# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 18:13:25 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 3-{[(trans-4-methylcyclohexyl)carbonyl](1-methylethyl)amino}-5-phenylthiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)N(C(=O)[C@H]1CC[C@H](C)CC1)c2cc(sc2C(O)=O)c3ccccc3
#
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
 NN3  NN3  '3-{[(trans-4-methylcyclohexyl)carbonyl](1-methylethyl)amino}-5-phenylthiophene-2-carboxylic acid'  ligand  54  27  .  2021-08-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NN3
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
 NN3  C4    C  CH1   0  -0.227   4.2432   1.7615  -1.8975
 NN3  C5    C  CH2   0  -0.407   3.5605   2.7554  -0.9610
 NN3  C6    C  CH2   0  -0.424   2.0470   2.5606  -0.9014
 NN3  C11   C  CR5   0   0.401  -0.2650  -0.6066   0.6451
 NN3  C7    C  CH3   0  -0.655   5.7549   1.9440  -1.8955
 NN3  C8    C  C     0   0.566   1.7631   0.7035   0.8201
 NN3  C10   C  CR5   0  -0.383  -0.5791  -1.7916   0.0168
 NN3  C12   C  CR15  0  -0.224  -1.3565   0.2945   0.6622
 NN3  C13   C  CR5   0  -0.199  -2.4770  -0.1951   0.0467
 NN3  C3    C  CH2   0  -0.412   3.8511   0.3333  -1.5249
 NN3  O27   O  O     0  -0.466   2.6196   1.1909   1.5374
 NN3  C1    C  CH1   0  -0.410   1.5926   1.1228  -0.6314
 NN3  C2    C  CH2   0  -0.434   2.3403   0.1389  -1.5499
 NN3  N14   N  NT    0  -0.558   0.9595  -0.3084   1.2722
 NN3  C22   C  CH1   0  -0.111   1.1347  -0.8957   2.6204
 NN3  C24   C  CH3   0  -0.667   2.5413  -1.4160   2.8841
 NN3  C23   C  CH3   0  -0.649   0.6508   0.0481   3.7157
 NN3  C15   C  C     0   0.532   0.2633  -2.9653  -0.2091
 NN3  O26   O  O     0  -0.420   1.4066  -3.0806   0.1578
 NN3  O25   O  OH1   0  -0.603  -0.3961  -3.9039  -0.8814
 NN3  S9    S  S2    0   0.296  -2.2059  -1.7842  -0.5432
 NN3  C16   C  CR6   0   0.140  -3.7763   0.4555  -0.1095
 NN3  C21   C  CR16  0  -0.315  -4.6349   0.1163  -1.1575
 NN3  C20   C  CR16  0  -0.236  -5.8671   0.7374  -1.2873
 NN3  C19   C  CR16  0  -0.260  -6.2587   1.7114  -0.3786
 NN3  C18   C  CR16  0  -0.234  -5.4096   2.0586   0.6646
 NN3  C17   C  CR16  0  -0.315  -4.1800   1.4350   0.8011
 NN3  H4    H  HCH1  0   0.202   3.8783   1.9499  -2.9166
 NN3  H51   H  HCH2  0   0.217   3.7747   3.7765  -1.2908
 NN3  H52   H  HCH2  0   0.216   3.9875   2.6565   0.0387
 NN3  H61   H  HCH2  0   0.225   1.6195   2.8466  -1.8679
 NN3  H62   H  HCH2  0   0.231   1.6078   3.2398  -0.1667
 NN3  H71   H  HCH3  0   0.211   6.1719   1.7402  -0.9061
 NN3  H72   H  HCH3  0   0.222   6.2379   1.2677  -2.6035
 NN3  H73   H  HCH3  0   0.222   6.0342   2.9634  -2.1683
 NN3  H12   H  HCR5  0   0.284  -1.2930   1.2811   1.0998
 NN3  H31   H  HCH2  0   0.225   4.3130  -0.3720  -2.2220
 NN3  H32   H  HCH2  0   0.211   4.2553   0.0926  -0.5356
 NN3  H1    H  HCH1  0   0.277   0.5358   1.0631  -0.8997
 NN3  H21A  H  HCH2  0   0.246   2.0828  -0.8904  -1.2953
 NN3  H22A  H  HCH2  0   0.231   1.9802   0.3050  -2.5703
 NN3  H22   H  HCH1  0   0.252   0.4727  -1.7628   2.6189
 NN3  H241  H  HCH3  0   0.227   2.5051  -2.0881   3.7423
 NN3  H242  H  HCH3  0   0.242   2.9130  -1.9815   2.0324
 NN3  H243  H  HCH3  0   0.231   3.2459  -0.6204   3.1108
 NN3  H231  H  HCH3  0   0.233   1.2889   0.9264   3.7944
 NN3  H232  H  HCH3  0   0.229  -0.3735   0.3783   3.5354
 NN3  H233  H  HCH3  0   0.232   0.6625  -0.4683   4.6766
 NN3  HO25  H  HOH1  0   0.493   0.1713  -4.6764  -1.0245
 NN3  H21   H  HCR6  0   0.259  -4.3390  -0.6240  -1.8916
 NN3  H20   H  HCR6  0   0.265  -6.5206   0.4617  -2.1043
 NN3  H19   H  HCR6  0   0.264  -7.2209   2.1953  -0.4811
 NN3  H18   H  HCR6  0   0.265  -5.7091   2.8113   1.3819
 NN3  H17   H  HCR6  0   0.259  -3.5385   1.7015   1.6317

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
 NN3  C4   C5    single    1.527  0.020  1.527
 NN3  C4   C7    single    1.523  0.020  1.523
 NN3  C4   C3    single    1.527  0.020  1.527
 NN3  C4   H4    single    0.970  0.020  1.090
 NN3  C5   C6    single    1.527  0.020  1.527
 NN3  C5   H51   single    0.970  0.020  1.090
 NN3  C5   H52   single    0.970  0.020  1.090
 NN3  C6   C1    single    1.532  0.020  1.532
 NN3  C6   H61   single    0.970  0.020  1.090
 NN3  C6   H62   single    0.970  0.020  1.090
 NN3  C11  C10   aromatic  1.377  0.020  1.377
 NN3  C11  C12   aromatic  1.416  0.020  1.416
 NN3  C11  N14   single    1.408  0.020  1.408
 NN3  C7   H71   single    0.970  0.020  1.090
 NN3  C7   H72   single    0.970  0.020  1.090
 NN3  C7   H73   single    0.970  0.020  1.090
 NN3  C8   O27   double    1.219  0.020  1.219
 NN3  C8   C1    single    1.520  0.020  1.520
 NN3  C8   N14   single    1.369  0.020  1.369
 NN3  C10  C15   single    1.462  0.020  1.462
 NN3  C10  S9    aromatic  1.721  0.020  1.721
 NN3  C12  C13   aromatic  1.369  0.020  1.369
 NN3  C12  H12   single    0.930  0.020  1.080
 NN3  C13  S9    aromatic  1.717  0.020  1.717
 NN3  C13  C16   single    1.461  0.020  1.461
 NN3  C3   C2    single    1.524  0.020  1.524
 NN3  C3   H31   single    0.970  0.020  1.090
 NN3  C3   H32   single    0.970  0.020  1.090
 NN3  C1   C2    single    1.540  0.020  1.540
 NN3  C1   H1    single    0.970  0.020  1.090
 NN3  C2   H21A  single    0.970  0.020  1.090
 NN3  C2   H22A  single    0.970  0.020  1.090
 NN3  N14  C22   single    1.481  0.020  1.481
 NN3  C22  C24   single    1.523  0.020  1.523
 NN3  C22  C23   single    1.525  0.020  1.525
 NN3  C22  H22   single    0.970  0.020  1.090
 NN3  C24  H241  single    0.970  0.020  1.090
 NN3  C24  H242  single    0.970  0.020  1.090
 NN3  C24  H243  single    0.970  0.020  1.090
 NN3  C23  H231  single    0.970  0.020  1.090
 NN3  C23  H232  single    0.970  0.020  1.090
 NN3  C23  H233  single    0.970  0.020  1.090
 NN3  C15  O26   double    1.206  0.020  1.206
 NN3  C15  O25   single    1.330  0.020  1.330
 NN3  O25  HO25  single    0.850  0.020  0.980
 NN3  C16  C21   aromatic  1.397  0.020  1.397
 NN3  C16  C17   aromatic  1.397  0.020  1.397
 NN3  C21  C20   aromatic  1.386  0.020  1.386
 NN3  C21  H21   single    0.930  0.020  1.080
 NN3  C20  C19   aromatic  1.388  0.020  1.388
 NN3  C20  H20   single    0.930  0.020  1.080
 NN3  C19  C18   aromatic  1.389  0.020  1.389
 NN3  C19  H19   single    0.930  0.020  1.080
 NN3  C18  C17   aromatic  1.385  0.020  1.385
 NN3  C18  H18   single    0.930  0.020  1.080
 NN3  C17  H17   single    0.930  0.020  1.080

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
 NN3  H4    C4   C3    107.54  3.000
 NN3  H4    C4   C7    108.08  3.000
 NN3  C3    C4   C7    111.51  3.000
 NN3  H4    C4   C5    107.98  3.000
 NN3  C3    C4   C5    110.14  3.000
 NN3  C7    C4   C5    111.41  3.000
 NN3  H52   C5   H51   106.50  3.000
 NN3  H52   C5   C6    109.90  3.000
 NN3  H51   C5   C6    108.96  3.000
 NN3  H52   C5   C4    109.14  3.000
 NN3  H51   C5   C4    109.58  3.000
 NN3  C6    C5   C4    112.58  3.000
 NN3  H62   C6   H61   105.92  3.000
 NN3  H62   C6   C1    110.22  3.000
 NN3  H61   C6   C1    106.55  3.000
 NN3  H62   C6   C5    110.20  3.000
 NN3  H61   C6   C5    108.62  3.000
 NN3  C1    C6   C5    114.87  3.000
 NN3  N14   C11  C12   122.04  3.000
 NN3  N14   C11  C10   125.72  3.000
 NN3  C12   C11  C10   112.16  3.000
 NN3  H73   C7   H72   107.65  3.000
 NN3  H73   C7   H71   107.62  3.000
 NN3  H72   C7   H71   107.62  3.000
 NN3  H73   C7   C4    111.44  3.000
 NN3  H72   C7   C4    111.35  3.000
 NN3  H71   C7   C4    110.96  3.000
 NN3  N14   C8   C1    116.95  3.000
 NN3  N14   C8   O27   120.91  3.000
 NN3  C1    C8   O27   122.03  3.000
 NN3  S9    C10  C15   119.86  3.000
 NN3  S9    C10  C11   111.13  3.000
 NN3  C15   C10  C11   129.02  3.000
 NN3  H12   C12  C13   123.81  3.000
 NN3  H12   C12  C11   122.72  3.000
 NN3  C13   C12  C11   113.46  3.000
 NN3  C16   C13  S9    121.05  3.000
 NN3  C16   C13  C12   128.06  3.000
 NN3  S9    C13  C12   110.88  3.000
 NN3  H32   C3   H31   106.15  3.000
 NN3  H32   C3   C2    110.65  3.000
 NN3  H31   C3   C2    109.03  3.000
 NN3  H32   C3   C4    109.33  3.000
 NN3  H31   C3   C4    109.81  3.000
 NN3  C2    C3   C4    111.71  3.000
 NN3  H1    C1   C2    106.77  3.000
 NN3  H1    C1   C8    109.15  3.000
 NN3  C2    C1   C8    109.81  3.000
 NN3  H1    C1   C6    107.16  3.000
 NN3  C2    C1   C6    110.52  3.000
 NN3  C8    C1   C6    113.19  3.000
 NN3  H22A  C2   H21A  106.43  3.000
 NN3  H22A  C2   C1    107.43  3.000
 NN3  H21A  C2   C1    110.43  3.000
 NN3  H22A  C2   C3    108.79  3.000
 NN3  H21A  C2   C3    110.52  3.000
 NN3  C1    C2   C3    112.97  3.000
 NN3  C22   N14  C8    121.62  3.000
 NN3  C22   N14  C11   115.12  3.000
 NN3  C8    N14  C11   121.34  3.000
 NN3  H22   C22  C23   107.48  3.000
 NN3  H22   C22  C24   106.81  3.000
 NN3  C23   C22  C24   112.35  3.000
 NN3  H22   C22  N14   104.01  3.000
 NN3  C23   C22  N14   111.77  3.000
 NN3  C24   C22  N14   113.73  3.000
 NN3  H243  C24  H242  108.80  3.000
 NN3  H243  C24  H241  107.98  3.000
 NN3  H242  C24  H241  107.88  3.000
 NN3  H243  C24  C22   112.64  3.000
 NN3  H242  C24  C22   110.96  3.000
 NN3  H241  C24  C22   108.43  3.000
 NN3  H233  C23  H232  107.39  3.000
 NN3  H233  C23  H231  108.18  3.000
 NN3  H232  C23  H231  108.55  3.000
 NN3  H233  C23  C22   109.65  3.000
 NN3  H232  C23  C22   111.51  3.000
 NN3  H231  C23  C22   111.43  3.000
 NN3  O25   C15  O26   123.81  3.000
 NN3  O25   C15  C10   111.04  3.000
 NN3  O26   C15  C10   125.15  3.000
 NN3  HO25  O25  C15   110.30  3.000
 NN3  C13   S9   C10    92.37  3.000
 NN3  C17   C16  C21   118.81  3.000
 NN3  C17   C16  C13   119.96  3.000
 NN3  C21   C16  C13   121.23  3.000
 NN3  H21   C21  C20   119.03  3.000
 NN3  H21   C21  C16   120.43  3.000
 NN3  C20   C21  C16   120.53  3.000
 NN3  H20   C20  C19   120.17  3.000
 NN3  H20   C20  C21   119.57  3.000
 NN3  C19   C20  C21   120.25  3.000
 NN3  H19   C19  C18   120.20  3.000
 NN3  H19   C19  C20   120.17  3.000
 NN3  C18   C19  C20   119.63  3.000
 NN3  H18   C18  C17   119.57  3.000
 NN3  H18   C18  C19   120.16  3.000
 NN3  C17   C18  C19   120.26  3.000
 NN3  H17   C17  C18   119.38  3.000
 NN3  H17   C17  C16   120.09  3.000
 NN3  C18   C17  C16   120.52  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
 NN3  CONST_01  C13   S9   C10  C11     0.00   0.0  0
 NN3  CONST_02  S9    C13  C12  C11     0.00   0.0  0
 NN3  CONST_03  C16   C13  C12  C11   180.00   0.0  0
 NN3  CONST_04  C13   C12  C11  C10     0.00   0.0  0
 NN3  CONST_05  C12   C13  S9   C10     0.00   0.0  0
 NN3  CONST_06  C16   C13  S9   C10   180.00   0.0  0
 NN3  CONST_07  S9    C10  C11  C12     0.00   0.0  0
 NN3  CONST_10  C20   C21  C16  C13   180.00   0.0  0
 NN3  CONST_11  C18   C17  C16  C13   180.00   0.0  0
 NN3  CONST_14  C19   C20  C21  C16     0.00   0.0  0
 NN3  CONST_15  C19   C18  C17  C16     0.00   0.0  0
 NN3  CONST_16  C18   C17  C16  C21     0.00   0.0  0
 NN3  CONST_17  C18   C19  C20  C21     0.00   0.0  0
 NN3  CONST_18  C17   C16  C21  C20     0.00   0.0  0
 NN3  CONST_19  C17   C18  C19  C20     0.00   0.0  0
 NN3  CONST_20  C15   C10  C11  C12   180.00   0.0  0
 NN3  CONST_21  N14   C11  C12  C13   180.00   0.0  0
 NN3  CONST_22  C15   C10  S9   C13   180.00   0.0  0
 NN3  CONST_23  S9    C10  C11  N14   180.00   0.0  0
 NN3  CONST_24  H12   C12  C11  C10   180.00   0.0  0
 NN3  CONST_25  H21   C21  C16  C13     0.00   0.0  0
 NN3  CONST_26  H17   C17  C16  C13     0.00   0.0  0
 NN3  CONST_27  H20   C20  C21  C16   180.00   0.0  0
 NN3  CONST_28  H18   C18  C17  C16   180.00   0.0  0
 NN3  CONST_29  H19   C19  C20  C21   180.00   0.0  0
 NN3  CONST_36  C22   N14  C8   C1    180.00   0.0  0
 NN3  CONST_37  HO25  O25  C15  C10   180.00   0.0  0
 NN3  CONST_38  C22   N14  C8   O27     0.00   0.0  0
 NN3  Var_01    C1    C6   C5   C4     50.60  30.0  1
 NN3  Var_02    C1    C2   C3   C4    -56.54  30.0  1
 NN3  Var_03    O26   C15  C10  C11     1.25  30.0  2
 NN3  Var_04    C24   C22  N14  C11   140.27  30.0  3
 NN3  Var_05    H241  C24  C22  N14  -162.77  30.0  3
 NN3  Var_06    H231  C23  C22  N14   -68.25  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
 NN3  chir_01  C4  C5  C7  C3  negativ
 NN3  chir_02  C1  C6  C8  C2  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
 NN3  plan-1  C11   0.020
 NN3  plan-1  C10   0.020
 NN3  plan-1  C12   0.020
 NN3  plan-1  C13   0.020
 NN3  plan-1  N14   0.020
 NN3  plan-1  C15   0.020
 NN3  plan-1  S9    0.020
 NN3  plan-1  C16   0.020
 NN3  plan-1  H12   0.020
 NN3  plan-2  C13   0.020
 NN3  plan-2  C16   0.020
 NN3  plan-2  C21   0.020
 NN3  plan-2  C20   0.020
 NN3  plan-2  C19   0.020
 NN3  plan-2  C18   0.020
 NN3  plan-2  C17   0.020
 NN3  plan-2  H21   0.020
 NN3  plan-2  H20   0.020
 NN3  plan-2  H19   0.020
 NN3  plan-2  H18   0.020
 NN3  plan-2  H17   0.020
 NN3  plan-3  C11   0.020
 NN3  plan-3  C8    0.020
 NN3  plan-3  O27   0.020
 NN3  plan-3  C1    0.020
 NN3  plan-3  N14   0.020
 NN3  plan-3  C22   0.020
 NN3  plan-4  C10   0.020
 NN3  plan-4  C15   0.020
 NN3  plan-4  O26   0.020
 NN3  plan-4  O25   0.020
 NN3  plan-4  HO25  0.020

