# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 16:25:27 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: methyl (3S)-3-(3-carbamimidoylphenyl)-5-(4-carbamimidoylphenyl)pentanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)C[C@H](CCc1ccc(cc1)C(N)=N)c2cccc(c2)C(N)=N
#
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
 IN4  IN4  'methyl (3S)-3-(3-carbamimidoylphenyl)-5-(4-carbamimidoylphenyl)pentanoate'  ligand  50  26  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_IN4
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
 IN4  C1    C  CR16  0  -0.312  -1.8658   1.5361   3.7170
 IN4  C2    C  CR16  0  -0.225  -1.0670   2.2792   2.8584
 IN4  C3    C  CR16  0  -0.314  -0.2012   1.6445   1.9822
 IN4  C4    C  CR6   0   0.185  -0.1167   0.2524   1.9523
 IN4  C5    C  CR16  0  -0.349  -0.9133  -0.4789   2.8230
 IN4  C6    C  CR6   0   0.066  -1.7946   0.1457   3.7030
 IN4  C10   C  CH1   0  -0.327   0.8130  -0.4485   0.9899
 IN4  C9    C  CH2   0  -0.405   0.3944  -0.1653  -0.4580
 IN4  C11   C  CH2   0  -0.527   1.1462  -0.9973  -1.5002
 IN4  C12   C  CR6   0   0.140   0.6387  -0.7140  -2.8851
 IN4  C20   C  C     0   0.335  -2.6172  -0.6871   4.6249
 IN4  N3    N  N     0  -0.652  -2.1830  -1.8409   4.9618
 IN4  N4    N  NH2   0  -0.823  -3.7626  -0.0977   5.0753
 IN4  C7    C  CR16  0  -0.304   1.2741   0.2096  -3.7125
 IN4  C13   C  CR16  0  -0.258   0.7713   0.5081  -4.9682
 IN4  C15   C  CR6   0   0.030  -0.3922  -0.1020  -5.4322
 IN4  C16   C  C     0   0.331  -0.9144   0.2457  -6.7825
 IN4  C17   C  CR16  0  -0.278  -1.0265  -1.0332  -4.6117
 IN4  C19   C  CR16  0  -0.294  -0.5146  -1.3338  -3.3588
 IN4  N2    N  N     0  -0.653  -0.0995   0.6888  -7.6616
 IN4  N1    N  NH2   0  -0.822  -2.2468   0.0077  -6.9720
 IN4  C14   C  CH2   0  -0.575   2.2677  -0.0415   1.2396
 IN4  C22   C  C     0   0.602   2.7194  -0.3328   2.6451
 IN4  O3    O  O     0  -0.446   2.3725  -1.2897   3.2915
 IN4  O4    O  O2    0  -0.452   3.5795   0.5752   3.0879
 IN4  C8    C  CH3   0  -0.425   4.1370   0.3775   4.3873
 IN4  H1    H  HCR6  0   0.256  -2.5218   2.0509   4.4072
 IN4  H2    H  HCR6  0   0.258  -1.1201   3.3599   2.8778
 IN4  H3    H  HCR6  0   0.253   0.4073   2.2455   1.3169
 IN4  H5    H  HCR6  0   0.244  -0.8556  -1.5599   2.8175
 IN4  H10   H  HCH1  0   0.255   0.7250  -1.5256   1.1598
 IN4  H91   H  HCH2  0   0.249  -0.6753  -0.3711  -0.5532
 IN4  H92   H  HCH2  0   0.232   0.5248   0.8982  -0.6821
 IN4  H111  H  HCH2  0   0.252   2.2167  -0.7852  -1.4549
 IN4  H112  H  HCH2  0   0.247   1.0229  -2.0594  -1.2693
 IN4  HN3   H  H     0   0.322  -2.8420  -2.3176   5.5716
 IN4  HN41  H  HNH2  0   0.391  -4.4076  -0.6706   5.5955
 IN4  HN42  H  HNH2  0   0.395  -4.2097   0.5933   4.4957
 IN4  H7    H  HCR6  0   0.248   2.1744   0.7053  -3.3686
 IN4  H13   H  HCR6  0   0.252   1.2777   1.2269  -5.5982
 IN4  H17   H  HCR6  0   0.255  -1.9163  -1.5501  -4.9482
 IN4  H19   H  HCR6  0   0.250  -1.0202  -2.0661  -2.7404
 IN4  HN2   H  H     0   0.322  -0.5830   0.9193  -8.5256
 IN4  HN11  H  HNH2  0   0.390  -2.6652   0.3738  -7.8126
 IN4  HN12  H  HNH2  0   0.394  -2.8558   0.0481  -6.1715
 IN4  H141  H  HCH2  0   0.263   2.4227   1.0122   1.0014
 IN4  H142  H  HCH2  0   0.297   2.9320  -0.6042   0.5762
 IN4  H81   H  HCH3  0   0.251   4.8182   1.2077   4.5494
 IN4  H82   H  HCH3  0   0.239   3.3665   0.3879   5.1578
 IN4  H83   H  HCH3  0   0.238   4.6906  -0.5593   4.4458

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
 IN4  C1   C2    aromatic  1.388  0.020  1.388
 IN4  C1   C6    aromatic  1.392  0.020  1.392
 IN4  C1   H1    single    0.930  0.020  1.080
 IN4  C2   C3    aromatic  1.386  0.020  1.386
 IN4  C2   H2    single    0.930  0.020  1.080
 IN4  C3   C4    aromatic  1.395  0.020  1.395
 IN4  C3   H3    single    0.930  0.020  1.080
 IN4  C4   C5    aromatic  1.388  0.020  1.388
 IN4  C4   C10   single    1.511  0.020  1.511
 IN4  C5   C6    aromatic  1.393  0.020  1.393
 IN4  C5   H5    single    0.930  0.020  1.080
 IN4  C6   C20   single    1.490  0.020  1.490
 IN4  C10  C9    single    1.534  0.020  1.534
 IN4  C10  C14   single    1.531  0.020  1.531
 IN4  C10  H10   single    0.970  0.020  1.090
 IN4  C9   C11   single    1.531  0.020  1.531
 IN4  C9   H91   single    0.970  0.020  1.090
 IN4  C9   H92   single    0.970  0.020  1.090
 IN4  C11  C12   single    1.502  0.020  1.502
 IN4  C11  H111  single    0.970  0.020  1.090
 IN4  C11  H112  single    0.970  0.020  1.090
 IN4  C12  C7    aromatic  1.393  0.020  1.393
 IN4  C12  C19   aromatic  1.392  0.020  1.392
 IN4  C20  N3    double    1.278  0.020  1.278
 IN4  C20  N4    single    1.365  0.020  1.365
 IN4  N3   HN3   single    0.890  0.020  1.040
 IN4  N4   HN41  single    0.890  0.020  1.040
 IN4  N4   HN42  single    0.890  0.020  1.040
 IN4  C7   C13   aromatic  1.385  0.020  1.385
 IN4  C7   H7    single    0.930  0.020  1.080
 IN4  C13  C15   aromatic  1.393  0.020  1.393
 IN4  C13  H13   single    0.930  0.020  1.080
 IN4  C15  C16   single    1.489  0.020  1.489
 IN4  C15  C17   aromatic  1.394  0.020  1.394
 IN4  C16  N2    double    1.278  0.020  1.278
 IN4  C16  N1    single    1.367  0.020  1.367
 IN4  C17  C19   aromatic  1.386  0.020  1.386
 IN4  C17  H17   single    0.930  0.020  1.080
 IN4  C19  H19   single    0.930  0.020  1.080
 IN4  N2   HN2   single    0.890  0.020  1.040
 IN4  N1   HN11  single    0.890  0.020  1.040
 IN4  N1   HN12  single    0.890  0.020  1.040
 IN4  C14  C22   single    1.505  0.020  1.505
 IN4  C14  H141  single    0.970  0.020  1.090
 IN4  C14  H142  single    0.970  0.020  1.090
 IN4  C22  O3    double    1.206  0.020  1.206
 IN4  C22  O4    single    1.327  0.020  1.327
 IN4  O4   C8    single    1.428  0.020  1.428
 IN4  C8   H81   single    0.970  0.020  1.090
 IN4  C8   H82   single    0.970  0.020  1.090
 IN4  C8   H83   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
 IN4  H1    C1   C6    120.82  3.000
 IN4  H1    C1   C2    119.24  3.000
 IN4  C6    C1   C2    119.93  3.000
 IN4  H2    C2   C3    119.96  3.000
 IN4  H2    C2   C1    119.69  3.000
 IN4  C3    C2   C1    120.36  3.000
 IN4  H3    C3   C4    120.42  3.000
 IN4  H3    C3   C2    119.02  3.000
 IN4  C4    C3   C2    120.56  3.000
 IN4  C10   C4   C5    120.55  3.000
 IN4  C10   C4   C3    120.93  3.000
 IN4  C5    C4   C3    118.52  3.000
 IN4  H5    C5   C6    118.99  3.000
 IN4  H5    C5   C4    119.49  3.000
 IN4  C6    C5   C4    121.53  3.000
 IN4  C20   C6   C5    119.30  3.000
 IN4  C20   C6   C1    121.58  3.000
 IN4  C5    C6   C1    119.10  3.000
 IN4  H10   C10  C14   108.23  3.000
 IN4  H10   C10  C9    107.84  3.000
 IN4  C14   C10  C9    111.36  3.000
 IN4  H10   C10  C4    107.96  3.000
 IN4  C14   C10  C4    110.95  3.000
 IN4  C9    C10  C4    110.35  3.000
 IN4  H92   C9   H91   106.35  3.000
 IN4  H92   C9   C11   109.28  3.000
 IN4  H91   C9   C11   108.60  3.000
 IN4  H92   C9   C10   109.89  3.000
 IN4  H91   C9   C10   108.33  3.000
 IN4  C11   C9   C10   114.10  3.000
 IN4  H112  C11  H111  106.87  3.000
 IN4  H112  C11  C12   109.86  3.000
 IN4  H111  C11  C12   109.44  3.000
 IN4  H112  C11  C9    109.18  3.000
 IN4  H111  C11  C9    110.34  3.000
 IN4  C12   C11  C9    111.06  3.000
 IN4  C19   C12  C7    118.08  3.000
 IN4  C19   C12  C11   120.64  3.000
 IN4  C7    C12  C11   121.23  3.000
 IN4  N4    C20  N3    126.02  3.000
 IN4  N4    C20  C6    115.23  3.000
 IN4  N3    C20  C6    118.69  3.000
 IN4  HN3   N3   C20   111.18  3.000
 IN4  HN42  N4   HN41  113.79  3.000
 IN4  HN42  N4   C20   118.64  3.000
 IN4  HN41  N4   C20   117.53  3.000
 IN4  H7    C7   C13   119.38  3.000
 IN4  H7    C7   C12   119.58  3.000
 IN4  C13   C7   C12   121.04  3.000
 IN4  H13   C13  C15   119.21  3.000
 IN4  H13   C13  C7    120.08  3.000
 IN4  C15   C13  C7    120.71  3.000
 IN4  C17   C15  C16   122.03  3.000
 IN4  C17   C15  C13   118.45  3.000
 IN4  C16   C15  C13   119.51  3.000
 IN4  N1    C16  N2    125.92  3.000
 IN4  N1    C16  C15   115.28  3.000
 IN4  N2    C16  C15   118.77  3.000
 IN4  H17   C17  C19   118.74  3.000
 IN4  H17   C17  C15   120.66  3.000
 IN4  C19   C17  C15   120.59  3.000
 IN4  H19   C19  C17   119.34  3.000
 IN4  H19   C19  C12   119.55  3.000
 IN4  C17   C19  C12   121.12  3.000
 IN4  HN2   N2   C16   111.10  3.000
 IN4  HN12  N1   HN11  113.42  3.000
 IN4  HN12  N1   C16   118.20  3.000
 IN4  HN11  N1   C16   117.21  3.000
 IN4  H142  C14  H141  106.13  3.000
 IN4  H142  C14  C22   106.52  3.000
 IN4  H141  C14  C22   110.37  3.000
 IN4  H142  C14  C10   109.95  3.000
 IN4  H141  C14  C10   110.85  3.000
 IN4  C22   C14  C10   112.71  3.000
 IN4  O4    C22  O3    123.42  3.000
 IN4  O4    C22  C14   111.95  3.000
 IN4  O3    C22  C14   124.61  3.000
 IN4  C8    O4   C22   117.53  3.000
 IN4  H83   C8   H82   109.23  3.000
 IN4  H83   C8   H81   109.30  3.000
 IN4  H82   C8   H81   109.32  3.000
 IN4  H83   C8   O4    111.48  3.000
 IN4  H82   C8   O4    111.47  3.000
 IN4  H81   C8   O4    105.96  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
 IN4  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 IN4  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 IN4  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 IN4  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 IN4  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 IN4  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 IN4  CONST_07  C15   C13  C7   C12     0.00   0.0  0
 IN4  CONST_08  C15   C17  C19  C12     0.00   0.0  0
 IN4  CONST_09  C17   C19  C12  C7      0.00   0.0  0
 IN4  CONST_10  C17   C15  C13  C7      0.00   0.0  0
 IN4  CONST_11  C19   C12  C7   C13     0.00   0.0  0
 IN4  CONST_12  C19   C17  C15  C13     0.00   0.0  0
 IN4  CONST_13  C20   C6   C1   C2    180.00   0.0  0
 IN4  CONST_14  C10   C4   C3   C2    180.00   0.0  0
 IN4  CONST_15  C20   C6   C5   C4    180.00   0.0  0
 IN4  CONST_16  C10   C4   C5   C6    180.00   0.0  0
 IN4  CONST_17  C13   C7   C12  C11   180.00   0.0  0
 IN4  CONST_18  C17   C19  C12  C11   180.00   0.0  0
 IN4  CONST_19  C16   C15  C13  C7    180.00   0.0  0
 IN4  CONST_20  C19   C17  C15  C16   180.00   0.0  0
 IN4  CONST_21  H3    C3   C2   C1    180.00   0.0  0
 IN4  CONST_22  H5    C5   C6   C1    180.00   0.0  0
 IN4  CONST_23  H1    C1   C2   C3    180.00   0.0  0
 IN4  CONST_24  H2    C2   C3   C4    180.00   0.0  0
 IN4  CONST_25  H13   C13  C7   C12   180.00   0.0  0
 IN4  CONST_26  H17   C17  C19  C12   180.00   0.0  0
 IN4  CONST_27  H19   C19  C12  C7    180.00   0.0  0
 IN4  CONST_28  H7    C7   C13  C15   180.00   0.0  0
 IN4  CONST_29  HN3   N3   C20  C6    180.00   0.0  0
 IN4  CONST_30  HN41  N4   C20  C6    180.00   0.0  0
 IN4  CONST_32  HN2   N2   C16  C15   180.00   0.0  0
 IN4  CONST_33  HN11  N1   C16  C15   180.00   0.0  0
 IN4  Var_01    N3    C20  C6   C1   -152.84  30.0  2
 IN4  Var_02    C7    C12  C11  C9     95.87  30.0  2
 IN4  Var_03    N2    C16  C15  C13    24.84  30.0  2
 IN4  Var_04    C12   C11  C9   C10   177.30  30.0  3
 IN4  Var_05    O3    C22  C14  C10    35.74  30.0  3
 IN4  Var_06    H81   C8   O4   C22   178.99  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
 IN4  chir_01  C10  C4  C9  C14  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
 IN4  plan-1  C1    0.020
 IN4  plan-1  C2    0.020
 IN4  plan-1  C3    0.020
 IN4  plan-1  C4    0.020
 IN4  plan-1  C5    0.020
 IN4  plan-1  C6    0.020
 IN4  plan-1  C10   0.020
 IN4  plan-1  C20   0.020
 IN4  plan-1  H1    0.020
 IN4  plan-1  H2    0.020
 IN4  plan-1  H3    0.020
 IN4  plan-1  H5    0.020
 IN4  plan-2  C11   0.020
 IN4  plan-2  C12   0.020
 IN4  plan-2  C7    0.020
 IN4  plan-2  C13   0.020
 IN4  plan-2  C15   0.020
 IN4  plan-2  C16   0.020
 IN4  plan-2  C17   0.020
 IN4  plan-2  C19   0.020
 IN4  plan-2  H7    0.020
 IN4  plan-2  H13   0.020
 IN4  plan-2  H17   0.020
 IN4  plan-2  H19   0.020
 IN4  plan-3  C6    0.020
 IN4  plan-3  C20   0.020
 IN4  plan-3  N3    0.020
 IN4  plan-3  N4    0.020
 IN4  plan-3  HN3   0.020
 IN4  plan-3  HN41  0.020
 IN4  plan-3  HN42  0.020
 IN4  plan-4  C15   0.020
 IN4  plan-4  C16   0.020
 IN4  plan-4  N2    0.020
 IN4  plan-4  N1    0.020
 IN4  plan-4  HN2   0.020
 IN4  plan-4  HN11  0.020
 IN4  plan-4  HN12  0.020
 IN4  plan-5  C14   0.020
 IN4  plan-5  C22   0.020
 IN4  plan-5  O3    0.020
 IN4  plan-5  O4    0.020

