# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 17:02:24 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: (7R)-8-(cyclopropylmethyl)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1N(CC2CC2)c3nc(Nc4cc(F)c(O)c(F)c4)ncc3N(CC#C)C1=O
#
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
 RTJ  RTJ  (7R)-8-(cyclopropylmethyl)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one  ligand  48  29  .  2022-08-10  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RTJ
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
 RTJ  C4   C  CR6   0   0.505  27.7030   0.3035  14.5520
 RTJ  C14  C  CH2   0  -0.482  31.7235   8.1944  12.8686
 RTJ  C5   C  CR6   0   0.044  26.8744  -0.5475  13.8380
 RTJ  C6   C  CR6   0   0.491  26.4430  -0.0575  12.6101
 RTJ  C11  C  C     0   0.551  31.7606   7.3101  15.1351
 RTJ  C7   C  CR6   0   0.591  28.7151   4.2763  12.7836
 RTJ  C8   C  CR16  0  -0.088  29.5380   6.3372  12.3623
 RTJ  C9   C  CR6   0   0.178  30.2754   6.3127  13.5247
 RTJ  C10  C  CR6   0   0.576  30.1162   5.1649  14.3285
 RTJ  C12  C  CH1   0  -0.248  31.1130   6.3668  16.1336
 RTJ  C13  C  CH3   0  -0.663  29.9113   7.0678  16.7732
 RTJ  N2   N  N     0  -0.479  28.7446   5.3381  11.9845
 RTJ  C3   C  CR16  0  -0.527  28.0923   1.5542  14.1171
 RTJ  N3   N  N     0  -0.522  29.3564   4.1522  13.9373
 RTJ  C1   C  CR16  0  -0.531  26.7959   1.1812  12.1304
 RTJ  C2   C  CR6   0   0.386  27.6310   2.0148  12.8840
 RTJ  N4   N  NT    0  -0.562  31.2233   7.2830  13.8846
 RTJ  N5   N  NT    0  -0.488  30.7764   5.1039  15.5008
 RTJ  F1   F  F     0  -0.310  25.6490  -0.8416  11.8699
 RTJ  F2   F  F     0  -0.320  28.1502  -0.1280  15.7454
 RTJ  O2   O  OH1   0  -0.620  26.4784  -1.7699  14.2392
 RTJ  C15  C  CSP   0   0.261  32.4618   7.4956  11.8208
 RTJ  C16  C  CSP1  0  -0.495  33.0673   6.9175  10.9597
 RTJ  C17  C  CH2   0  -0.333  30.8475   3.8696  16.2624
 RTJ  C18  C  CH1   0  -0.250  29.6870   3.6199  17.1913
 RTJ  C19  C  CH2   0  -0.493  29.8588   2.5991  18.2728
 RTJ  C20  C  CH2   0  -0.488  29.7560   4.0520  18.6241
 RTJ  H1   H  HCH2  0   0.318  32.3705   8.9200  13.3577
 RTJ  H2   H  HCH2  0   0.304  30.8968   8.7606  12.4338
 RTJ  H3   H  HCR6  0   0.282  29.5892   7.1799  11.6823
 RTJ  H4   H  HCH1  0   0.293  31.8630   6.1615  16.8980
 RTJ  H5   H  HCH3  0   0.275  29.4704   6.4350  17.5400
 RTJ  H6   H  HCH3  0   0.250  30.2223   8.0016  17.2412
 RTJ  H7   H  HCH3  0   0.238  29.1445   7.2948  16.0316
 RTJ  H8   H  HNH1  0   0.411  27.4986   3.4500  11.4451
 RTJ  H9   H  HCR6  0   0.334  28.7421   2.1513  14.7359
 RTJ  H10  H  HCR6  0   0.294  26.4184   1.4964  11.1651
 RTJ  H11  H  HOH1  0   0.477  26.8366  -1.9783  15.1098
 RTJ  H12  H  H     0   0.282  33.6105   6.4039  10.1993
 RTJ  H13  H  HCH2  0   0.266  30.9381   3.0491  15.5498
 RTJ  H14  H  HCH2  0   0.261  31.7798   3.8932  16.8331
 RTJ  H15  H  HCH1  0   0.262  28.7111   3.6612  16.7192
 RTJ  H16  H  HCH2  0   0.253  29.0233   1.9506  18.5021
 RTJ  H17  H  HCH2  0   0.245  30.8282   2.1242  18.3685
 RTJ  H18  H  HCH2  0   0.247  30.6555   4.5550  18.9605
 RTJ  H19  H  HCH2  0   0.253  28.8483   4.4037  19.0978
 RTJ  N1   N  NH1   0  -0.779  27.9318   3.2513  12.3343
 RTJ  O1   O  O     0  -0.452  32.6487   8.0718  15.4636

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
 RTJ  C16  C15  triple    1.201  0.020  1.201
 RTJ  N2   C8   aromatic  1.330  0.020  1.330
 RTJ  N2   C7   aromatic  1.329  0.020  1.329
 RTJ  C15  C14  single    1.460  0.020  1.460
 RTJ  C8   C9   aromatic  1.377  0.020  1.377
 RTJ  N1   C7   single    1.366  0.020  1.366
 RTJ  N1   C2   single    1.386  0.020  1.386
 RTJ  C1   C2   aromatic  1.400  0.020  1.400
 RTJ  C1   C6   aromatic  1.374  0.020  1.374
 RTJ  F1   C6   single    1.339  0.020  1.339
 RTJ  C7   N3   aromatic  1.326  0.020  1.326
 RTJ  C14  N4   single    1.454  0.020  1.454
 RTJ  C2   C3   aromatic  1.395  0.020  1.395
 RTJ  C6   C5   aromatic  1.391  0.020  1.391
 RTJ  C9   N4   single    1.403  0.020  1.403
 RTJ  C9   C10  aromatic  1.410  0.020  1.410
 RTJ  N4   C11  single    1.361  0.020  1.361
 RTJ  N3   C10  aromatic  1.325  0.020  1.325
 RTJ  C3   C4   aromatic  1.380  0.020  1.380
 RTJ  C10  N5   single    1.347  0.020  1.347
 RTJ  C5   C4   aromatic  1.386  0.020  1.386
 RTJ  C5   O2   single    1.346  0.020  1.346
 RTJ  C4   F2   single    1.346  0.020  1.346
 RTJ  C11  O1   double    1.215  0.020  1.215
 RTJ  C11  C12  single    1.519  0.020  1.519
 RTJ  N5   C12  single    1.452  0.020  1.452
 RTJ  N5   C17  single    1.452  0.020  1.452
 RTJ  C12  C13  single    1.531  0.020  1.531
 RTJ  C17  C18  single    1.507  0.020  1.507
 RTJ  C18  C19  single    1.497  0.020  1.497
 RTJ  C18  C20  single    1.498  0.020  1.498
 RTJ  C19  C20  single    1.498  0.020  1.498
 RTJ  C14  H1   single    0.939  0.020  1.096
 RTJ  C14  H2   single    0.939  0.020  1.096
 RTJ  C8   H3   single    0.929  0.020  1.085
 RTJ  C12  H4   single    0.939  0.020  1.096
 RTJ  C13  H5   single    0.939  0.020  1.096
 RTJ  C13  H6   single    0.939  0.020  1.096
 RTJ  C13  H7   single    0.939  0.020  1.096
 RTJ  N1   H8   single    0.868  0.020  1.013
 RTJ  C3   H9   single    0.929  0.020  1.085
 RTJ  C1   H10  single    0.929  0.020  1.085
 RTJ  O2   H11  single    0.832  0.020  0.971
 RTJ  C16  H12  single    0.913  0.020  1.066
 RTJ  C17  H13  single    0.939  0.020  1.096
 RTJ  C17  H14  single    0.939  0.020  1.096
 RTJ  C18  H15  single    0.939  0.020  1.096
 RTJ  C19  H16  single    0.939  0.020  1.096
 RTJ  C19  H17  single    0.939  0.020  1.096
 RTJ  C20  H18  single    0.939  0.020  1.096
 RTJ  C20  H19  single    0.939  0.020  1.096

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
 RTJ  F2   C4   C3   118.45  3.000
 RTJ  F2   C4   C5   117.31  3.000
 RTJ  C3   C4   C5   124.24  3.000
 RTJ  H2   C14  H1   106.45  3.000
 RTJ  H2   C14  C15  110.19  3.000
 RTJ  H1   C14  C15  109.94  3.000
 RTJ  H2   C14  N4   110.05  3.000
 RTJ  H1   C14  N4   107.97  3.000
 RTJ  C15  C14  N4   112.06  3.000
 RTJ  O2   C5   C6   119.46  3.000
 RTJ  O2   C5   C4   125.45  3.000
 RTJ  C6   C5   C4   115.09  3.000
 RTJ  F1   C6   C1   119.15  3.000
 RTJ  F1   C6   C5   117.76  3.000
 RTJ  C1   C6   C5   123.09  3.000
 RTJ  O1   C11  N4   123.32  3.000
 RTJ  O1   C11  C12  121.55  3.000
 RTJ  N4   C11  C12  115.04  3.000
 RTJ  N3   C7   N2   125.96  3.000
 RTJ  N3   C7   N1   119.56  3.000
 RTJ  N2   C7   N1   114.49  3.000
 RTJ  H3   C8   N2   115.71  3.000
 RTJ  H3   C8   C9   121.20  3.000
 RTJ  N2   C8   C9   123.08  3.000
 RTJ  N4   C9   C10  119.53  3.000
 RTJ  C10  C9   C8   115.79  3.000
 RTJ  N4   C9   C8   124.47  3.000
 RTJ  N5   C10  N3   120.23  3.000
 RTJ  N5   C10  C9   118.53  3.000
 RTJ  N3   C10  C9   121.23  3.000
 RTJ  H4   C12  N5   107.53  3.000
 RTJ  H4   C12  C13  109.46  3.000
 RTJ  N5   C12  C13  113.47  3.000
 RTJ  H4   C12  C11  106.54  3.000
 RTJ  C13  C12  C11  108.96  3.000
 RTJ  N5   C12  C11  110.64  3.000
 RTJ  H7   C13  H6   108.32  3.000
 RTJ  H7   C13  H5   108.39  3.000
 RTJ  H6   C13  H5   108.15  3.000
 RTJ  H7   C13  C12  111.28  3.000
 RTJ  H6   C13  C12  110.35  3.000
 RTJ  H5   C13  C12  110.26  3.000
 RTJ  C8   N2   C7   116.26  3.000
 RTJ  H9   C3   C2   121.61  3.000
 RTJ  H9   C3   C4   119.41  3.000
 RTJ  C2   C3   C4   118.98  3.000
 RTJ  C10  N3   C7   117.56  3.000
 RTJ  H10  C1   C2   120.94  3.000
 RTJ  H10  C1   C6   118.93  3.000
 RTJ  C2   C1   C6   120.13  3.000
 RTJ  C1   C2   C3   118.46  3.000
 RTJ  C3   C2   N1   124.98  3.000
 RTJ  C1   C2   N1   116.56  3.000
 RTJ  C9   N4   C11  121.06  3.000
 RTJ  C11  N4   C14  119.59  3.000
 RTJ  C9   N4   C14  119.12  3.000
 RTJ  C17  N5   C12  119.95  3.000
 RTJ  C17  N5   C10  121.27  3.000
 RTJ  C12  N5   C10  116.97  3.000
 RTJ  H11  O2   C5   110.87  3.000
 RTJ  C16  C15  C14  180.00  3.000
 RTJ  H12  C16  C15  180.00  3.000
 RTJ  H14  C17  H13  106.65  3.000
 RTJ  H14  C17  C18  109.78  3.000
 RTJ  H13  C17  C18  110.00  3.000
 RTJ  H14  C17  N5   107.29  3.000
 RTJ  H13  C17  N5   107.51  3.000
 RTJ  C18  C17  N5   115.23  3.000
 RTJ  H15  C18  C20  116.53  3.000
 RTJ  H15  C18  C19  116.33  3.000
 RTJ  C20  C18  C19   60.03  3.000
 RTJ  H15  C18  C17  114.72  3.000
 RTJ  C20  C18  C17  120.40  3.000
 RTJ  C19  C18  C17  118.02  3.000
 RTJ  H17  C19  H16  114.16  3.000
 RTJ  H17  C19  C20  117.75  3.000
 RTJ  H16  C19  C20  118.59  3.000
 RTJ  H17  C19  C18  117.72  3.000
 RTJ  H16  C19  C18  118.23  3.000
 RTJ  C20  C19  C18   60.02  3.000
 RTJ  H19  C20  H18  114.15  3.000
 RTJ  H19  C20  C19  118.37  3.000
 RTJ  H18  C20  C19  117.76  3.000
 RTJ  H19  C20  C18  118.27  3.000
 RTJ  H18  C20  C18  117.96  3.000
 RTJ  C19  C20  C18   59.95  3.000
 RTJ  H8   N1   C2   115.59  3.000
 RTJ  H8   N1   C7   112.85  3.000
 RTJ  C2   N1   C7   131.56  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
 RTJ  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 RTJ  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 RTJ  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 RTJ  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 RTJ  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 RTJ  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 RTJ  CONST_07  C9   C8   N2   C7      0.00   0.0  0
 RTJ  CONST_08  C9   C10  N3   C7      0.00   0.0  0
 RTJ  CONST_09  N3   C7   N2   C8      0.00   0.0  0
 RTJ  CONST_10  N3   C10  C9   C8      0.00   0.0  0
 RTJ  CONST_11  N2   C8   C9   C10     0.00   0.0  0
 RTJ  CONST_12  N2   C7   N3   C10     0.00   0.0  0
 RTJ  CONST_13  C12  C11  N4   C9      0.00   0.0  0
 RTJ  CONST_14  N1   C2   C3   C4    180.00   0.0  0
 RTJ  CONST_15  F1   C6   C5   C4    180.00   0.0  0
 RTJ  CONST_16  N1   C2   C1   C6    180.00   0.0  0
 RTJ  CONST_17  F2   C4   C5   C6    180.00   0.0  0
 RTJ  CONST_18  N1   C7   N2   C8    180.00   0.0  0
 RTJ  CONST_19  N1   C7   N3   C10   180.00   0.0  0
 RTJ  CONST_20  O2   C5   C4   C3    180.00   0.0  0
 RTJ  CONST_21  O2   C5   C6   C1    180.00   0.0  0
 RTJ  CONST_22  F1   C6   C1   C2    180.00   0.0  0
 RTJ  CONST_23  F2   C4   C3   C2    180.00   0.0  0
 RTJ  CONST_24  C12  C11  N4   C14   180.00   0.0  0
 RTJ  CONST_25  O1   C11  N4   C9    180.00   0.0  0
 RTJ  CONST_26  H10  C1   C6   C5    180.00   0.0  0
 RTJ  CONST_27  H9   C3   C4   C5    180.00   0.0  0
 RTJ  CONST_28  H3   C8   N2   C7    180.00   0.0  0
 RTJ  CONST_29  O1   C11  N4   C14     0.00   0.0  0
 RTJ  Var_01    C8   C9   N4   C11   169.59  30.0  1
 RTJ  Var_02    C12  N5   C10  C9     26.25  30.0  1
 RTJ  Var_03    C1   C2   N1   C7   -178.88  30.0  2
 RTJ  Var_04    C18  C17  N5   C10   -85.93  30.0  3
 RTJ  Var_05    C2   N1   C7   N2   -178.66  30.0  2
 RTJ  Var_06    C19  C18  C17  N5   -163.05  30.0  3
 RTJ  Var_07    C20  C19  C18  C17   110.79  30.0  1
 RTJ  Var_08    H18  C20  C19  C18  -107.92  30.0  1
 RTJ  Var_09    C15  C14  N4   C11   110.62  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
 RTJ  chir_01  C12  C11  N5   C13  positiv
 RTJ  chir_02  C18  C17  C19  C20  both

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
 RTJ  plan-1  C4   0.020
 RTJ  plan-1  C5   0.020
 RTJ  plan-1  C6   0.020
 RTJ  plan-1  C3   0.020
 RTJ  plan-1  C1   0.020
 RTJ  plan-1  C2   0.020
 RTJ  plan-1  F1   0.020
 RTJ  plan-1  F2   0.020
 RTJ  plan-1  O2   0.020
 RTJ  plan-1  H9   0.020
 RTJ  plan-1  H10  0.020
 RTJ  plan-1  N1   0.020
 RTJ  plan-2  C7   0.020
 RTJ  plan-2  C8   0.020
 RTJ  plan-2  C9   0.020
 RTJ  plan-2  C10  0.020
 RTJ  plan-2  N2   0.020
 RTJ  plan-2  N3   0.020
 RTJ  plan-2  N4   0.020
 RTJ  plan-2  N5   0.020
 RTJ  plan-2  H3   0.020
 RTJ  plan-2  N1   0.020
 RTJ  plan-3  C14  0.020
 RTJ  plan-3  C11  0.020
 RTJ  plan-3  C9   0.020
 RTJ  plan-3  C12  0.020
 RTJ  plan-3  N4   0.020
 RTJ  plan-3  O1   0.020

