# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 07:34:31 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 1-amino-3,6,9,12-tetraoxapentadecan-15-oic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCOCCOCCOCCOCCC(O)=O
#
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
 3V3  3V3  '1-amino-3,6,9,12-tetraoxapentadecan-15-oic acid'  ligand  40  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3V3
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
 3V3  C1   C  CH2    0  -0.317   6.4724   1.0088   1.4214
 3V3  C2   C  CH2    0  -0.141   5.4778   1.6729   0.4943
 3V3  C4   C  CH2    0  -0.169   3.7882   1.2630  -1.0692
 3V3  O3   O  O2     0  -0.481   4.7298   0.7013  -0.1928
 3V3  C5   C  CH2    0  -0.169   3.0233   0.1688  -1.7679
 3V3  C7   C  CH2    0  -0.169   1.5149  -1.5862  -1.4151
 3V3  C8   C  CH2    0  -0.168   0.6752  -2.2639  -0.3632
 3V3  C10  C  CH2    0  -0.168  -1.1083  -1.9260   1.1150
 3V3  O6   O  O2     0  -0.486   2.2472  -0.5379  -0.8342
 3V3  C11  C  CH2    0  -0.165  -2.2025  -0.9593   1.4897
 3V3  C13  C  CH2    0  -0.116  -4.1880   0.0305   0.7314
 3V3  C14  C  CH2    0  -0.626  -5.1251   0.0844  -0.4553
 3V3  C15  C  C      0   0.412  -6.3675   0.9690  -0.2450
 3V3  N1   N  NH2    0  -0.795   7.4505   0.2205   0.6897
 3V3  O9   O  O2     0  -0.486  -0.3191  -1.3806   0.0888
 3V3  O12  O  O2     0  -0.494  -3.1014  -0.8187   0.4225
 3V3  O16  O  O      0  -0.609  -6.4706   1.5680   0.8438
 3V3  H1   H  HCH2   0   0.200   6.9118   1.8041   2.0398
 3V3  H2   H  HCH2   0   0.223   5.9347   0.3502   2.1087
 3V3  H3   H  HCH2   0   0.201   4.8189   2.3242   1.0859
 3V3  H4   H  HCH2   0   0.193   6.0086   2.3273  -0.2151
 3V3  H5   H  HCH2   0   0.202   3.0900   1.9221  -0.5322
 3V3  H6   H  HCH2   0   0.204   4.2782   1.8804  -1.8355
 3V3  H7   H  HCH2   0   0.206   2.3902   0.6310  -2.5381
 3V3  H8   H  HCH2   0   0.203   3.7214  -0.5013  -2.2905
 3V3  H9   H  HCH2   0   0.207   2.1832  -2.3372  -1.8597
 3V3  H10  H  HCH2   0   0.204   0.8704  -1.2170  -2.2262
 3V3  H11  H  HCH2   0   0.207   0.2308  -3.1654  -0.8079
 3V3  H12  H  HCH2   0   0.203   1.3136  -2.6006   0.4667
 3V3  H13  H  HCH2   0   0.205  -0.5053  -2.1280   2.0115
 3V3  H14  H  HCH2   0   0.202  -1.5501  -2.8852   0.8073
 3V3  H15  H  HCH2   0   0.201  -2.7071  -1.3521   2.3841
 3V3  H16  H  HCH2   0   0.200  -1.7667   0.0102   1.7729
 3V3  H17  H  HCH2   0   0.188  -3.8265   1.0372   0.9805
 3V3  H18  H  HCH2   0   0.187  -4.7171  -0.3421   1.6191
 3V3  H19  H  HCH2   0   0.229  -4.5856   0.4482  -1.3367
 3V3  H20  H  HCH2   0   0.227  -5.4576  -0.9277  -0.7093
 3V3  O1   O  OC    -1  -0.627  -7.1763   1.0104  -1.1940
 3V3  H22  H  HNH2   0   0.337   8.0480   0.8401   0.1559
 3V3  H23  H  HNH2   0   0.348   8.0617  -0.2475   1.3460

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
 3V3  N1   C1   single  1.454  0.020  1.454
 3V3  C1   C2   single  1.513  0.020  1.513
 3V3  C2   O3   single  1.406  0.020  1.406
 3V3  O3   C4   single  1.404  0.020  1.404
 3V3  C4   C5   single  1.507  0.020  1.507
 3V3  O6   C5   single  1.405  0.020  1.405
 3V3  O6   C7   single  1.405  0.020  1.405
 3V3  O9   C8   single  1.405  0.020  1.405
 3V3  O9   C10  single  1.405  0.020  1.405
 3V3  C8   C7   single  1.507  0.020  1.507
 3V3  C14  C15  single  1.540  0.020  1.540
 3V3  C14  C13  single  1.513  0.020  1.513
 3V3  C15  O16  deloc   1.247  0.020  1.247
 3V3  O12  C13  single  1.413  0.020  1.413
 3V3  O12  C11  single  1.402  0.020  1.402
 3V3  C10  C11  single  1.507  0.020  1.507
 3V3  C1   H1   single  0.970  0.020  1.090
 3V3  C1   H2   single  0.970  0.020  1.090
 3V3  C2   H3   single  0.970  0.020  1.090
 3V3  C2   H4   single  0.970  0.020  1.090
 3V3  C4   H5   single  0.970  0.020  1.090
 3V3  C4   H6   single  0.970  0.020  1.090
 3V3  C5   H7   single  0.970  0.020  1.090
 3V3  C5   H8   single  0.970  0.020  1.090
 3V3  C7   H9   single  0.970  0.020  1.090
 3V3  C7   H10  single  0.970  0.020  1.090
 3V3  C8   H11  single  0.970  0.020  1.090
 3V3  C8   H12  single  0.970  0.020  1.090
 3V3  C10  H13  single  0.970  0.020  1.090
 3V3  C10  H14  single  0.970  0.020  1.090
 3V3  C11  H15  single  0.970  0.020  1.090
 3V3  C11  H16  single  0.970  0.020  1.090
 3V3  C13  H17  single  0.970  0.020  1.090
 3V3  C13  H18  single  0.970  0.020  1.090
 3V3  C14  H19  single  0.970  0.020  1.090
 3V3  C14  H20  single  0.970  0.020  1.090
 3V3  C15  O1   deloc   1.248  0.020  1.248
 3V3  N1   H22  single  0.890  0.020  1.040
 3V3  N1   H23  single  0.890  0.020  1.040

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
 3V3  H2   C1   H1   106.19  3.000
 3V3  H2   C1   N1   108.71  3.000
 3V3  H1   C1   N1   113.98  3.000
 3V3  H2   C1   C2   109.05  3.000
 3V3  H1   C1   C2   106.85  3.000
 3V3  N1   C1   C2   111.83  3.000
 3V3  H4   C2   H3   106.47  3.000
 3V3  H4   C2   O3   110.63  3.000
 3V3  H3   C2   O3   110.71  3.000
 3V3  H4   C2   C1   109.79  3.000
 3V3  H3   C2   C1   108.92  3.000
 3V3  O3   C2   C1   110.23  3.000
 3V3  H6   C4   H5   106.66  3.000
 3V3  H6   C4   C5   108.11  3.000
 3V3  H5   C4   C5   109.83  3.000
 3V3  H6   C4   O3   111.16  3.000
 3V3  H5   C4   O3   111.15  3.000
 3V3  C5   C4   O3   109.84  3.000
 3V3  C4   O3   C2   112.68  3.000
 3V3  H8   C5   H7   106.79  3.000
 3V3  H8   C5   O6   111.11  3.000
 3V3  H7   C5   O6   111.04  3.000
 3V3  H8   C5   C4   109.92  3.000
 3V3  H7   C5   C4   108.18  3.000
 3V3  O6   C5   C4   109.72  3.000
 3V3  H10  C7   H9   106.70  3.000
 3V3  H10  C7   O6   111.10  3.000
 3V3  H9   C7   O6   111.12  3.000
 3V3  H10  C7   C8   109.83  3.000
 3V3  H9   C7   C8   108.29  3.000
 3V3  O6   C7   C8   109.72  3.000
 3V3  H12  C8   H11  106.79  3.000
 3V3  H12  C8   O9   111.14  3.000
 3V3  H11  C8   O9   111.09  3.000
 3V3  H12  C8   C7   109.93  3.000
 3V3  H11  C8   C7   108.16  3.000
 3V3  O9   C8   C7   109.64  3.000
 3V3  H14  C10  H13  106.75  3.000
 3V3  H14  C10  O9   111.09  3.000
 3V3  H13  C10  O9   111.04  3.000
 3V3  H14  C10  C11  109.71  3.000
 3V3  H13  C10  C11  108.26  3.000
 3V3  O9   C10  C11  109.90  3.000
 3V3  C7   O6   C5   112.86  3.000
 3V3  H16  C11  H15  106.70  3.000
 3V3  H16  C11  O12  111.19  3.000
 3V3  H15  C11  O12  111.14  3.000
 3V3  H16  C11  C10  109.98  3.000
 3V3  H15  C11  C10  107.83  3.000
 3V3  O12  C11  C10  109.90  3.000
 3V3  H18  C13  H17  106.63  3.000
 3V3  H18  C13  O12  110.07  3.000
 3V3  H17  C13  O12  110.32  3.000
 3V3  H18  C13  C14  110.34  3.000
 3V3  H17  C13  C14  110.43  3.000
 3V3  O12  C13  C14  109.04  3.000
 3V3  H20  C14  H19  105.66  3.000
 3V3  H20  C14  C15  108.52  3.000
 3V3  H19  C14  C15  108.45  3.000
 3V3  H20  C14  C13  109.69  3.000
 3V3  H19  C14  C13  109.75  3.000
 3V3  C15  C14  C13  114.40  3.000
 3V3  O1   C15  O16  126.49  3.000
 3V3  O1   C15  C14  116.00  3.000
 3V3  O16  C15  C14  117.52  3.000
 3V3  H23  N1   H22  105.58  3.000
 3V3  H23  N1   C1   109.32  3.000
 3V3  H22  N1   C1   109.30  3.000
 3V3  C10  O9   C8   112.86  3.000
 3V3  C13  O12  C11  112.75  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
 3V3  Var_01  C5   C4   O3   C2   -179.91  30.0  3
 3V3  Var_02  N1   C1   C2   O3     63.30  30.0  1
 3V3  Var_03  O6   C5   C4   O3     66.00  30.0  3
 3V3  Var_04  C8   C7   O6   C5   -178.09  30.0  3
 3V3  Var_05  C11  C10  O9   C8   -176.54  30.0  3
 3V3  Var_06  O9   C8   C7   O6     66.97  30.0  1
 3V3  Var_07  C14  C13  O12  C11  -178.07  30.0  3
 3V3  Var_08  O16  C15  C14  C13     1.52  30.0  3
 3V3  Var_09  O12  C13  C14  C15   179.37  30.0  3
 3V3  Var_10  O12  C11  C10  O9     66.64  30.0  3
 3V3  Var_11  H22  N1   C1   C2     68.12  30.0  3
 3V3  Var_12  H3   C2   O3   C4     59.39  30.0  2
 3V3  Var_13  H11  C8   O9   C10    63.04  30.0  3
 3V3  Var_14  H15  C11  O12  C13    58.02  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
 3V3  plan-1  C14  0.020
 3V3  plan-1  C15  0.020
 3V3  plan-1  O16  0.020
 3V3  plan-1  O1   0.020

