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: 3K85L

Calculation Name: 1MPU-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1MPU

Chain ID: A

ChEMBL ID:

UniProt ID: P26718

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 124
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1144392.565383
FMO2-HF: Nuclear repulsion 1090157.419792
FMO2-HF: Total energy -54235.145591
FMO2-MP2: Total energy -54385.194224


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:88:GLN)


Summations of interaction energy for fragment #1(A:88:GLN)
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.
-13.241-11.581-0.021-0.678-0.9610
Interaction energy analysis for fragmet #1(A:88:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.827 / q_NPA : 0.891
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].
3A90PRO00.0320.0133.7170.4282.088-0.021-0.678-0.9610.000
4A91LEU00.0180.0155.0040.3280.3280.0000.0000.0000.000
5A92THR0-0.026-0.0088.2551.8441.8440.0000.0000.0000.000
6A93GLU-1-0.881-0.94011.634-21.608-21.6080.0000.0000.0000.000
7A94SER0-0.077-0.04914.3270.9140.9140.0000.0000.0000.000
8A95TYR0-0.0080.00817.961-0.057-0.0570.0000.0000.0000.000
9A96CYS0-0.048-0.01221.2770.2160.2160.0000.0000.0000.000
10A97GLY00.0350.01422.7130.3430.3430.0000.0000.0000.000
11A98PRO0-0.013-0.00926.2730.0040.0040.0000.0000.0000.000
12A99CYS00.0500.04026.863-0.312-0.3120.0000.0000.0000.000
13A100PRO00.0230.01730.3780.0690.0690.0000.0000.0000.000
14A101LYS10.9400.96330.4389.5969.5960.0000.0000.0000.000
15A102ASN0-0.029-0.03329.4940.0180.0180.0000.0000.0000.000
16A103TRP00.0270.03529.9200.0580.0580.0000.0000.0000.000
17A104ILE0-0.0030.01024.393-0.395-0.3950.0000.0000.0000.000
18A106TYR0-0.073-0.09018.933-0.907-0.9070.0000.0000.0000.000
19A107LYS10.8240.90719.50715.73215.7320.0000.0000.0000.000
20A108ASN00.0360.01922.7400.1640.1640.0000.0000.0000.000
21A109ASN0-0.0090.01025.5610.8620.8620.0000.0000.0000.000
22A111TYR00.003-0.01226.5130.4760.4760.0000.0000.0000.000
23A112GLN00.0250.00829.960-0.441-0.4410.0000.0000.0000.000
24A113PHE0-0.027-0.01329.1860.1830.1830.0000.0000.0000.000
25A114PHE00.0250.00833.566-0.029-0.0290.0000.0000.0000.000
26A115ASP-1-0.919-0.97037.025-8.316-8.3160.0000.0000.0000.000
27A116GLU-1-0.876-0.94838.834-7.637-7.6370.0000.0000.0000.000
28A117SER0-0.103-0.05342.3540.0580.0580.0000.0000.0000.000
29A118LYS10.8920.95542.8387.4797.4790.0000.0000.0000.000
30A119ASN00.0350.03145.309-0.141-0.1410.0000.0000.0000.000
31A120TRP00.033-0.00742.8120.0110.0110.0000.0000.0000.000
32A121TYR00.025-0.00245.494-0.095-0.0950.0000.0000.0000.000
33A122GLU-1-0.862-0.93447.241-6.588-6.5880.0000.0000.0000.000
34A123SER0-0.055-0.00141.667-0.156-0.1560.0000.0000.0000.000
35A124GLN00.0720.00742.084-0.280-0.2800.0000.0000.0000.000
36A125ALA00.000-0.00143.521-0.068-0.0680.0000.0000.0000.000
37A126SER0-0.055-0.03442.1630.0030.0030.0000.0000.0000.000
38A127CYS0-0.0460.01535.1170.0970.0970.0000.0000.0000.000
39A128MET00.0240.01340.496-0.036-0.0360.0000.0000.0000.000
40A129SER0-0.056-0.01743.0020.0090.0090.0000.0000.0000.000
41A130GLN0-0.055-0.03037.8870.0040.0040.0000.0000.0000.000
42A131ASN0-0.037-0.01038.473-0.078-0.0780.0000.0000.0000.000
43A132ALA0-0.033-0.00736.785-0.256-0.2560.0000.0000.0000.000
44A133SER00.0300.02437.7470.2390.2390.0000.0000.0000.000
45A134LEU0-0.021-0.02037.584-0.255-0.2550.0000.0000.0000.000
46A135LEU0-0.062-0.02931.887-0.083-0.0830.0000.0000.0000.000
47A136LYS10.9520.96834.4828.7378.7370.0000.0000.0000.000
48A137VAL0-0.039-0.02531.557-0.327-0.3270.0000.0000.0000.000
49A138TYR0-0.020-0.02628.1440.3680.3680.0000.0000.0000.000
50A139SER0-0.003-0.00727.389-0.013-0.0130.0000.0000.0000.000
51A140LYS10.8390.92427.11710.19510.1950.0000.0000.0000.000
52A141GLU-1-0.888-0.94223.723-12.292-12.2920.0000.0000.0000.000
53A142ASP-1-0.856-0.92322.837-13.083-13.0830.0000.0000.0000.000
54A143GLN00.037-0.01024.8330.1270.1270.0000.0000.0000.000
55A144ASP-1-0.754-0.83220.994-14.511-14.5110.0000.0000.0000.000
56A145LEU00.0080.01822.5500.1910.1910.0000.0000.0000.000
57A146LEU00.0390.01623.9270.2700.2700.0000.0000.0000.000
58A147LYS10.8620.94124.82412.59512.5950.0000.0000.0000.000
59A148LEU0-0.0090.00121.2060.0180.0180.0000.0000.0000.000
60A149VAL0-0.0150.01225.9350.1470.1470.0000.0000.0000.000
61A150LYS10.9840.98629.2759.9549.9540.0000.0000.0000.000
62A151SER0-0.009-0.01231.5650.1910.1910.0000.0000.0000.000
63A152TYR00.0190.02234.962-0.226-0.2260.0000.0000.0000.000
64A153HIS10.8320.90133.6879.0449.0440.0000.0000.0000.000
65A154TRP00.0010.00537.831-0.097-0.0970.0000.0000.0000.000
66A155MET0-0.056-0.01036.984-0.345-0.3450.0000.0000.0000.000
67A156GLY00.0650.02438.3950.2320.2320.0000.0000.0000.000
68A157LEU0-0.060-0.02339.7500.1290.1290.0000.0000.0000.000
69A158VAL00.0490.00741.6300.1020.1020.0000.0000.0000.000
70A159HIS10.8450.92445.4846.3406.3400.0000.0000.0000.000
71A160ILE00.0660.04048.4260.1310.1310.0000.0000.0000.000
72A161PRO00.0100.01151.250-0.002-0.0020.0000.0000.0000.000
73A162THR0-0.027-0.02653.5130.0850.0850.0000.0000.0000.000
74A163ASN0-0.038-0.03155.4930.0080.0080.0000.0000.0000.000
75A164GLY00.0180.03051.630-0.036-0.0360.0000.0000.0000.000
76A165SER0-0.002-0.01446.571-0.023-0.0230.0000.0000.0000.000
77A166TRP0-0.015-0.00343.8920.0460.0460.0000.0000.0000.000
78A167GLN0-0.049-0.02243.304-0.037-0.0370.0000.0000.0000.000
79A168TRP00.0420.01836.660-0.140-0.1400.0000.0000.0000.000
80A169GLU-1-0.815-0.90440.705-7.656-7.6560.0000.0000.0000.000
81A170ASP-1-0.808-0.85140.299-7.746-7.7460.0000.0000.0000.000
82A171GLY00.0060.01343.7010.0850.0850.0000.0000.0000.000
83A172SER0-0.124-0.08540.480-0.067-0.0670.0000.0000.0000.000
84A173ILE00.026-0.00940.8580.0210.0210.0000.0000.0000.000
85A174LEU0-0.0010.01337.936-0.238-0.2380.0000.0000.0000.000
86A175SER00.012-0.00136.3280.2200.2200.0000.0000.0000.000
87A176PRO00.0420.01537.804-0.070-0.0700.0000.0000.0000.000
88A177ASN0-0.001-0.01234.091-0.068-0.0680.0000.0000.0000.000
89A178LEU0-0.0160.01932.162-0.364-0.3640.0000.0000.0000.000
90A179LEU00.006-0.00333.758-0.241-0.2410.0000.0000.0000.000
91A180THR0-0.030-0.01036.0430.1780.1780.0000.0000.0000.000
92A181ILE00.004-0.00338.148-0.086-0.0860.0000.0000.0000.000
93A182ILE0-0.043-0.01939.4540.0460.0460.0000.0000.0000.000
94A183GLU-1-0.913-0.95542.864-6.500-6.5000.0000.0000.0000.000
95A184MET0-0.031-0.02143.9920.0430.0430.0000.0000.0000.000
96A185GLN0-0.025-0.02447.1580.1760.1760.0000.0000.0000.000
97A186LYS10.9841.00149.4755.6785.6780.0000.0000.0000.000
98A187GLY0-0.009-0.01449.7140.0400.0400.0000.0000.0000.000
99A188ASP-1-0.880-0.93549.419-6.237-6.2370.0000.0000.0000.000
100A189CYS0-0.030-0.00145.326-0.101-0.1010.0000.0000.0000.000
101A190ALA00.0370.01041.7490.0360.0360.0000.0000.0000.000
102A191LEU00.0020.01539.892-0.160-0.1600.0000.0000.0000.000
103A192TYR0-0.024-0.02830.341-0.040-0.0400.0000.0000.0000.000
104A193ALA00.029-0.00434.8550.0610.0610.0000.0000.0000.000
105A194SER0-0.0190.00029.190-0.129-0.1290.0000.0000.0000.000
106A195SER0-0.038-0.03829.3690.0050.0050.0000.0000.0000.000
107A196PHE00.0180.00827.2370.1690.1690.0000.0000.0000.000
108A197LYS10.9170.96932.5139.1559.1550.0000.0000.0000.000
109A198GLY00.0320.01436.099-0.107-0.1070.0000.0000.0000.000
110A199TYR0-0.010-0.01737.695-0.050-0.0500.0000.0000.0000.000
111A200ILE00.0070.00741.840-0.030-0.0300.0000.0000.0000.000
112A201GLU-1-0.794-0.89344.644-6.980-6.9800.0000.0000.0000.000
113A202ASN00.0380.00946.6020.0450.0450.0000.0000.0000.000
114A204SER00.006-0.00648.895-0.020-0.0200.0000.0000.0000.000
115A205THR0-0.037-0.01347.3050.1290.1290.0000.0000.0000.000
116A206PRO0-0.016-0.00146.834-0.123-0.1230.0000.0000.0000.000
117A207ASN0-0.012-0.02241.869-0.169-0.1690.0000.0000.0000.000
118A208THR00.0160.03038.145-0.096-0.0960.0000.0000.0000.000
119A209TYR0-0.0030.00138.2460.0820.0820.0000.0000.0000.000
120A210ILE0-0.0050.00031.966-0.211-0.2110.0000.0000.0000.000
121A212MET0-0.028-0.01931.366-0.432-0.4320.0000.0000.0000.000
122A213GLN0-0.024-0.02232.5300.1200.1200.0000.0000.0000.000
123A214ARG10.8790.93531.3919.3249.3240.0000.0000.0000.000
124A215THR-1-0.855-0.91828.557-10.108-10.1080.0000.0000.0000.000