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: 973J2

Calculation Name: 6SPD-F-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6SPD

Chain ID: F

ChEMBL ID:

UniProt ID: A0A2V3

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-04

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 175
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1753473.571016
FMO2-HF: Nuclear repulsion 1684503.24796
FMO2-HF: Total energy -68970.323056
FMO2-MP2: Total energy -69173.608372


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:3:ARG)


Summations of interaction energy for fragment #1(A:3:ARG)
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.
-133.426-129.22546.044-26.423-23.824-0.3
Interaction energy analysis for fragmet #1(A:3:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.620 / q_NPA : 1.772
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].
3A5LYS10.8860.9513.27376.22078.248-0.008-0.914-1.107-0.002
4A6GLU-1-0.768-0.8704.275-49.165-48.902-0.001-0.031-0.2310.000
5A7LEU00.0080.0153.7606.6406.9910.002-0.048-0.3050.000
95A97TYR00.0570.0003.709-0.971-0.7790.000-0.034-0.1580.000
96A98GLU-1-0.840-0.8931.815-241.939-241.29921.300-12.059-9.881-0.154
97A99PHE00.0240.0093.552-4.935-4.3000.007-0.285-0.357-0.002
99A101ASP-1-0.754-0.8811.806-205.536-206.91723.891-12.362-10.148-0.149
100A102ARG10.8880.9712.48998.808100.2810.853-0.690-1.6370.007
6A8TYR0-0.022-0.0326.7396.7666.7660.0000.0000.0000.000
7A9ARG10.8110.8728.66555.39355.3930.0000.0000.0000.000
8A10LYS10.9270.9539.41249.97249.9720.0000.0000.0000.000
9A11GLU-1-0.894-0.92210.339-37.027-37.0270.0000.0000.0000.000
10A12ILE0-0.020-0.0269.6022.1862.1860.0000.0000.0000.000
11A13ALA0-0.0080.00212.9022.5852.5850.0000.0000.0000.000
12A14PRO0-0.018-0.00614.2902.1972.1970.0000.0000.0000.000
13A15LYS10.8370.91315.51031.37131.3710.0000.0000.0000.000
14A16LEU0-0.002-0.01715.7271.0551.0550.0000.0000.0000.000
15A17LYS10.8530.95418.69926.78426.7840.0000.0000.0000.000
16A18GLU-1-0.891-0.94421.094-25.430-25.4300.0000.0000.0000.000
17A19GLU-1-0.875-0.91320.914-26.309-26.3090.0000.0000.0000.000
18A20LEU0-0.025-0.01621.3930.4050.4050.0000.0000.0000.000
19A21GLN0-0.029-0.01224.6100.5480.5480.0000.0000.0000.000
20A22LEU0-0.026-0.00521.6200.5350.5350.0000.0000.0000.000
21A23ALA00.0280.01925.416-0.165-0.1650.0000.0000.0000.000
22A24ASN0-0.071-0.05724.6370.0720.0720.0000.0000.0000.000
23A25VAL00.013-0.01218.417-0.742-0.7420.0000.0000.0000.000
24A26MET0-0.040-0.02019.488-1.797-1.7970.0000.0000.0000.000
25A27GLU-1-0.793-0.90321.433-24.425-24.4250.0000.0000.0000.000
26A28VAL00.0120.01916.810-0.215-0.2150.0000.0000.0000.000
27A29PRO00.0210.02817.683-1.031-1.0310.0000.0000.0000.000
28A30ARG10.9600.97713.58634.11034.1100.0000.0000.0000.000
29A31VAL00.0440.01211.2161.6811.6810.0000.0000.0000.000
30A32THR0-0.070-0.03012.618-1.652-1.6520.0000.0000.0000.000
31A33LYS10.8800.93513.62429.28729.2870.0000.0000.0000.000
32A34ILE00.0380.03310.7900.7900.7900.0000.0000.0000.000
33A35THR0-0.030-0.02514.962-0.193-0.1930.0000.0000.0000.000
34A36LEU0-0.0160.01613.9870.9900.9900.0000.0000.0000.000
35A37ASN00.019-0.01217.5171.4641.4640.0000.0000.0000.000
36A38MET0-0.042-0.01419.651-0.580-0.5800.0000.0000.0000.000
37A39GLY00.0140.01522.0780.7670.7670.0000.0000.0000.000
38A40LEU0-0.042-0.00125.584-0.100-0.1000.0000.0000.0000.000
39A41GLY00.009-0.02928.9280.4010.4010.0000.0000.0000.000
40A42GLU-1-0.875-0.94729.542-20.092-20.0920.0000.0000.0000.000
41A43ALA00.0210.00732.052-0.278-0.2780.0000.0000.0000.000
42A44VAL00.0000.02630.7230.1740.1740.0000.0000.0000.000
43A45GLY0-0.052-0.03633.9150.1310.1310.0000.0000.0000.000
44A46ASP-1-0.875-0.94335.492-16.960-16.9600.0000.0000.0000.000
45A47LYS10.8540.93633.58316.60116.6010.0000.0000.0000.000
46A48LYS10.9810.99732.05818.13818.1380.0000.0000.0000.000
47A49ILE00.0580.03428.858-0.243-0.2430.0000.0000.0000.000
48A50ILE0-0.020-0.01927.214-0.936-0.9360.0000.0000.0000.000
49A51GLU-1-0.895-0.96626.284-20.970-20.9700.0000.0000.0000.000
50A52ASN0-0.042-0.00625.3460.0970.0970.0000.0000.0000.000
51A53ALA00.0410.01223.424-1.010-1.0100.0000.0000.0000.000
52A54VAL0-0.069-0.03822.072-1.215-1.2150.0000.0000.0000.000
53A55ALA00.0490.01720.510-1.476-1.4760.0000.0000.0000.000
54A56ASP-1-0.886-0.93519.324-28.217-28.2170.0000.0000.0000.000
55A57LEU0-0.041-0.03415.423-1.982-1.9820.0000.0000.0000.000
56A58GLU-1-0.929-0.96715.592-30.909-30.9090.0000.0000.0000.000
57A59LYS10.8860.95615.22328.45828.4580.0000.0000.0000.000
58A60ILE0-0.0150.00612.441-2.824-2.8240.0000.0000.0000.000
59A61THR0-0.083-0.05810.915-3.912-3.9120.0000.0000.0000.000
60A62GLY00.0470.03211.135-3.602-3.6020.0000.0000.0000.000
61A63GLN0-0.117-0.07713.205-1.849-1.8490.0000.0000.0000.000
62A64LYS11.0261.02015.71525.96325.9630.0000.0000.0000.000
63A65PRO0-0.015-0.00319.1670.0370.0370.0000.0000.0000.000
64A66VAL0-0.050-0.02321.2850.8470.8470.0000.0000.0000.000
65A67VAL00.0110.00924.2520.4670.4670.0000.0000.0000.000
66A68THR0-0.063-0.01926.3250.4770.4770.0000.0000.0000.000
67A69TYR00.0610.02728.4100.3830.3830.0000.0000.0000.000
68A70ALA0-0.0110.00332.189-0.166-0.1660.0000.0000.0000.000
69A71ARG10.9920.99334.58317.67417.6740.0000.0000.0000.000
70A72LYS10.9310.94536.65214.94414.9440.0000.0000.0000.000
71A73SER0-0.089-0.05237.730-0.291-0.2910.0000.0000.0000.000
72A74ILE00.034-0.01039.1450.3730.3730.0000.0000.0000.000
73A75ALA0-0.009-0.00736.9460.2020.2020.0000.0000.0000.000
74A76GLY00.0740.05738.769-0.187-0.1870.0000.0000.0000.000
75A77PHE0-0.027-0.00938.7270.3780.3780.0000.0000.0000.000
76A78LYS10.9370.96640.60414.27514.2750.0000.0000.0000.000
77A79ILE00.014-0.00736.1080.1390.1390.0000.0000.0000.000
78A80ARG10.9450.99739.85014.99914.9990.0000.0000.0000.000
79A81GLU-1-0.802-0.88738.350-15.577-15.5770.0000.0000.0000.000
80A82GLY00.0300.03036.3490.2380.2380.0000.0000.0000.000
81A83TRP0-0.042-0.03735.5060.0460.0460.0000.0000.0000.000
82A84PRO00.006-0.00530.391-0.217-0.2170.0000.0000.0000.000
83A85ILE0-0.0070.00630.1350.3660.3660.0000.0000.0000.000
84A86GLY00.0470.03326.449-0.307-0.3070.0000.0000.0000.000
85A87VAL00.0260.00720.8660.2590.2590.0000.0000.0000.000
86A88LYS10.9260.96121.24024.30724.3070.0000.0000.0000.000
87A89VAL00.0740.04615.5060.3290.3290.0000.0000.0000.000
88A90THR0-0.037-0.02316.798-0.213-0.2130.0000.0000.0000.000
89A91LEU00.0180.02610.574-0.370-0.3700.0000.0000.0000.000
90A92ARG10.9950.96512.25335.54335.5430.0000.0000.0000.000
91A93SER00.016-0.0139.622-3.291-3.2910.0000.0000.0000.000
92A94ASP-1-0.826-0.9036.892-61.260-61.2600.0000.0000.0000.000
93A95ARG10.9330.9656.10740.82140.8210.0000.0000.0000.000
94A96MET0-0.0590.0048.046-3.365-3.3650.0000.0000.0000.000
98A100LEU00.0180.0046.1522.3992.3990.0000.0000.0000.000
101A103LEU00.0390.0096.3217.2727.2720.0000.0000.0000.000
102A104LEU0-0.014-0.0058.162-4.305-4.3050.0000.0000.0000.000
103A105SER0-0.022-0.0135.7335.2065.2060.0000.0000.0000.000
104A106ILE00.032-0.0026.8954.7184.7180.0000.0000.0000.000
105A107SER00.0210.0049.9073.8003.8000.0000.0000.0000.000
106A108LEU0-0.0040.00011.8303.0503.0500.0000.0000.0000.000
107A109PRO0-0.028-0.01113.2521.6791.6790.0000.0000.0000.000
108A110ARG10.8540.94412.83541.21241.2120.0000.0000.0000.000
109A111VAL0-0.0050.01916.0551.3201.3200.0000.0000.0000.000
110A112ARG10.9410.96618.34023.45923.4590.0000.0000.0000.000
111A113ASP-1-0.863-0.92421.097-25.157-25.1570.0000.0000.0000.000
112A114PHE0-0.015-0.00819.9610.3510.3510.0000.0000.0000.000
113A115ARG10.8350.91318.27826.98226.9820.0000.0000.0000.000
114A116GLY00.0400.02617.410-1.716-1.7160.0000.0000.0000.000
115A117LEU0-0.109-0.04518.3371.0061.0060.0000.0000.0000.000
116A118ASN00.0560.02120.906-0.292-0.2920.0000.0000.0000.000
117A119ALA00.0100.00923.5541.0201.0200.0000.0000.0000.000
118A120LYS10.8960.96421.63726.75326.7530.0000.0000.0000.000
119A121SER00.023-0.00624.4860.5820.5820.0000.0000.0000.000
120A122PHE0-0.033-0.00919.845-0.737-0.7370.0000.0000.0000.000
121A123ASP-1-0.739-0.85224.440-24.219-24.2190.0000.0000.0000.000
122A124GLY00.021-0.00526.315-0.305-0.3050.0000.0000.0000.000
123A125ARG10.8580.92125.81422.38622.3860.0000.0000.0000.000
124A126GLY00.0630.06822.751-0.441-0.4410.0000.0000.0000.000
125A127ASN0-0.089-0.05220.172-3.028-3.0280.0000.0000.0000.000
126A128TYR00.0610.02116.8940.5700.5700.0000.0000.0000.000
127A129SER0-0.006-0.02019.581-0.379-0.3790.0000.0000.0000.000
128A130MET0-0.027-0.00715.9481.4421.4420.0000.0000.0000.000
129A131GLY00.0990.06219.334-1.174-1.1740.0000.0000.0000.000
130A132VAL0-0.053-0.03716.9170.0090.0090.0000.0000.0000.000
131A133LYS10.8630.91320.24023.88623.8860.0000.0000.0000.000
132A134GLU-1-0.829-0.91419.938-27.058-27.0580.0000.0000.0000.000
133A135GLN0-0.012-0.01417.514-0.853-0.8530.0000.0000.0000.000
134A136ILE00.0390.02312.118-0.464-0.4640.0000.0000.0000.000
135A137ILE0-0.062-0.0368.8890.9950.9950.0000.0000.0000.000
136A138PHE0-0.007-0.00211.308-1.337-1.3370.0000.0000.0000.000
137A139PRO0-0.071-0.0477.628-1.940-1.9400.0000.0000.0000.000
138A140GLU-1-0.905-0.9389.405-42.031-42.0310.0000.0000.0000.000
139A141ILE0-0.021-0.01712.8560.2340.2340.0000.0000.0000.000
140A142ASP-1-0.813-0.91815.925-31.558-31.5580.0000.0000.0000.000
141A143TYR0-0.021-0.01813.4680.2540.2540.0000.0000.0000.000
142A144ASP-1-0.921-0.95119.384-24.407-24.4070.0000.0000.0000.000
143A145LYS10.8550.93920.43927.95827.9580.0000.0000.0000.000
144A146ILE0-0.057-0.03123.7260.5880.5880.0000.0000.0000.000
145A147ASP-1-0.831-0.91125.127-23.134-23.1340.0000.0000.0000.000
146A148ALA0-0.026-0.00927.9200.1250.1250.0000.0000.0000.000
147A149LEU00.0260.02620.916-0.307-0.3070.0000.0000.0000.000
148A150ARG10.9180.96724.77223.02623.0260.0000.0000.0000.000
149A151GLY00.0260.01122.518-0.916-0.9160.0000.0000.0000.000
150A152LEU00.000-0.01516.4850.4310.4310.0000.0000.0000.000
151A153ASP-1-0.835-0.90219.777-26.552-26.5520.0000.0000.0000.000
152A154ILE0-0.038-0.02913.709-1.651-1.6510.0000.0000.0000.000
153A155THR0-0.053-0.01516.756-0.069-0.0690.0000.0000.0000.000
154A156LEU0-0.019-0.01513.194-1.736-1.7360.0000.0000.0000.000
155A157THR0-0.035-0.02016.6811.7551.7550.0000.0000.0000.000
156A158THR00.007-0.01216.189-2.424-2.4240.0000.0000.0000.000
157A159THR0-0.018-0.01617.4630.1620.1620.0000.0000.0000.000
158A160ALA00.0170.01719.1550.4310.4310.0000.0000.0000.000
159A161ARG10.8460.94021.23926.75426.7540.0000.0000.0000.000
160A162THR0-0.006-0.02124.9270.7390.7390.0000.0000.0000.000
161A163ASP-1-0.814-0.90723.914-24.235-24.2350.0000.0000.0000.000
162A164ASP-1-0.839-0.90523.373-24.718-24.7180.0000.0000.0000.000
163A165GLU-1-0.806-0.91421.706-26.833-26.8330.0000.0000.0000.000
164A166GLY0-0.024-0.01619.387-1.890-1.8900.0000.0000.0000.000
165A167ARG10.8280.90418.90622.90222.9020.0000.0000.0000.000
166A168ALA00.0010.01919.320-0.702-0.7020.0000.0000.0000.000
167A169LEU00.0010.00013.973-2.427-2.4270.0000.0000.0000.000
168A170LEU0-0.034-0.02310.002-1.217-1.2170.0000.0000.0000.000
169A171ARG10.9830.99413.34128.13328.1330.0000.0000.0000.000
170A172ALA00.0310.01411.9460.1980.1980.0000.0000.0000.000
171A173PHE0-0.070-0.0456.625-2.746-2.7460.0000.0000.0000.000
172A174LYS10.8740.94410.44247.98247.9820.0000.0000.0000.000
173A175PHE00.0230.00113.385-0.716-0.7160.0000.0000.0000.000
174A176PRO0-0.029-0.00415.6571.1701.1700.0000.0000.0000.000
175A177PHE-1-0.855-0.92818.798-26.453-26.4530.0000.0000.0000.000