# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 22:15:48 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 1-(1,3-benzodioxol-5-yl)-~{N}-(pyridin-2-ylmethyl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1Oc2ccc(CNCc3ccccn3)cc2O1
#
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
 T3T  T3T  "1-(1,3-benzodioxol-5-yl)-~{N}-(pyridin-2-ylmethyl)methanamine"
  ligand  32  18  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T3T
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
 T3T  C10  C  CR6   0   0.083   3.0438  -4.8924  6.7398
 T3T  C13  C  CR56  0   0.285   0.4300  -5.2537  5.9444
 T3T  C15  C  CR16  0  -0.371   2.7544  -4.9559  5.3650
 T3T  C17  C  CH2   0   0.069  -0.4493  -5.5688  3.9308
 T3T  C01  C  CR16  0  -0.148   8.3541  -2.0986  5.8694
 T3T  C02  C  CR16  0  -0.327   8.1447  -2.1373  4.5006
 T3T  C03  C  CR16  0  -0.082   7.4898  -3.2419  3.9736
 T3T  C05  C  CR6   0   0.239   7.2544  -4.2214  6.0238
 T3T  C06  C  CR16  0  -0.340   7.9002  -3.1567  6.6426
 T3T  C07  C  CH2   0  -0.350   6.7547  -5.3964  6.8285
 T3T  C09  C  CH2   0  -0.334   4.4674  -4.6765  7.1749
 T3T  C11  C  CR16  0  -0.331   2.0246  -5.0201  7.6706
 T3T  C12  C  CR16  0  -0.331   0.6869  -5.2023  7.2897
 T3T  C14  C  CR56  0   0.312   1.4446  -5.1329  5.0052
 T3T  N04  N  N     0  -0.408   7.0560  -4.2575  4.7072
 T3T  N08  N  NH1   0  -0.586   5.3523  -5.6582  6.5782
 T3T  O16  O  O     0  -0.485   0.9113  -5.1984  3.7597
 T3T  O18  O  O     0  -0.484  -0.7581  -5.3974  5.3063
 T3T  H1   H  HCR6  0   0.259   3.5417  -4.8655  4.6275
 T3T  H2   H  HCH2  0   0.242  -1.0870  -4.9241  3.3253
 T3T  H3   H  HCH2  0   0.229  -0.5880  -6.6182  3.6463
 T3T  H5   H  HCR6  0   0.266   8.4753  -1.3365  3.8536
 T3T  H6   H  HCR6  0   0.258   7.3098  -3.3076  2.9057
 T3T  H7   H  HCR6  0   0.265   8.0371  -3.1567  7.7163
 T3T  H8   H  HCH2  0   0.214   6.9820  -5.2208  7.8905
 T3T  H9   H  HCH2  0   0.257   7.3187  -6.2851  6.5332
 T3T  H10  H  HCH2  0   0.219   4.5192  -4.6612  8.2738
 T3T  H11  H  HCH2  0   0.240   4.7937  -3.6848  6.8449
 T3T  H12  H  HCR6  0   0.250   2.2637  -4.9807  8.7261
 T3T  H13  H  HCR6  0   0.268  -0.0994  -5.2986  8.0263
 T3T  H14  H  HNH1  0   0.352   5.1156  -6.5790  6.9245
 T3T  H4   H  HCR6  0   0.270   8.8558  -1.2572  6.3296

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
 T3T  O16  C17  single    1.421  0.020  1.421
 T3T  O16  C14  single    1.356  0.020  1.356
 T3T  C17  O18  single    1.420  0.020  1.420
 T3T  C03  C02  aromatic  1.388  0.020  1.388
 T3T  C03  N04  aromatic  1.326  0.020  1.326
 T3T  C02  C01  aromatic  1.385  0.020  1.385
 T3T  N04  C05  aromatic  1.332  0.020  1.332
 T3T  C14  C15  aromatic  1.370  0.020  1.370
 T3T  C14  C13  aromatic  1.388  0.020  1.388
 T3T  C15  C10  aromatic  1.406  0.020  1.406
 T3T  N08  C09  single    1.450  0.020  1.450
 T3T  N08  C07  single    1.448  0.020  1.448
 T3T  O18  C13  single    1.356  0.020  1.356
 T3T  C13  C12  aromatic  1.371  0.020  1.371
 T3T  C10  C09  single    1.504  0.020  1.504
 T3T  C10  C11  aromatic  1.386  0.020  1.386
 T3T  C05  C06  aromatic  1.391  0.020  1.391
 T3T  C05  C07  single    1.509  0.020  1.509
 T3T  C01  C06  aromatic  1.387  0.020  1.387
 T3T  C12  C11  aromatic  1.403  0.020  1.403
 T3T  C15  H1   single    0.930  0.020  1.080
 T3T  C17  H2   single    0.970  0.020  1.090
 T3T  C17  H3   single    0.970  0.020  1.090
 T3T  C01  H4   single    0.930  0.020  1.080
 T3T  C02  H5   single    0.930  0.020  1.080
 T3T  C03  H6   single    0.930  0.020  1.080
 T3T  C06  H7   single    0.930  0.020  1.080
 T3T  C07  H8   single    0.970  0.020  1.090
 T3T  C07  H9   single    0.970  0.020  1.090
 T3T  C09  H10  single    0.970  0.020  1.090
 T3T  C09  H11  single    0.970  0.020  1.090
 T3T  C11  H12  single    0.930  0.020  1.080
 T3T  C12  H13  single    0.930  0.020  1.080
 T3T  N08  H14  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
 T3T  C11  C10  C09  120.99  3.000
 T3T  C11  C10  C15  120.06  3.000
 T3T  C09  C10  C15  118.95  3.000
 T3T  O18  C13  C14  109.35  3.000
 T3T  O18  C13  C12  129.04  3.000
 T3T  C14  C13  C12  121.60  3.000
 T3T  H1   C15  C14  121.82  3.000
 T3T  H1   C15  C10  120.83  3.000
 T3T  C14  C15  C10  117.35  3.000
 T3T  H3   C17  H2   110.37  3.000
 T3T  H3   C17  O18  109.85  3.000
 T3T  H2   C17  O18  109.83  3.000
 T3T  H3   C17  O16  109.85  3.000
 T3T  H2   C17  O16  109.82  3.000
 T3T  O18  C17  O16  107.06  3.000
 T3T  H4   C01  C06  120.51  3.000
 T3T  H4   C01  C02  120.80  3.000
 T3T  C06  C01  C02  118.69  3.000
 T3T  H5   C02  C03  120.43  3.000
 T3T  H5   C02  C01  121.62  3.000
 T3T  C03  C02  C01  117.95  3.000
 T3T  H6   C03  N04  116.36  3.000
 T3T  H6   C03  C02  120.01  3.000
 T3T  N04  C03  C02  123.64  3.000
 T3T  N04  C05  C07  117.18  3.000
 T3T  C07  C05  C06  120.83  3.000
 T3T  N04  C05  C06  121.99  3.000
 T3T  H7   C06  C05  120.02  3.000
 T3T  H7   C06  C01  120.77  3.000
 T3T  C05  C06  C01  119.21  3.000
 T3T  H9   C07  H8   106.50  3.000
 T3T  H9   C07  N08  107.81  3.000
 T3T  H8   C07  N08  113.31  3.000
 T3T  H9   C07  C05  108.55  3.000
 T3T  H8   C07  C05  108.79  3.000
 T3T  N08  C07  C05  111.66  3.000
 T3T  H11  C09  H10  105.93  3.000
 T3T  H11  C09  N08  107.90  3.000
 T3T  H10  C09  N08  113.06  3.000
 T3T  H11  C09  C10  108.95  3.000
 T3T  H10  C09  C10  109.60  3.000
 T3T  N08  C09  C10  111.18  3.000
 T3T  H12  C11  C12  118.68  3.000
 T3T  H12  C11  C10  119.26  3.000
 T3T  C12  C11  C10  122.06  3.000
 T3T  H13  C12  C11  121.32  3.000
 T3T  H13  C12  C13  121.93  3.000
 T3T  C11  C12  C13  116.75  3.000
 T3T  O16  C14  C15  128.56  3.000
 T3T  C15  C14  C13  122.18  3.000
 T3T  O16  C14  C13  109.26  3.000
 T3T  C05  N04  C03  118.52  3.000
 T3T  H14  N08  C09  109.42  3.000
 T3T  H14  N08  C07  109.38  3.000
 T3T  C09  N08  C07  113.41  3.000
 T3T  C14  O16  C17  106.18  3.000
 T3T  C17  O18  C13  106.14  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
 T3T  CONST_01  C13  C14  C15  C10     0.00   0.0  0
 T3T  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 T3T  CONST_03  C12  C13  C14  C15     0.00   0.0  0
 T3T  CONST_04  C12  C11  C10  C15     0.00   0.0  0
 T3T  CONST_05  N04  C03  C02  C01     0.00   0.0  0
 T3T  CONST_06  N04  C05  C06  C01     0.00   0.0  0
 T3T  CONST_07  C05  N04  C03  C02     0.00   0.0  0
 T3T  CONST_08  C05  C06  C01  C02     0.00   0.0  0
 T3T  CONST_09  C06  C01  C02  C03     0.00   0.0  0
 T3T  CONST_10  C06  C05  N04  C03     0.00   0.0  0
 T3T  CONST_11  C14  C15  C10  C11     0.00   0.0  0
 T3T  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 T3T  CONST_13  C07  C05  C06  C01   180.00   0.0  0
 T3T  CONST_14  C07  C05  N04  C03   180.00   0.0  0
 T3T  CONST_15  C14  C15  C10  C09   180.00   0.0  0
 T3T  CONST_16  C12  C11  C10  C09   180.00   0.0  0
 T3T  CONST_17  H13  C12  C11  C10   180.00   0.0  0
 T3T  CONST_18  H1   C15  C14  C13   180.00   0.0  0
 T3T  CONST_19  H12  C11  C12  C13   180.00   0.0  0
 T3T  CONST_20  H12  C11  C10  C15   180.00   0.0  0
 T3T  CONST_21  H6   C03  C02  C01   180.00   0.0  0
 T3T  CONST_22  H7   C06  C01  C02   180.00   0.0  0
 T3T  CONST_23  H4   C01  C02  C03   180.00   0.0  0
 T3T  CONST_24  H6   C03  N04  C05   180.00   0.0  0
 T3T  CONST_25  H4   C01  C06  C05   180.00   0.0  0
 T3T  CONST_26  H5   C02  C01  C06   180.00   0.0  0
 T3T  CONST_27  H1   C15  C10  C11   180.00   0.0  0
 T3T  CONST_28  H13  C12  C13  C14   180.00   0.0  0
 T3T  CONST_29  H5   C02  C03  N04   180.00   0.0  0
 T3T  CONST_30  H7   C06  C05  N04   180.00   0.0  0
 T3T  CONST_31  H1   C15  C14  O16     0.00   0.0  0
 T3T  CONST_32  H13  C12  C13  O18     0.00   0.0  0
 T3T  Var_01    C17  O16  C14  C13    -8.67  30.0  1
 T3T  Var_02    O16  C17  O18  C13   -13.83  30.0  1
 T3T  Var_03    C17  O16  C14  C15   172.35  30.0  1
 T3T  Var_04    C14  C13  O18  C17     8.66  30.0  1
 T3T  Var_05    C12  C13  O18  C17  -172.35  30.0  1
 T3T  Var_06    O18  C17  O16  C14    13.85  30.0  1
 T3T  Var_07    H2   C17  O18  C13  -133.03  30.0  1
 T3T  Var_08    H3   C17  O18  C13   105.40  30.0  1
 T3T  Var_09    H2   C17  O16  C14   133.05  30.0  1
 T3T  Var_10    H3   C17  O16  C14  -105.39  30.0  1
 T3T  Var_11    N08  C09  C10  C15   -53.78  30.0  2
 T3T  Var_12    N08  C07  C05  C06   126.60  30.0  2
 T3T  Var_13    N08  C09  C10  C11   126.60  30.0  2
 T3T  Var_14    N08  C07  C05  N04   -53.79  30.0  2
 T3T  Var_15    H10  C09  C10  C15  -179.50  30.0  2
 T3T  Var_16    H11  C09  C10  C15    65.01  30.0  2
 T3T  Var_17    H8   C07  C05  C06     0.81  30.0  2
 T3T  Var_18    H9   C07  C05  C06  -114.69  30.0  2
 T3T  Var_19    H10  C09  C10  C11     0.87  30.0  2
 T3T  Var_20    H11  C09  C10  C11  -114.62  30.0  2
 T3T  Var_21    H8   C07  C05  N04  -179.58  30.0  2
 T3T  Var_22    H9   C07  C05  N04    64.92  30.0  2
 T3T  Var_23    C07  N08  C09  C10   172.69  30.0  2
 T3T  Var_24    C09  N08  C07  C05   -72.79  30.0  2
 T3T  Var_25    H14  N08  C09  C10   -64.89  30.0  2
 T3T  Var_26    H14  N08  C07  C05   164.77  30.0  2
 T3T  Var_27    H10  C09  N08  C07   -63.53  30.0  3
 T3T  Var_28    H11  C09  N08  C07    53.27  30.0  3
 T3T  Var_29    H8   C07  N08  C09    50.46  30.0  3
 T3T  Var_30    H9   C07  N08  C09   168.06  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
 T3T  plan-1  C01  0.020
 T3T  plan-1  C02  0.020
 T3T  plan-1  C03  0.020
 T3T  plan-1  C05  0.020
 T3T  plan-1  C06  0.020
 T3T  plan-1  C07  0.020
 T3T  plan-1  N04  0.020
 T3T  plan-1  H5   0.020
 T3T  plan-1  H6   0.020
 T3T  plan-1  H7   0.020
 T3T  plan-1  H4   0.020
 T3T  plan-2  C10  0.020
 T3T  plan-2  C13  0.020
 T3T  plan-2  C15  0.020
 T3T  plan-2  C09  0.020
 T3T  plan-2  C11  0.020
 T3T  plan-2  C12  0.020
 T3T  plan-2  C14  0.020
 T3T  plan-2  O16  0.020
 T3T  plan-2  O18  0.020
 T3T  plan-2  H1   0.020
 T3T  plan-2  H12  0.020
 T3T  plan-2  H13  0.020

