# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 11:46:58 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 1-{5-deoxy-5-[4-(ethoxycarbonyl)piperidin-1-yl]-alpha-L-arabinofuranosyl}pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)[C@H]1CCN(CC1)C[C@@H]2O[C@H]([C@H](O)[C@H]2O)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
 U1S  U1S  1-{5-deoxy-5-[4-(ethoxycarbonyl)piperidin-1-yl]-alpha-L-arabinofuranosyl}pyrimidine-2,4(1H,3H)-dione  ligand  52  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_U1S
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
 U1S  C4    C  CR6   0   0.567  -4.4600  -3.2566  -0.5383
 U1S  C5    C  CR16  0  -0.513  -4.8104  -2.3079  -1.5656
 U1S  C6    C  CR16  0   0.101  -4.3017  -1.0667  -1.5192
 U1S  N1    N  NR6   0  -0.568  -3.4641  -0.6286  -0.5328
 U1S  N3    N  NR16  0  -0.734  -3.6001  -2.7371   0.4178
 U1S  CAV   C  CH1   0  -0.401   4.0925   0.6133  -0.3374
 U1S  CAK   C  CH2   0  -0.425   3.4415   1.1735  -1.5941
 U1S  CAM   C  CH2   0  -0.283   2.3034   2.1136  -1.2316
 U1S  CAJ   C  CH2   0  -0.430   3.0186  -0.0328   0.5438
 U1S  CAL   C  CH2   0  -0.291   1.8965   0.9548   0.8186
 U1S  NBA   N  NT    0  -0.422   1.3024   1.4548  -0.4086
 U1S  C4'   C  CH1   0   0.004  -1.0469   1.6376   0.3716
 U1S  O4'   O  O2    0  -0.485  -1.5645   0.7616  -0.6276
 U1S  C3'   C  CH1   0  -0.002  -2.2012   2.5817   0.6862
 U1S  O3'   O  OH1   0  -0.662  -2.0178   3.1715   1.9422
 U1S  C2'   C  CH1   0  -0.048  -3.3971   1.6365   0.5781
 U1S  O2'   O  OH1   0  -0.661  -4.6243   2.2301   0.2567
 U1S  C1'   C  CH1   0   0.209  -2.9579   0.7411  -0.5812
 U1S  O4    O  O     0  -0.464  -4.8430  -4.4094  -0.4652
 U1S  C2    C  CR6   0   0.747  -3.0787  -1.4721   0.4926
 U1S  O2    O  O     0  -0.468  -2.3414  -1.1321   1.3926
 U1S  H5    H  HCR6  0   0.294  -5.4677  -2.6019  -2.3689
 U1S  H6    H  HCR6  0   0.328  -4.5384  -0.3377  -2.2810
 U1S  HN3   H  HNR6  0   0.426  -3.3159  -3.3618   1.1626
 U1S  C15   C  CH3   0  -0.689   7.3115  -2.1161   1.7215
 U1S  HAV   H  HCH1  0   0.269   4.5359   1.4412   0.2318
 U1S  HAK   H  HCH2  0   0.242   4.1685   1.7158  -2.2014
 U1S  HAKA  H  HCH2  0   0.227   3.0521   0.3567  -2.2072
 U1S  HAM   H  HCH2  0   0.189   2.7141   3.0069  -0.7274
 U1S  HAMA  H  HCH2  0   0.241   1.8246   2.4654  -2.1482
 U1S  HAJ   H  HCH2  0   0.231   2.6132  -0.9160   0.0412
 U1S  HAJA  H  HCH2  0   0.249   3.4354  -0.3616   1.4963
 U1S  HAL   H  HCH2  0   0.246   1.1362   0.4507   1.4169
 U1S  HALA  H  HCH2  0   0.192   2.2883   1.7827   1.4377
 U1S  H4'   H  HCH1  0   0.236  -0.8125   1.0627   1.2754
 U1S  H3'   H  HCH1  0   0.225  -2.2799   3.3408  -0.1078
 U1S  HO3'  H  HOH1  0   0.460  -2.6056   3.9286   2.0185
 U1S  H2'   H  HCH1  0   0.252  -3.4628   1.0638   1.5094
 U1S  HO2'  H  HOH1  0   0.463  -5.0483   2.5202   1.0693
 U1S  H1'   H  HCH1  0   0.262  -3.3629   1.1545  -1.5112
 U1S  C16   C  CH2   0  -0.180   6.8623  -1.7460   0.3287
 U1S  H21   H  HCH3  0   0.236   6.5025  -2.5664   2.2967
 U1S  H22   H  HCH3  0   0.239   8.1200  -2.8433   1.6554
 U1S  H23   H  HCH3  0   0.236   7.6858  -1.2500   2.2672
 U1S  H24   H  HCH2  0   0.234   7.6831  -1.3071  -0.2424
 U1S  H25   H  HCH2  0   0.234   6.5103  -2.6261  -0.2132
 U1S  C5'   C  CH2   0  -0.277   0.1851   2.3429  -0.1512
 U1S  C17   C  C     0   0.625   5.2088  -0.3532  -0.6518
 U1S  H5'   H  HCH2  0   0.208   0.4508   3.1401   0.5647
 U1S  H5'A  H  HCH2  0   0.239  -0.0840   2.8426  -1.0862
 U1S  O6    O  O2    0  -0.457   5.7952  -0.7937   0.4526
 U1S  O7    O  O     0  -0.451   5.5401  -0.6962  -1.7606

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
 U1S  C4   C5    single  1.442  0.020  1.442
 U1S  C4   N3    single  1.387  0.020  1.387
 U1S  C4   O4    double  1.217  0.020  1.217
 U1S  C5   C6    double  1.342  0.020  1.342
 U1S  C5   H5    single  0.930  0.020  1.080
 U1S  C6   N1    single  1.366  0.020  1.366
 U1S  C6   H6    single  0.930  0.020  1.080
 U1S  N1   C1'   single  1.461  0.020  1.461
 U1S  N1   C2    single  1.383  0.020  1.383
 U1S  N3   C2    single  1.370  0.020  1.370
 U1S  N3   HN3   single  0.860  0.020  1.020
 U1S  CAV  CAK   single  1.522  0.020  1.522
 U1S  CAV  CAJ   single  1.532  0.020  1.532
 U1S  CAV  C17   single  1.510  0.020  1.510
 U1S  CAV  HAV   single  0.970  0.020  1.090
 U1S  CAK  CAM   single  1.520  0.020  1.520
 U1S  CAK  HAK   single  0.970  0.020  1.090
 U1S  CAK  HAKA  single  0.970  0.020  1.090
 U1S  CAM  NBA   single  1.454  0.020  1.454
 U1S  CAM  HAM   single  0.970  0.020  1.090
 U1S  CAM  HAMA  single  0.970  0.020  1.090
 U1S  CAJ  CAL   single  1.520  0.020  1.520
 U1S  CAJ  HAJ   single  0.970  0.020  1.090
 U1S  CAJ  HAJA  single  0.970  0.020  1.090
 U1S  CAL  NBA   single  1.452  0.020  1.452
 U1S  CAL  HAL   single  0.970  0.020  1.090
 U1S  CAL  HALA  single  0.970  0.020  1.090
 U1S  NBA  C5'   single  1.450  0.020  1.450
 U1S  C5'  C4'   single  1.513  0.020  1.513
 U1S  C5'  H5'   single  0.970  0.020  1.090
 U1S  C5'  H5'A  single  0.970  0.020  1.090
 U1S  C4'  O4'   single  1.426  0.020  1.426
 U1S  C4'  C3'   single  1.524  0.020  1.524
 U1S  C4'  H4'   single  0.970  0.020  1.090
 U1S  O4'  C1'   single  1.394  0.020  1.394
 U1S  C3'  O3'   single  1.400  0.020  1.400
 U1S  C3'  C2'   single  1.528  0.020  1.528
 U1S  C3'  H3'   single  0.970  0.020  1.090
 U1S  O3'  HO3'  single  0.850  0.020  0.980
 U1S  C2'  O2'   single  1.401  0.020  1.401
 U1S  C2'  C1'   single  1.529  0.020  1.529
 U1S  C2'  H2'   single  0.970  0.020  1.090
 U1S  O2'  HO2'  single  0.850  0.020  0.980
 U1S  C1'  H1'   single  0.970  0.020  1.090
 U1S  C2   O2    double  1.212  0.020  1.212
 U1S  C15  C16   single  1.509  0.020  1.509
 U1S  C16  O6    single  1.436  0.020  1.436
 U1S  O6   C17   single  1.326  0.020  1.326
 U1S  C17  O7    double  1.207  0.020  1.207
 U1S  C15  H21   single  0.970  0.020  1.090
 U1S  C15  H22   single  0.970  0.020  1.090
 U1S  C15  H23   single  0.970  0.020  1.090
 U1S  C16  H24   single  0.970  0.020  1.090
 U1S  C16  H25   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
 U1S  O4    C4   N3   120.57  3.000
 U1S  O4    C4   C5   126.14  3.000
 U1S  N3    C4   C5   113.29  3.000
 U1S  H5    C5   C6   120.58  3.000
 U1S  H5    C5   C4   119.96  3.000
 U1S  C6    C5   C4   119.46  3.000
 U1S  H6    C6   N1   115.27  3.000
 U1S  H6    C6   C5   121.09  3.000
 U1S  N1    C6   C5   123.63  3.000
 U1S  C2    N1   C1'  120.00  3.000
 U1S  C2    N1   C6   120.71  3.000
 U1S  C1'   N1   C6   119.29  3.000
 U1S  HN3   N3   C2   114.99  3.000
 U1S  HN3   N3   C4   116.74  3.000
 U1S  C2    N3   C4   128.27  3.000
 U1S  C17   CAV  HAV  106.98  3.000
 U1S  HAV   CAV  CAJ  107.62  3.000
 U1S  C17   CAV  CAJ  111.60  3.000
 U1S  HAV   CAV  CAK  108.85  3.000
 U1S  C17   CAV  CAK  112.33  3.000
 U1S  CAJ   CAV  CAK  109.28  3.000
 U1S  HAKA  CAK  HAK  107.25  3.000
 U1S  HAKA  CAK  CAM  109.22  3.000
 U1S  HAK   CAK  CAM  108.91  3.000
 U1S  HAKA  CAK  CAV  109.90  3.000
 U1S  HAK   CAK  CAV  110.93  3.000
 U1S  CAM   CAK  CAV  110.54  3.000
 U1S  HAMA  CAM  HAM  106.58  3.000
 U1S  HAMA  CAM  NBA  108.61  3.000
 U1S  HAM   CAM  NBA  111.34  3.000
 U1S  HAMA  CAM  CAK  109.10  3.000
 U1S  HAM   CAM  CAK  109.30  3.000
 U1S  NBA   CAM  CAK  111.74  3.000
 U1S  HAJA  CAJ  HAJ  107.42  3.000
 U1S  HAJA  CAJ  CAL  108.68  3.000
 U1S  HAJ   CAJ  CAL  109.52  3.000
 U1S  HAJA  CAJ  CAV  111.20  3.000
 U1S  HAJ   CAJ  CAV  109.62  3.000
 U1S  CAL   CAJ  CAV  110.33  3.000
 U1S  HALA  CAL  HAL  106.61  3.000
 U1S  HALA  CAL  NBA  111.12  3.000
 U1S  HAL   CAL  NBA  109.72  3.000
 U1S  HALA  CAL  CAJ  109.04  3.000
 U1S  HAL   CAL  CAJ  108.27  3.000
 U1S  NBA   CAL  CAJ  111.90  3.000
 U1S  C5'   NBA  CAL  112.09  3.000
 U1S  C5'   NBA  CAM  110.70  3.000
 U1S  CAL   NBA  CAM  110.65  3.000
 U1S  H4'   C4'  C3'  108.46  3.000
 U1S  H4'   C4'  O4'  109.45  3.000
 U1S  C3'   C4'  O4'  104.49  3.000
 U1S  H4'   C4'  C5'  110.81  3.000
 U1S  C3'   C4'  C5'  113.54  3.000
 U1S  O4'   C4'  C5'  109.86  3.000
 U1S  C1'   O4'  C4'  110.39  3.000
 U1S  H3'   C3'  C2'  108.63  3.000
 U1S  H3'   C3'  O3'  111.46  3.000
 U1S  C2'   C3'  O3'  115.25  3.000
 U1S  H3'   C3'  C4'  109.41  3.000
 U1S  C2'   C3'  C4'  101.24  3.000
 U1S  O3'   C3'  C4'  110.31  3.000
 U1S  HO3'  O3'  C3'  108.84  3.000
 U1S  H2'   C2'  C1'  110.84  3.000
 U1S  H2'   C2'  O2'  111.36  3.000
 U1S  C1'   C2'  O2'  109.02  3.000
 U1S  H2'   C2'  C3'  108.07  3.000
 U1S  C1'   C2'  C3'  101.01  3.000
 U1S  O2'   C2'  C3'  116.09  3.000
 U1S  HO2'  O2'  C2'  108.68  3.000
 U1S  H1'   C1'  C2'  108.45  3.000
 U1S  H1'   C1'  O4'  109.61  3.000
 U1S  C2'   C1'  O4'  107.68  3.000
 U1S  H1'   C1'  N1   104.70  3.000
 U1S  C2'   C1'  N1   115.11  3.000
 U1S  O4'   C1'  N1   111.17  3.000
 U1S  O2    C2   N3   122.07  3.000
 U1S  O2    C2   N1   123.30  3.000
 U1S  N3    C2   N1   114.62  3.000
 U1S  H23   C15  H22  107.81  3.000
 U1S  H23   C15  H21  108.60  3.000
 U1S  H22   C15  H21  107.88  3.000
 U1S  H23   C15  C16  111.67  3.000
 U1S  H22   C15  C16  109.18  3.000
 U1S  H21   C15  C16  111.55  3.000
 U1S  H25   C16  H24  107.86  3.000
 U1S  H25   C16  O6   109.75  3.000
 U1S  H24   C16  O6   109.71  3.000
 U1S  H25   C16  C15  110.87  3.000
 U1S  H24   C16  C15  110.94  3.000
 U1S  O6    C16  C15  107.71  3.000
 U1S  H5'A  C5'  H5'  106.48  3.000
 U1S  H5'A  C5'  C4'  107.94  3.000
 U1S  H5'   C5'  C4'  107.97  3.000
 U1S  H5'A  C5'  NBA  108.52  3.000
 U1S  H5'   C5'  NBA  111.83  3.000
 U1S  C4'   C5'  NBA  113.78  3.000
 U1S  O7    C17  O6   123.33  3.000
 U1S  O7    C17  CAV  125.18  3.000
 U1S  O6    C17  CAV  111.49  3.000
 U1S  C17   O6   C16  118.51  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
 U1S  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 U1S  CONST_02  C2   N3   C4   C5     0.00   0.0  0
 U1S  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 U1S  CONST_04  C1'  N1   C2   N3   180.00   0.0  0
 U1S  CONST_05  O2   C2   N3   C4   180.00   0.0  0
 U1S  CONST_06  O2   C2   N1   C6   180.00   0.0  0
 U1S  CONST_07  O2   C2   N1   C1'    0.00   0.0  0
 U1S  CONST_08  C2   N3   C4   O4   180.00   0.0  0
 U1S  CONST_09  HN3  N3   C4   C5   180.00   0.0  0
 U1S  Var_01    NBA  CAM  CAK  CAV  -57.32  30.0  1
 U1S  Var_02    NBA  CAL  CAJ  CAV   56.98  30.0  1
 U1S  Var_03    CAL  NBA  CAM  CAK   58.95  30.0  1
 U1S  Var_04    CAJ  CAL  NBA  CAM  -58.95  30.0  1
 U1S  Var_05    C4'  C5'  NBA  CAM  164.57  30.0  3
 U1S  Var_06    O7   C17  O6   C16   -1.20  30.0  3
 U1S  Var_07    H21  C15  C16  O6    60.60  30.0  3
 U1S  Var_08    H24  C16  O6   C17   61.26  30.0  2

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
 U1S  chir_01  CAV  CAK  CAJ  C17  negativ
 U1S  chir_02  C4'  O4'  C5'  C3'  negativ
 U1S  chir_03  C3'  O3'  C4'  C2'  negativ
 U1S  chir_04  C2'  O2'  C3'  C1'  positiv
 U1S  chir_05  C1'  O4'  N1   C2'  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
 U1S  plan-1  C4   0.020
 U1S  plan-1  C5   0.020
 U1S  plan-1  C6   0.020
 U1S  plan-1  N1   0.020
 U1S  plan-1  N3   0.020
 U1S  plan-1  C1'  0.020
 U1S  plan-1  O4   0.020
 U1S  plan-1  C2   0.020
 U1S  plan-1  O2   0.020
 U1S  plan-1  H5   0.020
 U1S  plan-1  H6   0.020
 U1S  plan-1  HN3  0.020
 U1S  plan-2  CAV  0.020
 U1S  plan-2  C17  0.020
 U1S  plan-2  O6   0.020
 U1S  plan-2  O7   0.020

