# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 17:55:56 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 2-(tert-butylamino)-3-methyl-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)C(=Nc34)NC(C)(C)C
#
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
 6CD  6CD  2-(tert-butylamino)-3-methyl-8-[(6R)-6-methyl-4-oxo-1,4,5,6-tetrahydropyrrolo[3,4-b]pyrrol-2-yl]quinazolin-4(3H)-one  ligand  50  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6CD
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
 6CD  C01  C  CH3   0  -0.658  -5.5606   2.3573   0.3548
 6CD  C02  C  CR15  0  -0.086  -4.8301   1.1363   0.8966
 6CD  N03  N  NR15  0  -0.671  -5.2921  -0.1119   0.3022
 6CD  C04  C  CR5   0   0.471  -4.3408  -0.8509  -0.3423
 6CD  O05  O  O     0  -0.490  -4.5290  -1.9235  -0.8960
 6CD  C06  C  CR55  0  -0.117  -3.1077  -0.0720  -0.2113
 6CD  C07  C  CR15  0  -0.430  -1.7325  -0.0395  -0.5384
 6CD  C08  C  CR5   0   0.327  -1.2390   1.1372  -0.0126
 6CD  N09  N  NR15  0  -0.712  -2.2854   1.7960   0.6163
 6CD  C10  C  CR55  0   0.335  -3.3965   1.0563   0.5001
 6CD  C11  C  CR6   0  -0.025   0.0766   1.7695  -0.0788
 6CD  C12  C  CR16  0  -0.320   0.1631   3.1525  -0.1541
 6CD  C13  C  CR16  0  -0.262   1.3860   3.8241  -0.1805
 6CD  C14  C  CR16  0  -0.290   2.5552   3.1024  -0.1351
 6CD  C15  C  CR66  0  -0.126   2.5026   1.7078  -0.0633
 6CD  C16  C  CR6   0   0.577   3.7411   0.9493   0.0158
 6CD  O17  O  O     0  -0.467   4.8480   1.4620  -0.0020
 6CD  N18  N  NR6   0  -0.588   3.5895  -0.4236   0.1269
 6CD  C19  C  CH3   0  -0.598   4.7874  -1.2424   0.2553
 6CD  C20  C  CR6   0   0.772   2.3353  -1.0136   0.1160
 6CD  N21  N  NH1   0  -0.713   2.3152  -2.3510   0.2267
 6CD  C22  C  CT    0   0.096   1.1473  -3.2370   0.0937
 6CD  C23  C  CH3   0  -0.655   0.0759  -2.9174   1.1355
 6CD  C24  C  CH3   0  -0.656   0.5876  -3.1697  -1.3277
 6CD  C25  C  CH3   0  -0.684   1.6793  -4.6457   0.3574
 6CD  N26  N  N     0  -0.524   1.2289  -0.3380   0.0230
 6CD  C27  C  CR66  0   0.231   1.2821   1.0155  -0.0440
 6CD  H1   H  HCH3  0   0.236  -5.4504   2.4248  -0.7273
 6CD  H2   H  HCH3  0   0.248  -6.6226   2.3069   0.5944
 6CD  H3   H  HCH3  0   0.240  -5.1604   3.2670   0.8022
 6CD  H4   H  HCR5  0   0.277  -4.9444   1.0977   1.9853
 6CD  H5   H  HNR5  0   0.397  -6.2440  -0.4261   0.4002
 6CD  H6   H  HCR5  0   0.262  -1.1645  -0.7605  -1.0984
 6CD  H7   H  HNR5  0   0.416  -2.1921   2.6484   1.1459
 6CD  H8   H  HCR6  0   0.259  -0.7447   3.7409  -0.2116
 6CD  H9   H  HCR6  0   0.259   1.4058   4.9033  -0.2431
 6CD  H10  H  HCR6  0   0.261   3.5136   3.6033  -0.1544
 6CD  H11  H  HCH3  0   0.296   5.6558  -0.5961   0.2758
 6CD  H12  H  HCH3  0   0.269   4.7653  -1.8127   1.1833
 6CD  H13  H  HCH3  0   0.268   4.8896  -1.9205  -0.5919
 6CD  H14  H  HNH1  0   0.424   3.1975  -2.8325   0.2179
 6CD  H15  H  HCH3  0   0.268  -0.3756  -1.9433   0.9709
 6CD  H16  H  HCH3  0   0.223  -0.7116  -3.6711   1.0881
 6CD  H17  H  HCH3  0   0.224   0.5010  -2.9400   2.1406
 6CD  H18  H  HCH3  0   0.231   1.3434  -3.4799  -2.0514
 6CD  H19  H  HCH3  0   0.228  -0.2691  -3.8377  -1.4284
 6CD  H20  H  HCH3  0   0.254   0.2657  -2.1627  -1.5857
 6CD  H21  H  HCH3  0   0.242   2.0861  -4.7320   1.3666
 6CD  H22  H  HCH3  0   0.247   0.8737  -5.3718   0.2575
 6CD  H23  H  HCH3  0   0.237   2.4606  -4.9203  -0.3547

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
 6CD  C25  C22  single    1.529  0.020  1.529
 6CD  C22  N21  single    1.472  0.020  1.472
 6CD  C22  C24  single    1.529  0.020  1.529
 6CD  C22  C23  single    1.528  0.020  1.528
 6CD  N21  C20  single    1.342  0.020  1.342
 6CD  C19  N18  single    1.457  0.020  1.457
 6CD  C20  N18  single    1.386  0.020  1.386
 6CD  C20  N26  double    1.300  0.020  1.300
 6CD  N18  C16  single    1.386  0.020  1.386
 6CD  C01  C02  single    1.522  0.020  1.522
 6CD  N26  C27  single    1.356  0.020  1.356
 6CD  C16  O17  double    1.220  0.020  1.220
 6CD  C16  C15  single    1.454  0.020  1.454
 6CD  C02  C10  single    1.489  0.020  1.489
 6CD  C02  N03  single    1.458  0.020  1.458
 6CD  N09  C10  aromatic  1.340  0.020  1.340
 6CD  N09  C08  aromatic  1.387  0.020  1.387
 6CD  C10  C06  aromatic  1.365  0.020  1.365
 6CD  C27  C15  aromatic  1.403  0.020  1.403
 6CD  C27  C11  aromatic  1.422  0.020  1.422
 6CD  C15  C14  aromatic  1.397  0.020  1.397
 6CD  N03  C04  single    1.366  0.020  1.366
 6CD  C08  C11  single    1.461  0.020  1.461
 6CD  C08  C07  aromatic  1.380  0.020  1.380
 6CD  C11  C12  aromatic  1.388  0.020  1.388
 6CD  C06  C04  single    1.464  0.020  1.464
 6CD  C06  C07  aromatic  1.414  0.020  1.414
 6CD  C14  C13  aromatic  1.375  0.020  1.375
 6CD  C04  O05  double    1.222  0.020  1.222
 6CD  C12  C13  aromatic  1.395  0.020  1.395
 6CD  C01  H1   single    0.970  0.020  1.090
 6CD  C01  H2   single    0.970  0.020  1.090
 6CD  C01  H3   single    0.970  0.020  1.090
 6CD  C02  H4   single    0.970  0.020  1.090
 6CD  N03  H5   single    0.860  0.020  1.020
 6CD  C07  H6   single    0.930  0.020  1.080
 6CD  N09  H7   single    0.860  0.020  1.020
 6CD  C12  H8   single    0.930  0.020  1.080
 6CD  C13  H9   single    0.930  0.020  1.080
 6CD  C14  H10  single    0.930  0.020  1.080
 6CD  C19  H11  single    0.970  0.020  1.090
 6CD  C19  H12  single    0.970  0.020  1.090
 6CD  C19  H13  single    0.970  0.020  1.090
 6CD  N21  H14  single    0.860  0.020  1.020
 6CD  C23  H15  single    0.970  0.020  1.090
 6CD  C23  H16  single    0.970  0.020  1.090
 6CD  C23  H17  single    0.970  0.020  1.090
 6CD  C24  H18  single    0.970  0.020  1.090
 6CD  C24  H19  single    0.970  0.020  1.090
 6CD  C24  H20  single    0.970  0.020  1.090
 6CD  C25  H21  single    0.970  0.020  1.090
 6CD  C25  H22  single    0.970  0.020  1.090
 6CD  C25  H23  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
 6CD  H3   C01  H2   107.83  3.000
 6CD  H3   C01  H1   108.59  3.000
 6CD  H2   C01  H1   108.64  3.000
 6CD  H3   C01  C02  110.31  3.000
 6CD  H2   C01  C02  110.63  3.000
 6CD  H1   C01  C02  110.76  3.000
 6CD  H4   C02  C10  111.29  3.000
 6CD  H4   C02  N03  110.00  3.000
 6CD  C10  C02  N03   98.65  3.000
 6CD  H4   C02  C01  109.38  3.000
 6CD  N03  C02  C01  112.92  3.000
 6CD  C10  C02  C01  114.22  3.000
 6CD  H5   N03  C04  122.36  3.000
 6CD  H5   N03  C02  121.80  3.000
 6CD  C04  N03  C02  115.78  3.000
 6CD  C06  C04  O05  129.59  3.000
 6CD  O05  C04  N03  125.56  3.000
 6CD  C06  C04  N03  104.86  3.000
 6CD  C10  C06  C07  107.91  3.000
 6CD  C07  C06  C04  144.15  3.000
 6CD  C10  C06  C04  107.95  3.000
 6CD  H6   C07  C08  125.54  3.000
 6CD  H6   C07  C06  128.23  3.000
 6CD  C08  C07  C06  106.21  3.000
 6CD  C11  C08  N09  119.62  3.000
 6CD  C11  C08  C07  132.35  3.000
 6CD  N09  C08  C07  107.93  3.000
 6CD  H7   N09  C10  126.11  3.000
 6CD  H7   N09  C08  124.75  3.000
 6CD  C10  N09  C08  108.91  3.000
 6CD  N09  C10  C06  109.03  3.000
 6CD  C06  C10  C02  112.76  3.000
 6CD  N09  C10  C02  138.19  3.000
 6CD  C27  C11  C12  118.48  3.000
 6CD  C12  C11  C08  119.33  3.000
 6CD  C27  C11  C08  122.18  3.000
 6CD  H8   C12  C13  118.17  3.000
 6CD  H8   C12  C11  119.47  3.000
 6CD  C13  C12  C11  122.36  3.000
 6CD  H9   C13  C14  120.69  3.000
 6CD  H9   C13  C12  119.83  3.000
 6CD  C14  C13  C12  119.48  3.000
 6CD  H10  C14  C15  119.77  3.000
 6CD  H10  C14  C13  120.66  3.000
 6CD  C15  C14  C13  119.57  3.000
 6CD  C27  C15  C16  118.85  3.000
 6CD  C27  C15  C14  121.72  3.000
 6CD  C16  C15  C14  119.42  3.000
 6CD  N18  C16  O17  121.12  3.000
 6CD  O17  C16  C15  123.55  3.000
 6CD  N18  C16  C15  115.33  3.000
 6CD  C20  N18  C19  120.37  3.000
 6CD  C20  N18  C16  121.34  3.000
 6CD  C19  N18  C16  118.29  3.000
 6CD  H13  C19  H12  109.78  3.000
 6CD  H13  C19  H11  108.11  3.000
 6CD  H12  C19  H11  108.22  3.000
 6CD  H13  C19  N18  110.99  3.000
 6CD  H12  C19  N18  110.65  3.000
 6CD  H11  C19  N18  109.01  3.000
 6CD  N26  C20  N21  120.74  3.000
 6CD  N26  C20  N18  123.34  3.000
 6CD  N21  C20  N18  115.92  3.000
 6CD  H14  N21  C22  114.04  3.000
 6CD  H14  N21  C20  117.60  3.000
 6CD  C22  N21  C20  127.18  3.000
 6CD  C25  C22  C24  109.16  3.000
 6CD  C24  C22  C23  111.58  3.000
 6CD  C25  C22  C23  108.61  3.000
 6CD  C23  C22  N21  111.64  3.000
 6CD  C24  C22  N21  110.36  3.000
 6CD  C25  C22  N21  105.25  3.000
 6CD  H17  C23  H16  107.86  3.000
 6CD  H17  C23  H15  108.66  3.000
 6CD  H16  C23  H15  108.23  3.000
 6CD  H17  C23  C22  110.51  3.000
 6CD  H16  C23  C22  109.39  3.000
 6CD  H15  C23  C22  112.07  3.000
 6CD  H20  C24  H19  108.21  3.000
 6CD  H20  C24  H18  108.10  3.000
 6CD  H19  C24  H18  107.97  3.000
 6CD  H20  C24  C22  111.67  3.000
 6CD  H19  C24  C22  110.26  3.000
 6CD  H18  C24  C22  110.51  3.000
 6CD  H23  C25  H22  107.56  3.000
 6CD  H23  C25  H21  108.45  3.000
 6CD  H22  C25  H21  107.92  3.000
 6CD  H23  C25  C22  111.60  3.000
 6CD  H22  C25  C22  109.94  3.000
 6CD  H21  C25  C22  111.23  3.000
 6CD  C27  N26  C20  119.27  3.000
 6CD  N26  C27  C15  121.81  3.000
 6CD  C15  C27  C11  118.38  3.000
 6CD  N26  C27  C11  119.81  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
 6CD  CONST_01  C08  N09  C10  C06     0.00   0.0  0
 6CD  CONST_02  N09  C08  C07  C06     0.00   0.0  0
 6CD  CONST_03  C11  C08  C07  C06   180.00   0.0  0
 6CD  CONST_04  C10  N09  C08  C07     0.00   0.0  0
 6CD  CONST_07  N09  C10  C06  C07     0.00   0.0  0
 6CD  CONST_08  C15  C27  C11  C08   180.00   0.0  0
 6CD  CONST_09  C13  C12  C11  C08   180.00   0.0  0
 6CD  CONST_10  C10  C06  C07  C08     0.00   0.0  0
 6CD  CONST_13  C11  C08  N09  C10   180.00   0.0  0
 6CD  CONST_14  C14  C15  C27  C11     0.00   0.0  0
 6CD  CONST_15  C14  C13  C12  C11     0.00   0.0  0
 6CD  CONST_16  C15  C27  C11  C12     0.00   0.0  0
 6CD  CONST_17  C15  C14  C13  C12     0.00   0.0  0
 6CD  CONST_18  C27  C15  C14  C13     0.00   0.0  0
 6CD  CONST_19  C27  C11  C12  C13     0.00   0.0  0
 6CD  CONST_20  N26  C27  C11  C08     0.00   0.0  0
 6CD  CONST_21  C06  C04  N03  C02     0.00   0.0  0
 6CD  CONST_22  C20  N18  C16  C15     0.00   0.0  0
 6CD  CONST_23  N26  C20  N18  C16     0.00   0.0  0
 6CD  CONST_24  C27  N26  C20  N18     0.00   0.0  0
 6CD  CONST_25  O05  C04  N03  C02   180.00   0.0  0
 6CD  CONST_26  C19  N18  C16  C15   180.00   0.0  0
 6CD  CONST_27  N21  C20  N18  C16   180.00   0.0  0
 6CD  CONST_28  C20  N18  C16  O17   180.00   0.0  0
 6CD  CONST_29  N26  C20  N18  C19   180.00   0.0  0
 6CD  CONST_30  C27  N26  C20  N21   180.00   0.0  0
 6CD  CONST_31  H7   N09  C10  C02     0.00   0.0  0
 6CD  CONST_32  H6   C07  C06  C04     0.00   0.0  0
 6CD  CONST_33  H8   C12  C11  C08     0.00   0.0  0
 6CD  CONST_34  H9   C13  C12  C11   180.00   0.0  0
 6CD  CONST_35  H10  C14  C13  C12   180.00   0.0  0
 6CD  CONST_36  H5   N03  C04  C06   180.00   0.0  0
 6CD  CONST_37  C19  N18  C16  O17     0.00   0.0  0
 6CD  CONST_38  C22  N21  C20  N18   180.00   0.0  0
 6CD  CONST_39  N21  C20  N18  C19     0.00   0.0  0
 6CD  CONST_40  N26  C20  N21  C22     0.00   0.0  0
 6CD  CONST_41  H14  N21  C20  N18     0.00   0.0  0
 6CD  Var_01    H11  C19  N18  C16     1.91  30.0  3
 6CD  Var_02    C25  C22  N21  C20  -178.16  30.0  3
 6CD  Var_03    H21  C25  C22  N21    61.67  30.0  3
 6CD  Var_04    H18  C24  C22  N21    59.90  30.0  3
 6CD  Var_05    H15  C23  C22  N21    67.13  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
 6CD  chir_01  C02  C01  C10  N03  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
 6CD  plan-1  C08  0.020
 6CD  plan-1  C11  0.020
 6CD  plan-1  C12  0.020
 6CD  plan-1  C13  0.020
 6CD  plan-1  C14  0.020
 6CD  plan-1  C15  0.020
 6CD  plan-1  C16  0.020
 6CD  plan-1  O17  0.020
 6CD  plan-1  N18  0.020
 6CD  plan-1  C19  0.020
 6CD  plan-1  C20  0.020
 6CD  plan-1  N21  0.020
 6CD  plan-1  C22  0.020
 6CD  plan-1  N26  0.020
 6CD  plan-1  C27  0.020
 6CD  plan-1  H8   0.020
 6CD  plan-1  H9   0.020
 6CD  plan-1  H10  0.020
 6CD  plan-1  H14  0.020
 6CD  plan-2  C02  0.020
 6CD  plan-2  N03  0.020
 6CD  plan-2  C04  0.020
 6CD  plan-2  O05  0.020
 6CD  plan-2  C06  0.020
 6CD  plan-2  C07  0.020
 6CD  plan-2  C08  0.020
 6CD  plan-2  N09  0.020
 6CD  plan-2  C10  0.020
 6CD  plan-2  C11  0.020
 6CD  plan-2  H5   0.020
 6CD  plan-2  H6   0.020
 6CD  plan-2  H7   0.020

