0.020  1.378
 NEO  N2   C3    aromatic  1.369  0.020  1.369
 NEO  N2   HN2   single    0.860  0.020  1.020
 NEO  C1   C10   aromatic  1.464  0.020  1.464
 NEO  C1   O11   double    1.212  0.020  1.212
 NEO  C10  N9    aromatic  1.326  0.020  1.326
 NEO  C10  C5    aromatic  1.405  0.020  1.405
 NEO  N9   C8    aromatic  1.315  0.020  1.315
 NEO  C8   C7    aromatic  1.406  0.020  1.406
 NEO  C8   C16   single    1.515  0.020  1.515
 NEO  C7   N6    aromatic  1.314  0.020  1.314
 NEO  C7   H7    single    0.930  0.020  1.080
 NEO  N6   C5    aromatic  1.341  0.020  1.341
 NEO  C5   N4    aromatic  1.352  0.020  1.352
 NEO  N4   C3    aromatic  1.304  0.020  1.304
 NEO  C3   N13   single    1.333  0.020  1.333
 NEO  N13  H131  single    0.860  0.020  1.020
 NEO  N13  H132  single    0.860  0.020  1.020
 NEO  C16  O21   single    1.402  0.020  1.402
 NEO  C16  C26   single    1.529  0.020  1.529
 NEO  C16  H16   single    0.970  0.020  1.090
 NEO  O21  H21   single    0.850  0.020  0.980
 NEO  C26  O22   single    1.410  0.020  1.410
 NEO  C26  C28   single    1.519  0.020  1.519
 NEO  C26  H26   single    0.970  0.020  1.090
 NEO  O22  H22   single    0.850  0.020  0.980
 NEO  C28  O24   single    1.412  0.020  1.412
 NEO  C28  H281  single    0.970  0.020  1.090
 NEO  C28  H282  single    0.970  0.020  1.090
 NEO  O24  H24   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
 NEO  HN2   N2   C3    119.02  3.000
 NEO  HN2   N2   C1    116.51  3.000
 NEO  C3    N2   C1    124.46  3.000
 NEO  O11   C1   C10   125.68  3.000
 NEO  O11   C1   N2    121.74  3.000
 NEO  C10   C1   N2    112.59  3.000
 NEO  C5    C10  N9    122.51  3.000
 NEO  C5    C10  C1    118.96  3.000
 NEO  N9    C10  C1    118.53  3.000
 NEO  C8    N9   C10   118.05  3.000
 NEO  C16   C8   C7    122.80  3.000
 NEO  C16   C8   N9    117.46  3.000
 NEO  C7    C8   N9    119.73  3.000
 NEO  H7    C7   N6    116.55  3.000
 NEO  H7    C7   C8    120.60  3.000
 NEO  N6    C7   C8    122.85  3.000
 NEO  C5    N6   C7    117.72  3.000
 NEO  N4    C5   N6    117.35  3.000
 NEO  N4    C5   C10   123.52  3.000
 NEO  N6    C5   C10   119.13  3.000
 NEO  C3    N4   C5    117.21  3.000
 NEO  N13   C3   N4    120.25  3.000
 NEO  N13   C3   N2    116.49  3.000
 NEO  N4    C3   N2    123.26  3.000
 NEO  H132  N13  H131  117.60  3.000
 NEO  H132  N13  C3    122.33  3.000
 NEO  H131  N13  C3    118.68  3.000
 NEO  H16   C16  C26   107.87  3.000
 NEO  H16   C16  O21   106.92  3.000
 NEO  C26   C16  O21   111.92  3.000
 NEO  H16   C16  C8    107.42  3.000
 NEO  C26   C16  C8    110.48  3.000
 NEO  O21   C16  C8    111.99  3.000
 NEO  H21   O21  C16   107.99  3.000
 NEO  H26   C26  C28   108.16  3.000
 NEO  H26   C26  O22   111.06  3.000
 NEO  C28   C26  O22   111.74  3.000
 NEO  H26   C26  C16   107.60  3.000
 NEO  C28   C26  C16   111.61  3.000
 NEO  O22   C26  C16   106.62  3.000
 NEO  H22   O22  C26   108.09  3.000
 NEO  H282  C28  H281  107.54  3.000
 NEO  H282  C28  O24   111.26  3.000
 NEO  H281  C28  O24   111.75  3.000
 NEO  H282  C28  C26   110.07  3.000
 NEO  H281  C28  C26   108.86  3.000
 NEO  O24   C28  C26   107.35  3.000
 NEO  H24   O24  C28   108.57  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
 NEO  CONST_01  N9    C10  C1   N2   180.00  0.0  0
 NEO  CONST_02  C5    C10  C1   N2     0.00  0.0  0
 NEO  CONST_03  C5    N4   C3   N2     0.00  0.0  0
 NEO  CONST_04  N4    C3   N2   C1     0.00  0.0  0
 NEO  CONST_05  C8    N9   C10  C1   180.00  0.0  0
 NEO  CONST_06  N6    C5   C10  C1   180.00  0.0  0
 NEO  CONST_07  N4    C5   C10  C1     0.00  0.0  0
 NEO  CONST_08  C3    N2   C1   C10    0.00  0.0  0
 NEO  CONST_09  C7    C8   N9   C10    0.00  0.0  0
 NEO  CONST_10  C7    N6   C5   C10    0.00  0.0  0
 NEO  CONST_11  C3    N4   C5   C10    0.00  0.0  0
 NEO  CONST_12  N6    C5   C10  N9     0.00  0.0  0
 NEO  CONST_13  N4    C5   C10  N9   180.00  0.0  0
 NEO  CONST_14  N6    C7   C8   N9     0.00  0.0  0
 NEO  CONST_15  C5    C10  N9   C8     0.00  0.0  0
 NEO  CONST_16  C5    N6   C7   C8     0.00  0.0  0
 NEO  CONST_17  N4    C5   N6   C7   180.00  0.0  0
 NEO  CONST_18  C3    N4   C5   N6   180.00  0.0  0
 NEO  CONST_19  N13   C3   N2   C1   180.00  0.0  0
 NEO  CONST_20  C16   C8   N9   C10  180.00  0.0  0
 NEO  CONST_21  O11   C1   C10  N9     0.00  0.0  0
 NEO  CONST_22  C16   C8   C7   N6   180.00  0.0  0
 NEO  CONST_23  O11   C1   C10  C5   180.00  0.0  0
 NEO  CONST_24  N13   C3   N4   C5   180.00  0.0  0
 NEO  CONST_25  O11   C1   N2   C3   180.00  0.0  0
 NEO  CONST_26  HN2   N2   C1   C10  180.00  0.0  0
 NEO  CONST_27  H7    C7   C8   N9   180.00  0.0  0
 NEO  CONST_28  H131  N13  C3   N2   180.00  0.0  0
 NEO  CONST_29  H132  N13  C3   N2     0.00  0.0  0

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
 NEO  chir_01  C16  C8   O21  C26  negativ
 NEO  chir_02  C26  O22  C16  C28  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
 NEO  plan-1  N2    0.020
 NEO  plan-1  C1    0.020
 NEO  plan-1  C10   0.020
 NEO  plan-1  N9    0.020
 NEO  plan-1  C8    0.020
 NEO  plan-1  C7    0.020
 NEO  plan-1  N6    0.020
 NEO  plan-1  C5    0.020
 NEO  plan-1  N4    0.020
 NEO  plan-1  C3    0.020
 NEO  plan-1  N13   0.020
 NEO  plan-1  C16   0.020
 NEO  plan-1  O11   0.020
 NEO  plan-1  HN2   0.020
 NEO  plan-1  H7    0.020
 NEO  plan-2  C3    0.020
 NEO  plan-2  N13   0.020
 NEO  plan-2  H131  0.020
 NEO  plan-2  H132  0.020

