# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 07:49:29 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (5~{S})-1-ethyl-5-(4-methylphenyl)-8,9-dihydro-5~{H}-furo[3,4]pyrido[3,5-~{b}]pyrimidine-2,4,6-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=O)NC(=O)C2=C1NC3=C([C@H]2c4ccc(C)cc4)C(=O)OC3
#
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
 6RX  6RX  (5~{S})-1-ethyl-5-(4-methylphenyl)-8,9-dihydro-5~{H}-furo[3,4]pyrido[3,5-~{b}]pyrimidine-2,4,6-trione  ligand  42  25  .  2022-07-23  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_6RX
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
 6RX  C10   C  C     0   0.721  -3.2809  -1.4207  -0.3799
 6RX  C13   C  CH3   0  -0.657  -3.7410   0.0677   2.5259
 6RX  C21   C  CR5   0  -0.137   0.6550   1.7093  -0.3941
 6RX  C22   C  CR5   0   0.551   1.7012   2.7094  -0.4732
 6RX  C24   C  CR16  0  -0.305   2.7464  -1.0852  -0.9433
 6RX  C02   C  CR6   0   0.081   3.5914  -2.1379   1.0667
 6RX  C03   C  CR16  0  -0.282   2.5153  -1.5872   1.7620
 6RX  C04   C  CR16  0  -0.284   1.5720  -0.8036   1.1157
 6RX  C05   C  CR6   0   0.192   1.6747  -0.5440  -0.2473
 6RX  C06   C  CH1   0  -0.393   0.6461   0.3259  -0.9460
 6RX  C07   C  C     0  -0.231  -0.7567  -0.2205  -0.7753
 6RX  C08   C  C     0   0.568  -1.0604  -1.4533  -1.4402
 6RX  N09   N  NH1   0  -0.733  -2.3212  -1.9614  -1.1810
 6RX  N11   N  NT    0  -0.603  -2.9639  -0.1957   0.1803
 6RX  C12   C  CH2   0  -0.380  -3.9688   0.4084   1.0637
 6RX  O14   O  O     0  -0.477  -4.3432  -1.9732  -0.1823
 6RX  O15   O  O     0  -0.460  -0.3003  -2.0518  -2.1829
 6RX  C16   C  C     0   0.692  -1.7229   0.3669  -0.0069
 6RX  N17   N  NH1   0  -0.782  -1.4956   1.5738   0.6065
 6RX  C18   C  CR5   0   0.283  -0.3356   2.2234   0.3387
 6RX  C19   C  CH2   0  -0.187   0.0173   3.5987   0.7864
 6RX  O20   O  O     0  -0.460   1.3063   3.8021   0.2272
 6RX  O23   O  O     0  -0.436   2.7651   2.6762  -1.0340
 6RX  C25   C  CR16  0  -0.291   3.6918  -1.8698  -0.2959
 6RX  H132  H  HCH3  0   0.246  -3.7975  -1.0081   2.6858
 6RX  H131  H  HCH3  0   0.233  -2.7740   0.4162   2.8885
 6RX  H133  H  HCH3  0   0.252  -4.5130   0.5394   3.1328
 6RX  H241  H  HCR6  0   0.243   2.8481  -0.8915  -2.0047
 6RX  H012  H  HCH3  0   0.247   4.2468  -4.0482   1.8037
 6RX  H011  H  HCH3  0   0.242   5.5529  -3.0123   1.2493
 6RX  H013  H  HCH3  0   0.242   4.7587  -2.6901   2.7914
 6RX  H031  H  HCR6  0   0.244   2.4134  -1.7737   2.8249
 6RX  H041  H  HCR6  0   0.242   0.7478  -0.3912   1.6873
 6RX  H061  H  HCH1  0   0.283   0.8962   0.3478  -2.0116
 6RX  H091  H  HNH1  0   0.426  -2.5559  -2.8495  -1.6060
 6RX  H121  H  HCH2  0   0.298  -4.9386   0.0460   0.7387
 6RX  H122  H  HCH2  0   0.272  -3.9950   1.4839   0.8931
 6RX  H171  H  HNH1  0   0.444  -2.2010   2.0333   1.1581
 6RX  H191  H  HCH2  0   0.286  -0.6779   4.3502   0.4055
 6RX  H192  H  HCH2  0   0.287   0.0642   3.6854   1.8742
 6RX  H251  H  HCR6  0   0.244   4.5195  -2.2814  -0.8620
 6RX  C01   C  CH3   0  -0.720   4.5923  -3.0129   1.7638

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
 6RX  C01  C02   single    1.501  0.020  1.501
 6RX  C25  C02   aromatic  1.392  0.020  1.392
 6RX  C25  C24   aromatic  1.389  0.020  1.389
 6RX  C02  C03   aromatic  1.394  0.020  1.394
 6RX  C24  C05   aromatic  1.388  0.020  1.388
 6RX  O15  C08   double    1.220  0.020  1.220
 6RX  C03  C04   aromatic  1.386  0.020  1.386
 6RX  C05  C04   aromatic  1.391  0.020  1.391
 6RX  C05  C06   single    1.518  0.020  1.518
 6RX  C08  N09   single    1.384  0.020  1.384
 6RX  C08  C07   single    1.433  0.020  1.433
 6RX  O23  C22   double    1.203  0.020  1.203
 6RX  C06  C07   single    1.515  0.020  1.515
 6RX  C06  C21   single    1.489  0.020  1.489
 6RX  N09  C10   single    1.362  0.020  1.362
 6RX  C07  C16   double    1.367  0.020  1.367
 6RX  C22  C21   single    1.450  0.020  1.450
 6RX  C22  O20   single    1.357  0.020  1.357
 6RX  C21  C18   double    1.335  0.020  1.335
 6RX  C10  O14   double    1.214  0.020  1.214
 6RX  C10  N11   single    1.384  0.020  1.384
 6RX  C16  N11   single    1.375  0.020  1.375
 6RX  C16  N17   single    1.373  0.020  1.373
 6RX  O20  C19   single    1.420  0.020  1.420
 6RX  C18  N17   single    1.356  0.020  1.356
 6RX  C18  C19   single    1.489  0.020  1.489
 6RX  N11  C12   single    1.468  0.020  1.468
 6RX  C12  C13   single    1.519  0.020  1.519
 6RX  C13  H132  single    0.970  0.020  1.090
 6RX  C13  H131  single    0.970  0.020  1.090
 6RX  C13  H133  single    0.970  0.020  1.090
 6RX  C24  H241  single    0.930  0.020  1.080
 6RX  C01  H012  single    0.970  0.020  1.090
 6RX  C01  H011  single    0.970  0.020  1.090
 6RX  C01  H013  single    0.970  0.020  1.090
 6RX  C03  H031  single    0.930  0.020  1.080
 6RX  C04  H041  single    0.930  0.020  1.080
 6RX  C06  H061  single    0.970  0.020  1.090
 6RX  N09  H091  single    0.860  0.020  1.020
 6RX  C12  H121  single    0.970  0.020  1.090
 6RX  C12  H122  single    0.970  0.020  1.090
 6RX  N17  H171  single    0.860  0.020  1.020
 6RX  C19  H191  single    0.970  0.020  1.090
 6RX  C19  H192  single    0.970  0.020  1.090
 6RX  C25  H251  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
 6RX  O14   C10  N11   122.52  3.000
 6RX  N11   C10  N09   115.35  3.000
 6RX  O14   C10  N09   122.13  3.000
 6RX  H133  C13  H131  107.75  3.000
 6RX  H133  C13  H132  108.01  3.000
 6RX  H131  C13  H132  108.24  3.000
 6RX  H133  C13  C12   109.45  3.000
 6RX  H131  C13  C12   112.44  3.000
 6RX  H132  C13  C12   110.81  3.000
 6RX  C18   C21  C06   123.82  3.000
 6RX  C18   C21  C22   107.45  3.000
 6RX  C06   C21  C22   128.67  3.000
 6RX  O23   C22  O20   121.35  3.000
 6RX  O20   C22  C21   108.51  3.000
 6RX  O23   C22  C21   130.14  3.000
 6RX  H241  C24  C25   119.59  3.000
 6RX  H241  C24  C05   119.60  3.000
 6RX  C25   C24  C05   120.81  3.000
 6RX  C25   C02  C03   117.87  3.000
 6RX  C03   C02  C01   120.88  3.000
 6RX  C25   C02  C01   121.24  3.000
 6RX  H031  C03  C04   119.37  3.000
 6RX  H031  C03  C02   119.57  3.000
 6RX  C04   C03  C02   121.06  3.000
 6RX  H041  C04  C05   120.10  3.000
 6RX  H041  C04  C03   119.10  3.000
 6RX  C05   C04  C03   120.80  3.000
 6RX  C06   C05  C04   120.53  3.000
 6RX  C06   C05  C24   121.07  3.000
 6RX  C04   C05  C24   118.40  3.000
 6RX  H061  C06  C07   109.17  3.000
 6RX  H061  C06  C05   107.74  3.000
 6RX  C07   C06  C05   111.65  3.000
 6RX  H061  C06  C21   109.92  3.000
 6RX  C07   C06  C21   107.38  3.000
 6RX  C05   C06  C21   110.97  3.000
 6RX  C16   C07  C08   118.72  3.000
 6RX  C16   C07  C06   124.24  3.000
 6RX  C08   C07  C06   117.01  3.000
 6RX  O15   C08  N09   120.11  3.000
 6RX  N09   C08  C07   114.96  3.000
 6RX  O15   C08  C07   124.93  3.000
 6RX  H091  N09  C08   117.05  3.000
 6RX  H091  N09  C10   115.59  3.000
 6RX  C08   N09  C10   127.32  3.000
 6RX  C16   N11  C12   122.09  3.000
 6RX  C12   N11  C10   116.81  3.000
 6RX  C16   N11  C10   120.91  3.000
 6RX  H122  C12  H121  105.15  3.000
 6RX  H122  C12  N11   109.18  3.000
 6RX  H121  C12  N11   107.11  3.000
 6RX  H122  C12  C13   112.08  3.000
 6RX  H121  C12  C13   110.34  3.000
 6RX  N11   C12  C13   112.61  3.000
 6RX  N17   C16  N11   116.63  3.000
 6RX  N17   C16  C07   120.79  3.000
 6RX  N11   C16  C07   122.58  3.000
 6RX  H171  N17  C18   119.28  3.000
 6RX  H171  N17  C16   122.02  3.000
 6RX  C18   N17  C16   118.32  3.000
 6RX  C19   C18  N17   125.86  3.000
 6RX  C19   C18  C21   110.18  3.000
 6RX  N17   C18  C21   123.96  3.000
 6RX  H192  C19  H191  108.66  3.000
 6RX  H192  C19  O20   110.00  3.000
 6RX  H191  C19  O20   109.99  3.000
 6RX  H192  C19  C18   112.52  3.000
 6RX  H191  C19  C18   112.32  3.000
 6RX  O20   C19  C18   103.25  3.000
 6RX  C19   O20  C22   110.62  3.000
 6RX  H251  C25  C02   119.54  3.000
 6RX  H251  C25  C24   119.40  3.000
 6RX  C02   C25  C24   121.06  3.000
 6RX  H013  C01  H011  108.09  3.000
 6RX  H013  C01  H012  107.13  3.000
 6RX  H011  C01  H012  107.26  3.000
 6RX  H013  C01  C02   111.53  3.000
 6RX  H011  C01  C02   111.61  3.000
 6RX  H012  C01  C02   111.01  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
 6RX  CONST_01  C03   C02  C25  C24     0.00   0.0  0
 6RX  CONST_02  C03   C04  C05  C24     0.00   0.0  0
 6RX  CONST_03  C05   C24  C25  C02     0.00   0.0  0
 6RX  CONST_04  C05   C04  C03  C02     0.00   0.0  0
 6RX  CONST_05  C25   C02  C03  C04     0.00   0.0  0
 6RX  CONST_06  C25   C24  C05  C04     0.00   0.0  0
 6RX  CONST_07  C06   C05  C04  C03   180.00   0.0  0
 6RX  CONST_08  C25   C24  C05  C06   180.00   0.0  0
 6RX  CONST_09  C07   C16  N11  C10     0.00   0.0  0
 6RX  CONST_10  N17   C16  N11  C10   180.00   0.0  0
 6RX  CONST_11  C18   N17  C16  C07     0.00   0.0  0
 6RX  CONST_12  N11   C10  N09  C08     0.00   0.0  0
 6RX  CONST_13  C16   N11  C10  N09     0.00   0.0  0
 6RX  CONST_14  C18   N17  C16  N11   180.00   0.0  0
 6RX  CONST_15  C01   C02  C25  C24   180.00   0.0  0
 6RX  CONST_16  C04   C03  C02  C01   180.00   0.0  0
 6RX  CONST_17  C12   N11  C16  C07   180.00   0.0  0
 6RX  CONST_18  O14   C10  N09  C08   180.00   0.0  0
 6RX  CONST_19  C12   N11  C10  N09   180.00   0.0  0
 6RX  CONST_20  N17   C16  N11  C12     0.00   0.0  0
 6RX  CONST_21  C16   N11  C10  O14   180.00   0.0  0
 6RX  CONST_22  H041  C04  C05  C24   180.00   0.0  0
 6RX  CONST_23  H241  C24  C25  C02   180.00   0.0  0
 6RX  CONST_24  H251  C25  C02  C03   180.00   0.0  0
 6RX  CONST_25  H031  C03  C04  C05   180.00   0.0  0
 6RX  CONST_26  H171  N17  C16  C07   180.00   0.0  0
 6RX  CONST_27  H091  N09  C10  N11   180.00   0.0  0
 6RX  CONST_28  O14   C10  N11  C12     0.00   0.0  0
 6RX  Var_01    C16   N17  C18  C21    -6.14  30.0  1
 6RX  Var_02    O20   C19  C18  C21     0.08  30.0  1
 6RX  Var_03    N17   C18  C21  C22   178.87  30.0  1
 6RX  Var_04    C18   C19  O20  C22     0.12  30.0  1
 6RX  Var_05    O20   C22  C21  C06  -176.97  30.0  1
 6RX  Var_06    C13   C12  N11  C10    93.63  30.0  3
 6RX  Var_07    H012  C01  C02  C03    84.84  30.0  2
 6RX  Var_08    H132  C13  C12  N11   -60.94  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
 6RX  chir_01  C06  C05  C07  C21  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
 6RX  plan-1  C24   0.020
 6RX  plan-1  C02   0.020
 6RX  plan-1  C03   0.020
 6RX  plan-1  C04   0.020
 6RX  plan-1  C05   0.020
 6RX  plan-1  C06   0.020
 6RX  plan-1  C25   0.020
 6RX  plan-1  H241  0.020
 6RX  plan-1  H031  0.020
 6RX  plan-1  H041  0.020
 6RX  plan-1  H251  0.020
 6RX  plan-1  C01   0.020
 6RX  plan-2  C21   0.020
 6RX  plan-2  C22   0.020
 6RX  plan-2  O20   0.020
 6RX  plan-2  O23   0.020
 6RX  plan-3  C10   0.020
 6RX  plan-3  C06   0.020
 6RX  plan-3  C07   0.020
 6RX  plan-3  C08   0.020
 6RX  plan-3  N09   0.020
 6RX  plan-3  N11   0.020
 6RX  plan-3  C12   0.020
 6RX  plan-3  O14   0.020
 6RX  plan-3  O15   0.020
 6RX  plan-3  C16   0.020
 6RX  plan-3  N17   0.020
 6RX  plan-3  C18   0.020
 6RX  plan-3  H091  0.020
 6RX  plan-3  H171  0.020

