# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 11:10:12 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: 7-methoxy-4-(2-methyl-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl)-3,4-dihydroquinoxalin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2N(CC(=O)Nc2c1)c3nc(C)nc4CCCc34
#
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
 Y5M  Y5M  "7-methoxy-4-(2-methyl-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl)-3,4-dihydroquinoxalin-2(1H)-one"
  ligand  41  23  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y5M
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
 Y5M  C01  C  CH3   0  -0.731  17.0115  -67.6083  -37.3076
 Y5M  C02  C  CR6   0   0.338  16.4257  -67.3000  -38.6499
 Y5M  C04  C  CR56  0   0.228  14.6181  -66.9559  -39.9297
 Y5M  C05  C  CR56  0  -0.041  15.3911  -66.7887  -41.0670
 Y5M  C06  C  CH2   0  -0.488  14.5239  -66.6292  -42.2811
 Y5M  C07  C  CH2   0  -0.460  13.1509  -67.1174  -41.7808
 Y5M  C08  C  CH2   0  -0.505  13.1594  -66.8713  -40.2660
 Y5M  C09  C  CR6   0   0.470  16.7720  -66.8752  -40.8773
 Y5M  C11  C  CR6   0   0.289  17.4832  -65.9344  -43.0191
 Y5M  C12  C  CR16  0  -0.294  16.8646  -64.6963  -43.0010
 Y5M  C13  C  CR16  0  -0.390  16.6907  -63.9636  -44.1686
 Y5M  C14  C  CR6   0   0.386  17.1812  -64.4615  -45.3732
 Y5M  C16  C  CH3   0  -0.436  16.4264  -62.5771  -46.5986
 Y5M  C17  C  CR16  0  -0.427  17.8592  -65.6810  -45.3922
 Y5M  C18  C  CR6   0   0.356  18.0083  -66.4083  -44.2254
 Y5M  C20  C  C     0   0.507  19.2305  -68.1697  -43.0957
 Y5M  C21  C  CH2   0  -0.446  18.9842  -67.3744  -41.8269
 Y5M  N03  N  N     0  -0.450  15.1000  -67.1908  -38.7175
 Y5M  N10  N  NT    0  -0.602  17.6894  -66.7310  -41.8869
 Y5M  N19  N  NH1   0  -0.725  18.6770  -67.6295  -44.2121
 Y5M  N23  N  N     0  -0.472  17.2617  -67.1534  -39.6653
 Y5M  O22  O  O     0  -0.446  19.8881  -69.1899  -43.1144
 Y5M  H1   H  HCH3  0   0.245  18.0932  -67.7009  -37.3611
 Y5M  H2   H  HCH3  0   0.252  16.7639  -66.8209  -36.5942
 Y5M  H3   H  HCH3  0   0.251  16.5985  -68.5371  -36.9123
 Y5M  H4   H  HCH2  0   0.254  14.8817  -67.1949  -43.1426
 Y5M  H5   H  HCH2  0   0.254  14.4744  -65.5824  -42.5951
 Y5M  H6   H  HCH2  0   0.242  12.3257  -66.6175  -42.2857
 Y5M  H7   H  HCH2  0   0.243  13.0531  -68.1875  -41.9726
 Y5M  H8   H  HCH2  0   0.259  12.7876  -65.8710  -40.0208
 Y5M  H9   H  HCH2  0   0.257  12.5576  -67.5848  -39.7030
 Y5M  H10  H  HCR6  0   0.283  16.4949  -64.2935  -42.0664
 Y5M  H11  H  HCR6  0   0.281  16.1850  -63.0100  -44.1122
 Y5M  H12  H  HCH3  0   0.259  16.4413  -62.2554  -47.6370
 Y5M  H13  H  HCH3  0   0.228  15.3872  -62.6357  -46.2642
 Y5M  H14  H  HCH3  0   0.228  16.9495  -61.8328  -45.9924
 Y5M  H15  H  HCR6  0   0.277  18.2679  -66.0561  -46.3231
 Y5M  H16  H  HCH2  0   0.299  19.0244  -68.0478  -40.9756
 Y5M  H17  H  HCH2  0   0.282  19.7927  -66.6425  -41.7065
 Y5M  H18  H  HNH1  0   0.413  18.8824  -68.0766  -45.0959
 Y5M  O15  O  O2    0  -0.470  17.0664  -63.8366  -46.5593

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
 Y5M  O15  C16  single    1.413  0.020  1.413
 Y5M  O15  C14  single    1.346  0.020  1.346
 Y5M  C17  C14  aromatic  1.395  0.020  1.395
 Y5M  C17  C18  aromatic  1.383  0.020  1.383
 Y5M  C14  C13  aromatic  1.393  0.020  1.393
 Y5M  N19  C18  single    1.392  0.020  1.392
 Y5M  N19  C20  single    1.358  0.020  1.358
 Y5M  C18  C11  aromatic  1.398  0.020  1.398
 Y5M  C13  C12  aromatic  1.389  0.020  1.389
 Y5M  O22  C20  double    1.214  0.020  1.214
 Y5M  C20  C21  single    1.518  0.020  1.518
 Y5M  C11  C12  aromatic  1.384  0.020  1.384
 Y5M  C11  N10  single    1.400  0.020  1.400
 Y5M  C06  C07  single    1.541  0.020  1.541
 Y5M  C06  C05  single    1.501  0.020  1.501
 Y5M  N10  C21  single    1.447  0.020  1.447
 Y5M  N10  C09  single    1.372  0.020  1.372
 Y5M  C07  C08  single    1.535  0.020  1.535
 Y5M  C05  C09  aromatic  1.397  0.020  1.397
 Y5M  C05  C04  aromatic  1.385  0.020  1.385
 Y5M  C09  N23  aromatic  1.336  0.020  1.336
 Y5M  C08  C04  single    1.499  0.020  1.499
 Y5M  C04  N03  aromatic  1.326  0.020  1.326
 Y5M  N23  C02  aromatic  1.323  0.020  1.323
 Y5M  N03  C02  aromatic  1.332  0.020  1.332
 Y5M  C02  C01  single    1.497  0.020  1.497
 Y5M  C01  H1   single    0.970  0.020  1.090
 Y5M  C01  H2   single    0.970  0.020  1.090
 Y5M  C01  H3   single    0.970  0.020  1.090
 Y5M  C06  H4   single    0.970  0.020  1.090
 Y5M  C06  H5   single    0.970  0.020  1.090
 Y5M  C07  H6   single    0.970  0.020  1.090
 Y5M  C07  H7   single    0.970  0.020  1.090
 Y5M  C08  H8   single    0.970  0.020  1.090
 Y5M  C08  H9   single    0.970  0.020  1.090
 Y5M  C12  H10  single    0.930  0.020  1.080
 Y5M  C13  H11  single    0.930  0.020  1.080
 Y5M  C16  H12  single    0.970  0.020  1.090
 Y5M  C16  H13  single    0.970  0.020  1.090
 Y5M  C16  H14  single    0.970  0.020  1.090
 Y5M  C17  H15  single    0.930  0.020  1.080
 Y5M  C21  H16  single    0.970  0.020  1.090
 Y5M  C21  H17  single    0.970  0.020  1.090
 Y5M  N19  H18  single    0.860  0.020  1.020

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
 Y5M  H3   C01  H2   106.96  3.000
 Y5M  H3   C01  H1   108.80  3.000
 Y5M  H2   C01  H1   108.64  3.000
 Y5M  H3   C01  C02  110.62  3.000
 Y5M  H2   C01  C02  110.42  3.000
 Y5M  H1   C01  C02  111.28  3.000
 Y5M  N23  C02  N03  125.51  3.000
 Y5M  N03  C02  C01  116.87  3.000
 Y5M  N23  C02  C01  117.62  3.000
 Y5M  N03  C04  C08  124.67  3.000
 Y5M  N03  C04  C05  124.71  3.000
 Y5M  C08  C04  C05  110.61  3.000
 Y5M  C09  C05  C06  133.47  3.000
 Y5M  C09  C05  C04  115.64  3.000
 Y5M  C06  C05  C04  110.77  3.000
 Y5M  H5   C06  H4   106.52  3.000
 Y5M  H5   C06  C07  110.87  3.000
 Y5M  H4   C06  C07  112.60  3.000
 Y5M  H5   C06  C05  111.10  3.000
 Y5M  H4   C06  C05  113.21  3.000
 Y5M  C07  C06  C05  102.63  3.000
 Y5M  H7   C07  H6   107.50  3.000
 Y5M  H7   C07  C08  109.34  3.000
 Y5M  H6   C07  C08  112.84  3.000
 Y5M  H7   C07  C06  109.48  3.000
 Y5M  H6   C07  C06  112.29  3.000
 Y5M  C08  C07  C06  105.35  3.000
 Y5M  H9   C08  H8   107.15  3.000
 Y5M  H9   C08  C07  113.69  3.000
 Y5M  H8   C08  C07  111.45  3.000
 Y5M  H9   C08  C04  112.60  3.000
 Y5M  H8   C08  C04  109.37  3.000
 Y5M  C07  C08  C04  102.57  3.000
 Y5M  N23  C09  N10  116.38  3.000
 Y5M  N23  C09  C05  119.90  3.000
 Y5M  N10  C09  C05  123.69  3.000
 Y5M  N10  C11  C18  116.72  3.000
 Y5M  N10  C11  C12  124.36  3.000
 Y5M  C18  C11  C12  118.83  3.000
 Y5M  H10  C12  C13  119.11  3.000
 Y5M  H10  C12  C11  119.78  3.000
 Y5M  C13  C12  C11  121.11  3.000
 Y5M  H11  C13  C14  121.69  3.000
 Y5M  H11  C13  C12  118.68  3.000
 Y5M  C14  C13  C12  119.62  3.000
 Y5M  O15  C14  C17  115.81  3.000
 Y5M  C17  C14  C13  119.69  3.000
 Y5M  O15  C14  C13  124.50  3.000
 Y5M  H14  C16  H13  108.77  3.000
 Y5M  H14  C16  H12  108.76  3.000
 Y5M  H13  C16  H12  108.72  3.000
 Y5M  H14  C16  O15  112.01  3.000
 Y5M  H13  C16  O15  111.97  3.000
 Y5M  H12  C16  O15  106.50  3.000
 Y5M  H15  C17  C18  120.14  3.000
 Y5M  H15  C17  C14  119.82  3.000
 Y5M  C18  C17  C14  120.04  3.000
 Y5M  N19  C18  C17  121.41  3.000
 Y5M  N19  C18  C11  117.99  3.000
 Y5M  C17  C18  C11  120.60  3.000
 Y5M  O22  C20  N19  122.85  3.000
 Y5M  O22  C20  C21  122.77  3.000
 Y5M  N19  C20  C21  114.37  3.000
 Y5M  H17  C21  H16  107.48  3.000
 Y5M  H17  C21  N10  111.55  3.000
 Y5M  H16  C21  N10  109.95  3.000
 Y5M  H17  C21  C20  108.77  3.000
 Y5M  H16  C21  C20  108.93  3.000
 Y5M  N10  C21  C20  110.09  3.000
 Y5M  C04  N03  C02  115.01  3.000
 Y5M  C21  N10  C11  114.74  3.000
 Y5M  C21  N10  C09  121.40  3.000
 Y5M  C11  N10  C09  123.83  3.000
 Y5M  H18  N19  C20  117.36  3.000
 Y5M  H18  N19  C18  118.48  3.000
 Y5M  C20  N19  C18  123.54  3.000
 Y5M  C09  N23  C02  119.17  3.000
 Y5M  C16  O15  C14  118.49  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
 Y5M  CONST_01  C05  C09  N23  C02     0.00   0.0  0
 Y5M  CONST_02  C05  C04  N03  C02     0.00   0.0  0
 Y5M  CONST_03  N23  C09  C05  C04     0.00   0.0  0
 Y5M  CONST_04  N23  C02  N03  C04     0.00   0.0  0
 Y5M  CONST_08  N03  C04  C05  C09     0.00   0.0  0
 Y5M  CONST_09  N03  C02  N23  C09     0.00   0.0  0
 Y5M  CONST_10  C14  C17  C18  C11     0.00   0.0  0
 Y5M  CONST_11  C14  C13  C12  C11     0.00   0.0  0
 Y5M  CONST_13  C17  C14  C13  C12     0.00   0.0  0
 Y5M  CONST_14  C17  C18  C11  C12     0.00   0.0  0
 Y5M  CONST_15  C18  C17  C14  C13     0.00   0.0  0
 Y5M  CONST_16  C18  C11  C12  C13     0.00   0.0  0
 Y5M  CONST_17  N10  C09  N23  C02   180.00   0.0  0
 Y5M  CONST_18  N10  C09  C05  C04   180.00   0.0  0
 Y5M  CONST_20  N10  C09  C05  C06     0.00   0.0  0
 Y5M  CONST_22  C21  C20  N19  C18     0.00   0.0  0
 Y5M  CONST_23  C09  N23  C02  C01   180.00   0.0  0
 Y5M  CONST_24  C04  N03  C02  C01   180.00   0.0  0
 Y5M  CONST_25  O15  C14  C13  C12   180.00   0.0  0
 Y5M  CONST_26  O15  C14  C17  C18   180.00   0.0  0
 Y5M  CONST_27  O22  C20  N19  C18   180.00   0.0  0
 Y5M  CONST_28  H15  C17  C18  C11   180.00   0.0  0
 Y5M  CONST_29  H11  C13  C12  C11   180.00   0.0  0
 Y5M  CONST_30  H15  C17  C14  C13   180.00   0.0  0
 Y5M  CONST_31  H10  C12  C13  C14   180.00   0.0  0
 Y5M  CONST_32  H11  C13  C14  C17   180.00   0.0  0
 Y5M  CONST_33  H10  C12  C11  C18   180.00   0.0  0
 Y5M  CONST_34  H10  C12  C11  N10     0.00   0.0  0
 Y5M  CONST_35  H15  C17  C18  N19     0.00   0.0  0
 Y5M  CONST_36  H18  N19  C20  C21   180.00   0.0  0
 Y5M  CONST_37  H18  N19  C20  O22     0.00   0.0  0
 Y5M  Var_01    C07  C06  C05  C04   -15.40  30.0  1
 Y5M  Var_02    C06  C07  C08  C04   -27.63  30.0  1
 Y5M  Var_03    C08  C07  C06  C05    26.43  30.0  1
 Y5M  Var_04    C07  C08  C04  C05    18.86  30.0  1
 Y5M  Var_05    C09  C05  C06  C07   160.37  30.0  1
 Y5M  Var_06    N03  C04  C08  C07  -159.62  30.0  1
 Y5M  Var_07    C20  C21  N10  C09   127.66  30.0  1
 Y5M  Var_08    C20  N19  C18  C11   -22.39  30.0  1
 Y5M  Var_09    C20  C21  N10  C11   -54.29  30.0  1
 Y5M  Var_10    C21  N10  C11  C12  -138.42  30.0  1
 Y5M  Var_11    C20  N19  C18  C17   157.82  30.0  1
 Y5M  Var_12    C21  N10  C11  C18    38.03  30.0  1
 Y5M  Var_13    N19  C20  C21  N10    33.01  30.0  1
 Y5M  Var_14    O22  C20  C21  N10  -148.29  30.0  1
 Y5M  Var_15    H4   C06  C05  C04  -137.05  30.0  1
 Y5M  Var_16    H5   C06  C05  C04   103.14  30.0  1
 Y5M  Var_17    H6   C07  C08  C04  -150.47  30.0  1
 Y5M  Var_18    H7   C07  C08  C04    89.95  30.0  1
 Y5M  Var_19    H6   C07  C06  C05   149.63  30.0  1
 Y5M  Var_20    H7   C07  C06  C05   -91.05  30.0  1
 Y5M  Var_21    H8   C08  C04  C05   -99.54  30.0  1
 Y5M  Var_22    H9   C08  C04  C05   141.46  30.0  1
 Y5M  Var_23    H8   C08  C07  C06    89.30  30.0  1
 Y5M  Var_24    H9   C08  C07  C06  -149.48  30.0  1
 Y5M  Var_25    H4   C06  C07  C08   148.49  30.0  1
 Y5M  Var_26    H5   C06  C07  C08   -92.27  30.0  1
 Y5M  Var_27    H16  C21  N10  C09     7.65  30.0  1
 Y5M  Var_28    H17  C21  N10  C09  -111.49  30.0  1
 Y5M  Var_29    H4   C06  C05  C09    38.72  30.0  1
 Y5M  Var_30    H5   C06  C05  C09   -81.09  30.0  1
 Y5M  Var_31    H18  N19  C18  C11   166.90  30.0  1
 Y5M  Var_32    H16  C21  N10  C11  -174.30  30.0  1
 Y5M  Var_33    H17  C21  N10  C11    66.56  30.0  1
 Y5M  Var_34    H18  N19  C18  C17   -12.90  30.0  1
 Y5M  Var_35    H8   C08  C04  N03    81.98  30.0  1
 Y5M  Var_36    H9   C08  C04  N03   -37.02  30.0  1
 Y5M  Var_37    H16  C21  C20  N19   153.64  30.0  1
 Y5M  Var_38    H17  C21  C20  N19   -89.49  30.0  1
 Y5M  Var_39    C16  O15  C14  C13     1.12  30.0  2
 Y5M  Var_40    C17  C14  O15  C16  -178.06  30.0  2
 Y5M  Var_41    H1   C01  C02  N03   178.62  30.0  2
 Y5M  Var_42    H2   C01  C02  N03   -60.66  30.0  2
 Y5M  Var_43    H3   C01  C02  N03    57.55  30.0  2
 Y5M  Var_44    H1   C01  C02  N23    -1.66  30.0  2
 Y5M  Var_45    H2   C01  C02  N23   119.06  30.0  2
 Y5M  Var_46    H3   C01  C02  N23  -122.73  30.0  2
 Y5M  Var_47    H16  C21  C20  O22   -27.66  30.0  1
 Y5M  Var_48    H17  C21  C20  O22    89.21  30.0  1
 Y5M  Var_49    H12  C16  O15  C14  -179.98  30.0  3
 Y5M  Var_50    H13  C16  O15  C14   -61.26  30.0  3
 Y5M  Var_51    H14  C16  O15  C14    61.24  30.0  3

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
 Y5M  plan-1  C01  0.020
 Y5M  plan-1  C02  0.020
 Y5M  plan-1  C04  0.020
 Y5M  plan-1  C05  0.020
 Y5M  plan-1  C06  0.020
 Y5M  plan-1  C08  0.020
 Y5M  plan-1  C09  0.020
 Y5M  plan-1  N03  0.020
 Y5M  plan-1  N10  0.020
 Y5M  plan-1  N23  0.020
 Y5M  plan-2  C11  0.020
 Y5M  plan-2  C12  0.020
 Y5M  plan-2  C13  0.020
 Y5M  plan-2  C14  0.020
 Y5M  plan-2  C17  0.020
 Y5M  plan-2  C18  0.020
 Y5M  plan-2  N10  0.020
 Y5M  plan-2  N19  0.020
 Y5M  plan-2  H10  0.020
 Y5M  plan-2  H11  0.020
 Y5M  plan-2  H15  0.020
 Y5M  plan-2  O15  0.020
 Y5M  plan-3  C18  0.020
 Y5M  plan-3  C20  0.020
 Y5M  plan-3  C21  0.020
 Y5M  plan-3  N19  0.020
 Y5M  plan-3  O22  0.020
 Y5M  plan-3  H18  0.020

