# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 03:23:57 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: 5'-{[(3S)-3-amino-3-carboxypropyl](methylidene)-lambda~4~-sulfanyl}-5'-deoxyuridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC[S](=C)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O)C(O)=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
 YQP  YQP  "(2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl-methyl-$l^{3}-sulfanyl]butanoic acid"  ligand  45  25  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YQP
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
 YQP  N    N  NH2    0  -0.788  8.1674  -59.0656  29.9380
 YQP  CA   C  CH1    0  -0.208  6.8957  -58.3612  29.8852
 YQP  C    C  C      0   0.387  5.6737  -59.1559  30.4214
 YQP  OXT  O  OC     0  -0.613  4.6389  -58.4890  30.6257
 YQP  CB   C  CH2    0  -0.425  6.6029  -57.9164  28.4450
 YQP  CG   C  CH2    0  -0.558  7.6728  -56.9773  27.9173
 YQP  SD   S  S3     0   0.331  7.5174  -56.5895  26.1306
 YQP  CE   C  C2     0  -0.869  8.7478  -55.6032  25.5633
 YQP  O    O  O     -1  -0.597  5.8179  -60.3840  30.5780
 YQP  CAH  C  CH2    0  -0.589  6.0322  -55.5349  26.2341
 YQP  CAK  C  CR15   0   0.066  5.6205  -55.0380  24.8737
 YQP  CAM  C  CR15   0   0.206  4.2814  -55.7534  23.1293
 YQP  CAN  C  CR15   0  -0.051  3.7735  -54.3520  23.5190
 YQP  CAO  C  CR15   0  -0.016  4.3999  -54.1183  24.9072
 YQP  CAS  C  CR16   0   0.100  3.1485  -57.4908  21.8470
 YQP  CAT  C  CR6    0   0.744  2.4919  -57.1226  24.1141
 YQP  CAV  C  CR16   0  -0.509  2.2736  -58.4909  21.6622
 YQP  CAW  C  CR6    0   0.565  1.4111  -58.8897  22.7474
 YQP  NAR  N  NR6    0  -0.570  3.2727  -56.7997  23.0208
 YQP  NAU  N  NR16   0  -0.734  1.6156  -58.1548  23.9074
 YQP  OAL  O  O      0  -0.486  5.2462  -56.1391  24.0649
 YQP  OAP  O  OH1    0  -0.658  4.8125  -52.7906  25.1017
 YQP  OAQ  O  OH1    0  -0.668  4.2865  -53.4392  22.5850
 YQP  OAX  O  O      0  -0.451  0.5746  -59.7705  22.7131
 YQP  OAY  O  O      0  -0.463  2.5645  -56.5421  25.1750
 YQP  H1   H  HNH2   0   0.336  8.4774  -59.1106  30.9010
 YQP  H2   H  HNH2   0   0.324  7.9889  -60.0313  29.6839
 YQP  H4   H  HCH1   0   0.213  6.9895  -57.4536  30.4922
 YQP  H6   H  HCH2   0   0.238  5.6241  -57.4358  28.4247
 YQP  H7   H  HCH2   0   0.225  6.5389  -58.8010  27.8019
 YQP  H8   H  HCH2   0   0.279  8.6577  -57.4374  27.9993
 YQP  H9   H  HCH2   0   0.266  7.6926  -56.0300  28.4633
 YQP  H10  H  H      0   0.205  9.1001  -54.8278  26.2360
 YQP  H11  H  H      0   0.215  9.5111  -56.1671  25.0427
 YQP  H13  H  HCH2   0   0.292  6.2733  -54.6910  26.8838
 YQP  H14  H  HCH2   0   0.287  5.2339  -56.1200  26.6931
 YQP  H15  H  HCR5   0   0.242  6.4663  -54.5049  24.4187
 YQP  H16  H  HCR5   0   0.264  4.7197  -55.6837  22.1295
 YQP  H17  H  HCR5   0   0.249  2.6789  -54.3068  23.5466
 YQP  H18  H  HCR5   0   0.260  3.7025  -54.4369  25.6833
 YQP  H19  H  HCR6   0   0.328  3.8108  -57.1761  21.0527
 YQP  H20  H  HCR6   0   0.292  2.2144  -59.0012  20.7135
 YQP  H21  H  HNR6   0   0.425  1.0392  -58.3945  24.7056
 YQP  H22  H  HOH1   0   0.468  4.1125  -52.3064  25.5509
 YQP  H23  H  HOH1   0   0.447  4.5433  -52.6475  23.0777

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
 YQP  CAV  CAS  double  1.342  0.020  1.342
 YQP  CAV  CAW  single  1.442  0.020  1.442
 YQP  CAS  NAR  single  1.368  0.020  1.368
 YQP  OAX  CAW  double  1.215  0.020  1.215
 YQP  OAQ  CAN  single  1.403  0.020  1.403
 YQP  CAW  NAU  single  1.388  0.020  1.388
 YQP  NAR  CAM  single  1.457  0.020  1.457
 YQP  NAR  CAT  single  1.382  0.020  1.382
 YQP  CAM  CAN  single  1.541  0.020  1.541
 YQP  CAM  OAL  single  1.398  0.020  1.398
 YQP  CAN  CAO  single  1.541  0.020  1.541
 YQP  NAU  CAT  single  1.370  0.020  1.370
 YQP  OAL  CAK  single  1.417  0.020  1.417
 YQP  CAT  OAY  double  1.211  0.020  1.211
 YQP  CAK  CAO  single  1.529  0.020  1.529
 YQP  CAK  CAH  single  1.506  0.020  1.506
 YQP  CAO  OAP  single  1.404  0.020  1.404
 YQP  CE   SD   double  1.676  0.020  1.676
 YQP  CAH  SD   single  1.824  0.020  1.824
 YQP  SD   CG   single  1.835  0.020  1.835
 YQP  CG   CB   single  1.518  0.020  1.518
 YQP  CB   CA   single  1.536  0.020  1.536
 YQP  O    C    deloc   1.246  0.020  1.246
 YQP  N    CA   single  1.455  0.020  1.455
 YQP  CA   C    single  1.553  0.020  1.553
 YQP  C    OXT  deloc   1.248  0.020  1.248
 YQP  N    H1   single  0.868  0.020  1.013
 YQP  N    H2   single  0.868  0.020  1.013
 YQP  CA   H4   single  0.939  0.020  1.096
 YQP  CB   H6   single  0.939  0.020  1.096
 YQP  CB   H7   single  0.939  0.020  1.096
 YQP  CG   H8   single  0.939  0.020  1.096
 YQP  CG   H9   single  0.939  0.020  1.096
 YQP  CE   H10  single  0.930  0.020  1.086
 YQP  CE   H11  single  0.930  0.020  1.086
 YQP  CAH  H13  single  0.939  0.020  1.096
 YQP  CAH  H14  single  0.939  0.020  1.096
 YQP  CAK  H15  single  0.939  0.020  1.096
 YQP  CAM  H16  single  0.939  0.020  1.096
 YQP  CAN  H17  single  0.939  0.020  1.096
 YQP  CAO  H18  single  0.939  0.020  1.096
 YQP  CAS  H19  single  0.930  0.020  1.086
 YQP  CAV  H20  single  0.930  0.020  1.086
 YQP  NAU  H21  single  0.868  0.020  1.013
 YQP  OAP  H22  single  0.832  0.020  0.971
 YQP  OAQ  H23  single  0.832  0.020  0.971

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
 YQP  H2   N    H1   104.47  3.000
 YQP  H2   N    CA   107.34  3.000
 YQP  H1   N    CA   108.88  3.000
 YQP  H4   CA   CB   107.21  3.000
 YQP  H4   CA   C    107.45  3.000
 YQP  CB   CA   C    108.78  3.000
 YQP  H4   CA   N    107.82  3.000
 YQP  C    CA   N    115.30  3.000
 YQP  CB   CA   N    109.94  3.000
 YQP  O    C    OXT  127.01  3.000
 YQP  OXT  C    CA   115.81  3.000
 YQP  O    C    CA   117.16  3.000
 YQP  H7   CB   H6   107.00  3.000
 YQP  H7   CB   CG   109.67  3.000
 YQP  H6   CB   CG   110.70  3.000
 YQP  H7   CB   CA   109.14  3.000
 YQP  H6   CB   CA   108.44  3.000
 YQP  CG   CB   CA   111.76  3.000
 YQP  H9   CG   H8   108.16  3.000
 YQP  H9   CG   SD   107.73  3.000
 YQP  H8   CG   SD   103.83  3.000
 YQP  H9   CG   CB   112.02  3.000
 YQP  H8   CG   CB   110.46  3.000
 YQP  SD   CG   CB   114.17  3.000
 YQP  CAH  SD   CE   106.06  3.000
 YQP  CAH  SD   CG    97.81  3.000
 YQP  CE   SD   CG   113.07  3.000
 YQP  H11  CE   H10  116.19  3.000
 YQP  H11  CE   SD   111.96  3.000
 YQP  H10  CE   SD   116.68  3.000
 YQP  H14  CAH  H13  109.01  3.000
 YQP  H14  CAH  CAK  110.91  3.000
 YQP  H13  CAH  CAK  110.05  3.000
 YQP  H14  CAH  SD   108.03  3.000
 YQP  H13  CAH  SD   107.50  3.000
 YQP  CAK  CAH  SD   111.23  3.000
 YQP  H15  CAK  OAL  110.13  3.000
 YQP  H15  CAK  CAO  109.38  3.000
 YQP  OAL  CAK  CAO  105.62  3.000
 YQP  H15  CAK  CAH  108.90  3.000
 YQP  CAO  CAK  CAH  113.40  3.000
 YQP  OAL  CAK  CAH  109.37  3.000
 YQP  H16  CAM  OAL  110.65  3.000
 YQP  H16  CAM  NAR  104.78  3.000
 YQP  OAL  CAM  NAR  109.23  3.000
 YQP  H16  CAM  CAN  107.78  3.000
 YQP  OAL  CAM  CAN  108.01  3.000
 YQP  NAR  CAM  CAN  116.33  3.000
 YQP  H17  CAN  OAQ  110.80  3.000
 YQP  H17  CAN  CAO  112.16  3.000
 YQP  OAQ  CAN  CAO  110.63  3.000
 YQP  H17  CAN  CAM  111.91  3.000
 YQP  CAO  CAN  CAM  103.40  3.000
 YQP  OAQ  CAN  CAM  107.63  3.000
 YQP  H18  CAO  OAP  111.44  3.000
 YQP  H18  CAO  CAN  109.68  3.000
 YQP  OAP  CAO  CAN  112.81  3.000
 YQP  H18  CAO  CAK  110.51  3.000
 YQP  OAP  CAO  CAK  109.72  3.000
 YQP  CAN  CAO  CAK  102.34  3.000
 YQP  H19  CAS  NAR  115.33  3.000
 YQP  H19  CAS  CAV  121.02  3.000
 YQP  NAR  CAS  CAV  123.65  3.000
 YQP  OAY  CAT  NAU  122.11  3.000
 YQP  OAY  CAT  NAR  123.16  3.000
 YQP  NAU  CAT  NAR  114.72  3.000
 YQP  H20  CAV  CAW  119.87  3.000
 YQP  H20  CAV  CAS  120.63  3.000
 YQP  CAW  CAV  CAS  119.50  3.000
 YQP  OAX  CAW  NAU  120.57  3.000
 YQP  NAU  CAW  CAV  113.22  3.000
 YQP  OAX  CAW  CAV  126.21  3.000
 YQP  CAT  NAR  CAS  120.64  3.000
 YQP  CAT  NAR  CAM  120.00  3.000
 YQP  CAS  NAR  CAM  119.30  3.000
 YQP  H21  NAU  CAW  116.69  3.000
 YQP  H21  NAU  CAT  115.04  3.000
 YQP  CAW  NAU  CAT  128.26  3.000
 YQP  CAM  OAL  CAK  110.49  3.000
 YQP  H22  OAP  CAO  109.07  3.000
 YQP  H23  OAQ  CAN  106.89  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
 YQP  CONST_01  NAU  CAT  NAR  CAM   180.00   0.0  0
 YQP  CONST_02  NAU  CAT  NAR  CAS     0.00   0.0  0
 YQP  CONST_03  CAV  CAW  NAU  CAT     0.00   0.0  0
 YQP  CONST_04  NAR  CAT  NAU  CAW     0.00   0.0  0
 YQP  CONST_05  OAY  CAT  NAR  CAM     0.00   0.0  0
 YQP  CONST_06  OAY  CAT  NAR  CAS   180.00   0.0  0
 YQP  CONST_07  OAX  CAW  NAU  CAT   180.00   0.0  0
 YQP  CONST_08  OAY  CAT  NAU  CAW   180.00   0.0  0
 YQP  CONST_09  H21  NAU  CAW  CAV   180.00   0.0  0
 YQP  CONST_10  H21  NAU  CAT  NAR   180.00   0.0  0
 YQP  CONST_11  H21  NAU  CAW  OAX     0.00   0.0  0
 YQP  CONST_12  H21  NAU  CAT  OAY     0.00   0.0  0
 YQP  Var_01    H19  CAS  NAR  CAM    -1.87  30.0  1
 YQP  Var_02    H19  CAS  NAR  CAT  -179.15  30.0  1
 YQP  Var_03    H19  CAS  CAV  CAW   179.61  30.0  1
 YQP  Var_04    H20  CAV  CAS  NAR   179.78  30.0  1
 YQP  Var_05    H20  CAV  CAW  NAU   179.16  30.0  1
 YQP  Var_06    H20  CAV  CAW  OAX    -0.72  30.0  1
 YQP  Var_07    CAK  CAH  SD   CG   -179.67  30.0  2
 YQP  Var_08    CAK  CAH  SD   CE     63.51  30.0  2
 YQP  Var_09    SD   CG   CB   CA    171.91  30.0  2
 YQP  Var_10    CE   SD   CG   CB   -177.59  30.0  1
 YQP  Var_11    CAH  SD   CG   CB     71.18  30.0  1
 YQP  Var_12    H10  CE   SD   CG    -37.07   0.0  2
 YQP  Var_13    H11  CE   SD   CG    100.25   0.0  2
 YQP  Var_14    H10  CE   SD   CAH    68.97   0.0  2
 YQP  Var_15    H11  CE   SD   CAH  -153.71   0.0  2
 YQP  Var_16    H8   CG   CB   CA     55.36  30.0  2
 YQP  Var_17    H9   CG   CB   CA    -65.29  30.0  2
 YQP  Var_18    H13  CAH  SD   CG     59.78  30.0  2
 YQP  Var_19    H14  CAH  SD   CG    -57.72  30.0  2
 YQP  Var_20    H6   CB   CG   SD    -67.10  30.0  3
 YQP  Var_21    H7   CB   CG   SD     50.74  30.0  3
 YQP  Var_22    H13  CAH  SD   CE    -57.03  30.0  2
 YQP  Var_23    H14  CAH  SD   CE   -174.54  30.0  2
 YQP  Var_24    H8   CG   SD   CE    -57.26  30.0  3
 YQP  Var_25    H9   CG   SD   CE     57.30  30.0  3
 YQP  Var_26    H8   CG   SD   CAH  -168.49  30.0  3
 YQP  Var_27    H9   CG   SD   CAH   -53.92  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
 YQP  chir_01  CA   CB   N    C    positiv
 YQP  chir_02  CAK  OAL  CAO  CAH  negativ
 YQP  chir_03  CAM  OAL  NAR  CAN  negativ
 YQP  chir_04  CAN  OAQ  CAM  CAO  negativ
 YQP  chir_05  CAO  OAP  CAK  CAN  positiv

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
 YQP  plan-1  CG   0.020
 YQP  plan-1  SD   0.020
 YQP  plan-1  CE   0.020
 YQP  plan-1  CAH  0.020
 YQP  plan-1  H10  0.020
 YQP  plan-1  H11  0.020
 YQP  plan-2  CAM  0.020
 YQP  plan-2  CAS  0.020
 YQP  plan-2  CAT  0.020
 YQP  plan-2  CAV  0.020
 YQP  plan-2  CAW  0.020
 YQP  plan-2  NAR  0.020
 YQP  plan-2  NAU  0.020
 YQP  plan-2  OAX  0.020
 YQP  plan-2  OAY  0.020
 YQP  plan-2  H21  0.020
 YQP  plan-3  CA   0.020
 YQP  plan-3  C    0.020
 YQP  plan-3  OXT  0.020
 YQP  plan-3  O    0.020

