# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 08:25:03 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 4-(1H,3H-benzo[de]isochromen-6-yl)-6-methylpyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(nc(N)n1)c2ccc3COCc4cccc2c34
#
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
 B2L  B2L  4-(1H,3H-benzo[de]isochromen-6-yl)-6-methylpyrimidin-2-amine  ligand  36  21  .  2022-07-24  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_B2L
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
 B2L  C1    C  CH2   0  -0.236  -3.9451   1.5406  -0.5952
 B2L  O2    O  O2    0  -0.473  -4.7269   0.7531   0.2690
 B2L  C3    C  CH2   0  -0.237  -4.5326  -0.6218   0.0411
 B2L  C4    C  CR6   0   0.004  -3.0965  -1.0192   0.2435
 B2L  C5    C  CR16  0  -0.323  -2.7405  -2.2700   0.6681
 B2L  C6    C  CR16  0  -0.239  -1.3829  -2.6011   0.8343
 B2L  C7    C  CR16  0  -0.357  -0.3977  -1.6897   0.5668
 B2L  C8    C  CR66  0   0.132  -0.7209  -0.3864   0.1168
 B2L  C9    C  CR66  0   0.128  -2.0943  -0.0529  -0.0274
 B2L  C10   C  CR6   0  -0.012  -2.4792   1.2482  -0.4379
 B2L  C11   C  CR16  0  -0.313  -1.5191   2.1914  -0.6793
 B2L  C12   C  CR16  0  -0.303  -0.1581   1.8715  -0.5413
 B2L  C13   C  CR6   0   0.021   0.2549   0.6157  -0.1652
 B2L  C14   C  CR6   0   0.230   1.7095   0.3553  -0.0790
 B2L  N15   N  N     0  -0.476   2.1830  -0.7227  -0.6905
 B2L  C16   C  CR16  0  -0.407   2.5448   1.2377   0.5968
 B2L  C17   C  CR6   0   0.286   3.9038   0.9447   0.6011
 B2L  C18   C  CH3   0  -0.725   4.8840   1.8147   1.3200
 B2L  N19   N  N     0  -0.475   4.3840  -0.1306  -0.0099
 B2L  C20   C  CR6   0   0.524   3.5022  -0.9227  -0.6255
 B2L  N21   N  NH2   0  -0.826   3.9819  -2.0371  -1.2150
 B2L  H1    H  HCH2  0   0.230  -4.2419   1.3774  -1.6425
 B2L  H1A   H  HCH2  0   0.258  -4.1522   2.5858  -0.3609
 B2L  H3    H  HCH2  0   0.256  -5.1803  -1.1605   0.7341
 B2L  H3A   H  HCH2  0   0.228  -4.8496  -0.8919  -0.9774
 B2L  H5    H  HCR6  0   0.255  -3.5026  -3.0084   0.8882
 B2L  H6    H  HCR6  0   0.260  -1.1158  -3.5886   1.1876
 B2L  H7    H  HCR6  0   0.254   0.6354  -1.9721   0.7020
 B2L  H11   H  HCR6  0   0.258  -1.8000   3.1926  -0.9828
 B2L  H12   H  HCR6  0   0.262   0.5808   2.6339  -0.7543
 B2L  H16   H  HCR6  0   0.265   2.1581   2.1075   1.1076
 B2L  H18   H  HCH3  0   0.261   5.2026   1.3287   2.2441
 B2L  H18A  H  HCH3  0   0.255   5.7757   1.9764   0.7157
 B2L  H18B  H  HCH3  0   0.248   4.4530   2.7795   1.5793
 B2L  HN21  H  HNH2  0   0.394   3.3878  -2.5393  -1.8514
 B2L  HN2A  H  HNH2  0   0.393   4.9736  -2.1163  -1.3582

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
 B2L  C1   O2    single    1.406  0.020  1.406
 B2L  C1   C10   single    1.503  0.020  1.503
 B2L  O2   C3    single    1.407  0.020  1.407
 B2L  C3   C4    single    1.504  0.020  1.504
 B2L  C4   C5    aromatic  1.368  0.020  1.368
 B2L  C4   C9    aromatic  1.418  0.020  1.418
 B2L  C5   C6    aromatic  1.407  0.020  1.407
 B2L  C6   C7    aromatic  1.369  0.020  1.369
 B2L  C7   C8    aromatic  1.416  0.020  1.416
 B2L  C8   C9    aromatic  1.421  0.020  1.421
 B2L  C8   C13   aromatic  1.427  0.020  1.427
 B2L  C9   C10   aromatic  1.418  0.020  1.418
 B2L  C10  C11   aromatic  1.367  0.020  1.367
 B2L  C11  C12   aromatic  1.405  0.020  1.405
 B2L  C12  C13   aromatic  1.374  0.020  1.374
 B2L  C13  C14   single    1.480  0.020  1.480
 B2L  C14  N15   aromatic  1.327  0.020  1.327
 B2L  C14  C16   aromatic  1.390  0.020  1.390
 B2L  N15  C20   aromatic  1.336  0.020  1.336
 B2L  C16  C17   aromatic  1.390  0.020  1.390
 B2L  C17  C18   single    1.495  0.020  1.495
 B2L  C17  N19   aromatic  1.327  0.020  1.327
 B2L  N19  C20   aromatic  1.336  0.020  1.336
 B2L  C20  N21   single    1.349  0.020  1.349
 B2L  C1   H1    single    0.970  0.020  1.090
 B2L  C1   H1A   single    0.970  0.020  1.090
 B2L  C3   H3    single    0.970  0.020  1.090
 B2L  C3   H3A   single    0.970  0.020  1.090
 B2L  C5   H5    single    0.930  0.020  1.080
 B2L  C6   H6    single    0.930  0.020  1.080
 B2L  C7   H7    single    0.930  0.020  1.080
 B2L  C11  H11   single    0.930  0.020  1.080
 B2L  C12  H12   single    0.930  0.020  1.080
 B2L  C16  H16   single    0.930  0.020  1.080
 B2L  C18  H18   single    0.970  0.020  1.090
 B2L  C18  H18A  single    0.970  0.020  1.090
 B2L  C18  H18B  single    0.970  0.020  1.090
 B2L  N21  HN21  single    0.890  0.020  1.040
 B2L  N21  HN2A  single    0.890  0.020  1.040

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
 B2L  H1A   C1   H1    107.17  3.000
 B2L  H1A   C1   C10   110.42  3.000
 B2L  H1    C1   C10   109.50  3.000
 B2L  H1A   C1   O2    107.39  3.000
 B2L  H1    C1   O2    110.59  3.000
 B2L  C10   C1   O2    111.65  3.000
 B2L  C3    O2   C1    111.76  3.000
 B2L  H3A   C3   H3    107.21  3.000
 B2L  H3A   C3   C4    109.56  3.000
 B2L  H3    C3   C4    110.55  3.000
 B2L  H3A   C3   O2    110.49  3.000
 B2L  H3    C3   O2    107.32  3.000
 B2L  C4    C3   O2    111.61  3.000
 B2L  C9    C4   C5    119.89  3.000
 B2L  C9    C4   C3    117.97  3.000
 B2L  C5    C4   C3    122.13  3.000
 B2L  H5    C5   C6    119.61  3.000
 B2L  H5    C5   C4    120.20  3.000
 B2L  C6    C5   C4    120.19  3.000
 B2L  H6    C6   C7    119.59  3.000
 B2L  H6    C6   C5    119.43  3.000
 B2L  C7    C6   C5    120.98  3.000
 B2L  H7    C7   C8    119.93  3.000
 B2L  H7    C7   C6    119.36  3.000
 B2L  C8    C7   C6    120.71  3.000
 B2L  C13   C8   C9    118.44  3.000
 B2L  C13   C8   C7    123.58  3.000
 B2L  C9    C8   C7    117.97  3.000
 B2L  C10   C9   C8    120.49  3.000
 B2L  C10   C9   C4    119.26  3.000
 B2L  C8    C9   C4    120.25  3.000
 B2L  C11   C10  C9    119.58  3.000
 B2L  C11   C10  C1    122.15  3.000
 B2L  C9    C10  C1    118.27  3.000
 B2L  H11   C11  C12   119.29  3.000
 B2L  H11   C11  C10   120.33  3.000
 B2L  C12   C11  C10   120.38  3.000
 B2L  H12   C12  C13   119.48  3.000
 B2L  H12   C12  C11   118.78  3.000
 B2L  C13   C12  C11   121.74  3.000
 B2L  C14   C13  C12   118.16  3.000
 B2L  C14   C13  C8    122.48  3.000
 B2L  C12   C13  C8    119.36  3.000
 B2L  C16   C14  N15   121.69  3.000
 B2L  C16   C14  C13   120.47  3.000
 B2L  N15   C14  C13   117.83  3.000
 B2L  C20   N15  C14   116.85  3.000
 B2L  H16   C16  C17   121.21  3.000
 B2L  H16   C16  C14   121.72  3.000
 B2L  C17   C16  C14   117.07  3.000
 B2L  N19   C17  C18   117.12  3.000
 B2L  N19   C17  C16   121.55  3.000
 B2L  C18   C17  C16   121.32  3.000
 B2L  H18B  C18  H18A  108.96  3.000
 B2L  H18B  C18  H18   107.98  3.000
 B2L  H18A  C18  H18   107.27  3.000
 B2L  H18B  C18  C17   111.77  3.000
 B2L  H18A  C18  C17   110.88  3.000
 B2L  H18   C18  C17   109.84  3.000
 B2L  C20   N19  C17   116.99  3.000
 B2L  N21   C20  N19   117.16  3.000
 B2L  N21   C20  N15   116.98  3.000
 B2L  N19   C20  N15   125.85  3.000
 B2L  HN2A  N21  HN21  116.98  3.000
 B2L  HN2A  N21  C20   118.57  3.000
 B2L  HN21  N21  C20   118.64  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
 B2L  CONST_01  C7    C6   C5   C4     0.00   0.0  0
 B2L  CONST_02  C7    C8   C9   C4     0.00   0.0  0
 B2L  CONST_03  C13   C8   C9   C4   180.00   0.0  0
 B2L  CONST_04  C11   C10  C9   C4   180.00   0.0  0
 B2L  CONST_05  C8    C9   C4   C5     0.00   0.0  0
 B2L  CONST_06  C10   C9   C4   C5   180.00   0.0  0
 B2L  CONST_07  C8    C7   C6   C5     0.00   0.0  0
 B2L  CONST_08  C9    C4   C5   C6     0.00   0.0  0
 B2L  CONST_09  C9    C8   C7   C6     0.00   0.0  0
 B2L  CONST_10  C13   C8   C7   C6   180.00   0.0  0
 B2L  CONST_11  C10   C9   C8   C7   180.00   0.0  0
 B2L  CONST_12  C12   C13  C8   C7   180.00   0.0  0
 B2L  CONST_13  C14   C13  C8   C7     0.00   0.0  0
 B2L  CONST_14  C11   C10  C9   C8     0.00   0.0  0
 B2L  CONST_15  C11   C12  C13  C8     0.00   0.0  0
 B2L  CONST_18  C12   C13  C8   C9     0.00   0.0  0
 B2L  CONST_19  C14   C13  C8   C9   180.00   0.0  0
 B2L  CONST_20  C12   C11  C10  C9     0.00   0.0  0
 B2L  CONST_21  C13   C8   C9   C10    0.00   0.0  0
 B2L  CONST_22  C13   C12  C11  C10    0.00   0.0  0
 B2L  CONST_23  C14   C13  C12  C11  180.00   0.0  0
 B2L  CONST_26  C20   N15  C14  C13  180.00   0.0  0
 B2L  CONST_27  C17   C16  C14  C13  180.00   0.0  0
 B2L  CONST_28  N19   C20  N15  C14    0.00   0.0  0
 B2L  CONST_29  N19   C17  C16  C14    0.00   0.0  0
 B2L  CONST_30  C17   C16  C14  N15    0.00   0.0  0
 B2L  CONST_31  C17   N19  C20  N15    0.00   0.0  0
 B2L  CONST_32  C20   N15  C14  C16    0.00   0.0  0
 B2L  CONST_33  C20   N19  C17  C16    0.00   0.0  0
 B2L  CONST_34  N21   C20  N15  C14  180.00   0.0  0
 B2L  CONST_35  C18   C17  C16  C14  180.00   0.0  0
 B2L  CONST_36  N21   C20  N19  C17  180.00   0.0  0
 B2L  CONST_37  C20   N19  C17  C18  180.00   0.0  0
 B2L  CONST_38  H11   C11  C10  C1     0.00   0.0  0
 B2L  CONST_39  H5    C5   C4   C3     0.00   0.0  0
 B2L  CONST_40  H6    C6   C5   C4   180.00   0.0  0
 B2L  CONST_41  H7    C7   C6   C5   180.00   0.0  0
 B2L  CONST_42  H12   C12  C13  C8   180.00   0.0  0
 B2L  CONST_43  H16   C16  C14  C13    0.00   0.0  0
 B2L  CONST_44  HN21  N21  C20  N15    0.00   0.0  0
 B2L  CONST_45  HN2A  N21  C20  N15  180.00   0.0  0
 B2L  Var_01    C4    C3   O2   C1    59.62  30.0  1
 B2L  Var_02    C9    C10  C1   O2    29.05  30.0  1
 B2L  Var_03    C5    C4   C3   O2   150.19  30.0  1
 B2L  Var_04    C10   C1   O2   C3   -59.00  30.0  1
 B2L  Var_05    H18   C18  C17  C16  104.80  30.0  2

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
 B2L  plan-1  C13   0.020
 B2L  plan-1  C14   0.020
 B2L  plan-1  N15   0.020
 B2L  plan-1  C16   0.020
 B2L  plan-1  C17   0.020
 B2L  plan-1  C18   0.020
 B2L  plan-1  N19   0.020
 B2L  plan-1  C20   0.020
 B2L  plan-1  N21   0.020
 B2L  plan-1  H16   0.020
 B2L  plan-2  C1    0.020
 B2L  plan-2  C3    0.020
 B2L  plan-2  C4    0.020
 B2L  plan-2  C5    0.020
 B2L  plan-2  C6    0.020
 B2L  plan-2  C7    0.020
 B2L  plan-2  C8    0.020
 B2L  plan-2  C9    0.020
 B2L  plan-2  C10   0.020
 B2L  plan-2  C11   0.020
 B2L  plan-2  C12   0.020
 B2L  plan-2  C13   0.020
 B2L  plan-2  C14   0.020
 B2L  plan-2  H5    0.020
 B2L  plan-2  H6    0.020
 B2L  plan-2  H7    0.020
 B2L  plan-2  H11   0.020
 B2L  plan-2  H12   0.020
 B2L  plan-3  C20   0.020
 B2L  plan-3  N21   0.020
 B2L  plan-3  HN21  0.020
 B2L  plan-3  HN2A  0.020

