# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 17:26:04 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (3-methoxy-5-pyridin-3-yl-phenyl)methyl 1~{H}-pyrazole-4-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(COC(=O)c2c[nH]nc2)cc(c1)c3cccnc3
#
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
 JDE  JDE  '(3-methoxy-5-pyridin-3-yl-phenyl)methyl 1~{H}-pyrazole-4-carboxylate'  ligand  38  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JDE
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
 JDE  C10  C  CR15  0  -0.054   3.8047  -0.4628  -1.5273
 JDE  N12  N  NR15  0  -0.416   5.8116  -1.0730  -1.4097
 JDE  C13  C  CR15  0   0.071   5.4807  -0.8394  -0.1415
 JDE  C15  C  CR16  0  -0.384  -0.9745  -0.1302   0.8603
 JDE  C17  C  CR6   0  -0.012  -3.1388  -1.0166   0.0157
 JDE  C20  C  CR16  0  -0.071  -4.8279  -3.1382  -0.3092
 JDE  C21  C  CR16  0  -0.315  -4.7678  -2.1769  -1.3069
 JDE  C22  C  CR16  0  -0.194  -3.9101  -1.1027  -1.1412
 JDE  C01  C  CH3   0  -0.440  -3.1511   4.0250  -0.8981
 JDE  C03  C  CR6   0   0.426  -1.6711   2.4483   0.0777
 JDE  C04  C  CR16  0  -0.394  -0.4412   2.2082   0.6944
 JDE  C05  C  CR6   0   0.116  -0.0966   0.9265   1.0855
 JDE  C06  C  CH2   0  -0.254   1.2367   0.6668   1.7191
 JDE  O07  O  O2    0  -0.458   2.1288   0.2783   0.6651
 JDE  C09  C  CR5   0  -0.273   4.1598  -0.4318  -0.1617
 JDE  N11  N  N     0  -0.258   4.8164  -0.8530  -2.2699
 JDE  O14  O  O     0  -0.459   3.7803  -0.0655   2.1393
 JDE  C16  C  CR6   0   0.134  -2.2021   0.0976   0.2504
 JDE  C18  C  CR16  0  -0.100  -3.2896  -2.0378   0.9548
 JDE  N19  N  N     0  -0.397  -4.1055  -3.0708   0.8032
 JDE  C23  C  CR16  0  -0.462  -2.5498   1.3932  -0.1406
 JDE  H1   H  HCR5  0   0.270   2.8565  -0.2149  -1.9789
 JDE  H2   H  HNR5  0   0.432   6.7069  -1.3861  -1.7516
 JDE  H3   H  HCR5  0   0.306   6.1766  -0.9712   0.6703
 JDE  H4   H  HCR6  0   0.255  -0.6866  -1.1341   1.1474
 JDE  H5   H  HCR6  0   0.267  -5.4840  -3.9949  -0.4126
 JDE  H6   H  HCR6  0   0.274  -5.3731  -2.2746  -2.1976
 JDE  H7   H  HCR6  0   0.271  -3.8270  -0.3491  -1.9142
 JDE  H8   H  HCH3  0   0.231  -4.0096   3.7793  -0.2677
 JDE  H9   H  HCH3  0   0.263  -3.1479   5.0961  -1.0829
 JDE  H10  H  HCH3  0   0.230  -3.2525   3.5030  -1.8532
 JDE  H11  H  HCR6  0   0.265   0.2368   3.0361   0.8669
 JDE  H12  H  HCH2  0   0.256   1.6155   1.5614   2.2169
 JDE  H13  H  HCH2  0   0.255   1.1649  -0.1313   2.4605
 JDE  H14  H  HCR6  0   0.262  -2.7290  -2.0033   1.8835
 JDE  H15  H  HCR6  0   0.282  -3.5208   1.5654  -0.5866
 JDE  C08  C  C     0   0.545   3.3671  -0.0635   1.0029
 JDE  O02  O  O2    0  -0.471  -1.9253   3.7245  -0.2597

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
 JDE  N19  C18  aromatic  1.325  0.020  1.325
 JDE  N19  C20  aromatic  1.328  0.020  1.328
 JDE  C18  C17  aromatic  1.396  0.020  1.396
 JDE  O02  C01  single    1.414  0.020  1.414
 JDE  O02  C03  single    1.344  0.020  1.344
 JDE  C20  C21  aromatic  1.387  0.020  1.387
 JDE  C23  C03  aromatic  1.390  0.020  1.390
 JDE  C23  C16  aromatic  1.397  0.020  1.397
 JDE  C03  C04  aromatic  1.397  0.020  1.397
 JDE  C17  C16  single    1.474  0.020  1.474
 JDE  C17  C22  aromatic  1.393  0.020  1.393
 JDE  C16  C15  aromatic  1.390  0.020  1.390
 JDE  C21  C22  aromatic  1.385  0.020  1.385
 JDE  C04  C05  aromatic  1.384  0.020  1.384
 JDE  C15  C05  aromatic  1.392  0.020  1.392
 JDE  C05  C06  single    1.499  0.020  1.499
 JDE  C06  O07  single    1.435  0.020  1.435
 JDE  O07  C08  single    1.328  0.020  1.328
 JDE  C10  C09  aromatic  1.411  0.020  1.411
 JDE  C10  N11  aromatic  1.314  0.020  1.314
 JDE  C08  C09  single    1.456  0.020  1.456
 JDE  C08  O14  double    1.209  0.020  1.209
 JDE  C09  C13  aromatic  1.382  0.020  1.382
 JDE  N11  N12  aromatic  1.334  0.020  1.334
 JDE  C13  N12  aromatic  1.331  0.020  1.331
 JDE  C10  H1   single    0.930  0.020  1.080
 JDE  N12  H2   single    0.860  0.020  1.020
 JDE  C13  H3   single    0.930  0.020  1.080
 JDE  C15  H4   single    0.930  0.020  1.080
 JDE  C20  H5   single    0.930  0.020  1.080
 JDE  C21  H6   single    0.930  0.020  1.080
 JDE  C22  H7   single    0.930  0.020  1.080
 JDE  C01  H8   single    0.970  0.020  1.090
 JDE  C01  H9   single    0.970  0.020  1.090
 JDE  C01  H10  single    0.970  0.020  1.090
 JDE  C04  H11  single    0.930  0.020  1.080
 JDE  C06  H12  single    0.970  0.020  1.090
 JDE  C06  H13  single    0.970  0.020  1.090
 JDE  C18  H14  single    0.930  0.020  1.080
 JDE  C23  H15  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
 JDE  H1   C10  N11  120.54  3.000
 JDE  H1   C10  C09  128.39  3.000
 JDE  N11  C10  C09  111.07  3.000
 JDE  H2   N12  N11  119.68  3.000
 JDE  H2   N12  C13  126.75  3.000
 JDE  N11  N12  C13  113.58  3.000
 JDE  H3   C13  C09  131.62  3.000
 JDE  H3   C13  N12  122.39  3.000
 JDE  C09  C13  N12  105.98  3.000
 JDE  H4   C15  C16  120.20  3.000
 JDE  H4   C15  C05  119.54  3.000
 JDE  C16  C15  C05  120.25  3.000
 JDE  C18  C17  C16  120.96  3.000
 JDE  C16  C17  C22  122.05  3.000
 JDE  C18  C17  C22  116.98  3.000
 JDE  H5   C20  N19  116.69  3.000
 JDE  H5   C20  C21  120.36  3.000
 JDE  N19  C20  C21  122.95  3.000
 JDE  H6   C21  C22  121.03  3.000
 JDE  H6   C21  C20  120.38  3.000
 JDE  C22  C21  C20  118.59  3.000
 JDE  H7   C22  C21  120.14  3.000
 JDE  H7   C22  C17  120.49  3.000
 JDE  C21  C22  C17  119.37  3.000
 JDE  H10  C01  H9   108.80  3.000
 JDE  H10  C01  H8   108.89  3.000
 JDE  H9   C01  H8   108.78  3.000
 JDE  H10  C01  O02  111.92  3.000
 JDE  H9   C01  O02  106.47  3.000
 JDE  H8   C01  O02  111.88  3.000
 JDE  C23  C03  C04  119.70  3.000
 JDE  C04  C03  O02  116.14  3.000
 JDE  C23  C03  O02  124.16  3.000
 JDE  H11  C04  C05  120.44  3.000
 JDE  H11  C04  C03  119.33  3.000
 JDE  C05  C04  C03  120.22  3.000
 JDE  C06  C05  C04  120.11  3.000
 JDE  C06  C05  C15  119.85  3.000
 JDE  C04  C05  C15  120.02  3.000
 JDE  H13  C06  H12  108.19  3.000
 JDE  H13  C06  O07  109.99  3.000
 JDE  H12  C06  O07  109.95  3.000
 JDE  H13  C06  C05  110.81  3.000
 JDE  H12  C06  C05  111.06  3.000
 JDE  O07  C06  C05  106.83  3.000
 JDE  C08  O07  C06  117.56  3.000
 JDE  C08  C09  C13  125.66  3.000
 JDE  C13  C09  C10  104.36  3.000
 JDE  C08  C09  C10  129.98  3.000
 JDE  N12  N11  C10  105.01  3.000
 JDE  C23  C16  C17  119.87  3.000
 JDE  C17  C16  C15  120.48  3.000
 JDE  C23  C16  C15  119.64  3.000
 JDE  H14  C18  N19  116.15  3.000
 JDE  H14  C18  C17  119.78  3.000
 JDE  N19  C18  C17  124.06  3.000
 JDE  C18  N19  C20  118.05  3.000
 JDE  H15  C23  C16  119.08  3.000
 JDE  H15  C23  C03  120.73  3.000
 JDE  C16  C23  C03  120.17  3.000
 JDE  O14  C08  C09  124.42  3.000
 JDE  O14  C08  O07  123.91  3.000
 JDE  C09  C08  O07  111.67  3.000
 JDE  C03  O02  C01  118.61  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
 JDE  CONST_01  N12  C13  C09  C10     0.00   0.0  0
 JDE  CONST_02  C13  N12  N11  C10     0.00   0.0  0
 JDE  CONST_03  C09  C10  N11  N12     0.00   0.0  0
 JDE  CONST_04  N11  C10  C09  C13     0.00   0.0  0
 JDE  CONST_05  C03  C23  C16  C15     0.00   0.0  0
 JDE  CONST_08  C03  C04  C05  C15     0.00   0.0  0
 JDE  CONST_09  C20  N19  C18  C17     0.00   0.0  0
 JDE  CONST_10  C03  C23  C16  C17   180.00   0.0  0
 JDE  CONST_11  C05  C15  C16  C17   180.00   0.0  0
 JDE  CONST_12  C20  C21  C22  C17     0.00   0.0  0
 JDE  CONST_13  C18  N19  C20  C21     0.00   0.0  0
 JDE  CONST_14  C18  C17  C22  C21     0.00   0.0  0
 JDE  CONST_15  C16  C17  C22  C21   180.00   0.0  0
 JDE  CONST_16  N19  C18  C17  C22     0.00   0.0  0
 JDE  CONST_18  N19  C20  C21  C22     0.00   0.0  0
 JDE  CONST_19  C16  C23  C03  C04     0.00   0.0  0
 JDE  CONST_20  C16  C15  C05  C04     0.00   0.0  0
 JDE  CONST_21  C23  C03  C04  C05     0.00   0.0  0
 JDE  CONST_22  C23  C16  C15  C05     0.00   0.0  0
 JDE  CONST_23  N11  N12  C13  C09     0.00   0.0  0
 JDE  CONST_24  N19  C18  C17  C16   180.00   0.0  0
 JDE  CONST_26  C08  C09  C13  N12   180.00   0.0  0
 JDE  CONST_27  C16  C23  C03  O02   180.00   0.0  0
 JDE  CONST_28  C05  C04  C03  O02   180.00   0.0  0
 JDE  CONST_29  C06  C05  C04  C03   180.00   0.0  0
 JDE  CONST_30  C16  C15  C05  C06   180.00   0.0  0
 JDE  CONST_31  N11  C10  C09  C08   180.00   0.0  0
 JDE  CONST_32  H3   C13  C09  C10   180.00   0.0  0
 JDE  CONST_33  H2   N12  N11  C10   180.00   0.0  0
 JDE  CONST_34  H1   C10  N11  N12   180.00   0.0  0
 JDE  CONST_35  H15  C23  C16  C15   180.00   0.0  0
 JDE  CONST_36  H11  C04  C05  C15   180.00   0.0  0
 JDE  CONST_37  H4   C15  C16  C17     0.00   0.0  0
 JDE  CONST_38  H6   C21  C22  C17   180.00   0.0  0
 JDE  CONST_39  H14  C18  N19  C20   180.00   0.0  0
 JDE  CONST_40  H7   C22  C21  C20   180.00   0.0  0
 JDE  CONST_41  H5   C20  C21  C22   180.00   0.0  0
 JDE  Var_01    O07  C08  C09  C10     0.42  30.0  2
 JDE  Var_02    O07  C06  C05  C15    84.72  30.0  2
 JDE  Var_03    C23  C03  O02  C01    -1.10  30.0  2
 JDE  Var_04    C09  C08  O07  C06  -179.93  30.0  3
 JDE  Var_05    H8   C01  O02  C03    61.56  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
 JDE  plan-1  C10  0.020
 JDE  plan-1  N12  0.020
 JDE  plan-1  C13  0.020
 JDE  plan-1  C09  0.020
 JDE  plan-1  N11  0.020
 JDE  plan-1  H1   0.020
 JDE  plan-1  H2   0.020
 JDE  plan-1  H3   0.020
 JDE  plan-1  C08  0.020
 JDE  plan-2  C17  0.020
 JDE  plan-2  C20  0.020
 JDE  plan-2  C21  0.020
 JDE  plan-2  C22  0.020
 JDE  plan-2  C16  0.020
 JDE  plan-2  C18  0.020
 JDE  plan-2  N19  0.020
 JDE  plan-2  H5   0.020
 JDE  plan-2  H6   0.020
 JDE  plan-2  H7   0.020
 JDE  plan-2  H14  0.020
 JDE  plan-3  C15  0.020
 JDE  plan-3  C17  0.020
 JDE  plan-3  C03  0.020
 JDE  plan-3  C04  0.020
 JDE  plan-3  C05  0.020
 JDE  plan-3  C06  0.020
 JDE  plan-3  C16  0.020
 JDE  plan-3  C23  0.020
 JDE  plan-3  H4   0.020
 JDE  plan-3  H11  0.020
 JDE  plan-3  H15  0.020
 JDE  plan-3  O02  0.020
 JDE  plan-4  O07  0.020
 JDE  plan-4  C09  0.020
 JDE  plan-4  O14  0.020
 JDE  plan-4  C08  0.020

