# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 11:44:22 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 3-methyl-2-[[(3~{R})-1-methylpiperidin-3-yl]amino]-5~{H}-pyrrolo[3,2-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC[C@H](C1)NC2=Nc3cc[nH]c3C(=O)N2C
#
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
 B4L  B4L  3-methyl-2-[[(3~{R})-1-methylpiperidin-3-yl]amino]-5~{H}-pyrrolo[3,2-d]pyrimidin-4-one  ligand  38  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B4L
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
 B4L  C10  C  CR15  0  -0.018  -3.7372  -2.4423   0.3551
 B4L  C13  C  CR16  0  -0.065   1.9288   0.3879   0.5449
 B4L  C17  C  C     0  -0.443   4.3269   0.5554   1.2233
 B4L  N01  N  NH1   0  -0.712   0.7247   1.1550   0.2943
 B4L  C02  C  CR6   0   0.744  -0.4960   0.5838   0.1825
 B4L  C04  C  CR6   0   0.536  -2.8575   0.9714  -0.3295
 B4L  C06  C  CR56  0   0.121  -2.9825  -0.4011  -0.0102
 B4L  C07  C  CR56  0   0.202  -1.8952  -1.1741   0.3690
 B4L  C09  C  CR15  0  -0.427  -2.3816  -2.4843   0.6024
 B4L  N11  N  NR15  0  -0.647  -4.0964  -1.1936  -0.0135
 B4L  C12  C  CH3   0  -0.590  -1.2612   2.8207  -0.4842
 B4L  C14  C  C     0  -0.264   2.4030  -0.3331  -0.7169
 B4L  C16  C  C     0  -0.276   4.6968  -0.1695  -0.0607
 B4L  C18  C  C     0  -0.456   3.0192   1.3192   1.0593
 B4L  N03  N  NR6   0  -0.590  -1.5335   1.4190  -0.1998
 B4L  N08  N  N     0  -0.533  -0.6348  -0.6796   0.4612
 B4L  N15  N  NR6   0  -0.414   3.6297  -1.0636  -0.4710
 B4L  O05  O  O     0  -0.496  -3.7620   1.7201  -0.6787
 B4L  H1   H  HCR5  0   0.285  -4.4713  -3.2286   0.4208
 B4L  H2   H  HCR6  0   0.244   1.7073  -0.3597   1.3088
 B4L  H3   H  H     0   0.222   4.2304  -0.1730   2.0331
 B4L  H4   H  H     0   0.237   5.1298   1.2407   1.5012
 B4L  H5   H  HNH1  0   0.412   0.8697   2.0750  -0.0861
 B4L  H6   H  HCR5  0   0.251  -1.8164  -3.3486   0.9121
 B4L  H7   H  HNR5  0   0.414  -5.0305  -0.8971  -0.2425
 B4L  H8   H  HCH3  0   0.262  -0.5870   2.9240  -1.3350
 B4L  H9   H  HCH3  0   0.290  -2.1922   3.3157  -0.7325
 B4L  H10  H  HCH3  0   0.265  -0.8300   3.3169   0.3848
 B4L  H11  H  H     0   0.241   1.6303  -1.0321  -1.0438
 B4L  H12  H  H     0   0.182   2.5296   0.4158  -1.5211
 B4L  H13  H  H     0   0.184   4.9222   0.5735  -0.8478
 B4L  H14  H  H     0   0.234   5.6066  -0.7557   0.0899
 B4L  H15  H  H     0   0.219   3.1637   2.1337   0.3398
 B4L  H16  H  H     0   0.247   2.7124   1.7747   2.0034
 B4L  H17  H  HCH3  0   0.231   4.9151  -2.4209  -1.4022
 B4L  H18  H  HCH3  0   0.232   3.2173  -2.5756  -1.8520
 B4L  H19  H  HCH3  0   0.190   4.1913  -1.2585  -2.5233
 B4L  C19  C  CH3   0  -0.516   4.0057  -1.8582  -1.6183

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
 B4L  C19  N15  single    1.445  0.020  1.445
 B4L  C16  N15  single    1.451  0.020  1.451
 B4L  C16  C17  single    1.520  0.020  1.520
 B4L  N15  C14  single    1.449  0.020  1.449
 B4L  C14  C13  single    1.529  0.020  1.529
 B4L  C17  C18  single    1.523  0.020  1.523
 B4L  C18  C13  single    1.523  0.020  1.523
 B4L  C13  N01  single    1.450  0.020  1.450
 B4L  N01  C02  single    1.352  0.020  1.352
 B4L  C02  N08  double    1.301  0.020  1.301
 B4L  C02  N03  single    1.386  0.020  1.386
 B4L  C12  N03  single    1.456  0.020  1.456
 B4L  N08  C07  single    1.357  0.020  1.357
 B4L  N03  C04  single    1.404  0.020  1.404
 B4L  C07  C06  aromatic  1.387  0.020  1.387
 B4L  C07  C09  aromatic  1.417  0.020  1.417
 B4L  C04  C06  single    1.415  0.020  1.415
 B4L  C04  O05  double    1.225  0.020  1.225
 B4L  C06  N11  aromatic  1.367  0.020  1.367
 B4L  C09  C10  aromatic  1.379  0.020  1.379
 B4L  N11  C10  aromatic  1.351  0.020  1.351
 B4L  C10  H1   single    0.930  0.020  1.080
 B4L  C13  H2   single    0.970  0.020  1.090
 B4L  C17  H3   single    0.970  0.020  1.090
 B4L  C17  H4   single    0.970  0.020  1.090
 B4L  N01  H5   single    0.860  0.020  1.020
 B4L  C09  H6   single    0.930  0.020  1.080
 B4L  N11  H7   single    0.860  0.020  1.020
 B4L  C12  H8   single    0.970  0.020  1.090
 B4L  C12  H9   single    0.970  0.020  1.090
 B4L  C12  H10  single    0.970  0.020  1.090
 B4L  C14  H11  single    0.970  0.020  1.090
 B4L  C14  H12  single    0.970  0.020  1.090
 B4L  C16  H13  single    0.970  0.020  1.090
 B4L  C16  H14  single    0.970  0.020  1.090
 B4L  C18  H15  single    0.970  0.020  1.090
 B4L  C18  H16  single    0.970  0.020  1.090
 B4L  C19  H17  single    0.970  0.020  1.090
 B4L  C19  H18  single    0.970  0.020  1.090
 B4L  C19  H19  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
 B4L  H1   C10  N11  120.66  3.000
 B4L  H1   C10  C09  129.55  3.000
 B4L  N11  C10  C09  109.79  3.000
 B4L  H2   C13  C18  109.13  3.000
 B4L  H2   C13  C14  108.51  3.000
 B4L  C18  C13  C14  110.18  3.000
 B4L  H2   C13  N01  108.35  3.000
 B4L  C18  C13  N01  109.24  3.000
 B4L  C14  C13  N01  111.38  3.000
 B4L  H4   C17  H3   107.13  3.000
 B4L  H4   C17  C18  110.13  3.000
 B4L  H3   C17  C18  109.76  3.000
 B4L  H4   C17  C16  109.60  3.000
 B4L  H3   C17  C16  109.23  3.000
 B4L  C18  C17  C16  110.92  3.000
 B4L  H5   N01  C02  119.02  3.000
 B4L  H5   N01  C13  115.44  3.000
 B4L  C02  N01  C13  122.73  3.000
 B4L  N08  C02  N03  124.36  3.000
 B4L  N03  C02  N01  116.36  3.000
 B4L  N08  C02  N01  119.26  3.000
 B4L  O05  C04  N03  121.87  3.000
 B4L  O05  C04  C06  126.30  3.000
 B4L  N03  C04  C06  111.83  3.000
 B4L  N11  C06  C07  108.44  3.000
 B4L  N11  C06  C04  129.33  3.000
 B4L  C07  C06  C04  122.22  3.000
 B4L  N08  C07  C09  130.14  3.000
 B4L  C09  C07  C06  106.94  3.000
 B4L  N08  C07  C06  122.93  3.000
 B4L  H6   C09  C07  127.49  3.000
 B4L  H6   C09  C10  126.26  3.000
 B4L  C07  C09  C10  106.25  3.000
 B4L  H7   N11  C06  125.88  3.000
 B4L  H7   N11  C10  125.55  3.000
 B4L  C06  N11  C10  108.57  3.000
 B4L  H10  C12  H9   108.35  3.000
 B4L  H10  C12  H8   109.54  3.000
 B4L  H9   C12  H8   108.01  3.000
 B4L  H10  C12  N03  110.89  3.000
 B4L  H9   C12  N03  108.90  3.000
 B4L  H8   C12  N03  111.05  3.000
 B4L  H12  C14  H11  107.26  3.000
 B4L  H12  C14  N15  111.59  3.000
 B4L  H11  C14  N15  109.10  3.000
 B4L  H12  C14  C13  108.43  3.000
 B4L  H11  C14  C13  109.24  3.000
 B4L  N15  C14  C13  111.12  3.000
 B4L  H14  C16  H13  106.80  3.000
 B4L  H14  C16  N15  108.70  3.000
 B4L  H13  C16  N15  111.26  3.000
 B4L  H14  C16  C17  110.00  3.000
 B4L  H13  C16  C17  109.30  3.000
 B4L  N15  C16  C17  110.71  3.000
 B4L  H16  C18  H15  107.13  3.000
 B4L  H16  C18  C17  110.93  3.000
 B4L  H15  C18  C17  109.27  3.000
 B4L  H16  C18  C13  110.23  3.000
 B4L  H15  C18  C13  109.08  3.000
 B4L  C17  C18  C13  110.14  3.000
 B4L  C12  N03  C04  117.73  3.000
 B4L  C04  N03  C02  122.66  3.000
 B4L  C12  N03  C02  119.61  3.000
 B4L  C07  N08  C02  116.00  3.000
 B4L  C19  N15  C16  111.83  3.000
 B4L  C16  N15  C14  111.10  3.000
 B4L  C19  N15  C14  111.27  3.000
 B4L  H19  C19  H18  107.68  3.000
 B4L  H19  C19  H17  107.64  3.000
 B4L  H18  C19  H17  107.79  3.000
 B4L  H19  C19  N15  113.37  3.000
 B4L  H18  C19  N15  110.09  3.000
 B4L  H17  C19  N15  110.07  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
 B4L  CONST_01  C06  C07  C09  C10     0.00   0.0  0
 B4L  CONST_02  C07  C06  N11  C10     0.00   0.0  0
 B4L  CONST_03  C09  C10  N11  C06     0.00   0.0  0
 B4L  CONST_04  N11  C10  C09  C07     0.00   0.0  0
 B4L  CONST_05  N11  C06  C07  C09     0.00   0.0  0
 B4L  CONST_06  C06  C04  N03  C02     0.00   0.0  0
 B4L  CONST_07  N08  C02  N03  C04     0.00   0.0  0
 B4L  CONST_08  N03  C02  N08  C07     0.00   0.0  0
 B4L  CONST_09  N08  C02  N01  C13     0.00   0.0  0
 B4L  CONST_10  N03  C02  N01  C13   180.00   0.0  0
 B4L  CONST_11  C07  N08  C02  N01   180.00   0.0  0
 B4L  CONST_12  C04  N03  C02  N01   180.00   0.0  0
 B4L  CONST_13  O05  C04  N03  C02   180.00   0.0  0
 B4L  CONST_14  C12  N03  C04  C06   180.00   0.0  0
 B4L  CONST_15  N08  C02  N03  C12   180.00   0.0  0
 B4L  CONST_16  H7   N11  C06  C04     0.00   0.0  0
 B4L  CONST_17  H6   C09  C07  C06   180.00   0.0  0
 B4L  CONST_18  H1   C10  N11  C06   180.00   0.0  0
 B4L  CONST_19  C12  N03  C02  N01     0.00   0.0  0
 B4L  CONST_20  O05  C04  N03  C12     0.00   0.0  0
 B4L  CONST_21  H5   N01  C02  N03     0.00   0.0  0
 B4L  Var_01    C16  N15  C14  C13   -60.73  30.0  1
 B4L  Var_02    C16  C17  C18  C13    53.19  30.0  1
 B4L  Var_03    C14  N15  C16  C17    60.45  30.0  1
 B4L  Var_04    N15  C16  C17  C18   -56.75  30.0  1
 B4L  Var_05    H8   C12  N03  C02    63.02  30.0  3
 B4L  Var_06    H17  C19  N15  C14  -178.42  30.0  3

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
 B4L  chir_01  C13  C14  C18  N01  negativ

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
 B4L  plan-1  C10  0.020
 B4L  plan-1  C13  0.020
 B4L  plan-1  N01  0.020
 B4L  plan-1  C02  0.020
 B4L  plan-1  C04  0.020
 B4L  plan-1  C06  0.020
 B4L  plan-1  C07  0.020
 B4L  plan-1  C09  0.020
 B4L  plan-1  N11  0.020
 B4L  plan-1  C12  0.020
 B4L  plan-1  N03  0.020
 B4L  plan-1  N08  0.020
 B4L  plan-1  O05  0.020
 B4L  plan-1  H1   0.020
 B4L  plan-1  H5   0.020
 B4L  plan-1  H6   0.020
 B4L  plan-1  H7   0.020

