# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 01:51:44 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 4-(2,4-dichloro-5-methoxyphenyl)-2-methyl-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(c(Cl)cc1Cl)c2nc(C)nc3[nH]cc(C#N)c23
#
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
 3RQ  3RQ  4-(2,4-dichloro-5-methoxyphenyl)-2-methyl-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile  ligand  32  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3RQ
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
 3RQ  N1    N   N     0  -0.428  -4.0217  -0.2536   0.5663
 3RQ  N3    N   NR15  0  -0.659  -3.8671   1.9056  -0.4535
 3RQ  C4    C   CR6   0  -0.149   0.8175  -1.4923  -0.5492
 3RQ  C5    C   CR16  0  -0.144   2.2011  -1.5535  -0.6191
 3RQ  C6    C   CR6   0  -0.168   2.9606  -0.5907   0.0148
 3RQ  C8    C   CR6   0   0.202  -1.2777  -0.3610   0.2601
 3RQ  C13   C   CR5   0  -0.187  -1.6700   2.0284  -0.8081
 3RQ  C15   C   CSP   0  -0.048  -0.4276   2.5389  -1.2355
 3RQ  C2    C   CR16  0  -0.446   0.9753   0.4915   0.7862
 3RQ  C14   C   CR15  0   0.068  -2.8737   2.6764  -0.9516
 3RQ  C12   C   CR56  0   0.092  -1.9576   0.7733  -0.1756
 3RQ  C3    C   CR6   0   0.132   0.1926  -0.4724   0.1566
 3RQ  C1    C   CR6   0   0.492   2.3627   0.4572   0.7222
 3RQ  C11   C   CR56  0   0.523  -3.3478   0.7416   0.0217
 3RQ  C9    C   CR6   0   0.339  -3.2747  -1.2841   0.9357
 3RQ  N4    N   NS    0  -0.252   0.5860   2.9647  -1.5857
 3RQ  N2    N   N     0  -0.418  -1.9446  -1.3655   0.8015
 3RQ  O1    O   O2    0  -0.451   3.1749   1.3528   1.2865
 3RQ  CL1   CL  CL    0  -0.089   4.6798  -0.6648  -0.0734
 3RQ  H5    H   HCR6  0   0.305   2.6868  -2.3450  -1.1726
 3RQ  H7    H   HCH3  0   0.270   3.4303   3.1019   2.2499
 3RQ  H7A   H   HCH3  0   0.236   1.9776   3.0580   1.2320
 3RQ  H7B   H   HCH3  0   0.238   2.0053   2.2001   2.7934
 3RQ  H10   H   HCH3  0   0.260  -3.9562  -3.3035   0.8448
 3RQ  H10A  H   HCH3  0   0.256  -3.4338  -2.7931   2.4408
 3RQ  H10B  H   HCH3  0   0.251  -4.9898  -2.2352   1.7978
 3RQ  H2    H   HCR6  0   0.306   0.4764   1.2725   1.3443
 3RQ  H14   H   HCR5  0   0.330  -3.0770   3.6425  -1.3832
 3RQ  HN3   H   HNR5  0   0.435  -4.8452   2.1547  -0.4462
 3RQ  C10   C   CH3   0  -0.734  -3.9580  -2.4654   1.5443
 3RQ  CL2   CL  CL    0  -0.118  -0.1008  -2.6769  -1.4093
 3RQ  C7    C   CH3   0  -0.445   2.5999   2.4830   1.9219

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
 3RQ  C11  N1    aromatic  1.319  0.020  1.319
 3RQ  N1   C9    aromatic  1.325  0.020  1.325
 3RQ  N3   C14   aromatic  1.352  0.020  1.352
 3RQ  N3   C11   aromatic  1.360  0.020  1.360
 3RQ  CL2  C4    single    1.728  0.020  1.728
 3RQ  C4   C3    aromatic  1.389  0.020  1.389
 3RQ  C4   C5    aromatic  1.387  0.020  1.387
 3RQ  C5   C6    aromatic  1.381  0.020  1.381
 3RQ  C5   H5    single    0.930  0.020  1.080
 3RQ  C6   C1    aromatic  1.399  0.020  1.399
 3RQ  C6   CL1   single    1.723  0.020  1.723
 3RQ  O1   C7    single    1.418  0.020  1.418
 3RQ  C7   H7    single    0.970  0.020  1.090
 3RQ  C7   H7A   single    0.970  0.020  1.090
 3RQ  C7   H7B   single    0.970  0.020  1.090
 3RQ  C12  C8    aromatic  1.392  0.020  1.392
 3RQ  C8   N2    aromatic  1.322  0.020  1.322
 3RQ  C8   C3    single    1.478  0.020  1.478
 3RQ  C9   C10   single    1.494  0.020  1.494
 3RQ  C10  H10   single    0.970  0.020  1.090
 3RQ  C10  H10A  single    0.970  0.020  1.090
 3RQ  C10  H10B  single    0.970  0.020  1.090
 3RQ  C14  C13   aromatic  1.375  0.020  1.375
 3RQ  C13  C12   aromatic  1.435  0.020  1.435
 3RQ  C13  C15   single    1.410  0.020  1.410
 3RQ  C15  N4    triple    1.154  0.020  1.154
 3RQ  C3   C2    aromatic  1.392  0.020  1.392
 3RQ  C2   C1    aromatic  1.389  0.020  1.389
 3RQ  C2   H2    single    0.930  0.020  1.080
 3RQ  C14  H14   single    0.930  0.020  1.080
 3RQ  C11  C12   aromatic  1.404  0.020  1.404
 3RQ  C1   O1    single    1.334  0.020  1.334
 3RQ  C9   N2    aromatic  1.339  0.020  1.339
 3RQ  N3   HN3   single    0.860  0.020  1.020

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
 3RQ  C9    N1   C11   114.44  3.000
 3RQ  HN3   N3   C11   125.35  3.000
 3RQ  HN3   N3   C14   125.02  3.000
 3RQ  C11   N3   C14   109.63  3.000
 3RQ  CL2   C4   C3    121.15  3.000
 3RQ  C3    C4   C5    120.46  3.000
 3RQ  CL2   C4   C5    118.35  3.000
 3RQ  H5    C5   C6    119.90  3.000
 3RQ  H5    C5   C4    120.43  3.000
 3RQ  C6    C5   C4    119.67  3.000
 3RQ  CL1   C6   C1    118.99  3.000
 3RQ  CL1   C6   C5    119.70  3.000
 3RQ  C1    C6   C5    121.31  3.000
 3RQ  N2    C8   C3    118.25  3.000
 3RQ  C3    C8   C12   121.68  3.000
 3RQ  N2    C8   C12   120.06  3.000
 3RQ  C12   C13  C14   106.44  3.000
 3RQ  C12   C13  C15   128.85  3.000
 3RQ  C14   C13  C15   124.71  3.000
 3RQ  N4    C15  C13   180.00  3.000
 3RQ  H2    C2   C1    120.14  3.000
 3RQ  H2    C2   C3    118.29  3.000
 3RQ  C1    C2   C3    121.57  3.000
 3RQ  H14   C14  C13   129.03  3.000
 3RQ  H14   C14  N3    121.33  3.000
 3RQ  C13   C14  N3    109.64  3.000
 3RQ  C11   C12  C13   106.27  3.000
 3RQ  C11   C12  C8    114.90  3.000
 3RQ  C13   C12  C8    138.83  3.000
 3RQ  C2    C3   C8    118.38  3.000
 3RQ  C2    C3   C4    119.04  3.000
 3RQ  C8    C3   C4    122.58  3.000
 3RQ  O1    C1   C2    124.88  3.000
 3RQ  O1    C1   C6    117.17  3.000
 3RQ  C2    C1   C6    117.95  3.000
 3RQ  C12   C11  N3    108.03  3.000
 3RQ  C12   C11  N1    125.48  3.000
 3RQ  N3    C11  N1    126.49  3.000
 3RQ  N2    C9   C10   116.55  3.000
 3RQ  N2    C9   N1    125.39  3.000
 3RQ  C10   C9   N1    118.07  3.000
 3RQ  C9    N2   C8    119.73  3.000
 3RQ  C1    O1   C7    118.53  3.000
 3RQ  H10B  C10  H10A  109.18  3.000
 3RQ  H10B  C10  H10   108.27  3.000
 3RQ  H10A  C10  H10   107.20  3.000
 3RQ  H10B  C10  C9    111.20  3.000
 3RQ  H10A  C10  C9    110.68  3.000
 3RQ  H10   C10  C9    110.20  3.000
 3RQ  H7B   C7   H7A   109.27  3.000
 3RQ  H7B   C7   H7    108.83  3.000
 3RQ  H7A   C7   H7    109.04  3.000
 3RQ  H7B   C7   O1    111.83  3.000
 3RQ  H7A   C7   O1    111.55  3.000
 3RQ  H7    C7   O1    106.22  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
 3RQ  CONST_01  C14  N3   C11  N1    180.00   0.0  0
 3RQ  CONST_02  C8   C12  C11  N1      0.00   0.0  0
 3RQ  CONST_03  C13  C12  C11  N1    180.00   0.0  0
 3RQ  CONST_04  C8   N2   C9   N1      0.00   0.0  0
 3RQ  CONST_05  C12  C13  C14  N3      0.00   0.0  0
 3RQ  CONST_06  C9   N1   C11  N3    180.00   0.0  0
 3RQ  CONST_07  C8   C12  C11  N3    180.00   0.0  0
 3RQ  CONST_08  C13  C12  C11  N3      0.00   0.0  0
 3RQ  CONST_11  C1   C2   C3   C4      0.00   0.0  0
 3RQ  CONST_12  C1   C6   C5   C4      0.00   0.0  0
 3RQ  CONST_13  C8   C3   C4   C5    180.00   0.0  0
 3RQ  CONST_14  C2   C3   C4   C5      0.00   0.0  0
 3RQ  CONST_15  C2   C1   C6   C5      0.00   0.0  0
 3RQ  CONST_16  C3   C4   C5   C6      0.00   0.0  0
 3RQ  CONST_17  C3   C2   C1   C6      0.00   0.0  0
 3RQ  CONST_18  C14  C13  C12  C8    180.00   0.0  0
 3RQ  CONST_19  C1   C2   C3   C8    180.00   0.0  0
 3RQ  CONST_20  C11  N3   C14  C13     0.00   0.0  0
 3RQ  CONST_21  N2   C8   C12  C13   180.00   0.0  0
 3RQ  CONST_22  C3   C8   C12  C13     0.00   0.0  0
 3RQ  CONST_25  C12  C11  N3   C14     0.00   0.0  0
 3RQ  CONST_26  C11  C12  C13  C14     0.00   0.0  0
 3RQ  CONST_27  C9   N2   C8   C12     0.00   0.0  0
 3RQ  CONST_28  C9   N1   C11  C12     0.00   0.0  0
 3RQ  CONST_29  C11  C12  C8   C3    180.00   0.0  0
 3RQ  CONST_30  C9   N2   C8   C3    180.00   0.0  0
 3RQ  CONST_31  N2   C9   N1   C11     0.00   0.0  0
 3RQ  CONST_32  N2   C8   C12  C11     0.00   0.0  0
 3RQ  CONST_33  C15  C13  C14  N3    180.00   0.0  0
 3RQ  CONST_34  CL1  C6   C5   C4    180.00   0.0  0
 3RQ  CONST_35  O1   C1   C6   C5    180.00   0.0  0
 3RQ  CONST_36  CL2  C4   C5   C6    180.00   0.0  0
 3RQ  CONST_37  C15  C13  C12  C8      0.00   0.0  0
 3RQ  CONST_38  C10  C9   N2   C8    180.00   0.0  0
 3RQ  CONST_39  CL2  C4   C3   C8      0.00   0.0  0
 3RQ  CONST_40  C11  N1   C9   C10   180.00   0.0  0
 3RQ  CONST_41  C11  C12  C13  C15   180.00   0.0  0
 3RQ  CONST_42  CL2  C4   C3   C2    180.00   0.0  0
 3RQ  CONST_43  CL1  C6   C1   C2    180.00   0.0  0
 3RQ  CONST_44  O1   C1   C2   C3    180.00   0.0  0
 3RQ  CONST_45  HN3  N3   C11  N1      0.00   0.0  0
 3RQ  CONST_46  H2   C2   C3   C4    180.00   0.0  0
 3RQ  CONST_47  H14  C14  C13  C12   180.00   0.0  0
 3RQ  CONST_48  H5   C5   C4   C3    180.00   0.0  0
 3RQ  Var_01    C2   C1   O1   C7     -4.78  30.0  2
 3RQ  Var_02    H10  C10  C9   N1    108.07  30.0  2
 3RQ  Var_03    H7   C7   O1   C1   -176.46  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
 3RQ  plan-1  C4   0.020
 3RQ  plan-1  C5   0.020
 3RQ  plan-1  C6   0.020
 3RQ  plan-1  C8   0.020
 3RQ  plan-1  C2   0.020
 3RQ  plan-1  C3   0.020
 3RQ  plan-1  C1   0.020
 3RQ  plan-1  O1   0.020
 3RQ  plan-1  CL1  0.020
 3RQ  plan-1  H5   0.020
 3RQ  plan-1  H2   0.020
 3RQ  plan-1  CL2  0.020
 3RQ  plan-2  N1   0.020
 3RQ  plan-2  N3   0.020
 3RQ  plan-2  C8   0.020
 3RQ  plan-2  C13  0.020
 3RQ  plan-2  C15  0.020
 3RQ  plan-2  C14  0.020
 3RQ  plan-2  C12  0.020
 3RQ  plan-2  C3   0.020
 3RQ  plan-2  C11  0.020
 3RQ  plan-2  C9   0.020
 3RQ  plan-2  N4   0.020
 3RQ  plan-2  N2   0.020
 3RQ  plan-2  H14  0.020
 3RQ  plan-2  HN3  0.020
 3RQ  plan-2  C10  0.020

