# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 20:04:50 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: ~{N}1,~{N}1,~{N}8,~{N}8-tetramethylnaphthalene-1,8-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1cccc2cccc(N(C)C)c12
#
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
 U1E  U1E  "~{N}1,~{N}1,~{N}8,~{N}8-tetramethylnaphthalene-1,8-diamine"
  ligand  34  16  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_U1E
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
 U1E  C10  C  CR16  0  -0.247   -8.7482   1.9003   1.6217
 U1E  C15  C  CH3   0  -0.547  -11.7454   0.1651  -0.7585
 U1E  C01  C  CH3   0  -0.546  -14.3738   4.5750  -0.2648
 U1E  C03  C  CH3   0  -0.522  -13.9404   2.6491   1.0948
 U1E  C04  C  CR6   0   0.283  -12.1746   4.2559   0.7218
 U1E  C05  C  CR16  0  -0.352  -12.1155   5.5973   1.0480
 U1E  C06  C  CR16  0  -0.247  -10.9748   6.1696   1.6324
 U1E  C07  C  CR16  0  -0.338   -9.9067   5.3860   1.9565
 U1E  C08  C  CR66  0   0.079   -9.8993   4.0154   1.6055
 U1E  C09  C  CR16  0  -0.338   -8.7959   3.2145   1.9829
 U1E  C11  C  CR16  0  -0.353   -9.7391   1.3648   0.7838
 U1E  C12  C  CR6   0   0.284  -10.8194   2.1144   0.3584
 U1E  C14  C  CH3   0  -0.522  -11.8169   2.3025  -1.8364
 U1E  C16  C  CR66  0   0.037  -10.9888   3.4491   0.8799
 U1E  N02  N  NT    0  -0.466  -13.3661   3.6913   0.2657
 U1E  N13  N  NT    0  -0.466  -11.7170   1.5946  -0.5744
 U1E  H1   H  HCR6  0   0.248   -7.9171   1.2761   1.9241
 U1E  H2   H  HCH3  0   0.242  -11.8091  -0.3468   0.2016
 U1E  H3   H  HCH3  0   0.245  -12.6357  -0.0961  -1.3321
 U1E  H4   H  HCH3  0   0.206  -10.8780  -0.2337  -1.3038
 U1E  H5   H  HCH3  0   0.242  -13.9393   5.2560  -0.9962
 U1E  H6   H  HCH3  0   0.244  -15.1280   3.9753  -0.7760
 U1E  H7   H  HCH3  0   0.206  -14.8944   5.1731   0.4969
 U1E  H8   H  HCH3  0   0.248  -13.1715   2.0302   1.5468
 U1E  H9   H  HCH3  0   0.208  -14.5505   3.0720   1.9052
 U1E  H10  H  HCH3  0   0.228  -14.5794   2.0008   0.4937
 U1E  H11  H  HCR6  0   0.261  -12.9866   6.2234   0.9134
 U1E  H12  H  HCR6  0   0.248  -10.9789   7.2242   1.8775
 U1E  H13  H  HCR6  0   0.244   -9.0500   5.7973   2.4760
 U1E  H14  H  HCR6  0   0.244   -8.0002   3.6626   2.5651
 U1E  H15  H  HCR6  0   0.261   -9.6067   0.3551   0.4208
 U1E  H16  H  HCH3  0   0.248  -11.7247   3.3755  -1.7019
 U1E  H17  H  HCH3  0   0.208  -11.0340   1.9830  -2.5383
 U1E  H18  H  HCH3  0   0.228  -12.7850   2.1066  -2.2994

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
 U1E  C14  N13  single    1.450  0.020  1.450
 U1E  C01  N02  single    1.442  0.020  1.442
 U1E  N13  C15  single    1.442  0.020  1.442
 U1E  N13  C12  single    1.395  0.020  1.395
 U1E  N02  C03  single    1.450  0.020  1.450
 U1E  N02  C04  single    1.395  0.020  1.395
 U1E  C12  C11  aromatic  1.382  0.020  1.382
 U1E  C12  C16  aromatic  1.443  0.020  1.443
 U1E  C11  C10  aromatic  1.404  0.020  1.404
 U1E  C16  C04  aromatic  1.443  0.020  1.443
 U1E  C16  C08  aromatic  1.426  0.020  1.426
 U1E  C04  C05  aromatic  1.382  0.020  1.382
 U1E  C10  C09  aromatic  1.364  0.020  1.364
 U1E  C08  C09  aromatic  1.415  0.020  1.415
 U1E  C08  C07  aromatic  1.415  0.020  1.415
 U1E  C05  C06  aromatic  1.404  0.020  1.404
 U1E  C06  C07  aromatic  1.364  0.020  1.364
 U1E  C10  H1   single    0.930  0.020  1.080
 U1E  C15  H2   single    0.970  0.020  1.090
 U1E  C15  H3   single    0.970  0.020  1.090
 U1E  C15  H4   single    0.970  0.020  1.090
 U1E  C01  H5   single    0.970  0.020  1.090
 U1E  C01  H6   single    0.970  0.020  1.090
 U1E  C01  H7   single    0.970  0.020  1.090
 U1E  C03  H8   single    0.970  0.020  1.090
 U1E  C03  H9   single    0.970  0.020  1.090
 U1E  C03  H10  single    0.970  0.020  1.090
 U1E  C05  H11  single    0.930  0.020  1.080
 U1E  C06  H12  single    0.930  0.020  1.080
 U1E  C07  H13  single    0.930  0.020  1.080
 U1E  C09  H14  single    0.930  0.020  1.080
 U1E  C11  H15  single    0.930  0.020  1.080
 U1E  C14  H16  single    0.970  0.020  1.090
 U1E  C14  H17  single    0.970  0.020  1.090
 U1E  C14  H18  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
 U1E  H1   C10  C11  119.25  3.000
 U1E  H1   C10  C09  120.57  3.000
 U1E  C11  C10  C09  120.07  3.000
 U1E  H4   C15  H3   107.24  3.000
 U1E  H4   C15  H2   108.22  3.000
 U1E  H3   C15  H2   107.64  3.000
 U1E  H4   C15  N13  114.05  3.000
 U1E  H3   C15  N13  108.70  3.000
 U1E  H2   C15  N13  110.75  3.000
 U1E  H7   C01  H6   107.24  3.000
 U1E  H7   C01  H5   108.29  3.000
 U1E  H6   C01  H5   107.74  3.000
 U1E  H7   C01  N02  114.18  3.000
 U1E  H6   C01  N02  108.59  3.000
 U1E  H5   C01  N02  110.57  3.000
 U1E  H10  C03  H9   108.05  3.000
 U1E  H10  C03  H8   107.78  3.000
 U1E  H9   C03  H8   107.79  3.000
 U1E  H10  C03  N02  110.12  3.000
 U1E  H9   C03  N02  111.40  3.000
 U1E  H8   C03  N02  111.54  3.000
 U1E  N02  C04  C16  120.76  3.000
 U1E  C16  C04  C05  118.80  3.000
 U1E  N02  C04  C05  120.44  3.000
 U1E  H11  C05  C06  118.06  3.000
 U1E  H11  C05  C04  119.89  3.000
 U1E  C06  C05  C04  121.93  3.000
 U1E  H12  C06  C07  120.59  3.000
 U1E  H12  C06  C05  119.23  3.000
 U1E  C07  C06  C05  120.07  3.000
 U1E  H13  C07  C08  118.86  3.000
 U1E  H13  C07  C06  121.02  3.000
 U1E  C08  C07  C06  120.12  3.000
 U1E  C16  C08  C09  120.45  3.000
 U1E  C09  C08  C07  119.10  3.000
 U1E  C16  C08  C07  120.45  3.000
 U1E  H14  C09  C08  118.83  3.000
 U1E  H14  C09  C10  121.03  3.000
 U1E  C08  C09  C10  120.14  3.000
 U1E  H15  C11  C12  119.93  3.000
 U1E  H15  C11  C10  118.05  3.000
 U1E  C12  C11  C10  121.91  3.000
 U1E  N13  C12  C16  120.71  3.000
 U1E  C16  C12  C11  118.83  3.000
 U1E  N13  C12  C11  120.45  3.000
 U1E  H18  C14  H17  108.00  3.000
 U1E  H18  C14  H16  107.79  3.000
 U1E  H17  C14  H16  107.82  3.000
 U1E  H18  C14  N13  110.05  3.000
 U1E  H17  C14  N13  111.40  3.000
 U1E  H16  C14  N13  111.64  3.000
 U1E  C12  C16  C08  117.48  3.000
 U1E  C08  C16  C04  117.49  3.000
 U1E  C12  C16  C04  125.03  3.000
 U1E  C04  N02  C03  116.24  3.000
 U1E  C04  N02  C01  117.98  3.000
 U1E  C03  N02  C01  111.97  3.000
 U1E  C14  N13  C12  116.38  3.000
 U1E  C12  N13  C15  117.88  3.000
 U1E  C14  N13  C15  111.80  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
 U1E  CONST_01  C16  C12  C11  C10     0.00   0.0  0
 U1E  CONST_02  C16  C08  C09  C10     0.00   0.0  0
 U1E  CONST_03  C07  C08  C09  C10   180.00   0.0  0
 U1E  CONST_04  C11  C12  C16  C04   180.00   0.0  0
 U1E  CONST_05  C09  C08  C16  C04   180.00   0.0  0
 U1E  CONST_06  C07  C08  C16  C04     0.00   0.0  0
 U1E  CONST_07  C07  C06  C05  C04     0.00   0.0  0
 U1E  CONST_08  C12  C16  C04  C05   180.00   0.0  0
 U1E  CONST_09  C08  C16  C04  C05     0.00   0.0  0
 U1E  CONST_10  C08  C07  C06  C05     0.00   0.0  0
 U1E  CONST_11  C16  C04  C05  C06     0.00   0.0  0
 U1E  CONST_12  C16  C08  C07  C06     0.00   0.0  0
 U1E  CONST_13  C09  C08  C07  C06   180.00   0.0  0
 U1E  CONST_14  C12  C16  C08  C07   180.00   0.0  0
 U1E  CONST_15  C11  C12  C16  C08     0.00   0.0  0
 U1E  CONST_16  C11  C10  C09  C08     0.00   0.0  0
 U1E  CONST_17  C12  C11  C10  C09     0.00   0.0  0
 U1E  CONST_18  C12  C16  C08  C09     0.00   0.0  0
 U1E  CONST_19  N13  C12  C11  C10   180.00   0.0  0
 U1E  CONST_20  N13  C12  C16  C04     0.00   0.0  0
 U1E  CONST_21  N02  C04  C05  C06   180.00   0.0  0
 U1E  CONST_22  N13  C12  C16  C08   180.00   0.0  0
 U1E  CONST_23  N02  C04  C16  C08   180.00   0.0  0
 U1E  CONST_24  N02  C04  C16  C12     0.00   0.0  0
 U1E  CONST_25  H12  C06  C05  C04   180.00   0.0  0
 U1E  CONST_26  H13  C07  C06  C05   180.00   0.0  0
 U1E  CONST_27  H14  C09  C08  C07     0.00   0.0  0
 U1E  CONST_28  H11  C05  C06  C07   180.00   0.0  0
 U1E  CONST_29  H1   C10  C09  C08   180.00   0.0  0
 U1E  CONST_30  H12  C06  C07  C08   180.00   0.0  0
 U1E  CONST_31  H15  C11  C10  C09   180.00   0.0  0
 U1E  CONST_32  H13  C07  C08  C09     0.00   0.0  0
 U1E  CONST_33  H14  C09  C10  C11   180.00   0.0  0
 U1E  CONST_34  H1   C10  C11  C12   180.00   0.0  0
 U1E  CONST_35  H15  C11  C12  C16   180.00   0.0  0
 U1E  CONST_36  H11  C05  C04  C16   180.00   0.0  0
 U1E  CONST_37  H14  C09  C08  C16   180.00   0.0  0
 U1E  CONST_38  H13  C07  C08  C16   180.00   0.0  0
 U1E  Var_01    H5   C01  N02  C04    49.32  30.0  3
 U1E  Var_02    H6   C01  N02  C04   167.33  30.0  3
 U1E  Var_03    H7   C01  N02  C04   -73.09  30.0  3
 U1E  Var_04    H8   C03  N02  C04   -36.27  30.0  3
 U1E  Var_05    H9   C03  N02  C04    84.22  30.0  3
 U1E  Var_06    H10  C03  N02  C04  -155.90  30.0  3
 U1E  Var_07    H16  C14  N13  C12   -36.46  30.0  3
 U1E  Var_08    H17  C14  N13  C12    84.14  30.0  3
 U1E  Var_09    H18  C14  N13  C12  -156.10  30.0  3
 U1E  Var_10    H2   C15  N13  C12    49.02  30.0  3
 U1E  Var_11    H3   C15  N13  C12   167.08  30.0  3
 U1E  Var_12    H4   C15  N13  C12   -73.34  30.0  3
 U1E  Var_13    H16  C14  N13  C15  -175.97  30.0  3
 U1E  Var_14    H17  C14  N13  C15   -55.37  30.0  3
 U1E  Var_15    H18  C14  N13  C15    64.39  30.0  3
 U1E  Var_16    H8   C03  N02  C01  -176.00  30.0  3
 U1E  Var_17    H9   C03  N02  C01   -55.50  30.0  3
 U1E  Var_18    H10  C03  N02  C01    64.38  30.0  3
 U1E  Var_19    H5   C01  N02  C03  -171.72  30.0  3
 U1E  Var_20    H6   C01  N02  C03   -53.71  30.0  3
 U1E  Var_21    H7   C01  N02  C03    65.87  30.0  3
 U1E  Var_22    H2   C15  N13  C14  -172.14  30.0  3
 U1E  Var_23    H3   C15  N13  C14   -54.08  30.0  3
 U1E  Var_24    H4   C15  N13  C14    65.50  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
 U1E  plan-1  C10  0.020
 U1E  plan-1  C04  0.020
 U1E  plan-1  C05  0.020
 U1E  plan-1  C06  0.020
 U1E  plan-1  C07  0.020
 U1E  plan-1  C08  0.020
 U1E  plan-1  C09  0.020
 U1E  plan-1  C11  0.020
 U1E  plan-1  C12  0.020
 U1E  plan-1  C16  0.020
 U1E  plan-1  N02  0.020
 U1E  plan-1  N13  0.020
 U1E  plan-1  H1   0.020
 U1E  plan-1  H11  0.020
 U1E  plan-1  H12  0.020
 U1E  plan-1  H13  0.020
 U1E  plan-1  H14  0.020
 U1E  plan-1  H15  0.020
 U1E  plan-2  C01  0.020
 U1E  plan-2  C03  0.020
 U1E  plan-2  C04  0.020
 U1E  plan-2  N02  0.020
 U1E  plan-3  C15  0.020
 U1E  plan-3  C12  0.020
 U1E  plan-3  C14  0.020
 U1E  plan-3  N13  0.020

