# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 17:50:13 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 1-(3,4-dimethoxyphenyl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CN)cc1OC
#
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
 JHD  JHD  1-(3,4-dimethoxyphenyl)methanamine  ligand  25  12  .  2021-08-12  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JHD
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
 JHD  C10   C  CH3   0  -0.436   0.7628   3.1743  -0.2853
 JHD  N12   N  NH2   0  -0.796  -3.7783  -1.3533   0.3097
 JHD  C01   C  CH3   0  -0.435   3.2482  -1.5888   0.2334
 JHD  O02   O  O2    0  -0.466   2.5505  -0.3725   0.0701
 JHD  C03   C  CR6   0   0.293   1.2041  -0.4213   0.0067
 JHD  C04   C  CR16  0  -0.369   0.4434  -1.5754   0.0602
 JHD  C05   C  CR16  0  -0.316  -0.9495  -1.5166  -0.0126
 JHD  C06   C  CR6   0   0.072  -1.5980  -0.3031  -0.1357
 JHD  C07   C  CR16  0  -0.434  -0.8298   0.8659  -0.1835
 JHD  C08   C  CR6   0   0.325   0.5519   0.8232  -0.1186
 JHD  O09   O  O2    0  -0.467   1.3600   1.9011  -0.1572
 JHD  H103  H  HCH3  0   0.226   0.1890   3.2649  -1.2117
 JHD  H101  H  HCH3  0   0.226   0.1050   3.4048   0.5573
 JHD  H102  H  HCH3  0   0.259   1.5746   3.8972  -0.3034
 JHD  H121  H  HNH2  0   0.343  -3.6820  -1.3496   1.3175
 JHD  H122  H  HNH2  0   0.354  -4.7698  -1.2802   0.1232
 JHD  H011  H  HCH3  0   0.225   2.9714  -2.0979   1.1608
 JHD  H012  H  HCH3  0   0.226   3.0819  -2.2741  -0.6025
 JHD  H013  H  HCH3  0   0.257   4.3053  -1.3372   0.2740
 JHD  H041  H  HCR6  0   0.275   0.9184  -2.5424   0.1613
 JHD  H051  H  HCR6  0   0.245  -1.5233  -2.4322   0.0344
 JHD  H071  H  HCR6  0   0.271  -1.3416   1.8170  -0.2712
 JHD  H111  H  HCH2  0   0.238  -3.3706  -0.1254  -1.3029
 JHD  H112  H  HCH2  0   0.210  -3.4131   0.7564   0.2040
 JHD  C11   C  CH2   0  -0.326  -3.0998  -0.1967  -0.2447

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
 JHD  C10  O09   single    1.412  0.020  1.412
 JHD  O09  C08   single    1.348  0.020  1.348
 JHD  O02  C01   single    1.412  0.020  1.412
 JHD  O02  C03   single    1.349  0.020  1.349
 JHD  C08  C03   aromatic  1.411  0.020  1.411
 JHD  C08  C07   aromatic  1.384  0.020  1.384
 JHD  C03  C04   aromatic  1.383  0.020  1.383
 JHD  C07  C06   aromatic  1.400  0.020  1.400
 JHD  C04  C05   aromatic  1.396  0.020  1.396
 JHD  C06  C05   aromatic  1.381  0.020  1.381
 JHD  C06  C11   single    1.509  0.020  1.509
 JHD  N12  C11   single    1.451  0.020  1.451
 JHD  C10  H103  single    0.970  0.020  1.090
 JHD  C10  H101  single    0.970  0.020  1.090
 JHD  C10  H102  single    0.970  0.020  1.090
 JHD  N12  H121  single    0.890  0.020  1.040
 JHD  N12  H122  single    0.890  0.020  1.040
 JHD  C01  H011  single    0.970  0.020  1.090
 JHD  C01  H012  single    0.970  0.020  1.090
 JHD  C01  H013  single    0.970  0.020  1.090
 JHD  C04  H041  single    0.930  0.020  1.080
 JHD  C05  H051  single    0.930  0.020  1.080
 JHD  C07  H071  single    0.930  0.020  1.080
 JHD  C11  H111  single    0.970  0.020  1.090
 JHD  C11  H112  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
 JHD  H102  C10  H101  108.77  3.000
 JHD  H102  C10  H103  108.82  3.000
 JHD  H101  C10  H103  108.65  3.000
 JHD  H102  C10  O09   106.57  3.000
 JHD  H101  C10  O09   112.00  3.000
 JHD  H103  C10  O09   111.93  3.000
 JHD  H122  N12  H121  106.05  3.000
 JHD  H122  N12  C11   109.29  3.000
 JHD  H121  N12  C11   109.45  3.000
 JHD  H013  C01  H012  108.75  3.000
 JHD  H013  C01  H011  108.79  3.000
 JHD  H012  C01  H011  108.54  3.000
 JHD  H013  C01  O02   106.59  3.000
 JHD  H012  C01  O02   112.11  3.000
 JHD  H011  C01  O02   111.97  3.000
 JHD  C03   O02  C01   117.88  3.000
 JHD  C08   C03  C04   119.03  3.000
 JHD  C04   C03  O02   125.26  3.000
 JHD  C08   C03  O02   115.70  3.000
 JHD  H041  C04  C05   118.72  3.000
 JHD  H041  C04  C03   120.52  3.000
 JHD  C05   C04  C03   120.76  3.000
 JHD  H051  C05  C06   119.90  3.000
 JHD  H051  C05  C04   119.44  3.000
 JHD  C06   C05  C04   120.67  3.000
 JHD  C11   C06  C07   119.00  3.000
 JHD  C11   C06  C05   122.37  3.000
 JHD  C07   C06  C05   118.62  3.000
 JHD  H071  C07  C08   120.16  3.000
 JHD  H071  C07  C06   118.46  3.000
 JHD  C08   C07  C06   121.38  3.000
 JHD  O09   C08  C07   124.94  3.000
 JHD  C07   C08  C03   119.53  3.000
 JHD  O09   C08  C03   115.53  3.000
 JHD  C08   O09  C10   118.04  3.000
 JHD  H112  C11  H111  105.52  3.000
 JHD  H112  C11  C06   108.38  3.000
 JHD  H111  C11  C06   108.69  3.000
 JHD  H112  C11  N12   113.70  3.000
 JHD  H111  C11  N12   107.80  3.000
 JHD  C06   C11  N12   112.43  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
 JHD  CONST_01  C06   C07  C08  C03     0.00   0.0  0
 JHD  CONST_02  C06   C05  C04  C03     0.00   0.0  0
 JHD  CONST_03  C07   C08  C03  C04     0.00   0.0  0
 JHD  CONST_04  C07   C06  C05  C04     0.00   0.0  0
 JHD  CONST_05  C08   C03  C04  C05     0.00   0.0  0
 JHD  CONST_06  C08   C07  C06  C05     0.00   0.0  0
 JHD  CONST_07  C07   C08  C03  O02   180.00   0.0  0
 JHD  CONST_08  C05   C04  C03  O02   180.00   0.0  0
 JHD  CONST_09  O09   C08  C03  C04   180.00   0.0  0
 JHD  CONST_10  C11   C06  C05  C04   180.00   0.0  0
 JHD  CONST_11  O09   C08  C07  C06   180.00   0.0  0
 JHD  CONST_12  C11   C06  C07  C08   180.00   0.0  0
 JHD  CONST_13  H071  C07  C08  C03   180.00   0.0  0
 JHD  CONST_14  H051  C05  C04  C03   180.00   0.0  0
 JHD  CONST_15  H041  C04  C05  C06   180.00   0.0  0
 JHD  Var_01    C03   C08  O09  C10   179.84  30.0  2
 JHD  Var_02    C07   C06  C11  N12  -158.16  30.0  2
 JHD  Var_03    C08   C03  O02  C01   178.27  30.0  2
 JHD  Var_04    H011  C01  O02  C03   -60.42  30.0  3
 JHD  Var_05    H121  N12  C11  C06    70.33  30.0  3
 JHD  Var_06    H103  C10  O09  C08   -60.78  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
 JHD  plan-1  O02   0.020
 JHD  plan-1  C03   0.020
 JHD  plan-1  C04   0.020
 JHD  plan-1  C05   0.020
 JHD  plan-1  C06   0.020
 JHD  plan-1  C07   0.020
 JHD  plan-1  C08   0.020
 JHD  plan-1  O09   0.020
 JHD  plan-1  H041  0.020
 JHD  plan-1  H051  0.020
 JHD  plan-1  H071  0.020
 JHD  plan-1  C11   0.020

