# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:28:15 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 4,7-dimethyl-1,10-phenanthroline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccnc2c1ccc3c(C)ccnc23
#
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
 DPT  DPT  4,7-dimethyl-1,10-phenanthroline  ligand  28  16  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DPT
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
 DPT  N1    N  N     0  -0.411  -1.8188   0.0180   1.3526
 DPT  C2    C  CR16  0  -0.077  -1.8199   0.0181   2.6634
 DPT  C3    C  CR16  0  -0.384  -0.6585   0.0067   3.4454
 DPT  C4    C  CR6   0   0.200   0.5724  -0.0059   2.8335
 DPT  C4A   C  CR66  0   0.021   0.5957  -0.0043   1.4168
 DPT  C5    C  CR16  0  -0.323   1.8184  -0.0146   0.6797
 DPT  C6    C  CR16  0  -0.323   1.8203  -0.0140  -0.6739
 DPT  C6A   C  CR66  0   0.021   0.5996  -0.0034  -1.4145
 DPT  C7    C  CR6   0   0.199   0.5804  -0.0044  -2.8313
 DPT  C8    C  CR16  0  -0.384  -0.6490   0.0057  -3.4465
 DPT  C9    C  CR16  0  -0.077  -1.8124   0.0169  -2.6677
 DPT  N10   N  N     0  -0.411  -1.8150   0.0179  -1.3569
 DPT  C10   C  CR66  0   0.154  -0.6301   0.0076  -0.7253
 DPT  C1A   C  CR66  0   0.153  -0.6322   0.0075   0.7241
 DPT  C11   C  CH3   0  -0.751   1.8351  -0.0229   3.6351
 DPT  C12   C  CH3   0  -0.750   1.8453  -0.0176  -3.6293
 DPT  H2    H  HCR6  0   0.262  -2.7902   0.0274   3.1495
 DPT  H3    H  HCR6  0   0.266  -0.7409   0.0076   4.5245
 DPT  H5    H  HCR6  0   0.265   2.7588  -0.0228   1.2145
 DPT  H6    H  HCR6  0   0.265   2.7624  -0.0224  -1.2057
 DPT  H8    H  HCR6  0   0.266  -0.7287   0.0049  -4.5260
 DPT  H9    H  HCR6  0   0.261  -2.7812   0.0253  -3.1571
 DPT  H111  H  HCH3  0   0.258   2.4360  -0.9066   3.4139
 DPT  H112  H  HCH3  0   0.258   2.4576   0.8471   3.4198
 DPT  H113  H  HCH3  0   0.263   1.6185  -0.0235   4.7014
 DPT  H121  H  HCH3  0   0.258   2.4477  -0.9001  -3.4083
 DPT  H122  H  HCH3  0   0.263   1.6318  -0.0169  -4.6962
 DPT  H123  H  HCH3  0   0.258   2.4652   0.8536  -3.4112

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
 DPT  N1   C2    aromatic  1.311  0.020  1.311
 DPT  N1   C1A   aromatic  1.343  0.020  1.343
 DPT  C2   C3    aromatic  1.400  0.020  1.400
 DPT  C2   H2    single    0.930  0.020  1.080
 DPT  C3   C4    aromatic  1.375  0.020  1.375
 DPT  C3   H3    single    0.930  0.020  1.080
 DPT  C4   C4A   aromatic  1.417  0.020  1.417
 DPT  C4   C11   single    1.496  0.020  1.496
 DPT  C4A  C5    aromatic  1.428  0.020  1.428
 DPT  C4A  C1A   aromatic  1.410  0.020  1.410
 DPT  C5   C6    aromatic  1.354  0.020  1.354
 DPT  C5   H5    single    0.930  0.020  1.080
 DPT  C6   C6A   aromatic  1.428  0.020  1.428
 DPT  C6   H6    single    0.930  0.020  1.080
 DPT  C6A  C7    aromatic  1.417  0.020  1.417
 DPT  C6A  C10   aromatic  1.410  0.020  1.410
 DPT  C7   C8    aromatic  1.375  0.020  1.375
 DPT  C7   C12   single    1.496  0.020  1.496
 DPT  C8   C9    aromatic  1.400  0.020  1.400
 DPT  C8   H8    single    0.930  0.020  1.080
 DPT  C9   N10   aromatic  1.311  0.020  1.311
 DPT  C9   H9    single    0.930  0.020  1.080
 DPT  N10  C10   aromatic  1.343  0.020  1.343
 DPT  C10  C1A   aromatic  1.449  0.020  1.449
 DPT  C11  H111  single    0.970  0.020  1.090
 DPT  C11  H112  single    0.970  0.020  1.090
 DPT  C11  H113  single    0.970  0.020  1.090
 DPT  C12  H121  single    0.970  0.020  1.090
 DPT  C12  H122  single    0.970  0.020  1.090
 DPT  C12  H123  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
 DPT  C1A   N1   C2    117.95  3.000
 DPT  H2    C2   C3    119.44  3.000
 DPT  H2    C2   N1    116.66  3.000
 DPT  C3    C2   N1    123.90  3.000
 DPT  H3    C3   C4    120.80  3.000
 DPT  H3    C3   C2    119.59  3.000
 DPT  C4    C3   C2    119.62  3.000
 DPT  C11   C4   C4A   121.46  3.000
 DPT  C11   C4   C3    121.16  3.000
 DPT  C4A   C4   C3    117.37  3.000
 DPT  C1A   C4A  C5    119.49  3.000
 DPT  C1A   C4A  C4    118.49  3.000
 DPT  C5    C4A  C4    122.02  3.000
 DPT  H5    C5   C6    119.55  3.000
 DPT  H5    C5   C4A   119.29  3.000
 DPT  C6    C5   C4A   121.16  3.000
 DPT  H6    C6   C6A   119.32  3.000
 DPT  H6    C6   C5    119.52  3.000
 DPT  C6A   C6   C5    121.16  3.000
 DPT  C10   C6A  C7    118.49  3.000
 DPT  C10   C6A  C6    119.49  3.000
 DPT  C7    C6A  C6    122.02  3.000
 DPT  C12   C7   C8    121.17  3.000
 DPT  C12   C7   C6A   121.47  3.000
 DPT  C8    C7   C6A   117.36  3.000
 DPT  H8    C8   C9    119.58  3.000
 DPT  H8    C8   C7    120.81  3.000
 DPT  C9    C8   C7    119.62  3.000
 DPT  H9    C9   N10   116.69  3.000
 DPT  H9    C9   C8    119.40  3.000
 DPT  N10   C9   C8    123.91  3.000
 DPT  C10   N10  C9    117.95  3.000
 DPT  C1A   C10  N10   117.98  3.000
 DPT  C1A   C10  C6A   119.35  3.000
 DPT  N10   C10  C6A   122.67  3.000
 DPT  C10   C1A  C4A   119.34  3.000
 DPT  C10   C1A  N1    117.99  3.000
 DPT  C4A   C1A  N1    122.67  3.000
 DPT  H113  C11  H112  107.90  3.000
 DPT  H113  C11  H111  107.93  3.000
 DPT  H112  C11  H111  106.95  3.000
 DPT  H113  C11  C4    110.92  3.000
 DPT  H112  C11  C4    111.51  3.000
 DPT  H111  C11  C4    111.44  3.000
 DPT  H123  C12  H122  107.88  3.000
 DPT  H123  C12  H121  106.96  3.000
 DPT  H122  C12  H121  107.90  3.000
 DPT  H123  C12  C7    111.52  3.000
 DPT  H122  C12  C7    110.93  3.000
 DPT  H121  C12  C7    111.47  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
 DPT  CONST_01  C4    C3   C2   N1     0.00   0.0  0
 DPT  CONST_02  C4    C4A  C1A  N1     0.00   0.0  0
 DPT  CONST_03  C5    C4A  C1A  N1   180.00   0.0  0
 DPT  CONST_04  C6A   C10  C1A  N1   180.00   0.0  0
 DPT  CONST_05  N10   C10  C1A  N1     0.00   0.0  0
 DPT  CONST_06  C4A   C1A  N1   C2     0.00   0.0  0
 DPT  CONST_07  C10   C1A  N1   C2   180.00   0.0  0
 DPT  CONST_08  C4A   C4   C3   C2     0.00   0.0  0
 DPT  CONST_09  C1A   N1   C2   C3     0.00   0.0  0
 DPT  CONST_10  C5    C4A  C4   C3   180.00   0.0  0
 DPT  CONST_11  C1A   C4A  C4   C3     0.00   0.0  0
 DPT  CONST_12  C6    C5   C4A  C4   180.00   0.0  0
 DPT  CONST_13  C10   C1A  C4A  C4   180.00   0.0  0
 DPT  CONST_14  C6A   C6   C5   C4A    0.00   0.0  0
 DPT  CONST_15  C6A   C10  C1A  C4A    0.00   0.0  0
 DPT  CONST_16  N10   C10  C1A  C4A  180.00   0.0  0
 DPT  CONST_17  C10   C1A  C4A  C5     0.00   0.0  0
 DPT  CONST_18  C7    C6A  C6   C5   180.00   0.0  0
 DPT  CONST_19  C10   C6A  C6   C5     0.00   0.0  0
 DPT  CONST_20  C1A   C4A  C5   C6     0.00   0.0  0
 DPT  CONST_21  C8    C7   C6A  C6   180.00   0.0  0
 DPT  CONST_22  N10   C10  C6A  C6   180.00   0.0  0
 DPT  CONST_23  C1A   C10  C6A  C6     0.00   0.0  0
 DPT  CONST_24  C9    C8   C7   C6A    0.00   0.0  0
 DPT  CONST_25  C9    N10  C10  C6A    0.00   0.0  0
 DPT  CONST_26  N10   C10  C6A  C7     0.00   0.0  0
 DPT  CONST_27  C1A   C10  C6A  C7   180.00   0.0  0
 DPT  CONST_28  N10   C9   C8   C7     0.00   0.0  0
 DPT  CONST_29  C10   C6A  C7   C8     0.00   0.0  0
 DPT  CONST_30  C10   N10  C9   C8     0.00   0.0  0
 DPT  CONST_31  C1A   C10  N10  C9   180.00   0.0  0
 DPT  CONST_32  C11   C4   C3   C2   180.00   0.0  0
 DPT  CONST_33  C11   C4   C4A  C5     0.00   0.0  0
 DPT  CONST_34  C12   C7   C6A  C6     0.00   0.0  0
 DPT  CONST_35  C12   C7   C8   C9   180.00   0.0  0
 DPT  CONST_36  C12   C7   C6A  C10  180.00   0.0  0
 DPT  CONST_37  C11   C4   C4A  C1A  180.00   0.0  0
 DPT  CONST_38  H3    C3   C2   N1   180.00   0.0  0
 DPT  CONST_39  H2    C2   C3   C4   180.00   0.0  0
 DPT  CONST_40  H5    C5   C4A  C4     0.00   0.0  0
 DPT  CONST_41  H6    C6   C5   C4A  180.00   0.0  0
 DPT  CONST_42  H8    C8   C7   C6A  180.00   0.0  0
 DPT  CONST_43  H9    C9   C8   C7   180.00   0.0  0
 DPT  Var_01    H111  C11  C4   C3   120.28  30.0  2
 DPT  Var_02    H121  C12  C7   C6A   59.70  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
 DPT  plan-1  N1   0.020
 DPT  plan-1  C2   0.020
 DPT  plan-1  C3   0.020
 DPT  plan-1  C4   0.020
 DPT  plan-1  C4A  0.020
 DPT  plan-1  C5   0.020
 DPT  plan-1  C6   0.020
 DPT  plan-1  C6A  0.020
 DPT  plan-1  C7   0.020
 DPT  plan-1  C8   0.020
 DPT  plan-1  C9   0.020
 DPT  plan-1  N10  0.020
 DPT  plan-1  C10  0.020
 DPT  plan-1  C1A  0.020
 DPT  plan-1  C11  0.020
 DPT  plan-1  C12  0.020
 DPT  plan-1  H2   0.020
 DPT  plan-1  H3   0.020
 DPT  plan-1  H5   0.020
 DPT  plan-1  H6   0.020
 DPT  plan-1  H8   0.020
 DPT  plan-1  H9   0.020

