# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 10:53:40 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: tert-butyl (2S)-3-[4-amino-7-(3-hydroxypropyl)-5-(4-methylphenyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]-2-cyanopropanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)c2c(C[C@@H](C#N)C(=O)OC(C)(C)C)n(CCCO)c3ncnc(N)c23
#
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
 0JH  0JH  'tert-butyl (2S)-3-[4-amino-7-(3-hydroxypropyl)-5-(4-methylphenyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]-2-cyanopropanoate'  ligand  61  32  .  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_0JH
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
 0JH  N01  N  NH2   0  -0.829   4.0184   2.4991  -0.7770
 0JH  C02  C  CR6   0   0.400   3.8999   1.1684  -0.8807
 0JH  C03  C  CR56  0  -0.074   2.7589   0.4606  -0.4470
 0JH  C04  C  CR56  0   0.486   2.8313  -0.9279  -0.5805
 0JH  N05  N  NR5   0  -0.565   1.6822  -1.4661  -0.1007
 0JH  C06  C  CH2   0  -0.335   1.4125  -2.8882  -0.0465
 0JH  C07  C  CH2   0  -0.471   1.7831  -3.5068   1.2946
 0JH  C08  C  CH2   0  -0.141   1.4965  -4.9962   1.2976
 0JH  O09  O  OH1   0  -0.671   1.8584  -5.5227   2.5543
 0JH  C10  C  CR5   0   0.349   0.8761  -0.4444   0.3618
 0JH  C11  C  CH2   0  -0.548  -0.5042  -0.6790   0.8778
 0JH  C12  C  CH1   0  -0.504  -1.5654  -0.1846  -0.1197
 0JH  C13  C  C     0   0.678  -2.9919  -0.3803   0.3978
 0JH  O14  O  O2    0  -0.466  -3.8473  -0.3114  -0.5907
 0JH  C15  C  CT    0   0.172  -5.2985  -0.4473  -0.4267
 0JH  C16  C  CH3   0  -0.656  -5.8163  -0.2473  -1.8437
 0JH  C17  C  CH3   0  -0.671  -5.6388  -1.8447   0.0709
 0JH  C18  C  CH3   0  -0.674  -5.8443   0.6388   0.4898
 0JH  O19  O  O     0  -0.427  -3.2332  -0.5387   1.5636
 0JH  C20  C  CSP   0   0.159  -1.3850  -0.8136  -1.4215
 0JH  N21  N  NS    0  -0.255  -1.1990  -1.3273  -2.4332
 0JH  C22  C  CR5   0  -0.033   1.4999   0.7604   0.1583
 0JH  C23  C  CR6   0  -0.054   0.9295   2.0861   0.4418
 0JH  C24  C  CR16  0  -0.314   0.7126   2.9940  -0.5951
 0JH  C25  C  CR16  0  -0.285   0.1737   4.2481  -0.3433
 0JH  C26  C  CR6   0   0.091  -0.1758   4.6340   0.9477
 0JH  C27  C  CH3   0  -0.724  -0.7804   5.9791   1.2251
 0JH  C28  C  CR16  0  -0.280   0.0396   3.7237   1.9819
 0JH  C29  C  CR16  0  -0.285   0.5859   2.4740   1.7375
 0JH  N30  N  N     0  -0.466   3.8586  -1.6145  -1.0861
 0JH  C31  C  CR16  0   0.036   4.8483  -0.8363  -1.4725
 0JH  N32  N  N     0  -0.476   4.9278   0.4905  -1.3997
 0JH  H1   H  HNH2  0   0.414   3.2461   3.0767  -0.4943
 0JH  H2   H  HNH2  0   0.398   4.8182   2.9539  -1.1827
 0JH  H3   H  HCH2  0   0.262   0.3607  -3.0584  -0.2799
 0JH  H4   H  HCH2  0   0.274   1.9850  -3.3545  -0.8477
 0JH  H5   H  HCH2  0   0.244   2.8446  -3.3337   1.4899
 0JH  H6   H  HCH2  0   0.238   1.2222  -3.0226   2.0992
 0JH  H7   H  HCH2  0   0.195   0.4319  -5.1602   1.0833
 0JH  H8   H  HCH2  0   0.197   2.0587  -5.4731   0.4837
 0JH  H9   H  HOH1  0   0.454   1.7019  -6.4709   2.5384
 0JH  H10  H  HCH2  0   0.297  -0.6799  -1.7308   1.1021
 0JH  H11  H  HCH2  0   0.305  -0.6522  -0.1417   1.8133
 0JH  H12  H  HCH1  0   0.366  -1.4343   0.8952  -0.2707
 0JH  H13  H  HCH3  0   0.242  -5.3999  -0.9883  -2.5270
 0JH  H14  H  HCH3  0   0.235  -6.9008  -0.3512  -1.8566
 0JH  H15  H  HCH3  0   0.242  -5.5714   0.7468  -2.2203
 0JH  H16  H  HCH3  0   0.248  -5.3255  -2.0102   1.0997
 0JH  H17  H  HCH3  0   0.244  -6.7202  -1.9793   0.0307
 0JH  H18  H  HCH3  0   0.242  -5.1853  -2.6091  -0.5616
 0JH  H19  H  HCH3  0   0.243  -5.5051   1.6264   0.1745
 0JH  H20  H  HCH3  0   0.244  -6.9330   0.6297   0.4283
 0JH  H21  H  HCH3  0   0.249  -5.5717   0.4892   1.5321
 0JH  H22  H  HCR6  0   0.261   0.9554   2.7102  -1.6125
 0JH  H23  H  HCR6  0   0.252   0.0203   4.9330  -1.1688
 0JH  H24  H  HCH3  0   0.249  -1.8466   5.8916   1.4427
 0JH  H25  H  HCH3  0   0.246  -0.3154   6.4526   2.0902
 0JH  H26  H  HCH3  0   0.245  -0.6728   6.6510   0.3749
 0JH  H27  H  HCR6  0   0.251  -0.2125   4.0017   2.9987
 0JH  H28  H  HCR6  0   0.250   0.7609   1.7962   2.5644
 0JH  H29  H  HCR6  0   0.245   5.7121  -1.3332  -1.9022

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
 0JH  C08  O09  single    1.410  0.020  1.410
 0JH  C08  C07  single    1.517  0.020  1.517
 0JH  C07  C06  single    1.523  0.020  1.523
 0JH  C06  N05  single    1.448  0.020  1.448
 0JH  N30  C31  aromatic  1.317  0.020  1.317
 0JH  N30  C04  aromatic  1.335  0.020  1.335
 0JH  C31  N32  aromatic  1.331  0.020  1.331
 0JH  N05  C04  aromatic  1.357  0.020  1.357
 0JH  N05  C10  aromatic  1.381  0.020  1.381
 0JH  C04  C03  aromatic  1.397  0.020  1.397
 0JH  N32  C02  aromatic  1.336  0.020  1.336
 0JH  C16  C15  single    1.522  0.020  1.522
 0JH  C12  C20  single    1.457  0.020  1.457
 0JH  C12  C13  single    1.530  0.020  1.530
 0JH  C12  C11  single    1.538  0.020  1.538
 0JH  C20  N21  triple    1.150  0.020  1.150
 0JH  O14  C13  single    1.309  0.020  1.309
 0JH  O14  C15  single    1.467  0.020  1.467
 0JH  C10  C11  single    1.492  0.020  1.492
 0JH  C10  C22  aromatic  1.372  0.020  1.372
 0JH  C03  C02  aromatic  1.411  0.020  1.411
 0JH  C03  C22  aromatic  1.429  0.020  1.429
 0JH  C17  C15  single    1.522  0.020  1.522
 0JH  C13  O19  double    1.201  0.020  1.201
 0JH  C02  N01  single    1.340  0.020  1.340
 0JH  C15  C18  single    1.522  0.020  1.522
 0JH  C22  C23  single    1.471  0.020  1.471
 0JH  C23  C24  aromatic  1.395  0.020  1.395
 0JH  C23  C29  aromatic  1.395  0.020  1.395
 0JH  C24  C25  aromatic  1.388  0.020  1.388
 0JH  C29  C28  aromatic  1.386  0.020  1.386
 0JH  C25  C26  aromatic  1.392  0.020  1.392
 0JH  C28  C26  aromatic  1.395  0.020  1.395
 0JH  C26  C27  single    1.501  0.020  1.501
 0JH  N01  H1   single    0.860  0.020  1.020
 0JH  N01  H2   single    0.860  0.020  1.020
 0JH  C06  H3   single    0.970  0.020  1.090
 0JH  C06  H4   single    0.970  0.020  1.090
 0JH  C07  H5   single    0.970  0.020  1.090
 0JH  C07  H6   single    0.970  0.020  1.090
 0JH  C08  H7   single    0.970  0.020  1.090
 0JH  C08  H8   single    0.970  0.020  1.090
 0JH  O09  H9   single    0.850  0.020  0.980
 0JH  C11  H10  single    0.970  0.020  1.090
 0JH  C11  H11  single    0.970  0.020  1.090
 0JH  C12  H12  single    0.970  0.020  1.090
 0JH  C16  H13  single    0.970  0.020  1.090
 0JH  C16  H14  single    0.970  0.020  1.090
 0JH  C16  H15  single    0.970  0.020  1.090
 0JH  C17  H16  single    0.970  0.020  1.090
 0JH  C17  H17  single    0.970  0.020  1.090
 0JH  C17  H18  single    0.970  0.020  1.090
 0JH  C18  H19  single    0.970  0.020  1.090
 0JH  C18  H20  single    0.970  0.020  1.090
 0JH  C18  H21  single    0.970  0.020  1.090
 0JH  C24  H22  single    0.930  0.020  1.080
 0JH  C25  H23  single    0.930  0.020  1.080
 0JH  C27  H24  single    0.970  0.020  1.090
 0JH  C27  H25  single    0.970  0.020  1.090
 0JH  C27  H26  single    0.970  0.020  1.090
 0JH  C28  H27  single    0.930  0.020  1.080
 0JH  C29  H28  single    0.930  0.020  1.080
 0JH  C31  H29  single    0.930  0.020  1.080

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
 0JH  H2   N01  H1   117.69  3.000
 0JH  H2   N01  C02  119.23  3.000
 0JH  H1   N01  C02  121.64  3.000
 0JH  N32  C02  C03  119.14  3.000
 0JH  C03  C02  N01  123.09  3.000
 0JH  N32  C02  N01  117.76  3.000
 0JH  C22  C03  C04  107.14  3.000
 0JH  C22  C03  C02  137.52  3.000
 0JH  C04  C03  C02  115.30  3.000
 0JH  N30  C04  N05  125.57  3.000
 0JH  N05  C04  C03  108.46  3.000
 0JH  N30  C04  C03  125.97  3.000
 0JH  C10  N05  C06  127.24  3.000
 0JH  C10  N05  C04  108.62  3.000
 0JH  C06  N05  C04  124.08  3.000
 0JH  H4   C06  H3   106.41  3.000
 0JH  H4   C06  C07  110.24  3.000
 0JH  H3   C06  C07  111.09  3.000
 0JH  H4   C06  N05  107.15  3.000
 0JH  H3   C06  N05  108.95  3.000
 0JH  C07  C06  N05  112.74  3.000
 0JH  H6   C07  H5   107.24  3.000
 0JH  H6   C07  C08  109.65  3.000
 0JH  H5   C07  C08  109.80  3.000
 0JH  H6   C07  C06  110.08  3.000
 0JH  H5   C07  C06  109.23  3.000
 0JH  C08  C07  C06  110.77  3.000
 0JH  H8   C08  H7   106.67  3.000
 0JH  H8   C08  O09  111.53  3.000
 0JH  H7   C08  O09  111.53  3.000
 0JH  H8   C08  C07  109.16  3.000
 0JH  H7   C08  C07  109.23  3.000
 0JH  O09  C08  C07  108.66  3.000
 0JH  H9   O09  C08  108.17  3.000
 0JH  C22  C10  C11  127.59  3.000
 0JH  C22  C10  N05  109.55  3.000
 0JH  C11  C10  N05  122.64  3.000
 0JH  H11  C11  H10  106.11  3.000
 0JH  H11  C11  C12  107.74  3.000
 0JH  H10  C11  C12  109.43  3.000
 0JH  H11  C11  C10  110.19  3.000
 0JH  H10  C11  C10  111.85  3.000
 0JH  C12  C11  C10  111.31  3.000
 0JH  H12  C12  C20  106.66  3.000
 0JH  H12  C12  C13  106.48  3.000
 0JH  C20  C12  C13  111.25  3.000
 0JH  H12  C12  C11  108.84  3.000
 0JH  C13  C12  C11  112.51  3.000
 0JH  C20  C12  C11  110.81  3.000
 0JH  O19  C13  O14  127.49  3.000
 0JH  O19  C13  C12  122.17  3.000
 0JH  O14  C13  C12  110.31  3.000
 0JH  C15  O14  C13  123.86  3.000
 0JH  C18  C15  C17  112.22  3.000
 0JH  C18  C15  C16  110.17  3.000
 0JH  C17  C15  C16  110.43  3.000
 0JH  C18  C15  O14  110.85  3.000
 0JH  C17  C15  O14  110.05  3.000
 0JH  C16  C15  O14  102.73  3.000
 0JH  H15  C16  H14  107.83  3.000
 0JH  H15  C16  H13  108.49  3.000
 0JH  H14  C16  H13  107.93  3.000
 0JH  H15  C16  C15  111.40  3.000
 0JH  H14  C16  C15  109.70  3.000
 0JH  H13  C16  C15  111.36  3.000
 0JH  H18  C17  H17  107.73  3.000
 0JH  H18  C17  H16  108.78  3.000
 0JH  H17  C17  H16  107.55  3.000
 0JH  H18  C17  C15  111.15  3.000
 0JH  H17  C17  C15  108.84  3.000
 0JH  H16  C17  C15  112.61  3.000
 0JH  H21  C18  H20  107.64  3.000
 0JH  H21  C18  H19  108.88  3.000
 0JH  H20  C18  H19  107.56  3.000
 0JH  H21  C18  C15  112.89  3.000
 0JH  H20  C18  C15  108.54  3.000
 0JH  H19  C18  C15  111.13  3.000
 0JH  N21  C20  C12  180.00  3.000
 0JH  C23  C22  C10  125.92  3.000
 0JH  C23  C22  C03  127.77  3.000
 0JH  C10  C22  C03  106.21  3.000
 0JH  C29  C23  C24  118.09  3.000
 0JH  C29  C23  C22  121.67  3.000
 0JH  C24  C23  C22  120.23  3.000
 0JH  H22  C24  C25  119.60  3.000
 0JH  H22  C24  C23  119.50  3.000
 0JH  C25  C24  C23  120.90  3.000
 0JH  H23  C25  C26  119.72  3.000
 0JH  H23  C25  C24  119.20  3.000
 0JH  C26  C25  C24  121.07  3.000
 0JH  C28  C26  C27  120.68  3.000
 0JH  C27  C26  C25  121.40  3.000
 0JH  C28  C26  C25  117.91  3.000
 0JH  H26  C27  H25  108.02  3.000
 0JH  H26  C27  H24  107.55  3.000
 0JH  H25  C27  H24  107.05  3.000
 0JH  H26  C27  C26  111.65  3.000
 0JH  H25  C27  C26  111.35  3.000
 0JH  H24  C27  C26  111.01  3.000
 0JH  H27  C28  C29  119.24  3.000
 0JH  H27  C28  C26  119.50  3.000
 0JH  C29  C28  C26  121.25  3.000
 0JH  H28  C29  C28  119.55  3.000
 0JH  H28  C29  C23  119.67  3.000
 0JH  C28  C29  C23  120.77  3.000
 0JH  C31  N30  C04  112.67  3.000
 0JH  H29  C31  N32  115.50  3.000
 0JH  H29  C31  N30  116.35  3.000
 0JH  N32  C31  N30  128.15  3.000
 0JH  C31  N32  C02  118.75  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
 0JH  CONST_01  N30  C31  N32  C02     0.00   0.0  0
 0JH  CONST_02  N30  C04  C03  C02     0.00   0.0  0
 0JH  CONST_03  N05  C04  C03  C02   180.00   0.0  0
 0JH  CONST_04  C10  C22  C03  C02   180.00   0.0  0
 0JH  CONST_05  C23  C22  C03  C02     0.00   0.0  0
 0JH  CONST_06  C31  N30  C04  C03     0.00   0.0  0
 0JH  CONST_07  C10  N05  C04  C03     0.00   0.0  0
 0JH  CONST_08  C31  N32  C02  C03     0.00   0.0  0
 0JH  CONST_09  N05  C10  C22  C03     0.00   0.0  0
 0JH  CONST_12  N32  C31  N30  C04     0.00   0.0  0
 0JH  CONST_13  C22  C10  N05  C04     0.00   0.0  0
 0JH  CONST_14  N32  C02  C03  C04     0.00   0.0  0
 0JH  CONST_15  C10  C22  C03  C04     0.00   0.0  0
 0JH  CONST_16  C23  C22  C03  C04   180.00   0.0  0
 0JH  CONST_17  C31  N30  C04  N05   180.00   0.0  0
 0JH  CONST_18  C22  C03  C04  N05     0.00   0.0  0
 0JH  CONST_19  C23  C22  C10  N05   180.00   0.0  0
 0JH  CONST_20  N30  C04  N05  C10   180.00   0.0  0
 0JH  CONST_23  N30  C04  C03  C22   180.00   0.0  0
 0JH  CONST_24  N32  C02  C03  C22   180.00   0.0  0
 0JH  CONST_25  C25  C24  C23  C22   180.00   0.0  0
 0JH  CONST_26  C28  C29  C23  C22   180.00   0.0  0
 0JH  CONST_27  C26  C25  C24  C23     0.00   0.0  0
 0JH  CONST_28  C26  C28  C29  C23     0.00   0.0  0
 0JH  CONST_29  C28  C29  C23  C24     0.00   0.0  0
 0JH  CONST_30  C28  C26  C25  C24     0.00   0.0  0
 0JH  CONST_31  C29  C23  C24  C25     0.00   0.0  0
 0JH  CONST_32  C29  C28  C26  C25     0.00   0.0  0
 0JH  CONST_33  C31  N32  C02  N01   180.00   0.0  0
 0JH  CONST_34  C04  C03  C02  N01   180.00   0.0  0
 0JH  CONST_35  C22  C03  C02  N01     0.00   0.0  0
 0JH  CONST_36  C06  N05  C04  C03   180.00   0.0  0
 0JH  CONST_37  C11  C10  C22  C03   180.00   0.0  0
 0JH  CONST_38  C11  C10  N05  C04   180.00   0.0  0
 0JH  CONST_39  N30  C04  N05  C06     0.00   0.0  0
 0JH  CONST_40  C22  C10  N05  C06   180.00   0.0  0
 0JH  CONST_41  C23  C22  C10  C11     0.00   0.0  0
 0JH  CONST_42  C27  C26  C25  C24   180.00   0.0  0
 0JH  CONST_43  C29  C28  C26  C27   180.00   0.0  0
 0JH  CONST_44  H29  C31  N32  C02   180.00   0.0  0
 0JH  CONST_45  H22  C24  C23  C22     0.00   0.0  0
 0JH  CONST_46  H28  C29  C23  C22     0.00   0.0  0
 0JH  CONST_47  H23  C25  C24  C23   180.00   0.0  0
 0JH  CONST_48  H27  C28  C29  C23   180.00   0.0  0
 0JH  CONST_49  H1   N01  C02  C03     0.00   0.0  0
 0JH  CONST_50  H2   N01  C02  C03   180.00   0.0  0
 0JH  Var_01    C07  C06  N05  C04    93.75  30.0  1
 0JH  Var_02    C12  C11  C10  N05  -106.85  30.0  2
 0JH  Var_03    H24  C27  C26  C25   106.10  30.0  2
 0JH  Var_04    C08  C07  C06  N05  -179.42  30.0  2
 0JH  Var_05    O09  C08  C07  C06   179.83  30.0  1
 0JH  Var_06    C16  C15  O14  C13   178.25  30.0  3
 0JH  Var_07    O19  C13  O14  C15    -1.22  30.0  3
 0JH  Var_08    H13  C16  C15  O14    59.21  30.0  3
 0JH  Var_09    H16  C17  C15  O14    69.98  30.0  3
 0JH  Var_10    H19  C18  C15  O14    50.69  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
 0JH  chir_01  C12  C20  C13  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
 0JH  plan-1  C22  0.020
 0JH  plan-1  C23  0.020
 0JH  plan-1  C24  0.020
 0JH  plan-1  C25  0.020
 0JH  plan-1  C26  0.020
 0JH  plan-1  C27  0.020
 0JH  plan-1  C28  0.020
 0JH  plan-1  C29  0.020
 0JH  plan-1  H22  0.020
 0JH  plan-1  H23  0.020
 0JH  plan-1  H27  0.020
 0JH  plan-1  H28  0.020
 0JH  plan-2  N01  0.020
 0JH  plan-2  C02  0.020
 0JH  plan-2  C03  0.020
 0JH  plan-2  C04  0.020
 0JH  plan-2  N05  0.020
 0JH  plan-2  C06  0.020
 0JH  plan-2  C10  0.020
 0JH  plan-2  C11  0.020
 0JH  plan-2  C22  0.020
 0JH  plan-2  C23  0.020
 0JH  plan-2  N30  0.020
 0JH  plan-2  C31  0.020
 0JH  plan-2  N32  0.020
 0JH  plan-2  H29  0.020
 0JH  plan-3  N01  0.020
 0JH  plan-3  C02  0.020
 0JH  plan-3  H1   0.020
 0JH  plan-3  H2   0.020
 0JH  plan-4  C12  0.020
 0JH  plan-4  C13  0.020
 0JH  plan-4  O14  0.020
 0JH  plan-4  O19  0.020

