# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 00:58:21 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: 7-(3-cyano-4-hydroxyphenyl)-N-[2-(morpholin-4-yl)ethyl]dibenzo[b,f]oxepine-10-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1C#N)c2ccc3c(Oc4ccccc4C=C3C(=O)NCCN5CCOCC5)c2
#
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
 M3D  M3D  7-(3-cyano-4-hydroxyphenyl)-N-[2-(morpholin-4-yl)ethyl]dibenzo[b,f]oxepine-10-carboxamide  ligand  60  35  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_M3D
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
 M3D  C1   C  C1    0  -0.279   0.0709   3.8028   0.4814
 M3D  C2   C  C     0  -0.016   0.5331   2.5448   0.3756
 M3D  C3   C  CR6   0   0.289  -2.2209   3.5894  -0.4785
 M3D  O1   O  O2    0  -0.531  -1.7905   2.5505  -1.2689
 M3D  O2   O  O     0  -0.488   2.7126   3.1357   1.1529
 M3D  O3   O  OH1   0  -0.598  -5.5523  -5.2626  -0.3459
 M3D  C11  C  CR16  0  -0.381  -2.3448   0.3290  -0.6706
 M3D  C12  C  CR6   0   0.099  -2.0675  -0.8593   0.0013
 M3D  C13  C  CR16  0  -0.302  -0.9173  -0.9164   0.7904
 M3D  C14  C  CR16  0  -0.299  -0.0743   0.1734   0.8944
 M3D  C15  C  C     0   0.502   2.0206   2.3660   0.4999
 M3D  C16  C  CR6   0   0.084  -2.9763  -2.0148  -0.1089
 M3D  C17  C  CR16  0  -0.279  -3.6842  -2.2757  -1.2871
 M3D  C18  C  CR16  0  -0.360  -4.5482  -3.3479  -1.3997
 M3D  C19  C  CR6   0   0.372  -4.7360  -4.2095  -0.3231
 M3D  C20  C  CR6   0  -0.072  -4.0302  -3.9645   0.8616
 M3D  C21  C  CR16  0  -0.301  -3.1633  -2.8783   0.9616
 M3D  C22  C  CH2   0  -0.258   3.9430   1.0150  -0.1978
 M3D  C23  C  CH2   0  -0.300   4.1414  -0.4472  -0.5748
 M3D  C24  C  CH2   0  -0.305   5.7993  -1.9858  -1.3886
 M3D  C25  C  CH2   0  -0.188   7.2839  -2.2963  -1.4014
 M3D  C26  C  CH2   0  -0.185   7.5374  -1.3673   0.7106
 M3D  C27  C  CH2   0  -0.311   6.0596  -1.0296   0.7696
 M3D  C28  C  CSP   0   0.068  -4.2171  -4.8319   1.9741
 M3D  C10  C  CR6   0   0.318  -1.4897   1.4113  -0.5639
 M3D  C4   C  CR6   0   0.087  -1.3131   4.2351   0.3633
 M3D  C5   C  CR16  0  -0.318  -1.7591   5.3567   1.0683
 M3D  C6   C  CR16  0  -0.245  -3.0697   5.7909   0.9661
 M3D  C7   C  CR16  0  -0.260  -3.9582   5.1179   0.1358
 M3D  C8   C  CR16  0  -0.312  -3.5340   4.0140  -0.5902
 M3D  C9   C  CR6   0  -0.018  -0.3359   1.3696   0.2180
 M3D  N1   N  NH1   0  -0.644   2.5318   1.3303  -0.1826
 M3D  N2   N  NT    0  -0.431   5.5423  -0.8130  -0.5707
 M3D  N3   N  NS    0  -0.251  -4.3594  -5.5296   2.8804
 M3D  O4   O  O2    0  -0.485   7.7827  -2.4966  -0.0971
 M3D  H1   H  H     0   0.275   0.7873   4.5856   0.7060
 M3D  H2   H  HOH1  0   0.491  -6.0082  -5.3315  -1.1937
 M3D  H3   H  HCR6  0   0.268  -3.2359   0.4292  -1.2779
 M3D  H4   H  HCR6  0   0.263  -0.6615  -1.8258   1.3183
 M3D  H5   H  HCR6  0   0.270   0.8018   0.0948   1.5242
 M3D  H6   H  HCR6  0   0.276  -3.5469  -1.6380  -2.1509
 M3D  H7   H  HCR6  0   0.293  -5.0739  -3.5214  -2.3309
 M3D  H8   H  HCR6  0   0.284  -2.6532  -2.7090   1.9007
 M3D  H9   H  HCH2  0   0.243   4.3499   1.2239   0.7912
 M3D  H10  H  HCH2  0   0.239   4.4800   1.6483  -0.9100
 M3D  H11  H  HCH2  0   0.208   3.5426  -1.0883   0.0934
 M3D  H12  H  HCH2  0   0.246   3.7556  -0.6010  -1.5864
 M3D  H14  H  HCH2  0   0.199   5.2423  -2.8680  -1.0290
 M3D  H15  H  HCH2  0   0.237   7.4718  -3.2093  -1.9684
 M3D  H16  H  HCH2  0   0.200   7.8226  -1.4754  -1.8958
 M3D  H17  H  HCH2  0   0.201   8.0933  -0.4966   0.3345
 M3D  H18  H  HCH2  0   0.237   7.9070  -1.5949   1.7116
 M3D  H19  H  HCH2  0   0.201   5.5126  -1.8378   1.2857
 M3D  H20  H  HCH2  0   0.243   5.9412  -0.1280   1.3741
 M3D  H21  H  HCR6  0   0.265  -1.0640   5.8837   1.7102
 M3D  H22  H  HCR6  0   0.265  -3.3964   6.6577   1.5247
 M3D  H23  H  HCR6  0   0.269  -4.9820   5.4556   0.0448
 M3D  H24  H  HCR6  0   0.272  -4.2110   3.4963  -1.2577
 M3D  H25  H  HNH1  0   0.407   1.9276   0.8128  -0.8026
 M3D  H13  H  HCH2  0   0.244   5.4717  -1.7916  -2.4127

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
 M3D  C24  C25  single    1.517  0.020  1.517
 M3D  C24  N2   single    1.453  0.020  1.453
 M3D  C25  O4   single    1.411  0.020  1.411
 M3D  O4   C26  single    1.410  0.020  1.410
 M3D  C27  N2   single    1.453  0.020  1.453
 M3D  C27  C26  single    1.517  0.020  1.517
 M3D  N2   C23  single    1.448  0.020  1.448
 M3D  C23  C22  single    1.523  0.020  1.523
 M3D  C6   C5   aromatic  1.384  0.020  1.384
 M3D  C6   C7   aromatic  1.390  0.020  1.390
 M3D  C5   C4   aromatic  1.398  0.020  1.398
 M3D  C22  N1   single    1.446  0.020  1.446
 M3D  N1   C15  single    1.342  0.020  1.342
 M3D  C7   C8   aromatic  1.388  0.020  1.388
 M3D  C4   C1   single    1.455  0.020  1.455
 M3D  C4   C3   aromatic  1.396  0.020  1.396
 M3D  C1   C2   double    1.344  0.020  1.344
 M3D  C2   C15  single    1.503  0.020  1.503
 M3D  C2   C9   single    1.470  0.020  1.470
 M3D  C15  O2   double    1.224  0.020  1.224
 M3D  C8   C3   aromatic  1.385  0.020  1.385
 M3D  C3   O1   single    1.374  0.020  1.374
 M3D  C14  C9   aromatic  1.399  0.020  1.399
 M3D  C14  C13  aromatic  1.382  0.020  1.382
 M3D  C9   C10  aromatic  1.394  0.020  1.394
 M3D  C13  C12  aromatic  1.396  0.020  1.396
 M3D  C10  O1   single    1.373  0.020  1.373
 M3D  C10  C11  aromatic  1.383  0.020  1.383
 M3D  C12  C11  aromatic  1.393  0.020  1.393
 M3D  C12  C16  single    1.474  0.020  1.474
 M3D  C16  C17  aromatic  1.399  0.020  1.399
 M3D  C16  C21  aromatic  1.388  0.020  1.388
 M3D  C17  C18  aromatic  1.382  0.020  1.382
 M3D  C21  C20  aromatic  1.393  0.020  1.393
 M3D  C18  C19  aromatic  1.392  0.020  1.392
 M3D  C20  C19  aromatic  1.401  0.020  1.401
 M3D  C20  C28  single    1.423  0.020  1.423
 M3D  C19  O3   single    1.333  0.020  1.333
 M3D  C28  N3   triple    1.153  0.020  1.153
 M3D  C1   H1   single    0.930  0.020  1.080
 M3D  O3   H2   single    0.850  0.020  0.980
 M3D  C11  H3   single    0.930  0.020  1.080
 M3D  C13  H4   single    0.930  0.020  1.080
 M3D  C14  H5   single    0.930  0.020  1.080
 M3D  C17  H6   single    0.930  0.020  1.080
 M3D  C18  H7   single    0.930  0.020  1.080
 M3D  C21  H8   single    0.930  0.020  1.080
 M3D  C22  H9   single    0.970  0.020  1.090
 M3D  C22  H10  single    0.970  0.020  1.090
 M3D  C23  H11  single    0.970  0.020  1.090
 M3D  C23  H12  single    0.970  0.020  1.090
 M3D  C24  H13  single    0.970  0.020  1.090
 M3D  C24  H14  single    0.970  0.020  1.090
 M3D  C25  H15  single    0.970  0.020  1.090
 M3D  C25  H16  single    0.970  0.020  1.090
 M3D  C26  H17  single    0.970  0.020  1.090
 M3D  C26  H18  single    0.970  0.020  1.090
 M3D  C27  H19  single    0.970  0.020  1.090
 M3D  C27  H20  single    0.970  0.020  1.090
 M3D  C5   H21  single    0.930  0.020  1.080
 M3D  C6   H22  single    0.930  0.020  1.080
 M3D  C7   H23  single    0.930  0.020  1.080
 M3D  C8   H24  single    0.930  0.020  1.080
 M3D  N1   H25  single    0.860  0.020  1.020

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
 M3D  H1   C1   C4   115.51  3.000
 M3D  H1   C1   C2   117.68  3.000
 M3D  C4   C1   C2   126.78  3.000
 M3D  C9   C2   C15  119.91  3.000
 M3D  C9   C2   C1   123.59  3.000
 M3D  C15  C2   C1   116.42  3.000
 M3D  C8   C3   C4   121.56  3.000
 M3D  C8   C3   O1   118.84  3.000
 M3D  C4   C3   O1   119.52  3.000
 M3D  C10  O1   C3   113.61  3.000
 M3D  H2   O3   C19  111.16  3.000
 M3D  H3   C11  C10  118.65  3.000
 M3D  H3   C11  C12  120.88  3.000
 M3D  C10  C11  C12  120.47  3.000
 M3D  C16  C12  C13  121.20  3.000
 M3D  C16  C12  C11  120.66  3.000
 M3D  C13  C12  C11  118.13  3.000
 M3D  H4   C13  C14  118.81  3.000
 M3D  H4   C13  C12  120.32  3.000
 M3D  C14  C13  C12  120.86  3.000
 M3D  H5   C14  C9   119.68  3.000
 M3D  H5   C14  C13  118.72  3.000
 M3D  C9   C14  C13  121.60  3.000
 M3D  N1   C15  O2   122.79  3.000
 M3D  O2   C15  C2   121.93  3.000
 M3D  N1   C15  C2   115.26  3.000
 M3D  C21  C16  C17  117.73  3.000
 M3D  C21  C16  C12  120.87  3.000
 M3D  C17  C16  C12  121.40  3.000
 M3D  H6   C17  C18  118.14  3.000
 M3D  H6   C17  C16  119.86  3.000
 M3D  C18  C17  C16  121.99  3.000
 M3D  H7   C18  C19  120.02  3.000
 M3D  H7   C18  C17  119.85  3.000
 M3D  C19  C18  C17  120.12  3.000
 M3D  C20  C19  C18  118.56  3.000
 M3D  C20  C19  O3   117.48  3.000
 M3D  C18  C19  O3   123.96  3.000
 M3D  C28  C20  C21  120.05  3.000
 M3D  C28  C20  C19  119.24  3.000
 M3D  C21  C20  C19  120.70  3.000
 M3D  H8   C21  C20  118.53  3.000
 M3D  H8   C21  C16  120.57  3.000
 M3D  C20  C21  C16  120.89  3.000
 M3D  H10  C22  H9   107.25  3.000
 M3D  H10  C22  N1   111.08  3.000
 M3D  H9   C22  N1   108.25  3.000
 M3D  H10  C22  C23  109.31  3.000
 M3D  H9   C22  C23  111.10  3.000
 M3D  N1   C22  C23  109.82  3.000
 M3D  H12  C23  H11  106.69  3.000
 M3D  H12  C23  N2   107.96  3.000
 M3D  H11  C23  N2   112.14  3.000
 M3D  H12  C23  C22  108.54  3.000
 M3D  H11  C23  C22  109.72  3.000
 M3D  N2   C23  C22  111.59  3.000
 M3D  H14  C24  H13  107.22  3.000
 M3D  H14  C24  N2   111.88  3.000
 M3D  H13  C24  N2   109.34  3.000
 M3D  H14  C24  C25  109.46  3.000
 M3D  H13  C24  C25  108.78  3.000
 M3D  N2   C24  C25  110.07  3.000
 M3D  H16  C25  H15  107.86  3.000
 M3D  H16  C25  O4   110.41  3.000
 M3D  H15  C25  O4   107.51  3.000
 M3D  H16  C25  C24  109.30  3.000
 M3D  H15  C25  C24  110.13  3.000
 M3D  O4   C25  C24  111.55  3.000
 M3D  H18  C26  H17  107.93  3.000
 M3D  H18  C26  O4   107.43  3.000
 M3D  H17  C26  O4   110.51  3.000
 M3D  H18  C26  C27  109.93  3.000
 M3D  H17  C26  C27  109.24  3.000
 M3D  O4   C26  C27  111.72  3.000
 M3D  H20  C27  H19  106.98  3.000
 M3D  H20  C27  N2   110.43  3.000
 M3D  H19  C27  N2   111.35  3.000
 M3D  H20  C27  C26  108.11  3.000
 M3D  H19  C27  C26  109.74  3.000
 M3D  N2   C27  C26  110.13  3.000
 M3D  N3   C28  C20  180.00  3.000
 M3D  C9   C10  C11  122.09  3.000
 M3D  C11  C10  O1   118.30  3.000
 M3D  C9   C10  O1   119.60  3.000
 M3D  C5   C4   C3   117.89  3.000
 M3D  C3   C4   C1   122.01  3.000
 M3D  C5   C4   C1   120.07  3.000
 M3D  H21  C5   C6   119.92  3.000
 M3D  H21  C5   C4   118.99  3.000
 M3D  C6   C5   C4   121.10  3.000
 M3D  H22  C6   C7   120.22  3.000
 M3D  H22  C6   C5   119.94  3.000
 M3D  C7   C6   C5   119.83  3.000
 M3D  H23  C7   C8   119.58  3.000
 M3D  H23  C7   C6   120.27  3.000
 M3D  C8   C7   C6   120.15  3.000
 M3D  H24  C8   C7   120.79  3.000
 M3D  H24  C8   C3   119.75  3.000
 M3D  C7   C8   C3   119.45  3.000
 M3D  C10  C9   C14  116.84  3.000
 M3D  C10  C9   C2   121.69  3.000
 M3D  C14  C9   C2   121.41  3.000
 M3D  H25  N1   C22  117.79  3.000
 M3D  H25  N1   C15  118.73  3.000
 M3D  C22  N1   C15  123.06  3.000
 M3D  C27  N2   C24  109.63  3.000
 M3D  C27  N2   C23  112.63  3.000
 M3D  C24  N2   C23  111.93  3.000
 M3D  C26  O4   C25  110.76  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
 M3D  CONST_01  C6   C5   C4   C3      0.00   0.0  0
 M3D  CONST_02  C6   C7   C8   C3      0.00   0.0  0
 M3D  CONST_03  C14  C9   C10  C11     0.00   0.0  0
 M3D  CONST_04  C14  C13  C12  C11     0.00   0.0  0
 M3D  CONST_07  C9   C14  C13  C12     0.00   0.0  0
 M3D  CONST_08  C9   C10  C11  C12     0.00   0.0  0
 M3D  CONST_09  C18  C17  C16  C12   180.00   0.0  0
 M3D  CONST_10  C20  C21  C16  C12   180.00   0.0  0
 M3D  CONST_11  C10  C9   C14  C13     0.00   0.0  0
 M3D  CONST_12  C10  C11  C12  C13     0.00   0.0  0
 M3D  CONST_15  C16  C12  C13  C14   180.00   0.0  0
 M3D  CONST_16  C10  C11  C12  C16   180.00   0.0  0
 M3D  CONST_17  C19  C18  C17  C16     0.00   0.0  0
 M3D  CONST_18  C19  C20  C21  C16     0.00   0.0  0
 M3D  CONST_19  C20  C21  C16  C17     0.00   0.0  0
 M3D  CONST_20  C20  C19  C18  C17     0.00   0.0  0
 M3D  CONST_21  C21  C16  C17  C18     0.00   0.0  0
 M3D  CONST_22  C21  C20  C19  C18     0.00   0.0  0
 M3D  CONST_23  C7   C6   C5   C4      0.00   0.0  0
 M3D  CONST_24  C7   C8   C3   C4      0.00   0.0  0
 M3D  CONST_25  C8   C7   C6   C5      0.00   0.0  0
 M3D  CONST_26  C8   C3   C4   C5      0.00   0.0  0
 M3D  CONST_27  C17  C18  C19  O3    180.00   0.0  0
 M3D  CONST_28  C21  C20  C19  O3    180.00   0.0  0
 M3D  CONST_29  C28  C20  C21  C16   180.00   0.0  0
 M3D  CONST_30  C28  C20  C19  C18   180.00   0.0  0
 M3D  CONST_31  H21  C5   C4   C1      0.00   0.0  0
 M3D  CONST_32  H5   C14  C9   C2      0.00   0.0  0
 M3D  CONST_33  H23  C7   C8   C3    180.00   0.0  0
 M3D  CONST_34  H24  C8   C3   O1      0.00   0.0  0
 M3D  CONST_35  H3   C11  C10  O1      0.00   0.0  0
 M3D  CONST_36  H4   C13  C12  C11   180.00   0.0  0
 M3D  CONST_37  H6   C17  C16  C12     0.00   0.0  0
 M3D  CONST_38  H8   C21  C16  C12     0.00   0.0  0
 M3D  CONST_39  H7   C18  C17  C16   180.00   0.0  0
 M3D  CONST_40  H22  C6   C5   C4    180.00   0.0  0
 M3D  CONST_41  C22  N1   C15  C2    180.00   0.0  0
 M3D  CONST_42  H25  N1   C15  C2      0.00   0.0  0
 M3D  CONST_43  C22  N1   C15  O2      0.00   0.0  0
 M3D  Var_01    C14  C9   C2   C1   -139.19  30.0  1
 M3D  Var_02    C5   C4   C1   C2    149.98  30.0  1
 M3D  Var_03    C9   C10  O1   C3    -72.58  30.0  1
 M3D  Var_04    C26  C27  N2   C24    56.38  30.0  1
 M3D  Var_05    C27  N2   C24  C25   -56.64  30.0  1
 M3D  Var_06    C27  C26  O4   C25    57.15  30.0  1
 M3D  Var_07    C4   C3   O1   C10    70.55  30.0  1
 M3D  Var_08    C9   C2   C1   C4     -4.85  30.0  1
 M3D  Var_09    O4   C25  C24  N2     57.50  30.0  1
 M3D  Var_10    O4   C26  C27  N2    -57.05  30.0  1
 M3D  Var_11    H15  C25  O4   C26  -178.18  30.0  1
 M3D  Var_12    N1   C15  C2   C1   -150.30  30.0  2
 M3D  Var_13    C24  N2   C23  C22  -158.06  30.0  2
 M3D  Var_14    N2   C23  C22  N1   -178.64  30.0  1
 M3D  Var_15    C23  C22  N1   C15   158.14  30.0  3

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
 M3D  plan-1  O3   0.020
 M3D  plan-1  C12  0.020
 M3D  plan-1  C16  0.020
 M3D  plan-1  C17  0.020
 M3D  plan-1  C18  0.020
 M3D  plan-1  C19  0.020
 M3D  plan-1  C20  0.020
 M3D  plan-1  C21  0.020
 M3D  plan-1  C28  0.020
 M3D  plan-1  N3   0.020
 M3D  plan-1  H6   0.020
 M3D  plan-1  H7   0.020
 M3D  plan-1  H8   0.020
 M3D  plan-2  C2   0.020
 M3D  plan-2  O1   0.020
 M3D  plan-2  C11  0.020
 M3D  plan-2  C12  0.020
 M3D  plan-2  C13  0.020
 M3D  plan-2  C14  0.020
 M3D  plan-2  C16  0.020
 M3D  plan-2  C10  0.020
 M3D  plan-2  C9   0.020
 M3D  plan-2  H3   0.020
 M3D  plan-2  H4   0.020
 M3D  plan-2  H5   0.020
 M3D  plan-3  C1   0.020
 M3D  plan-3  C3   0.020
 M3D  plan-3  O1   0.020
 M3D  plan-3  C4   0.020
 M3D  plan-3  C5   0.020
 M3D  plan-3  C6   0.020
 M3D  plan-3  C7   0.020
 M3D  plan-3  C8   0.020
 M3D  plan-3  H21  0.020
 M3D  plan-3  H22  0.020
 M3D  plan-3  H23  0.020
 M3D  plan-3  H24  0.020
 M3D  plan-4  C2   0.020
 M3D  plan-4  O2   0.020
 M3D  plan-4  C15  0.020
 M3D  plan-4  C22  0.020
 M3D  plan-4  N1   0.020
 M3D  plan-4  H25  0.020

