# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 20:28:50 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: 1-[3-(4-carboxypiperidin-1-yl)-3-deoxy-beta-D-arabinofuranosyl]pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@@H](O)[C@@H]1N2CC[C@H](CC2)C(O)=O)N3C=CC(=O)NC3=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
 N3E  N3E  1-[3-(4-carboxypiperidin-1-yl)-3-deoxy-beta-D-arabinofuranosyl]pyrimidine-2,4(1H,3H)-dione  ligand  45  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N3E
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
 N3E  O2    O  OC     0  -0.482  -2.2989  -2.5039   0.6518
 N3E  C2    C  CR6    0   0.710  -3.0827  -1.5940   0.4737
 N3E  N3    N  NR16   0  -0.636  -4.4342  -1.7972   0.3968
 N3E  C4    C  CR6    0   0.580  -5.4251  -0.8576   0.1520
 N3E  O4    O  OC     0  -0.614  -6.5948  -1.1923   0.1028
 N3E  C5    C  CR16   0  -0.474  -4.9147   0.4774  -0.0246
 N3E  C6    C  CR16   0  -0.013  -3.5933   0.7057   0.0675
 N3E  N1    N  NR6    0  -0.422  -2.6865  -0.2812   0.3292
 N3E  C1'   C  CR15   0   0.125  -1.2563   0.0112   0.3848
 N3E  O4'   O  O      0  -0.529  -1.0861   1.2932   0.9010
 N3E  C4'   C  CR15   0   0.035  -0.0032   1.9578   0.2476
 N3E  C5'   C  CH2    0  -0.173  -0.4721   3.2330  -0.4184
 N3E  O5'   O  OH1    0  -0.684  -1.0039   4.0842   0.5693
 N3E  C2'   C  CR15   0   0.033  -0.5896   0.0158  -0.9937
 N3E  O2'   O  OH1    0  -0.647  -1.4148   0.6059  -1.9648
 N3E  C3'   C  CR15   0  -0.169   0.6058   0.9444  -0.7449
 N3E  N7    N  NT     0  -0.435   1.7635   0.2747  -0.1591
 N3E  C13   C  CH2    0  -0.309   2.8621   1.2327  -0.0345
 N3E  C8    C  CH2    0  -0.328   2.2160  -0.8680  -0.9540
 N3E  C9    C  CH2    0  -0.386   3.4573  -1.5303  -0.3750
 N3E  C10   C  CH1    0  -0.365   4.6069  -0.5464  -0.2186
 N3E  C12   C  CH2    0  -0.444   4.1023   0.6289   0.6037
 N3E  C11   C  C      0   0.426   5.9001  -1.1903   0.3203
 N3E  O13   O  OC    -1  -0.792   6.1172  -2.3733  -0.0105
 N3E  O12   O  O      0  -0.477   6.6429  -0.4750   1.0225
 N3E  HN3   H  HNR6   0   0.391  -4.7338  -2.7578   0.5143
 N3E  H5    H  HCR6   0   0.306  -5.5987   1.2891  -0.2183
 N3E  H6    H  HCR6   0   0.341  -3.1919   1.7020  -0.0323
 N3E  H1'   H  HCR5   0   0.315  -0.7947  -0.7404   1.0299
 N3E  H4'   H  HCR5   0   0.259   0.7144   2.2249   1.0263
 N3E  H5'1  H  HCH2   0   0.226  -1.2060   3.0070  -1.1993
 N3E  H5'2  H  HCH2   0   0.194   0.3992   3.6810  -0.9155
 N3E  H5'   H  HOH1   0   0.448  -1.4245   4.8285   0.1302
 N3E  H2'   H  HCR5   0   0.244  -0.3114  -0.9953  -1.2877
 N3E  H1    H  HOH1   0   0.451  -1.9491  -0.0781  -2.3793
 N3E  H3'   H  HCR5   0   0.294   0.8832   1.4355  -1.6932
 N3E  H131  H  HCH2   0   0.244   3.1291   1.6356  -1.0286
 N3E  H132  H  HCH2   0   0.212   2.5400   2.0873   0.5617
 N3E  H81   H  HCH2   0   0.231   1.4313  -1.6227  -0.9955
 N3E  H82   H  HCH2   0   0.218   2.4174  -0.5646  -1.9966
 N3E  H91   H  HCH2   0   0.238   3.7382  -2.3599  -1.0244
 N3E  H92   H  HCH2   0   0.141   3.2069  -1.9624   0.6001
 N3E  H10   H  HCH1   0   0.258   4.8337  -0.1395  -1.2212
 N3E  H121  H  HCH2   0   0.202   4.8655   1.4040   0.6832
 N3E  H122  H  HCH2   0   0.259   3.8684   0.3078   1.6240

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
 N3E  O2   C2    double    1.214  0.020  1.214
 N3E  C2   N3    aromatic  1.369  0.020  1.369
 N3E  C2   N1    aromatic  1.379  0.020  1.379
 N3E  N3   C4    aromatic  1.387  0.020  1.387
 N3E  N3   HN3   single    0.860  0.020  1.020
 N3E  C4   O4    double    1.218  0.020  1.218
 N3E  C4   C5    aromatic  1.440  0.020  1.440
 N3E  C5   C6    aromatic  1.344  0.020  1.344
 N3E  C5   H5    single    0.930  0.020  1.080
 N3E  C6   N1    aromatic  1.366  0.020  1.366
 N3E  C6   H6    single    0.930  0.020  1.080
 N3E  N1   C1'   single    1.461  0.020  1.461
 N3E  C1'  O4'   single    1.392  0.020  1.392
 N3E  C1'  C2'   single    1.531  0.020  1.531
 N3E  C1'  H1'   single    0.970  0.020  1.090
 N3E  O4'  C4'   single    1.429  0.020  1.429
 N3E  C4'  C5'   single    1.513  0.020  1.513
 N3E  C4'  C3'   single    1.544  0.020  1.544
 N3E  C4'  H4'   single    0.970  0.020  1.090
 N3E  C5'  O5'   single    1.408  0.020  1.408
 N3E  C5'  H5'1  single    0.970  0.020  1.090
 N3E  C5'  H5'2  single    0.970  0.020  1.090
 N3E  O5'  H5'   single    0.850  0.020  0.980
 N3E  C2'  O2'   single    1.404  0.020  1.404
 N3E  C2'  C3'   single    1.534  0.020  1.534
 N3E  C2'  H2'   single    0.970  0.020  1.090
 N3E  O2'  H1    single    0.850  0.020  0.980
 N3E  C3'  N7    single    1.460  0.020  1.460
 N3E  C3'  H3'   single    0.970  0.020  1.090
 N3E  N7   C13   single    1.463  0.020  1.463
 N3E  N7   C8    single    1.464  0.020  1.464
 N3E  C13  C12   single    1.520  0.020  1.520
 N3E  C13  H131  single    0.970  0.020  1.090
 N3E  C13  H132  single    0.970  0.020  1.090
 N3E  C8   C9    single    1.521  0.020  1.521
 N3E  C8   H81   single    0.970  0.020  1.090
 N3E  C8   H82   single    0.970  0.020  1.090
 N3E  C9   C10   single    1.521  0.020  1.521
 N3E  C9   H91   single    0.970  0.020  1.090
 N3E  C9   H92   single    0.970  0.020  1.090
 N3E  C10  C12   single    1.521  0.020  1.521
 N3E  C10  C11   single    1.542  0.020  1.542
 N3E  C10  H10   single    0.970  0.020  1.090
 N3E  C12  H121  single    0.970  0.020  1.090
 N3E  C12  H122  single    0.970  0.020  1.090
 N3E  C11  O13   deloc     1.247  0.020  1.247
 N3E  C11  O12   deloc     1.248  0.020  1.248

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
 N3E  N1    C2   N3    114.78  3.000
 N3E  N1    C2   O2    122.92  3.000
 N3E  N3    C2   O2    122.31  3.000
 N3E  HN3   N3   C4    116.84  3.000
 N3E  HN3   N3   C2    115.23  3.000
 N3E  C4    N3   C2    127.92  3.000
 N3E  C5    C4   O4    126.18  3.000
 N3E  C5    C4   N3    113.35  3.000
 N3E  O4    C4   N3    120.47  3.000
 N3E  H5    C5   C6    120.52  3.000
 N3E  H5    C5   C4    119.65  3.000
 N3E  C6    C5   C4    119.83  3.000
 N3E  H6    C6   N1    115.99  3.000
 N3E  H6    C6   C5    121.08  3.000
 N3E  N1    C6   C5    122.90  3.000
 N3E  C1'   N1   C6    120.84  3.000
 N3E  C1'   N1   C2    117.90  3.000
 N3E  C6    N1   C2    121.16  3.000
 N3E  H1'   C1'  C2'   110.46  3.000
 N3E  H1'   C1'  O4'   111.27  3.000
 N3E  C2'   C1'  O4'   106.13  3.000
 N3E  H1'   C1'  N1    107.36  3.000
 N3E  C2'   C1'  N1    113.12  3.000
 N3E  O4'   C1'  N1    108.55  3.000
 N3E  C4'   O4'  C1'   110.57  3.000
 N3E  H4'   C4'  C3'   111.08  3.000
 N3E  H4'   C4'  C5'   108.14  3.000
 N3E  C3'   C4'  C5'   113.11  3.000
 N3E  H4'   C4'  O4'   106.60  3.000
 N3E  C3'   C4'  O4'   106.72  3.000
 N3E  C5'   C4'  O4'   111.01  3.000
 N3E  H5'2  C5'  H5'1  107.03  3.000
 N3E  H5'2  C5'  O5'   111.75  3.000
 N3E  H5'1  C5'  O5'   111.83  3.000
 N3E  H5'2  C5'  C4'   107.28  3.000
 N3E  H5'1  C5'  C4'   110.33  3.000
 N3E  O5'   C5'  C4'   108.53  3.000
 N3E  H5'   O5'  C5'   108.24  3.000
 N3E  H2'   C2'  C3'   114.00  3.000
 N3E  H2'   C2'  O2'   110.70  3.000
 N3E  C3'   C2'  O2'   108.40  3.000
 N3E  H2'   C2'  C1'   110.58  3.000
 N3E  C3'   C2'  C1'   101.25  3.000
 N3E  O2'   C2'  C1'   111.58  3.000
 N3E  H1    O2'  C2'   109.00  3.000
 N3E  H3'   C3'  N7    110.46  3.000
 N3E  H3'   C3'  C2'   109.03  3.000
 N3E  N7    C3'  C2'   113.91  3.000
 N3E  H3'   C3'  C4'   111.08  3.000
 N3E  N7    C3'  C4'   110.85  3.000
 N3E  C2'   C3'  C4'   101.20  3.000
 N3E  C8    N7   C13   108.99  3.000
 N3E  C8    N7   C3'   112.67  3.000
 N3E  C13   N7   C3'   109.22  3.000
 N3E  H132  C13  H131  106.10  3.000
 N3E  H132  C13  C12   108.83  3.000
 N3E  H131  C13  C12   108.99  3.000
 N3E  H132  C13  N7    109.75  3.000
 N3E  H131  C13  N7    110.09  3.000
 N3E  C12   C13  N7    112.86  3.000
 N3E  H82   C8   H81   106.59  3.000
 N3E  H82   C8   C9    109.27  3.000
 N3E  H81   C8   C9    107.49  3.000
 N3E  H82   C8   N7    110.77  3.000
 N3E  H81   C8   N7    109.81  3.000
 N3E  C9    C8   N7    112.67  3.000
 N3E  H92   C9   H91   106.79  3.000
 N3E  H92   C9   C10   109.65  3.000
 N3E  H91   C9   C10   111.01  3.000
 N3E  H92   C9   C8    108.90  3.000
 N3E  H91   C9   C8    108.35  3.000
 N3E  C10   C9   C8    111.97  3.000
 N3E  H10   C10  C11   107.38  3.000
 N3E  H10   C10  C12   105.90  3.000
 N3E  C11   C10  C12   114.34  3.000
 N3E  H10   C10  C9    107.44  3.000
 N3E  C11   C10  C9    113.56  3.000
 N3E  C12   C10  C9    107.74  3.000
 N3E  H122  C12  H121  106.86  3.000
 N3E  H122  C12  C10   110.37  3.000
 N3E  H121  C12  C10   110.88  3.000
 N3E  H122  C12  C13   109.48  3.000
 N3E  H121  C12  C13   108.62  3.000
 N3E  C10   C12  C13   110.54  3.000
 N3E  O12   C11  O13   126.11  3.000
 N3E  O12   C11  C10   117.18  3.000
 N3E  O13   C11  C10   116.70  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
 N3E  CONST_01  C5   C4   N3   C2     0.00   0.0  0
 N3E  CONST_02  C5   C6   N1   C2     0.00   0.0  0
 N3E  CONST_03  C6   N1   C2   N3     0.00   0.0  0
 N3E  CONST_04  C6   C5   C4   N3     0.00   0.0  0
 N3E  CONST_05  N1   C2   N3   C4     0.00   0.0  0
 N3E  CONST_06  N1   C6   C5   C4     0.00   0.0  0
 N3E  CONST_07  C1'  N1   C2   N3   180.00   0.0  0
 N3E  CONST_08  C1'  N1   C6   C5   180.00   0.0  0
 N3E  CONST_09  C4   N3   C2   O2   180.00   0.0  0
 N3E  CONST_10  C6   N1   C2   O2   180.00   0.0  0
 N3E  CONST_11  C1'  N1   C2   O2     0.00   0.0  0
 N3E  CONST_12  O4   C4   N3   C2   180.00   0.0  0
 N3E  CONST_13  C6   C5   C4   O4   180.00   0.0  0
 N3E  CONST_14  H6   C6   N1   C2   180.00   0.0  0
 N3E  CONST_15  H5   C5   C4   N3   180.00   0.0  0
 N3E  CONST_16  HN3  N3   C4   C5   180.00   0.0  0
 N3E  Var_01    C12  C13  N7   C3'  178.45  30.0  1
 N3E  Var_02    C9   C8   N7   C3'  177.60  30.0  1
 N3E  Var_03    C10  C12  C13  N7    59.40  30.0  1
 N3E  Var_04    C10  C9   C8   N7   -56.57  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
 N3E  chir_01  C1'  N1   O4'  C2'  positiv
 N3E  chir_02  C4'  O4'  C3'  C5'  negativ
 N3E  chir_03  C2'  O2'  C3'  C1'  negativ
 N3E  chir_04  C3'  N7   C2'  C4'  negativ
 N3E  chir_05  C10  C9   C12  C11  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
 N3E  plan-1  O2   0.020
 N3E  plan-1  C2   0.020
 N3E  plan-1  N3   0.020
 N3E  plan-1  C4   0.020
 N3E  plan-1  O4   0.020
 N3E  plan-1  C5   0.020
 N3E  plan-1  C6   0.020
 N3E  plan-1  N1   0.020
 N3E  plan-1  C1'  0.020
 N3E  plan-1  HN3  0.020
 N3E  plan-1  H5   0.020
 N3E  plan-1  H6   0.020
 N3E  plan-2  C10  0.020
 N3E  plan-2  C11  0.020
 N3E  plan-2  O13  0.020
 N3E  plan-2  O12  0.020

