# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 17:21:59 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: methyl (2S)-3-{4-amino-7-[(1E)-3-hydroxyprop-1-en-1-yl]-5-(4-methylphenyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl}-2-cyanopropanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](Cc1n(/C=C/CO)c2ncnc(N)c2c1c3ccc(C)cc3)C#N
#
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
 0JG  0JG  'methyl (2S)-3-{4-amino-7-[(1E)-3-hydroxyprop-1-en-1-yl]-5-(4-methylphenyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl}-2-cyanopropanoate'  ligand  50  29  .  2022-08-09  2022-08-09
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0JG
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
 0JG  N01  N  NH2   0  -0.827   1.7376   3.8319   0.7453
 0JG  C02  C  CR6   0   0.409   0.4549   3.5062   0.5469
 0JG  C03  C  CR56  0  -0.076   0.0435   2.2317   0.1010
 0JG  C04  C  CR56  0   0.483  -1.3308   2.0717  -0.0783
 0JG  N05  N  NR5   0  -0.608  -1.5539   0.8097  -0.5567
 0JG  C06  C  C1    0  -0.052  -2.7943   0.2515  -0.9075
 0JG  C07  C  C1    0  -0.260  -3.9404   0.4845  -0.2806
 0JG  C08  C  CH2   0  -0.202  -5.2341  -0.0677  -0.7785
 0JG  O09  O  OH1   0  -0.670  -5.8696  -0.7460   0.2846
 0JG  C10  C  CR5   0   0.351  -0.3279   0.1689  -0.6886
 0JG  C11  C  CH2   0  -0.539  -0.2057  -1.2687  -1.0655
 0JG  C12  C  CH1   0  -0.511   0.1000  -2.1434   0.1650
 0JG  C13  C  C     0   0.671   0.2674  -3.6111  -0.2085
 0JG  O14  O  O2    0  -0.444  -0.0284  -4.4061   0.7948
 0JG  C15  C  CH3   0  -0.430   0.1425  -5.8160   0.5995
 0JG  O16  O  O     0  -0.425   0.6612  -3.9659  -1.2858
 0JG  C17  C  CSP   0   0.157  -0.9001  -1.9552   1.2079
 0JG  N18  N  NS    0  -0.245  -1.6969  -1.7698   2.0150
 0JG  C19  C  CR5   0  -0.035   0.6741   1.0095  -0.2891
 0JG  C20  C  CR6   0  -0.052   2.1010   0.6637  -0.2149
 0JG  C21  C  CR16  0  -0.285   2.8116   0.2758  -1.3507
 0JG  C22  C  CR16  0  -0.283   4.1498  -0.0748  -1.2655
 0JG  C23  C  CR6   0   0.090   4.8286  -0.0405  -0.0489
 0JG  C24  C  CH3   0  -0.723   6.2868  -0.3840   0.0320
 0JG  C25  C  CR16  0  -0.279   4.1179   0.3497   1.0838
 0JG  C26  C  CR16  0  -0.309   2.7764   0.6938   1.0062
 0JG  N27  N  N     0  -0.458  -2.2573   3.0037   0.1440
 0JG  C28  C  CR16  0   0.039  -1.7477   4.1394   0.5768
 0JG  N29  N  N     0  -0.472  -0.4699   4.4391   0.7902
 0JG  H1   H  HNH2  0   0.414   2.4874   3.2093   0.5022
 0JG  H2   H  HNH2  0   0.400   1.9743   4.7762   0.9969
 0JG  H3   H  H     0   0.283  -2.7639  -0.3927  -1.7778
 0JG  H4   H  H     0   0.267  -3.9806   1.1221   0.5937
 0JG  H5   H  HCH2  0   0.215  -5.8543   0.7619  -1.1429
 0JG  H6   H  HCH2  0   0.207  -5.0533  -0.7266  -1.6379
 0JG  H7   H  HOH1  0   0.456  -6.7709  -0.9436   0.0139
 0JG  H8   H  HCH2  0   0.302  -1.1030  -1.6407  -1.5574
 0JG  H9   H  HCH2  0   0.306   0.6093  -1.3997  -1.7750
 0JG  H10  H  HCH1  0   0.371   1.0622  -1.8271   0.5903
 0JG  H11  H  HCH3  0   0.250  -0.5011  -6.1798  -0.1998
 0JG  H12  H  HCH3  0   0.250   1.1800  -6.0555   0.3718
 0JG  H13  H  HCH3  0   0.261  -0.1424  -6.2804   1.5378
 0JG  H14  H  HCR6  0   0.253   2.3163   0.2619  -2.3140
 0JG  H15  H  HCR6  0   0.251   4.6758  -0.3734  -2.1646
 0JG  H16  H  HCH3  0   0.251   6.9039   0.4827  -0.2143
 0JG  H17  H  HCH3  0   0.245   6.5666  -0.7078   1.0337
 0JG  H18  H  HCH3  0   0.245   6.5517  -1.1761  -0.6681
 0JG  H19  H  HCR6  0   0.252   4.6168   0.3763   2.0454
 0JG  H20  H  HCR6  0   0.260   2.2449   0.9745   1.9078
 0JG  H21  H  HCR6  0   0.248  -2.4565   4.9344   0.7846

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
 0JG  O09  C08  single    1.412  0.020  1.412
 0JG  C08  C07  single    1.492  0.020  1.492
 0JG  C07  C06  double    1.327  0.020  1.327
 0JG  C06  N05  single    1.405  0.020  1.405
 0JG  N27  C28  aromatic  1.318  0.020  1.318
 0JG  N27  C04  aromatic  1.333  0.020  1.333
 0JG  C28  N29  aromatic  1.330  0.020  1.330
 0JG  N05  C04  aromatic  1.368  0.020  1.368
 0JG  N05  C10  aromatic  1.390  0.020  1.390
 0JG  C04  C03  aromatic  1.395  0.020  1.395
 0JG  N29  C02  aromatic  1.336  0.020  1.336
 0JG  C10  C11  single    1.491  0.020  1.491
 0JG  C10  C19  aromatic  1.368  0.020  1.368
 0JG  C03  C02  aromatic  1.411  0.020  1.411
 0JG  C03  C19  aromatic  1.430  0.020  1.430
 0JG  C17  N18  triple    1.149  0.020  1.149
 0JG  C17  C12  single    1.457  0.020  1.457
 0JG  C12  C11  single    1.540  0.020  1.540
 0JG  C12  C13  single    1.524  0.020  1.524
 0JG  C02  N01  single    1.338  0.020  1.338
 0JG  O14  C13  single    1.314  0.020  1.314
 0JG  O14  C15  single    1.434  0.020  1.434
 0JG  C19  C20  single    1.470  0.020  1.470
 0JG  C13  O16  double    1.201  0.020  1.201
 0JG  C20  C26  aromatic  1.396  0.020  1.396
 0JG  C20  C21  aromatic  1.395  0.020  1.395
 0JG  C26  C25  aromatic  1.387  0.020  1.387
 0JG  C21  C22  aromatic  1.386  0.020  1.386
 0JG  C25  C23  aromatic  1.393  0.020  1.393
 0JG  C22  C23  aromatic  1.394  0.020  1.394
 0JG  C23  C24  single    1.500  0.020  1.500
 0JG  N01  H1   single    0.860  0.020  1.020
 0JG  N01  H2   single    0.860  0.020  1.020
 0JG  C06  H3   single    0.930  0.020  1.080
 0JG  C07  H4   single    0.930  0.020  1.080
 0JG  C08  H5   single    0.970  0.020  1.090
 0JG  C08  H6   single    0.970  0.020  1.090
 0JG  O09  H7   single    0.850  0.020  0.980
 0JG  C11  H8   single    0.970  0.020  1.090
 0JG  C11  H9   single    0.970  0.020  1.090
 0JG  C12  H10  single    0.970  0.020  1.090
 0JG  C15  H11  single    0.970  0.020  1.090
 0JG  C15  H12  single    0.970  0.020  1.090
 0JG  C15  H13  single    0.970  0.020  1.090
 0JG  C21  H14  single    0.930  0.020  1.080
 0JG  C22  H15  single    0.930  0.020  1.080
 0JG  C24  H16  single    0.970  0.020  1.090
 0JG  C24  H17  single    0.970  0.020  1.090
 0JG  C24  H18  single    0.970  0.020  1.090
 0JG  C25  H19  single    0.930  0.020  1.080
 0JG  C26  H20  single    0.930  0.020  1.080
 0JG  C28  H21  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
 0JG  H2   N01  H1   117.84  3.000
 0JG  H2   N01  C02  119.43  3.000
 0JG  H1   N01  C02  121.92  3.000
 0JG  N29  C02  C03  119.10  3.000
 0JG  C03  C02  N01  123.09  3.000
 0JG  N29  C02  N01  117.81  3.000
 0JG  C19  C03  C04  107.54  3.000
 0JG  C19  C03  C02  136.85  3.000
 0JG  C04  C03  C02  115.55  3.000
 0JG  N27  C04  N05  126.16  3.000
 0JG  N05  C04  C03  108.14  3.000
 0JG  N27  C04  C03  125.67  3.000
 0JG  C10  N05  C06  124.90  3.000
 0JG  C10  N05  C04  108.34  3.000
 0JG  C06  N05  C04  126.72  3.000
 0JG  H3   C06  C07  120.54  3.000
 0JG  H3   C06  N05  114.34  3.000
 0JG  C07  C06  N05  125.10  3.000
 0JG  H4   C07  C08  117.07  3.000
 0JG  H4   C07  C06  121.12  3.000
 0JG  C08  C07  C06  121.76  3.000
 0JG  H6   C08  H5   106.66  3.000
 0JG  H6   C08  O09  112.03  3.000
 0JG  H5   C08  O09  111.02  3.000
 0JG  H6   C08  C07  109.91  3.000
 0JG  H5   C08  C07  108.72  3.000
 0JG  O09  C08  C07  108.47  3.000
 0JG  H7   O09  C08  107.97  3.000
 0JG  C19  C10  C11  127.33  3.000
 0JG  C19  C10  N05  109.59  3.000
 0JG  C11  C10  N05  122.74  3.000
 0JG  H9   C11  H8   106.35  3.000
 0JG  H9   C11  C12  107.68  3.000
 0JG  H8   C11  C12  109.29  3.000
 0JG  H9   C11  C10  110.01  3.000
 0JG  H8   C11  C10  112.09  3.000
 0JG  C12  C11  C10  111.21  3.000
 0JG  H10  C12  C17  106.67  3.000
 0JG  H10  C12  C13  106.02  3.000
 0JG  C17  C12  C13  112.04  3.000
 0JG  H10  C12  C11  108.64  3.000
 0JG  C13  C12  C11  111.90  3.000
 0JG  C17  C12  C11  111.24  3.000
 0JG  O16  C13  O14  125.47  3.000
 0JG  O16  C13  C12  122.72  3.000
 0JG  O14  C13  C12  111.77  3.000
 0JG  C15  O14  C13  117.66  3.000
 0JG  H13  C15  H12  109.69  3.000
 0JG  H13  C15  H11  109.67  3.000
 0JG  H12  C15  H11  109.65  3.000
 0JG  H13  C15  O14  105.77  3.000
 0JG  H12  C15  O14  111.00  3.000
 0JG  H11  C15  O14  110.99  3.000
 0JG  N18  C17  C12  180.00  3.000
 0JG  C20  C19  C10  125.54  3.000
 0JG  C20  C19  C03  127.99  3.000
 0JG  C10  C19  C03  106.38  3.000
 0JG  C26  C20  C21  118.16  3.000
 0JG  C21  C20  C19  121.25  3.000
 0JG  C26  C20  C19  120.59  3.000
 0JG  H14  C21  C22  119.53  3.000
 0JG  H14  C21  C20  119.66  3.000
 0JG  C22  C21  C20  120.81  3.000
 0JG  H15  C22  C23  119.65  3.000
 0JG  H15  C22  C21  119.17  3.000
 0JG  C23  C22  C21  121.18  3.000
 0JG  C25  C23  C24  121.08  3.000
 0JG  C24  C23  C22  120.98  3.000
 0JG  C25  C23  C22  117.92  3.000
 0JG  H18  C24  H17  108.19  3.000
 0JG  H18  C24  H16  107.13  3.000
 0JG  H17  C24  H16  107.35  3.000
 0JG  H18  C24  C23  111.60  3.000
 0JG  H17  C24  C23  111.55  3.000
 0JG  H16  C24  C23  110.82  3.000
 0JG  H19  C25  C26  119.26  3.000
 0JG  H19  C25  C23  119.58  3.000
 0JG  C26  C25  C23  121.16  3.000
 0JG  H20  C26  C25  119.48  3.000
 0JG  H20  C26  C20  119.75  3.000
 0JG  C25  C26  C20  120.77  3.000
 0JG  C28  N27  C04  112.87  3.000
 0JG  H21  C28  N29  115.58  3.000
 0JG  H21  C28  N27  116.21  3.000
 0JG  N29  C28  N27  128.21  3.000
 0JG  C28  N29  C02  118.59  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
 0JG  CONST_01  N27  C28  N29  C02     0.00   0.0  0
 0JG  CONST_02  N27  C04  C03  C02     0.00   0.0  0
 0JG  CONST_03  N05  C04  C03  C02   180.00   0.0  0
 0JG  CONST_04  C10  C19  C03  C02   180.00   0.0  0
 0JG  CONST_05  C20  C19  C03  C02     0.00   0.0  0
 0JG  CONST_06  C28  N27  C04  C03     0.00   0.0  0
 0JG  CONST_07  C10  N05  C04  C03     0.00   0.0  0
 0JG  CONST_08  C28  N29  C02  C03     0.00   0.0  0
 0JG  CONST_09  N05  C10  C19  C03     0.00   0.0  0
 0JG  CONST_12  N29  C28  N27  C04     0.00   0.0  0
 0JG  CONST_13  C19  C10  N05  C04     0.00   0.0  0
 0JG  CONST_14  N29  C02  C03  C04     0.00   0.0  0
 0JG  CONST_15  C10  C19  C03  C04     0.00   0.0  0
 0JG  CONST_16  C20  C19  C03  C04   180.00   0.0  0
 0JG  CONST_17  C28  N27  C04  N05   180.00   0.0  0
 0JG  CONST_18  C19  C03  C04  N05     0.00   0.0  0
 0JG  CONST_19  C20  C19  C10  N05   180.00   0.0  0
 0JG  CONST_20  N27  C04  N05  C10   180.00   0.0  0
 0JG  CONST_23  N27  C04  C03  C19   180.00   0.0  0
 0JG  CONST_24  N29  C02  C03  C19   180.00   0.0  0
 0JG  CONST_25  C25  C26  C20  C19   180.00   0.0  0
 0JG  CONST_26  C22  C21  C20  C19   180.00   0.0  0
 0JG  CONST_27  C23  C25  C26  C20     0.00   0.0  0
 0JG  CONST_28  C23  C22  C21  C20     0.00   0.0  0
 0JG  CONST_29  C25  C26  C20  C21     0.00   0.0  0
 0JG  CONST_30  C25  C23  C22  C21     0.00   0.0  0
 0JG  CONST_31  C26  C20  C21  C22     0.00   0.0  0
 0JG  CONST_32  C26  C25  C23  C22     0.00   0.0  0
 0JG  CONST_33  C28  N29  C02  N01   180.00   0.0  0
 0JG  CONST_34  C04  C03  C02  N01   180.00   0.0  0
 0JG  CONST_35  C19  C03  C02  N01     0.00   0.0  0
 0JG  CONST_36  C06  N05  C04  C03   180.00   0.0  0
 0JG  CONST_37  C11  C10  C19  C03   180.00   0.0  0
 0JG  CONST_38  C11  C10  N05  C04   180.00   0.0  0
 0JG  CONST_39  N27  C04  N05  C06     0.00   0.0  0
 0JG  CONST_40  C19  C10  N05  C06   180.00   0.0  0
 0JG  CONST_41  C20  C19  C10  C11     0.00   0.0  0
 0JG  CONST_42  C24  C23  C22  C21   180.00   0.0  0
 0JG  CONST_43  C26  C25  C23  C24   180.00   0.0  0
 0JG  CONST_44  H21  C28  N29  C02   180.00   0.0  0
 0JG  CONST_45  H20  C26  C20  C19     0.00   0.0  0
 0JG  CONST_46  H14  C21  C20  C19     0.00   0.0  0
 0JG  CONST_47  H19  C25  C26  C20   180.00   0.0  0
 0JG  CONST_48  H15  C22  C21  C20   180.00   0.0  0
 0JG  CONST_49  H1   N01  C02  C03     0.00   0.0  0
 0JG  CONST_50  H2   N01  C02  C03   180.00   0.0  0
 0JG  Var_01    C07  C06  N05  C04   -36.07  30.0  2
 0JG  Var_02    C12  C11  C10  N05  -102.18  30.0  2
 0JG  Var_03    H16  C24  C23  C22    83.90  30.0  2
 0JG  Var_04    C08  C07  C06  N05   175.32   0.0  2
 0JG  Var_05    O09  C08  C07  C06   127.70  30.0  2
 0JG  Var_06    O16  C13  O14  C15     0.63  30.0  3
 0JG  Var_07    H11  C15  O14  C13   -61.74  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
 0JG  chir_01  C12  C17  C11  C13  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
 0JG  plan-1  C19  0.020
 0JG  plan-1  C20  0.020
 0JG  plan-1  C21  0.020
 0JG  plan-1  C22  0.020
 0JG  plan-1  C23  0.020
 0JG  plan-1  C24  0.020
 0JG  plan-1  C25  0.020
 0JG  plan-1  C26  0.020
 0JG  plan-1  H14  0.020
 0JG  plan-1  H15  0.020
 0JG  plan-1  H19  0.020
 0JG  plan-1  H20  0.020
 0JG  plan-2  N01  0.020
 0JG  plan-2  C02  0.020
 0JG  plan-2  C03  0.020
 0JG  plan-2  C04  0.020
 0JG  plan-2  N05  0.020
 0JG  plan-2  C06  0.020
 0JG  plan-2  C10  0.020
 0JG  plan-2  C11  0.020
 0JG  plan-2  C19  0.020
 0JG  plan-2  C20  0.020
 0JG  plan-2  N27  0.020
 0JG  plan-2  C28  0.020
 0JG  plan-2  N29  0.020
 0JG  plan-2  H21  0.020
 0JG  plan-3  N01  0.020
 0JG  plan-3  C02  0.020
 0JG  plan-3  H1   0.020
 0JG  plan-3  H2   0.020
 0JG  plan-4  N05  0.020
 0JG  plan-4  C06  0.020
 0JG  plan-4  C07  0.020
 0JG  plan-4  C08  0.020
 0JG  plan-4  H3   0.020
 0JG  plan-4  H4   0.020
 0JG  plan-5  C12  0.020
 0JG  plan-5  C13  0.020
 0JG  plan-5  O14  0.020
 0JG  plan-5  O16  0.020

