# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 19:49:48 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: decyl(dimethyl)phosphane oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC[P](C)(C)=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
 DCX  DCX  'decyl(dimethyl)phosphane oxide'  ligand  41  14  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DCX
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
 DCX  C3    C  CH3   0  -0.894   5.9526  -1.0937   0.2062
 DCX  O4    O  O     0  -0.751   4.7469   0.7099  -1.5378
 DCX  C6    C  CH2   0  -0.427   1.8596   0.1220  -0.0538
 DCX  C14   C  CH3   0  -0.662  -8.3000   0.5049  -0.0846
 DCX  C13   C  CH2   0  -0.418  -7.0685  -0.3755   0.0764
 DCX  C12   C  CH2   0  -0.406  -5.7646   0.3991  -0.0693
 DCX  C11   C  CH2   0  -0.411  -4.5238  -0.4696   0.0926
 DCX  C10   C  CH2   0  -0.411  -3.2215   0.3059  -0.0601
 DCX  C9    C  CH2   0  -0.412  -1.9807  -0.5626   0.1043
 DCX  C8    C  CH2   0  -0.414  -0.6788   0.2120  -0.0570
 DCX  C7    C  CH2   0  -0.405   0.5605  -0.6564   0.1159
 DCX  C4    C  CH2   0  -0.680   3.0907  -0.7573   0.1498
 DCX  P1    P  P     0   1.027   4.6555   0.1191  -0.1542
 DCX  C2    C  CH3   0  -0.908   4.7904   1.3573   1.1632
 DCX  H31   H  HCH3  0   0.273   6.9315  -0.6196   0.1359
 DCX  H32   H  HCH3  0   0.265   5.8382  -1.5082   1.2075
 DCX  H33   H  HCH3  0   0.273   5.9081  -1.9082  -0.5167
 DCX  H61   H  HCH2  0   0.228   1.8885   0.5697  -1.0512
 DCX  H62   H  HCH2  0   0.227   1.8732   0.9536   0.6577
 DCX  H141  H  HCH3  0   0.225  -9.2220  -0.0712   0.0031
 DCX  H142  H  HCH3  0   0.215  -8.3269   1.2895   0.6741
 DCX  H143  H  HCH3  0   0.215  -8.3092   0.9937  -1.0609
 DCX  H131  H  HCH2  0   0.210  -7.0912  -0.8646   1.0554
 DCX  H132  H  HCH2  0   0.209  -7.0955  -1.1812  -0.6640
 DCX  H121  H  HCH2  0   0.205  -5.7419   0.8862  -1.0510
 DCX  H122  H  HCH2  0   0.205  -5.7413   1.2088   0.6689
 DCX  H111  H  HCH2  0   0.206  -4.5444  -0.9531   1.0758
 DCX  H112  H  HCH2  0   0.206  -4.5501  -1.2810  -0.6434
 DCX  H101  H  HCH2  0   0.206  -3.1999   0.7881  -1.0439
 DCX  H102  H  HCH2  0   0.206  -3.1952   1.1184   0.6748
 DCX  H91   H  HCH2  0   0.207  -1.9993  -1.0387   1.0912
 DCX  H92   H  HCH2  0   0.207  -2.0089  -1.3795  -0.6256
 DCX  H81   H  HCH2  0   0.209  -0.6583   0.6846  -1.0453
 DCX  H82   H  HCH2  0   0.208  -0.6525   1.0307   0.6707
 DCX  H71   H  HCH2  0   0.213   0.5355  -1.4786  -0.6075
 DCX  H72   H  HCH2  0   0.212   0.5441  -1.1223   1.1072
 DCX  H41   H  HCH2  0   0.262   3.1094  -1.1706   1.1625
 DCX  H42   H  HCH2  0   0.267   3.0674  -1.6086  -0.5380
 DCX  H21   H  HCH3  0   0.275   5.7581   1.8552   1.1018
 DCX  H22   H  HCH3  0   0.274   4.0091   2.1085   1.0520
 DCX  H23   H  HCH3  0   0.265   4.6966   0.8970   2.1464

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
 DCX  C3   P1    single  1.812  0.020  1.812
 DCX  C3   H31   single  0.970  0.020  1.090
 DCX  C3   H32   single  0.970  0.020  1.090
 DCX  C3   H33   single  0.970  0.020  1.090
 DCX  O4   P1    double  1.507  0.020  1.507
 DCX  C6   C7    single  1.524  0.020  1.524
 DCX  C6   C4    single  1.527  0.020  1.527
 DCX  C6   H61   single  0.970  0.020  1.090
 DCX  C6   H62   single  0.970  0.020  1.090
 DCX  C14  C13   single  1.522  0.020  1.522
 DCX  C14  H141  single  0.970  0.020  1.090
 DCX  C14  H142  single  0.970  0.020  1.090
 DCX  C14  H143  single  0.970  0.020  1.090
 DCX  C13  C12   single  1.524  0.020  1.524
 DCX  C13  H131  single  0.970  0.020  1.090
 DCX  C13  H132  single  0.970  0.020  1.090
 DCX  C12  C11   single  1.523  0.020  1.523
 DCX  C12  H121  single  0.970  0.020  1.090
 DCX  C12  H122  single  0.970  0.020  1.090
 DCX  C11  C10   single  1.523  0.020  1.523
 DCX  C11  H111  single  0.970  0.020  1.090
 DCX  C11  H112  single  0.970  0.020  1.090
 DCX  C10  C9    single  1.523  0.020  1.523
 DCX  C10  H101  single  0.970  0.020  1.090
 DCX  C10  H102  single  0.970  0.020  1.090
 DCX  C9   C8    single  1.523  0.020  1.523
 DCX  C9   H91   single  0.970  0.020  1.090
 DCX  C9   H92   single  0.970  0.020  1.090
 DCX  C8   C7    single  1.523  0.020  1.523
 DCX  C8   H81   single  0.970  0.020  1.090
 DCX  C8   H82   single  0.970  0.020  1.090
 DCX  C7   H71   single  0.970  0.020  1.090
 DCX  C7   H72   single  0.970  0.020  1.090
 DCX  C4   P1    single  1.819  0.020  1.819
 DCX  C4   H41   single  0.970  0.020  1.090
 DCX  C4   H42   single  0.970  0.020  1.090
 DCX  P1   C2    single  1.813  0.020  1.813
 DCX  C2   H21   single  0.970  0.020  1.090
 DCX  C2   H22   single  0.970  0.020  1.090
 DCX  C2   H23   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
 DCX  H33   C3   H32   108.72  3.000
 DCX  H33   C3   H31   108.60  3.000
 DCX  H32   C3   H31   108.60  3.000
 DCX  H33   C3   P1    109.82  3.000
 DCX  H32   C3   P1    111.23  3.000
 DCX  H31   C3   P1    109.81  3.000
 DCX  H62   C6   H61   106.35  3.000
 DCX  H62   C6   C4    109.93  3.000
 DCX  H61   C6   C4    109.64  3.000
 DCX  H62   C6   C7    109.04  3.000
 DCX  H61   C6   C7    109.47  3.000
 DCX  C4    C6   C7    112.24  3.000
 DCX  H143  C14  H142  107.43  3.000
 DCX  H143  C14  H141  107.53  3.000
 DCX  H142  C14  H141  107.63  3.000
 DCX  H143  C14  C13   111.12  3.000
 DCX  H142  C14  C13   111.23  3.000
 DCX  H141  C14  C13   111.70  3.000
 DCX  H132  C13  H131  106.00  3.000
 DCX  H132  C13  C12   109.30  3.000
 DCX  H131  C13  C12   109.29  3.000
 DCX  H132  C13  C14   109.53  3.000
 DCX  H131  C13  C14   109.65  3.000
 DCX  C12   C13  C14   112.84  3.000
 DCX  H122  C12  H121  105.93  3.000
 DCX  H122  C12  C11   109.42  3.000
 DCX  H121  C12  C11   109.38  3.000
 DCX  H122  C12  C13   109.23  3.000
 DCX  H121  C12  C13   109.22  3.000
 DCX  C11   C12  C13   113.39  3.000
 DCX  H112  C11  H111  105.99  3.000
 DCX  H112  C11  C10   109.28  3.000
 DCX  H111  C11  C10   109.31  3.000
 DCX  H112  C11  C12   109.35  3.000
 DCX  H111  C11  C12   109.37  3.000
 DCX  C10   C11  C12   113.29  3.000
 DCX  H102  C10  H101  105.98  3.000
 DCX  H102  C10  C9    109.32  3.000
 DCX  H101  C10  C9    109.37  3.000
 DCX  H102  C10  C11   109.32  3.000
 DCX  H101  C10  C11   109.32  3.000
 DCX  C9    C10  C11   113.28  3.000
 DCX  H92   C9   H91   105.99  3.000
 DCX  H92   C9   C8    109.30  3.000
 DCX  H91   C9   C8    109.32  3.000
 DCX  H92   C9   C10   109.40  3.000
 DCX  H91   C9   C10   109.33  3.000
 DCX  C8    C9   C10   113.25  3.000
 DCX  H82   C8   H81   106.04  3.000
 DCX  H82   C8   C7    109.34  3.000
 DCX  H81   C8   C7    109.46  3.000
 DCX  H82   C8   C9    109.28  3.000
 DCX  H81   C8   C9    109.32  3.000
 DCX  C7    C8   C9    113.17  3.000
 DCX  H72   C7   H71   106.15  3.000
 DCX  H72   C7   C8    109.45  3.000
 DCX  H71   C7   C8    109.53  3.000
 DCX  H72   C7   C6    109.32  3.000
 DCX  H71   C7   C6    109.23  3.000
 DCX  C8    C7   C6    112.94  3.000
 DCX  H42   C4   H41   106.75  3.000
 DCX  H42   C4   P1    106.74  3.000
 DCX  H41   C4   P1    108.78  3.000
 DCX  H42   C4   C6    110.31  3.000
 DCX  H41   C4   C6    110.78  3.000
 DCX  P1    C4   C6    113.20  3.000
 DCX  C2    P1   C4    105.76  3.000
 DCX  C2    P1   O4    113.25  3.000
 DCX  C4    P1   O4    113.23  3.000
 DCX  C2    P1   C3    105.03  3.000
 DCX  C4    P1   C3    105.07  3.000
 DCX  O4    P1   C3    113.68  3.000
 DCX  H23   C2   H22   108.76  3.000
 DCX  H23   C2   H21   108.67  3.000
 DCX  H22   C2   H21   108.42  3.000
 DCX  H23   C2   P1    111.15  3.000
 DCX  H22   C2   P1    110.09  3.000
 DCX  H21   C2   P1    109.70  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
 DCX  Var_01  C6    C4   P1   C3   177.95  30.0  2
 DCX  Var_02  C9    C8   C7   C6   179.69  30.0  1
 DCX  Var_03  C11   C12  C13  C14  179.87  30.0  3
 DCX  Var_04  C10   C11  C12  C13  179.73  30.0  3
 DCX  Var_05  C9    C10  C11  C12  179.90  30.0  3
 DCX  Var_06  C8    C9   C10  C11  179.65  30.0  3
 DCX  Var_07  C7    C8   C9   C10  179.66  30.0  3
 DCX  Var_08  P1    C4   C6   C7   176.21  30.0  3
 DCX  Var_09  H21   C2   P1   C3    63.48  30.0  3
 DCX  Var_10  H31   C3   P1   O4    60.81  30.0  3
 DCX  Var_11  H141  C14  C13  C12  178.85  30.0  3

