# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 19:45:52 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: N-[(1S)-1-carboxy-3-methylbutyl]-3-(3,5-dichlorobenzyl)-L-histidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N[C@@H](Cc1cncn1Cc2cc(Cl)cc(Cl)c2)C(O)=O)C(O)=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
 XX5  XX5  N-[(1S)-1-carboxy-3-methylbutyl]-3-(3,5-dichlorobenzyl)-L-histidine  ligand  51  28  .  2022-07-22  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XX5
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
 XX5  O1    O   O     0  -0.433   4.4656  -0.4167   3.4295
 XX5  C2    C   C     0   0.540   4.1431  -1.3165   4.1650
 XX5  O3    O   OH1   0  -0.590   5.0017  -1.9889   4.9209
 XX5  C4    C   CH1   0  -0.214   2.7166  -1.8418   4.3049
 XX5  C5    C   CH2   0  -0.444   2.5928  -3.1146   3.4532
 XX5  C6    C   CH1   0  -0.217   1.3270  -3.9580   3.6565
 XX5  C7    C   CH3   0  -0.677   1.1145  -4.3346   5.1191
 XX5  C8    C   CH3   0  -0.654   0.0594  -3.3464   3.0678
 XX5  N9    N   NH1   0  -0.573   1.7244  -0.8691   3.9324
 XX5  C10   C   CH1   0  -0.156   1.6323   0.2979   4.7686
 XX5  C11   C   C     0   0.550   0.9745  -0.0500   6.0956
 XX5  O12   O   OH1   0  -0.583   1.5476   0.5904   7.1054
 XX5  O13   O   O     0  -0.424   0.0269  -0.7814   6.2182
 XX5  C14   C   CH2   0  -0.568   0.7432   1.3396   4.0645
 XX5  C15   C   CR5   0   0.301   0.4533   2.5538   4.8710
 XX5  C16   C   CR15  0  -0.254  -0.6985   2.9405   5.4974
 XX5  N17   N   N     0  -0.449  -0.5195   4.1210   6.1595
 XX5  C18   C   CR15  0   0.085   0.7243   4.4505   5.9397
 XX5  N19   N   NR5   0  -0.451   1.3624   3.5403   5.1686
 XX5  C20   C   CH2   0  -0.397   2.7334   3.6380   4.7202
 XX5  C21   C   CR6   0   0.086   2.8457   3.8106   3.2267
 XX5  C22   C   CR16  0  -0.229   2.1278   4.8147   2.5864
 XX5  C23   C   CR6   0  -0.029   2.2545   4.9672   1.2175
 XX5  CL24  CL  CL    0  -0.109   1.3679   6.2184   0.4181
 XX5  C25   C   CR16  0  -0.182   3.0794   4.1458   0.4627
 XX5  C26   C   CR16  0  -0.257   3.6733   2.9712   2.4941
 XX5  C27   C   CR6   0  -0.034   3.7811   3.1525   1.1232
 XX5  CL28  CL  CL    0  -0.108   4.8083   2.1036   0.2104
 XX5  HC4   H   HCH1  0   0.275   2.5682  -2.1165   5.3542
 XX5  HC51  H   HCH2  0   0.238   2.6819  -2.8386   2.3971
 XX5  HC52  H   HCH2  0   0.248   3.4519  -3.7551   3.6685
 XX5  HC6   H   HCH1  0   0.222   1.5250  -4.8852   3.1065
 XX5  HC71  H   HCH3  0   0.223   2.0244  -4.7315   5.5741
 XX5  HC72  H   HCH3  0   0.224   0.7907  -3.4743   5.7081
 XX5  HC73  H   HCH3  0   0.231   0.3400  -5.0977   5.2123
 XX5  HC81  H   HCH3  0   0.237  -0.2476  -2.4648   3.6272
 XX5  HC82  H   HCH3  0   0.213   0.2030  -3.0485   2.0272
 XX5  HC83  H   HCH3  0   0.213  -0.7567  -4.0717   3.0912
 XX5  HN9   H   HNH1  0   0.357   1.8328  -0.6033   2.9617
 XX5  H10   H   HCH1  0   0.241   2.6080   0.7557   4.9851
 XX5  H12   H   HOH1  0   0.481   1.0672   0.4133   7.9287
 XX5  H141  H   HCH2  0   0.279   1.2215   1.6023   3.1170
 XX5  H142  H   HCH2  0   0.286  -0.2051   0.8612   3.8129
 XX5  H16   H   HCR5  0   0.256  -1.6441   2.4182   5.4991
 XX5  H18   H   HCR5  0   0.285   1.2261   5.3335   6.3076
 XX5  H201  H   HCH2  0   0.288   3.2937   2.7598   5.0411
 XX5  H202  H   HCH2  0   0.309   3.1806   4.4934   5.2288
 XX5  H22   H   HCR6  0   0.284   1.4774   5.4729   3.1488
 XX5  H25   H   HCR6  0   0.304   3.1705   4.2809  -0.6062
 XX5  H26   H   HCR6  0   0.293   4.2216   2.1756   2.9817
 XX5  HO1   H   HOH1  0   0.481   5.9044  -1.6684   4.7721

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
 XX5  O1   C2    double    1.206  0.020  1.206
 XX5  C2   O3    single    1.327  0.020  1.327
 XX5  C2   C4    single    1.527  0.020  1.527
 XX5  C4   C5    single    1.536  0.020  1.536
 XX5  C4   N9    single    1.439  0.020  1.439
 XX5  C4   HC4   single    0.970  0.020  1.090
 XX5  C5   C6    single    1.535  0.020  1.535
 XX5  C5   HC51  single    0.970  0.020  1.090
 XX5  C5   HC52  single    0.970  0.020  1.090
 XX5  C6   C7    single    1.525  0.020  1.525
 XX5  C6   C8    single    1.526  0.020  1.526
 XX5  C6   HC6   single    0.970  0.020  1.090
 XX5  C7   HC71  single    0.970  0.020  1.090
 XX5  C7   HC72  single    0.970  0.020  1.090
 XX5  C7   HC73  single    0.970  0.020  1.090
 XX5  C8   HC81  single    0.970  0.020  1.090
 XX5  C8   HC82  single    0.970  0.020  1.090
 XX5  C8   HC83  single    0.970  0.020  1.090
 XX5  N9   C10   single    1.439  0.020  1.439
 XX5  N9   HN9   single    0.890  0.020  1.040
 XX5  C10  C11   single    1.521  0.020  1.521
 XX5  C10  C14   single    1.540  0.020  1.540
 XX5  C10  H10   single    0.970  0.020  1.090
 XX5  C11  O12   single    1.326  0.020  1.326
 XX5  C11  O13   double    1.203  0.020  1.203
 XX5  O12  H12   single    0.850  0.020  0.980
 XX5  C14  C15   single    1.486  0.020  1.486
 XX5  C14  H141  single    0.970  0.020  1.090
 XX5  C14  H142  single    0.970  0.020  1.090
 XX5  C15  C16   aromatic  1.367  0.020  1.367
 XX5  C15  N19   aromatic  1.374  0.020  1.374
 XX5  C16  N17   aromatic  1.365  0.020  1.365
 XX5  C16  H16   single    0.930  0.020  1.080
 XX5  N17  C18   aromatic  1.305  0.020  1.305
 XX5  C18  N19   aromatic  1.353  0.020  1.353
 XX5  C18  H18   single    0.930  0.020  1.080
 XX5  N19  C20   single    1.446  0.020  1.446
 XX5  C20  C21   single    1.508  0.020  1.508
 XX5  C20  H201  single    0.970  0.020  1.090
 XX5  C20  H202  single    0.970  0.020  1.090
 XX5  C21  C22   aromatic  1.391  0.020  1.391
 XX5  C21  C26   aromatic  1.388  0.020  1.388
 XX5  C22  C23   aromatic  1.383  0.020  1.383
 XX5  C22  H22   single    0.930  0.020  1.080
 XX5  C23  CL24  single    1.729  0.020  1.729
 XX5  C23  C25   aromatic  1.387  0.020  1.387
 XX5  C25  C27   aromatic  1.384  0.020  1.384
 XX5  C25  H25   single    0.930  0.020  1.080
 XX5  C26  C27   aromatic  1.387  0.020  1.387
 XX5  C26  H26   single    0.930  0.020  1.080
 XX5  C27  CL28  single    1.729  0.020  1.729
 XX5  HO1  O3    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
 XX5  C4    C2   O3    112.21  3.000
 XX5  C4    C2   O1    124.23  3.000
 XX5  O3    C2   O1    123.53  3.000
 XX5  HO1   O3   C2    110.34  3.000
 XX5  HC4   C4   N9    108.93  3.000
 XX5  HC4   C4   C5    108.21  3.000
 XX5  N9    C4   C5    111.16  3.000
 XX5  HC4   C4   C2    107.51  3.000
 XX5  N9    C4   C2    112.84  3.000
 XX5  C5    C4   C2    108.03  3.000
 XX5  HC52  C5   HC51  105.88  3.000
 XX5  HC52  C5   C6    107.47  3.000
 XX5  HC51  C5   C6    109.47  3.000
 XX5  HC52  C5   C4    108.24  3.000
 XX5  HC51  C5   C4    108.61  3.000
 XX5  C6    C5   C4    116.64  3.000
 XX5  HC6   C6   C8    107.19  3.000
 XX5  HC6   C6   C7    107.31  3.000
 XX5  C8    C6   C7    110.68  3.000
 XX5  HC6   C6   C5    104.45  3.000
 XX5  C8    C6   C5    114.45  3.000
 XX5  C7    C6   C5    112.19  3.000
 XX5  HC73  C7   HC72  107.12  3.000
 XX5  HC73  C7   HC71  107.55  3.000
 XX5  HC72  C7   HC71  107.98  3.000
 XX5  HC73  C7   C6    110.70  3.000
 XX5  HC72  C7   C6    111.36  3.000
 XX5  HC71  C7   C6    111.91  3.000
 XX5  HC83  C8   HC82  107.45  3.000
 XX5  HC83  C8   HC81  108.43  3.000
 XX5  HC82  C8   HC81  107.82  3.000
 XX5  HC83  C8   C6    110.27  3.000
 XX5  HC82  C8   C6    111.58  3.000
 XX5  HC81  C8   C6    111.15  3.000
 XX5  HN9   N9   C10   110.56  3.000
 XX5  HN9   N9   C4    110.61  3.000
 XX5  C10   N9   C4    116.24  3.000
 XX5  H10   C10  C14   108.71  3.000
 XX5  H10   C10  C11   107.89  3.000
 XX5  C14   C10  C11   107.69  3.000
 XX5  H10   C10  N9    113.29  3.000
 XX5  C14   C10  N9    108.66  3.000
 XX5  C11   C10  N9    110.44  3.000
 XX5  O13   C11  O12   123.81  3.000
 XX5  O13   C11  C10   124.63  3.000
 XX5  O12   C11  C10   111.53  3.000
 XX5  H12   O12  C11   110.14  3.000
 XX5  H142  C14  H141  106.59  3.000
 XX5  H142  C14  C15   108.28  3.000
 XX5  H141  C14  C15   111.06  3.000
 XX5  H142  C14  C10   108.09  3.000
 XX5  H141  C14  C10   107.83  3.000
 XX5  C15   C14  C10   114.66  3.000
 XX5  N19   C15  C16   104.78  3.000
 XX5  N19   C15  C14   125.10  3.000
 XX5  C16   C15  C14   130.10  3.000
 XX5  H16   C16  N17   122.14  3.000
 XX5  H16   C16  C15   126.98  3.000
 XX5  N17   C16  C15   110.88  3.000
 XX5  C18   N17  C16   105.15  3.000
 XX5  H18   C18  N19   121.66  3.000
 XX5  H18   C18  N17   126.27  3.000
 XX5  N19   C18  N17   112.07  3.000
 XX5  C20   N19  C18   125.35  3.000
 XX5  C20   N19  C15   127.50  3.000
 XX5  C18   N19  C15   107.12  3.000
 XX5  H202  C20  H201  106.48  3.000
 XX5  H202  C20  C21   109.97  3.000
 XX5  H201  C20  C21   110.22  3.000
 XX5  H202  C20  N19   107.28  3.000
 XX5  H201  C20  N19   109.98  3.000
 XX5  C21   C20  N19   112.68  3.000
 XX5  C26   C21  C22   120.10  3.000
 XX5  C26   C21  C20   119.87  3.000
 XX5  C22   C21  C20   120.03  3.000
 XX5  H22   C22  C23   120.14  3.000
 XX5  H22   C22  C21   120.65  3.000
 XX5  C23   C22  C21   119.21  3.000
 XX5  C25   C23  CL24  118.80  3.000
 XX5  C25   C23  C22   121.84  3.000
 XX5  CL24  C23  C22   119.36  3.000
 XX5  H25   C25  C27   121.25  3.000
 XX5  H25   C25  C23   120.92  3.000
 XX5  C27   C25  C23   117.82  3.000
 XX5  H26   C26  C27   120.14  3.000
 XX5  H26   C26  C21   120.59  3.000
 XX5  C27   C26  C21   119.27  3.000
 XX5  CL28  C27  C26   119.26  3.000
 XX5  CL28  C27  C25   118.99  3.000
 XX5  C26   C27  C25   121.75  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
 XX5  CONST_01  C18   N17  C16  C15      0.00   0.0  0
 XX5  CONST_02  N17   C18  N19  C15      0.00   0.0  0
 XX5  CONST_03  C18   N19  C15  C16      0.00   0.0  0
 XX5  CONST_04  N19   C18  N17  C16      0.00   0.0  0
 XX5  CONST_05  N19   C15  C16  N17      0.00   0.0  0
 XX5  CONST_06  C25   C23  C22  C21      0.00   0.0  0
 XX5  CONST_07  C25   C27  C26  C21      0.00   0.0  0
 XX5  CONST_08  C27   C26  C21  C22      0.00   0.0  0
 XX5  CONST_09  C27   C25  C23  C22      0.00   0.0  0
 XX5  CONST_10  C26   C21  C22  C23      0.00   0.0  0
 XX5  CONST_11  C26   C27  C25  C23      0.00   0.0  0
 XX5  CONST_12  N17   C16  C15  C14    180.00   0.0  0
 XX5  CONST_13  C18   N19  C15  C14    180.00   0.0  0
 XX5  CONST_14  C20   N19  C15  C16    180.00   0.0  0
 XX5  CONST_15  C20   N19  C18  N17    180.00   0.0  0
 XX5  CONST_16  C23   C22  C21  C20    180.00   0.0  0
 XX5  CONST_17  C27   C26  C21  C20    180.00   0.0  0
 XX5  CONST_18  CL24  C23  C22  C21    180.00   0.0  0
 XX5  CONST_19  CL28  C27  C26  C21    180.00   0.0  0
 XX5  CONST_20  CL28  C27  C25  C23    180.00   0.0  0
 XX5  CONST_21  C27   C25  C23  CL24   180.00   0.0  0
 XX5  CONST_22  H18   C18  N19  C15    180.00   0.0  0
 XX5  CONST_23  H16   C16  N17  C18    180.00   0.0  0
 XX5  CONST_24  H26   C26  C21  C22    180.00   0.0  0
 XX5  CONST_25  H25   C25  C23  C22    180.00   0.0  0
 XX5  CONST_26  H22   C22  C23  C25    180.00   0.0  0
 XX5  CONST_27  HO1   O3   C2   O1       0.00   0.0  0
 XX5  CONST_28  H12   O12  C11  C10    180.00   0.0  0
 XX5  Var_01    C21   C20  N19  C15     64.27  30.0  2
 XX5  Var_02    C22   C21  C20  N19     52.08  30.0  2
 XX5  Var_03    C16   C15  C14  C10   -106.69  30.0  2
 XX5  Var_04    C7    C6   C5   C4     -54.12  30.0  3
 XX5  Var_05    HC71  C7   C6   C5     -48.14  30.0  3
 XX5  Var_06    HC81  C8   C6   C5     -69.75  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
 XX5  chir_01  C4   C2  C5   N9   positiv
 XX5  chir_02  C10  N9  C11  C14  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
 XX5  plan-1  C14   0.020
 XX5  plan-1  C15   0.020
 XX5  plan-1  C16   0.020
 XX5  plan-1  N17   0.020
 XX5  plan-1  C18   0.020
 XX5  plan-1  N19   0.020
 XX5  plan-1  C20   0.020
 XX5  plan-1  H16   0.020
 XX5  plan-1  H18   0.020
 XX5  plan-2  C20   0.020
 XX5  plan-2  C21   0.020
 XX5  plan-2  C22   0.020
 XX5  plan-2  C23   0.020
 XX5  plan-2  CL24  0.020
 XX5  plan-2  C25   0.020
 XX5  plan-2  C26   0.020
 XX5  plan-2  C27   0.020
 XX5  plan-2  CL28  0.020
 XX5  plan-2  H22   0.020
 XX5  plan-2  H25   0.020
 XX5  plan-2  H26   0.020
 XX5  plan-3  O1    0.020
 XX5  plan-3  C2    0.020
 XX5  plan-3  O3    0.020
 XX5  plan-3  C4    0.020
 XX5  plan-3  HO1   0.020
 XX5  plan-4  C10   0.020
 XX5  plan-4  C11   0.020
 XX5  plan-4  O12   0.020
 XX5  plan-4  O13   0.020
 XX5  plan-4  H12   0.020

