# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 10:07:27 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: (3S)-1-(5-deoxy-alpha-D-ribofuranosyl)-1,2,3,6-tetrahydropyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H]([C@H](O)[C@@H]1O)N2CC=C[C@@H](C2)C(N)=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
 NIR  NIR  (3S)-1-(5-deoxy-alpha-D-ribofuranosyl)-1,2,3,6-tetrahydropyridine-3-carboxamide  ligand  35  17  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NIR
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
 NIR  N1    N  NH2   0  -0.802  -4.0003  -1.6539  -0.8300
 NIR  C4    C  C     0  -0.276  -1.4125  -0.2686   0.3162
 NIR  C5    C  CR16  0  -0.449  -2.6485   0.2956  -0.3909
 NIR  C6    C  C     0   0.521  -3.8447  -0.5789  -0.0442
 NIR  O6    O  O     0  -0.481  -4.5774  -0.3286   0.9014
 NIR  C8    C  C     0  -0.319  -0.5615   1.8879   0.9085
 NIR  N9    N  NR6   0  -0.460  -0.2987   0.6577   0.1795
 NIR  C1'   C  CR15  0   0.254   0.9415   0.0648   0.6140
 NIR  C2'   C  CR15  0  -0.077   2.1667   0.9624   0.4537
 NIR  O2'   O  OH1   0  -0.663   2.0764   1.6800  -0.7496
 NIR  C3'   C  CR15  0  -0.005   3.2574  -0.1020   0.3847
 NIR  C4N   C  CR16  0  -0.159  -2.8785   1.7131   0.0314
 NIR  O3'   O  OH1   0  -0.666   4.4460   0.4301  -0.1280
 NIR  C4'   C  CR15  0   0.046   2.5929  -1.1611  -0.4996
 NIR  C5N   C  CR16  0  -0.276  -1.9314   2.4181   0.6360
 NIR  O4'   O  O     0  -0.516   1.2145  -1.0959  -0.1470
 NIR  C5'   C  CH3   0  -0.689   3.1175  -2.5648  -0.3014
 NIR  H1N1  H  HNH2  0   0.408  -3.3864  -1.8346  -1.6052
 NIR  H1N2  H  HNH2  0   0.400  -4.7197  -2.3319  -0.6385
 NIR  H41   H  H     0   0.260  -1.1453  -1.2224  -0.1354
 NIR  H55   H  HCR6  0   0.276  -2.4782   0.2517  -1.4731
 NIR  H8    H  H     0   0.260   0.1676   2.6463   0.6166
 NIR  H81   H  H     0   0.215  -0.4421   1.7554   1.9997
 NIR  H1'   H  HCR5  0   0.189   0.8749  -0.2206   1.6831
 NIR  H2'   H  HCR5  0   0.250   2.2936   1.6271   1.3174
 NIR  HB    H  HOH1  0   0.454   2.9187   2.1245  -0.8926
 NIR  H3'   H  HCR5  0   0.224   3.4056  -0.5149   1.3932
 NIR  H4N   H  HCR6  0   0.249  -3.8435   2.1612  -0.1753
 NIR  HA    H  HOH1  0   0.462   5.1651  -0.1855   0.0405
 NIR  H4'   H  HCR5  0   0.213   2.7178  -0.8713  -1.5514
 NIR  H5N   H  HCR6  0   0.251  -2.1230   3.4370   0.9513
 NIR  H5'1  H  HCH3  0   0.243   2.5874  -3.2831  -0.9277
 NIR  H5'2  H  HCH3  0   0.229   4.1723  -2.6139  -0.5766
 NIR  H5'3  H  HCH3  0   0.227   3.0246  -2.8792   0.7399
 NIR  H4    H  H     0   0.211  -1.6508  -0.4624   1.3761

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
 NIR  N1   C6    single  1.341  0.020  1.341
 NIR  N1   H1N1  single  0.860  0.020  1.020
 NIR  N1   H1N2  single  0.860  0.020  1.020
 NIR  C4   C5    single  1.532  0.020  1.532
 NIR  C4   N9    single  1.455  0.020  1.455
 NIR  C4   H4    single  0.970  0.020  1.090
 NIR  C4   H41   single  0.970  0.020  1.090
 NIR  C5   C6    single  1.522  0.020  1.522
 NIR  C5   C4N   single  1.497  0.020  1.497
 NIR  C5   H55   single  0.970  0.020  1.090
 NIR  C6   O6    double  1.222  0.020  1.222
 NIR  C8   N9    single  1.454  0.020  1.454
 NIR  C8   C5N   single  1.494  0.020  1.494
 NIR  C8   H8    single  0.970  0.020  1.090
 NIR  C8   H81   single  0.970  0.020  1.090
 NIR  N9   C1'   single  1.442  0.020  1.442
 NIR  C1'  C2'   single  1.527  0.020  1.527
 NIR  C1'  O4'   single  1.415  0.020  1.415
 NIR  C1'  H1'   single  0.970  0.020  1.090
 NIR  C2'  O2'   single  1.404  0.020  1.404
 NIR  C2'  C3'   single  1.526  0.020  1.526
 NIR  C2'  H2'   single  0.970  0.020  1.090
 NIR  O2'  HB    single  0.850  0.020  0.980
 NIR  C3'  O3'   single  1.400  0.020  1.400
 NIR  C3'  C4'   single  1.531  0.020  1.531
 NIR  C3'  H3'   single  0.970  0.020  1.090
 NIR  C4N  C5N   double  1.326  0.020  1.326
 NIR  C4N  H4N   single  0.930  0.020  1.080
 NIR  O3'  HA    single  0.850  0.020  0.980
 NIR  C4'  O4'   single  1.424  0.020  1.424
 NIR  C4'  C5'   single  1.512  0.020  1.512
 NIR  C4'  H4'   single  0.970  0.020  1.090
 NIR  C5N  H5N   single  0.930  0.020  1.080
 NIR  C5'  H5'1  single  0.970  0.020  1.090
 NIR  C5'  H5'2  single  0.970  0.020  1.090
 NIR  C5'  H5'3  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
 NIR  H1N2  N1   H1N1  117.51  3.000
 NIR  H1N2  N1   C6    120.76  3.000
 NIR  H1N1  N1   C6    121.69  3.000
 NIR  H41   C4   H4    107.31  3.000
 NIR  H41   C4   N9    109.32  3.000
 NIR  H4    C4   N9    111.55  3.000
 NIR  H41   C4   C5    109.23  3.000
 NIR  H4    C4   C5    109.50  3.000
 NIR  N9    C4   C5    109.86  3.000
 NIR  H55   C5   C4N   109.89  3.000
 NIR  H55   C5   C6    108.90  3.000
 NIR  C4N   C5   C6    111.05  3.000
 NIR  H55   C5   C4    108.39  3.000
 NIR  C4N   C5   C4    110.04  3.000
 NIR  C6    C5   C4    108.51  3.000
 NIR  O6    C6   C5    121.99  3.000
 NIR  O6    C6   N1    123.24  3.000
 NIR  C5    C6   N1    114.74  3.000
 NIR  H81   C8   H8    105.96  3.000
 NIR  H81   C8   C5N   108.76  3.000
 NIR  H8    C8   C5N   108.49  3.000
 NIR  H81   C8   N9    111.96  3.000
 NIR  H8    C8   N9    109.45  3.000
 NIR  C5N   C8   N9    112.00  3.000
 NIR  C1'   N9   C8    110.63  3.000
 NIR  C1'   N9   C4    111.62  3.000
 NIR  C8    N9   C4    110.68  3.000
 NIR  H1'   C1'  O4'   108.61  3.000
 NIR  H1'   C1'  C2'   107.51  3.000
 NIR  O4'   C1'  C2'   105.72  3.000
 NIR  H1'   C1'  N9    110.17  3.000
 NIR  O4'   C1'  N9    109.96  3.000
 NIR  C2'   C1'  N9    114.63  3.000
 NIR  H2'   C2'  C3'   112.06  3.000
 NIR  H2'   C2'  O2'   111.87  3.000
 NIR  C3'   C2'  O2'   111.34  3.000
 NIR  H2'   C2'  C1'   111.48  3.000
 NIR  C3'   C2'  C1'    99.68  3.000
 NIR  O2'   C2'  C1'   109.81  3.000
 NIR  HB    O2'  C2'   107.88  3.000
 NIR  H3'   C3'  C4'   109.17  3.000
 NIR  H3'   C3'  O3'   111.36  3.000
 NIR  C4'   C3'  O3'   114.83  3.000
 NIR  H3'   C3'  C2'   108.47  3.000
 NIR  C4'   C3'  C2'   101.44  3.000
 NIR  O3'   C3'  C2'   111.00  3.000
 NIR  H4N   C4N  C5N   120.20  3.000
 NIR  H4N   C4N  C5    118.33  3.000
 NIR  C5N   C4N  C5    121.48  3.000
 NIR  HA    O3'  C3'   109.12  3.000
 NIR  H4'   C4'  C5'   109.34  3.000
 NIR  H4'   C4'  O4'   109.58  3.000
 NIR  C5'   C4'  O4'   110.24  3.000
 NIR  H4'   C4'  C3'   108.73  3.000
 NIR  C5'   C4'  C3'   114.58  3.000
 NIR  O4'   C4'  C3'   104.20  3.000
 NIR  H5N   C5N  C4N   120.41  3.000
 NIR  H5N   C5N  C8    116.27  3.000
 NIR  C4N   C5N  C8    123.32  3.000
 NIR  C4'   O4'  C1'   110.95  3.000
 NIR  H5'3  C5'  H5'2  108.05  3.000
 NIR  H5'3  C5'  H5'1  108.47  3.000
 NIR  H5'2  C5'  H5'1  107.19  3.000
 NIR  H5'3  C5'  C4'   111.28  3.000
 NIR  H5'2  C5'  C4'   110.13  3.000
 NIR  H5'1  C5'  C4'   111.57  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
 NIR  CONST_01  H1N1  N1   C6   C5    0.00   0.0  0
 NIR  CONST_02  H1N2  N1   C6   C5  180.00   0.0  0
 NIR  Var_01    C5N   C8   N9   C4  -47.05  30.0  1
 NIR  Var_02    C8    N9   C4   C5   66.84  30.0  1
 NIR  Var_03    C8    C5N  C4N  C5    1.90  30.0  1
 NIR  Var_04    C4N   C5N  C8   N9   13.04  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
 NIR  chir_01  C5   C4   C6   C4N  negativ
 NIR  chir_02  C1'  O4'  N9   C2'  positiv
 NIR  chir_03  C2'  O2'  C1'  C3'  negativ
 NIR  chir_04  C3'  O3'  C4'  C2'  positiv
 NIR  chir_05  C4'  O4'  C3'  C5'  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
 NIR  plan-1  N1    0.020
 NIR  plan-1  C5    0.020
 NIR  plan-1  C6    0.020
 NIR  plan-1  O6    0.020
 NIR  plan-1  H1N1  0.020
 NIR  plan-1  H1N2  0.020

