# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 15:21:59 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: ethyl 4-[(2S)-2-(aminomethyl)morpholin-4-yl]-1H-pyrazolo[3,4-b]pyridine-5-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)c1cnc2[nH]ncc2c1N3CCO[C@@H](CN)C3
#
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
 YM3  YM3  'ethyl 4-[(2S)-2-(aminomethyl)morpholin-4-yl]-1H-pyrazolo[3,4-b]pyridine-5-carboxylate'  ligand  41  22  .  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_YM3
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
 YM3  CAC   C  CH3   0  -0.688   5.0955   1.8634   1.3114
 YM3  CAB   C  CH2   0  -0.178   3.7601   2.1396   0.6652
 YM3  CAQ   C  C     0   0.553   1.8528   0.8930   0.0099
 YM3  CAR   C  CR6   0  -0.253   1.3087  -0.4756  -0.1419
 YM3  CAG   C  CR16  0  -0.076   2.2131  -1.4816  -0.5331
 YM3  NAN   N  N     0  -0.442   1.8957  -2.6908  -0.9415
 YM3  CAU   C  CR56  0   0.518   0.5822  -2.9097  -0.9650
 YM3  NAO   N  NR15  0  -0.516  -0.0186  -4.0639  -1.3036
 YM3  NAM   N  N     0  -0.232  -1.3475  -4.0034  -1.1733
 YM3  CAH   C  CR15  0  -0.111  -1.6293  -2.8017  -0.7436
 YM3  CAT   C  CR56  0  -0.210  -0.4446  -2.0239  -0.5922
 YM3  CAS   C  CR6   0   0.478  -0.0813  -0.7393  -0.1218
 YM3  NAV   N  NT    0  -0.509  -0.9885   0.1510   0.3494
 YM3  CAL   C  CH2   0  -0.355  -2.3925   0.0734  -0.0024
 YM3  CAK   C  CH2   0  -0.344  -0.7920   0.8697   1.6009
 YM3  CAJ   C  CH2   0  -0.193  -1.4051   2.2507   1.5201
 YM3  OAP   O  O2    0  -0.491  -2.7682   2.1770   1.1528
 YM3  CAW   C  CH1   0   0.014  -2.9910   1.4783  -0.0581
 YM3  CAI   C  CH2   0  -0.317  -2.5087   2.2546  -1.2798
 YM3  NAA   N  NH2   0  -0.803  -3.1032   3.5812  -1.3056
 YM3  O03   O  O2    0  -0.459   3.0547   0.8914   0.5715
 YM3  O05   O  O     0  -0.437   1.3026   1.8989  -0.3720
 YM3  HAC1  H  HCH3  0   0.237   4.9789   1.4505   2.3134
 YM3  HAC2  H  HCH3  0   0.237   5.6944   1.1737   0.7168
 YM3  HAC3  H  HCH3  0   0.240   5.6490   2.7979   1.3987
 YM3  HAB1  H  HCH2  0   0.235   3.1767   2.8450   1.2604
 YM3  HAB2  H  HCH2  0   0.236   3.8889   2.5661  -0.3318
 YM3  HAG   H  HCR6  0   0.272   3.2724  -1.2529  -0.5336
 YM3  HAO   H  HNR5  0   0.419   0.4246  -4.9149  -1.6116
 YM3  HAH   H  HCR5  0   0.273  -2.6563  -2.5331  -0.5586
 YM3  HAL1  H  HCH2  0   0.270  -2.5087  -0.3808  -0.9851
 YM3  HAL2  H  HCH2  0   0.253  -2.9476  -0.5359   0.7226
 YM3  HAK1  H  HCH2  0   0.254  -1.2838   0.3005   2.4014
 YM3  HAK2  H  HCH2  0   0.271   0.2571   0.9379   1.8726
 YM3  HAW   H  HCH1  0   0.247  -4.0766   1.3717  -0.1352
 YM3  HAJ1  H  HCH2  0   0.245  -1.3672   2.7233   2.5024
 YM3  HAJ2  H  HCH2  0   0.224  -0.8321   2.8740   0.8262
 YM3  HAI1  H  HCH2  0   0.215  -1.4117   2.2529  -1.3302
 YM3  HAI2  H  HCH2  0   0.233  -2.8539   1.7077  -2.1611
 YM3  HAA1  H  HNH2  0   0.342  -2.7130   4.1437  -0.5602
 YM3  HAA2  H  HNH2  0   0.349  -2.8375   4.0464  -2.1638

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
 YM3  CAC  CAB   single    1.509  0.020  1.509
 YM3  CAB  O03   single    1.437  0.020  1.437
 YM3  CAQ  CAR   single    1.481  0.020  1.481
 YM3  CAQ  O03   single    1.327  0.020  1.327
 YM3  CAQ  O05   double    1.208  0.020  1.208
 YM3  CAR  CAG   aromatic  1.408  0.020  1.408
 YM3  CAR  CAS   aromatic  1.415  0.020  1.415
 YM3  CAG  NAN   aromatic  1.315  0.020  1.315
 YM3  NAN  CAU   aromatic  1.332  0.020  1.332
 YM3  CAU  NAO   aromatic  1.345  0.020  1.345
 YM3  CAU  CAT   aromatic  1.406  0.020  1.406
 YM3  NAO  NAM   aromatic  1.337  0.020  1.337
 YM3  NAM  CAH   aromatic  1.307  0.020  1.307
 YM3  CAH  CAT   aromatic  1.425  0.020  1.425
 YM3  CAT  CAS   aromatic  1.415  0.020  1.415
 YM3  CAS  NAV   single    1.356  0.020  1.356
 YM3  NAV  CAL   single    1.449  0.020  1.449
 YM3  NAV  CAK   single    1.457  0.020  1.457
 YM3  CAL  CAW   single    1.528  0.020  1.528
 YM3  CAK  CAJ   single    1.513  0.020  1.513
 YM3  CAJ  OAP   single    1.414  0.020  1.414
 YM3  OAP  CAW   single    1.416  0.020  1.416
 YM3  CAW  CAI   single    1.526  0.020  1.526
 YM3  CAI  NAA   single    1.454  0.020  1.454
 YM3  CAC  HAC1  single    0.970  0.020  1.090
 YM3  CAC  HAC2  single    0.970  0.020  1.090
 YM3  CAC  HAC3  single    0.970  0.020  1.090
 YM3  CAB  HAB1  single    0.970  0.020  1.090
 YM3  CAB  HAB2  single    0.970  0.020  1.090
 YM3  CAG  HAG   single    0.930  0.020  1.080
 YM3  NAO  HAO   single    0.860  0.020  1.020
 YM3  CAH  HAH   single    0.930  0.020  1.080
 YM3  CAL  HAL1  single    0.970  0.020  1.090
 YM3  CAL  HAL2  single    0.970  0.020  1.090
 YM3  CAK  HAK1  single    0.970  0.020  1.090
 YM3  CAK  HAK2  single    0.970  0.020  1.090
 YM3  CAW  HAW   single    0.970  0.020  1.090
 YM3  CAJ  HAJ1  single    0.970  0.020  1.090
 YM3  CAJ  HAJ2  single    0.970  0.020  1.090
 YM3  CAI  HAI1  single    0.970  0.020  1.090
 YM3  CAI  HAI2  single    0.970  0.020  1.090
 YM3  NAA  HAA1  single    0.890  0.020  1.040
 YM3  NAA  HAA2  single    0.890  0.020  1.040

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
 YM3  HAC3  CAC  HAC2  107.90  3.000
 YM3  HAC3  CAC  HAC1  107.79  3.000
 YM3  HAC2  CAC  HAC1  108.69  3.000
 YM3  HAC3  CAC  CAB   109.08  3.000
 YM3  HAC2  CAC  CAB   111.62  3.000
 YM3  HAC1  CAC  CAB   111.61  3.000
 YM3  HAB2  CAB  HAB1  107.96  3.000
 YM3  HAB2  CAB  O03   109.73  3.000
 YM3  HAB1  CAB  O03   109.54  3.000
 YM3  HAB2  CAB  CAC   110.99  3.000
 YM3  HAB1  CAB  CAC   110.96  3.000
 YM3  O03   CAB  CAC   107.66  3.000
 YM3  O05   CAQ  O03   123.18  3.000
 YM3  O05   CAQ  CAR   124.73  3.000
 YM3  O03   CAQ  CAR   112.04  3.000
 YM3  CAS   CAR  CAG   120.12  3.000
 YM3  CAS   CAR  CAQ   122.13  3.000
 YM3  CAG   CAR  CAQ   116.93  3.000
 YM3  HAG   CAG  NAN   115.45  3.000
 YM3  HAG   CAG  CAR   118.50  3.000
 YM3  NAN   CAG  CAR   126.02  3.000
 YM3  CAU   NAN  CAG   113.24  3.000
 YM3  CAT   CAU  NAO   106.33  3.000
 YM3  CAT   CAU  NAN   127.72  3.000
 YM3  NAO   CAU  NAN   125.89  3.000
 YM3  HAO   NAO  NAM   120.35  3.000
 YM3  HAO   NAO  CAU   127.26  3.000
 YM3  NAM   NAO  CAU   112.38  3.000
 YM3  CAH   NAM  NAO   106.74  3.000
 YM3  HAH   CAH  CAT   129.64  3.000
 YM3  HAH   CAH  NAM   119.41  3.000
 YM3  CAT   CAH  NAM   110.95  3.000
 YM3  CAS   CAT  CAH   138.07  3.000
 YM3  CAS   CAT  CAU   118.19  3.000
 YM3  CAH   CAT  CAU   103.59  3.000
 YM3  NAV   CAS  CAT   122.67  3.000
 YM3  NAV   CAS  CAR   122.69  3.000
 YM3  CAT   CAS  CAR   114.62  3.000
 YM3  CAK   NAV  CAL   111.45  3.000
 YM3  CAK   NAV  CAS   122.17  3.000
 YM3  CAL   NAV  CAS   121.92  3.000
 YM3  HAL2  CAL  HAL1  108.09  3.000
 YM3  HAL2  CAL  CAW   109.65  3.000
 YM3  HAL1  CAL  CAW   107.99  3.000
 YM3  HAL2  CAL  NAV   111.05  3.000
 YM3  HAL1  CAL  NAV   110.17  3.000
 YM3  CAW   CAL  NAV   109.81  3.000
 YM3  HAK2  CAK  HAK1  106.43  3.000
 YM3  HAK2  CAK  CAJ   110.33  3.000
 YM3  HAK1  CAK  CAJ   109.30  3.000
 YM3  HAK2  CAK  NAV   112.10  3.000
 YM3  HAK1  CAK  NAV   108.06  3.000
 YM3  CAJ   CAK  NAV   110.47  3.000
 YM3  HAJ2  CAJ  HAJ1  107.82  3.000
 YM3  HAJ2  CAJ  OAP   111.70  3.000
 YM3  HAJ1  CAJ  OAP   106.86  3.000
 YM3  HAJ2  CAJ  CAK   109.97  3.000
 YM3  HAJ1  CAJ  CAK   109.46  3.000
 YM3  OAP   CAJ  CAK   110.91  3.000
 YM3  CAW   OAP  CAJ   113.56  3.000
 YM3  HAW   CAW  CAI   107.87  3.000
 YM3  HAW   CAW  OAP   105.35  3.000
 YM3  CAI   CAW  OAP   112.59  3.000
 YM3  HAW   CAW  CAL   107.56  3.000
 YM3  CAI   CAW  CAL   111.91  3.000
 YM3  OAP   CAW  CAL   111.16  3.000
 YM3  HAI2  CAI  HAI1  106.12  3.000
 YM3  HAI2  CAI  NAA   108.24  3.000
 YM3  HAI1  CAI  NAA   114.14  3.000
 YM3  HAI2  CAI  CAW   106.93  3.000
 YM3  HAI1  CAI  CAW   110.59  3.000
 YM3  NAA   CAI  CAW   110.44  3.000
 YM3  HAA2  NAA  HAA1  105.54  3.000
 YM3  HAA2  NAA  CAI   109.10  3.000
 YM3  HAA1  NAA  CAI   109.65  3.000
 YM3  CAQ   O03  CAB   118.12  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
 YM3  CONST_01  CAU   NAN  CAG  CAR     0.00   0.0  0
 YM3  CONST_02  CAU   CAT  CAS  CAR     0.00   0.0  0
 YM3  CONST_03  CAH   CAT  CAS  CAR   180.00   0.0  0
 YM3  CONST_04  CAT   CAS  CAR  CAG     0.00   0.0  0
 YM3  CONST_05  NAO   CAU  NAN  CAG   180.00   0.0  0
 YM3  CONST_06  CAT   CAU  NAN  CAG     0.00   0.0  0
 YM3  CONST_07  CAS   CAR  CAG  NAN     0.00   0.0  0
 YM3  CONST_08  NAM   NAO  CAU  NAN   180.00   0.0  0
 YM3  CONST_09  CAH   CAT  CAU  NAN   180.00   0.0  0
 YM3  CONST_10  CAS   CAT  CAU  NAN     0.00   0.0  0
 YM3  CONST_11  CAH   NAM  NAO  CAU     0.00   0.0  0
 YM3  CONST_12  NAM   CAH  CAT  CAU     0.00   0.0  0
 YM3  CONST_13  CAH   CAT  CAU  NAO     0.00   0.0  0
 YM3  CONST_14  CAS   CAT  CAU  NAO   180.00   0.0  0
 YM3  CONST_15  CAT   CAH  NAM  NAO     0.00   0.0  0
 YM3  CONST_16  CAT   CAU  NAO  NAM     0.00   0.0  0
 YM3  CONST_17  CAS   CAT  CAH  NAM   180.00   0.0  0
 YM3  CONST_18  NAV   CAS  CAR  CAG   180.00   0.0  0
 YM3  CONST_19  NAV   CAS  CAT  CAU   180.00   0.0  0
 YM3  CONST_20  NAV   CAS  CAT  CAH     0.00   0.0  0
 YM3  CONST_21  NAN   CAG  CAR  CAQ   180.00   0.0  0
 YM3  CONST_22  CAT   CAS  CAR  CAQ   180.00   0.0  0
 YM3  CONST_24  HAO   NAO  CAU  NAN     0.00   0.0  0
 YM3  CONST_25  HAG   CAG  NAN  CAU   180.00   0.0  0
 YM3  CONST_26  HAH   CAH  CAT  CAU   180.00   0.0  0
 YM3  Var_01    CAL   NAV  CAS  CAR   160.29  30.0  2
 YM3  Var_02    CAW   CAL  NAV  CAS  -147.57  30.0  1
 YM3  Var_03    CAJ   CAK  NAV  CAS   147.09  30.0  1
 YM3  Var_04    OAP   CAJ  CAK  NAV    54.85  30.0  1
 YM3  Var_05    O03   CAQ  CAR  CAG   -39.78  30.0  2
 YM3  Var_06    CAR   CAQ  O03  CAB   174.17  30.0  1
 YM3  Var_07    HAA1  NAA  CAI  CAW    69.94  30.0  3
 YM3  Var_08    HAB1  CAB  O03  CAQ    60.30  30.0  1
 YM3  Var_09    HAC1  CAC  CAB  O03   -60.71  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
 YM3  chir_01  CAW  CAL  OAP  CAI  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
 YM3  plan-1  CAQ  0.020
 YM3  plan-1  CAR  0.020
 YM3  plan-1  CAG  0.020
 YM3  plan-1  NAN  0.020
 YM3  plan-1  CAU  0.020
 YM3  plan-1  NAO  0.020
 YM3  plan-1  NAM  0.020
 YM3  plan-1  CAH  0.020
 YM3  plan-1  CAT  0.020
 YM3  plan-1  CAS  0.020
 YM3  plan-1  NAV  0.020
 YM3  plan-1  HAG  0.020
 YM3  plan-1  HAO  0.020
 YM3  plan-1  HAH  0.020
 YM3  plan-2  CAQ  0.020
 YM3  plan-2  CAR  0.020
 YM3  plan-2  O03  0.020
 YM3  plan-2  O05  0.020

