# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 18:37:00 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: methyl hydrogen (S)-undecylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCC[P@@](O)(=O)OC
#
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
 MUP  MUP  'methyl hydrogen (S)-undecylphosphonate'  ligand  43  16  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MUP
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
 MUP  C1    C  CH2   0  -0.749  -0.6385   0.0855  -3.1176
 MUP  C2    C  CH2   0  -0.432   0.2624  -0.0314  -1.8882
 MUP  C3    C  CH2   0  -0.407  -0.5346   0.0880  -0.5954
 MUP  C4    C  CH2   0  -0.414   0.3336  -0.0252   0.6510
 MUP  C5    C  CH2   0  -0.413  -0.4661   0.0781   1.9435
 MUP  C6    C  CH2   0  -0.412   0.3955  -0.0218   3.1961
 MUP  C7    C  CH2   0  -0.411  -0.4111   0.0611   4.4860
 MUP  C8    C  CH2   0  -0.412   0.4479  -0.0166   5.7422
 MUP  C9    C  CH2   0  -0.406  -0.3649   0.0452   7.0292
 MUP  C10   C  CH2   0  -0.419   0.4900  -0.0127   8.2896
 MUP  C11   C  CH3   0  -0.662  -0.3392   0.0438   9.5654
 MUP  CM    C  CH3   0  -0.414  -0.6128  -0.0612  -7.1376
 MUP  O1P   O  O     0  -0.722   1.0501  -1.3518  -4.8216
 MUP  O2P   O  O2    0  -0.591  -0.8849   0.1387  -5.7485
 MUP  O3P   O  OH1   0  -0.755   1.2760   1.1551  -4.7807
 MUP  P     P  P     0   1.389   0.2711  -0.1001  -4.6574
 MUP  H11   H  HCH2  0   0.284  -1.4088  -0.6899  -3.0966
 MUP  H12   H  HCH2  0   0.282  -1.1591   1.0471  -3.1230
 MUP  H21   H  HCH2  0   0.232   1.0323   0.7448  -1.9143
 MUP  H22   H  HCH2  0   0.233   0.7867  -0.9908  -1.9054
 MUP  H31   H  HCH2  0   0.215  -1.3064  -0.6888  -0.5738
 MUP  H32   H  HCH2  0   0.215  -1.0658   1.0459  -0.5842
 MUP  H41   H  HCH2  0   0.210   1.1002   0.7574   0.6330
 MUP  H42   H  HCH2  0   0.210   0.8731  -0.9788   0.6333
 MUP  H51   H  HCH2  0   0.208  -1.2264  -0.7107   1.9624
 MUP  H52   H  HCH2  0   0.207  -1.0148   1.0267   1.9561
 MUP  H61   H  HCH2  0   0.207   1.1463   0.7763   3.1845
 MUP  H62   H  HCH2  0   0.206   0.9552  -0.9639   3.1786
 MUP  H71   H  HCH2  0   0.206  -1.1516  -0.7465   4.5025
 MUP  H72   H  HCH2  0   0.206  -0.9835   0.9957   4.4964
 MUP  H81   H  HCH2  0   0.206   1.1773   0.8012   5.7334
 MUP  H82   H  HCH2  0   0.206   1.0326  -0.9435   5.7264
 MUP  H91   H  HCH2  0   0.206  -1.0857  -0.7803   7.0434
 MUP  H92   H  HCH2  0   0.205  -0.9604   0.9655   7.0392
 MUP  H101  H  HCH2  0   0.210   1.2050   0.8157   8.2793
 MUP  H102  H  HCH2  0   0.210   1.0884  -0.9293   8.2796
 MUP  H111  H  HCH3  0   0.225   0.2876   0.0064  10.4572
 MUP  H112  H  HCH3  0   0.215  -0.9251   0.9639   9.6120
 MUP  H113  H  HCH3  0   0.215  -1.0382  -0.7932   9.6177
 MUP  HM1   H  HCH3  0   0.251  -1.5300   0.1612  -7.6768
 MUP  HM2   H  HCH3  0   0.233   0.1732   0.6072  -7.4916
 MUP  HM3   H  HCH3  0   0.236  -0.3224  -1.0920  -7.3396
 MUP  HOP3  H  HOH1  0   0.488   0.8646   2.0247  -4.6914

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
 MUP  C1   C2    single  1.529  0.020  1.529
 MUP  C1   P     single  1.798  0.020  1.798
 MUP  C1   H11   single  0.970  0.020  1.090
 MUP  C1   H12   single  0.970  0.020  1.090
 MUP  C2   C3    single  1.523  0.020  1.523
 MUP  C2   H21   single  0.970  0.020  1.090
 MUP  C2   H22   single  0.970  0.020  1.090
 MUP  C3   C4    single  1.523  0.020  1.523
 MUP  C3   H31   single  0.970  0.020  1.090
 MUP  C3   H32   single  0.970  0.020  1.090
 MUP  C4   C5    single  1.523  0.020  1.523
 MUP  C4   H41   single  0.970  0.020  1.090
 MUP  C4   H42   single  0.970  0.020  1.090
 MUP  C5   C6    single  1.524  0.020  1.524
 MUP  C5   H51   single  0.970  0.020  1.090
 MUP  C5   H52   single  0.970  0.020  1.090
 MUP  C6   C7    single  1.524  0.020  1.524
 MUP  C6   H61   single  0.970  0.020  1.090
 MUP  C6   H62   single  0.970  0.020  1.090
 MUP  C7   C8    single  1.524  0.020  1.524
 MUP  C7   H71   single  0.970  0.020  1.090
 MUP  C7   H72   single  0.970  0.020  1.090
 MUP  C8   C9    single  1.523  0.020  1.523
 MUP  C8   H81   single  0.970  0.020  1.090
 MUP  C8   H82   single  0.970  0.020  1.090
 MUP  C9   C10   single  1.524  0.020  1.524
 MUP  C9   H91   single  0.970  0.020  1.090
 MUP  C9   H92   single  0.970  0.020  1.090
 MUP  C10  C11   single  1.523  0.020  1.523
 MUP  C10  H101  single  0.970  0.020  1.090
 MUP  C10  H102  single  0.970  0.020  1.090
 MUP  C11  H111  single  0.970  0.020  1.090
 MUP  C11  H112  single  0.970  0.020  1.090
 MUP  C11  H113  single  0.970  0.020  1.090
 MUP  CM   O2P   single  1.430  0.020  1.430
 MUP  CM   HM1   single  0.970  0.020  1.090
 MUP  CM   HM2   single  0.970  0.020  1.090
 MUP  CM   HM3   single  0.970  0.020  1.090
 MUP  O1P  P     double  1.483  0.020  1.483
 MUP  O2P  P     single  1.607  0.020  1.607
 MUP  O3P  P     single  1.613  0.020  1.613
 MUP  O3P  HOP3  single  0.850  0.020  0.980

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
 MUP  H12   C1   H11   106.76  3.000
 MUP  H12   C1   P     109.11  3.000
 MUP  H11   C1   P     107.44  3.000
 MUP  H12   C1   C2    110.60  3.000
 MUP  H11   C1   C2    110.22  3.000
 MUP  P     C1   C2    112.50  3.000
 MUP  H22   C2   H21   106.55  3.000
 MUP  H22   C2   C3    109.45  3.000
 MUP  H21   C2   C3    109.45  3.000
 MUP  H22   C2   C1    109.70  3.000
 MUP  H21   C2   C1    109.96  3.000
 MUP  C3    C2   C1    111.60  3.000
 MUP  H32   C3   H31   106.16  3.000
 MUP  H32   C3   C4    109.45  3.000
 MUP  H31   C3   C4    109.44  3.000
 MUP  H32   C3   C2    109.32  3.000
 MUP  H31   C3   C2    109.26  3.000
 MUP  C4    C3   C2    112.98  3.000
 MUP  H42   C4   H41   106.08  3.000
 MUP  H42   C4   C5    109.34  3.000
 MUP  H41   C4   C5    109.44  3.000
 MUP  H42   C4   C3    109.40  3.000
 MUP  H41   C4   C3    109.41  3.000
 MUP  C5    C4   C3    112.95  3.000
 MUP  H52   C5   H51   106.00  3.000
 MUP  H52   C5   C6    109.29  3.000
 MUP  H51   C5   C6    109.33  3.000
 MUP  H52   C5   C4    109.34  3.000
 MUP  H51   C5   C4    109.28  3.000
 MUP  C6    C5   C4    113.34  3.000
 MUP  H62   C6   H61   106.02  3.000
 MUP  H62   C6   C7    109.31  3.000
 MUP  H61   C6   C7    109.39  3.000
 MUP  H62   C6   C5    109.39  3.000
 MUP  H61   C6   C5    109.33  3.000
 MUP  C7    C6   C5    113.15  3.000
 MUP  H72   C7   H71   105.98  3.000
 MUP  H72   C7   C8    109.27  3.000
 MUP  H71   C7   C8    109.33  3.000
 MUP  H72   C7   C6    109.32  3.000
 MUP  H71   C7   C6    109.29  3.000
 MUP  C8    C7   C6    113.38  3.000
 MUP  H82   C8   H81   106.02  3.000
 MUP  H82   C8   C9    109.33  3.000
 MUP  H81   C8   C9    109.37  3.000
 MUP  H82   C8   C7    109.39  3.000
 MUP  H81   C8   C7    109.30  3.000
 MUP  C9    C8   C7    113.18  3.000
 MUP  H92   C9   H91   105.96  3.000
 MUP  H92   C9   C10   109.21  3.000
 MUP  H91   C9   C10   109.24  3.000
 MUP  H92   C9   C8    109.36  3.000
 MUP  H91   C9   C8    109.35  3.000
 MUP  C10   C9   C8    113.44  3.000
 MUP  H102  C10  H101  106.05  3.000
 MUP  H102  C10  C11   109.66  3.000
 MUP  H101  C10  C11   109.61  3.000
 MUP  H102  C10  C9    109.32  3.000
 MUP  H101  C10  C9    109.27  3.000
 MUP  C11   C10  C9    112.71  3.000
 MUP  H113  C11  H112  107.48  3.000
 MUP  H113  C11  H111  107.61  3.000
 MUP  H112  C11  H111  107.60  3.000
 MUP  H113  C11  C10   111.12  3.000
 MUP  H112  C11  C10   111.05  3.000
 MUP  H111  C11  C10   111.77  3.000
 MUP  HM3   CM   HM2   109.11  3.000
 MUP  HM3   CM   HM1   109.05  3.000
 MUP  HM2   CM   HM1   108.76  3.000
 MUP  HM3   CM   O2P   111.29  3.000
 MUP  HM2   CM   O2P   111.52  3.000
 MUP  HM1   CM   O2P   107.03  3.000
 MUP  P     O2P  CM    120.12  3.000
 MUP  HOP3  O3P  P     115.35  3.000
 MUP  O3P   P    O2P   106.30  3.000
 MUP  O3P   P    O1P   108.73  3.000
 MUP  O2P   P    O1P   115.34  3.000
 MUP  O3P   P    C1    107.48  3.000
 MUP  O2P   P    C1    101.66  3.000
 MUP  O1P   P    C1    116.59  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
 MUP  Var_01  C4    C3   C2   C1   179.96  30.0  3
 MUP  Var_02  O1P   P    C1   C2    56.47  30.0  3
 MUP  Var_03  C5    C4   C3   C2  -179.33  30.0  3
 MUP  Var_04  P     C1   C2   C3  -178.33  30.0  1
 MUP  Var_05  C6    C5   C4   C3  -179.49  30.0  3
 MUP  Var_06  C7    C6   C5   C4  -179.14  30.0  3
 MUP  Var_07  C8    C7   C6   C5  -179.11  30.0  3
 MUP  Var_08  C9    C8   C7   C6  -179.12  30.0  3
 MUP  Var_09  C10   C9   C8   C7  -179.21  30.0  3
 MUP  Var_10  C11   C10  C9   C8  -179.74  30.0  3
 MUP  Var_11  H111  C11  C10  C9  -179.71  30.0  3
 MUP  Var_12  HM1   CM   O2P  P   -179.77  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
 MUP  chir_01  P  O1P  O2P  O3P  both

