# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 02:34:55 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 5-{2-amino-4-chloro-7-[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]-7H-pyrrolo[2,3-d]pyrimidin-5-yl}-2-methylpent-4-yn-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1c(C)cnc(Cn2cc(C#CCC(C)(C)O)c3c(Cl)nc(N)nc23)c1C
#
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
 7PP  7PP  5-{2-amino-4-chloro-7-[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]-7H-pyrrolo[2,3-d]pyrimidin-5-yl}-2-methylpent-4-yn-2-ol  ligand  53  29  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7PP
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
 7PP  CL    CL  CL    0  -0.094  -2.7469   3.1122   0.8032
 7PP  C1    C   CR6   0   0.022  -1.2506   2.6816   0.0547
 7PP  N5    N   N     0  -0.452  -0.3779   3.6369  -0.1110
 7PP  C21   C   CR6   0   0.541   0.8002   3.3231  -0.6927
 7PP  N4    N   NH2   0  -0.824   1.6605   4.3449  -0.8804
 7PP  N3    N   N     0  -0.486   1.1585   2.1157  -1.1149
 7PP  C20   C   CR56  0   0.559   0.2400   1.1849  -0.9280
 7PP  C2    C   CR56  0   0.048  -1.0232   1.3739  -0.3354
 7PP  N1    N   NR5   0  -0.506   0.3465  -0.1174  -1.2806
 7PP  C11   C   CH2   0  -0.376   1.5386  -0.7411  -1.7844
 7PP  C12   C   CR6   0   0.170   2.5162  -1.0954  -0.6850
 7PP  C18   C   CR6   0  -0.022   3.7564  -1.6465  -1.0241
 7PP  C19   C   CH3   0  -0.762   4.1233  -1.9108  -2.4537
 7PP  C16   C   CR6   0   0.393   4.6209  -1.9346   0.0288
 7PP  O2    O   O2    0  -0.484   5.8397  -2.4831  -0.2111
 7PP  C17   C   CH3   0  -0.415   6.8561  -1.5408  -0.5360
 7PP  C14   C   CR6   0  -0.067   4.2415  -1.6946   1.3514
 7PP  C15   C   CH3   0  -0.719   5.1447  -2.0066   2.5039
 7PP  C13   C   CR16  0  -0.134   2.9777  -1.1605   1.5423
 7PP  N2    N   N     0  -0.410   2.1387  -0.8608   0.5585
 7PP  C10   C   CR15  0  -0.050  -0.7956  -0.7740  -0.8972
 7PP  C3    C   CR5   0  -0.180  -1.6811   0.0965  -0.3230
 7PP  C4    C   CSP   0   0.103  -2.9713  -0.2253   0.1578
 7PP  C5    C   CSP   0   0.051  -4.0735  -0.5128   0.5534
 7PP  C6    C   CH2   0  -0.645  -5.3996  -0.8744   1.0289
 7PP  C7    C   CT    0   0.191  -5.8080  -2.3130   0.6419
 7PP  C9    C   CH3   0  -0.659  -4.8756  -3.3231   1.2939
 7PP  C8    C   CH3   0  -0.675  -7.2466  -2.5508   1.0943
 7PP  O1    O   OH1   0  -0.667  -5.6848  -2.4950  -0.7559
 7PP  HN4   H   HNH2  0   0.398   1.5060   5.1982  -0.3716
 7PP  HN4A  H   HNH2  0   0.397   2.6137   4.1288  -1.1164
 7PP  H11   H   HCH2  0   0.295   1.2450  -1.6364  -2.3366
 7PP  H11A  H   HCH2  0   0.290   2.0072  -0.0714  -2.5079
 7PP  H19   H   HCH3  0   0.259   4.3909  -0.9875  -2.9727
 7PP  H19A  H   HCH3  0   0.266   4.9668  -2.5921  -2.5355
 7PP  H19B  H   HCH3  0   0.258   3.2930  -2.3556  -3.0024
 7PP  H17   H   HCH3  0   0.230   6.6326  -1.0074  -1.4632
 7PP  H17A  H   HCH3  0   0.229   6.9929  -0.8080   0.2634
 7PP  H17B  H   HCH3  0   0.246   7.7806  -2.0991  -0.6647
 7PP  H15   H   HCH3  0   0.247   6.0339  -1.3733   2.5051
 7PP  H15A  H   HCH3  0   0.248   4.6283  -1.8454   3.4492
 7PP  H15B  H   HCH3  0   0.250   5.4867  -3.0413   2.4805
 7PP  H13   H   HCR6  0   0.256   2.6286  -0.9601   2.5506
 7PP  H10   H   HCR5  0   0.301  -0.9067  -1.8314  -1.0773
 7PP  H6    H   HCH2  0   0.267  -5.4464  -0.7666   2.1167
 7PP  H6A   H   HCH2  0   0.269  -6.1335  -0.1681   0.6248
 7PP  H9    H   HCH3  0   0.227  -4.9250  -3.2378   2.3797
 7PP  H9A   H   HCH3  0   0.236  -5.1592  -4.3412   1.0236
 7PP  H9B   H   HCH3  0   0.238  -3.8392  -3.1664   0.9913
 7PP  H8    H   HCH3  0   0.231  -7.9347  -1.8489   0.6169
 7PP  H8A   H   HCH3  0   0.240  -7.5677  -3.5632   0.8443
 7PP  H8B   H   HCH3  0   0.228  -7.3468  -2.4251   2.1731
 7PP  HO1   H   HOH1  0   0.444  -6.3116  -1.9127  -1.1987

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
 7PP  C1   CL    single    1.728  0.020  1.728
 7PP  N5   C1    aromatic  1.304  0.020  1.304
 7PP  C2   C1    aromatic  1.383  0.020  1.383
 7PP  C21  N5    aromatic  1.351  0.020  1.351
 7PP  N4   C21   single    1.349  0.020  1.349
 7PP  N3   C21   aromatic  1.328  0.020  1.328
 7PP  N4   HN4   single    0.890  0.020  1.040
 7PP  N4   HN4A  single    0.890  0.020  1.040
 7PP  N3   C20   aromatic  1.321  0.020  1.321
 7PP  N1   C20   aromatic  1.353  0.020  1.353
 7PP  C20  C2    aromatic  1.408  0.020  1.408
 7PP  C2   C3    aromatic  1.437  0.020  1.437
 7PP  C11  N1    single    1.437  0.020  1.437
 7PP  N1   C10   aromatic  1.372  0.020  1.372
 7PP  C11  C12   single    1.513  0.020  1.513
 7PP  C11  H11   single    0.970  0.020  1.090
 7PP  C11  H11A  single    0.970  0.020  1.090
 7PP  N2   C12   aromatic  1.321  0.020  1.321
 7PP  C12  C18   aromatic  1.399  0.020  1.399
 7PP  C18  C19   single    1.499  0.020  1.499
 7PP  C18  C16   aromatic  1.392  0.020  1.392
 7PP  C19  H19   single    0.970  0.020  1.090
 7PP  C19  H19A  single    0.970  0.020  1.090
 7PP  C19  H19B  single    0.970  0.020  1.090
 7PP  C14  C16   aromatic  1.397  0.020  1.397
 7PP  C16  O2    single    1.358  0.020  1.358
 7PP  O2   C17   single    1.424  0.020  1.424
 7PP  C17  H17   single    0.970  0.020  1.090
 7PP  C17  H17A  single    0.970  0.020  1.090
 7PP  C17  H17B  single    0.970  0.020  1.090
 7PP  C13  C14   aromatic  1.385  0.020  1.385
 7PP  C14  C15   single    1.497  0.020  1.497
 7PP  C15  H15   single    0.970  0.020  1.090
 7PP  C15  H15A  single    0.970  0.020  1.090
 7PP  C15  H15B  single    0.970  0.020  1.090
 7PP  N2   C13   aromatic  1.327  0.020  1.327
 7PP  C13  H13   single    0.930  0.020  1.080
 7PP  C10  C3    aromatic  1.368  0.020  1.368
 7PP  C10  H10   single    0.930  0.020  1.080
 7PP  C3   C4    single    1.414  0.020  1.414
 7PP  C4   C5    triple    1.206  0.020  1.206
 7PP  C5   C6    single    1.454  0.020  1.454
 7PP  C6   C7    single    1.545  0.020  1.545
 7PP  C6   H6    single    0.970  0.020  1.090
 7PP  C6   H6A   single    0.970  0.020  1.090
 7PP  C8   C7    single    1.527  0.020  1.527
 7PP  C7   O1    single    1.415  0.020  1.415
 7PP  C7   C9    single    1.522  0.020  1.522
 7PP  C9   H9    single    0.970  0.020  1.090
 7PP  C9   H9A   single    0.970  0.020  1.090
 7PP  C9   H9B   single    0.970  0.020  1.090
 7PP  C8   H8    single    0.970  0.020  1.090
 7PP  C8   H8A   single    0.970  0.020  1.090
 7PP  C8   H8B   single    0.970  0.020  1.090
 7PP  O1   HO1   single    0.850  0.020  0.980

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
 7PP  C2    C1   N5    123.13  3.000
 7PP  C2    C1   CL    120.01  3.000
 7PP  N5    C1   CL    116.87  3.000
 7PP  C21   N5   C1    117.91  3.000
 7PP  N3    C21  N4    118.19  3.000
 7PP  N3    C21  N5    125.68  3.000
 7PP  N4    C21  N5    116.11  3.000
 7PP  HN4A  N4   HN4   116.54  3.000
 7PP  HN4A  N4   C21   118.32  3.000
 7PP  HN4   N4   C21   118.33  3.000
 7PP  C20   N3   C21   114.08  3.000
 7PP  N1    C20  C2    108.02  3.000
 7PP  C2    C20  N3    126.07  3.000
 7PP  N1    C20  N3    125.90  3.000
 7PP  C3    C2   C20   107.16  3.000
 7PP  C3    C2   C1    139.70  3.000
 7PP  C20   C2   C1    113.14  3.000
 7PP  C10   N1   C11   125.51  3.000
 7PP  C10   N1   C20   108.80  3.000
 7PP  C11   N1   C20   125.06  3.000
 7PP  H11A  C11  H11   106.45  3.000
 7PP  H11A  C11  C12   110.36  3.000
 7PP  H11   C11  C12   110.43  3.000
 7PP  H11A  C11  N1    108.80  3.000
 7PP  H11   C11  N1    108.07  3.000
 7PP  C12   C11  N1    112.52  3.000
 7PP  N2    C12  C18   123.48  3.000
 7PP  C18   C12  C11   119.27  3.000
 7PP  N2    C12  C11   117.25  3.000
 7PP  C16   C18  C19   122.18  3.000
 7PP  C16   C18  C12   116.66  3.000
 7PP  C19   C18  C12   121.16  3.000
 7PP  H19B  C19  H19A  107.30  3.000
 7PP  H19B  C19  H19   107.00  3.000
 7PP  H19A  C19  H19   107.68  3.000
 7PP  H19B  C19  C18   111.44  3.000
 7PP  H19A  C19  C18   111.84  3.000
 7PP  H19   C19  C18   111.34  3.000
 7PP  C14   C16  O2    118.72  3.000
 7PP  O2    C16  C18   120.48  3.000
 7PP  C14   C16  C18   120.78  3.000
 7PP  C17   O2   C16   114.44  3.000
 7PP  H17B  C17  H17A  108.92  3.000
 7PP  H17B  C17  H17   108.90  3.000
 7PP  H17A  C17  H17   108.60  3.000
 7PP  H17B  C17  O2    107.11  3.000
 7PP  H17A  C17  O2    111.48  3.000
 7PP  H17   C17  O2    111.76  3.000
 7PP  C13   C14  C15   121.65  3.000
 7PP  C15   C14  C16   121.95  3.000
 7PP  C13   C14  C16   116.40  3.000
 7PP  H15B  C15  H15A  107.93  3.000
 7PP  H15B  C15  H15   107.17  3.000
 7PP  H15A  C15  H15   107.42  3.000
 7PP  H15B  C15  C14   111.75  3.000
 7PP  H15A  C15  C14   110.56  3.000
 7PP  H15   C15  C14   111.80  3.000
 7PP  H13   C13  N2    116.33  3.000
 7PP  H13   C13  C14   119.50  3.000
 7PP  N2    C13  C14   124.17  3.000
 7PP  C13   N2   C12   118.50  3.000
 7PP  H10   C10  C3    128.86  3.000
 7PP  H10   C10  N1    120.56  3.000
 7PP  C3    C10  N1    110.58  3.000
 7PP  C4    C3   C10   126.05  3.000
 7PP  C4    C3   C2    128.53  3.000
 7PP  C10   C3   C2    105.41  3.000
 7PP  C5    C4   C3    180.00  3.000
 7PP  C6    C5   C4    180.00  3.000
 7PP  H6A   C6   H6    105.93  3.000
 7PP  H6A   C6   C7    109.31  3.000
 7PP  H6    C6   C7    109.24  3.000
 7PP  H6A   C6   C5    109.26  3.000
 7PP  H6    C6   C5    109.85  3.000
 7PP  C7    C6   C5    113.00  3.000
 7PP  O1    C7   C8    110.78  3.000
 7PP  O1    C7   C9    106.54  3.000
 7PP  C8    C7   C9    110.31  3.000
 7PP  C9    C7   C6    110.42  3.000
 7PP  O1    C7   C6    110.14  3.000
 7PP  C8    C7   C6    108.66  3.000
 7PP  H9B   C9   H9A   108.20  3.000
 7PP  H9B   C9   H9    107.94  3.000
 7PP  H9A   C9   H9    107.94  3.000
 7PP  H9B   C9   C7    111.59  3.000
 7PP  H9A   C9   C7    110.74  3.000
 7PP  H9    C9   C7    110.31  3.000
 7PP  H8B   C8   H8A   107.85  3.000
 7PP  H8B   C8   H8    107.48  3.000
 7PP  H8A   C8   H8    108.09  3.000
 7PP  H8B   C8   C7    111.21  3.000
 7PP  H8A   C8   C7    110.73  3.000
 7PP  H8    C8   C7    111.33  3.000
 7PP  HO1   O1   C7    108.64  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
 7PP  CONST_01  N3    C21  N5   C1      0.00   0.0  0
 7PP  CONST_02  N3    C20  C2   C1      0.00   0.0  0
 7PP  CONST_03  N1    C20  C2   C1    180.00   0.0  0
 7PP  CONST_04  C10   C3   C2   C1    180.00   0.0  0
 7PP  CONST_05  C20   C2   C1   N5      0.00   0.0  0
 7PP  CONST_06  C3    C2   C1   N5    180.00   0.0  0
 7PP  CONST_07  C20   N3   C21  N5      0.00   0.0  0
 7PP  CONST_08  C2    C1   N5   C21     0.00   0.0  0
 7PP  CONST_09  N1    C20  N3   C21   180.00   0.0  0
 7PP  CONST_10  C2    C20  N3   C21     0.00   0.0  0
 7PP  CONST_11  C10   N1   C20  N3    180.00   0.0  0
 7PP  CONST_12  C3    C2   C20  N3    180.00   0.0  0
 7PP  CONST_13  C3    C10  N1   C20     0.00   0.0  0
 7PP  CONST_14  C10   C3   C2   C20     0.00   0.0  0
 7PP  CONST_15  C10   N1   C20  C2      0.00   0.0  0
 7PP  CONST_16  N1    C10  C3   C2      0.00   0.0  0
 7PP  CONST_17  C3    C2   C20  N1      0.00   0.0  0
 7PP  CONST_18  C14   C13  N2   C12     0.00   0.0  0
 7PP  CONST_19  C14   C16  C18  C12     0.00   0.0  0
 7PP  CONST_20  C13   N2   C12  C18     0.00   0.0  0
 7PP  CONST_21  C13   C14  C16  C18     0.00   0.0  0
 7PP  CONST_22  N2    C12  C18  C16     0.00   0.0  0
 7PP  CONST_23  N2    C13  C14  C16     0.00   0.0  0
 7PP  CONST_24  C21   N5   C1   CL    180.00   0.0  0
 7PP  CONST_25  C20   C2   C1   CL    180.00   0.0  0
 7PP  CONST_26  C3    C2   C1   CL      0.00   0.0  0
 7PP  CONST_27  N4    C21  N5   C1    180.00   0.0  0
 7PP  CONST_28  C4    C3   C2   C1      0.00   0.0  0
 7PP  CONST_29  C20   N3   C21  N4    180.00   0.0  0
 7PP  CONST_30  C11   N1   C20  N3      0.00   0.0  0
 7PP  CONST_31  C4    C3   C2   C20   180.00   0.0  0
 7PP  CONST_32  C11   N1   C20  C2    180.00   0.0  0
 7PP  CONST_33  C4    C3   C10  N1    180.00   0.0  0
 7PP  CONST_34  C3    C10  N1   C11   180.00   0.0  0
 7PP  CONST_35  C13   N2   C12  C11   180.00   0.0  0
 7PP  CONST_36  C16   C18  C12  C11   180.00   0.0  0
 7PP  CONST_37  O2    C16  C18  C12   180.00   0.0  0
 7PP  CONST_38  C15   C14  C16  C18   180.00   0.0  0
 7PP  CONST_39  N2    C12  C18  C19   180.00   0.0  0
 7PP  CONST_40  C14   C16  C18  C19   180.00   0.0  0
 7PP  CONST_41  C13   C14  C16  O2    180.00   0.0  0
 7PP  CONST_42  N2    C13  C14  C15   180.00   0.0  0
 7PP  CONST_43  H10   C10  N1   C20   180.00   0.0  0
 7PP  CONST_44  H13   C13  N2   C12   180.00   0.0  0
 7PP  CONST_46  HN4A  N4   C21  N5    180.00   0.0  0
 7PP  Var_01    C12   C11  N1   C20    79.86  30.0  1
 7PP  Var_02    N2    C12  C11  N1      3.31  30.0  2
 7PP  Var_03    C14   C16  O2   C17   -97.02  30.0  2
 7PP  Var_04    H19   C19  C18  C12    76.29  30.0  2
 7PP  Var_05    H15   C15  C14  C16    66.26  30.0  2
 7PP  Var_06    H17   C17  O2   C16   -62.97  30.0  3
 7PP  Var_07    C7    C6   C5   C4    -19.07  30.0  3
 7PP  Var_08    C8    C7   C6   C5   -175.77  30.0  3
 7PP  Var_09    H8    C8   C7   C6     60.20  30.0  3
 7PP  Var_10    H9    C9   C7   C6     60.59  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
 7PP  plan-1  C11   0.020
 7PP  plan-1  C12   0.020
 7PP  plan-1  C18   0.020
 7PP  plan-1  C19   0.020
 7PP  plan-1  C16   0.020
 7PP  plan-1  O2    0.020
 7PP  plan-1  C14   0.020
 7PP  plan-1  C15   0.020
 7PP  plan-1  C13   0.020
 7PP  plan-1  N2    0.020
 7PP  plan-1  H13   0.020
 7PP  plan-2  CL    0.020
 7PP  plan-2  C1    0.020
 7PP  plan-2  N5    0.020
 7PP  plan-2  C21   0.020
 7PP  plan-2  N4    0.020
 7PP  plan-2  N3    0.020
 7PP  plan-2  C20   0.020
 7PP  plan-2  C2    0.020
 7PP  plan-2  N1    0.020
 7PP  plan-2  C11   0.020
 7PP  plan-2  C10   0.020
 7PP  plan-2  C3    0.020
 7PP  plan-2  C4    0.020
 7PP  plan-2  C5    0.020
 7PP  plan-2  H10   0.020
 7PP  plan-3  C21   0.020
 7PP  plan-3  N4    0.020
 7PP  plan-3  HN4   0.020
 7PP  plan-3  HN4A  0.020

