# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 10:12:56 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: 4-(2-chloro-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl)-7-methoxy-3,4-dihydroquinoxalin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2N(CC(=O)Nc2c1)c3nc(Cl)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
 Y5L  Y5L  "4-(2-chloro-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl)-7-methoxy-3,4-dihydroquinoxalin-2(1H)-one"
  ligand  38  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_Y5L
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
 Y5L  C02   C   CR6   0   0.273  16.2243  -67.2738  -39.0834
 Y5L  C04   C   CR56  0   0.243  14.4733  -66.8906  -40.3734
 Y5L  C05   C   CR56  0  -0.033  15.2838  -66.6149  -41.4600
 Y5L  C06   C   CH2   0  -0.491  14.4514  -66.4393  -42.6994
 Y5L  C07   C   CH2   0  -0.460  13.0324  -66.2258  -42.1380
 Y5L  C08   C   CH2   0  -0.505  13.0259  -66.8780  -40.7504
 Y5L  C09   C   CR6   0   0.491  16.6659  -66.7057  -41.2316
 Y5L  C11   C   CR6   0   0.283  17.4691  -65.6706  -43.2970
 Y5L  C12   C   CR16  0  -0.291  16.8731  -64.4227  -43.2562
 Y5L  C13   C   CR16  0  -0.389  16.7491  -63.6509  -44.4040
 Y5L  C14   C   CR6   0   0.392  17.2677  -64.1225  -45.6087
 Y5L  C16   C   CH3   0  -0.437  16.5847  -62.1879  -46.7976
 Y5L  C17   C   CR16  0  -0.427  17.9264  -65.3521  -45.6452
 Y5L  C18   C   CR6   0   0.363  18.0285  -66.1167  -44.4970
 Y5L  C20   C   C     0   0.511  19.2024  -67.9147  -43.3772
 Y5L  C21   C   CH2   0  -0.451  18.9197  -67.1503  -42.0961
 Y5L  N03   N   N     0  -0.415  14.9172  -67.2148  -39.1585
 Y5L  N10   N   NT    0  -0.601  17.6247  -66.5056  -42.1820
 Y5L  N19   N   NH1   0  -0.726  18.6846  -67.3440  -44.4964
 Y5L  N23   N   N     0  -0.435  17.1119  -67.0449  -40.0148
 Y5L  O22   O   O     0  -0.442  19.8564  -68.9361  -43.4001
 Y5L  CL01  CL  CL    0  -0.110  16.8699  -67.7130  -37.5327
 Y5L  H1    H   HCH2  0   0.259  14.5145  -67.3428  -43.3136
 Y5L  H2    H   HCH2  0   0.268  14.7571  -65.6109  -43.3343
 Y5L  H3    H   HCH2  0   0.246  12.8474  -65.1554  -42.0368
 Y5L  H4    H   HCH2  0   0.247  12.2636  -66.6285  -42.7950
 Y5L  H5    H   HCH2  0   0.266  12.4123  -66.3483  -40.0208
 Y5L  H6    H   HCH2  0   0.266  12.6606  -67.9089  -40.7846
 Y5L  H7    H   HCR6  0   0.285  16.4728  -64.0492  -42.3219
 Y5L  H8    H   HCR6  0   0.283  16.2562  -62.6916  -44.3340
 Y5L  H9    H   HCH3  0   0.260  16.6403  -61.8352  -47.8244
 Y5L  H10   H   HCH3  0   0.229  15.5343  -62.2349  -46.4987
 Y5L  H11   H   HCH3  0   0.229  17.1037  -61.4747  -46.1520
 Y5L  H12   H   HCR6  0   0.280  18.3592  -65.7044  -46.5740
 Y5L  H13   H   HCH2  0   0.304  18.9390  -67.8435  -41.2606
 Y5L  H14   H   HCH2  0   0.290  19.7185  -66.4162  -41.9376
 Y5L  H15   H   HNH1  0   0.414  18.9162  -67.7687  -45.3848
 Y5L  O15   O   O2    0  -0.468  17.1972  -63.4621  -46.7773

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
 Y5L  O15  C16   single    1.414  0.020  1.414
 Y5L  O15  C14   single    1.344  0.020  1.344
 Y5L  C17  C14   aromatic  1.395  0.020  1.395
 Y5L  C17  C18   aromatic  1.383  0.020  1.383
 Y5L  C14  C13   aromatic  1.394  0.020  1.394
 Y5L  N19  C18   single    1.392  0.020  1.392
 Y5L  N19  C20   single    1.359  0.020  1.359
 Y5L  C18  C11   aromatic  1.397  0.020  1.397
 Y5L  C13  C12   aromatic  1.389  0.020  1.389
 Y5L  C20  O22   double    1.213  0.020  1.213
 Y5L  C20  C21   single    1.518  0.020  1.518
 Y5L  C11  C12   aromatic  1.383  0.020  1.383
 Y5L  C11  N10   single    1.402  0.020  1.402
 Y5L  C06  C07   single    1.541  0.020  1.541
 Y5L  C06  C05   single    1.503  0.020  1.503
 Y5L  C07  C08   single    1.533  0.020  1.533
 Y5L  N10  C21   single    1.449  0.020  1.449
 Y5L  N10  C09   single    1.365  0.020  1.365
 Y5L  C05  C09   aromatic  1.404  0.020  1.404
 Y5L  C05  C04   aromatic  1.383  0.020  1.383
 Y5L  C09  N23   aromatic  1.340  0.020  1.340
 Y5L  C08  C04   single    1.496  0.020  1.496
 Y5L  C04  N03   aromatic  1.333  0.020  1.333
 Y5L  N23  C02   aromatic  1.307  0.020  1.307
 Y5L  N03  C02   aromatic  1.311  0.020  1.311
 Y5L  C02  CL01  single    1.736  0.020  1.736
 Y5L  C06  H1    single    0.970  0.020  1.090
 Y5L  C06  H2    single    0.970  0.020  1.090
 Y5L  C07  H3    single    0.970  0.020  1.090
 Y5L  C07  H4    single    0.970  0.020  1.090
 Y5L  C08  H5    single    0.970  0.020  1.090
 Y5L  C08  H6    single    0.970  0.020  1.090
 Y5L  C12  H7    single    0.930  0.020  1.080
 Y5L  C13  H8    single    0.930  0.020  1.080
 Y5L  C16  H9    single    0.970  0.020  1.090
 Y5L  C16  H10   single    0.970  0.020  1.090
 Y5L  C16  H11   single    0.970  0.020  1.090
 Y5L  C17  H12   single    0.930  0.020  1.080
 Y5L  C21  H13   single    0.970  0.020  1.090
 Y5L  C21  H14   single    0.970  0.020  1.090
 Y5L  N19  H15   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
 Y5L  CL01  C02  N23  115.36  3.000
 Y5L  CL01  C02  N03  115.69  3.000
 Y5L  N23   C02  N03  128.95  3.000
 Y5L  N03   C04  C08  123.62  3.000
 Y5L  N03   C04  C05  124.69  3.000
 Y5L  C08   C04  C05  111.55  3.000
 Y5L  C09   C05  C06  133.38  3.000
 Y5L  C09   C05  C04  115.86  3.000
 Y5L  C06   C05  C04  110.28  3.000
 Y5L  H2    C06  H1   106.56  3.000
 Y5L  H2    C06  C07  111.47  3.000
 Y5L  H1    C06  C07  111.84  3.000
 Y5L  H2    C06  C05  114.50  3.000
 Y5L  H1    C06  C05  109.53  3.000
 Y5L  C07   C06  C05  103.04  3.000
 Y5L  H4    C07  H3   107.41  3.000
 Y5L  H4    C07  C08  112.70  3.000
 Y5L  H3    C07  C08  109.43  3.000
 Y5L  H4    C07  C06  112.29  3.000
 Y5L  H3    C07  C06  109.02  3.000
 Y5L  C08   C07  C06  105.94  3.000
 Y5L  H6    C08  H5   106.90  3.000
 Y5L  H6    C08  C07  111.95  3.000
 Y5L  H5    C08  C07  113.65  3.000
 Y5L  H6    C08  C04  108.85  3.000
 Y5L  H5    C08  C04  112.33  3.000
 Y5L  C07   C08  C04  103.16  3.000
 Y5L  N23   C09  N10  115.83  3.000
 Y5L  N23   C09  C05  119.47  3.000
 Y5L  N10   C09  C05  124.68  3.000
 Y5L  N10   C11  C18  116.65  3.000
 Y5L  N10   C11  C12  124.17  3.000
 Y5L  C18   C11  C12  119.06  3.000
 Y5L  H7    C12  C13  119.23  3.000
 Y5L  H7    C12  C11  119.72  3.000
 Y5L  C13   C12  C11  121.02  3.000
 Y5L  H8    C13  C14  121.74  3.000
 Y5L  H8    C13  C12  118.71  3.000
 Y5L  C14   C13  C12  119.55  3.000
 Y5L  O15   C14  C17  115.78  3.000
 Y5L  C17   C14  C13  119.76  3.000
 Y5L  O15   C14  C13  124.45  3.000
 Y5L  H11   C16  H10  108.83  3.000
 Y5L  H11   C16  H9   108.77  3.000
 Y5L  H10   C16  H9   108.75  3.000
 Y5L  H11   C16  O15  111.96  3.000
 Y5L  H10   C16  O15  111.94  3.000
 Y5L  H9    C16  O15  106.48  3.000
 Y5L  H12   C17  C18  120.15  3.000
 Y5L  H12   C17  C14  119.83  3.000
 Y5L  C18   C17  C14  120.02  3.000
 Y5L  N19   C18  C17  121.51  3.000
 Y5L  N19   C18  C11  118.03  3.000
 Y5L  C17   C18  C11  120.46  3.000
 Y5L  O22   C20  N19  122.92  3.000
 Y5L  O22   C20  C21  122.70  3.000
 Y5L  N19   C20  C21  114.37  3.000
 Y5L  H14   C21  H13  107.65  3.000
 Y5L  H14   C21  N10  111.21  3.000
 Y5L  H13   C21  N10  110.21  3.000
 Y5L  H14   C21  C20  108.87  3.000
 Y5L  H13   C21  C20  108.94  3.000
 Y5L  N10   C21  C20  109.90  3.000
 Y5L  C04   N03  C02  113.27  3.000
 Y5L  C21   N10  C11  114.29  3.000
 Y5L  C21   N10  C09  121.42  3.000
 Y5L  C11   N10  C09  124.28  3.000
 Y5L  H15   N19  C20  117.38  3.000
 Y5L  H15   N19  C18  118.54  3.000
 Y5L  C20   N19  C18  123.40  3.000
 Y5L  C09   N23  C02  117.75  3.000
 Y5L  C16   O15  C14  118.55  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
 Y5L  CONST_01  C05   C09  N23  C02     0.00   0.0  0
 Y5L  CONST_02  C05   C04  N03  C02     0.00   0.0  0
 Y5L  CONST_03  N23   C09  C05  C04     0.00   0.0  0
 Y5L  CONST_04  N23   C02  N03  C04     0.00   0.0  0
 Y5L  CONST_08  N03   C04  C05  C09     0.00   0.0  0
 Y5L  CONST_09  N03   C02  N23  C09     0.00   0.0  0
 Y5L  CONST_10  C14   C17  C18  C11     0.00   0.0  0
 Y5L  CONST_11  C14   C13  C12  C11     0.00   0.0  0
 Y5L  CONST_13  C17   C14  C13  C12     0.00   0.0  0
 Y5L  CONST_14  C17   C18  C11  C12     0.00   0.0  0
 Y5L  CONST_15  C18   C17  C14  C13     0.00   0.0  0
 Y5L  CONST_16  C18   C11  C12  C13     0.00   0.0  0
 Y5L  CONST_17  N10   C09  N23  C02   180.00   0.0  0
 Y5L  CONST_18  N10   C09  C05  C04   180.00   0.0  0
 Y5L  CONST_20  N10   C09  C05  C06     0.00   0.0  0
 Y5L  CONST_22  C21   C20  N19  C18     0.00   0.0  0
 Y5L  CONST_23  CL01  C02  N03  C04   180.00   0.0  0
 Y5L  CONST_24  CL01  C02  N23  C09   180.00   0.0  0
 Y5L  CONST_25  O15   C14  C13  C12   180.00   0.0  0
 Y5L  CONST_26  O15   C14  C17  C18   180.00   0.0  0
 Y5L  CONST_27  O22   C20  N19  C18   180.00   0.0  0
 Y5L  CONST_28  H12   C17  C18  C11   180.00   0.0  0
 Y5L  CONST_29  H8    C13  C12  C11   180.00   0.0  0
 Y5L  CONST_30  H12   C17  C14  C13   180.00   0.0  0
 Y5L  CONST_31  H7    C12  C13  C14   180.00   0.0  0
 Y5L  CONST_32  H8    C13  C14  C17   180.00   0.0  0
 Y5L  CONST_33  H7    C12  C11  C18   180.00   0.0  0
 Y5L  CONST_34  H7    C12  C11  N10     0.00   0.0  0
 Y5L  CONST_35  H12   C17  C18  N19     0.00   0.0  0
 Y5L  CONST_36  H15   N19  C20  C21   180.00   0.0  0
 Y5L  CONST_37  H15   N19  C20  O22     0.00   0.0  0
 Y5L  Var_01    C07   C06  C05  C04    16.47  30.0  1
 Y5L  Var_02    C06   C07  C08  C04    22.82  30.0  1
 Y5L  Var_03    C08   C07  C06  C05   -24.03  30.0  1
 Y5L  Var_04    C07   C08  C04  C05   -13.21  30.0  1
 Y5L  Var_05    C09   C05  C06  C07  -172.10  30.0  1
 Y5L  Var_06    N03   C04  C08  C07   170.87  30.0  1
 Y5L  Var_07    C20   C21  N10  C09   125.60  30.0  1
 Y5L  Var_08    C20   N19  C18  C11   -22.79  30.0  1
 Y5L  Var_09    C20   C21  N10  C11   -55.08  30.0  1
 Y5L  Var_10    C21   N10  C11  C12  -137.21  30.0  1
 Y5L  Var_11    C20   N19  C18  C17   157.23  30.0  1
 Y5L  Var_12    C21   N10  C11  C18    38.95  30.0  1
 Y5L  Var_13    N19   C20  C21  N10    33.22  30.0  1
 Y5L  Var_14    O22   C20  C21  N10  -148.05  30.0  1
 Y5L  Var_15    H1    C06  C05  C04  -102.70  30.0  1
 Y5L  Var_16    H2    C06  C05  C04   137.70  30.0  1
 Y5L  Var_17    H3    C07  C08  C04   -94.58  30.0  1
 Y5L  Var_18    H4    C07  C08  C04   145.98  30.0  1
 Y5L  Var_19    H3    C07  C06  C05    93.65  30.0  1
 Y5L  Var_20    H4    C07  C06  C05  -147.46  30.0  1
 Y5L  Var_21    H5    C08  C04  C05  -135.99  30.0  1
 Y5L  Var_22    H6    C08  C04  C05   105.83  30.0  1
 Y5L  Var_23    H5    C08  C07  C06   144.72  30.0  1
 Y5L  Var_24    H6    C08  C07  C06   -94.04  30.0  1
 Y5L  Var_25    H1    C06  C07  C08    93.52  30.0  1
 Y5L  Var_26    H2    C06  C07  C08  -147.30  30.0  1
 Y5L  Var_27    H13   C21  N10  C09     5.53  30.0  1
 Y5L  Var_28    H14   C21  N10  C09  -113.77  30.0  1
 Y5L  Var_29    H1    C06  C05  C09    68.73  30.0  1
 Y5L  Var_30    H2    C06  C05  C09   -50.87  30.0  1
 Y5L  Var_31    H15   N19  C18  C11   166.99  30.0  1
 Y5L  Var_32    H13   C21  N10  C11  -175.15  30.0  1
 Y5L  Var_33    H14   C21  N10  C11    65.54  30.0  1
 Y5L  Var_34    H15   N19  C18  C17   -12.99  30.0  1
 Y5L  Var_35    H5    C08  C04  N03    48.09  30.0  1
 Y5L  Var_36    H6    C08  C04  N03   -70.09  30.0  1
 Y5L  Var_37    H13   C21  C20  N19   154.06  30.0  1
 Y5L  Var_38    H14   C21  C20  N19   -88.81  30.0  1
 Y5L  Var_39    C16   O15  C14  C13     1.48  30.0  2
 Y5L  Var_40    C17   C14  O15  C16  -177.75  30.0  2
 Y5L  Var_41    H13   C21  C20  O22   -27.20  30.0  1
 Y5L  Var_42    H14   C21  C20  O22    89.93  30.0  1
 Y5L  Var_43    H9    C16  O15  C14   179.63  30.0  3
 Y5L  Var_44    H10   C16  O15  C14   -61.64  30.0  3
 Y5L  Var_45    H11   C16  O15  C14    60.87  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
 Y5L  plan-1  C02   0.020
 Y5L  plan-1  C04   0.020
 Y5L  plan-1  C05   0.020
 Y5L  plan-1  C06   0.020
 Y5L  plan-1  C08   0.020
 Y5L  plan-1  C09   0.020
 Y5L  plan-1  N03   0.020
 Y5L  plan-1  N10   0.020
 Y5L  plan-1  N23   0.020
 Y5L  plan-1  CL01  0.020
 Y5L  plan-2  C11   0.020
 Y5L  plan-2  C12   0.020
 Y5L  plan-2  C13   0.020
 Y5L  plan-2  C14   0.020
 Y5L  plan-2  C17   0.020
 Y5L  plan-2  C18   0.020
 Y5L  plan-2  N10   0.020
 Y5L  plan-2  N19   0.020
 Y5L  plan-2  H7    0.020
 Y5L  plan-2  H8    0.020
 Y5L  plan-2  H12   0.020
 Y5L  plan-2  O15   0.020
 Y5L  plan-3  C18   0.020
 Y5L  plan-3  C20   0.020
 Y5L  plan-3  C21   0.020
 Y5L  plan-3  N19   0.020
 Y5L  plan-3  O22   0.020
 Y5L  plan-3  H15   0.020

