FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

tag_button

FMODB ID: Z74GN

Calculation Name: 1WT9-A-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1WT9

Chain ID: A

ChEMBL ID:

UniProt ID: Q9DEF8

Base Structure: X-ray

Registration Date: 2025-10-03

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 126
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1093160.866605
FMO2-HF: Nuclear repulsion 1040526.905896
FMO2-HF: Total energy -52633.96071
FMO2-MP2: Total energy -52784.189794


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-3.087-1.202-0.019-0.934-0.9320
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.076 / q_NPA : -0.039
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A3SER00.0460.0293.8492.7974.682-0.019-0.934-0.9320.000
4A4SER00.0240.0056.662-0.016-0.0160.0000.0000.0000.000
5A5GLY0-0.004-0.0098.773-0.174-0.1740.0000.0000.0000.000
6A6TRP0-0.046-0.0267.7020.2230.2230.0000.0000.0000.000
7A7SER0-0.034-0.0127.8620.3600.3600.0000.0000.0000.000
8A8SER00.023-0.0064.8480.1610.1610.0000.0000.0000.000
9A9TYR0-0.0010.0076.8191.7101.7100.0000.0000.0000.000
10A10GLU-1-0.888-0.9458.223-3.833-3.8330.0000.0000.0000.000
11A11GLY0-0.037-0.0115.0510.2890.2890.0000.0000.0000.000
12A12HIS10.8710.9465.6153.1973.1970.0000.0000.0000.000
13A14TYR00.025-0.0137.4331.0531.0530.0000.0000.0000.000
14A15LYS10.8510.93610.9782.3612.3610.0000.0000.0000.000
15A16VAL00.0160.02813.4990.2120.2120.0000.0000.0000.000
16A17PHE0-0.007-0.01615.6770.0920.0920.0000.0000.0000.000
17A18LYS10.9670.97519.5370.7670.7670.0000.0000.0000.000
18A19GLN0-0.0010.00521.5650.0460.0460.0000.0000.0000.000
19A20SER0-0.015-0.01024.772-0.051-0.0510.0000.0000.0000.000
20A21LYS10.8980.95623.9720.9390.9390.0000.0000.0000.000
21A22THR00.0830.04427.611-0.034-0.0340.0000.0000.0000.000
22A23TRP00.0320.00924.474-0.036-0.0360.0000.0000.0000.000
23A24THR00.0440.00525.237-0.102-0.1020.0000.0000.0000.000
24A25ASP-1-0.882-0.93025.643-0.844-0.8440.0000.0000.0000.000
25A26ALA0-0.042-0.01922.660-0.055-0.0550.0000.0000.0000.000
26A27GLU-1-0.731-0.83520.369-1.854-1.8540.0000.0000.0000.000
27A28SER0-0.013-0.01020.697-0.117-0.1170.0000.0000.0000.000
28A29PHE0-0.043-0.03218.8190.0010.0010.0000.0000.0000.000
29A30CYS0-0.055-0.00914.8760.0830.0830.0000.0000.0000.000
30A31THR0-0.044-0.00916.234-0.192-0.1920.0000.0000.0000.000
31A32LYS10.8880.94817.3631.0441.0440.0000.0000.0000.000
32A33GLN0-0.106-0.04514.8120.0950.0950.0000.0000.0000.000
33A34VAL00.0120.0109.257-0.151-0.1510.0000.0000.0000.000
34A35ASN0-0.017-0.01011.3510.1900.1900.0000.0000.0000.000
35A36GLY00.0310.01511.395-0.493-0.4930.0000.0000.0000.000
36A37GLY0-0.0220.00613.356-0.092-0.0920.0000.0000.0000.000
37A38HIS10.8330.88614.1462.5772.5770.0000.0000.0000.000
38A39LEU0-0.025-0.02616.289-0.207-0.2070.0000.0000.0000.000
39A40VAL0-0.069-0.02715.021-0.031-0.0310.0000.0000.0000.000
40A41SER0-0.026-0.02216.1140.2600.2600.0000.0000.0000.000
41A42ILE0-0.035-0.03016.644-0.117-0.1170.0000.0000.0000.000
42A43GLU-1-0.862-0.91617.279-1.861-1.8610.0000.0000.0000.000
43A44SER0-0.020-0.01016.6560.1260.1260.0000.0000.0000.000
44A45SER00.007-0.01419.202-0.064-0.0640.0000.0000.0000.000
45A46GLY00.0570.03717.3610.0180.0180.0000.0000.0000.000
46A47GLU-1-0.783-0.85813.960-2.816-2.8160.0000.0000.0000.000
47A48ALA00.010-0.00316.157-0.041-0.0410.0000.0000.0000.000
48A49ASP-1-0.889-0.92318.884-0.963-0.9630.0000.0000.0000.000
49A50PHE0-0.013-0.00310.7890.0420.0420.0000.0000.0000.000
50A51VAL00.0320.00515.0400.0060.0060.0000.0000.0000.000
51A52GLY00.0350.01816.8170.0880.0880.0000.0000.0000.000
52A53GLN0-0.037-0.03618.1010.1260.1260.0000.0000.0000.000
53A54LEU0-0.033-0.00813.0570.1360.1360.0000.0000.0000.000
54A55ILE0-0.025-0.01416.7760.0840.0840.0000.0000.0000.000
55A56ALA00.0240.02119.8010.1010.1010.0000.0000.0000.000
56A57GLN0-0.026-0.00415.0050.1280.1280.0000.0000.0000.000
57A58LYS10.8000.88715.2911.6121.6120.0000.0000.0000.000
58A59ILE0-0.030-0.01321.3740.0870.0870.0000.0000.0000.000
59A60LYS10.9420.97123.4800.5570.5570.0000.0000.0000.000
60A61SER00.006-0.01027.2910.0730.0730.0000.0000.0000.000
61A62ALA00.1030.05129.690-0.041-0.0410.0000.0000.0000.000
62A63LYS10.8750.94131.6210.4970.4970.0000.0000.0000.000
63A64ILE0-0.049-0.00827.5710.0120.0120.0000.0000.0000.000
64A65HIS10.8270.93827.3430.7940.7940.0000.0000.0000.000
65A66VAL0-0.030-0.01721.721-0.011-0.0110.0000.0000.0000.000
66A67TRP0-0.033-0.02523.527-0.017-0.0170.0000.0000.0000.000
67A68ILE00.0190.00820.848-0.121-0.1210.0000.0000.0000.000
68A69GLY00.0280.01720.5200.1200.1200.0000.0000.0000.000
69A70LEU0-0.040-0.01221.6620.0260.0260.0000.0000.0000.000
70A71ARG10.9110.95524.8720.8760.8760.0000.0000.0000.000
71A72ALA00.0140.01428.214-0.013-0.0130.0000.0000.0000.000
72A73GLN0-0.008-0.02428.0450.0080.0080.0000.0000.0000.000
73A74ASN0-0.042-0.01031.842-0.004-0.0040.0000.0000.0000.000
74A75LYS10.9390.98335.4610.5420.5420.0000.0000.0000.000
75A76GLU-1-0.790-0.90837.760-0.502-0.5020.0000.0000.0000.000
76A77LYS10.8540.95139.0020.3940.3940.0000.0000.0000.000
77A78GLN00.018-0.00539.713-0.014-0.0140.0000.0000.0000.000
78A79CYS0-0.055-0.03436.6420.0050.0050.0000.0000.0000.000
79A80SER00.0010.00940.251-0.004-0.0040.0000.0000.0000.000
80A81ILE00.0210.01143.6180.0010.0010.0000.0000.0000.000
81A82GLU-1-0.956-0.98246.375-0.294-0.2940.0000.0000.0000.000
82A83TRP0-0.0100.00148.473-0.017-0.0170.0000.0000.0000.000
83A84SER0-0.030-0.02951.0270.0030.0030.0000.0000.0000.000
84A85ASP-1-0.860-0.90552.280-0.248-0.2480.0000.0000.0000.000
85A86GLY00.0050.01653.4180.0090.0090.0000.0000.0000.000
86A87SER0-0.094-0.06054.388-0.001-0.0010.0000.0000.0000.000
87A88SER00.035-0.00451.238-0.008-0.0080.0000.0000.0000.000
88A89ILE0-0.0120.00046.2090.0090.0090.0000.0000.0000.000
89A90SER0-0.049-0.01949.652-0.009-0.0090.0000.0000.0000.000
90A91TYR0-0.020-0.01851.5060.0060.0060.0000.0000.0000.000
91A92GLU-1-0.829-0.90845.180-0.397-0.3970.0000.0000.0000.000
92A93ASN0-0.049-0.03248.7730.0130.0130.0000.0000.0000.000
93A94TRP0-0.042-0.02142.119-0.001-0.0010.0000.0000.0000.000
94A95ILE00.0260.02742.9170.0080.0080.0000.0000.0000.000
95A96GLU-1-0.814-0.90940.306-0.454-0.4540.0000.0000.0000.000
96A97GLU-1-0.906-0.97038.488-0.439-0.4390.0000.0000.0000.000
97A98GLU-1-0.850-0.92438.534-0.448-0.4480.0000.0000.0000.000
98A99SER0-0.024-0.00238.586-0.018-0.0180.0000.0000.0000.000
99A100LYS10.7830.88034.8630.4390.4390.0000.0000.0000.000
100A101LYS10.8360.89833.3290.5550.5550.0000.0000.0000.000
101A102CYS0-0.078-0.02828.405-0.063-0.0630.0000.0000.0000.000
102A103LEU00.0440.02626.4070.0410.0410.0000.0000.0000.000
103A104GLY00.004-0.00725.266-0.076-0.0760.0000.0000.0000.000
104A105VAL0-0.0020.01522.7780.0480.0480.0000.0000.0000.000
105A106HIS00.0870.03426.056-0.016-0.0160.0000.0000.0000.000
106A107ILE0-0.038-0.00727.447-0.019-0.0190.0000.0000.0000.000
107A108GLU-1-0.888-0.94828.632-0.461-0.4610.0000.0000.0000.000
108A109THR0-0.024-0.00528.5180.0000.0000.0000.0000.0000.000
109A110GLY00.0160.00426.725-0.035-0.0350.0000.0000.0000.000
110A111PHE0-0.058-0.03623.109-0.065-0.0650.0000.0000.0000.000
111A112HIS10.8320.90022.6910.8340.8340.0000.0000.0000.000
112A113LYS10.9270.96224.8840.6490.6490.0000.0000.0000.000
113A114TRP00.0020.00022.4610.0160.0160.0000.0000.0000.000
114A115GLU-1-0.901-0.95727.498-0.611-0.6110.0000.0000.0000.000
115A116ASN0-0.032-0.02929.845-0.051-0.0510.0000.0000.0000.000
116A117PHE00.001-0.00629.2450.0410.0410.0000.0000.0000.000
117A118TYR00.0420.03032.641-0.024-0.0240.0000.0000.0000.000
118A120GLU-1-0.867-0.94130.756-0.730-0.7300.0000.0000.0000.000
119A121GLN0-0.028-0.00432.0780.0040.0040.0000.0000.0000.000
120A122GLN0-0.019-0.02130.148-0.070-0.0700.0000.0000.0000.000
121A123ASP-1-0.759-0.89027.833-0.666-0.6660.0000.0000.0000.000
122A124PRO0-0.031-0.01523.697-0.055-0.0550.0000.0000.0000.000
123A125PHE00.0190.00919.364-0.001-0.0010.0000.0000.0000.000
124A126VAL00.016-0.00315.543-0.004-0.0040.0000.0000.0000.000
125A128GLU-1-0.796-0.92011.496-3.643-3.6430.0000.0000.0000.000
126A129ALA-1-0.795-0.8738.635-6.883-6.8830.0000.0000.0000.000