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

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FMODB ID: KVJR3

Calculation Name: 3PH9-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3PH9

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TD06

Base Structure: X-ray

Registration Date: 2025-10-05

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 133
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1319697.896851
FMO2-HF: Nuclear repulsion 1264350.561394
FMO2-HF: Total energy -55347.335457
FMO2-MP2: Total energy -55506.6067


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:31:PRO)


Summations of interaction energy for fragment #1(A:31:PRO)
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.
-30.909-29.617-0.011-0.436-0.8450
Interaction energy analysis for fragmet #1(A:31:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.878 / q_NPA : 0.915
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].
3A33THR00.0570.0373.8441.0912.383-0.011-0.436-0.8450.000
4A34LEU00.0220.0096.1140.8450.8450.0000.0000.0000.000
5A35SER00.031-0.0079.5760.3880.3880.0000.0000.0000.000
6A36ARG10.8570.9318.26830.83430.8340.0000.0000.0000.000
7A37GLY00.0440.0249.4101.1061.1060.0000.0000.0000.000
8A38TRP0-0.002-0.00710.7042.4532.4530.0000.0000.0000.000
9A39GLY00.0740.02113.0871.6751.6750.0000.0000.0000.000
10A40ASP-1-0.894-0.91510.247-29.445-29.4450.0000.0000.0000.000
11A41ASP-1-0.895-0.93812.695-18.421-18.4210.0000.0000.0000.000
12A42ILE0-0.062-0.02515.5781.1701.1700.0000.0000.0000.000
13A43THR0-0.036-0.01715.010-1.135-1.1350.0000.0000.0000.000
14A44TRP0-0.058-0.03013.3770.8340.8340.0000.0000.0000.000
15A45VAL0-0.0030.00915.800-0.142-0.1420.0000.0000.0000.000
16A46GLN0-0.063-0.04613.605-1.285-1.2850.0000.0000.0000.000
17A47THR0-0.037-0.05016.034-0.363-0.3630.0000.0000.0000.000
18A48TYR00.000-0.02519.0860.1510.1510.0000.0000.0000.000
19A49GLU-1-0.817-0.90021.930-13.744-13.7440.0000.0000.0000.000
20A50GLU-1-0.844-0.91318.690-16.120-16.1200.0000.0000.0000.000
21A51GLY00.028-0.00422.2620.2850.2850.0000.0000.0000.000
22A52LEU00.007-0.00123.1060.4470.4470.0000.0000.0000.000
23A53PHE0-0.033-0.00225.6030.5830.5830.0000.0000.0000.000
24A54TYR00.021-0.00822.1050.6580.6580.0000.0000.0000.000
25A55ALA0-0.0070.03026.1810.2620.2620.0000.0000.0000.000
26A56GLN00.0400.01427.7490.2180.2180.0000.0000.0000.000
27A57LYS10.8760.94429.18610.49110.4910.0000.0000.0000.000
28A58SER0-0.069-0.05527.7950.1680.1680.0000.0000.0000.000
29A59LYS10.9310.96730.2078.5818.5810.0000.0000.0000.000
30A60LYS10.9230.97325.36612.00912.0090.0000.0000.0000.000
31A61PRO00.0090.00128.380-0.034-0.0340.0000.0000.0000.000
32A62LEU0-0.027-0.00122.259-0.422-0.4220.0000.0000.0000.000
33A63MET0-0.040-0.00922.4970.3510.3510.0000.0000.0000.000
34A64VAL00.0130.00120.615-0.721-0.7210.0000.0000.0000.000
35A65ILE0-0.008-0.00117.7020.4940.4940.0000.0000.0000.000
36A66HIS00.0230.00417.486-1.238-1.2380.0000.0000.0000.000
37A67HIS10.8040.88711.30523.98223.9820.0000.0000.0000.000
38A68LEU00.0430.02214.036-0.483-0.4830.0000.0000.0000.000
39A69GLU-1-0.783-0.9268.099-31.113-31.1130.0000.0000.0000.000
40A70ASP-1-0.918-0.94711.568-24.100-24.1000.0000.0000.0000.000
41A71CYS-1-0.800-0.74913.870-15.358-15.3580.0000.0000.0000.000
42A72GLN00.0490.00016.158-0.228-0.2280.0000.0000.0000.000
43A73TYR00.0220.00118.2390.0550.0550.0000.0000.0000.000
44A74SER0-0.054-0.15015.5100.1830.1830.0000.0000.0000.000
45A75GLN0-0.071-0.04510.474-0.282-0.2820.0000.0000.0000.000
46A76ALA0-0.035-0.01615.382-0.016-0.0160.0000.0000.0000.000
47A77LEU0-0.021-0.01118.8580.2640.2640.0000.0000.0000.000
48A78LYS10.8390.92010.03128.20228.2020.0000.0000.0000.000
49A79LYS10.9550.98315.57317.19617.1960.0000.0000.0000.000
50A80VAL0-0.031-0.01816.4470.4170.4170.0000.0000.0000.000
51A81PHE0-0.002-0.00818.1730.4910.4910.0000.0000.0000.000
52A82ALA0-0.009-0.00215.0600.4090.4090.0000.0000.0000.000
53A83GLN0-0.041-0.01216.0740.3580.3580.0000.0000.0000.000
54A84ASN0-0.0100.01019.5860.8600.8600.0000.0000.0000.000
55A85GLU-1-0.858-0.94022.818-12.195-12.1950.0000.0000.0000.000
56A86GLU-1-0.849-0.91524.359-10.307-10.3070.0000.0000.0000.000
57A87ILE0-0.010-0.02221.7960.1150.1150.0000.0000.0000.000
58A88GLN0-0.011-0.00717.889-0.547-0.5470.0000.0000.0000.000
59A89GLU-1-0.765-0.85422.006-11.184-11.1840.0000.0000.0000.000
60A90MET0-0.035-0.02725.0170.2560.2560.0000.0000.0000.000
61A91ALA00.006-0.01620.4920.1080.1080.0000.0000.0000.000
62A92GLN0-0.019-0.00719.586-0.274-0.2740.0000.0000.0000.000
63A93ASN0-0.050-0.03321.871-0.113-0.1130.0000.0000.0000.000
64A94LYS10.7900.89125.51510.90310.9030.0000.0000.0000.000
65A95PHE0-0.008-0.00224.0990.4070.4070.0000.0000.0000.000
66A96ILE0-0.0260.01021.908-0.230-0.2300.0000.0000.0000.000
67A97MET00.0150.02218.6250.4960.4960.0000.0000.0000.000
68A98LEU00.0400.02616.934-0.680-0.6800.0000.0000.0000.000
69A99ASN0-0.027-0.00712.944-0.718-0.7180.0000.0000.0000.000
70A100LEU0-0.020-0.00614.880-1.130-1.1300.0000.0000.0000.000
71A101MET0-0.034-0.0169.191-0.286-0.2860.0000.0000.0000.000
72A102HIS0-0.039-0.02214.6750.0510.0510.0000.0000.0000.000
73A103GLU-1-0.774-0.85517.494-14.015-14.0150.0000.0000.0000.000
74A104THR00.0310.02521.137-0.137-0.1370.0000.0000.0000.000
75A105THR0-0.003-0.01222.9980.1920.1920.0000.0000.0000.000
76A106ASP-1-0.805-0.87126.115-10.342-10.3420.0000.0000.0000.000
77A107LYS10.9920.98027.5979.7229.7220.0000.0000.0000.000
78A108ASN0-0.049-0.02729.7420.3220.3220.0000.0000.0000.000
79A109LEU00.0150.00924.0300.0040.0040.0000.0000.0000.000
80A110SER0-0.011-0.01525.946-0.513-0.5130.0000.0000.0000.000
81A111PRO0-0.0170.01627.7310.2020.2020.0000.0000.0000.000
82A112ASP-1-0.776-0.86730.119-10.222-10.2220.0000.0000.0000.000
83A113GLY00.000-0.00328.848-0.018-0.0180.0000.0000.0000.000
84A114GLN0-0.035-0.02823.723-0.307-0.3070.0000.0000.0000.000
85A115TYR0-0.078-0.05123.300-0.654-0.6540.0000.0000.0000.000
86A116VAL00.0010.01618.473-0.236-0.2360.0000.0000.0000.000
87A117PRO00.0170.00319.0810.2700.2700.0000.0000.0000.000
88A118ARG10.7310.83020.54814.08614.0860.0000.0000.0000.000
89A119ILE0-0.037-0.00521.500-0.567-0.5670.0000.0000.0000.000
90A120MET0-0.0210.01623.5680.6040.6040.0000.0000.0000.000
91A121PHE00.0520.00525.149-0.421-0.4210.0000.0000.0000.000
92A122VAL0-0.010-0.00126.9370.3180.3180.0000.0000.0000.000
93A123ASP-1-0.711-0.83529.390-9.386-9.3860.0000.0000.0000.000
94A124PRO0-0.0050.01131.275-0.090-0.0900.0000.0000.0000.000
95A125SER0-0.090-0.07932.2370.0800.0800.0000.0000.0000.000
96A126LEU0-0.030-0.02230.3720.1180.1180.0000.0000.0000.000
97A127THR0-0.0120.01232.477-0.040-0.0400.0000.0000.0000.000
98A128VAL00.013-0.00429.466-0.148-0.1480.0000.0000.0000.000
99A129ARG10.7920.86831.2199.5129.5120.0000.0000.0000.000
100A130ALA00.0220.01132.235-0.155-0.1550.0000.0000.0000.000
101A131ASP-1-0.794-0.86233.487-8.961-8.9610.0000.0000.0000.000
102A132ILE0-0.082-0.02630.7290.1870.1870.0000.0000.0000.000
103A133ALA00.0370.02730.792-0.370-0.3700.0000.0000.0000.000
104A134GLY00.0440.02630.0920.1070.1070.0000.0000.0000.000
105A135ARG10.8140.87731.04010.05610.0560.0000.0000.0000.000
106A136TYR0-0.054-0.02628.7560.4110.4110.0000.0000.0000.000
107A137SER00.0320.00832.850-0.184-0.1840.0000.0000.0000.000
108A138ASN0-0.037-0.01533.470-0.048-0.0480.0000.0000.0000.000
109A139ARG10.9440.96225.70411.29111.2910.0000.0000.0000.000
110A140LEU00.0540.04429.365-0.257-0.2570.0000.0000.0000.000
111A141TYR0-0.002-0.02327.0970.0430.0430.0000.0000.0000.000
112A142THR0-0.071-0.04024.046-0.612-0.6120.0000.0000.0000.000
113A143TYR00.005-0.00524.6130.6370.6370.0000.0000.0000.000
114A144GLU-1-0.819-0.88224.021-11.976-11.9760.0000.0000.0000.000
115A145PRO00.024-0.00922.1880.2450.2450.0000.0000.0000.000
116A146ARG10.8230.89524.71810.67310.6730.0000.0000.0000.000
117A147ASP-1-0.775-0.86627.531-10.302-10.3020.0000.0000.0000.000
118A148LEU00.0340.01723.0790.0930.0930.0000.0000.0000.000
119A149PRO00.0220.00527.2080.0360.0360.0000.0000.0000.000
120A150LEU00.0040.01830.7760.1720.1720.0000.0000.0000.000
121A151LEU00.006-0.00223.6830.0670.0670.0000.0000.0000.000
122A152ILE0-0.0040.00427.250-0.050-0.0500.0000.0000.0000.000
123A153GLU-1-0.842-0.92929.280-9.152-9.1520.0000.0000.0000.000
124A154ASN0-0.051-0.04830.2320.4980.4980.0000.0000.0000.000
125A155MET0-0.0240.00024.421-0.014-0.0140.0000.0000.0000.000
126A156LYS10.8480.90029.4699.8989.8980.0000.0000.0000.000
127A157LYS10.7720.89632.8159.1729.1720.0000.0000.0000.000
128A158ALA00.0070.00030.1800.1910.1910.0000.0000.0000.000
129A159LEU0-0.020-0.02129.2140.1100.1100.0000.0000.0000.000
130A160ARG10.8780.96232.8178.9318.9310.0000.0000.0000.000
131A161LEU00.0260.01833.322-0.065-0.0650.0000.0000.0000.000
132A162ILE0-0.031-0.01836.3500.1920.1920.0000.0000.0000.000
133A163GLN-1-1.008-0.99038.781-7.640-7.6400.0000.0000.0000.000