# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:13:05 2021
#   Inital geometry file: a 109 line input string
#   Ligand name: N-[(1S,2S)-2-aminocyclopentyl]-N-[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN(CC(=O)N(CC(O)=O)[C@H]2CCC[C@@H]2N)C(=O)NC1=O
#
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
 XDY  XDY  N-[(1S,2S)-2-aminocyclopentyl]-N-[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]glycine  peptide  43  23  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XDY
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
 XDY  C02   C  C     0   0.548  -38.0728   6.8260  -16.8261
 XDY  C03   C  CH2   0  -0.449  -39.3689   7.6066  -16.8246
 XDY  C05   C  CH1   0  -0.148  -39.4726  10.1001  -16.9966
 XDY  C06   C  CH1   0  -0.067  -40.8732  10.2383  -17.6143
 XDY  C08   C  CH2   0  -0.449  -40.6855  11.4234  -18.5629
 XDY  C09   C  CH2   0  -0.449  -39.2018  11.3924  -18.9974
 XDY  C10   C  CH2   0  -0.434  -38.5399  10.2606  -18.1921
 XDY  C11   C  C     0   0.582  -39.0386   8.8931  -14.8709
 XDY  C12   C  CH2   0  -0.475  -38.9777  10.2328  -14.1430
 XDY  C14   C  CR6   0   0.725  -37.3353   9.8002  -12.4330
 XDY  C16   C  CR6   0   0.560  -38.0612   9.3884  -10.1049
 XDY  C17   C  CR6   0  -0.180  -39.4316   9.5906  -10.5336
 XDY  C18   C  CR16  0   0.061  -39.6477   9.8841  -11.8273
 XDY  C19   C  CH3   0  -0.706  -40.5278   9.4704   -9.5267
 XDY  N04   N  NT    0  -0.465  -39.2877   8.9025  -16.1945
 XDY  N07   N  NH2   0  -0.793  -41.9828  10.4043  -16.7043
 XDY  N13   N  NR6   0  -0.512  -38.6515  10.0279  -12.7539
 XDY  N15   N  NR16  0  -0.732  -37.1190   9.5170  -11.1105
 XDY  O01   O  O     0  -0.448  -38.0377   5.6245  -16.9169
 XDY  O21   O  O     0  -0.478  -36.4384   9.8586  -13.2482
 XDY  O22   O  O     0  -0.481  -38.8807   7.8528  -14.2533
 XDY  H032  H  HCH2  0   0.304  -39.6724   7.7300  -17.8654
 XDY  H031  H  HCH2  0   0.303  -40.1336   6.9845  -16.3584
 XDY  H051  H  HCH1  0   0.276  -39.3312  10.9671  -16.3475
 XDY  H061  H  HCH1  0   0.231  -41.0738   9.3411  -18.2121
 XDY  H081  H  HCH2  0   0.232  -40.9071  12.3501  -18.0266
 XDY  H082  H  HCH2  0   0.243  -41.3734  11.3761  -19.4066
 XDY  H092  H  HCH2  0   0.239  -39.0929  11.2283  -20.0689
 XDY  H091  H  HCH2  0   0.237  -38.7229  12.3463  -18.7754
 XDY  H101  H  HCH2  0   0.231  -38.5141   9.3424  -18.7833
 XDY  H102  H  HCH2  0   0.250  -37.5155  10.4836  -17.8960
 XDY  H121  H  HCH2  0   0.319  -38.2440  10.8986  -14.5948
 XDY  H122  H  HCH2  0   0.307  -39.9408  10.7429  -14.1971
 XDY  H181  H  HCR6  0   0.311  -40.6484  10.0478  -12.2042
 XDY  H191  H  HCH3  0   0.247  -40.5254   8.4890   -9.0509
 XDY  H192  H  HCH3  0   0.247  -40.4215  10.2134   -8.7351
 XDY  H193  H  HCH3  0   0.247  -41.5013   9.6144   -9.9923
 XDY  H071  H  HNH2  0   0.346  -42.0624   9.6064  -16.0855
 XDY  H2    H  HNH2  0   0.340  -41.8426  11.2192  -16.1181
 XDY  H151  H  HNR6  0   0.425  -36.1518   9.3673  -10.8504
 XDY  O1    O  OH1   0  -0.574  -37.0034   7.5989  -16.7775
 XDY  H1    H  HOH1  0   0.485  -36.2006   7.0565  -16.8041
 XDY  O20   O  O     0  -0.455  -37.7189   9.1229   -8.9672

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
 XDY  C09  C08   single  1.546  0.020  1.546
 XDY  C09  C10   single  1.539  0.020  1.539
 XDY  C08  C06   single  1.530  0.020  1.530
 XDY  C10  C05   single  1.525  0.020  1.525
 XDY  O01  C02   double  1.205  0.020  1.205
 XDY  C06  C05   single  1.537  0.020  1.537
 XDY  C06  N07   single  1.445  0.020  1.445
 XDY  C02  C03   single  1.513  0.020  1.513
 XDY  C03  N04   single  1.443  0.020  1.443
 XDY  C05  N04   single  1.453  0.020  1.453
 XDY  N04  C11   single  1.347  0.020  1.347
 XDY  C11  O22   double  1.220  0.020  1.220
 XDY  C11  C12   single  1.526  0.020  1.526
 XDY  C12  N13   single  1.442  0.020  1.442
 XDY  O21  C14   double  1.213  0.020  1.213
 XDY  N13  C14   single  1.374  0.020  1.374
 XDY  N13  C18   single  1.368  0.020  1.368
 XDY  C14  N15   single  1.370  0.020  1.370
 XDY  C18  C17   double  1.344  0.020  1.344
 XDY  N15  C16   single  1.384  0.020  1.384
 XDY  C17  C16   single  1.450  0.020  1.450
 XDY  C17  C19   single  1.493  0.020  1.493
 XDY  C16  O20   double  1.217  0.020  1.217
 XDY  C03  H032  single  0.970  0.020  1.090
 XDY  C03  H031  single  0.970  0.020  1.090
 XDY  C05  H051  single  0.970  0.020  1.090
 XDY  C06  H061  single  0.970  0.020  1.090
 XDY  C08  H081  single  0.970  0.020  1.090
 XDY  C08  H082  single  0.970  0.020  1.090
 XDY  C09  H092  single  0.970  0.020  1.090
 XDY  C09  H091  single  0.970  0.020  1.090
 XDY  C10  H101  single  0.970  0.020  1.090
 XDY  C10  H102  single  0.970  0.020  1.090
 XDY  C12  H121  single  0.970  0.020  1.090
 XDY  C12  H122  single  0.970  0.020  1.090
 XDY  C18  H181  single  0.930  0.020  1.080
 XDY  C19  H191  single  0.970  0.020  1.090
 XDY  C19  H192  single  0.970  0.020  1.090
 XDY  C19  H193  single  0.970  0.020  1.090
 XDY  N07  H071  single  0.890  0.020  1.040
 XDY  N07  H2    single  0.890  0.020  1.040
 XDY  N15  H151  single  0.860  0.020  1.020
 XDY  C02  O1    single  1.320  0.020  1.320
 XDY  O1   H1    single  0.850  0.020  0.980

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
 XDY  O1    C02  O01   124.24  3.000
 XDY  O1    C02  C03   113.06  3.000
 XDY  O01   C02  C03   122.63  3.000
 XDY  H031  C03  H032  106.09  3.000
 XDY  H031  C03  N04   111.41  3.000
 XDY  H032  C03  N04   109.30  3.000
 XDY  H031  C03  C02   107.87  3.000
 XDY  H032  C03  C02   107.20  3.000
 XDY  N04   C03  C02   114.55  3.000
 XDY  H051  C05  N04   108.04  3.000
 XDY  H051  C05  C10   107.65  3.000
 XDY  N04   C05  C10   116.21  3.000
 XDY  H051  C05  C06   106.59  3.000
 XDY  N04   C05  C06   114.32  3.000
 XDY  C10   C05  C06   103.47  3.000
 XDY  H061  C06  N07   107.27  3.000
 XDY  H061  C06  C08   108.56  3.000
 XDY  N07   C06  C08   113.33  3.000
 XDY  H061  C06  C05   108.19  3.000
 XDY  N07   C06  C05   117.20  3.000
 XDY  C08   C06  C05   101.95  3.000
 XDY  H082  C08  H081  106.78  3.000
 XDY  H082  C08  C09   112.79  3.000
 XDY  H081  C08  C09   110.45  3.000
 XDY  H082  C08  C06   111.65  3.000
 XDY  H081  C08  C06   109.12  3.000
 XDY  C09   C08  C06   106.05  3.000
 XDY  H091  C09  H092  106.75  3.000
 XDY  H091  C09  C10   110.37  3.000
 XDY  H092  C09  C10   111.16  3.000
 XDY  H091  C09  C08   110.29  3.000
 XDY  H092  C09  C08   112.04  3.000
 XDY  C10   C09  C08   106.29  3.000
 XDY  H102  C10  H101  107.28  3.000
 XDY  H102  C10  C09   113.34  3.000
 XDY  H101  C10  C09   110.19  3.000
 XDY  H102  C10  C05   112.56  3.000
 XDY  H101  C10  C05   110.50  3.000
 XDY  C09   C10  C05   102.98  3.000
 XDY  O22   C11  N04   121.83  3.000
 XDY  O22   C11  C12   120.13  3.000
 XDY  N04   C11  C12   118.03  3.000
 XDY  H122  C12  H121  106.76  3.000
 XDY  H122  C12  N13   108.30  3.000
 XDY  H121  C12  N13   109.52  3.000
 XDY  H122  C12  C11   110.59  3.000
 XDY  H121  C12  C11   111.46  3.000
 XDY  N13   C12  C11   110.11  3.000
 XDY  O21   C14  N15   122.81  3.000
 XDY  N15   C14  N13   114.27  3.000
 XDY  O21   C14  N13   122.91  3.000
 XDY  O20   C16  N15   120.52  3.000
 XDY  O20   C16  C17   124.92  3.000
 XDY  N15   C16  C17   114.56  3.000
 XDY  C19   C17  C18   123.27  3.000
 XDY  C19   C17  C16   118.89  3.000
 XDY  C18   C17  C16   117.83  3.000
 XDY  H181  C18  N13   114.95  3.000
 XDY  H181  C18  C17   121.13  3.000
 XDY  N13   C18  C17   123.90  3.000
 XDY  H193  C19  H192  107.91  3.000
 XDY  H193  C19  H191  107.91  3.000
 XDY  H192  C19  H191  107.23  3.000
 XDY  H193  C19  C17   110.94  3.000
 XDY  H192  C19  C17   111.28  3.000
 XDY  H191  C19  C17   111.41  3.000
 XDY  C11   N04  C05   124.87  3.000
 XDY  C11   N04  C03   115.67  3.000
 XDY  C05   N04  C03   119.46  3.000
 XDY  H2    N07  H071  106.91  3.000
 XDY  H2    N07  C06   110.51  3.000
 XDY  H071  N07  C06   110.78  3.000
 XDY  C18   N13  C14   121.47  3.000
 XDY  C18   N13  C12   120.18  3.000
 XDY  C14   N13  C12   117.74  3.000
 XDY  H151  N15  C16   116.73  3.000
 XDY  H151  N15  C14   115.43  3.000
 XDY  C16   N15  C14   127.82  3.000
 XDY  H1    O1   C02   110.01  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
 XDY  CONST_01  C17   C16  N15  C14     0.00   0.0  0
 XDY  CONST_02  N13   C14  N15  C16     0.00   0.0  0
 XDY  CONST_03  N15   C14  N13  C18     0.00   0.0  0
 XDY  CONST_04  N15   C14  N13  C12   180.00   0.0  0
 XDY  CONST_05  O20   C16  N15  C14   180.00   0.0  0
 XDY  CONST_06  O21   C14  N15  C16   180.00   0.0  0
 XDY  CONST_07  O21   C14  N13  C18   180.00   0.0  0
 XDY  CONST_08  H151  N15  C16  C17   180.00   0.0  0
 XDY  CONST_09  O21   C14  N13  C12     0.00   0.0  0
 XDY  CONST_10  O22   C11  N04  C05   180.00   0.0  0
 XDY  CONST_11  C12   C11  N04  C05     0.00   0.0  0
 XDY  CONST_12  O22   C11  N04  C03     0.00   0.0  0
 XDY  CONST_13  C12   C11  N04  C03   180.00   0.0  0
 XDY  CONST_14  H1    O1   C02  C03   180.00   0.0  0
 XDY  Var_01    C08   C09  C10  C05   -21.85  30.0  1
 XDY  Var_02    C10   C09  C08  C06    -4.79  30.0  1
 XDY  Var_03    C14   N13  C12  C11    79.18  30.0  3
 XDY  Var_04    H191  C19  C17  C16   -57.93  30.0  3
 XDY  Var_05    C05   N04  C03  C02   114.57  30.0  3
 XDY  Var_06    N13   C12  C11  N04  -177.77  30.0  3
 XDY  Var_07    O01   C02  C03  N04   156.44  30.0  1

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
 XDY  chir_01  C05  C10  C06  N04  negativ
 XDY  chir_02  C06  N07  C08  C05  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
 XDY  plan-1  C12   0.020
 XDY  plan-1  C14   0.020
 XDY  plan-1  C16   0.020
 XDY  plan-1  C17   0.020
 XDY  plan-1  C18   0.020
 XDY  plan-1  C19   0.020
 XDY  plan-1  N13   0.020
 XDY  plan-1  N15   0.020
 XDY  plan-1  O21   0.020
 XDY  plan-1  H181  0.020
 XDY  plan-1  H151  0.020
 XDY  plan-1  O20   0.020
 XDY  plan-2  C03   0.020
 XDY  plan-2  C05   0.020
 XDY  plan-2  C11   0.020
 XDY  plan-2  C12   0.020
 XDY  plan-2  N04   0.020
 XDY  plan-2  O22   0.020
 XDY  plan-3  C02   0.020
 XDY  plan-3  C03   0.020
 XDY  plan-3  O01   0.020
 XDY  plan-3  O1    0.020
 XDY  plan-3  H1    0.020

