# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 02:31:24 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 4-(2,4-dichloro-5-methoxyphenyl)-2,6-dimethyl-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]c(C)c(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
 3RR  3RR  4-(2,4-dichloro-5-methoxyphenyl)-2,6-dimethyl-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile  ligand  35  23  .  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_3RR
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
 3RR  N1    N   N     0  -0.431  -3.8030  -0.8948   0.6794
 3RR  N3    N   NR15  0  -0.705  -3.9140   1.3403  -0.1633
 3RR  C4    C   CR56  0   0.124  -1.8863   0.4073  -0.0222
 3RR  C5    C   CR5   0  -0.218  -1.7620   1.7309  -0.5624
 3RR  C6    C   CR5   0   0.421  -3.0338   2.2639  -0.6295
 3RR  C8    C   CR6   0   0.134   0.3956  -0.6136   0.1762
 3RR  C10   C   CR16  0  -0.144   2.4942  -1.4252  -0.6864
 3RR  C13   C   CR16  0  -0.446   1.0836   0.3874   0.8571
 3RR  C15   C   CSP   0  -0.075  -0.5983   2.4026  -0.9836
 3RR  C12   C   CR6   0   0.491   2.4657   0.5043   0.7777
 3RR  C9    C   CR6   0  -0.150   1.1133  -1.5152  -0.5995
 3RR  C11   C   CR6   0  -0.169   3.1589  -0.4291   0.0006
 3RR  C2    C   CR6   0   0.192  -1.0751  -0.6719   0.3106
 3RR  C3    C   CR56  0   0.502  -3.2573   0.2068   0.2043
 3RR  C1    C   CR6   0   0.337  -2.9372  -1.8646   0.9474
 3RR  C16   C   CH3   0  -0.729  -3.4765   3.5931  -1.1058
 3RR  C14   C   CH3   0  -0.446   2.5092   2.4820   2.0773
 3RR  N4    N   NS    0  -0.253   0.3488   2.9649  -1.3298
 3RR  N2    N   N     0  -0.419  -1.6129  -1.7855   0.7839
 3RR  O1    O   O2    0  -0.451   3.1887   1.4435   1.3904
 3RR  CL2   CL  CL    0  -0.118   0.3117  -2.7371  -1.5224
 3RR  CL1   CL  CL    0  -0.089   4.8749  -0.3170  -0.1072
 3RR  H7    H   HCH3  0   0.259  -3.3682  -3.9385   0.7027
 3RR  H7A   H   HCH3  0   0.255  -2.9123  -3.4905   2.3368
 3RR  H7B   H   HCH3  0   0.250  -4.5244  -3.0776   1.7236
 3RR  H10   H   HCR6  0   0.305   3.0514  -2.1253  -1.2934
 3RR  H13   H   HCR6  0   0.305   0.5154   1.0741   1.4703
 3RR  H16   H   HCH3  0   0.281  -3.9334   4.1603  -0.2938
 3RR  H16A  H   HCH3  0   0.267  -2.6387   4.1674  -1.4938
 3RR  H16B  H   HCH3  0   0.279  -4.2193   3.4915  -1.8973
 3RR  H14   H   HCH3  0   0.236   1.8281   3.0211   1.4146
 3RR  H14A  H   HCH3  0   0.239   1.9512   2.1035   2.9367
 3RR  H14B  H   HCH3  0   0.269   3.2767   3.1654   2.4300
 3RR  HN3   H   HNR5  0   0.431  -4.9138   1.4711  -0.1086
 3RR  C7    C   CH3   0  -0.735  -3.4724  -3.1615   1.4622

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
 3RR  C3   N1    aromatic  1.318  0.020  1.318
 3RR  N1   C1    aromatic  1.327  0.020  1.327
 3RR  N3   C6    aromatic  1.358  0.020  1.358
 3RR  N3   C3    aromatic  1.361  0.020  1.361
 3RR  C3   C4    aromatic  1.404  0.020  1.404
 3RR  C5   C4    aromatic  1.435  0.020  1.435
 3RR  C4   C2    aromatic  1.391  0.020  1.391
 3RR  C6   C5    aromatic  1.381  0.020  1.381
 3RR  C5   C15   single    1.408  0.020  1.408
 3RR  C16  C6    single    1.480  0.020  1.480
 3RR  C1   C7    single    1.494  0.020  1.494
 3RR  C7   H7    single    0.970  0.020  1.090
 3RR  C7   H7A   single    0.970  0.020  1.090
 3RR  C7   H7B   single    0.970  0.020  1.090
 3RR  C2   C8    single    1.478  0.020  1.478
 3RR  C9   C8    aromatic  1.389  0.020  1.389
 3RR  C8   C13   aromatic  1.392  0.020  1.392
 3RR  C9   C10   aromatic  1.387  0.020  1.387
 3RR  C10  C11   aromatic  1.381  0.020  1.381
 3RR  C10  H10   single    0.930  0.020  1.080
 3RR  C13  C12   aromatic  1.389  0.020  1.389
 3RR  C13  H13   single    0.930  0.020  1.080
 3RR  C15  N4    triple    1.155  0.020  1.155
 3RR  C11  C12   aromatic  1.398  0.020  1.398
 3RR  C12  O1    single    1.334  0.020  1.334
 3RR  CL2  C9    single    1.728  0.020  1.728
 3RR  C11  CL1   single    1.723  0.020  1.723
 3RR  C2   N2    aromatic  1.324  0.020  1.324
 3RR  C1   N2    aromatic  1.337  0.020  1.337
 3RR  C16  H16   single    0.970  0.020  1.090
 3RR  C16  H16A  single    0.970  0.020  1.090
 3RR  C16  H16B  single    0.970  0.020  1.090
 3RR  O1   C14   single    1.418  0.020  1.418
 3RR  C14  H14   single    0.970  0.020  1.090
 3RR  C14  H14A  single    0.970  0.020  1.090
 3RR  C14  H14B  single    0.970  0.020  1.090
 3RR  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
 3RR  C1    N1   C3    114.42  3.000
 3RR  HN3   N3   C3    124.84  3.000
 3RR  HN3   N3   C6    124.89  3.000
 3RR  C3    N3   C6    110.27  3.000
 3RR  C3    C4   C2    114.85  3.000
 3RR  C2    C4   C5    139.07  3.000
 3RR  C3    C4   C5    106.09  3.000
 3RR  C15   C5   C6    124.24  3.000
 3RR  C15   C5   C4    128.62  3.000
 3RR  C6    C5   C4    107.13  3.000
 3RR  C16   C6   C5    129.64  3.000
 3RR  C16   C6   N3    121.83  3.000
 3RR  C5    C6   N3    108.53  3.000
 3RR  C2    C8   C9    122.63  3.000
 3RR  C9    C8   C13   118.97  3.000
 3RR  C2    C8   C13   118.39  3.000
 3RR  H10   C10  C11   119.90  3.000
 3RR  H10   C10  C9    120.42  3.000
 3RR  C11   C10  C9    119.67  3.000
 3RR  H13   C13  C12   120.09  3.000
 3RR  H13   C13  C8    118.29  3.000
 3RR  C12   C13  C8    121.61  3.000
 3RR  N4    C15  C5    180.00  3.000
 3RR  O1    C12  C11   117.16  3.000
 3RR  O1    C12  C13   124.90  3.000
 3RR  C11   C12  C13   117.95  3.000
 3RR  CL2   C9   C10   118.31  3.000
 3RR  CL2   C9   C8    121.16  3.000
 3RR  C10   C9   C8    120.49  3.000
 3RR  CL1   C11  C12   119.01  3.000
 3RR  CL1   C11  C10   119.69  3.000
 3RR  C12   C11  C10   121.30  3.000
 3RR  N2    C2   C8    118.03  3.000
 3RR  N2    C2   C4    120.09  3.000
 3RR  C8    C2   C4    121.88  3.000
 3RR  C4    C3   N3    107.98  3.000
 3RR  C4    C3   N1    125.58  3.000
 3RR  N3    C3   N1    126.43  3.000
 3RR  N2    C1   C7    116.64  3.000
 3RR  N2    C1   N1    125.33  3.000
 3RR  C7    C1   N1    118.03  3.000
 3RR  H16B  C16  H16A  108.38  3.000
 3RR  H16B  C16  H16   107.67  3.000
 3RR  H16A  C16  H16   108.28  3.000
 3RR  H16B  C16  C6    110.72  3.000
 3RR  H16A  C16  C6    111.03  3.000
 3RR  H16   C16  C6    110.65  3.000
 3RR  H14B  C14  H14A  108.87  3.000
 3RR  H14B  C14  H14   109.08  3.000
 3RR  H14A  C14  H14   109.25  3.000
 3RR  H14B  C14  O1    106.22  3.000
 3RR  H14A  C14  O1    111.84  3.000
 3RR  H14   C14  O1    111.48  3.000
 3RR  C1    N2   C2    119.73  3.000
 3RR  C14   O1   C12   118.57  3.000
 3RR  H7B   C7   H7A   109.14  3.000
 3RR  H7B   C7   H7    108.34  3.000
 3RR  H7A   C7   H7    107.12  3.000
 3RR  H7B   C7   C1    111.25  3.000
 3RR  H7A   C7   C1    110.76  3.000
 3RR  H7    C7   C1    110.11  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
 3RR  CONST_01  C6   N3   C3   N1   180.00   0.0  0
 3RR  CONST_02  C5   C4   C3   N1   180.00   0.0  0
 3RR  CONST_03  C2   C4   C3   N1     0.00   0.0  0
 3RR  CONST_04  C2   N2   C1   N1     0.00   0.0  0
 3RR  CONST_05  C4   C5   C6   N3     0.00   0.0  0
 3RR  CONST_06  C1   N1   C3   N3   180.00   0.0  0
 3RR  CONST_07  C5   C4   C3   N3     0.00   0.0  0
 3RR  CONST_08  C2   C4   C3   N3   180.00   0.0  0
 3RR  CONST_09  C1   N1   C3   C4     0.00   0.0  0
 3RR  CONST_10  C6   N3   C3   C4     0.00   0.0  0
 3RR  CONST_13  C1   N2   C2   C4     0.00   0.0  0
 3RR  CONST_14  C8   C2   C4   C5     0.00   0.0  0
 3RR  CONST_15  N2   C2   C4   C5   180.00   0.0  0
 3RR  CONST_16  C3   N3   C6   C5     0.00   0.0  0
 3RR  CONST_17  C3   C4   C5   C6     0.00   0.0  0
 3RR  CONST_18  C2   C4   C5   C6   180.00   0.0  0
 3RR  CONST_19  C3   C4   C2   C8   180.00   0.0  0
 3RR  CONST_20  C1   N2   C2   C8   180.00   0.0  0
 3RR  CONST_21  C11  C10  C9   C8     0.00   0.0  0
 3RR  CONST_22  C11  C12  C13  C8     0.00   0.0  0
 3RR  CONST_23  C2   C8   C9   C10  180.00   0.0  0
 3RR  CONST_24  C13  C8   C9   C10    0.00   0.0  0
 3RR  CONST_25  C13  C12  C11  C10    0.00   0.0  0
 3RR  CONST_27  C2   C8   C13  C12  180.00   0.0  0
 3RR  CONST_28  C9   C8   C13  C12    0.00   0.0  0
 3RR  CONST_29  C9   C10  C11  C12    0.00   0.0  0
 3RR  CONST_31  N2   C1   N1   C3     0.00   0.0  0
 3RR  CONST_32  N2   C2   C4   C3     0.00   0.0  0
 3RR  CONST_33  C15  C5   C6   N3   180.00   0.0  0
 3RR  CONST_34  C16  C6   C5   C4   180.00   0.0  0
 3RR  CONST_35  C3   N1   C1   C7   180.00   0.0  0
 3RR  CONST_36  C2   N2   C1   C7   180.00   0.0  0
 3RR  CONST_37  O1   C12  C13  C8   180.00   0.0  0
 3RR  CONST_38  O1   C12  C11  C10  180.00   0.0  0
 3RR  CONST_39  CL2  C9   C8   C13  180.00   0.0  0
 3RR  CONST_40  CL1  C11  C12  C13  180.00   0.0  0
 3RR  CONST_41  C3   C4   C5   C15  180.00   0.0  0
 3RR  CONST_42  C2   C4   C5   C15    0.00   0.0  0
 3RR  CONST_43  CL1  C11  C10  C9   180.00   0.0  0
 3RR  CONST_44  CL2  C9   C10  C11  180.00   0.0  0
 3RR  CONST_45  CL2  C9   C8   C2     0.00   0.0  0
 3RR  CONST_46  C16  C6   N3   C3   180.00   0.0  0
 3RR  CONST_47  HN3  N3   C3   N1     0.00   0.0  0
 3RR  CONST_48  H10  C10  C9   C8   180.00   0.0  0
 3RR  CONST_49  H13  C13  C8   C9   180.00   0.0  0
 3RR  Var_01    H7   C7   C1   N1   109.77  30.0  2
 3RR  Var_02    H16  C16  C6   N3    63.12  30.0  2
 3RR  Var_03    H14  C14  O1   C12  -57.08  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
 3RR  plan-1  C8   0.020
 3RR  plan-1  C10  0.020
 3RR  plan-1  C13  0.020
 3RR  plan-1  C12  0.020
 3RR  plan-1  C9   0.020
 3RR  plan-1  C11  0.020
 3RR  plan-1  C2   0.020
 3RR  plan-1  O1   0.020
 3RR  plan-1  CL2  0.020
 3RR  plan-1  CL1  0.020
 3RR  plan-1  H10  0.020
 3RR  plan-1  H13  0.020
 3RR  plan-2  N1   0.020
 3RR  plan-2  N3   0.020
 3RR  plan-2  C4   0.020
 3RR  plan-2  C5   0.020
 3RR  plan-2  C6   0.020
 3RR  plan-2  C8   0.020
 3RR  plan-2  C15  0.020
 3RR  plan-2  C2   0.020
 3RR  plan-2  C3   0.020
 3RR  plan-2  C1   0.020
 3RR  plan-2  C16  0.020
 3RR  plan-2  N4   0.020
 3RR  plan-2  N2   0.020
 3RR  plan-2  HN3  0.020
 3RR  plan-2  C7   0.020

