# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:19:24 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: (17R)-3,6,9,12,15-pentaoxaoctadecan-17-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOCCOCCOCCOCCOC[C@@H](C)N
#
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
 2NV  2NV  (17R)-3,6,9,12,15-pentaoxaoctadecan-17-amine  ligand  48  19  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2NV
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
 2NV  N1    N  NH2   0  -0.755   5.4066  -1.7051  -0.5393
 2NV  C2    C  CH1   0  -0.152   6.1578  -0.7833   0.3033
 2NV  C3    C  CH2   0  -0.112   5.2048   0.0129   1.1782
 2NV  O4    O  O2    0  -0.512   4.3108   0.7535   0.3904
 2NV  C5    C  CH2   0  -0.170   3.3853   1.4755   1.1595
 2NV  C6    C  CH2   0  -0.194   2.4558   2.2446   0.2569
 2NV  O7    O  O2    0  -0.536   1.6869   1.3510  -0.5080
 2NV  C8    C  CH2   0  -0.153   0.7428   2.0046  -1.3158
 2NV  C9    C  CH2   0  -0.193   0.0055   0.9996  -2.1621
 2NV  O10   O  O2    0  -0.523  -0.7345   0.1292  -1.3444
 2NV  C11   C  CH2   0  -0.163  -1.5093  -0.7757  -2.0887
 2NV  C12   C  CH2   0  -0.146  -2.2328  -1.7199  -1.1637
 2NV  O13   O  O2    0  -0.515  -3.1352  -1.0057  -0.3595
 2NV  C14   C  CH2   0  -0.228  -3.8898  -1.8425   0.4802
 2NV  C15   C  CH2   0  -0.146  -4.7710  -1.0104   1.3758
 2NV  O16   O  O2    0  -0.519  -5.7134  -0.3110   0.6059
 2NV  C17   C  CH2   0  -0.175  -6.5865   0.4695   1.3896
 2NV  C18   C  CH3   0  -0.672  -7.5400   1.2157   0.4839
 2NV  C2A   C  CH3   0  -0.715   7.2009  -1.4657   1.1871
 2NV  HN1   H  HNH2  0   0.346   6.0560  -2.2422  -1.1017
 2NV  HN1A  H  HNH2  0   0.318   4.9400  -2.3857   0.0514
 2NV  H2    H  HCH1  0   0.263   6.6763  -0.0814  -0.3591
 2NV  H3    H  HCH2  0   0.173   4.6586  -0.6794   1.8397
 2NV  H3A   H  HCH2  0   0.214   5.7861   0.6775   1.8343
 2NV  H5    H  HCH2  0   0.284   2.8029   0.8046   1.8082
 2NV  H5A   H  HCH2  0   0.171   3.8903   2.1940   1.8212
 2NV  H6    H  HCH2  0   0.224   1.8159   2.8766   0.8883
 2NV  H6A   H  HCH2  0   0.262   3.0310   2.9216  -0.3913
 2NV  H8    H  HCH2  0   0.217   0.0303   2.5776  -0.7047
 2NV  H8A   H  HCH2  0   0.208   1.2284   2.7221  -1.9923
 2NV  H9    H  HCH2  0   0.233  -0.6520   1.5543  -2.8462
 2NV  H9A   H  HCH2  0   0.210   0.7161   0.4409  -2.7882
 2NV  H11   H  HCH2  0   0.178  -2.2321  -0.2427  -2.7233
 2NV  H11A  H  HCH2  0   0.182  -0.8813  -1.3779  -2.7602
 2NV  H12   H  HCH2  0   0.175  -2.7538  -2.4636  -1.7833
 2NV  H12A  H  HCH2  0   0.233  -1.5090  -2.2727  -0.5473
 2NV  H14   H  HCH2  0   0.259  -4.5024  -2.5410  -0.1083
 2NV  H14A  H  HCH2  0   0.218  -3.2378  -2.4532   1.1200
 2NV  H15   H  HCH2  0   0.189  -5.2638  -1.6864   2.0893
 2NV  H15A  H  HCH2  0   0.242  -4.1543  -0.3195   1.9691
 2NV  H17   H  HCH2  0   0.231  -7.1494  -0.1674   2.0864
 2NV  H17A  H  HCH2  0   0.223  -6.0175   1.1806   2.0046
 2NV  H18   H  HCH3  0   0.230  -7.0060   1.8834  -0.1933
 2NV  H18A  H  HCH3  0   0.194  -8.1420   0.5297  -0.1125
 2NV  H18B  H  HCH3  0   0.237  -8.2199   1.8210   1.0830
 2NV  H2A   H  HCH3  0   0.185   7.8973  -2.0451   0.5794
 2NV  H2AA  H  HCH3  0   0.207   7.7857  -0.7464   1.7631
 2NV  H2AB  H  HCH3  0   0.274   6.7235  -2.1521   1.8914

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
 2NV  N1   C2    single  1.457  0.020  1.457
 2NV  N1   HN1   single  0.890  0.020  1.040
 2NV  N1   HN1A  single  0.890  0.020  1.040
 2NV  C3   C2    single  1.519  0.020  1.519
 2NV  C2   C2A   single  1.528  0.020  1.528
 2NV  C2   H2    single  0.970  0.020  1.090
 2NV  O4   C3    single  1.403  0.020  1.403
 2NV  C3   H3    single  0.970  0.020  1.090
 2NV  C3   H3A   single  0.970  0.020  1.090
 2NV  C5   O4    single  1.403  0.020  1.403
 2NV  C5   C6    single  1.507  0.020  1.507
 2NV  C5   H5    single  0.970  0.020  1.090
 2NV  C5   H5A   single  0.970  0.020  1.090
 2NV  O7   C6    single  1.405  0.020  1.405
 2NV  C6   H6    single  0.970  0.020  1.090
 2NV  C6   H6A   single  0.970  0.020  1.090
 2NV  O7   C8    single  1.404  0.020  1.404
 2NV  C8   C9    single  1.507  0.020  1.507
 2NV  C8   H8    single  0.970  0.020  1.090
 2NV  C8   H8A   single  0.970  0.020  1.090
 2NV  O10  C9    single  1.405  0.020  1.405
 2NV  C9   H9    single  0.970  0.020  1.090
 2NV  C9   H9A   single  0.970  0.020  1.090
 2NV  O10  C11   single  1.405  0.020  1.405
 2NV  C11  C12   single  1.507  0.020  1.507
 2NV  C11  H11   single  0.970  0.020  1.090
 2NV  C11  H11A  single  0.970  0.020  1.090
 2NV  C12  O13   single  1.404  0.020  1.404
 2NV  C12  H12   single  0.970  0.020  1.090
 2NV  C12  H12A  single  0.970  0.020  1.090
 2NV  O13  C14   single  1.405  0.020  1.405
 2NV  C14  C15   single  1.507  0.020  1.507
 2NV  C14  H14   single  0.970  0.020  1.090
 2NV  C14  H14A  single  0.970  0.020  1.090
 2NV  C15  O16   single  1.404  0.020  1.404
 2NV  C15  H15   single  0.970  0.020  1.090
 2NV  C15  H15A  single  0.970  0.020  1.090
 2NV  O16  C17   single  1.409  0.020  1.409
 2NV  C17  C18   single  1.512  0.020  1.512
 2NV  C17  H17   single  0.970  0.020  1.090
 2NV  C17  H17A  single  0.970  0.020  1.090
 2NV  C18  H18   single  0.970  0.020  1.090
 2NV  C18  H18A  single  0.970  0.020  1.090
 2NV  C18  H18B  single  0.970  0.020  1.090
 2NV  C2A  H2A   single  0.970  0.020  1.090
 2NV  C2A  H2AA  single  0.970  0.020  1.090
 2NV  C2A  H2AB  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
 2NV  HN1A  N1   HN1   105.20  3.000
 2NV  HN1A  N1   C2    108.94  3.000
 2NV  HN1   N1   C2    109.01  3.000
 2NV  H2    C2   C2A   108.22  3.000
 2NV  H2    C2   C3    108.02  3.000
 2NV  C2A   C2   C3    109.22  3.000
 2NV  H2    C2   N1    107.43  3.000
 2NV  C2A   C2   N1    113.82  3.000
 2NV  C3    C2   N1    109.95  3.000
 2NV  H3A   C3   H3    106.46  3.000
 2NV  H3A   C3   O4    110.65  3.000
 2NV  H3    C3   O4    110.65  3.000
 2NV  H3A   C3   C2    109.19  3.000
 2NV  H3    C3   C2    109.10  3.000
 2NV  O4    C3   C2    110.68  3.000
 2NV  C5    O4   C3    112.59  3.000
 2NV  H5A   C5   H5    106.67  3.000
 2NV  H5A   C5   C6    108.08  3.000
 2NV  H5    C5   C6    109.75  3.000
 2NV  H5A   C5   O4    111.29  3.000
 2NV  H5    C5   O4    111.01  3.000
 2NV  C6    C5   O4    109.95  3.000
 2NV  H6A   C6   H6    106.81  3.000
 2NV  H6A   C6   O7    110.91  3.000
 2NV  H6    C6   O7    111.10  3.000
 2NV  H6A   C6   C5    110.16  3.000
 2NV  H6    C6   C5    107.97  3.000
 2NV  O7    C6   C5    109.82  3.000
 2NV  C8    O7   C6    112.64  3.000
 2NV  H8A   C8   H8    106.74  3.000
 2NV  H8A   C8   C9    107.81  3.000
 2NV  H8    C8   C9    110.04  3.000
 2NV  H8A   C8   O7    111.16  3.000
 2NV  H8    C8   O7    111.01  3.000
 2NV  C9    C8   O7    109.98  3.000
 2NV  H9A   C9   H9    106.77  3.000
 2NV  H9A   C9   O10   110.92  3.000
 2NV  H9    C9   O10   111.09  3.000
 2NV  H9A   C9   C8    110.03  3.000
 2NV  H9    C9   C8    107.80  3.000
 2NV  O10   C9   C8    110.12  3.000
 2NV  C11   O10  C9    112.41  3.000
 2NV  H11A  C11  H11   106.77  3.000
 2NV  H11A  C11  C12   107.82  3.000
 2NV  H11   C11  C12   110.02  3.000
 2NV  H11A  C11  O10   111.19  3.000
 2NV  H11   C11  O10   110.86  3.000
 2NV  C12   C11  O10   110.07  3.000
 2NV  H12A  C12  H12   106.73  3.000
 2NV  H12A  C12  O13   110.95  3.000
 2NV  H12   C12  O13   111.24  3.000
 2NV  H12A  C12  C11   110.06  3.000
 2NV  H12   C12  C11   107.79  3.000
 2NV  O13   C12  C11   109.97  3.000
 2NV  C14   O13  C12   112.61  3.000
 2NV  H14A  C14  H14   106.81  3.000
 2NV  H14A  C14  C15   107.92  3.000
 2NV  H14   C14  C15   110.06  3.000
 2NV  H14A  C14  O13   111.12  3.000
 2NV  H14   C14  O13   110.95  3.000
 2NV  C15   C14  O13   109.90  3.000
 2NV  H15A  C15  H15   106.71  3.000
 2NV  H15A  C15  O16   111.06  3.000
 2NV  H15   C15  O16   111.19  3.000
 2NV  H15A  C15  C14   109.85  3.000
 2NV  H15   C15  C14   107.96  3.000
 2NV  O16   C15  C14   109.98  3.000
 2NV  C17   O16  C15   112.76  3.000
 2NV  H17A  C17  H17   106.58  3.000
 2NV  H17A  C17  C18   110.03  3.000
 2NV  H17   C17  C18   110.04  3.000
 2NV  H17A  C17  O16   110.42  3.000
 2NV  H17   C17  O16   110.42  3.000
 2NV  C18   C17  O16   109.32  3.000
 2NV  H18B  C18  H18A  107.81  3.000
 2NV  H18B  C18  H18   107.87  3.000
 2NV  H18A  C18  H18   108.41  3.000
 2NV  H18B  C18  C17   109.77  3.000
 2NV  H18A  C18  C17   111.43  3.000
 2NV  H18   C18  C17   111.42  3.000
 2NV  H2AB  C2A  H2AA  107.92  3.000
 2NV  H2AB  C2A  H2A   107.71  3.000
 2NV  H2AA  C2A  H2A   107.58  3.000
 2NV  H2AB  C2A  C2    110.79  3.000
 2NV  H2AA  C2A  C2    112.13  3.000
 2NV  H2A   C2A  C2    110.54  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
 2NV  Var_01  C6   C5   O4   C3   -179.90  30.0  1
 2NV  Var_02  O7   C6   C5   O4     64.53  30.0  3
 2NV  Var_03  C9   C8   O7   C6    176.95  30.0  3
 2NV  Var_04  O10  C9   C8   O7     64.01  30.0  3
 2NV  Var_05  C12  C11  O10  C9    177.56  30.0  3
 2NV  Var_06  O13  C12  C11  O10    63.50  30.0  3
 2NV  Var_07  C15  C14  O13  C12   176.38  30.0  3
 2NV  Var_08  O16  C15  C14  O13    64.51  30.0  3
 2NV  Var_09  C18  C17  O16  C15   178.46  30.0  3
 2NV  Var_10  H3   C3   O4   C5     57.20  30.0  3
 2NV  Var_11  H18  C18  C17  O16   -60.66  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 2NV  chir_01  C2  N1  C3  C2A  negativ

