# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 00:35:21 2021
#   Inital geometry file: a 149 line input string
#   Ligand name: (1~{R},3~{S})-~{N}-(6,7-dimethoxy-2-oxidanylidene-chromen-3-yl)-3-[(phenylmethyl)amino]cyclohexane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2OC(=O)C(=Cc2cc1OC)NC(=O)[C@@H]3CCC[C@@H](C3)NCc4ccccc4
#
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
 N9T  N9T  (1~{R},3~{S})-~{N}-(6,7-dimethoxy-2-oxidanylidene-chromen-3-yl)-3-[(phenylmethyl)amino]cyclohexane-1-carboxamide  ligand  60  32  .  2022-03-23  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N9T
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
 N9T  C10  C  CH1   0  -0.377  -1.9740  60.4704  297.3769
 N9T  C13  C  CH2   0  -0.439  -0.3970  57.9942  297.2300
 N9T  C15  C  CH2   0  -0.462  -0.4753  60.4956  297.0804
 N9T  C17  C  CR6   0   0.097   1.4416  58.8583  293.6430
 N9T  C20  C  CR16  0  -0.272   0.8060  59.6950  291.0468
 N9T  C21  C  CR16  0  -0.242   0.8255  58.3427  291.3602
 N9T  C22  C  CR16  0  -0.313   1.1367  57.9313  292.6505
 N9T  C24  C  CR66  0   0.385  -2.0438  66.0922  300.7549
 N9T  C01  C  CH3   0  -0.444  -2.1614  69.7100  302.8553
 N9T  C02  C  CR6   0   0.332  -3.2197  67.9609  301.6642
 N9T  C03  C  CR6   0   0.288  -4.4253  67.4192  301.1580
 N9T  C04  C  CH3   0  -0.411  -6.2518  67.8192  302.5624
 N9T  C05  C  CR16  0  -0.408  -4.4100  66.2286  300.4738
 N9T  C06  C  CR66  0   0.028  -3.2104  65.5373  300.2503
 N9T  C07  C  CR16  0  -0.221  -3.1340  64.3015  299.5335
 N9T  C08  C  CR6   0   0.132  -1.9366  63.6971  299.3529
 N9T  C09  C  C     0   0.560  -2.5526  61.7226  298.0087
 N9T  C11  C  CH2   0  -0.419  -2.3408  59.2519  298.2361
 N9T  C12  C  CH2   0  -0.437  -1.8828  57.9618  297.5668
 N9T  C14  C  CH1   0  -0.059  -0.0305  59.2130  296.3805
 N9T  C18  C  CR16  0  -0.284   1.4135  60.2134  293.3201
 N9T  C19  C  CR16  0  -0.242   1.0989  60.6289  292.0336
 N9T  C23  C  CR6   0   0.518  -0.7244  64.3055  299.9028
 N9T  C25  C  CR16  0  -0.468  -2.0240  67.2888  301.4561
 N9T  N01  N  NH1   0  -0.740  -1.6754  62.5125  298.6789
 N9T  N02  N  NH1   0  -0.599   1.3858  59.3028  296.0606
 N9T  O02  O  O2    0  -0.490  -5.5857  68.1009  301.3370
 N9T  O03  O  O     0  -0.470  -3.7440  61.9734  297.9394
 N9T  O04  O  O     0  -0.432   0.3805  63.8294  299.7948
 N9T  O05  O  O     0  -0.452  -0.8566  65.4622  300.5694
 N9T  H1   H  HCH1  0   0.263  -2.5027  60.3719  296.4221
 N9T  H2   H  HCH2  0   0.236  -0.1122  57.0736  296.7145
 N9T  H3   H  HCH2  0   0.211   0.1903  58.0275  298.1559
 N9T  H4   H  HCH2  0   0.218   0.1055  60.5858  298.0078
 N9T  H5   H  HCH2  0   0.255  -0.2192  61.3507  296.4500
 N9T  H6   H  HCR6  0   0.252   0.5583  60.0193  290.0443
 N9T  H7   H  HCR6  0   0.252   0.5918  57.6057  290.6021
 N9T  H8   H  HCR6  0   0.245   1.1400  56.8735  292.8882
 N9T  H9   H  HCH3  0   0.269  -2.4773  70.6274  303.3442
 N9T  H10  H  HCH3  0   0.237  -1.6862  69.0594  303.5930
 N9T  H11  H  HCH3  0   0.236  -1.4373  69.9548  302.0747
 N9T  H12  H  HCH3  0   0.242  -7.1488  68.4347  302.5875
 N9T  H13  H  HCH3  0   0.224  -6.5431  66.7674  302.6229
 N9T  H14  H  HCH3  0   0.225  -5.6338  68.0634  303.4293
 N9T  H15  H  HCR6  0   0.279  -5.3393  65.8237  300.0914
 N9T  H16  H  HCR6  0   0.305  -4.0436  63.8718  299.1451
 N9T  H17  H  HCH2  0   0.245  -3.4197  59.2239  298.4000
 N9T  H18  H  HCH2  0   0.226  -1.8715  59.3483  299.2208
 N9T  H19  H  HCH2  0   0.220  -2.4593  57.8085  296.6486
 N9T  H20  H  HCH2  0   0.237  -2.1040  57.1123  298.2165
 N9T  H21  H  HCH1  0   0.226  -0.5740  59.1514  295.4298
 N9T  H22  H  HCH2  0   0.213   1.4953  57.3580  295.1608
 N9T  H23  H  HCH2  0   0.254   2.9275  58.3549  295.0795
 N9T  H24  H  HCR6  0   0.245   1.6320  60.9442  294.0884
 N9T  H25  H  HCR6  0   0.250   1.0810  61.6861  291.8003
 N9T  H26  H  HCR6  0   0.309  -1.0800  67.6694  301.8219
 N9T  H27  H  HNH1  0   0.420  -0.7053  62.2332  298.6896
 N9T  H28  H  HNH1  0   0.347   1.9315  59.1517  296.9001
 N9T  C16  C  CH2   0  -0.349   1.8358  58.3957  295.0253
 N9T  O01  O  O2    0  -0.451  -3.3314  69.1200  302.3164

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
 N9T  C20  C19  aromatic  1.390  0.020  1.390
 N9T  C20  C21  aromatic  1.388  0.020  1.388
 N9T  C19  C18  aromatic  1.388  0.020  1.388
 N9T  C21  C22  aromatic  1.390  0.020  1.390
 N9T  C18  C17  aromatic  1.393  0.020  1.393
 N9T  C22  C17  aromatic  1.392  0.020  1.392
 N9T  C17  C16  single    1.510  0.020  1.510
 N9T  C16  N02  single    1.448  0.020  1.448
 N9T  N02  C14  single    1.455  0.020  1.455
 N9T  C14  C13  single    1.530  0.020  1.530
 N9T  C14  C15  single    1.527  0.020  1.527
 N9T  C13  C12  single    1.524  0.020  1.524
 N9T  C15  C10  single    1.528  0.020  1.528
 N9T  C12  C11  single    1.524  0.020  1.524
 N9T  C10  C11  single    1.535  0.020  1.535
 N9T  C10  C09  single    1.517  0.020  1.517
 N9T  C09  O03  double    1.219  0.020  1.219
 N9T  C09  N01  single    1.357  0.020  1.357
 N9T  N01  C08  single    1.388  0.020  1.388
 N9T  C08  C07  double    1.353  0.020  1.353
 N9T  C08  C23  single    1.464  0.020  1.464
 N9T  C07  C06  single    1.431  0.020  1.431
 N9T  O04  C23  double    1.208  0.020  1.208
 N9T  C23  O05  single    1.342  0.020  1.342
 N9T  C06  C05  aromatic  1.402  0.020  1.402
 N9T  C06  C24  aromatic  1.387  0.020  1.387
 N9T  O05  C24  single    1.357  0.020  1.357
 N9T  C05  C03  aromatic  1.373  0.020  1.373
 N9T  C24  C25  aromatic  1.387  0.020  1.387
 N9T  C03  O02  single    1.358  0.020  1.358
 N9T  C03  C02  aromatic  1.415  0.020  1.415
 N9T  C25  C02  aromatic  1.387  0.020  1.387
 N9T  O02  C04  single    1.423  0.020  1.423
 N9T  C02  O01  single    1.335  0.020  1.335
 N9T  O01  C01  single    1.417  0.020  1.417
 N9T  C10  H1   single    0.970  0.020  1.090
 N9T  C13  H2   single    0.970  0.020  1.090
 N9T  C13  H3   single    0.970  0.020  1.090
 N9T  C15  H4   single    0.970  0.020  1.090
 N9T  C15  H5   single    0.970  0.020  1.090
 N9T  C20  H6   single    0.930  0.020  1.080
 N9T  C21  H7   single    0.930  0.020  1.080
 N9T  C22  H8   single    0.930  0.020  1.080
 N9T  C01  H9   single    0.970  0.020  1.090
 N9T  C01  H10  single    0.970  0.020  1.090
 N9T  C01  H11  single    0.970  0.020  1.090
 N9T  C04  H12  single    0.970  0.020  1.090
 N9T  C04  H13  single    0.970  0.020  1.090
 N9T  C04  H14  single    0.970  0.020  1.090
 N9T  C05  H15  single    0.930  0.020  1.080
 N9T  C07  H16  single    0.930  0.020  1.080
 N9T  C11  H17  single    0.970  0.020  1.090
 N9T  C11  H18  single    0.970  0.020  1.090
 N9T  C12  H19  single    0.970  0.020  1.090
 N9T  C12  H20  single    0.970  0.020  1.090
 N9T  C14  H21  single    0.970  0.020  1.090
 N9T  C16  H22  single    0.970  0.020  1.090
 N9T  C16  H23  single    0.970  0.020  1.090
 N9T  C18  H24  single    0.930  0.020  1.080
 N9T  C19  H25  single    0.930  0.020  1.080
 N9T  C25  H26  single    0.930  0.020  1.080
 N9T  N01  H27  single    0.860  0.020  1.020
 N9T  N02  H28  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
 N9T  H1   C10  C11  107.51  3.000
 N9T  H1   C10  C09  104.66  3.000
 N9T  C11  C10  C09  109.32  3.000
 N9T  H1   C10  C15  107.80  3.000
 N9T  C09  C10  C15  116.19  3.000
 N9T  C11  C10  C15  110.86  3.000
 N9T  H3   C13  H2   106.51  3.000
 N9T  H3   C13  C14  108.43  3.000
 N9T  H2   C13  C14  110.29  3.000
 N9T  H3   C13  C12  109.64  3.000
 N9T  H2   C13  C12  109.91  3.000
 N9T  C14  C13  C12  111.91  3.000
 N9T  H5   C15  H4   107.39  3.000
 N9T  H5   C15  C14  108.93  3.000
 N9T  H4   C15  C14  107.57  3.000
 N9T  H5   C15  C10  110.78  3.000
 N9T  H4   C15  C10  110.87  3.000
 N9T  C14  C15  C10  111.15  3.000
 N9T  C18  C17  C16  121.02  3.000
 N9T  C16  C17  C22  120.39  3.000
 N9T  C18  C17  C22  118.56  3.000
 N9T  H6   C20  C19  120.30  3.000
 N9T  H6   C20  C21  120.27  3.000
 N9T  C19  C20  C21  119.42  3.000
 N9T  H7   C21  C22  119.80  3.000
 N9T  H7   C21  C20  120.13  3.000
 N9T  C22  C21  C20  120.07  3.000
 N9T  H8   C22  C21  119.54  3.000
 N9T  H8   C22  C17  119.53  3.000
 N9T  C21  C22  C17  120.93  3.000
 N9T  O05  C24  C25  117.21  3.000
 N9T  C25  C24  C06  122.76  3.000
 N9T  O05  C24  C06  120.03  3.000
 N9T  H11  C01  H10  109.12  3.000
 N9T  H11  C01  H9   108.97  3.000
 N9T  H10  C01  H9   109.00  3.000
 N9T  H11  C01  O01  111.65  3.000
 N9T  H10  C01  O01  111.60  3.000
 N9T  H9   C01  O01  106.42  3.000
 N9T  O01  C02  C25  124.49  3.000
 N9T  O01  C02  C03  115.84  3.000
 N9T  C25  C02  C03  119.67  3.000
 N9T  O02  C03  C05  120.70  3.000
 N9T  O02  C03  C02  119.26  3.000
 N9T  C05  C03  C02  120.03  3.000
 N9T  H14  C04  H13  108.79  3.000
 N9T  H14  C04  H12  108.77  3.000
 N9T  H13  C04  H12  108.87  3.000
 N9T  H14  C04  O02  111.98  3.000
 N9T  H13  C04  O02  111.28  3.000
 N9T  H12  C04  O02  107.08  3.000
 N9T  H15  C05  C06  119.55  3.000
 N9T  H15  C05  C03  119.36  3.000
 N9T  C06  C05  C03  121.09  3.000
 N9T  C07  C06  C05  123.46  3.000
 N9T  C05  C06  C24  117.66  3.000
 N9T  C07  C06  C24  118.88  3.000
 N9T  H16  C07  C08  121.34  3.000
 N9T  H16  C07  C06  118.66  3.000
 N9T  C08  C07  C06  120.00  3.000
 N9T  N01  C08  C23  112.42  3.000
 N9T  C23  C08  C07  119.80  3.000
 N9T  N01  C08  C07  127.78  3.000
 N9T  O03  C09  N01  122.67  3.000
 N9T  N01  C09  C10  116.06  3.000
 N9T  O03  C09  C10  121.24  3.000
 N9T  H18  C11  H17  106.90  3.000
 N9T  H18  C11  C12  109.92  3.000
 N9T  H17  C11  C12  109.95  3.000
 N9T  H18  C11  C10  109.33  3.000
 N9T  H17  C11  C10  109.91  3.000
 N9T  C12  C11  C10  110.75  3.000
 N9T  H20  C12  H19  106.46  3.000
 N9T  H20  C12  C11  109.66  3.000
 N9T  H19  C12  C11  109.19  3.000
 N9T  H20  C12  C13  110.21  3.000
 N9T  H19  C12  C13  109.32  3.000
 N9T  C11  C12  C13  111.85  3.000
 N9T  H21  C14  N02  107.18  3.000
 N9T  H21  C14  C15  107.46  3.000
 N9T  N02  C14  C15  109.42  3.000
 N9T  H21  C14  C13  108.52  3.000
 N9T  C15  C14  C13  110.16  3.000
 N9T  N02  C14  C13  113.86  3.000
 N9T  H24  C18  C19  120.10  3.000
 N9T  H24  C18  C17  119.21  3.000
 N9T  C19  C18  C17  120.69  3.000
 N9T  H25  C19  C18  119.71  3.000
 N9T  H25  C19  C20  119.98  3.000
 N9T  C18  C19  C20  120.31  3.000
 N9T  O05  C23  O04  118.32  3.000
 N9T  O05  C23  C08  117.61  3.000
 N9T  O04  C23  C08  124.07  3.000
 N9T  H26  C25  C02  122.07  3.000
 N9T  H26  C25  C24  119.14  3.000
 N9T  C02  C25  C24  118.78  3.000
 N9T  H27  N01  C09  117.72  3.000
 N9T  H27  N01  C08  114.32  3.000
 N9T  C09  N01  C08  127.94  3.000
 N9T  H28  N02  C16  109.38  3.000
 N9T  H28  N02  C14  109.46  3.000
 N9T  C16  N02  C14  114.90  3.000
 N9T  C04  O02  C03  114.47  3.000
 N9T  C23  O05  C24  123.68  3.000
 N9T  H23  C16  H22  105.51  3.000
 N9T  H23  C16  N02  107.34  3.000
 N9T  H22  C16  N02  113.98  3.000
 N9T  H23  C16  C17  108.50  3.000
 N9T  H22  C16  C17  108.72  3.000
 N9T  N02  C16  C17  112.42  3.000
 N9T  C02  O01  C01  118.58  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
 N9T  CONST_01  C20  C19  C18  C17     0.00   0.0  0
 N9T  CONST_02  C20  C21  C22  C17     0.00   0.0  0
 N9T  CONST_03  C18  C19  C20  C21     0.00   0.0  0
 N9T  CONST_04  C18  C17  C22  C21     0.00   0.0  0
 N9T  CONST_05  C19  C20  C21  C22     0.00   0.0  0
 N9T  CONST_06  C19  C18  C17  C22     0.00   0.0  0
 N9T  CONST_07  C03  C05  C06  C24     0.00   0.0  0
 N9T  CONST_08  C03  C02  C25  C24     0.00   0.0  0
 N9T  CONST_09  C06  C05  C03  C02     0.00   0.0  0
 N9T  CONST_10  C06  C24  C25  C02     0.00   0.0  0
 N9T  CONST_11  C25  C24  C06  C05     0.00   0.0  0
 N9T  CONST_12  C25  C02  C03  C05     0.00   0.0  0
 N9T  CONST_13  C16  C17  C22  C21   180.00   0.0  0
 N9T  CONST_14  O01  C02  C25  C24   180.00   0.0  0
 N9T  CONST_15  O01  C02  C03  C05   180.00   0.0  0
 N9T  CONST_16  O02  C03  C05  C06   180.00   0.0  0
 N9T  CONST_17  C19  C18  C17  C16   180.00   0.0  0
 N9T  CONST_18  O02  C03  C02  C25   180.00   0.0  0
 N9T  CONST_19  H25  C19  C18  C17   180.00   0.0  0
 N9T  CONST_20  H7   C21  C22  C17   180.00   0.0  0
 N9T  CONST_21  H24  C18  C19  C20   180.00   0.0  0
 N9T  CONST_22  H8   C22  C21  C20   180.00   0.0  0
 N9T  CONST_23  H6   C20  C21  C22   180.00   0.0  0
 N9T  CONST_24  H15  C05  C06  C24   180.00   0.0  0
 N9T  CONST_25  H26  C25  C02  C03   180.00   0.0  0
 N9T  CONST_26  C08  N01  C09  C10   180.00   0.0  0
 N9T  CONST_27  O03  C09  N01  C08     0.00   0.0  0
 N9T  CONST_28  H27  N01  C09  C10     0.00   0.0  0
 N9T  Var_01    C13  C12  C11  C10    54.39  30.0  1
 N9T  Var_02    C08  C07  C06  C24    -0.27  30.0  1
 N9T  Var_03    C08  C23  O05  C24    -0.19  30.0  1
 N9T  Var_04    C23  C08  C07  C06     0.54  30.0  1
 N9T  Var_05    O05  C23  C08  C07    -0.32  30.0  1
 N9T  Var_06    C14  C13  C12  C11   -54.71  30.0  1
 N9T  Var_07    C25  C24  O05  C23  -179.47  30.0  1
 N9T  Var_08    C14  N02  C16  C17    76.58  30.0  3
 N9T  Var_09    N02  C16  C17  C22  -146.63  30.0  2
 N9T  Var_10    C03  C02  O01  C01   179.58  30.0  2
 N9T  Var_11    C05  C03  O02  C04    93.75  30.0  2
 N9T  Var_12    C09  N01  C08  C07     2.70  30.0  2
 N9T  Var_13    H9   C01  O01  C02  -179.48  30.0  3
 N9T  Var_14    H12  C04  O02  C03   179.16  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
 N9T  chir_01  C10  C15  C11  C09  negativ
 N9T  chir_02  C14  N02  C13  C15  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
 N9T  plan-1  C17  0.020
 N9T  plan-1  C20  0.020
 N9T  plan-1  C21  0.020
 N9T  plan-1  C22  0.020
 N9T  plan-1  C18  0.020
 N9T  plan-1  C19  0.020
 N9T  plan-1  H6   0.020
 N9T  plan-1  H7   0.020
 N9T  plan-1  H8   0.020
 N9T  plan-1  H24  0.020
 N9T  plan-1  H25  0.020
 N9T  plan-1  C16  0.020
 N9T  plan-2  C24  0.020
 N9T  plan-2  C02  0.020
 N9T  plan-2  C03  0.020
 N9T  plan-2  C05  0.020
 N9T  plan-2  C06  0.020
 N9T  plan-2  C07  0.020
 N9T  plan-2  C25  0.020
 N9T  plan-2  O02  0.020
 N9T  plan-2  O05  0.020
 N9T  plan-2  H15  0.020
 N9T  plan-2  H26  0.020
 N9T  plan-2  O01  0.020
 N9T  plan-3  C10  0.020
 N9T  plan-3  C08  0.020
 N9T  plan-3  C09  0.020
 N9T  plan-3  N01  0.020
 N9T  plan-3  O03  0.020
 N9T  plan-3  H27  0.020
 N9T  plan-4  C08  0.020
 N9T  plan-4  C23  0.020
 N9T  plan-4  O04  0.020
 N9T  plan-4  O05  0.020

