# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 14:03:38 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: N-(4-carbamimidoylbenzyl)-1-[(cyclopentyloxy)acetyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(CNC(=O)[C@@H]2CCCN2C(=O)COC3CCCC3)cc1
#
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
 45U  45U  N-(4-carbamimidoylbenzyl)-1-[(cyclopentyloxy)acetyl]-L-prolinamide  peptide  55  27  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_45U
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
 45U  O32   O  O     0  -0.491   1.9336  -0.6842   0.5544
 45U  C14   C  C     0   0.513   2.5237   0.3623   0.3360
 45U  C5    C  CH2   0  -0.267   4.0226   0.4186   0.1100
 45U  O21   O  O2    0  -0.487   4.5541  -0.8555   0.2915
 45U  C44   C  CR15  0   0.069   5.8997  -0.9627  -0.1126
 45U  C49   C  CH2   0  -0.474   6.3563  -2.4225  -0.0357
 45U  C48   C  CH2   0  -0.447   7.8749  -2.3671   0.2326
 45U  C47   C  CH2   0  -0.456   8.2266  -0.8718   0.3288
 45U  C45   C  CH2   0  -0.481   6.9174  -0.2069   0.7412
 45U  N1    N  NT    0  -0.462   1.8901   1.5452   0.2812
 45U  C1    C  CH1   0  -0.217   0.4527   1.6107   0.4175
 45U  C7    C  C     0   0.578  -0.2311   0.9545  -0.7796
 45U  O22   O  O     0  -0.492   0.3064   0.8641  -1.8721
 45U  C2    C  CH2   0  -0.469   0.1748   3.1204   0.4563
 45U  C3    C  CH2   0  -0.475   1.2991   3.7119  -0.3865
 45U  C4    C  CH2   0  -0.275   2.4960   2.8334  -0.0418
 45U  N23   N  NH1   0  -0.637  -1.4828   0.5395  -0.5446
 45U  C24   C  CH2   0  -0.314  -2.3217  -0.0212  -1.5891
 45U  C25   C  CR6   0   0.043  -3.6862  -0.3269  -1.0404
 45U  C30   C  CR16  0  -0.275  -4.7270   0.5837  -1.1764
 45U  C29   C  CR16  0  -0.280  -5.9797   0.3157  -0.6428
 45U  C28   C  CR6   0   0.039  -6.2175  -0.8733   0.0426
 45U  C21   C  C     0   0.335  -7.5520  -1.1990   0.6191
 45U  N47   N  N     0  -0.650  -7.8526  -2.4270   0.8040
 45U  N46   N  NH2   0  -0.823  -8.3659  -0.1280   0.8554
 45U  C27   C  CR16  0  -0.260  -5.1750  -1.7892   0.1736
 45U  C26   C  CR16  0  -0.269  -3.9260  -1.5170  -0.3571
 45U  H5    H  HCH2  0   0.236   4.2106   0.7924  -0.9089
 45U  H5A   H  HCH2  0   0.240   4.4683   1.1572   0.7918
 45U  H44   H  HCR5  0   0.202   5.9964  -0.6056  -1.1505
 45U  H49   H  HCH2  0   0.232   5.8357  -2.9157   0.7883
 45U  H49A  H  HCH2  0   0.239   6.1079  -2.9706  -0.9451
 45U  H48   H  HCH2  0   0.230   8.1103  -2.8688   1.1722
 45U  H48A  H  HCH2  0   0.232   8.4523  -2.8694  -0.5435
 45U  H47   H  HCH2  0   0.236   9.0441  -0.6733   1.0222
 45U  H47A  H  HCH2  0   0.225   8.5363  -0.4915  -0.6481
 45U  H45   H  HCH2  0   0.239   6.9143   0.8721   0.5759
 45U  H45A  H  HCH2  0   0.224   6.7127  -0.3862   1.8022
 45U  H1    H  HCH1  0   0.288   0.1230   1.1263   1.3402
 45U  H2    H  HCH2  0   0.264  -0.8206   3.3716   0.0915
 45U  H2A   H  HCH2  0   0.260   0.2464   3.4683   1.4881
 45U  H3    H  HCH2  0   0.247   1.0665   3.6327  -1.4488
 45U  H3A   H  HCH2  0   0.259   1.4870   4.7608  -0.1629
 45U  H4    H  HCH2  0   0.247   3.0416   3.2296   0.8193
 45U  H4A   H  HCH2  0   0.257   3.1958   2.7521  -0.8742
 45U  HN23  H  HNH1  0   0.406  -1.8692   0.6358   0.3809
 45U  H24   H  HCH2  0   0.256  -2.4007   0.6846  -2.4188
 45U  H24A  H  HCH2  0   0.257  -1.8615  -0.9304  -1.9836
 45U  H30   H  HCR6  0   0.258  -4.5657   1.5102  -1.7140
 45U  H29   H  HCR6  0   0.260  -6.7725   1.0372  -0.7926
 45U  HN47  H  H     0   0.324  -8.7715  -2.5202   1.2284
 45U  HN46  H  HNH2  0   0.395  -7.9405   0.7610   1.0613
 45U  HN4A  H  HNH2  0   0.392  -9.2084  -0.2994   1.3813
 45U  H27   H  HCR6  0   0.257  -5.3497  -2.7186   0.6985
 45U  H26   H  HCR6  0   0.259  -3.1280  -2.2406  -0.2408

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
 45U  C2   C3    single    1.525  0.020  1.525
 45U  C2   C1    single    1.536  0.020  1.536
 45U  C24  N23   single    1.452  0.020  1.452
 45U  C24  C25   single    1.502  0.020  1.502
 45U  C3   C4    single    1.524  0.020  1.524
 45U  N23  C7    single    1.339  0.020  1.339
 45U  C26  C25   aromatic  1.393  0.020  1.393
 45U  C26  C27   aromatic  1.384  0.020  1.384
 45U  C7   C1    single    1.527  0.020  1.527
 45U  C7   O22   double    1.221  0.020  1.221
 45U  C25  C30   aromatic  1.390  0.020  1.390
 45U  C1   N1    single    1.445  0.020  1.445
 45U  C4   N1    single    1.460  0.020  1.460
 45U  C27  C28   aromatic  1.394  0.020  1.394
 45U  N1   C14   single    1.343  0.020  1.343
 45U  C30  C29   aromatic  1.388  0.020  1.388
 45U  C28  C29   aromatic  1.393  0.020  1.393
 45U  C28  C21   single    1.490  0.020  1.490
 45U  C14  O32   double    1.221  0.020  1.221
 45U  C14  C5    single    1.517  0.020  1.517
 45U  N46  C21   single    1.366  0.020  1.366
 45U  C21  N47   double    1.278  0.020  1.278
 45U  C5   O21   single    1.392  0.020  1.392
 45U  O21  C44   single    1.409  0.020  1.409
 45U  C45  C44   single    1.528  0.020  1.528
 45U  C45  C47   single    1.525  0.020  1.525
 45U  C44  C49   single    1.531  0.020  1.531
 45U  C49  C48   single    1.543  0.020  1.543
 45U  C47  C48   single    1.539  0.020  1.539
 45U  C5   H5    single    0.970  0.020  1.090
 45U  C5   H5A   single    0.970  0.020  1.090
 45U  C44  H44   single    0.970  0.020  1.090
 45U  C49  H49   single    0.970  0.020  1.090
 45U  C49  H49A  single    0.970  0.020  1.090
 45U  C48  H48   single    0.970  0.020  1.090
 45U  C48  H48A  single    0.970  0.020  1.090
 45U  C47  H47   single    0.970  0.020  1.090
 45U  C47  H47A  single    0.970  0.020  1.090
 45U  C45  H45   single    0.970  0.020  1.090
 45U  C45  H45A  single    0.970  0.020  1.090
 45U  C1   H1    single    0.970  0.020  1.090
 45U  C2   H2    single    0.970  0.020  1.090
 45U  C2   H2A   single    0.970  0.020  1.090
 45U  C3   H3    single    0.970  0.020  1.090
 45U  C3   H3A   single    0.970  0.020  1.090
 45U  C4   H4    single    0.970  0.020  1.090
 45U  C4   H4A   single    0.970  0.020  1.090
 45U  N23  HN23  single    0.860  0.020  1.020
 45U  C24  H24   single    0.970  0.020  1.090
 45U  C24  H24A  single    0.970  0.020  1.090
 45U  C26  H26   single    0.930  0.020  1.080
 45U  C27  H27   single    0.930  0.020  1.080
 45U  N46  HN46  single    0.890  0.020  1.040
 45U  N46  HN4A  single    0.890  0.020  1.040
 45U  N47  HN47  single    0.890  0.020  1.040
 45U  C29  H29   single    0.930  0.020  1.080
 45U  C30  H30   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
 45U  N1    C14  C5    115.30  3.000
 45U  C5    C14  O32   122.41  3.000
 45U  N1    C14  O32   122.29  3.000
 45U  H5A   C5   H5    106.05  3.000
 45U  H5A   C5   O21   112.27  3.000
 45U  H5    C5   O21   111.46  3.000
 45U  H5A   C5   C14   109.46  3.000
 45U  H5    C5   C14   108.61  3.000
 45U  O21   C5   C14   108.89  3.000
 45U  C44   O21  C5    113.37  3.000
 45U  H44   C44  C45   107.91  3.000
 45U  H44   C44  C49   109.27  3.000
 45U  C45   C44  C49   104.17  3.000
 45U  H44   C44  O21   109.23  3.000
 45U  C49   C44  O21   110.05  3.000
 45U  C45   C44  O21   115.98  3.000
 45U  H49A  C49  H49   107.07  3.000
 45U  H49A  C49  C48   112.78  3.000
 45U  H49   C49  C48   110.73  3.000
 45U  H49A  C49  C44   111.67  3.000
 45U  H49   C49  C44   109.04  3.000
 45U  C48   C49  C44   105.54  3.000
 45U  H48A  C48  H48   106.69  3.000
 45U  H48A  C48  C47   111.79  3.000
 45U  H48   C48  C47   110.10  3.000
 45U  H48A  C48  C49   112.39  3.000
 45U  H48   C48  C49   110.22  3.000
 45U  C47   C48  C49   105.70  3.000
 45U  H47A  C47  H47   107.01  3.000
 45U  H47A  C47  C45   109.46  3.000
 45U  H47   C47  C45   113.10  3.000
 45U  H47A  C47  C48   110.29  3.000
 45U  H47   C47  C48   112.83  3.000
 45U  C45   C47  C48   104.14  3.000
 45U  H45A  C45  H45   107.93  3.000
 45U  H45A  C45  C47   110.55  3.000
 45U  H45   C45  C47   113.10  3.000
 45U  H45A  C45  C44   109.62  3.000
 45U  H45   C45  C44   113.72  3.000
 45U  C47   C45  C44   101.83  3.000
 45U  C4    N1   C1    113.18  3.000
 45U  C4    N1   C14   126.20  3.000
 45U  C1    N1   C14   120.35  3.000
 45U  H1    C1   C2    111.09  3.000
 45U  H1    C1   C7    109.65  3.000
 45U  C2    C1   C7    111.18  3.000
 45U  H1    C1   N1    111.07  3.000
 45U  C7    C1   N1    110.61  3.000
 45U  C2    C1   N1    103.12  3.000
 45U  N23   C7   O22   123.05  3.000
 45U  O22   C7   C1    122.43  3.000
 45U  N23   C7   C1    114.46  3.000
 45U  H2A   C2   H2    107.64  3.000
 45U  H2A   C2   C3    110.53  3.000
 45U  H2    C2   C3    113.53  3.000
 45U  H2A   C2   C1    108.99  3.000
 45U  H2    C2   C1    112.55  3.000
 45U  C3    C2   C1    103.54  3.000
 45U  H3A   C3   H3    107.87  3.000
 45U  H3A   C3   C4    111.92  3.000
 45U  H3    C3   C4    110.25  3.000
 45U  H3A   C3   C2    112.80  3.000
 45U  H3    C3   C2    110.67  3.000
 45U  C4    C3   C2    103.33  3.000
 45U  H4A   C4   H4    107.93  3.000
 45U  H4A   C4   C3    111.98  3.000
 45U  H4    C4   C3    111.16  3.000
 45U  H4A   C4   N1    111.68  3.000
 45U  H4    C4   N1    110.64  3.000
 45U  C3    C4   N1    103.46  3.000
 45U  HN23  N23  C24   118.43  3.000
 45U  HN23  N23  C7    119.33  3.000
 45U  C24   N23  C7    122.22  3.000
 45U  H24A  C24  H24   107.09  3.000
 45U  H24A  C24  C25   110.19  3.000
 45U  H24   C24  C25   110.08  3.000
 45U  H24A  C24  N23   109.73  3.000
 45U  H24   C24  N23   109.80  3.000
 45U  C25   C24  N23   109.91  3.000
 45U  C26   C25  C30   118.61  3.000
 45U  C30   C25  C24   120.75  3.000
 45U  C26   C25  C24   120.62  3.000
 45U  H30   C30  C29   119.37  3.000
 45U  H30   C30  C25   119.83  3.000
 45U  C29   C30  C25   120.80  3.000
 45U  H29   C29  C28   120.81  3.000
 45U  H29   C29  C30   118.64  3.000
 45U  C28   C29  C30   120.54  3.000
 45U  C27   C28  C21   119.34  3.000
 45U  C21   C28  C29   122.00  3.000
 45U  C27   C28  C29   118.65  3.000
 45U  N46   C21  N47   126.05  3.000
 45U  N47   C21  C28   118.48  3.000
 45U  N46   C21  C28   115.42  3.000
 45U  HN47  N47  C21   111.17  3.000
 45U  HN4A  N46  HN46  113.37  3.000
 45U  HN4A  N46  C21   117.07  3.000
 45U  HN46  N46  C21   118.43  3.000
 45U  H27   C27  C26   120.06  3.000
 45U  H27   C27  C28   119.30  3.000
 45U  C26   C27  C28   120.64  3.000
 45U  H26   C26  C27   119.49  3.000
 45U  H26   C26  C25   119.76  3.000
 45U  C27   C26  C25   120.76  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
 45U  CONST_01  C28   C27  C26  C25     0.00   0.0  0
 45U  CONST_02  C28   C29  C30  C25     0.00   0.0  0
 45U  CONST_03  C27   C26  C25  C30     0.00   0.0  0
 45U  CONST_04  C27   C28  C29  C30     0.00   0.0  0
 45U  CONST_05  C26   C25  C30  C29     0.00   0.0  0
 45U  CONST_06  C26   C27  C28  C29     0.00   0.0  0
 45U  CONST_07  C27   C26  C25  C24   180.00   0.0  0
 45U  CONST_08  C29   C30  C25  C24   180.00   0.0  0
 45U  CONST_09  C21   C28  C29  C30   180.00   0.0  0
 45U  CONST_10  C26   C27  C28  C21   180.00   0.0  0
 45U  CONST_11  H27   C27  C26  C25   180.00   0.0  0
 45U  CONST_12  H29   C29  C30  C25   180.00   0.0  0
 45U  CONST_13  H26   C26  C25  C30   180.00   0.0  0
 45U  CONST_14  H30   C30  C29  C28   180.00   0.0  0
 45U  CONST_15  C1    N1   C14  O32     0.00   0.0  0
 45U  CONST_16  C4    N1   C14  O32   180.00   0.0  0
 45U  CONST_17  C1    N1   C14  C5    180.00   0.0  0
 45U  CONST_18  C4    N1   C14  C5      0.00   0.0  0
 45U  CONST_19  C24   N23  C7   C1    180.00   0.0  0
 45U  CONST_20  HN23  N23  C7   C1      0.00   0.0  0
 45U  CONST_22  HN4A  N46  C21  C28   180.00   0.0  0
 45U  CONST_23  HN47  N47  C21  C28   180.00   0.0  0
 45U  CONST_24  C24   N23  C7   O22     0.00   0.0  0
 45U  Var_01    C48   C47  C45  C44   -40.89  30.0  1
 45U  Var_02    C47   C48  C49  C44     1.15  30.0  1
 45U  Var_03    C45   C47  C48  C49    24.69  30.0  1
 45U  Var_04    C2    C3   C4   N1     29.40  30.0  1
 45U  Var_05    C4    C3   C2   C1    -36.85  30.0  1
 45U  Var_06    C3    C4   N1   C1    -11.07  30.0  1
 45U  Var_07    C26   C25  C24  N23   -83.12  30.0  2
 45U  Var_08    N46   C21  C28  C29   -22.01  30.0  2
 45U  Var_09    N1    C14  C5   O21   175.71  30.0  1
 45U  Var_10    C25   C24  N23  C7   -177.11  30.0  1
 45U  Var_11    H5    C5   O21  C44    50.12  30.0  2

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
 45U  chir_01  C44  O21  C45  C49  negativ
 45U  chir_02  C1   N1   C7   C2   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
 45U  plan-1  O32   0.020
 45U  plan-1  C14   0.020
 45U  plan-1  C5    0.020
 45U  plan-1  N1    0.020
 45U  plan-1  C1    0.020
 45U  plan-1  C4    0.020
 45U  plan-2  C24   0.020
 45U  plan-2  C25   0.020
 45U  plan-2  C30   0.020
 45U  plan-2  C29   0.020
 45U  plan-2  C28   0.020
 45U  plan-2  C21   0.020
 45U  plan-2  C27   0.020
 45U  plan-2  C26   0.020
 45U  plan-2  H30   0.020
 45U  plan-2  H29   0.020
 45U  plan-2  H27   0.020
 45U  plan-2  H26   0.020
 45U  plan-3  C1    0.020
 45U  plan-3  C7    0.020
 45U  plan-3  O22   0.020
 45U  plan-3  N23   0.020
 45U  plan-3  C24   0.020
 45U  plan-3  HN23  0.020
 45U  plan-4  C28   0.020
 45U  plan-4  C21   0.020
 45U  plan-4  N47   0.020
 45U  plan-4  N46   0.020
 45U  plan-4  HN47  0.020
 45U  plan-4  HN46  0.020
 45U  plan-4  HN4A  0.020

