# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 18:44:19 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-(methylsulfanyl)but-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSC\C=C(NCc1c(O)c(C)ncc1CO[P](O)(O)=O)/C(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
 3LM  3LM  '(2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-(methylsulfanyl)but-2-enoic acid'  ligand  43  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3LM
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
 3LM  C     C  C     0   0.486  -3.0877  -0.2707  -1.5179
 3LM  N     N  NH1   0  -0.714  -1.4677  -0.5857   0.2549
 3LM  O1    O  O     0  -0.427  -2.8890  -1.3611  -1.9937
 3LM  P     P  P     0   1.464   4.5627   2.2704   0.1888
 3LM  N1    N  N     0  -0.407   2.8618  -3.0834   0.4179
 3LM  C2    C  CR6   0   0.132   1.6174  -3.4983   0.2574
 3LM  C3    C  CR6   0   0.270   0.5802  -2.5944  -0.0209
 3LM  O3    O  OH1   0  -0.639  -0.6509  -3.0956  -0.1955
 3LM  C4    C  CR6   0   0.025   0.8638  -1.2323  -0.1219
 3LM  C5    C  CR6   0  -0.076   2.1890  -0.8212   0.0527
 3LM  C6    C  CR16  0  -0.143   3.1445  -1.7879   0.3188
 3LM  CA    C  C     0   0.259  -2.6250   0.1035  -0.1471
 3LM  CB    C  C1    0  -0.294  -3.3109   0.8827   0.6983
 3LM  SD    S  S2    0  -0.029  -5.9236   0.2041   0.5653
 3LM  CE    C  CH3   0  -0.770  -7.4078   1.2092   0.3465
 3LM  CG    C  CH2   0  -0.602  -4.6529   1.5098   0.4965
 3LM  C4A   C  CH2   0  -0.354  -0.2318  -0.2524  -0.4581
 3LM  C5A   C  CH2   0  -0.214   2.5392   0.6364  -0.0669
 3LM  OP1   O  O     0  -0.708   4.1110   3.2493  -0.8162
 3LM  OP2   O  OH1   0  -0.728   6.0907   1.8256   0.1740
 3LM  OP3   O  OH1   0  -0.739   4.2152   2.8053   1.6527
 3LM  OP4   O  O2    0  -0.593   3.9452   0.7995   0.0789
 3LM  O2    O  OH1   0  -0.576  -3.7111   0.7066  -2.1482
 3LM  HN    H  HNH1  0   0.394  -1.3264  -0.4870   1.2533
 3LM  HO3   H  HOH1  0   0.479  -1.2924  -2.3514  -0.1331
 3LM  H6    H  HCR6  0   0.255   4.1826  -1.5189   0.4625
 3LM  HB    H  H     0   0.281  -2.8896   1.0059   1.6909
 3LM  HE    H  HCH3  0   0.276  -8.2654   0.5391   0.3651
 3LM  HEA   H  HCH3  0   0.263  -7.5151   1.9349   1.1518
 3LM  HEB   H  HCH3  0   0.263  -7.3916   1.7294  -0.6104
 3LM  HG    H  HCH2  0   0.286  -4.8371   2.2215   1.3006
 3LM  HGA   H  HCH2  0   0.291  -4.7369   2.0412  -0.4488
 3LM  H2A   H  HCH3  0   0.245   0.5725  -5.1689   1.1276
 3LM  H2A1  H  HCH3  0   0.246   0.9636  -5.3791  -0.5684
 3LM  H2A2  H  HCH3  0   0.246   2.2410  -5.4973   0.6438
 3LM  H4A   H  HCH2  0   0.287  -0.4210  -0.2947  -1.5339
 3LM  H4A1  H  HCH2  0   0.271   0.0717   0.7745  -0.2403
 3LM  H5A   H  HCH2  0   0.264   2.2268   1.0258  -1.0399
 3LM  H5A1  H  HCH2  0   0.257   2.0073   1.2090   0.7015
 3LM  H2    H  HOH1  0   0.490  -4.0367   0.3962  -3.0071
 3LM  HOP2  H  HOH1  0   0.506   6.7152   2.5575   0.0803
 3LM  HOP3  H  HOH1  0   0.497   4.5042   2.2460   2.3864
 3LM  C2A   C  CH3   0  -0.721   1.3324  -4.9640   0.3716

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
 3LM  C    O1    double    1.206  0.020  1.206
 3LM  C    CA    single    1.494  0.020  1.494
 3LM  C    O2    single    1.320  0.020  1.320
 3LM  N    CA    single    1.406  0.020  1.406
 3LM  N    C4A   single    1.465  0.020  1.465
 3LM  P    OP1   double    1.474  0.020  1.474
 3LM  P    OP2   single    1.592  0.020  1.592
 3LM  P    OP3   single    1.597  0.020  1.597
 3LM  P    OP4   single    1.599  0.020  1.599
 3LM  N1   C2    aromatic  1.322  0.020  1.322
 3LM  N1   C6    aromatic  1.330  0.020  1.330
 3LM  C2   C3    aromatic  1.404  0.020  1.404
 3LM  C2   C2A   single    1.498  0.020  1.498
 3LM  C3   O3    single    1.341  0.020  1.341
 3LM  C3   C4    aromatic  1.395  0.020  1.395
 3LM  C4   C5    aromatic  1.398  0.020  1.398
 3LM  C4   C4A   single    1.508  0.020  1.508
 3LM  C5   C6    aromatic  1.385  0.020  1.385
 3LM  C5   C5A   single    1.504  0.020  1.504
 3LM  CA   CB    double    1.339  0.020  1.339
 3LM  CB   CG    single    1.495  0.020  1.495
 3LM  SD   CE    single    1.806  0.020  1.806
 3LM  SD   CG    single    1.823  0.020  1.823
 3LM  C5A  OP4   single    1.423  0.020  1.423
 3LM  N    HN    single    0.890  0.020  1.040
 3LM  O3   HO3   single    0.850  0.020  0.980
 3LM  C6   H6    single    0.930  0.020  1.080
 3LM  CB   HB    single    0.930  0.020  1.080
 3LM  CE   HE    single    0.970  0.020  1.090
 3LM  CE   HEA   single    0.970  0.020  1.090
 3LM  CE   HEB   single    0.970  0.020  1.090
 3LM  CG   HG    single    0.970  0.020  1.090
 3LM  CG   HGA   single    0.970  0.020  1.090
 3LM  C2A  H2A   single    0.970  0.020  1.090
 3LM  C2A  H2A1  single    0.970  0.020  1.090
 3LM  C2A  H2A2  single    0.970  0.020  1.090
 3LM  C4A  H4A   single    0.970  0.020  1.090
 3LM  C4A  H4A1  single    0.970  0.020  1.090
 3LM  C5A  H5A   single    0.970  0.020  1.090
 3LM  C5A  H5A1  single    0.970  0.020  1.090
 3LM  O2   H2    single    0.850  0.020  0.980
 3LM  OP2  HOP2  single    0.850  0.020  0.980
 3LM  OP3  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
 3LM  O2    C    CA    113.51  3.000
 3LM  O2    C    O1    123.99  3.000
 3LM  CA    C    O1    122.49  3.000
 3LM  HN    N    C4A   109.86  3.000
 3LM  HN    N    CA    110.42  3.000
 3LM  C4A   N    CA    116.35  3.000
 3LM  OP4   P    OP3   106.68  3.000
 3LM  OP4   P    OP2    96.49  3.000
 3LM  OP3   P    OP2   108.12  3.000
 3LM  OP4   P    OP1   116.47  3.000
 3LM  OP3   P    OP1   109.63  3.000
 3LM  OP2   P    OP1   118.26  3.000
 3LM  C6    N1   C2    119.80  3.000
 3LM  C2A   C2   C3    120.32  3.000
 3LM  C2A   C2   N1    118.50  3.000
 3LM  C3    C2   N1    121.18  3.000
 3LM  C4    C3   O3    122.84  3.000
 3LM  C4    C3   C2    119.53  3.000
 3LM  O3    C3   C2    117.62  3.000
 3LM  HO3   O3   C3    107.91  3.000
 3LM  C4A   C4   C5    121.69  3.000
 3LM  C4A   C4   C3    120.20  3.000
 3LM  C5    C4   C3    118.08  3.000
 3LM  C5A   C5   C6    122.08  3.000
 3LM  C5A   C5   C4    119.72  3.000
 3LM  C6    C5   C4    118.20  3.000
 3LM  H6    C6   C5    120.93  3.000
 3LM  H6    C6   N1    115.87  3.000
 3LM  C5    C6   N1    123.20  3.000
 3LM  CB    CA   N     121.78  3.000
 3LM  CB    CA   C     124.49  3.000
 3LM  N     CA   C     113.23  3.000
 3LM  HB    CB   CG    115.10  3.000
 3LM  HB    CB   CA    116.41  3.000
 3LM  CG    CB   CA    128.24  3.000
 3LM  CG    SD   CE     99.76  3.000
 3LM  HEB   CE   HEA   109.43  3.000
 3LM  HEB   CE   HE    108.71  3.000
 3LM  HEA   CE   HE    108.66  3.000
 3LM  HEB   CE   SD    111.10  3.000
 3LM  HEA   CE   SD    111.24  3.000
 3LM  HE    CE   SD    107.63  3.000
 3LM  HGA   CG   HG    108.01  3.000
 3LM  HGA   CG   SD    109.20  3.000
 3LM  HG    CG   SD    108.80  3.000
 3LM  HGA   CG   CB    113.05  3.000
 3LM  HG    CG   CB    109.04  3.000
 3LM  SD    CG   CB    108.67  3.000
 3LM  H4A1  C4A  H4A   106.29  3.000
 3LM  H4A1  C4A  C4    111.38  3.000
 3LM  H4A   C4A  C4    108.67  3.000
 3LM  H4A1  C4A  N     110.55  3.000
 3LM  H4A   C4A  N     108.91  3.000
 3LM  C4    C4A  N     110.89  3.000
 3LM  H5A1  C5A  H5A   107.40  3.000
 3LM  H5A1  C5A  OP4   110.36  3.000
 3LM  H5A   C5A  OP4   109.43  3.000
 3LM  H5A1  C5A  C5    109.73  3.000
 3LM  H5A   C5A  C5    110.44  3.000
 3LM  OP4   C5A  C5    109.46  3.000
 3LM  HOP2  OP2  P     114.17  3.000
 3LM  HOP3  OP3  P     115.91  3.000
 3LM  C5A   OP4  P     119.61  3.000
 3LM  H2    O2   C     110.16  3.000
 3LM  H2A2  C2A  H2A1  108.12  3.000
 3LM  H2A2  C2A  H2A   108.43  3.000
 3LM  H2A1  C2A  H2A   106.85  3.000
 3LM  H2A2  C2A  C2    109.87  3.000
 3LM  H2A1  C2A  C2    111.76  3.000
 3LM  H2A   C2A  C2    111.67  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
 3LM  CONST_01  C4   C3   C2   N1      0.00   0.0  0
 3LM  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 3LM  CONST_03  C5   C6   N1   C2      0.00   0.0  0
 3LM  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 3LM  CONST_05  C6   N1   C2   C3      0.00   0.0  0
 3LM  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 3LM  CONST_07  O3   C3   C2   N1    180.00   0.0  0
 3LM  CONST_08  C5A  C5   C6   N1    180.00   0.0  0
 3LM  CONST_09  C4A  C4   C3   C2    180.00   0.0  0
 3LM  CONST_10  C5A  C5   C4   C3    180.00   0.0  0
 3LM  CONST_11  C5   C4   C3   O3    180.00   0.0  0
 3LM  CONST_12  C2A  C2   C3   C4    180.00   0.0  0
 3LM  CONST_13  C2A  C2   N1   C6    180.00   0.0  0
 3LM  CONST_14  C4A  C4   C5   C6    180.00   0.0  0
 3LM  CONST_15  H6   C6   N1   C2    180.00   0.0  0
 3LM  CONST_16  H2   O2   C    O1      0.00   0.0  0
 3LM  Var_01    C3   C4   C4A  N      41.14  30.0  3
 3LM  Var_02    OP4  C5A  C5   C4   -176.95  30.0  2
 3LM  Var_03    H2A  C2A  C2   N1    123.80  30.0  2
 3LM  Var_04    C5   C5A  OP4  P    -171.84  30.0  1
 3LM  Var_05    CA   N    C4A  C4   -169.19  30.0  2
 3LM  Var_06    CG   CB   CA   C       1.46   0.0  2
 3LM  Var_07    C4A  N    CA   C      68.39  30.0  2
 3LM  Var_08    O1   C    CA   N      28.98  30.0  2
 3LM  Var_09    SD   CG   CB   CA     71.67  30.0  3
 3LM  Var_10    OP1  P    OP4  C5A   -48.40  30.0  1
 3LM  Var_11    HE   CE   SD   CG    179.84  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
 3LM  plan-1  N1   0.020
 3LM  plan-1  C2   0.020
 3LM  plan-1  C3   0.020
 3LM  plan-1  O3   0.020
 3LM  plan-1  C4   0.020
 3LM  plan-1  C5   0.020
 3LM  plan-1  C6   0.020
 3LM  plan-1  C4A  0.020
 3LM  plan-1  C5A  0.020
 3LM  plan-1  H6   0.020
 3LM  plan-1  C2A  0.020
 3LM  plan-2  C    0.020
 3LM  plan-2  O1   0.020
 3LM  plan-2  CA   0.020
 3LM  plan-2  O2   0.020
 3LM  plan-2  H2   0.020
 3LM  plan-3  C    0.020
 3LM  plan-3  N    0.020
 3LM  plan-3  CA   0.020
 3LM  plan-3  CB   0.020
 3LM  plan-3  CG   0.020
 3LM  plan-3  HB   0.020

