# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 20:10:14 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (2~{S})-~{N}-[[4-(aminomethyl)-2-(2-azanyl-2-oxidanylidene-ethoxy)phenyl]methyl]-2-(4-hydroxyphenyl)-2-methoxy-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H](C(=O)NCc1ccc(CN)cc1OCC(N)=O)c2ccc(O)cc2
#
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
 7YP  7YP  (2~{S})-~{N}-[[4-(aminomethyl)-2-(2-azanyl-2-oxidanylidene-ethoxy)phenyl]methyl]-2-(4-hydroxyphenyl)-2-methoxy-ethanamide  ligand  50  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7YP
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
 7YP  C5   C  CH2   0  -0.327   5.1050   0.3234  -1.6509
 7YP  C6   C  CH1   0  -0.110  -2.5525  -1.7030  -0.3166
 7YP  C7   C  C     0   0.489  -0.1645   2.3306   1.8292
 7YP  C10  C  CH2   0  -0.334   0.8306  -2.2953   1.3000
 7YP  C15  C  CR6   0   0.085   4.0372  -0.3818  -0.8506
 7YP  C17  C  CR16  0  -0.288  -1.6662   0.1246  -1.8007
 7YP  C20  C  CR6   0   0.328  -2.1563   2.4427  -1.3986
 7YP  C21  C  CR16  0  -0.323   4.0580  -1.7508  -0.6378
 7YP  C22  C  CR16  0  -0.308  -2.9522   2.0718  -0.3167
 7YP  C1   C  C     0   0.527  -1.5686  -1.9214   0.8449
 7YP  C2   C  CR6   0   0.403   1.9682  -0.2303   0.3989
 7YP  C3   C  CR6   0  -0.048   1.9745  -1.6207   0.5972
 7YP  N4   N  NH1   0  -0.616  -0.3432  -2.2922   0.4494
 7YP  O8   O  O2    0  -0.449   0.9387   0.4278   0.9633
 7YP  C9   C  CR6   0   0.086  -2.4489  -0.2554  -0.7197
 7YP  C11  C  CR16  0  -0.427   2.9865   0.3744  -0.3259
 7YP  O12  O  O     0  -0.481  -1.8930  -1.7246   2.0024
 7YP  O13  O  O     0  -0.464  -0.4395   1.7138   2.8401
 7YP  C14  C  CR16  0  -0.267   3.0270  -2.3530   0.0774
 7YP  C16  C  CR16  0  -0.263  -3.0861   0.7377   0.0206
 7YP  C18  C  CH2   0  -0.287   0.8458   1.8161   0.8157
 7YP  N19  N  NH2   0  -0.804  -0.6332   3.5556   1.5418
 7YP  C23  C  CR16  0  -0.365  -1.5143   1.4606  -2.1451
 7YP  O24  O  O2    0  -0.477  -3.8638  -1.9851   0.0623
 7YP  O25  O  OH1   0  -0.637  -2.0328   3.7604  -1.6650
 7YP  N27  N  NH2   0  -0.798   6.2940  -0.4852  -1.8342
 7YP  H1   H  HCH2  0   0.245   4.6953   0.5502  -2.6397
 7YP  H2   H  HCH2  0   0.216   5.2993   1.2985  -1.1830
 7YP  H3   H  HCH1  0   0.245  -2.2525  -2.3331  -1.1696
 7YP  H4   H  HCH2  0   0.256   1.1136  -3.3198   1.5535
 7YP  H5   H  HCH2  0   0.263   0.5725  -1.7908   2.2301
 7YP  H6   H  HCR6  0   0.250  -1.1555  -0.6269  -2.3917
 7YP  H7   H  HCR6  0   0.245   4.8679  -2.3475  -1.0340
 7YP  H8   H  HCR6  0   0.260  -3.4512   2.8338   0.2681
 7YP  H9   H  HCH3  0   0.241  -5.1672  -3.4630   0.5206
 7YP  H10  H  HCH3  0   0.209  -3.9107  -3.9462  -0.6321
 7YP  H11  H  HCH3  0   0.214  -3.5223  -3.7742   1.0901
 7YP  H12  H  HNH1  0   0.391  -0.1885  -2.4653  -0.5311
 7YP  H13  H  HCR6  0   0.270   2.9861   1.4439  -0.4989
 7YP  H14  H  HCR6  0   0.249   3.0419  -3.4260   0.2319
 7YP  H15  H  HCR6  0   0.249  -3.6907   0.4742   0.8779
 7YP  H16  H  HCH2  0   0.248   0.5575   2.0881  -0.2060
 7YP  H17  H  HCH2  0   0.263   1.7985   2.3159   1.0327
 7YP  H18  H  HNH2  0   0.405  -0.5248   3.9592   0.6268
 7YP  H19  H  HNH2  0   0.403  -1.3287   3.9745   2.1375
 7YP  H20  H  HCR6  0   0.271  -0.8966   1.7303  -2.9944
 7YP  H21  H  HOH1  0   0.474  -1.4562   3.8966  -2.4250
 7YP  H22  H  HNH2  0   0.357   6.9202  -0.0180  -2.4764
 7YP  H23  H  HNH2  0   0.345   6.7959  -0.5579  -0.9579
 7YP  C26  C  CH3   0  -0.413  -4.1130  -3.3567   0.2692

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
 7YP  C26  O24  single    1.409  0.020  1.409
 7YP  O24  C6   single    1.394  0.020  1.394
 7YP  C6   C1   single    1.538  0.020  1.538
 7YP  C6   C9   single    1.506  0.020  1.506
 7YP  C16  C9   aromatic  1.393  0.020  1.393
 7YP  C16  C22  aromatic  1.383  0.020  1.383
 7YP  C1   N4   single    1.340  0.020  1.340
 7YP  C1   O12  double    1.218  0.020  1.218
 7YP  N4   C10  single    1.450  0.020  1.450
 7YP  C9   C17  aromatic  1.388  0.020  1.388
 7YP  C10  C3   single    1.502  0.020  1.502
 7YP  C22  C20  aromatic  1.393  0.020  1.393
 7YP  C14  C3   aromatic  1.384  0.020  1.384
 7YP  C14  C21  aromatic  1.392  0.020  1.392
 7YP  C3   C2   aromatic  1.405  0.020  1.405
 7YP  C17  C23  aromatic  1.388  0.020  1.388
 7YP  C20  C23  aromatic  1.391  0.020  1.391
 7YP  C20  O25  single    1.350  0.020  1.350
 7YP  C21  C15  aromatic  1.386  0.020  1.386
 7YP  C2   O8   single    1.346  0.020  1.346
 7YP  C2   C11  aromatic  1.389  0.020  1.389
 7YP  O8   C18  single    1.399  0.020  1.399
 7YP  N19  C7   single    1.343  0.020  1.343
 7YP  C15  C11  aromatic  1.397  0.020  1.397
 7YP  C15  C5   single    1.509  0.020  1.509
 7YP  C7   C18  single    1.521  0.020  1.521
 7YP  C7   O13  double    1.216  0.020  1.216
 7YP  N27  C5   single    1.450  0.020  1.450
 7YP  C5   H1   single    0.970  0.020  1.090
 7YP  C5   H2   single    0.970  0.020  1.090
 7YP  C6   H3   single    0.970  0.020  1.090
 7YP  C10  H4   single    0.970  0.020  1.090
 7YP  C10  H5   single    0.970  0.020  1.090
 7YP  C17  H6   single    0.930  0.020  1.080
 7YP  C21  H7   single    0.930  0.020  1.080
 7YP  C22  H8   single    0.930  0.020  1.080
 7YP  C26  H9   single    0.970  0.020  1.090
 7YP  C26  H10  single    0.970  0.020  1.090
 7YP  C26  H11  single    0.970  0.020  1.090
 7YP  N4   H12  single    0.860  0.020  1.020
 7YP  C11  H13  single    0.930  0.020  1.080
 7YP  C14  H14  single    0.930  0.020  1.080
 7YP  C16  H15  single    0.930  0.020  1.080
 7YP  C18  H16  single    0.970  0.020  1.090
 7YP  C18  H17  single    0.970  0.020  1.090
 7YP  N19  H18  single    0.860  0.020  1.020
 7YP  N19  H19  single    0.860  0.020  1.020
 7YP  C23  H20  single    0.930  0.020  1.080
 7YP  O25  H21  single    0.850  0.020  0.980
 7YP  N27  H22  single    0.890  0.020  1.040
 7YP  N27  H23  single    0.890  0.020  1.040

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
 7YP  H2   C5   H1   105.49  3.000
 7YP  H2   C5   N27  113.81  3.000
 7YP  H1   C5   N27  107.97  3.000
 7YP  H2   C5   C15  108.30  3.000
 7YP  H1   C5   C15  108.13  3.000
 7YP  N27  C5   C15  112.75  3.000
 7YP  H3   C6   O24  110.53  3.000
 7YP  H3   C6   C9   108.88  3.000
 7YP  O24  C6   C9   109.39  3.000
 7YP  H3   C6   C1   109.22  3.000
 7YP  C9   C6   C1   107.14  3.000
 7YP  O24  C6   C1   111.59  3.000
 7YP  N19  C7   C18  113.45  3.000
 7YP  C18  C7   O13  122.19  3.000
 7YP  N19  C7   O13  124.19  3.000
 7YP  H5   C10  H4   107.31  3.000
 7YP  H5   C10  N4   107.95  3.000
 7YP  H4   C10  N4   110.35  3.000
 7YP  H5   C10  C3   111.84  3.000
 7YP  H4   C10  C3   109.41  3.000
 7YP  N4   C10  C3   109.94  3.000
 7YP  C11  C15  C21  119.25  3.000
 7YP  C11  C15  C5   118.58  3.000
 7YP  C21  C15  C5   122.17  3.000
 7YP  H6   C17  C23  118.72  3.000
 7YP  H6   C17  C9   120.04  3.000
 7YP  C23  C17  C9   121.24  3.000
 7YP  O25  C20  C23  122.76  3.000
 7YP  O25  C20  C22  117.73  3.000
 7YP  C23  C20  C22  119.51  3.000
 7YP  H7   C21  C14  120.30  3.000
 7YP  H7   C21  C15  120.02  3.000
 7YP  C14  C21  C15  119.68  3.000
 7YP  H8   C22  C16  120.19  3.000
 7YP  H8   C22  C20  119.70  3.000
 7YP  C16  C22  C20  120.11  3.000
 7YP  O12  C1   N4   124.66  3.000
 7YP  O12  C1   C6   121.62  3.000
 7YP  N4   C1   C6   113.67  3.000
 7YP  C11  C2   O8   124.53  3.000
 7YP  C11  C2   C3   120.10  3.000
 7YP  O8   C2   C3   115.36  3.000
 7YP  C14  C3   C2   118.31  3.000
 7YP  C2   C3   C10  120.47  3.000
 7YP  C14  C3   C10  121.15  3.000
 7YP  H12  N4   C1   118.37  3.000
 7YP  H12  N4   C10  116.51  3.000
 7YP  C1   N4   C10  124.61  3.000
 7YP  C18  O8   C2   119.45  3.000
 7YP  C16  C9   C17  118.47  3.000
 7YP  C17  C9   C6   120.69  3.000
 7YP  C16  C9   C6   120.77  3.000
 7YP  H13  C11  C2   120.86  3.000
 7YP  H13  C11  C15  118.34  3.000
 7YP  C2   C11  C15  120.79  3.000
 7YP  H14  C14  C3   118.73  3.000
 7YP  H14  C14  C21  119.42  3.000
 7YP  C3   C14  C21  121.85  3.000
 7YP  H15  C16  C9   120.21  3.000
 7YP  H15  C16  C22  118.86  3.000
 7YP  C9   C16  C22  120.93  3.000
 7YP  H17  C18  H16  107.44  3.000
 7YP  H17  C18  O8   111.92  3.000
 7YP  H16  C18  O8   111.22  3.000
 7YP  H17  C18  C7   106.91  3.000
 7YP  H16  C18  C7   111.26  3.000
 7YP  O8   C18  C7   108.03  3.000
 7YP  H19  N19  H18  116.46  3.000
 7YP  H19  N19  C7   119.60  3.000
 7YP  H18  N19  C7   121.54  3.000
 7YP  H20  C23  C20  120.51  3.000
 7YP  H20  C23  C17  119.75  3.000
 7YP  C20  C23  C17  119.74  3.000
 7YP  C26  O24  C6   113.78  3.000
 7YP  H21  O25  C20  110.38  3.000
 7YP  H23  N27  H22  106.01  3.000
 7YP  H23  N27  C5   109.71  3.000
 7YP  H22  N27  C5   109.30  3.000
 7YP  H11  C26  H10  108.18  3.000
 7YP  H11  C26  H9   108.20  3.000
 7YP  H10  C26  H9   108.43  3.000
 7YP  H11  C26  O24  112.71  3.000
 7YP  H10  C26  O24  111.72  3.000
 7YP  H9   C26  O24  107.46  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
 7YP  CONST_01  C3   C14  C21  C15     0.00   0.0  0
 7YP  CONST_02  C3   C2   C11  C15     0.00   0.0  0
 7YP  CONST_03  C22  C16  C9   C17     0.00   0.0  0
 7YP  CONST_04  C22  C20  C23  C17     0.00   0.0  0
 7YP  CONST_05  C9   C16  C22  C20     0.00   0.0  0
 7YP  CONST_06  C9   C17  C23  C20     0.00   0.0  0
 7YP  CONST_07  C2   C3   C14  C21     0.00   0.0  0
 7YP  CONST_08  C2   C11  C15  C21     0.00   0.0  0
 7YP  CONST_09  C14  C3   C2   C11     0.00   0.0  0
 7YP  CONST_10  C14  C21  C15  C11     0.00   0.0  0
 7YP  CONST_11  C23  C17  C9   C16     0.00   0.0  0
 7YP  CONST_12  C23  C20  C22  C16     0.00   0.0  0
 7YP  CONST_13  C14  C21  C15  C5    180.00   0.0  0
 7YP  CONST_14  C2   C11  C15  C5    180.00   0.0  0
 7YP  CONST_15  C22  C16  C9   C6    180.00   0.0  0
 7YP  CONST_16  C23  C17  C9   C6    180.00   0.0  0
 7YP  CONST_17  C21  C14  C3   C10   180.00   0.0  0
 7YP  CONST_18  C11  C2   C3   C10   180.00   0.0  0
 7YP  CONST_19  O8   C2   C11  C15   180.00   0.0  0
 7YP  CONST_20  O25  C20  C23  C17   180.00   0.0  0
 7YP  CONST_21  C14  C3   C2   O8    180.00   0.0  0
 7YP  CONST_22  O25  C20  C22  C16   180.00   0.0  0
 7YP  CONST_23  H14  C14  C21  C15   180.00   0.0  0
 7YP  CONST_24  H15  C16  C9   C17   180.00   0.0  0
 7YP  CONST_25  H6   C17  C23  C20   180.00   0.0  0
 7YP  CONST_26  H13  C11  C15  C21   180.00   0.0  0
 7YP  CONST_27  H20  C23  C20  C22   180.00   0.0  0
 7YP  CONST_28  H7   C21  C14  C3    180.00   0.0  0
 7YP  CONST_29  H8   C22  C16  C9    180.00   0.0  0
 7YP  CONST_30  C10  N4   C1   C6    180.00   0.0  0
 7YP  CONST_31  O12  C1   N4   C10     0.00   0.0  0
 7YP  CONST_32  H12  N4   C1   C6      0.00   0.0  0
 7YP  CONST_33  H18  N19  C7   O13   180.00   0.0  0
 7YP  CONST_34  H19  N19  C7   O13     0.00   0.0  0
 7YP  Var_01    N27  C5   C15  C21   -16.10  30.0  2
 7YP  Var_02    N4   C10  C3   C2     71.17  30.0  2
 7YP  Var_03    C3   C10  N4   C1   -131.86  30.0  3
 7YP  Var_04    H22  N27  C5   C15   172.42  30.0  3
 7YP  Var_05    H16  C18  O8   C2     72.33  30.0  3
 7YP  Var_06    N19  C7   C18  O8   -161.60  30.0  1
 7YP  Var_07    H9   C26  O24  C6   -177.83  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
 7YP  chir_01  C6  O24  C1  C9  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
 7YP  plan-1  C5   0.020
 7YP  plan-1  C10  0.020
 7YP  plan-1  C15  0.020
 7YP  plan-1  C21  0.020
 7YP  plan-1  C2   0.020
 7YP  plan-1  C3   0.020
 7YP  plan-1  O8   0.020
 7YP  plan-1  C11  0.020
 7YP  plan-1  C14  0.020
 7YP  plan-1  H7   0.020
 7YP  plan-1  H13  0.020
 7YP  plan-1  H14  0.020
 7YP  plan-2  C6   0.020
 7YP  plan-2  C17  0.020
 7YP  plan-2  C20  0.020
 7YP  plan-2  C22  0.020
 7YP  plan-2  C9   0.020
 7YP  plan-2  C16  0.020
 7YP  plan-2  C23  0.020
 7YP  plan-2  O25  0.020
 7YP  plan-2  H6   0.020
 7YP  plan-2  H8   0.020
 7YP  plan-2  H15  0.020
 7YP  plan-2  H20  0.020
 7YP  plan-3  C7   0.020
 7YP  plan-3  O13  0.020
 7YP  plan-3  C18  0.020
 7YP  plan-3  N19  0.020
 7YP  plan-3  H18  0.020
 7YP  plan-3  H19  0.020
 7YP  plan-4  C6   0.020
 7YP  plan-4  C10  0.020
 7YP  plan-4  C1   0.020
 7YP  plan-4  N4   0.020
 7YP  plan-4  O12  0.020
 7YP  plan-4  H12  0.020

