# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 01:41:13 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 4-amino-2-[(3S)-3-(propanoylamino)pyrrolidin-1-yl]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N[C@H]1CCN(C1)c2ncc(C(N)=O)c(N)n2
#
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
 GJD  GJD  4-amino-2-[(3S)-3-(propanoylamino)pyrrolidin-1-yl]pyrimidine-5-carboxamide  ligand  38  20  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GJD
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
 GJD  C2   C  CR6   0   0.639  -0.7734   0.4052   0.2633
 GJD  C4   C  CR6   0   0.508  -2.7911   0.3616  -0.8096
 GJD  C5   C  CR6   0  -0.286  -3.2067  -0.7254   0.0163
 GJD  C6   C  CR16  0  -0.031  -2.2430  -1.1696   0.9123
 GJD  CAT  C  CH3   0  -0.658   5.8017  -2.1710  -1.1602
 GJD  CAS  C  CH2   0  -0.574   4.5592  -1.3285  -1.3944
 GJD  OAR  O  O     0  -0.503   4.1731  -1.2119   0.9771
 GJD  NAN  N  NH1   0  -0.640   3.3299   0.4384  -0.3003
 GJD  CAL  C  CH1   0  -0.130   2.7226   1.1720   0.7925
 GJD  CAM  C  CH2   0  -0.252   1.4537   0.4948   1.3108
 GJD  CAK  C  CH2   0  -0.519   2.1857   2.5044   0.2791
 GJD  CAJ  C  CH2   0  -0.262   0.8529   2.1359  -0.3672
 GJD  NAI  N  NT    0  -0.492   0.4262   0.9807   0.4051
 GJD  N3   N  N     0  -0.521  -1.5870   0.9108  -0.6602
 GJD  NAH  N  NH2   0  -0.823  -3.5776   0.8944  -1.7459
 GJD  N1   N  N     0  -0.493  -1.0453  -0.6428   1.0635
 GJD  CAG  C  C     0   0.519  -4.5338  -1.3522  -0.1090
 GJD  OAO  O  O     0  -0.511  -5.2563  -1.1625  -1.0895
 GJD  NAP  N  NH2   0  -0.821  -4.9252  -2.1630   0.8920
 GJD  H1   H  HCR6  0   0.256  -2.4444  -2.0286   1.5455
 GJD  H2   H  HCH3  0   0.229   5.6081  -2.9788  -0.4567
 GJD  H3   H  HCH3  0   0.234   6.1352  -2.6172  -2.0963
 GJD  H4   H  HCH3  0   0.228   6.6234  -1.5723  -0.7666
 GJD  H5   H  HCH2  0   0.251   4.7562  -0.5537  -2.1383
 GJD  H6   H  HCH2  0   0.270   3.7634  -1.9503  -1.8168
 GJD  H7   H  HNH1  0   0.401   3.2817   0.8303  -1.2278
 GJD  H8   H  HCH1  0   0.275   3.4513   1.3002   1.5942
 GJD  H9   H  HCH2  0   0.259   1.5187  -0.5910   1.2986
 GJD  H10  H  HCH2  0   0.241   1.2561   0.8053   2.3417
 GJD  H11  H  HCH2  0   0.268   2.0257   3.1719   1.1264
 GJD  H12  H  HCH2  0   0.269   2.8645   3.0052  -0.4112
 GJD  H13  H  HCH2  0   0.253   0.1254   2.9454  -0.3106
 GJD  H14  H  HCH2  0   0.239   0.9693   1.8780  -1.4243
 GJD  H15  H  HNH2  0   0.412  -4.4433   0.4408  -1.9868
 GJD  H16  H  HNH2  0   0.392  -3.2069   1.6174  -2.3383
 GJD  H17  H  HNH2  0   0.409  -4.4673  -2.1868   1.7858
 GJD  H18  H  HNH2  0   0.403  -5.8398  -2.5815   0.8455
 GJD  CAQ  C  C     0   0.563   4.0175  -0.7043  -0.1253

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
 GJD  CAJ  CAK  single    1.526  0.020  1.526
 GJD  CAJ  NAI  single    1.454  0.020  1.454
 GJD  CAK  CAL  single    1.526  0.020  1.526
 GJD  N1   C6   aromatic  1.317  0.020  1.317
 GJD  N1   C2   aromatic  1.346  0.020  1.346
 GJD  C6   C5   aromatic  1.389  0.020  1.389
 GJD  NAP  CAG  single    1.346  0.020  1.346
 GJD  NAI  C2   single    1.338  0.020  1.338
 GJD  NAI  CAM  single    1.453  0.020  1.453
 GJD  NAN  CAL  single    1.450  0.020  1.450
 GJD  NAN  CAQ  single    1.345  0.020  1.345
 GJD  C2   N3   aromatic  1.331  0.020  1.331
 GJD  CAL  CAM  single    1.529  0.020  1.529
 GJD  C5   CAG  single    1.473  0.020  1.473
 GJD  C5   C4   aromatic  1.427  0.020  1.427
 GJD  CAS  CAQ  single    1.514  0.020  1.514
 GJD  CAS  CAT  single    1.519  0.020  1.519
 GJD  CAG  OAO  double    1.233  0.020  1.233
 GJD  CAQ  OAR  double    1.224  0.020  1.224
 GJD  N3   C4   aromatic  1.332  0.020  1.332
 GJD  C4   NAH  single    1.334  0.020  1.334
 GJD  C6   H1   single    0.930  0.020  1.080
 GJD  CAT  H2   single    0.970  0.020  1.090
 GJD  CAT  H3   single    0.970  0.020  1.090
 GJD  CAT  H4   single    0.970  0.020  1.090
 GJD  CAS  H5   single    0.970  0.020  1.090
 GJD  CAS  H6   single    0.970  0.020  1.090
 GJD  NAN  H7   single    0.860  0.020  1.020
 GJD  CAL  H8   single    0.970  0.020  1.090
 GJD  CAM  H9   single    0.970  0.020  1.090
 GJD  CAM  H10  single    0.970  0.020  1.090
 GJD  CAK  H11  single    0.970  0.020  1.090
 GJD  CAK  H12  single    0.970  0.020  1.090
 GJD  CAJ  H13  single    0.970  0.020  1.090
 GJD  CAJ  H14  single    0.970  0.020  1.090
 GJD  NAH  H15  single    0.860  0.020  1.020
 GJD  NAH  H16  single    0.860  0.020  1.020
 GJD  NAP  H17  single    0.860  0.020  1.020
 GJD  NAP  H18  single    0.860  0.020  1.020

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
 GJD  N1   C2   N3   125.79  3.000
 GJD  N3   C2   NAI  117.28  3.000
 GJD  N1   C2   NAI  116.93  3.000
 GJD  NAH  C4   N3   116.56  3.000
 GJD  NAH  C4   C5   122.60  3.000
 GJD  N3   C4   C5   120.83  3.000
 GJD  CAG  C5   C6   122.95  3.000
 GJD  CAG  C5   C4   122.50  3.000
 GJD  C6   C5   C4   114.51  3.000
 GJD  H1   C6   N1   114.71  3.000
 GJD  H1   C6   C5   120.03  3.000
 GJD  N1   C6   C5   125.25  3.000
 GJD  H4   CAT  H3   107.73  3.000
 GJD  H4   CAT  H2   107.96  3.000
 GJD  H3   CAT  H2   107.81  3.000
 GJD  H4   CAT  CAS  111.56  3.000
 GJD  H3   CAT  CAS  110.18  3.000
 GJD  H2   CAT  CAS  111.45  3.000
 GJD  H6   CAS  H5   105.74  3.000
 GJD  H6   CAS  CAQ  107.31  3.000
 GJD  H5   CAS  CAQ  110.06  3.000
 GJD  H6   CAS  CAT  109.81  3.000
 GJD  H5   CAS  CAT  110.54  3.000
 GJD  CAQ  CAS  CAT  113.07  3.000
 GJD  H7   NAN  CAL  118.48  3.000
 GJD  H7   NAN  CAQ  118.33  3.000
 GJD  CAL  NAN  CAQ  123.09  3.000
 GJD  H8   CAL  CAK  112.32  3.000
 GJD  H8   CAL  CAM  110.93  3.000
 GJD  CAK  CAL  CAM  102.05  3.000
 GJD  H8   CAL  NAN  109.49  3.000
 GJD  CAM  CAL  NAN  112.28  3.000
 GJD  CAK  CAL  NAN  109.62  3.000
 GJD  H10  CAM  H9   107.73  3.000
 GJD  H10  CAM  NAI  111.37  3.000
 GJD  H9   CAM  NAI  111.65  3.000
 GJD  H10  CAM  CAL  110.09  3.000
 GJD  H9   CAM  CAL  112.87  3.000
 GJD  NAI  CAM  CAL  103.15  3.000
 GJD  H12  CAK  H11  107.59  3.000
 GJD  H12  CAK  CAJ  112.74  3.000
 GJD  H11  CAK  CAJ  110.41  3.000
 GJD  H12  CAK  CAL  113.28  3.000
 GJD  H11  CAK  CAL  108.95  3.000
 GJD  CAJ  CAK  CAL  103.83  3.000
 GJD  H14  CAJ  H13  107.23  3.000
 GJD  H14  CAJ  NAI  110.93  3.000
 GJD  H13  CAJ  NAI  111.51  3.000
 GJD  H14  CAJ  CAK  111.91  3.000
 GJD  H13  CAJ  CAK  112.43  3.000
 GJD  NAI  CAJ  CAK  102.90  3.000
 GJD  CAJ  NAI  CAM  112.91  3.000
 GJD  CAM  NAI  C2   123.79  3.000
 GJD  CAJ  NAI  C2   123.28  3.000
 GJD  C4   N3   C2   118.29  3.000
 GJD  H16  NAH  H15  120.01  3.000
 GJD  H16  NAH  C4   118.90  3.000
 GJD  H15  NAH  C4   119.68  3.000
 GJD  C6   N1   C2   115.26  3.000
 GJD  NAP  CAG  OAO  120.90  3.000
 GJD  OAO  CAG  C5   122.03  3.000
 GJD  NAP  CAG  C5   117.06  3.000
 GJD  H18  NAP  H17  116.44  3.000
 GJD  H18  NAP  CAG  118.70  3.000
 GJD  H17  NAP  CAG  122.91  3.000
 GJD  NAN  CAQ  OAR  122.32  3.000
 GJD  OAR  CAQ  CAS  122.58  3.000
 GJD  NAN  CAQ  CAS  115.08  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
 GJD  CONST_01  C5   C6   N1   C2      0.00   0.0  0
 GJD  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 GJD  CONST_03  N1   C6   C5   C4      0.00   0.0  0
 GJD  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 GJD  CONST_05  N3   C2   N1   C6      0.00   0.0  0
 GJD  CONST_06  N3   C4   C5   C6      0.00   0.0  0
 GJD  CONST_07  NAI  C2   N3   C4    180.00   0.0  0
 GJD  CONST_08  NAI  C2   N1   C6    180.00   0.0  0
 GJD  CONST_09  NAH  C4   N3   C2    180.00   0.0  0
 GJD  CONST_10  NAH  C4   C5   C6    180.00   0.0  0
 GJD  CONST_11  CAG  C5   C4   N3    180.00   0.0  0
 GJD  CONST_12  CAG  C5   C6   N1    180.00   0.0  0
 GJD  CONST_13  H1   C6   N1   C2    180.00   0.0  0
 GJD  CONST_14  H15  NAH  C4   C5      0.00   0.0  0
 GJD  CONST_15  H16  NAH  C4   C5    180.00   0.0  0
 GJD  CONST_16  CAL  NAN  CAQ  CAS   180.00   0.0  0
 GJD  CONST_17  CAL  NAN  CAQ  OAR     0.00   0.0  0
 GJD  CONST_18  H17  NAP  CAG  C5      0.00   0.0  0
 GJD  CONST_19  H18  NAP  CAG  C5    180.00   0.0  0
 GJD  CONST_20  H7   NAN  CAQ  CAS     0.00   0.0  0
 GJD  Var_01    CAK  CAJ  NAI  C2    173.12  30.0  1
 GJD  Var_02    CAL  CAM  NAI  C2    162.58  30.0  1
 GJD  Var_03    NAI  CAJ  CAK  CAL    29.61  30.0  1
 GJD  Var_04    N1   C2   NAI  CAM     3.37  30.0  2
 GJD  Var_05    NAP  CAG  C5   C4   -166.16  30.0  2
 GJD  Var_06    NAN  CAQ  CAS  CAT   153.10  30.0  3
 GJD  Var_07    H2   CAT  CAS  CAQ    58.88  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
 GJD  chir_01  CAL  CAK  NAN  CAM  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
 GJD  plan-1  C2   0.020
 GJD  plan-1  C4   0.020
 GJD  plan-1  C5   0.020
 GJD  plan-1  C6   0.020
 GJD  plan-1  NAI  0.020
 GJD  plan-1  N3   0.020
 GJD  plan-1  NAH  0.020
 GJD  plan-1  N1   0.020
 GJD  plan-1  CAG  0.020
 GJD  plan-1  H1   0.020
 GJD  plan-2  CAS  0.020
 GJD  plan-2  OAR  0.020
 GJD  plan-2  NAN  0.020
 GJD  plan-2  CAL  0.020
 GJD  plan-2  H7   0.020
 GJD  plan-2  CAQ  0.020
 GJD  plan-3  C4   0.020
 GJD  plan-3  NAH  0.020
 GJD  plan-3  H15  0.020
 GJD  plan-3  H16  0.020
 GJD  plan-4  C5   0.020
 GJD  plan-4  CAG  0.020
 GJD  plan-4  OAO  0.020
 GJD  plan-4  NAP  0.020
 GJD  plan-4  H17  0.020
 GJD  plan-4  H18  0.020

