# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 16:57:25 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: N,N'-dibuta-2,3-dien-1-ylbutane-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [CH2]=[C]=[CH]CNCCCCNC[CH]=[C]=[CH2]
#
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
 MD2  MD2  N,N'-dibuta-2,3-dien-1-ylbutane-1,4-diamine  ligand  34  14  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MD2
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
 MD2  C1    C  C2    0  -0.691   1.2891  -0.0441   7.4865
 MD2  C6    C  CH2   0  -0.250  -0.3379   0.5386   1.8661
 MD2  C7    C  CH2   0  -0.444  -0.3004  -0.3843   0.6583
 MD2  C11   C  CH2   0  -0.300  -0.3360  -0.6466  -4.2779
 MD2  C12   C  C1    0  -0.407  -0.4330   0.1693  -5.5381
 MD2  C2    C  CSP   0   0.271   0.4326  -0.1262   6.5088
 MD2  C3    C  C1    0  -0.403  -0.4218  -0.2024   5.5277
 MD2  C4    C  CH2   0  -0.304  -0.3527   0.6360   4.2821
 MD2  N5    N  NH1   0  -0.600  -0.3104  -0.2140   3.1070
 MD2  C8    C  CH2   0  -0.445  -0.3389   0.3804  -0.6581
 MD2  C9    C  CH2   0  -0.251  -0.3125  -0.5418  -1.8667
 MD2  N10   N  NH1   0  -0.598  -0.3419   0.2125  -3.1065
 MD2  C13   C  CSP   0   0.275   0.4675   0.1767  -6.4794
 MD2  C14   C  C2    0  -0.692   1.3677   0.1723  -7.4205
 MD2  HC11  H  H     0   0.263   1.1373   0.6377   8.3152
 MD2  HC1A  H  H     0   0.263   2.1826  -0.6576   7.5066
 MD2  HC61  H  HCH2  0   0.216  -1.2629   1.1244   1.8434
 MD2  HC62  H  HCH2  0   0.188   0.4870   1.2664   1.7948
 MD2  HC71  H  HCH2  0   0.217   0.6074  -0.9969   0.6966
 MD2  HC72  H  HCH2  0   0.219  -1.1454  -1.0776   0.7134
 MD2  H111  H  HCH2  0   0.235   0.5899  -1.2264  -4.2847
 MD2  H112  H  HCH2  0   0.208  -1.1623  -1.3753  -4.2676
 MD2  HC12  H  H     0   0.269  -1.3203   0.7871  -5.6592
 MD2  HC3   H  H     0   0.268  -1.2413  -0.9128   5.5957
 MD2  HC41  H  HCH2  0   0.235  -1.2586   1.2481   4.2219
 MD2  HC42  H  HCH2  0   0.212   0.4924   1.3358   4.3483
 MD2  HN5   H  HNH1  0   0.340   0.5406  -0.7647   3.1376
 MD2  HC81  H  HCH2  0   0.216  -1.2437   0.9979  -0.6930
 MD2  HC82  H  HCH2  0   0.219   0.5092   1.0692  -0.7153
 MD2  HC91  H  HCH2  0   0.216   0.6085  -1.1343  -1.8489
 MD2  HC92  H  HCH2  0   0.188  -1.1420  -1.2642  -1.7927
 MD2  HN10  H  HNH1  0   0.340  -1.1853   0.7763  -3.1212
 MD2  H141  H  H     0   0.263   2.1949   0.8729  -7.4136
 MD2  H142  H  H     0   0.263   1.3218  -0.5322  -8.2429

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
 MD2  C1   C2    double  1.302  0.020  1.302
 MD2  C1   HC11  single  0.930  0.020  1.080
 MD2  C1   HC1A  single  0.930  0.020  1.080
 MD2  C6   C7    single  1.521  0.020  1.521
 MD2  C6   N5    single  1.452  0.020  1.452
 MD2  C6   HC61  single  0.970  0.020  1.090
 MD2  C6   HC62  single  0.970  0.020  1.090
 MD2  C7   C8    single  1.523  0.020  1.523
 MD2  C7   HC71  single  0.970  0.020  1.090
 MD2  C7   HC72  single  0.970  0.020  1.090
 MD2  C11  C12   single  1.504  0.020  1.504
 MD2  C11  N10   single  1.453  0.020  1.453
 MD2  C11  H111  single  0.970  0.020  1.090
 MD2  C11  H112  single  0.970  0.020  1.090
 MD2  C12  C13   double  1.303  0.020  1.303
 MD2  C12  HC12  single  0.930  0.020  1.080
 MD2  C2   C3    double  1.303  0.020  1.303
 MD2  C3   C4    single  1.503  0.020  1.503
 MD2  C3   HC3   single  0.930  0.020  1.080
 MD2  C4   N5    single  1.451  0.020  1.451
 MD2  C4   HC41  single  0.970  0.020  1.090
 MD2  C4   HC42  single  0.970  0.020  1.090
 MD2  N5   HN5   single  0.890  0.020  1.040
 MD2  C8   C9    single  1.520  0.020  1.520
 MD2  C8   HC81  single  0.970  0.020  1.090
 MD2  C8   HC82  single  0.970  0.020  1.090
 MD2  C9   N10   single  1.452  0.020  1.452
 MD2  C9   HC91  single  0.970  0.020  1.090
 MD2  C9   HC92  single  0.970  0.020  1.090
 MD2  N10  HN10  single  0.890  0.020  1.040
 MD2  C13  C14   double  1.302  0.020  1.302
 MD2  C14  H141  single  0.930  0.020  1.080
 MD2  C14  H142  single  0.930  0.020  1.080

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
 MD2  HC1A  C1   HC11  117.21  3.000
 MD2  HC1A  C1   C2    121.35  3.000
 MD2  HC11  C1   C2    121.43  3.000
 MD2  HC62  C6   HC61  106.12  3.000
 MD2  HC62  C6   N5    112.54  3.000
 MD2  HC61  C6   N5    108.12  3.000
 MD2  HC62  C6   C7    109.32  3.000
 MD2  HC61  C6   C7    109.21  3.000
 MD2  N5    C6   C7    111.34  3.000
 MD2  HC72  C7   HC71  106.48  3.000
 MD2  HC72  C7   C8    110.00  3.000
 MD2  HC71  C7   C8    109.38  3.000
 MD2  HC72  C7   C6    109.00  3.000
 MD2  HC71  C7   C6    109.39  3.000
 MD2  C8    C7   C6    112.41  3.000
 MD2  H112  C11  H111  106.54  3.000
 MD2  H112  C11  N10   112.37  3.000
 MD2  H111  C11  N10   108.80  3.000
 MD2  H112  C11  C12   108.56  3.000
 MD2  H111  C11  C12   109.71  3.000
 MD2  N10   C11  C12   110.76  3.000
 MD2  HC12  C12  C13   118.69  3.000
 MD2  HC12  C12  C11   116.98  3.000
 MD2  C13   C12  C11   124.32  3.000
 MD2  C3    C2   C1    180.00  3.000
 MD2  HC3   C3   C4    116.82  3.000
 MD2  HC3   C3   C2    119.05  3.000
 MD2  C4    C3   C2    124.13  3.000
 MD2  HC42  C4   HC41  106.46  3.000
 MD2  HC42  C4   N5    113.54  3.000
 MD2  HC41  C4   N5    107.89  3.000
 MD2  HC42  C4   C3    109.91  3.000
 MD2  HC41  C4   C3    108.62  3.000
 MD2  N5    C4   C3    110.23  3.000
 MD2  HN5   N5   C4    108.55  3.000
 MD2  HN5   N5   C6    108.86  3.000
 MD2  C4    N5   C6    112.83  3.000
 MD2  HC82  C8   HC81  106.47  3.000
 MD2  HC82  C8   C9    109.08  3.000
 MD2  HC81  C8   C9    109.31  3.000
 MD2  HC82  C8   C7    109.98  3.000
 MD2  HC81  C8   C7    109.35  3.000
 MD2  C9    C8   C7    112.46  3.000
 MD2  HC92  C9   HC91  106.09  3.000
 MD2  HC92  C9   N10   112.50  3.000
 MD2  HC91  C9   N10   108.18  3.000
 MD2  HC92  C9   C8    109.33  3.000
 MD2  HC91  C9   C8    109.25  3.000
 MD2  N10   C9   C8    111.31  3.000
 MD2  HN10  N10  C9    108.54  3.000
 MD2  HN10  N10  C11   108.68  3.000
 MD2  C9    N10  C11   112.42  3.000
 MD2  C14   C13  C12   180.00  3.000
 MD2  H142  C14  H141  117.21  3.000
 MD2  H142  C14  C13   121.41  3.000
 MD2  H141  C14  C13   121.38  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
 MD2  Var_01  C4    C3   C2   C1     11.65   0.0  2
 MD2  Var_02  C9    C8   C7   C6   -179.55  30.0  3
 MD2  Var_03  C3    C4   N5   C6    175.92  30.0  2
 MD2  Var_04  C4    N5   C6   C7   -179.67  30.0  3
 MD2  Var_05  N10   C9   C8   C7   -179.65  30.0  3
 MD2  Var_06  C8    C9   N10  C11  -179.21  30.0  1
 MD2  Var_07  C9    N10  C11  C12   177.31  30.0  3
 MD2  Var_08  N5    C4   C3   C2    123.69  30.0  3
 MD2  Var_09  C8    C7   C6   N5    179.57  30.0  3
 MD2  Var_10  C13   C12  C11  N10   119.67  30.0  3
 MD2  Var_11  H141  C14  C13  C12  -139.67   0.0  2
 MD2  Var_12  HC11  C1   C2   C3     78.29   0.0  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
 MD2  plan-1  C1    0.020
 MD2  plan-1  C2    0.020
 MD2  plan-1  C3    0.020
 MD2  plan-1  C4    0.020
 MD2  plan-1  HC11  0.020
 MD2  plan-1  HC1A  0.020
 MD2  plan-1  HC3   0.020
 MD2  plan-2  C11   0.020
 MD2  plan-2  C12   0.020
 MD2  plan-2  C13   0.020
 MD2  plan-2  C14   0.020
 MD2  plan-2  HC12  0.020
 MD2  plan-2  H141  0.020
 MD2  plan-2  H142  0.020

