# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 23:59:13 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 4-(6-{[(cis-4-methylcyclohexyl)amino]methyl}-1,4-dihydroindeno[1,2-c]pyrazol-3-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CC[C@@H](CC1)NCc2ccc3c(Cc4c3[nH]nc4c5ccc(cc5)C(O)=O)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
 A58  A58  '4-(6-{[(cis-4-methylcyclohexyl)amino]methyl}-1,4-dihydroindeno[1,2-c]pyrazol-3-yl)benzoic acid'  ligand  56  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A58
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
 A58  C1    C  CH3    0  -0.654  -7.2380   0.5738  -3.1814
 A58  C2    C  CH1    0  -0.030  -4.6683  -2.2823  -1.0880
 A58  C3    C  CH2    0  -0.453  -5.0495  -0.9872  -0.3791
 A58  C4    C  CH2    0  -0.415  -6.2529  -0.3285  -1.0443
 A58  C5    C  CH1    0  -0.226  -6.0125  -0.0489  -2.5270
 A58  C6    C  CH2    0  -0.416  -5.5879  -1.3337  -3.2373
 A58  C7    C  CH2    0  -0.428  -4.3910  -1.9928  -2.5619
 A58  N8    N  NH1    0  -0.603  -3.5055  -2.8874  -0.4513
 A58  C9    C  CH2    0  -0.348  -3.3877  -4.3117  -0.7079
 A58  C10   C  CR6    0   0.107  -2.0799  -4.8559  -0.2021
 A58  C11   C  CR16   0  -0.361  -0.8802  -4.4130  -0.7690
 A58  C12   C  CR56   0   0.064   0.3174  -4.9388  -0.3359
 A58  C13   C  CR56   0   0.112   0.3313  -5.9040   0.6924
 A58  C14   C  CR16   0  -0.300  -0.8459  -6.3351   1.2781
 A58  C15   C  CR16   0  -0.327  -2.0467  -5.8017   0.8185
 A58  C16   C  CH2    0  -0.571   1.7192  -4.6363  -0.8307
 A58  C17   C  CR55   0  -0.097   2.5389  -5.5498   0.0254
 A58  C18   C  CR55   0   0.346   1.7241  -6.2490   0.8826
 A58  C19   C  CR5    0   0.161   3.8374  -6.0157   0.3028
 A58  N20   N  N      0  -0.287   3.7883  -6.9296   1.2718
 A58  N21   N  NR15   0  -0.525   2.5067  -7.0580   1.6082
 A58  C22   C  CR6    0   0.043   5.1099  -5.6456  -0.3175
 A58  C23   C  CR16   0  -0.281   6.2983  -6.2972   0.0211
 A58  C24   C  CR16   0  -0.278   7.4943  -5.9434  -0.5789
 A58  C25   C  CR6    0  -0.112   7.5524  -4.9308  -1.5353
 A58  C26   C  CR16   0  -0.269   6.3673  -4.2831  -1.8714
 A58  C27   C  CR16   0  -0.345   5.1655  -4.6316  -1.2744
 A58  C28   C  C      0   0.395   8.8719  -4.5476  -2.1904
 A58  O29   O  OC    -1  -0.593   8.8304  -3.6428  -3.0467
 A58  O30   O  O      0  -0.594   9.8832  -5.1709  -1.8136
 A58  H11A  H  HCH3   0   0.212  -8.0872  -0.1137  -3.1551
 A58  H12   H  HCH3   0   0.223  -7.5385   1.4905  -2.6708
 A58  H13   H  HCH3   0   0.223  -7.0487   0.8246  -4.2268
 A58  H5    H  HCH1   0   0.207  -5.1819   0.6656  -2.6028
 A58  H61   H  HCH2   0   0.225  -5.3550  -1.1228  -4.2847
 A58  H62   H  HCH2   0   0.205  -6.4337  -2.0323  -3.2455
 A58  H71   H  HCH2   0   0.228  -4.1260  -2.9112  -3.0931
 A58  H72   H  HCH2   0   0.207  -3.5183  -1.3330  -2.6220
 A58  H2    H  HCH1   0   0.182  -5.5444  -2.9545  -1.0308
 A58  H41   H  HCH2   0   0.206  -7.1260  -0.9852  -0.9451
 A58  H42   H  HCH2   0   0.226  -6.5045   0.6005  -0.5249
 A58  HN8   H  HNH1   0   0.340  -3.5678  -2.7513   0.5514
 A58  H91   H  HCH2   0   0.240  -3.4366  -4.4689  -1.7884
 A58  H92   H  HCH2   0   0.218  -4.2183  -4.8917  -0.2780
 A58  H15   H  HCR6   0   0.251  -2.9783  -6.1348   1.2603
 A58  H14   H  HCR6   0   0.252  -0.8413  -7.0729   2.0698
 A58  H11   H  HCR6   0   0.244  -0.9025  -3.6696  -1.5579
 A58  H161  H  HCH2   0   0.277   1.8186  -4.8454  -1.8996
 A58  H162  H  HCH2   0   0.276   1.9687  -3.5799  -0.6951
 A58  H21   H  HNR5   0   0.417   2.2468  -7.7052   2.3349
 A58  H27   H  HCR6   0   0.256   4.2653  -4.1012  -1.5598
 A58  H26   H  HCR6   0   0.244   6.3828  -3.4933  -2.6106
 A58  H24   H  HCR6   0   0.242   8.4016  -6.4647  -0.3025
 A58  H23   H  HCR6   0   0.243   6.2836  -7.0901   0.7576
 A58  H31   H  HCH2   0   0.214  -4.1926  -0.3043  -0.3989
 A58  H32   H  HCH2   0   0.228  -5.2681  -1.1909   0.6739

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
 A58  C1   C5    single    1.522  0.020  1.522
 A58  C1   H11A  single    0.970  0.020  1.090
 A58  C1   H12   single    0.970  0.020  1.090
 A58  C1   H13   single    0.970  0.020  1.090
 A58  C2   C7    single    1.527  0.020  1.527
 A58  C2   C3    single    1.525  0.020  1.525
 A58  C2   N8    single    1.457  0.020  1.457
 A58  C2   H2    single    0.970  0.020  1.090
 A58  C3   C4    single    1.525  0.020  1.525
 A58  C3   H31   single    0.970  0.020  1.090
 A58  C3   H32   single    0.970  0.020  1.090
 A58  C4   C5    single    1.528  0.020  1.528
 A58  C4   H41   single    0.970  0.020  1.090
 A58  C4   H42   single    0.970  0.020  1.090
 A58  C5   C6    single    1.528  0.020  1.528
 A58  C5   H5    single    0.970  0.020  1.090
 A58  C6   C7    single    1.524  0.020  1.524
 A58  C6   H61   single    0.970  0.020  1.090
 A58  C6   H62   single    0.970  0.020  1.090
 A58  C7   H71   single    0.970  0.020  1.090
 A58  C7   H72   single    0.970  0.020  1.090
 A58  N8   C9    single    1.452  0.020  1.452
 A58  N8   HN8   single    0.890  0.020  1.040
 A58  C9   C10   single    1.504  0.020  1.504
 A58  C9   H91   single    0.970  0.020  1.090
 A58  C9   H92   single    0.970  0.020  1.090
 A58  C10  C15   aromatic  1.392  0.020  1.392
 A58  C10  C11   aromatic  1.399  0.020  1.399
 A58  C11  C12   aromatic  1.378  0.020  1.378
 A58  C11  H11   single    0.930  0.020  1.080
 A58  C12  C13   aromatic  1.410  0.020  1.410
 A58  C12  C16   single    1.517  0.020  1.517
 A58  C13  C14   aromatic  1.384  0.020  1.384
 A58  C13  C18   aromatic  1.448  0.020  1.448
 A58  C14  C15   aromatic  1.392  0.020  1.392
 A58  C14  H14   single    0.930  0.020  1.080
 A58  C15  H15   single    0.930  0.020  1.080
 A58  C16  C17   single    1.496  0.020  1.496
 A58  C16  H161  single    0.970  0.020  1.090
 A58  C16  H162  single    0.970  0.020  1.090
 A58  C17  C19   aromatic  1.407  0.020  1.407
 A58  C17  C18   aromatic  1.374  0.020  1.374
 A58  C18  N21   aromatic  1.339  0.020  1.339
 A58  C19  N20   aromatic  1.333  0.020  1.333
 A58  C19  C22   single    1.463  0.020  1.463
 A58  N20  N21   aromatic  1.331  0.020  1.331
 A58  N21  H21   single    0.860  0.020  1.020
 A58  C22  C27   aromatic  1.395  0.020  1.395
 A58  C22  C23   aromatic  1.397  0.020  1.397
 A58  C23  C24   aromatic  1.384  0.020  1.384
 A58  C23  H23   single    0.930  0.020  1.080
 A58  C24  C25   aromatic  1.394  0.020  1.394
 A58  C24  H24   single    0.930  0.020  1.080
 A58  C25  C26   aromatic  1.392  0.020  1.392
 A58  C25  C28   single    1.522  0.020  1.522
 A58  C26  C27   aromatic  1.386  0.020  1.386
 A58  C26  H26   single    0.930  0.020  1.080
 A58  C27  H27   single    0.930  0.020  1.080
 A58  C28  O29   deloc     1.246  0.020  1.246
 A58  C28  O30   deloc     1.246  0.020  1.246

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
 A58  H13   C1   H12   107.62  3.000
 A58  H13   C1   H11A  107.60  3.000
 A58  H12   C1   H11A  107.65  3.000
 A58  H13   C1   C5    111.47  3.000
 A58  H12   C1   C5    111.34  3.000
 A58  H11A  C1   C5    110.97  3.000
 A58  H2    C2   N8    110.93  3.000
 A58  H2    C2   C7    108.00  3.000
 A58  N8    C2   C7    110.82  3.000
 A58  H2    C2   C3    107.11  3.000
 A58  N8    C2   C3    110.42  3.000
 A58  C7    C2   C3    109.45  3.000
 A58  H32   C3   H31   106.82  3.000
 A58  H32   C3   C4    110.03  3.000
 A58  H31   C3   C4    109.88  3.000
 A58  H32   C3   C2    109.82  3.000
 A58  H31   C3   C2    108.99  3.000
 A58  C4    C3   C2    111.19  3.000
 A58  H42   C4   H41   106.41  3.000
 A58  H42   C4   C5    109.98  3.000
 A58  H41   C4   C5    108.82  3.000
 A58  H42   C4   C3    109.96  3.000
 A58  H41   C4   C3    109.28  3.000
 A58  C5    C4   C3    112.22  3.000
 A58  H5    C5   C6    107.75  3.000
 A58  H5    C5   C4    107.76  3.000
 A58  C6    C5   C4    109.93  3.000
 A58  H5    C5   C1    108.24  3.000
 A58  C6    C5   C1    111.57  3.000
 A58  C4    C5   C1    111.43  3.000
 A58  H62   C6   H61   106.26  3.000
 A58  H62   C6   C7    109.47  3.000
 A58  H61   C6   C7    109.91  3.000
 A58  H62   C6   C5    108.94  3.000
 A58  H61   C6   C5    110.01  3.000
 A58  C7    C6   C5    112.07  3.000
 A58  H72   C7   H71   106.62  3.000
 A58  H72   C7   C6    109.93  3.000
 A58  H71   C7   C6    109.77  3.000
 A58  H72   C7   C2    108.16  3.000
 A58  H71   C7   C2    110.70  3.000
 A58  C6    C7   C2    111.53  3.000
 A58  HN8   N8   C9    108.15  3.000
 A58  HN8   N8   C2    109.11  3.000
 A58  C9    N8   C2    113.25  3.000
 A58  H92   C9   H91   106.06  3.000
 A58  H92   C9   C10   109.52  3.000
 A58  H91   C9   C10   108.62  3.000
 A58  H92   C9   N8    112.75  3.000
 A58  H91   C9   N8    108.19  3.000
 A58  C10   C9   N8    111.47  3.000
 A58  C15   C10  C11   119.46  3.000
 A58  C11   C10  C9    119.66  3.000
 A58  C15   C10  C9    120.88  3.000
 A58  H11   C11  C12   120.55  3.000
 A58  H11   C11  C10   119.63  3.000
 A58  C12   C11  C10   119.82  3.000
 A58  C16   C12  C13   111.42  3.000
 A58  C16   C12  C11   128.65  3.000
 A58  C13   C12  C11   119.93  3.000
 A58  C18   C13  C14   133.53  3.000
 A58  C18   C13  C12   105.57  3.000
 A58  C14   C13  C12   120.89  3.000
 A58  H14   C14  C15   120.43  3.000
 A58  H14   C14  C13   121.23  3.000
 A58  C15   C14  C13   118.34  3.000
 A58  H15   C15  C14   119.29  3.000
 A58  H15   C15  C10   119.17  3.000
 A58  C14   C15  C10   121.54  3.000
 A58  H162  C16  H161  106.56  3.000
 A58  H162  C16  C17   113.18  3.000
 A58  H161  C16  C17   113.12  3.000
 A58  H162  C16  C12   111.28  3.000
 A58  H161  C16  C12   111.39  3.000
 A58  C17   C16  C12   101.41  3.000
 A58  C19   C17  C18   104.81  3.000
 A58  C18   C17  C16   110.05  3.000
 A58  C19   C17  C16   145.13  3.000
 A58  N21   C18  C17   107.40  3.000
 A58  N21   C18  C13   141.03  3.000
 A58  C17   C18  C13   111.55  3.000
 A58  C22   C19  N20   120.90  3.000
 A58  C22   C19  C17   129.43  3.000
 A58  N20   C19  C17   109.66  3.000
 A58  N21   N20  C19   106.58  3.000
 A58  H21   N21  N20   119.52  3.000
 A58  H21   N21  C18   128.92  3.000
 A58  N20   N21  C18   111.56  3.000
 A58  C27   C22  C23   118.12  3.000
 A58  C23   C22  C19   121.27  3.000
 A58  C27   C22  C19   120.61  3.000
 A58  H23   C23  C24   119.61  3.000
 A58  H23   C23  C22   119.67  3.000
 A58  C24   C23  C22   120.72  3.000
 A58  H24   C24  C25   119.35  3.000
 A58  H24   C24  C23   119.38  3.000
 A58  C25   C24  C23   121.27  3.000
 A58  C28   C25  C26   121.13  3.000
 A58  C28   C25  C24   120.95  3.000
 A58  C26   C25  C24   117.92  3.000
 A58  H26   C26  C27   119.36  3.000
 A58  H26   C26  C25   119.51  3.000
 A58  C27   C26  C25   121.14  3.000
 A58  H27   C27  C26   118.93  3.000
 A58  H27   C27  C22   120.24  3.000
 A58  C26   C27  C22   120.83  3.000
 A58  O30   C28  O29   126.72  3.000
 A58  O30   C28  C25   116.57  3.000
 A58  O29   C28  C25   116.71  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
 A58  CONST_01  C13   C14  C15  C10    0.00   0.0  0
 A58  CONST_02  C13   C12  C11  C10    0.00   0.0  0
 A58  CONST_03  C14   C15  C10  C11    0.00   0.0  0
 A58  CONST_04  C14   C13  C12  C11    0.00   0.0  0
 A58  CONST_05  C18   C13  C12  C11  180.00   0.0  0
 A58  CONST_06  C15   C10  C11  C12    0.00   0.0  0
 A58  CONST_07  C15   C14  C13  C12    0.00   0.0  0
 A58  CONST_08  C17   C18  C13  C12    0.00   0.0  0
 A58  CONST_09  N21   C18  C13  C12  180.00   0.0  0
 A58  CONST_10  C19   C17  C18  C13  180.00   0.0  0
 A58  CONST_11  N20   N21  C18  C13  180.00   0.0  0
 A58  CONST_12  C17   C18  C13  C14  180.00   0.0  0
 A58  CONST_13  N21   C18  C13  C14    0.00   0.0  0
 A58  CONST_14  C18   C13  C14  C15  180.00   0.0  0
 A58  CONST_15  N21   N20  C19  C17    0.00   0.0  0
 A58  CONST_16  C27   C22  C19  C17    0.00   0.0  0
 A58  CONST_17  C23   C22  C19  C17  180.00   0.0  0
 A58  CONST_18  N20   N21  C18  C17    0.00   0.0  0
 A58  CONST_19  N20   C19  C17  C18    0.00   0.0  0
 A58  CONST_20  C22   C19  C17  C18  180.00   0.0  0
 A58  CONST_21  C19   N20  N21  C18    0.00   0.0  0
 A58  CONST_22  N21   C18  C17  C19    0.00   0.0  0
 A58  CONST_23  C26   C27  C22  C19  180.00   0.0  0
 A58  CONST_24  C24   C23  C22  C19  180.00   0.0  0
 A58  CONST_25  C27   C22  C19  N20  180.00   0.0  0
 A58  CONST_26  C23   C22  C19  N20    0.00   0.0  0
 A58  CONST_27  C22   C19  N20  N21  180.00   0.0  0
 A58  CONST_28  C25   C26  C27  C22    0.00   0.0  0
 A58  CONST_29  C25   C24  C23  C22    0.00   0.0  0
 A58  CONST_30  C26   C27  C22  C23    0.00   0.0  0
 A58  CONST_31  C26   C25  C24  C23    0.00   0.0  0
 A58  CONST_32  C27   C22  C23  C24    0.00   0.0  0
 A58  CONST_33  C27   C26  C25  C24    0.00   0.0  0
 A58  CONST_34  C22   C19  C17  C16    0.00   0.0  0
 A58  CONST_35  C14   C15  C10  C9   180.00   0.0  0
 A58  CONST_36  C12   C11  C10  C9   180.00   0.0  0
 A58  CONST_37  C28   C25  C24  C23  180.00   0.0  0
 A58  CONST_38  C28   C25  C26  C27  180.00   0.0  0
 A58  CONST_39  H14   C14  C15  C10  180.00   0.0  0
 A58  CONST_40  H15   C15  C10  C11  180.00   0.0  0
 A58  CONST_41  H11   C11  C12  C13  180.00   0.0  0
 A58  CONST_42  H21   N21  C18  C13    0.00   0.0  0
 A58  CONST_43  H27   C27  C22  C19    0.00   0.0  0
 A58  CONST_44  H23   C23  C22  C19    0.00   0.0  0
 A58  CONST_45  H26   C26  C27  C22  180.00   0.0  0
 A58  CONST_46  H24   C24  C23  C22  180.00   0.0  0
 A58  Var_01    C5    C6   C7   C2    56.37  30.0  1
 A58  Var_02    C5    C4   C3   C2   -56.87  30.0  1
 A58  Var_03    H161  C16  C12  C11  -58.22  30.0  1
 A58  Var_04    C10   C9   N8   C2   171.88  30.0  3
 A58  Var_05    C15   C10  C9   N8   116.08  30.0  2
 A58  Var_06    O29   C28  C25  C24  179.16  30.0  2

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
 A58  chir_01  C2  C7  C3  N8  positiv
 A58  chir_02  C5  C6  C4  C1  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
 A58  plan-1  C19  0.020
 A58  plan-1  C22  0.020
 A58  plan-1  C23  0.020
 A58  plan-1  C24  0.020
 A58  plan-1  C25  0.020
 A58  plan-1  C26  0.020
 A58  plan-1  C27  0.020
 A58  plan-1  C28  0.020
 A58  plan-1  H27  0.020
 A58  plan-1  H26  0.020
 A58  plan-1  H24  0.020
 A58  plan-1  H23  0.020
 A58  plan-2  C9   0.020
 A58  plan-2  C10  0.020
 A58  plan-2  C11  0.020
 A58  plan-2  C12  0.020
 A58  plan-2  C13  0.020
 A58  plan-2  C14  0.020
 A58  plan-2  C15  0.020
 A58  plan-2  C16  0.020
 A58  plan-2  C17  0.020
 A58  plan-2  C18  0.020
 A58  plan-2  C19  0.020
 A58  plan-2  N20  0.020
 A58  plan-2  N21  0.020
 A58  plan-2  C22  0.020
 A58  plan-2  H15  0.020
 A58  plan-2  H14  0.020
 A58  plan-2  H11  0.020
 A58  plan-2  H21  0.020
 A58  plan-3  C25  0.020
 A58  plan-3  C28  0.020
 A58  plan-3  O29  0.020
 A58  plan-3  O30  0.020

