# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 08:50:02 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 1-[3-(pyrrolidin-1-yl)phenyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc(c1)N2CCCC2
#
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
 7Z3  7Z3  1-[3-(pyrrolidin-1-yl)phenyl]methanamine  ligand  29  13  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7Z3
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
 7Z3  C1    C  CH2   0  -0.330  -3.3766   0.8712  -0.2623
 7Z3  N1    N  NH2   0  -0.796  -3.1004   2.1810   0.2983
 7Z3  C2    C  CR6   0   0.096  -2.2078  -0.0793  -0.1485
 7Z3  N2    N  NT    0  -0.533   1.4634   0.0054   0.0989
 7Z3  C3    C  CR16  0  -0.357  -2.4414  -1.4539  -0.1558
 7Z3  C4    C  CR16  0  -0.227  -1.3637  -2.3257  -0.0955
 7Z3  C5    C  CR16  0  -0.385  -0.0620  -1.8593  -0.0165
 7Z3  C6    C  CR6   0   0.425   0.1938  -0.4758   0.0069
 7Z3  C7    C  CH2   0  -0.268   2.6300  -0.8342   0.2895
 7Z3  C8    C  CH2   0  -0.473   3.7155   0.1569   0.6927
 7Z3  C9    C  CH2   0  -0.479   3.3144   1.4289  -0.0477
 7Z3  C10   C  CH2   0  -0.266   1.7908   1.4168   0.0303
 7Z3  C11   C  CR16  0  -0.417  -0.9079   0.3982  -0.0658
 7Z3  H11C  H  HCH2  0   0.211  -4.2605   0.3823   0.1697
 7Z3  H12C  H  HCH2  0   0.239  -3.6055   1.0061  -1.3240
 7Z3  H11N  H  HNH2  0   0.354  -3.8687   2.8035   0.0856
 7Z3  H12N  H  HNH2  0   0.343  -3.0613   2.1183   1.3079
 7Z3  H3    H  HCR6  0   0.231  -3.4541  -1.8362  -0.2083
 7Z3  H11   H  HCR6  0   0.254  -0.7598   1.4694  -0.0452
 7Z3  H71C  H  HCH2  0   0.235   2.4579  -1.5897   1.0608
 7Z3  H72C  H  HCH2  0   0.221   2.9003  -1.3660  -0.6319
 7Z3  H101  H  HCH2  0   0.234   1.3362   1.8921  -0.8438
 7Z3  H102  H  HCH2  0   0.221   1.4304   1.9556   0.9158
 7Z3  H4    H  HCR6  0   0.243  -1.5357  -3.3953  -0.1055
 7Z3  H5    H  HCR6  0   0.257   0.7520  -2.5705   0.0227
 7Z3  H81C  H  HCH2  0   0.236   3.6869   0.3221   1.7719
 7Z3  H82C  H  HCH2  0   0.246   4.7143  -0.1945   0.4362
 7Z3  H91C  H  HCH2  0   0.248   3.7424   2.3323   0.3847
 7Z3  H92C  H  HCH2  0   0.236   3.6360   1.3747  -1.0902

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
 7Z3  C1   N1    single    1.451  0.020  1.451
 7Z3  C1   C2    single    1.511  0.020  1.511
 7Z3  C2   C3    aromatic  1.394  0.020  1.394
 7Z3  C2   C11   aromatic  1.387  0.020  1.387
 7Z3  N2   C6    single    1.361  0.020  1.361
 7Z3  N2   C7    single    1.450  0.020  1.450
 7Z3  N2   C10   single    1.450  0.020  1.450
 7Z3  C3   C4    aromatic  1.387  0.020  1.387
 7Z3  C4   C5    aromatic  1.385  0.020  1.385
 7Z3  C5   C6    aromatic  1.407  0.020  1.407
 7Z3  C6   C11   aromatic  1.408  0.020  1.408
 7Z3  C7   C8    single    1.524  0.020  1.524
 7Z3  C8   C9    single    1.525  0.020  1.525
 7Z3  C9   C10   single    1.526  0.020  1.526
 7Z3  C1   H11C  single    0.970  0.020  1.090
 7Z3  C1   H12C  single    0.970  0.020  1.090
 7Z3  N1   H11N  single    0.890  0.020  1.040
 7Z3  N1   H12N  single    0.890  0.020  1.040
 7Z3  C3   H3    single    0.930  0.020  1.080
 7Z3  C11  H11   single    0.930  0.020  1.080
 7Z3  C7   H71C  single    0.970  0.020  1.090
 7Z3  C7   H72C  single    0.970  0.020  1.090
 7Z3  C10  H101  single    0.970  0.020  1.090
 7Z3  C10  H102  single    0.970  0.020  1.090
 7Z3  C4   H4    single    0.930  0.020  1.080
 7Z3  C5   H5    single    0.930  0.020  1.080
 7Z3  C8   H81C  single    0.970  0.020  1.090
 7Z3  C8   H82C  single    0.970  0.020  1.090
 7Z3  C9   H91C  single    0.970  0.020  1.090
 7Z3  C9   H92C  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
 7Z3  H12C  C1   H11C  105.55  3.000
 7Z3  H12C  C1   C2    108.21  3.000
 7Z3  H11C  C1   C2    108.23  3.000
 7Z3  H12C  C1   N1    107.65  3.000
 7Z3  H11C  C1   N1    113.76  3.000
 7Z3  C2    C1   N1    113.05  3.000
 7Z3  H12N  N1   H11N  106.09  3.000
 7Z3  H12N  N1   C1    109.67  3.000
 7Z3  H11N  N1   C1    109.25  3.000
 7Z3  C11   C2   C3    119.77  3.000
 7Z3  C11   C2   C1    120.86  3.000
 7Z3  C3    C2   C1    119.36  3.000
 7Z3  C10   N2   C7    112.83  3.000
 7Z3  C10   N2   C6    123.47  3.000
 7Z3  C7    N2   C6    123.70  3.000
 7Z3  H3    C3   C4    120.42  3.000
 7Z3  H3    C3   C2    120.30  3.000
 7Z3  C4    C3   C2    119.28  3.000
 7Z3  H4    C4   C5    118.82  3.000
 7Z3  H4    C4   C3    119.78  3.000
 7Z3  C5    C4   C3    121.39  3.000
 7Z3  H5    C5   C6    120.60  3.000
 7Z3  H5    C5   C4    119.21  3.000
 7Z3  C6    C5   C4    120.19  3.000
 7Z3  C11   C6   C5    117.86  3.000
 7Z3  C11   C6   N2    120.92  3.000
 7Z3  C5    C6   N2    121.22  3.000
 7Z3  H72C  C7   H71C  107.23  3.000
 7Z3  H72C  C7   C8    111.21  3.000
 7Z3  H71C  C7   C8    112.02  3.000
 7Z3  H72C  C7   N2    111.61  3.000
 7Z3  H71C  C7   N2    111.48  3.000
 7Z3  C8    C7   N2    103.37  3.000
 7Z3  H82C  C8   H81C  107.79  3.000
 7Z3  H82C  C8   C9    113.31  3.000
 7Z3  H81C  C8   C9    110.28  3.000
 7Z3  H82C  C8   C7    112.39  3.000
 7Z3  H81C  C8   C7    109.94  3.000
 7Z3  C9    C8   C7    103.10  3.000
 7Z3  H92C  C9   H91C  107.71  3.000
 7Z3  H92C  C9   C10   110.03  3.000
 7Z3  H91C  C9   C10   112.26  3.000
 7Z3  H92C  C9   C8    110.15  3.000
 7Z3  H91C  C9   C8    113.30  3.000
 7Z3  C10   C9   C8    103.36  3.000
 7Z3  H102  C10  H101  107.15  3.000
 7Z3  H102  C10  C9    111.43  3.000
 7Z3  H101  C10  C9    111.76  3.000
 7Z3  H102  C10  N2    111.44  3.000
 7Z3  H101  C10  N2    111.52  3.000
 7Z3  C9    C10  N2    103.63  3.000
 7Z3  H11   C11  C6    120.44  3.000
 7Z3  H11   C11  C2    118.05  3.000
 7Z3  C6    C11  C2    121.50  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
 7Z3  CONST_01  C5    C4   C3   C2     0.00   0.0  0
 7Z3  CONST_02  C5    C6   C11  C2     0.00   0.0  0
 7Z3  CONST_03  C6    C11  C2   C3     0.00   0.0  0
 7Z3  CONST_04  C6    C5   C4   C3     0.00   0.0  0
 7Z3  CONST_05  C11   C2   C3   C4     0.00   0.0  0
 7Z3  CONST_06  C11   C6   C5   C4     0.00   0.0  0
 7Z3  CONST_07  N2    C6   C11  C2   180.00   0.0  0
 7Z3  CONST_08  C4    C5   C6   N2   180.00   0.0  0
 7Z3  CONST_09  C4    C3   C2   C1   180.00   0.0  0
 7Z3  CONST_10  C6    C11  C2   C1   180.00   0.0  0
 7Z3  CONST_11  H4    C4   C3   C2   180.00   0.0  0
 7Z3  CONST_12  H5    C5   C6   N2     0.00   0.0  0
 7Z3  CONST_13  H11   C11  C6   N2     0.00   0.0  0
 7Z3  CONST_14  H3    C3   C4   C5   180.00   0.0  0
 7Z3  Var_01    C9    C8   C7   N2   -31.19  30.0  1
 7Z3  Var_02    C8    C9   C10  N2   -28.69  30.0  1
 7Z3  Var_03    C7    N2   C6   C5    -5.26  30.0  2
 7Z3  Var_04    C8    C7   N2   C6  -165.58  30.0  1
 7Z3  Var_05    C9    C10  N2   C6  -171.18  30.0  1
 7Z3  Var_06    C10   C9   C8   C7    37.16  30.0  1
 7Z3  Var_07    C3    C2   C1   N1   155.84  30.0  2
 7Z3  Var_08    H11N  N1   C1   C2   172.67  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
 7Z3  plan-1  C1   0.020
 7Z3  plan-1  C2   0.020
 7Z3  plan-1  N2   0.020
 7Z3  plan-1  C3   0.020
 7Z3  plan-1  C4   0.020
 7Z3  plan-1  C5   0.020
 7Z3  plan-1  C6   0.020
 7Z3  plan-1  C11  0.020
 7Z3  plan-1  H3   0.020
 7Z3  plan-1  H11  0.020
 7Z3  plan-1  H4   0.020
 7Z3  plan-1  H5   0.020

