# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 02:43:39 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 3-(1-methylcyclopropyl)-2-[(1-methylcyclopropyl)amino]-8-[(6R)-6-methyl-4-oxo-1,4,5,6-tetrahydropyrrolo[3,4-b]pyrrol-2-yl]quinazolin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1NC(=O)c2cc([nH]c12)c3cccc4C(=O)N(C(=Nc34)NC5(C)CC5)C6(C)CC6
#
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
 JYG  JYG  3-(1-methylcyclopropyl)-2-[(1-methylcyclopropyl)amino]-8-[(6R)-6-methyl-4-oxo-1,4,5,6-tetrahydropyrrolo[3,4-b]pyrrol-2-yl]quinazolin-4(3H)-one  ligand  55  30  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JYG
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
 JYG  C01  C  CH3   0  -0.657   6.2996   1.6077   0.5479
 JYG  C02  C  CR15  0  -0.085   5.5070   0.7392  -0.4190
 JYG  N03  N  NR15  0  -0.671   5.6948  -0.6873  -0.1825
 JYG  C04  C  CR5   0   0.467   4.5599  -1.3991   0.0863
 JYG  O05  O  O     0  -0.489   4.5057  -2.6007   0.2998
 JYG  C06  C  CR55  0  -0.105   3.4824  -0.4100   0.0537
 JYG  C07  C  CR15  0  -0.466   2.0878  -0.2399   0.1885
 JYG  C08  C  CR5   0   0.343   1.8378   1.1045  -0.0232
 JYG  N09  N  NR15  0  -0.734   3.0549   1.7237  -0.2827
 JYG  C10  C  CR55  0   0.331   4.0288   0.8047  -0.2411
 JYG  C11  C  CR6   0   0.003   0.6029   1.8826   0.0134
 JYG  C12  C  CR16  0  -0.331   0.6453   3.2679   0.1154
 JYG  C13  C  CR16  0  -0.257  -0.5052   4.0562   0.1143
 JYG  C14  C  CR16  0  -0.299  -1.7414   3.4598   0.0232
 JYG  C15  C  CR66  0  -0.111  -1.8242   2.0682  -0.0545
 JYG  C16  C  CR6   0   0.582  -3.1316   1.4290  -0.1297
 JYG  O17  O  O     0  -0.455  -4.1808   2.0405  -0.2083
 JYG  N18  N  NR6   0  -0.604  -3.1189   0.0392  -0.0841
 JYG  C19  C  CR6   0   0.753  -1.9272  -0.6571  -0.1919
 JYG  N20  N  NH1   0  -0.704  -2.0059  -1.9920  -0.3280
 JYG  C21  C  CT    0   0.172  -0.8593  -2.8400  -0.4807
 JYG  C22  C  CH3   0  -0.664  -0.1728  -2.7673  -1.8218
 JYG  C23  C  CH2   0  -0.481  -0.0554  -3.1210   0.7520
 JYG  C24  C  CH2   0  -0.513  -0.9809  -4.1657   0.2052
 JYG  N25  N  N     0  -0.531  -0.7625  -0.0879  -0.1660
 JYG  C26  C  CR66  0   0.213  -0.6765   1.2614  -0.0604
 JYG  C27  C  CT    0   0.083  -4.3983  -0.6418  -0.0641
 JYG  C28  C  CH3   0  -0.648  -4.9942  -0.8767  -1.4314
 JYG  C29  C  CH2   0  -0.472  -5.3102  -0.3272   1.0761
 JYG  C30  C  CH2   0  -0.516  -4.6265  -1.6527   1.0305
 JYG  H1   H  HCH3  0   0.248   7.3696   1.4445   0.4190
 JYG  H2   H  HCH3  0   0.240   6.0992   2.6627   0.3612
 JYG  H3   H  HCH3  0   0.236   6.0333   1.3796   1.5795
 JYG  H4   H  HCR5  0   0.277   5.7917   0.9897  -1.4466
 JYG  H5   H  HNR5  0   0.397   6.6005  -1.1218  -0.2570
 JYG  H6   H  HCR5  0   0.307   1.3401  -0.9814   0.3974
 JYG  H7   H  HNR5  0   0.418   3.1782   2.6938  -0.5232
 JYG  H8   H  HCR6  0   0.251   1.5954   3.7776   0.2156
 JYG  H9   H  HCR6  0   0.259  -0.4162   5.1310   0.1917
 JYG  H10  H  HCR6  0   0.259  -2.6440   4.0555   0.0226
 JYG  H11  H  HNH1  0   0.426  -2.9070  -2.4162  -0.4673
 JYG  H12  H  HCH3  0   0.242   0.2139  -1.7652  -2.0042
 JYG  H13  H  HCH3  0   0.226   0.6642  -3.4642  -1.8674
 JYG  H14  H  HCH3  0   0.229  -0.8660  -3.0232  -2.6250
 JYG  H15  H  HCH2  0   0.251   1.0121  -3.2659   0.6341
 JYG  H16  H  HCH2  0   0.261  -0.3433  -2.6180   1.6662
 JYG  H17  H  HCH2  0   0.259  -1.8899  -4.3748   0.7562
 JYG  H18  H  HCH2  0   0.257  -0.5546  -5.0269  -0.2929
 JYG  H19  H  HCH3  0   0.231  -4.3295  -1.4624  -2.0690
 JYG  H20  H  HCH3  0   0.238  -5.9354  -1.4196  -1.3479
 JYG  H21  H  HCH3  0   0.249  -5.1978   0.0695  -1.9324
 JYG  H22  H  HCH2  0   0.267  -4.9740   0.3750   1.8269
 JYG  H23  H  HCH2  0   0.264  -6.3681  -0.2685   0.8542
 JYG  H24  H  HCH2  0   0.278  -5.1950  -2.5369   0.7694
 JYG  H25  H  HCH2  0   0.277  -3.8354  -1.8247   1.7495

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
 JYG  O05  C04  double    1.222  0.020  1.222
 JYG  C13  C12  aromatic  1.395  0.020  1.395
 JYG  C13  C14  aromatic  1.376  0.020  1.376
 JYG  C12  C11  aromatic  1.390  0.020  1.390
 JYG  C07  C06  aromatic  1.411  0.020  1.411
 JYG  C07  C08  aromatic  1.384  0.020  1.384
 JYG  C04  C06  single    1.463  0.020  1.463
 JYG  C04  N03  single    1.366  0.020  1.366
 JYG  C06  C10  aromatic  1.364  0.020  1.364
 JYG  C14  C15  aromatic  1.396  0.020  1.396
 JYG  C11  C08  single    1.460  0.020  1.460
 JYG  C11  C26  aromatic  1.424  0.020  1.424
 JYG  C08  N09  aromatic  1.390  0.020  1.390
 JYG  N03  C02  single    1.458  0.020  1.458
 JYG  C10  N09  aromatic  1.340  0.020  1.340
 JYG  C10  C02  single    1.490  0.020  1.490
 JYG  C15  C26  aromatic  1.403  0.020  1.403
 JYG  C15  C16  single    1.457  0.020  1.457
 JYG  C26  N25  single    1.356  0.020  1.356
 JYG  C02  C01  single    1.522  0.020  1.522
 JYG  O17  C16  double    1.217  0.020  1.217
 JYG  C16  N18  single    1.391  0.020  1.391
 JYG  N25  C19  double    1.297  0.020  1.297
 JYG  N18  C19  single    1.384  0.020  1.384
 JYG  N18  C27  single    1.449  0.020  1.449
 JYG  C19  N20  single    1.344  0.020  1.344
 JYG  C22  C21  single    1.508  0.020  1.508
 JYG  C23  C21  single    1.498  0.020  1.498
 JYG  C23  C24  single    1.499  0.020  1.499
 JYG  C27  C30  single    1.507  0.020  1.507
 JYG  C27  C28  single    1.510  0.020  1.510
 JYG  C27  C29  single    1.494  0.020  1.494
 JYG  C30  C29  single    1.492  0.020  1.492
 JYG  N20  C21  single    1.434  0.020  1.434
 JYG  C21  C24  single    1.498  0.020  1.498
 JYG  C01  H1   single    0.970  0.020  1.090
 JYG  C01  H2   single    0.970  0.020  1.090
 JYG  C01  H3   single    0.970  0.020  1.090
 JYG  C02  H4   single    0.970  0.020  1.090
 JYG  N03  H5   single    0.860  0.020  1.020
 JYG  C07  H6   single    0.930  0.020  1.080
 JYG  N09  H7   single    0.860  0.020  1.020
 JYG  C12  H8   single    0.930  0.020  1.080
 JYG  C13  H9   single    0.930  0.020  1.080
 JYG  C14  H10  single    0.930  0.020  1.080
 JYG  N20  H11  single    0.860  0.020  1.020
 JYG  C22  H12  single    0.970  0.020  1.090
 JYG  C22  H13  single    0.970  0.020  1.090
 JYG  C22  H14  single    0.970  0.020  1.090
 JYG  C23  H15  single    0.970  0.020  1.090
 JYG  C23  H16  single    0.970  0.020  1.090
 JYG  C24  H17  single    0.970  0.020  1.090
 JYG  C24  H18  single    0.970  0.020  1.090
 JYG  C28  H19  single    0.970  0.020  1.090
 JYG  C28  H20  single    0.970  0.020  1.090
 JYG  C28  H21  single    0.970  0.020  1.090
 JYG  C29  H22  single    0.970  0.020  1.090
 JYG  C29  H23  single    0.970  0.020  1.090
 JYG  C30  H24  single    0.970  0.020  1.090
 JYG  C30  H25  single    0.970  0.020  1.090

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
 JYG  H3   C01  H2   108.66  3.000
 JYG  H3   C01  H1   108.70  3.000
 JYG  H2   C01  H1   107.76  3.000
 JYG  H3   C01  C02  110.78  3.000
 JYG  H2   C01  C02  110.35  3.000
 JYG  H1   C01  C02  110.52  3.000
 JYG  H4   C02  C10  111.09  3.000
 JYG  H4   C02  N03  110.03  3.000
 JYG  C10  C02  N03   98.71  3.000
 JYG  H4   C02  C01  109.28  3.000
 JYG  C10  C02  C01  114.55  3.000
 JYG  N03  C02  C01  112.83  3.000
 JYG  H5   N03  C04  122.46  3.000
 JYG  H5   N03  C02  121.72  3.000
 JYG  C04  N03  C02  115.76  3.000
 JYG  C06  C04  O05  129.51  3.000
 JYG  C06  C04  N03  104.79  3.000
 JYG  O05  C04  N03  125.70  3.000
 JYG  C10  C06  C07  108.00  3.000
 JYG  C10  C06  C04  108.17  3.000
 JYG  C07  C06  C04  143.82  3.000
 JYG  H6   C07  C08  125.11  3.000
 JYG  H6   C07  C06  128.57  3.000
 JYG  C08  C07  C06  106.32  3.000
 JYG  C11  C08  N09  120.53  3.000
 JYG  N09  C08  C07  107.65  3.000
 JYG  C11  C08  C07  131.81  3.000
 JYG  H7   N09  C10  125.40  3.000
 JYG  H7   N09  C08  125.51  3.000
 JYG  C10  N09  C08  108.97  3.000
 JYG  N09  C10  C06  109.05  3.000
 JYG  N09  C10  C02  138.37  3.000
 JYG  C06  C10  C02  112.58  3.000
 JYG  C26  C11  C12  117.77  3.000
 JYG  C26  C11  C08  121.75  3.000
 JYG  C12  C11  C08  120.48  3.000
 JYG  H8   C12  C13  117.25  3.000
 JYG  H8   C12  C11  120.18  3.000
 JYG  C13  C12  C11  122.57  3.000
 JYG  H9   C13  C14  120.65  3.000
 JYG  H9   C13  C12  119.59  3.000
 JYG  C14  C13  C12  119.76  3.000
 JYG  H10  C14  C15  119.97  3.000
 JYG  H10  C14  C13  120.75  3.000
 JYG  C15  C14  C13  119.28  3.000
 JYG  C26  C15  C16  118.78  3.000
 JYG  C16  C15  C14  119.56  3.000
 JYG  C26  C15  C14  121.66  3.000
 JYG  N18  C16  O17  120.81  3.000
 JYG  N18  C16  C15  115.37  3.000
 JYG  O17  C16  C15  123.81  3.000
 JYG  C27  N18  C19  121.64  3.000
 JYG  C27  N18  C16  117.51  3.000
 JYG  C19  N18  C16  120.53  3.000
 JYG  N25  C19  N20  119.38  3.000
 JYG  N20  C19  N18  117.19  3.000
 JYG  N25  C19  N18  123.43  3.000
 JYG  H11  N20  C21  116.88  3.000
 JYG  H11  N20  C19  119.04  3.000
 JYG  C21  N20  C19  123.44  3.000
 JYG  C24  C21  C23   60.05  3.000
 JYG  C24  C21  C22  119.13  3.000
 JYG  C23  C21  C22  119.76  3.000
 JYG  C24  C21  N20  114.19  3.000
 JYG  C23  C21  N20  116.89  3.000
 JYG  C22  C21  N20  115.47  3.000
 JYG  H14  C22  H13  107.88  3.000
 JYG  H14  C22  H12  108.54  3.000
 JYG  H13  C22  H12  107.97  3.000
 JYG  H14  C22  C21  110.73  3.000
 JYG  H13  C22  C21  110.84  3.000
 JYG  H12  C22  C21  110.77  3.000
 JYG  H16  C23  H15  114.58  3.000
 JYG  H16  C23  C24  117.89  3.000
 JYG  H15  C23  C24  118.38  3.000
 JYG  H16  C23  C21  117.71  3.000
 JYG  H15  C23  C21  117.65  3.000
 JYG  C24  C23  C21   59.96  3.000
 JYG  H18  C24  H17  114.26  3.000
 JYG  H18  C24  C23  118.64  3.000
 JYG  H17  C24  C23  117.84  3.000
 JYG  H18  C24  C21  117.49  3.000
 JYG  H17  C24  C21  118.16  3.000
 JYG  C23  C24  C21   60.00  3.000
 JYG  C26  N25  C19  119.69  3.000
 JYG  N25  C26  C15  121.38  3.000
 JYG  N25  C26  C11  119.67  3.000
 JYG  C15  C26  C11  118.94  3.000
 JYG  C30  C27  C29   59.63  3.000
 JYG  C29  C27  C28  118.89  3.000
 JYG  C30  C27  C28  119.58  3.000
 JYG  C29  C27  N18  116.77  3.000
 JYG  C28  C27  N18  114.14  3.000
 JYG  C30  C27  N18  117.31  3.000
 JYG  H21  C28  H20  107.84  3.000
 JYG  H21  C28  H19  108.13  3.000
 JYG  H20  C28  H19  107.66  3.000
 JYG  H21  C28  C27  110.79  3.000
 JYG  H20  C28  C27  110.42  3.000
 JYG  H19  C28  C27  111.85  3.000
 JYG  H23  C29  H22  114.26  3.000
 JYG  H23  C29  C30  119.32  3.000
 JYG  H22  C29  C30  117.10  3.000
 JYG  H23  C29  C27  116.84  3.000
 JYG  H22  C29  C27  118.48  3.000
 JYG  C30  C29  C27   60.65  3.000
 JYG  H25  C30  H24  114.44  3.000
 JYG  H25  C30  C29  117.10  3.000
 JYG  H24  C30  C29  119.48  3.000
 JYG  H25  C30  C27  118.56  3.000
 JYG  H24  C30  C27  116.86  3.000
 JYG  C29  C30  C27   59.73  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
 JYG  CONST_01  C11  C08  C07  C06   180.00   0.0  0
 JYG  CONST_02  N09  C08  C07  C06     0.00   0.0  0
 JYG  CONST_03  C08  N09  C10  C06     0.00   0.0  0
 JYG  CONST_04  N09  C10  C06  C07     0.00   0.0  0
 JYG  CONST_07  C10  N09  C08  C07     0.00   0.0  0
 JYG  CONST_08  C10  C06  C07  C08     0.00   0.0  0
 JYG  CONST_09  C13  C12  C11  C08   180.00   0.0  0
 JYG  CONST_10  C15  C26  C11  C08   180.00   0.0  0
 JYG  CONST_13  C11  C08  N09  C10   180.00   0.0  0
 JYG  CONST_14  C14  C13  C12  C11     0.00   0.0  0
 JYG  CONST_15  C14  C15  C26  C11     0.00   0.0  0
 JYG  CONST_16  C15  C14  C13  C12     0.00   0.0  0
 JYG  CONST_17  C15  C26  C11  C12     0.00   0.0  0
 JYG  CONST_18  C26  C11  C12  C13     0.00   0.0  0
 JYG  CONST_19  C26  C15  C14  C13     0.00   0.0  0
 JYG  CONST_20  N25  C26  C11  C08     0.00   0.0  0
 JYG  CONST_21  C06  C04  N03  C02     0.00   0.0  0
 JYG  CONST_22  C19  N18  C16  C15     0.00   0.0  0
 JYG  CONST_23  C27  N18  C16  C15   180.00   0.0  0
 JYG  CONST_24  N25  C19  N18  C16     0.00   0.0  0
 JYG  CONST_25  C26  N25  C19  N18     0.00   0.0  0
 JYG  CONST_26  C27  N18  C19  N25   180.00   0.0  0
 JYG  CONST_27  O05  C04  N03  C02   180.00   0.0  0
 JYG  CONST_28  N20  C19  N18  C16   180.00   0.0  0
 JYG  CONST_29  C19  N18  C16  O17   180.00   0.0  0
 JYG  CONST_30  C27  N18  C16  O17     0.00   0.0  0
 JYG  CONST_31  C21  N20  C19  N18   180.00   0.0  0
 JYG  CONST_32  C26  N25  C19  N20   180.00   0.0  0
 JYG  CONST_33  C27  N18  C19  N20     0.00   0.0  0
 JYG  CONST_34  N25  C19  N20  C21     0.00   0.0  0
 JYG  CONST_35  H7   N09  C10  C02     0.00   0.0  0
 JYG  CONST_36  H6   C07  C06  C04     0.00   0.0  0
 JYG  CONST_37  H8   C12  C11  C08     0.00   0.0  0
 JYG  CONST_38  H9   C13  C12  C11   180.00   0.0  0
 JYG  CONST_39  H10  C14  C13  C12   180.00   0.0  0
 JYG  CONST_40  H5   N03  C04  C06   180.00   0.0  0
 JYG  CONST_41  H11  N20  C19  N18     0.00   0.0  0
 JYG  Var_01    C30  C27  N18  C16  -127.59  30.0  3
 JYG  Var_02    C29  C30  C27  N18   106.56  30.0  1
 JYG  Var_03    C23  C21  N20  C19    76.18  30.0  3
 JYG  Var_04    C24  C23  C21  N20   103.77  30.0  1
 JYG  Var_05    H17  C24  C23  C21  -108.14  30.0  1
 JYG  Var_06    H19  C28  C27  N18    58.26  30.0  3
 JYG  Var_07    H12  C22  C21  C23   -86.03  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
 JYG  chir_01  C02  N03  C10  C01  negativ
 JYG  chir_02  C21  C23  N20  C24  both
 JYG  chir_03  C27  C29  C28  C30  both

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
 JYG  plan-1  C02  0.020
 JYG  plan-1  N03  0.020
 JYG  plan-1  C04  0.020
 JYG  plan-1  O05  0.020
 JYG  plan-1  C06  0.020
 JYG  plan-1  C07  0.020
 JYG  plan-1  C08  0.020
 JYG  plan-1  N09  0.020
 JYG  plan-1  C10  0.020
 JYG  plan-1  C11  0.020
 JYG  plan-1  H5   0.020
 JYG  plan-1  H6   0.020
 JYG  plan-1  H7   0.020
 JYG  plan-2  C08  0.020
 JYG  plan-2  C11  0.020
 JYG  plan-2  C12  0.020
 JYG  plan-2  C13  0.020
 JYG  plan-2  C14  0.020
 JYG  plan-2  C15  0.020
 JYG  plan-2  C16  0.020
 JYG  plan-2  O17  0.020
 JYG  plan-2  N18  0.020
 JYG  plan-2  C19  0.020
 JYG  plan-2  N20  0.020
 JYG  plan-2  C21  0.020
 JYG  plan-2  N25  0.020
 JYG  plan-2  C26  0.020
 JYG  plan-2  C27  0.020
 JYG  plan-2  H8   0.020
 JYG  plan-2  H9   0.020
 JYG  plan-2  H10  0.020
 JYG  plan-2  H11  0.020

