# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 02:28:35 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: (7~{S})-2-azanyl-4-(4-methoxyphenyl)-7-naphthalen-1-yl-5-oxidanylidene-4,6,7,8-tetrahydrochromene-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[C@@H]2C(=C(N)OC3=C2C(=O)C[C@H](C3)c4cccc5ccccc45)C#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
 6Z6  6Z6  (7~{S})-2-azanyl-4-(4-methoxyphenyl)-7-naphthalen-1-yl-5-oxidanylidene-4,6,7,8-tetrahydrochromene-3-carbonitrile  ligand  54  32  .  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_6Z6
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
 6Z6  N1   N  NS    0  -0.286   4.2656   3.7114  -0.6001
 6Z6  C2   C  CR16  0  -0.328   4.2150  -1.3723   1.2125
 6Z6  O2   O  O     0  -0.460   0.2038   2.0299   1.1626
 6Z6  C4   C  CR6   0   0.185   3.1111   0.0013  -0.4437
 6Z6  C5   C  CR16  0  -0.309   4.0418  -0.4262  -1.3756
 6Z6  C6   C  CR16  0  -0.373   5.0592  -1.3139  -1.0395
 6Z6  O1   O  O     0  -0.402   0.8662  -1.1639  -2.2138
 6Z6  C9   C  C     0   0.391   0.2020  -0.7296  -1.2932
 6Z6  C8   C  CR6   0  -0.111   0.6556   0.4383  -0.5289
 6Z6  C13  C  CR6   0   0.377  -0.1456   0.9576   0.4109
 6Z6  C14  C  CR6   0   0.601   1.3332   2.7117   0.8895
 6Z6  N    N  NH2   0  -0.837   1.4446   3.7982   1.6542
 6Z6  C15  C  CR6   0  -0.177   2.1946   2.2960  -0.0810
 6Z6  C16  C  CSP   0   0.031   3.3284   3.0759  -0.3579
 6Z6  C7   C  CR16  0  -0.368   2.0240   0.9893  -0.8192
 6Z6  C3   C  CR16  0  -0.280   3.2171  -0.4855   0.8583
 6Z6  C1   C  CR6   0   0.367   5.1491  -1.7959   0.2625
 6Z6  O    O  O2    0  -0.472   6.0891  -2.6603   0.6929
 6Z6  C    C  CH3   0  -0.435   7.0513  -3.1231  -0.2329
 6Z6  C10  C  CH2   0  -0.557  -1.0853  -1.3890  -0.8637
 6Z6  C11  C  CH1   0  -0.408  -2.1035  -0.3655  -0.3681
 6Z6  C12  C  CH2   0  -0.510  -1.4963   0.4462   0.7754
 6Z6  C17  C  CR6   0   0.169  -3.4255  -0.9655   0.0534
 6Z6  C18  C  CR16  0  -0.346  -3.4613  -2.1691   0.7123
 6Z6  C19  C  CR16  0  -0.239  -4.6686  -2.7431   1.1538
 6Z6  C20  C  CR16  0  -0.332  -5.8528  -2.1014   0.9334
 6Z6  C21  C  CR66  0   0.110  -5.8724  -0.8528   0.2714
 6Z6  C26  C  CR66  0   0.090  -4.6523  -0.2680  -0.1722
 6Z6  C22  C  CR16  0  -0.308  -7.0946  -0.1751   0.0499
 6Z6  C23  C  CR16  0  -0.263  -7.1230   1.0393  -0.5760
 6Z6  C24  C  CR16  0  -0.247  -5.9199   1.6284  -1.0109
 6Z6  C25  C  CR16  0  -0.348  -4.7230   0.9939  -0.8156
 6Z6  H1   H  HCR6  0   0.260   4.2812  -1.7439   2.2276
 6Z6  H2   H  HCR6  0   0.250   3.9826  -0.0649  -2.3954
 6Z6  H3   H  HCR6  0   0.276   5.7618  -1.6159  -1.8044
 6Z6  H4   H  HNH2  0   0.421   0.7494   4.0093   2.3502
 6Z6  H5   H  HNH2  0   0.424   2.2961   4.3324   1.6760
 6Z6  H6   H  HCR6  0   0.246   2.5085  -0.1704   1.6164
 6Z6  H7   H  HCH3  0   0.259   7.7052  -3.7993   0.3122
 6Z6  H8   H  HCH3  0   0.227   6.5929  -3.6702  -1.0612
 6Z6  H9   H  HCH3  0   0.227   7.6539  -2.3072  -0.6408
 6Z6  H10  H  HCH2  0   0.280  -1.4852  -1.9670  -1.6973
 6Z6  H11  H  HCH2  0   0.276  -0.8280  -2.1009  -0.0713
 6Z6  H12  H  HCH1  0   0.276  -2.2721   0.3220  -1.1993
 6Z6  H13  H  HCH2  0   0.288  -1.4104  -0.1750   1.6741
 6Z6  H14  H  HCH2  0   0.288  -2.1416   1.2872   1.0401
 6Z6  H15  H  HCR6  0   0.254  -2.5415  -2.7045   0.9091
 6Z6  H16  H  HCR6  0   0.258  -4.6472  -3.6957   1.6669
 6Z6  H17  H  HCR6  0   0.256  -6.7885  -2.5365   1.2630
 6Z6  H18  H  HCR6  0   0.256  -8.0140  -0.6387   0.3867
 6Z6  H19  H  HCR6  0   0.259  -8.0635   1.5490  -0.7390
 6Z6  H20  H  HCR6  0   0.260  -5.9421   2.5904  -1.5063
 6Z6  H21  H  HCR6  0   0.249  -3.8229   1.4787  -1.1676
 6Z6  H22  H  HCR6  0   0.286   2.1013   1.1734  -1.8957

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
 6Z6  C    O    single    1.413  0.020  1.413
 6Z6  O    C1   single    1.348  0.020  1.348
 6Z6  C1   C2   aromatic  1.398  0.020  1.398
 6Z6  C1   C6   aromatic  1.391  0.020  1.391
 6Z6  C2   C3   aromatic  1.381  0.020  1.381
 6Z6  C6   C5   aromatic  1.391  0.020  1.391
 6Z6  C3   C4   aromatic  1.394  0.020  1.394
 6Z6  C5   C4   aromatic  1.385  0.020  1.385
 6Z6  C4   C7   single    1.516  0.020  1.516
 6Z6  N1   C16  triple    1.158  0.020  1.158
 6Z6  C16  C15  single    1.404  0.020  1.404
 6Z6  C7   C15  single    1.511  0.020  1.511
 6Z6  C7   C8   single    1.503  0.020  1.503
 6Z6  O1   C9   double    1.215  0.020  1.215
 6Z6  C15  C14  double    1.363  0.020  1.363
 6Z6  C8   C9   single    1.468  0.020  1.468
 6Z6  C8   C13  double    1.340  0.020  1.340
 6Z6  C9   C10  single    1.509  0.020  1.509
 6Z6  C14  N    single    1.333  0.020  1.333
 6Z6  C14  O2   single    1.347  0.020  1.347
 6Z6  C24  C25  aromatic  1.369  0.020  1.369
 6Z6  C24  C23  aromatic  1.408  0.020  1.408
 6Z6  C13  O2   single    1.355  0.020  1.355
 6Z6  C13  C12  single    1.490  0.020  1.490
 6Z6  C10  C11  single    1.526  0.020  1.526
 6Z6  C25  C26  aromatic  1.418  0.020  1.418
 6Z6  C23  C22  aromatic  1.367  0.020  1.367
 6Z6  C12  C11  single    1.528  0.020  1.528
 6Z6  C11  C17  single    1.512  0.020  1.512
 6Z6  C26  C17  aromatic  1.429  0.020  1.429
 6Z6  C26  C21  aromatic  1.424  0.020  1.424
 6Z6  C17  C18  aromatic  1.373  0.020  1.373
 6Z6  C22  C21  aromatic  1.415  0.020  1.415
 6Z6  C21  C20  aromatic  1.413  0.020  1.413
 6Z6  C18  C19  aromatic  1.408  0.020  1.408
 6Z6  C20  C19  aromatic  1.365  0.020  1.365
 6Z6  C2   H1   single    0.930  0.020  1.080
 6Z6  C5   H2   single    0.930  0.020  1.080
 6Z6  C6   H3   single    0.930  0.020  1.080
 6Z6  N    H4   single    0.860  0.020  1.020
 6Z6  N    H5   single    0.860  0.020  1.020
 6Z6  C3   H6   single    0.930  0.020  1.080
 6Z6  C    H7   single    0.970  0.020  1.090
 6Z6  C    H8   single    0.970  0.020  1.090
 6Z6  C    H9   single    0.970  0.020  1.090
 6Z6  C10  H10  single    0.970  0.020  1.090
 6Z6  C10  H11  single    0.970  0.020  1.090
 6Z6  C11  H12  single    0.970  0.020  1.090
 6Z6  C12  H13  single    0.970  0.020  1.090
 6Z6  C12  H14  single    0.970  0.020  1.090
 6Z6  C18  H15  single    0.930  0.020  1.080
 6Z6  C19  H16  single    0.930  0.020  1.080
 6Z6  C20  H17  single    0.930  0.020  1.080
 6Z6  C22  H18  single    0.930  0.020  1.080
 6Z6  C23  H19  single    0.930  0.020  1.080
 6Z6  C24  H20  single    0.930  0.020  1.080
 6Z6  C25  H21  single    0.930  0.020  1.080
 6Z6  C7   H22  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
 6Z6  H1   C2   C1   119.48  3.000
 6Z6  H1   C2   C3   120.32  3.000
 6Z6  C1   C2   C3   120.20  3.000
 6Z6  C14  O2   C13  120.27  3.000
 6Z6  C3   C4   C7   120.89  3.000
 6Z6  C7   C4   C5   121.09  3.000
 6Z6  C3   C4   C5   118.01  3.000
 6Z6  H2   C5   C6   118.69  3.000
 6Z6  H2   C5   C4   119.58  3.000
 6Z6  C6   C5   C4   121.72  3.000
 6Z6  H3   C6   C1   121.53  3.000
 6Z6  H3   C6   C5   118.83  3.000
 6Z6  C1   C6   C5   119.63  3.000
 6Z6  C10  C9   C8   117.60  3.000
 6Z6  C10  C9   O1   121.72  3.000
 6Z6  C8   C9   O1   120.65  3.000
 6Z6  C7   C8   C13  122.53  3.000
 6Z6  C13  C8   C9   119.27  3.000
 6Z6  C7   C8   C9   118.19  3.000
 6Z6  C12  C13  C8   125.51  3.000
 6Z6  C12  C13  O2   111.69  3.000
 6Z6  C8   C13  O2   122.79  3.000
 6Z6  C15  C14  N    127.18  3.000
 6Z6  N    C14  O2   111.48  3.000
 6Z6  C15  C14  O2   121.33  3.000
 6Z6  H5   N    H4   117.30  3.000
 6Z6  H5   N    C14  121.07  3.000
 6Z6  H4   N    C14  120.67  3.000
 6Z6  C7   C15  C16  118.39  3.000
 6Z6  C7   C15  C14  122.73  3.000
 6Z6  C16  C15  C14  118.79  3.000
 6Z6  C15  C16  N1   180.00  3.000
 6Z6  H22  C7   C15  109.09  3.000
 6Z6  H22  C7   C8   108.41  3.000
 6Z6  C15  C7   C8   108.99  3.000
 6Z6  H22  C7   C4   107.60  3.000
 6Z6  C8   C7   C4   111.47  3.000
 6Z6  C15  C7   C4   111.20  3.000
 6Z6  H6   C3   C4   120.12  3.000
 6Z6  H6   C3   C2   118.64  3.000
 6Z6  C4   C3   C2   121.24  3.000
 6Z6  O    C1   C6   124.49  3.000
 6Z6  C6   C1   C2   119.19  3.000
 6Z6  O    C1   C2   116.32  3.000
 6Z6  C    O    C1   118.41  3.000
 6Z6  H9   C    H8   108.77  3.000
 6Z6  H9   C    H7   108.64  3.000
 6Z6  H8   C    H7   108.71  3.000
 6Z6  H9   C    O    112.04  3.000
 6Z6  H8   C    O    112.01  3.000
 6Z6  H7   C    O    106.55  3.000
 6Z6  H11  C10  H10  107.13  3.000
 6Z6  H11  C10  C11  110.94  3.000
 6Z6  H10  C10  C11  111.04  3.000
 6Z6  H11  C10  C9   106.83  3.000
 6Z6  H10  C10  C9   109.09  3.000
 6Z6  C11  C10  C9   111.63  3.000
 6Z6  H12  C11  C17  109.09  3.000
 6Z6  H12  C11  C12  107.26  3.000
 6Z6  C17  C11  C12  110.47  3.000
 6Z6  H12  C11  C10  106.14  3.000
 6Z6  C17  C11  C10  114.06  3.000
 6Z6  C12  C11  C10  109.52  3.000
 6Z6  H14  C12  H13  106.50  3.000
 6Z6  H14  C12  C11  110.82  3.000
 6Z6  H13  C12  C11  110.11  3.000
 6Z6  H14  C12  C13  109.31  3.000
 6Z6  H13  C12  C13  108.91  3.000
 6Z6  C11  C12  C13  111.07  3.000
 6Z6  C26  C17  C18  118.77  3.000
 6Z6  C18  C17  C11  120.31  3.000
 6Z6  C26  C17  C11  120.86  3.000
 6Z6  H15  C18  C19  118.03  3.000
 6Z6  H15  C18  C17  119.93  3.000
 6Z6  C19  C18  C17  122.04  3.000
 6Z6  H16  C19  C20  120.50  3.000
 6Z6  H16  C19  C18  119.39  3.000
 6Z6  C20  C19  C18  120.11  3.000
 6Z6  H17  C20  C21  119.04  3.000
 6Z6  H17  C20  C19  120.76  3.000
 6Z6  C21  C20  C19  120.20  3.000
 6Z6  C22  C21  C26  119.65  3.000
 6Z6  C22  C21  C20  120.56  3.000
 6Z6  C26  C21  C20  119.80  3.000
 6Z6  C25  C26  C21  117.65  3.000
 6Z6  C21  C26  C17  119.07  3.000
 6Z6  C25  C26  C17  123.28  3.000
 6Z6  H18  C22  C23  120.34  3.000
 6Z6  H18  C22  C21  118.65  3.000
 6Z6  C23  C22  C21  121.01  3.000
 6Z6  H19  C23  C24  119.93  3.000
 6Z6  H19  C23  C22  120.37  3.000
 6Z6  C24  C23  C22  119.70  3.000
 6Z6  H20  C24  C25  119.70  3.000
 6Z6  H20  C24  C23  119.70  3.000
 6Z6  C25  C24  C23  120.60  3.000
 6Z6  H21  C25  C24  118.27  3.000
 6Z6  H21  C25  C26  120.34  3.000
 6Z6  C24  C25  C26  121.39  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
 6Z6  CONST_01  C5   C6   C1   C2     0.00   0.0  0
 6Z6  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 6Z6  CONST_03  C1   C2   C3   C4     0.00   0.0  0
 6Z6  CONST_04  C1   C6   C5   C4     0.00   0.0  0
 6Z6  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 6Z6  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 6Z6  CONST_07  C24  C25  C26  C17  180.00   0.0  0
 6Z6  CONST_08  C22  C21  C26  C17  180.00   0.0  0
 6Z6  CONST_09  C20  C21  C26  C17    0.00   0.0  0
 6Z6  CONST_10  C20  C19  C18  C17    0.00   0.0  0
 6Z6  CONST_11  C25  C26  C17  C18  180.00   0.0  0
 6Z6  CONST_12  C21  C26  C17  C18    0.00   0.0  0
 6Z6  CONST_13  C21  C20  C19  C18    0.00   0.0  0
 6Z6  CONST_14  C26  C17  C18  C19    0.00   0.0  0
 6Z6  CONST_15  C26  C21  C20  C19    0.00   0.0  0
 6Z6  CONST_16  C22  C21  C20  C19  180.00   0.0  0
 6Z6  CONST_17  C25  C26  C21  C20  180.00   0.0  0
 6Z6  CONST_18  C23  C22  C21  C20  180.00   0.0  0
 6Z6  CONST_19  C24  C25  C26  C21    0.00   0.0  0
 6Z6  CONST_20  C24  C23  C22  C21    0.00   0.0  0
 6Z6  CONST_21  C23  C24  C25  C26    0.00   0.0  0
 6Z6  CONST_22  C23  C22  C21  C26    0.00   0.0  0
 6Z6  CONST_23  C25  C24  C23  C22    0.00   0.0  0
 6Z6  CONST_24  C25  C26  C21  C22    0.00   0.0  0
 6Z6  CONST_25  C7   C4   C3   C2   180.00   0.0  0
 6Z6  CONST_26  C7   C4   C5   C6   180.00   0.0  0
 6Z6  CONST_27  C25  C26  C17  C11    0.00   0.0  0
 6Z6  CONST_28  C21  C26  C17  C11  180.00   0.0  0
 6Z6  CONST_29  C19  C18  C17  C11  180.00   0.0  0
 6Z6  CONST_30  O    C1   C6   C5   180.00   0.0  0
 6Z6  CONST_31  O    C1   C2   C3   180.00   0.0  0
 6Z6  CONST_32  H3   C6   C1   C2   180.00   0.0  0
 6Z6  CONST_33  H1   C2   C3   C4   180.00   0.0  0
 6Z6  CONST_34  H6   C3   C4   C5   180.00   0.0  0
 6Z6  CONST_35  H2   C5   C4   C7     0.00   0.0  0
 6Z6  CONST_36  H15  C18  C17  C11    0.00   0.0  0
 6Z6  CONST_37  H21  C25  C26  C17    0.00   0.0  0
 6Z6  CONST_38  H16  C19  C18  C17  180.00   0.0  0
 6Z6  CONST_39  H17  C20  C19  C18  180.00   0.0  0
 6Z6  CONST_40  H18  C22  C21  C20    0.00   0.0  0
 6Z6  CONST_41  H19  C23  C22  C21  180.00   0.0  0
 6Z6  CONST_42  H20  C24  C25  C26  180.00   0.0  0
 6Z6  Var_01    C7   C15  C14  O2    -6.12  30.0  1
 6Z6  Var_02    C7   C8   C13  O2     0.89  30.0  1
 6Z6  Var_03    C11  C12  C13  O2   158.16  30.0  1
 6Z6  Var_04    C11  C10  C9   C8    35.92  30.0  1
 6Z6  Var_05    C10  C9   C8   C13   -7.16  30.0  1
 6Z6  Var_06    C15  C14  O2   C13   -4.44  30.0  1
 6Z6  Var_07    H4   N    C14  O2     1.73  30.0  2
 6Z6  Var_08    H7   C    O    C1   179.96  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
 6Z6  chir_01  C7   C4   C15  C8   positiv
 6Z6  chir_02  C11  C10  C12  C17  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
 6Z6  plan-1  C2   0.020
 6Z6  plan-1  C4   0.020
 6Z6  plan-1  C5   0.020
 6Z6  plan-1  C6   0.020
 6Z6  plan-1  C7   0.020
 6Z6  plan-1  C3   0.020
 6Z6  plan-1  C1   0.020
 6Z6  plan-1  O    0.020
 6Z6  plan-1  H1   0.020
 6Z6  plan-1  H2   0.020
 6Z6  plan-1  H3   0.020
 6Z6  plan-1  H6   0.020
 6Z6  plan-2  C11  0.020
 6Z6  plan-2  C17  0.020
 6Z6  plan-2  C18  0.020
 6Z6  plan-2  C19  0.020
 6Z6  plan-2  C20  0.020
 6Z6  plan-2  C21  0.020
 6Z6  plan-2  C26  0.020
 6Z6  plan-2  C22  0.020
 6Z6  plan-2  C23  0.020
 6Z6  plan-2  C24  0.020
 6Z6  plan-2  C25  0.020
 6Z6  plan-2  H15  0.020
 6Z6  plan-2  H16  0.020
 6Z6  plan-2  H17  0.020
 6Z6  plan-2  H18  0.020
 6Z6  plan-2  H19  0.020
 6Z6  plan-2  H20  0.020
 6Z6  plan-2  H21  0.020
 6Z6  plan-3  O1   0.020
 6Z6  plan-3  C9   0.020
 6Z6  plan-3  C8   0.020
 6Z6  plan-3  C10  0.020

