# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:00:26 2022
#   Inital geometry file: a 147 line input string
#   Ligand name: N-cycloheptylglycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(CNC(=O)[C@@H]2CCCN2C(=O)CNC3CCCCCC3)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
 12U  12U  N-cycloheptylglycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide  ligand  62  29  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_12U
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
 12U  C14   C  C     0   0.541  -1.7350   0.8578  -0.2757
 12U  O32   O  O     0  -0.499  -0.9751  -0.1012  -0.3223
 12U  C5    C  CH2   0  -0.391  -3.2433   0.6965  -0.2650
 12U  N21   N  NH1   0  -0.603  -3.6101  -0.6712  -0.0127
 12U  C49   C  CH1   0  -0.060  -5.0482  -0.9280  -0.0168
 12U  C48   C  CH2   0  -0.425  -5.2645  -2.3211   0.5801
 12U  C47   C  CH2   0  -0.434  -6.6910  -2.6921   0.9700
 12U  C46   C  CH2   0  -0.434  -7.7675  -2.5288  -0.1012
 12U  C52   C  CH2   0  -0.441  -8.0705  -1.0660  -0.4254
 12U  C51   C  CH2   0  -0.424  -7.1548  -0.4176  -1.4652
 12U  C50   C  CH2   0  -0.465  -5.6804  -0.8182  -1.4140
 12U  N1    N  NT    0  -0.480  -1.2707   2.1170  -0.2586
 12U  C1    C  CH1   0  -0.163   0.1573   2.3702  -0.2704
 12U  C7    C  C     0   0.569   0.8498   1.6739   0.8941
 12U  O22   O  O     0  -0.499   0.3584   1.6479   2.0120
 12U  C2    C  CH2   0  -0.477   0.2494   3.8972  -0.1386
 12U  C3    C  CH2   0  -0.473  -1.0687   4.3867  -0.7282
 12U  C4    C  CH2   0  -0.276  -2.0659   3.3380  -0.2562
 12U  N23   N  NH1   0  -0.635   2.0562   1.1675   0.6132
 12U  C24   C  CH2   0  -0.314   2.8603   0.4888   1.6132
 12U  C25   C  CR6   0   0.042   4.0767  -0.1135   0.9693
 12U  C30   C  CR16  0  -0.270   4.0138  -1.3778   0.3940
 12U  C29   C  CR16  0  -0.277   5.1252  -1.9332  -0.2216
 12U  C28   C  CR6   0   0.038   6.3264  -1.2295  -0.2820
 12U  C9    C  C     0   0.333   7.5333  -1.7966  -0.9457
 12U  N10   N  N     0  -0.650   8.3979  -0.9915  -1.4315
 12U  N11   N  NH2   0  -0.822   7.5704  -3.1596  -1.0191
 12U  C27   C  CR16  0  -0.260   6.3861   0.0424   0.2829
 12U  C26   C  CR16  0  -0.274   5.2758   0.5905   0.9041
 12U  H5    H  HCH2  0   0.258  -3.6707   1.3300   0.5191
 12U  H5A   H  HCH2  0   0.233  -3.6226   1.1108  -1.2153
 12U  HN21  H  HNH1  0   0.337  -3.1556  -1.2781  -0.6856
 12U  H49   H  HCH1  0   0.214  -5.4992  -0.1813   0.6497
 12U  H48   H  HCH2  0   0.207  -4.8824  -3.0562  -0.1384
 12U  H48A  H  HCH2  0   0.223  -4.6340  -2.4092   1.4685
 12U  H47   H  HCH2  0   0.225  -6.6805  -3.7311   1.3111
 12U  H47A  H  HCH2  0   0.209  -6.9912  -2.0982   1.8404
 12U  H46   H  HCH2  0   0.213  -7.4968  -3.0788  -1.0090
 12U  H46A  H  HCH2  0   0.226  -8.6805  -3.0017   0.2699
 12U  H52   H  HCH2  0   0.227  -9.1012  -0.9719  -0.7766
 12U  H52A  H  HCH2  0   0.212  -8.0306  -0.4935   0.5073
 12U  H51   H  HCH2  0   0.218  -7.5279  -0.6502  -2.4666
 12U  H51A  H  HCH2  0   0.218  -7.2350   0.6684  -1.3635
 12U  H50   H  HCH2  0   0.234  -5.1280  -0.0894  -2.0144
 12U  H50A  H  HCH2  0   0.215  -5.5364  -1.7767  -1.9234
 12U  H1    H  HCH1  0   0.272   0.5920   2.0425  -1.2212
 12U  H2    H  HCH2  0   0.250   0.3134   4.1819   0.9138
 12U  H2A   H  HCH2  0   0.265   1.1266   4.2936  -0.6467
 12U  H3    H  HCH2  0   0.258  -1.3348   5.3894  -0.3978
 12U  H3A   H  HCH2  0   0.245  -1.0216   4.3923  -1.8189
 12U  H4    H  HCH2  0   0.245  -2.4356   3.5637   0.7487
 12U  H4A   H  HCH2  0   0.259  -2.9251   3.2547  -0.9223
 12U  HN23  H  HNH1  0   0.404   2.3797   1.1690  -0.3406
 12U  H24   H  HCH2  0   0.256   3.1551   1.1906   2.3969
 12U  H24A  H  HCH2  0   0.256   2.2661  -0.2938   2.0907
 12U  H30   H  HCR6  0   0.258   3.0881  -1.9398   0.4263
 12U  H29   H  HCR6  0   0.260   5.0385  -2.9149  -0.6695
 12U  HN10  H  H     0   0.324   9.1841  -1.4962  -1.8321
 12U  HN11  H  HNH2  0   0.395   7.1090  -3.6902  -0.2985
 12U  HN1A  H  HNH2  0   0.392   8.4261  -3.5818  -1.3430
 12U  H27   H  HCR6  0   0.257   7.3124   0.5996   0.2452
 12U  H26   H  HCR6  0   0.257   5.3467   1.5747   1.3515

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
 12U  O22  C7    double    1.221  0.020  1.221
 12U  C7   N23   single    1.338  0.020  1.338
 12U  C7   C1    single    1.523  0.020  1.523
 12U  N23  C24   single    1.452  0.020  1.452
 12U  C24  C25   single    1.502  0.020  1.502
 12U  C25  C26   aromatic  1.392  0.020  1.392
 12U  C25  C30   aromatic  1.390  0.020  1.390
 12U  C26  C27   aromatic  1.385  0.020  1.385
 12U  C27  C28   aromatic  1.393  0.020  1.393
 12U  C28  C9    single    1.489  0.020  1.489
 12U  C28  C29   aromatic  1.393  0.020  1.393
 12U  C9   N10   double    1.277  0.020  1.277
 12U  C9   N11   single    1.365  0.020  1.365
 12U  C29  C30   aromatic  1.387  0.020  1.387
 12U  C1   C2    single    1.535  0.020  1.535
 12U  C1   N1    single    1.450  0.020  1.450
 12U  C2   C3    single    1.525  0.020  1.525
 12U  C3   C4    single    1.522  0.020  1.522
 12U  C4   N1    single    1.457  0.020  1.457
 12U  N1   C14   single    1.342  0.020  1.342
 12U  C14  O32   double    1.224  0.020  1.224
 12U  C14  C5    single    1.517  0.020  1.517
 12U  C5   N21   single    1.438  0.020  1.438
 12U  N21  C49   single    1.461  0.020  1.461
 12U  C49  C48   single    1.531  0.020  1.531
 12U  C49  C50   single    1.538  0.020  1.538
 12U  C48  C47   single    1.525  0.020  1.525
 12U  C47  C46   single    1.527  0.020  1.527
 12U  C46  C52   single    1.529  0.020  1.529
 12U  C52  C51   single    1.530  0.020  1.530
 12U  C51  C50   single    1.529  0.020  1.529
 12U  N23  HN23  single    0.860  0.020  1.020
 12U  C24  H24   single    0.970  0.020  1.090
 12U  C24  H24A  single    0.970  0.020  1.090
 12U  C26  H26   single    0.930  0.020  1.080
 12U  C27  H27   single    0.930  0.020  1.080
 12U  N10  HN10  single    0.890  0.020  1.040
 12U  N11  HN11  single    0.890  0.020  1.040
 12U  N11  HN1A  single    0.890  0.020  1.040
 12U  C29  H29   single    0.930  0.020  1.080
 12U  C30  H30   single    0.930  0.020  1.080
 12U  C1   H1    single    0.970  0.020  1.090
 12U  C2   H2    single    0.970  0.020  1.090
 12U  C2   H2A   single    0.970  0.020  1.090
 12U  C3   H3    single    0.970  0.020  1.090
 12U  C3   H3A   single    0.970  0.020  1.090
 12U  C4   H4    single    0.970  0.020  1.090
 12U  C4   H4A   single    0.970  0.020  1.090
 12U  C5   H5    single    0.970  0.020  1.090
 12U  C5   H5A   single    0.970  0.020  1.090
 12U  N21  HN21  single    0.890  0.020  1.040
 12U  C49  H49   single    0.970  0.020  1.090
 12U  C48  H48   single    0.970  0.020  1.090
 12U  C48  H48A  single    0.970  0.020  1.090
 12U  C47  H47   single    0.970  0.020  1.090
 12U  C47  H47A  single    0.970  0.020  1.090
 12U  C46  H46   single    0.970  0.020  1.090
 12U  C46  H46A  single    0.970  0.020  1.090
 12U  C52  H52   single    0.970  0.020  1.090
 12U  C52  H52A  single    0.970  0.020  1.090
 12U  C51  H51   single    0.970  0.020  1.090
 12U  C51  H51A  single    0.970  0.020  1.090
 12U  C50  H50   single    0.970  0.020  1.090
 12U  C50  H50A  single    0.970  0.020  1.090

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
 12U  N1    C14  C5    116.34  3.000
 12U  C5    C14  O32   122.28  3.000
 12U  N1    C14  O32   121.37  3.000
 12U  H5A   C5   H5    105.38  3.000
 12U  H5A   C5   N21   114.85  3.000
 12U  H5    C5   N21   108.96  3.000
 12U  H5A   C5   C14   107.20  3.000
 12U  H5    C5   C14   109.37  3.000
 12U  N21   C5   C14   110.85  3.000
 12U  HN21  N21  C49   109.53  3.000
 12U  HN21  N21  C5    109.78  3.000
 12U  C49   N21  C5    114.69  3.000
 12U  H49   C49  C50   109.53  3.000
 12U  H49   C49  C48   108.92  3.000
 12U  C50   C49  C48   111.18  3.000
 12U  H49   C49  N21   106.45  3.000
 12U  C50   C49  N21   113.25  3.000
 12U  C48   C49  N21   107.34  3.000
 12U  H48A  C48  H48   106.11  3.000
 12U  H48A  C48  C47   108.20  3.000
 12U  H48   C48  C47   109.30  3.000
 12U  H48A  C48  C49   107.99  3.000
 12U  H48   C48  C49   107.77  3.000
 12U  C47   C48  C49   116.96  3.000
 12U  H47A  C47  H47   105.66  3.000
 12U  H47A  C47  C46   107.82  3.000
 12U  H47   C47  C46   109.09  3.000
 12U  H47A  C47  C48   109.13  3.000
 12U  H47   C47  C48   107.57  3.000
 12U  C46   C47  C48   117.00  3.000
 12U  H46A  C46  H46   105.70  3.000
 12U  H46A  C46  C52   108.68  3.000
 12U  H46   C46  C52   110.71  3.000
 12U  H46A  C46  C47   107.72  3.000
 12U  H46   C46  C47   110.69  3.000
 12U  C52   C46  C47   113.00  3.000
 12U  H52A  C52  H52   105.25  3.000
 12U  H52A  C52  C51   109.61  3.000
 12U  H52   C52  C51   108.04  3.000
 12U  H52A  C52  C46   108.20  3.000
 12U  H52   C52  C46   109.72  3.000
 12U  C51   C52  C46   115.54  3.000
 12U  H51A  C51  H51   105.75  3.000
 12U  H51A  C51  C50   109.14  3.000
 12U  H51   C51  C50   107.70  3.000
 12U  H51A  C51  C52   108.28  3.000
 12U  H51   C51  C52   109.15  3.000
 12U  C50   C51  C52   116.33  3.000
 12U  H50A  C50  H50   105.16  3.000
 12U  H50A  C50  C51   109.91  3.000
 12U  H50   C50  C51   107.10  3.000
 12U  H50A  C50  C49   107.83  3.000
 12U  H50   C50  C49   109.80  3.000
 12U  C51   C50  C49   116.47  3.000
 12U  C4    N1   C1    113.02  3.000
 12U  C4    N1   C14   126.68  3.000
 12U  C1    N1   C14   120.28  3.000
 12U  H1    C1   C2    110.37  3.000
 12U  H1    C1   C7    110.26  3.000
 12U  C2    C1   C7    111.20  3.000
 12U  H1    C1   N1    110.22  3.000
 12U  C2    C1   N1    103.41  3.000
 12U  C7    C1   N1    111.20  3.000
 12U  N23   C7   O22   123.15  3.000
 12U  N23   C7   C1    114.98  3.000
 12U  O22   C7   C1    121.77  3.000
 12U  H2A   C2   H2    107.92  3.000
 12U  H2A   C2   C3    113.53  3.000
 12U  H2    C2   C3    109.85  3.000
 12U  H2A   C2   C1    111.75  3.000
 12U  H2    C2   C1    110.21  3.000
 12U  C3    C2   C1    103.54  3.000
 12U  H3A   C3   H3    107.99  3.000
 12U  H3A   C3   C4    109.98  3.000
 12U  H3    C3   C4    112.35  3.000
 12U  H3A   C3   C2    110.53  3.000
 12U  H3    C3   C2    112.93  3.000
 12U  C4    C3   C2    103.02  3.000
 12U  H4A   C4   H4    108.09  3.000
 12U  H4A   C4   C3    112.30  3.000
 12U  H4    C4   C3    111.35  3.000
 12U  H4A   C4   N1    111.41  3.000
 12U  H4    C4   N1    111.02  3.000
 12U  C3    C4   N1    102.67  3.000
 12U  HN23  N23  C24   118.37  3.000
 12U  HN23  N23  C7    119.20  3.000
 12U  C24   N23  C7    122.12  3.000
 12U  H24A  C24  H24   107.06  3.000
 12U  H24A  C24  C25   109.91  3.000
 12U  H24   C24  C25   110.27  3.000
 12U  H24A  C24  N23   109.56  3.000
 12U  H24   C24  N23   110.08  3.000
 12U  C25   C24  N23   109.92  3.000
 12U  C26   C25  C30   118.65  3.000
 12U  C30   C25  C24   120.35  3.000
 12U  C26   C25  C24   120.99  3.000
 12U  H30   C30  C29   119.36  3.000
 12U  H30   C30  C25   119.87  3.000
 12U  C29   C30  C25   120.77  3.000
 12U  H29   C29  C28   120.60  3.000
 12U  H29   C29  C30   118.86  3.000
 12U  C28   C29  C30   120.53  3.000
 12U  C27   C28  C9    119.58  3.000
 12U  C9    C28  C29   121.70  3.000
 12U  C27   C28  C29   118.71  3.000
 12U  N11   C9   N10   126.18  3.000
 12U  N11   C9   C28   115.22  3.000
 12U  N10   C9   C28   118.55  3.000
 12U  HN10  N10  C9    111.13  3.000
 12U  HN1A  N11  HN11  113.48  3.000
 12U  HN1A  N11  C9    117.30  3.000
 12U  HN11  N11  C9    118.37  3.000
 12U  H27   C27  C26   119.88  3.000
 12U  H27   C27  C28   119.53  3.000
 12U  C26   C27  C28   120.58  3.000
 12U  H26   C26  C27   119.48  3.000
 12U  H26   C26  C25   119.76  3.000
 12U  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
 12U  CONST_01  C28   C27  C26  C25     0.00   0.0  0
 12U  CONST_02  C28   C29  C30  C25     0.00   0.0  0
 12U  CONST_03  C27   C26  C25  C30     0.00   0.0  0
 12U  CONST_04  C27   C28  C29  C30     0.00   0.0  0
 12U  CONST_05  C26   C27  C28  C29     0.00   0.0  0
 12U  CONST_06  C26   C25  C30  C29     0.00   0.0  0
 12U  CONST_07  C27   C26  C25  C24   180.00   0.0  0
 12U  CONST_08  C29   C30  C25  C24   180.00   0.0  0
 12U  CONST_09  C9    C28  C29  C30   180.00   0.0  0
 12U  CONST_10  C26   C27  C28  C9    180.00   0.0  0
 12U  CONST_11  H27   C27  C26  C25   180.00   0.0  0
 12U  CONST_12  H29   C29  C30  C25   180.00   0.0  0
 12U  CONST_13  H26   C26  C25  C30   180.00   0.0  0
 12U  CONST_14  H30   C30  C29  C28   180.00   0.0  0
 12U  CONST_15  C1    N1   C14  O32     0.00   0.0  0
 12U  CONST_16  C4    N1   C14  O32   180.00   0.0  0
 12U  CONST_17  C1    N1   C14  C5    180.00   0.0  0
 12U  CONST_18  C4    N1   C14  C5      0.00   0.0  0
 12U  CONST_19  C24   N23  C7   C1    180.00   0.0  0
 12U  CONST_20  HN23  N23  C7   C1      0.00   0.0  0
 12U  CONST_21  HN10  N10  C9   C28   180.00   0.0  0
 12U  CONST_23  HN1A  N11  C9   C28   180.00   0.0  0
 12U  CONST_24  C24   N23  C7   O22     0.00   0.0  0
 12U  Var_01    C2    C3   C4   N1    -33.83  30.0  1
 12U  Var_02    C4    C3   C2   C1     37.58  30.0  1
 12U  Var_03    C3    C4   N1   C1     18.08  30.0  1
 12U  Var_04    C26   C25  C24  N23    92.35  30.0  2
 12U  Var_05    N10   C9   C28  C29   153.21  30.0  2
 12U  Var_06    C49   N21  C5   C14  -178.57  30.0  3
 12U  Var_07    N1    C14  C5   N21  -168.32  30.0  2
 12U  Var_08    C25   C24  N23  C7    173.09  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
 12U  chir_01  C49  N21  C48  C50  positiv
 12U  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
 12U  plan-1  C24   0.020
 12U  plan-1  C25   0.020
 12U  plan-1  C30   0.020
 12U  plan-1  C29   0.020
 12U  plan-1  C28   0.020
 12U  plan-1  C9    0.020
 12U  plan-1  C27   0.020
 12U  plan-1  C26   0.020
 12U  plan-1  H30   0.020
 12U  plan-1  H29   0.020
 12U  plan-1  H27   0.020
 12U  plan-1  H26   0.020
 12U  plan-2  C1    0.020
 12U  plan-2  C7    0.020
 12U  plan-2  O22   0.020
 12U  plan-2  N23   0.020
 12U  plan-2  C24   0.020
 12U  plan-2  HN23  0.020
 12U  plan-3  C14   0.020
 12U  plan-3  O32   0.020
 12U  plan-3  C5    0.020
 12U  plan-3  N1    0.020
 12U  plan-3  C1    0.020
 12U  plan-3  C4    0.020
 12U  plan-4  C28   0.020
 12U  plan-4  C9    0.020
 12U  plan-4  N10   0.020
 12U  plan-4  N11   0.020
 12U  plan-4  HN10  0.020
 12U  plan-4  HN11  0.020
 12U  plan-4  HN1A  0.020

