# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 01:00:16 2021
#   Inital geometry file: a 87 line input string
#   Ligand name: 5-ethyl-~{N}4-methyl-6-piperidin-1-yl-pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1c(NC)nc(N)nc1N2CCCCC2
#
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
 C9L  C9L  5-ethyl-~{N}4-methyl-6-piperidin-1-yl-pyrimidine-2,4-diamine  ligand  38  17  .  2022-03-15  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C9L
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
 C9L  C11  C  CH3   0  -0.524  25.8425   7.5125  -18.6958
 C9L  C13  C  CH2   0  -0.284  30.9694   9.1703  -14.5550
 C9L  C15  C  CH2   0  -0.441  33.1109   8.7359  -15.8236
 C9L  C16  C  CH2   0  -0.431  32.2698   8.5012  -17.0731
 C9L  C17  C  CH2   0  -0.326  30.9528   9.2488  -16.9663
 C9L  C01  C  CH3   0  -0.705  29.0124   7.4316  -18.9884
 C9L  C03  C  CR6   0  -0.108  28.0654   8.2513  -16.6729
 C9L  C04  C  CR6   0   0.467  28.8519   8.9672  -15.7484
 C9L  N05  N  N     0  -0.517  28.3325   9.7129  -14.7738
 C9L  C06  C  CR6   0   0.517  27.0070   9.7702  -14.7035
 C9L  N07  N  NH2   0  -0.827  26.4779  10.5332  -13.7091
 C9L  N08  N  N     0  -0.526  26.1594   9.2060  -15.5478
 C9L  C09  C  CR6   0   0.453  26.6790   8.4488  -16.5242
 C9L  N10  N  NH1   0  -0.648  25.7309   7.8452  -17.2927
 C9L  N12  N  NT    0  -0.491  30.2288   8.8585  -15.7646
 C9L  C14  C  CH2   0  -0.434  32.3028   8.4313  -14.5675
 C9L  H1   H  HCH3  0   0.230  26.2992   6.5390  -18.8704
 C9L  H2   H  HCH3  0   0.260  24.8367   7.4746  -19.1078
 C9L  H3   H  HCH3  0   0.233  26.4024   8.2613  -19.2583
 C9L  H4   H  HCH2  0   0.201  31.1442  10.2521  -14.4592
 C9L  H5   H  HCH2  0   0.243  30.3872   8.8659  -13.6873
 C9L  H6   H  HCH2  0   0.233  34.0168   8.1262  -15.8492
 C9L  H7   H  HCH2  0   0.212  33.4382   9.7810  -15.8016
 C9L  H8   H  HCH2  0   0.218  32.0691   7.4328  -17.1988
 C9L  H9   H  HCH2  0   0.231  32.8025   8.8352  -17.9662
 C9L  H10  H  HCH2  0   0.220  31.1554  10.3309  -16.9313
 C9L  H11  H  HCH2  0   0.278  30.3373   9.0849  -17.8444
 C9L  H12  H  HCH3  0   0.236  30.0803   7.3056  -19.1666
 C9L  H13  H  HCH3  0   0.240  28.4996   6.7546  -19.6705
 C9L  H14  H  HCH3  0   0.230  28.7486   8.4456  -19.2874
 C9L  H15  H  HCH2  0   0.247  27.9571   6.2975  -17.4803
 C9L  H16  H  HCH2  0   0.254  29.5424   6.7919  -16.9960
 C9L  H17  H  HNH2  0   0.383  25.5096  10.3843  -13.4815
 C9L  H18  H  HNH2  0   0.383  27.0764  10.7444  -12.9291
 C9L  H19  H  HNH1  0   0.378  24.8030   8.1072  -17.0018
 C9L  H20  H  HCH2  0   0.216  32.1100   7.3561  -14.5047
 C9L  H21  H  HCH2  0   0.230  32.8669   8.7060  -13.6732
 C9L  C02  C  CH2   0  -0.532  28.6479   7.1421  -17.5150

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
 C9L  C01  C02  single    1.545  0.020  1.545
 C9L  C11  N10  single    1.446  0.020  1.446
 C9L  C02  C03  single    1.509  0.020  1.509
 C9L  N10  C09  single    1.362  0.020  1.362
 C9L  C17  C16  single    1.518  0.020  1.518
 C9L  C17  N12  single    1.456  0.020  1.456
 C9L  C16  C15  single    1.524  0.020  1.524
 C9L  C03  C09  aromatic  1.408  0.020  1.408
 C9L  C03  C04  aromatic  1.409  0.020  1.409
 C9L  C09  N08  aromatic  1.340  0.020  1.340
 C9L  C04  N12  single    1.381  0.020  1.381
 C9L  C04  N05  aromatic  1.333  0.020  1.333
 C9L  N08  C06  aromatic  1.323  0.020  1.323
 C9L  N12  C13  single    1.452  0.020  1.452
 C9L  C15  C14  single    1.524  0.020  1.524
 C9L  N05  C06  aromatic  1.329  0.020  1.329
 C9L  C06  N07  single    1.361  0.020  1.361
 C9L  C13  C14  single    1.525  0.020  1.525
 C9L  C11  H1   single    0.970  0.020  1.090
 C9L  C11  H2   single    0.970  0.020  1.090
 C9L  C11  H3   single    0.970  0.020  1.090
 C9L  C13  H4   single    0.970  0.020  1.090
 C9L  C13  H5   single    0.970  0.020  1.090
 C9L  C15  H6   single    0.970  0.020  1.090
 C9L  C15  H7   single    0.970  0.020  1.090
 C9L  C16  H8   single    0.970  0.020  1.090
 C9L  C16  H9   single    0.970  0.020  1.090
 C9L  C17  H10  single    0.970  0.020  1.090
 C9L  C17  H11  single    0.970  0.020  1.090
 C9L  C01  H12  single    0.970  0.020  1.090
 C9L  C01  H13  single    0.970  0.020  1.090
 C9L  C01  H14  single    0.970  0.020  1.090
 C9L  C02  H15  single    0.970  0.020  1.090
 C9L  C02  H16  single    0.970  0.020  1.090
 C9L  N07  H17  single    0.890  0.020  1.040
 C9L  N07  H18  single    0.890  0.020  1.040
 C9L  N10  H19  single    0.890  0.020  1.040
 C9L  C14  H20  single    0.970  0.020  1.090
 C9L  C14  H21  single    0.970  0.020  1.090

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
 C9L  H3   C11  H2   107.65  3.000
 C9L  H3   C11  H1   108.39  3.000
 C9L  H2   C11  H1   107.21  3.000
 C9L  H3   C11  N10  112.44  3.000
 C9L  H2   C11  N10  107.71  3.000
 C9L  H1   C11  N10  113.16  3.000
 C9L  H5   C13  H4   106.90  3.000
 C9L  H5   C13  C14  109.81  3.000
 C9L  H4   C13  C14  109.78  3.000
 C9L  H5   C13  N12  109.34  3.000
 C9L  H4   C13  N12  111.39  3.000
 C9L  C14  C13  N12  109.58  3.000
 C9L  H7   C15  H6   106.57  3.000
 C9L  H7   C15  C14  109.42  3.000
 C9L  H6   C15  C14  110.33  3.000
 C9L  H7   C15  C16  109.16  3.000
 C9L  H6   C15  C16  110.64  3.000
 C9L  C14  C15  C16  110.62  3.000
 C9L  H9   C16  H8   107.10  3.000
 C9L  H9   C16  C17  109.27  3.000
 C9L  H8   C16  C17  109.25  3.000
 C9L  H9   C16  C15  110.74  3.000
 C9L  H8   C16  C15  110.22  3.000
 C9L  C17  C16  C15  110.19  3.000
 C9L  H11  C17  H10  106.17  3.000
 C9L  H11  C17  N12  110.21  3.000
 C9L  H10  C17  N12  109.19  3.000
 C9L  H11  C17  C16  111.15  3.000
 C9L  H10  C17  C16  109.05  3.000
 C9L  N12  C17  C16  110.94  3.000
 C9L  H14  C01  H13  107.01  3.000
 C9L  H14  C01  H12  107.45  3.000
 C9L  H13  C01  H12  106.67  3.000
 C9L  H14  C01  C02  112.27  3.000
 C9L  H13  C01  C02  111.69  3.000
 C9L  H12  C01  C02  111.43  3.000
 C9L  C09  C03  C04  114.14  3.000
 C9L  C04  C03  C02  121.59  3.000
 C9L  C09  C03  C02  122.81  3.000
 C9L  N12  C04  N05  116.18  3.000
 C9L  N05  C04  C03  123.13  3.000
 C9L  N12  C04  C03  120.58  3.000
 C9L  C06  N05  C04  116.85  3.000
 C9L  N08  C06  N07  117.16  3.000
 C9L  N07  C06  N05  116.80  3.000
 C9L  N08  C06  N05  125.95  3.000
 C9L  H18  N07  H17  115.38  3.000
 C9L  H18  N07  C06  116.95  3.000
 C9L  H17  N07  C06  117.18  3.000
 C9L  C09  N08  C06  117.22  3.000
 C9L  N10  C09  N08  113.05  3.000
 C9L  N08  C09  C03  122.54  3.000
 C9L  N10  C09  C03  124.31  3.000
 C9L  H19  N10  C09  111.30  3.000
 C9L  H19  N10  C11  114.27  3.000
 C9L  C09  N10  C11  126.57  3.000
 C9L  C04  N12  C17  118.96  3.000
 C9L  C04  N12  C13  118.79  3.000
 C9L  C17  N12  C13  112.10  3.000
 C9L  H21  C14  H20  106.92  3.000
 C9L  H21  C14  C15  110.52  3.000
 C9L  H20  C14  C15  109.70  3.000
 C9L  H21  C14  C13  108.84  3.000
 C9L  H20  C14  C13  108.77  3.000
 C9L  C15  C14  C13  111.93  3.000
 C9L  H16  C02  H15  104.78  3.000
 C9L  H16  C02  C03  106.66  3.000
 C9L  H15  C02  C03  107.86  3.000
 C9L  H16  C02  C01  108.67  3.000
 C9L  H15  C02  C01  108.93  3.000
 C9L  C03  C02  C01  119.03  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
 C9L  CONST_01  C06  N08  C09  C03     0.00   0.0  0
 C9L  CONST_02  C06  N05  C04  C03     0.00   0.0  0
 C9L  CONST_03  N08  C09  C03  C04     0.00   0.0  0
 C9L  CONST_04  N08  C06  N05  C04     0.00   0.0  0
 C9L  CONST_05  C09  C03  C04  N05     0.00   0.0  0
 C9L  CONST_06  C09  N08  C06  N05     0.00   0.0  0
 C9L  CONST_07  N12  C04  N05  C06   180.00   0.0  0
 C9L  CONST_08  N12  C04  C03  C09   180.00   0.0  0
 C9L  CONST_10  N12  C04  C03  C02     0.00   0.0  0
 C9L  CONST_12  N10  C09  C03  C04   180.00   0.0  0
 C9L  CONST_13  N07  C06  N05  C04   180.00   0.0  0
 C9L  CONST_14  N10  C09  N08  C06   180.00   0.0  0
 C9L  CONST_15  C09  N08  C06  N07   180.00   0.0  0
 C9L  CONST_18  H19  N10  C09  C03   180.00   0.0  0
 C9L  Var_01    C16  C17  N12  C13    61.53  30.0  1
 C9L  Var_02    C03  C04  N12  C13  -157.13  30.0  2
 C9L  Var_03    C16  C15  C14  C13   -52.15  30.0  1
 C9L  Var_04    N12  C17  C16  C15   -56.47  30.0  1
 C9L  Var_05    N12  C13  C14  C15    55.24  30.0  1
 C9L  Var_06    C14  C15  C16  C17    51.98  30.0  1
 C9L  Var_07    C14  C13  N12  C17   -59.91  30.0  1
 C9L  Var_08    C09  C03  C02  C01    93.41  30.0  2
 C9L  Var_09    H12  C01  C02  C03   117.59  30.0  3
 C9L  Var_10    H1   C11  N10  C09    86.92  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
 C9L  plan-1  C03  0.020
 C9L  plan-1  C04  0.020
 C9L  plan-1  N05  0.020
 C9L  plan-1  C06  0.020
 C9L  plan-1  N07  0.020
 C9L  plan-1  N08  0.020
 C9L  plan-1  C09  0.020
 C9L  plan-1  N10  0.020
 C9L  plan-1  N12  0.020
 C9L  plan-1  C02  0.020
 C9L  plan-2  C06  0.020
 C9L  plan-2  N07  0.020
 C9L  plan-2  H17  0.020
 C9L  plan-2  H18  0.020
 C9L  plan-3  C11  0.020
 C9L  plan-3  C09  0.020
 C9L  plan-3  N10  0.020
 C9L  plan-3  H19  0.020

