# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 03:14:00 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: (2S)-2-(5-methylfuran-2-yl)oxane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc(cc1)[C@@H]2CCCCO2
#
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
 N1X  N1X  "(2S)-2-(5-methylfuran-2-yl)oxane"
  ligand  26  12  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N1X
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
 N1X  C1   C  CH3   0  -0.753   8.2955   -8.5257  -15.9447
 N1X  C2   C  CR5   0   0.343   8.9089   -8.3959  -17.2870
 N1X  C4   C  CR5   0   0.374   9.1585   -8.9440  -19.3973
 N1X  C5   C  CR15  0  -0.371  10.0428   -7.9473  -19.1552
 N1X  C6   C  CR15  0  -0.371   9.8818   -7.5912  -17.7808
 N1X  C7   C  CH1   0  -0.045   8.8066   -9.7291  -20.6112
 N1X  C8   C  CH2   0  -0.504   9.8627   -9.6011  -21.6994
 N1X  C9   C  CH2   0  -0.427   9.4961  -10.4695  -22.9100
 N1X  C10  C  CH2   0  -0.496   7.9731  -10.5949  -23.0587
 N1X  C11  C  CH2   0  -0.164   7.2833   -9.3922  -22.4458
 N1X  O3   O  O     0  -0.435   8.4677   -9.2195  -18.2641
 N1X  O12  O  O2    0  -0.502   7.5257   -9.2880  -21.0521
 N1X  H1   H  HCH3  0   0.251   8.4377   -9.5250  -15.5290
 N1X  H2   H  HCH3  0   0.256   8.7539   -7.8114  -15.2638
 N1X  H3   H  HCH3  0   0.252   7.2222   -8.3278  -15.9655
 N1X  H4   H  HCR5  0   0.255  10.7321   -7.5139  -19.8623
 N1X  H5   H  HCR5  0   0.254  10.4221   -6.8374  -17.2309
 N1X  H6   H  HCH1  0   0.219   8.7400  -10.7906  -20.3256
 N1X  H7   H  HCH2  0   0.254  10.8344   -9.8916  -21.2979
 N1X  H8   H  HCH2  0   0.238   9.9492   -8.5517  -21.9948
 N1X  H9   H  HCH2  0   0.233   9.9363  -11.4624  -22.8044
 N1X  H10  H  HCH2  0   0.234   9.9303  -10.0304  -23.8093
 N1X  H11  H  HCH2  0   0.245   7.6872  -10.6824  -24.1084
 N1X  H12  H  HCH2  0   0.233   7.6137  -11.5012  -22.5644
 N1X  H13  H  HCH2  0   0.197   7.6079   -8.4786  -22.9625
 N1X  H14  H  HCH2  0   0.230   6.2001   -9.4587  -22.5678

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
 N1X  C10  C9   single    1.535  0.020  1.535
 N1X  C10  C11  single    1.516  0.020  1.516
 N1X  C9   C8   single    1.534  0.020  1.534
 N1X  C11  O12  single    1.418  0.020  1.418
 N1X  C8   C7   single    1.522  0.020  1.522
 N1X  O12  C7   single    1.425  0.020  1.425
 N1X  C7   C4   single    1.488  0.020  1.488
 N1X  C4   C5   aromatic  1.354  0.020  1.354
 N1X  C4   O3   aromatic  1.355  0.020  1.355
 N1X  C5   C6   aromatic  1.429  0.020  1.429
 N1X  O3   C2   aromatic  1.352  0.020  1.352
 N1X  C6   C2   aromatic  1.356  0.020  1.356
 N1X  C2   C1   single    1.482  0.020  1.482
 N1X  C1   H1   single    0.970  0.020  1.090
 N1X  C1   H2   single    0.970  0.020  1.090
 N1X  C1   H3   single    0.970  0.020  1.090
 N1X  C5   H4   single    0.930  0.020  1.080
 N1X  C6   H5   single    0.930  0.020  1.080
 N1X  C7   H6   single    0.970  0.020  1.090
 N1X  C8   H7   single    0.970  0.020  1.090
 N1X  C8   H8   single    0.970  0.020  1.090
 N1X  C9   H9   single    0.970  0.020  1.090
 N1X  C9   H10  single    0.970  0.020  1.090
 N1X  C10  H11  single    0.970  0.020  1.090
 N1X  C10  H12  single    0.970  0.020  1.090
 N1X  C11  H13  single    0.970  0.020  1.090
 N1X  C11  H14  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
 N1X  H3   C1   H2   107.89  3.000
 N1X  H3   C1   H1   107.54  3.000
 N1X  H2   C1   H1   107.93  3.000
 N1X  H3   C1   C2   111.96  3.000
 N1X  H2   C1   C2   109.57  3.000
 N1X  H1   C1   C2   111.80  3.000
 N1X  O3   C2   C6   109.42  3.000
 N1X  C6   C2   C1   132.78  3.000
 N1X  O3   C2   C1   117.80  3.000
 N1X  O3   C4   C7   117.03  3.000
 N1X  O3   C4   C5   109.44  3.000
 N1X  C7   C4   C5   133.52  3.000
 N1X  H4   C5   C6   127.05  3.000
 N1X  H4   C5   C4   126.58  3.000
 N1X  C6   C5   C4   106.37  3.000
 N1X  H5   C6   C5   127.47  3.000
 N1X  H5   C6   C2   126.07  3.000
 N1X  C5   C6   C2   106.46  3.000
 N1X  H6   C7   O12  108.92  3.000
 N1X  H6   C7   C8   107.97  3.000
 N1X  O12  C7   C8   112.13  3.000
 N1X  H6   C7   C4   108.14  3.000
 N1X  O12  C7   C4   107.57  3.000
 N1X  C8   C7   C4   112.02  3.000
 N1X  H8   C8   H7   106.54  3.000
 N1X  H8   C8   C9   110.42  3.000
 N1X  H7   C8   C9   110.64  3.000
 N1X  H8   C8   C7   109.19  3.000
 N1X  H7   C8   C7   109.43  3.000
 N1X  C9   C8   C7   110.54  3.000
 N1X  H10  C9   H9   106.58  3.000
 N1X  H10  C9   C10  110.36  3.000
 N1X  H9   C9   C10  109.59  3.000
 N1X  H10  C9   C8   109.12  3.000
 N1X  H9   C9   C8   110.01  3.000
 N1X  C10  C9   C8   111.08  3.000
 N1X  H12  C10  H11  106.40  3.000
 N1X  H12  C10  C11  108.98  3.000
 N1X  H11  C10  C11  109.46  3.000
 N1X  H12  C10  C9   110.49  3.000
 N1X  H11  C10  C9   111.07  3.000
 N1X  C11  C10  C9   110.33  3.000
 N1X  H14  C11  H13  106.93  3.000
 N1X  H14  C11  O12  106.48  3.000
 N1X  H13  C11  O12  110.52  3.000
 N1X  H14  C11  C10  110.97  3.000
 N1X  H13  C11  C10  109.58  3.000
 N1X  O12  C11  C10  112.19  3.000
 N1X  C4   O3   C2   108.31  3.000
 N1X  C11  O12  C7   115.78  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
 N1X  CONST_01  C5   C4   O3   C2      0.00   0.0  0
 N1X  CONST_02  C4   C5   C6   C2      0.00   0.0  0
 N1X  CONST_03  C6   C2   O3   C4      0.00   0.0  0
 N1X  CONST_04  O3   C2   C6   C5      0.00   0.0  0
 N1X  CONST_05  O3   C4   C5   C6      0.00   0.0  0
 N1X  CONST_06  C7   C4   O3   C2    180.00   0.0  0
 N1X  CONST_07  C7   C4   C5   C6    180.00   0.0  0
 N1X  CONST_08  C4   O3   C2   C1    180.00   0.0  0
 N1X  CONST_09  C5   C6   C2   C1    180.00   0.0  0
 N1X  CONST_10  H4   C5   C6   C2    180.00   0.0  0
 N1X  CONST_11  H5   C6   C5   C4    180.00   0.0  0
 N1X  CONST_12  H4   C5   C4   C7      0.00   0.0  0
 N1X  CONST_13  H4   C5   C4   O3    180.00   0.0  0
 N1X  CONST_14  H5   C6   C2   O3    180.00   0.0  0
 N1X  Var_01    C10  C9   C8   C7     30.59  30.0  1
 N1X  Var_02    C10  C11  O12  C7     33.66  30.0  1
 N1X  Var_03    C11  C10  C9   C8     26.32  30.0  1
 N1X  Var_04    O12  C11  C10  C9    -62.43  30.0  1
 N1X  Var_05    H9   C9   C8   C7    -90.92  30.0  1
 N1X  Var_06    H10  C9   C8   C7    152.47  30.0  1
 N1X  Var_07    H13  C11  O12  C7    -88.97  30.0  1
 N1X  Var_08    H14  C11  O12  C7    155.24  30.0  1
 N1X  Var_09    H11  C10  C9   C8    147.89  30.0  1
 N1X  Var_10    H12  C10  C9   C8    -94.27  30.0  1
 N1X  Var_11    H13  C11  C10  C9     60.73  30.0  1
 N1X  Var_12    H14  C11  C10  C9    178.59  30.0  1
 N1X  Var_13    H7   C8   C9   C10   151.97  30.0  1
 N1X  Var_14    H8   C8   C9   C10   -90.34  30.0  1
 N1X  Var_15    H9   C9   C10  C11   148.08  30.0  1
 N1X  Var_16    H10  C9   C10  C11   -94.84  30.0  1
 N1X  Var_17    H11  C10  C11  O12   175.06  30.0  1
 N1X  Var_18    H12  C10  C11  O12    59.06  30.0  1
 N1X  Var_19    H1   C1   C2   C6   -119.58  30.0  2
 N1X  Var_20    H2   C1   C2   C6      0.03  30.0  2
 N1X  Var_21    H3   C1   C2   C6    119.68  30.0  2
 N1X  Var_22    H1   C1   C2   O3     59.80  30.0  2
 N1X  Var_23    H2   C1   C2   O3    179.41  30.0  2
 N1X  Var_24    H3   C1   C2   O3    -60.94  30.0  2

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
 N1X  chir_01  C7  C8  O12  C4  positiv

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
 N1X  plan-1  C1  0.020
 N1X  plan-1  C2  0.020
 N1X  plan-1  C4  0.020
 N1X  plan-1  C5  0.020
 N1X  plan-1  C6  0.020
 N1X  plan-1  C7  0.020
 N1X  plan-1  O3  0.020
 N1X  plan-1  H4  0.020
 N1X  plan-1  H5  0.020

