FMODB

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

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: QK3LY

Calculation Name: 2FDB-P-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 2FDB

Chain ID: P

ChEMBL ID:

UniProt ID: P55075

Base Structure: X-ray

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 197
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1875185.399599
FMO2-HF: Nuclear repulsion 1796668.266752
FMO2-HF: Total energy -78517.132847
FMO2-MP2: Total energy -78745.14315


3D Structure
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:2151:LYS)


Summations of interaction energy for fragment #1(A:2151:LYS)
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.
-90.999-82.41516.285-11.855-13.014-0.13
Interaction energy analysis for fragmet #1(A:2151:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.791 / q_NPA : 1.899
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].
3A2153ALA00.1190.0893.882-2.571-0.554-0.015-1.051-0.951-0.002
34A2184ASN0-0.095-0.0372.188-15.678-14.3956.405-2.802-4.886-0.026
35A2185PRO00.1640.0711.897-44.056-43.2997.984-4.666-4.076-0.065
36A2186MET0-0.0050.0065.0611.6311.617-0.001-0.0020.0180.000
86A2236GLU-1-0.880-0.9452.423-134.317-130.2021.912-3.250-2.777-0.037
87A2237TYR0-0.020-0.0033.7701.1351.5610.000-0.084-0.3420.000
4A2154PRO0-0.009-0.0066.578-1.900-1.9000.0000.0000.0000.000
5A2155TYR0-0.047-0.0227.302-0.345-0.3450.0000.0000.0000.000
6A2156TRP00.0620.01311.553-0.791-0.7910.0000.0000.0000.000
7A2157THR0-0.049-0.04311.710-0.227-0.2270.0000.0000.0000.000
8A2158ASN0-0.004-0.02014.3962.1542.1540.0000.0000.0000.000
9A2159THR00.1030.03818.0230.0930.0930.0000.0000.0000.000
10A2160GLU-1-0.913-0.93220.317-23.480-23.4800.0000.0000.0000.000
11A2161LYS10.8600.91721.90925.75225.7520.0000.0000.0000.000
12A2162MET0-0.0280.00418.9340.2120.2120.0000.0000.0000.000
13A2163GLU-1-0.769-0.86923.635-24.804-24.8040.0000.0000.0000.000
14A2164LYS10.8670.95825.88621.03321.0330.0000.0000.0000.000
15A2165ARG10.8680.89623.57624.87624.8760.0000.0000.0000.000
16A2166LEU00.0140.01228.774-0.006-0.0060.0000.0000.0000.000
17A2167HIS0-0.013-0.01428.3210.5690.5690.0000.0000.0000.000
18A2168ALA00.0650.04133.2570.1220.1220.0000.0000.0000.000
19A2169VAL0-0.069-0.03535.268-0.165-0.1650.0000.0000.0000.000
20A2170PRO00.0080.01038.2770.2600.2600.0000.0000.0000.000
21A2171ALA00.0340.01139.844-0.469-0.4690.0000.0000.0000.000
22A2172ALA00.0050.00140.9390.1020.1020.0000.0000.0000.000
23A2173ASN0-0.0030.00536.8350.0990.0990.0000.0000.0000.000
24A2174THR0-0.019-0.00932.2890.0050.0050.0000.0000.0000.000
25A2175VAL0-0.0040.01430.489-0.118-0.1180.0000.0000.0000.000
26A2176LYS10.8660.92925.49323.05823.0580.0000.0000.0000.000
27A2177PHE00.0180.03125.200-0.144-0.1440.0000.0000.0000.000
28A2178ARG10.8290.89419.23428.65828.6580.0000.0000.0000.000
29A2179CYS0-0.0310.00018.5951.1461.1460.0000.0000.0000.000
30A2180PRO00.0020.00016.957-1.669-1.6690.0000.0000.0000.000
31A2181ALA00.0510.04412.605-0.402-0.4020.0000.0000.0000.000
32A2182GLY00.0090.0149.5490.0820.0820.0000.0000.0000.000
33A2183GLY00.0330.0016.3942.6722.6720.0000.0000.0000.000
37A2187PRO0-0.0360.0008.1361.5741.5740.0000.0000.0000.000
38A2188THR0-0.0020.0039.6703.8473.8470.0000.0000.0000.000
39A2189MET00.0000.01213.079-0.160-0.1600.0000.0000.0000.000
40A2190ARG10.8290.89715.82434.20034.2000.0000.0000.0000.000
41A2191TRP00.028-0.02419.327-0.132-0.1320.0000.0000.0000.000
42A2192LEU0-0.034-0.00522.3600.5650.5650.0000.0000.0000.000
43A2193LYS10.9400.98525.20318.14918.1490.0000.0000.0000.000
44A2194ASN0-0.007-0.01728.910-0.041-0.0410.0000.0000.0000.000
45A2195GLY00.0320.02526.4270.3060.3060.0000.0000.0000.000
46A2196LYS10.9240.95826.83919.98119.9810.0000.0000.0000.000
47A2197GLU-1-0.849-0.92324.817-22.925-22.9250.0000.0000.0000.000
48A2198PHE0-0.006-0.00325.9550.9290.9290.0000.0000.0000.000
49A2199LYS10.8900.94927.23619.92019.9200.0000.0000.0000.000
50A2200GLN00.0280.00728.1890.7380.7380.0000.0000.0000.000
51A2201GLU-1-0.828-0.92931.774-18.379-18.3790.0000.0000.0000.000
52A2202HIS0-0.053-0.01930.8030.0740.0740.0000.0000.0000.000
53A2203ARG10.7370.83833.05517.93817.9380.0000.0000.0000.000
54A2204ILE00.0510.02836.183-0.141-0.1410.0000.0000.0000.000
55A2205GLY00.0000.00137.006-0.121-0.1210.0000.0000.0000.000
56A2206GLY00.0080.03033.245-0.389-0.3890.0000.0000.0000.000
57A2207TYR0-0.095-0.07325.523-0.296-0.2960.0000.0000.0000.000
58A2208LYS10.8700.92328.12619.01119.0110.0000.0000.0000.000
59A2209VAL00.0450.00922.465-0.279-0.2790.0000.0000.0000.000
60A2210ARG10.8220.88922.50925.83325.8330.0000.0000.0000.000
61A2211ASN00.0620.01917.215-0.246-0.2460.0000.0000.0000.000
62A2212GLN00.0460.03416.893-0.693-0.6930.0000.0000.0000.000
63A2213HIS-1-0.818-0.90417.582-26.918-26.9180.0000.0000.0000.000
64A2214TRP00.0450.02712.2571.4141.4140.0000.0000.0000.000
65A2215SER0-0.020-0.01918.8610.9380.9380.0000.0000.0000.000
66A2216LEU00.0360.04522.625-0.082-0.0820.0000.0000.0000.000
67A2217ILE0-0.041-0.03625.0380.2060.2060.0000.0000.0000.000
68A2218MET00.0250.02628.6470.1690.1690.0000.0000.0000.000
69A2219GLU-1-0.811-0.88731.903-18.781-18.7810.0000.0000.0000.000
70A2220SER00.0330.01834.9150.3450.3450.0000.0000.0000.000
71A2221VAL0-0.045-0.01734.5200.1490.1490.0000.0000.0000.000
72A2222VAL00.0650.02737.6130.4810.4810.0000.0000.0000.000
73A2223PRO00.0550.00939.072-0.399-0.3990.0000.0000.0000.000
74A2224SER00.0310.02338.958-0.021-0.0210.0000.0000.0000.000
75A2225ASP-1-0.809-0.88334.835-17.759-17.7590.0000.0000.0000.000
76A2226LYS10.8290.93434.53614.82614.8260.0000.0000.0000.000
77A2227GLY0-0.0050.00633.7530.0900.0900.0000.0000.0000.000
78A2228ASN0-0.0090.00729.007-0.196-0.1960.0000.0000.0000.000
79A2229TYR0-0.018-0.04026.888-0.045-0.0450.0000.0000.0000.000
80A2230THR00.0160.01621.729-0.095-0.0950.0000.0000.0000.000
81A2231CYS0-0.0050.02818.719-0.077-0.0770.0000.0000.0000.000
82A2232VAL00.000-0.00915.9840.0150.0150.0000.0000.0000.000
83A2233VAL0-0.006-0.00611.973-0.072-0.0720.0000.0000.0000.000
84A2234GLU-1-0.755-0.83310.692-37.946-37.9460.0000.0000.0000.000
85A2235ASN0-0.052-0.0484.8661.9401.9400.0000.0000.0000.000
88A2238GLY00.0450.0165.8122.9742.9740.0000.0000.0000.000
89A2239SER0-0.036-0.0519.495-1.002-1.0020.0000.0000.0000.000
90A2240ILE0-0.0230.00912.2861.0521.0520.0000.0000.0000.000
91A2241ASN0-0.023-0.02714.7201.3421.3420.0000.0000.0000.000
92A2242HIS00.0290.00918.176-0.789-0.7890.0000.0000.0000.000
93A2243THR0-0.049-0.02921.076-0.024-0.0240.0000.0000.0000.000
94A2244TYR0-0.057-0.03723.4800.1970.1970.0000.0000.0000.000
95A2245HIS0-0.019-0.02827.392-0.105-0.1050.0000.0000.0000.000
96A2246LEU0-0.037-0.01031.103-0.090-0.0900.0000.0000.0000.000
97A2247ASP-1-0.801-0.90033.342-15.697-15.6970.0000.0000.0000.000
98A2248VAL0-0.001-0.00137.068-0.173-0.1730.0000.0000.0000.000
99A2249VAL0-0.008-0.00939.5190.3400.3400.0000.0000.0000.000
100A2250GLU-1-0.838-0.92743.083-14.201-14.2010.0000.0000.0000.000
101A2251ARG10.7630.83944.85013.98513.9850.0000.0000.0000.000
102A2252SER00.0220.00847.7060.1220.1220.0000.0000.0000.000
103A2253ARG10.9550.97747.96712.84512.8450.0000.0000.0000.000
104A2254HIS0-0.035-0.02452.0330.1680.1680.0000.0000.0000.000
105A2255ARG10.9551.00155.76610.13710.1370.0000.0000.0000.000
106A2256PRO0-0.0060.00558.812-0.072-0.0720.0000.0000.0000.000
107A2257ILE00.000-0.00357.8880.1670.1670.0000.0000.0000.000
108A2258LEU00.0180.01661.206-0.087-0.0870.0000.0000.0000.000
109A2259GLN00.0350.01662.7770.1000.1000.0000.0000.0000.000
110A2260ALA00.0220.00264.7610.1340.1340.0000.0000.0000.000
111A2261GLY00.0060.00267.5800.0060.0060.0000.0000.0000.000
112A2262LEU0-0.0510.00366.6630.0850.0850.0000.0000.0000.000
113A2263PRO00.012-0.00569.133-0.128-0.1280.0000.0000.0000.000
114A2264ALA00.0370.02272.0090.0380.0380.0000.0000.0000.000
115A2265ASN00.008-0.01374.6390.0050.0050.0000.0000.0000.000
116A2266ALA00.0340.03078.365-0.016-0.0160.0000.0000.0000.000
117A2267SER0-0.041-0.04280.2370.1070.1070.0000.0000.0000.000
118A2268THR0-0.020-0.00483.580-0.060-0.0600.0000.0000.0000.000
119A2269VAL00.0190.02285.7710.0450.0450.0000.0000.0000.000
120A2270VAL00.020-0.00387.983-0.095-0.0950.0000.0000.0000.000
121A2271GLY0-0.039-0.01188.4370.0490.0490.0000.0000.0000.000
122A2272GLY0-0.0340.00185.911-0.036-0.0360.0000.0000.0000.000
123A2273ASP-1-0.872-0.94280.441-7.942-7.9420.0000.0000.0000.000
124A2274VAL0-0.031-0.02278.8820.0030.0030.0000.0000.0000.000
125A2275GLU-1-0.882-0.93772.759-8.925-8.9250.0000.0000.0000.000
126A2276PHE0-0.020-0.00173.7820.0170.0170.0000.0000.0000.000
127A2277VAL00.0190.01267.623-0.107-0.1070.0000.0000.0000.000
128A2278CYS0-0.059-0.04166.9630.0150.0150.0000.0000.0000.000
129A2279LYS10.8890.94462.4509.8179.8170.0000.0000.0000.000
130A2280VAL00.0220.00960.3030.0460.0460.0000.0000.0000.000
131A2281TYR00.0330.01956.685-0.072-0.0720.0000.0000.0000.000
132A2282SER0-0.023-0.04556.1670.1270.1270.0000.0000.0000.000
133A2283ASP-1-0.760-0.80949.569-13.306-13.3060.0000.0000.0000.000
134A2284ALA00.0090.00052.459-0.080-0.0800.0000.0000.0000.000
135A2285GLN00.0410.02453.3830.0450.0450.0000.0000.0000.000
136A2286PRO0-0.024-0.00655.3750.0880.0880.0000.0000.0000.000
137A2287HIS00.0110.01359.154-0.088-0.0880.0000.0000.0000.000
138A2288ILE00.013-0.01462.1280.0210.0210.0000.0000.0000.000
139A2289GLN0-0.034-0.01565.3510.1150.1150.0000.0000.0000.000
140A2290TRP00.0270.00568.4410.0820.0820.0000.0000.0000.000
141A2291ILE0-0.022-0.02371.6000.0670.0670.0000.0000.0000.000
142A2292LYS10.9160.98775.1927.8977.8970.0000.0000.0000.000
143A2293HIS10.8180.88976.4018.3708.3700.0000.0000.0000.000
144A2294VAL00.0290.01880.7930.0950.0950.0000.0000.0000.000
145A2308TYR10.8530.91881.0297.9297.9290.0000.0000.0000.000
146A2309LEU00.0680.03975.4600.0310.0310.0000.0000.0000.000
147A2310LYS11.0131.01278.3128.0488.0480.0000.0000.0000.000
148A2311VAL00.0020.00571.778-0.022-0.0220.0000.0000.0000.000
149A2312LEU0-0.018-0.00874.1580.1050.1050.0000.0000.0000.000
150A2313LYS10.8790.92767.0699.4599.4590.0000.0000.0000.000
151A2314ALA00.0350.03669.5830.1000.1000.0000.0000.0000.000
152A2315ALA00.0090.01168.539-0.095-0.0950.0000.0000.0000.000
153A2316GLY00.023-0.00165.0730.0230.0230.0000.0000.0000.000
154A2317VAL0-0.048-0.01759.762-0.029-0.0290.0000.0000.0000.000
155A2318ASN0-0.012-0.01654.945-0.125-0.1250.0000.0000.0000.000
156A2319THR0-0.069-0.05555.8450.0060.0060.0000.0000.0000.000
157A2320THR00.009-0.01149.840-0.009-0.0090.0000.0000.0000.000
158A2321ASP-1-0.884-0.93151.852-11.876-11.8760.0000.0000.0000.000
159A2322LYS10.8460.92053.91911.22111.2210.0000.0000.0000.000
160A2323GLU-1-0.810-0.86557.154-11.305-11.3050.0000.0000.0000.000
161A2324ILE0-0.043-0.03059.9490.1170.1170.0000.0000.0000.000
162A2325GLU-1-0.867-0.93363.114-9.837-9.8370.0000.0000.0000.000
163A2326VAL00.011-0.00566.3720.0430.0430.0000.0000.0000.000
164A2327LEU0-0.0070.00569.9000.0050.0050.0000.0000.0000.000
165A2328TYR0-0.046-0.03671.4350.0250.0250.0000.0000.0000.000
166A2329ILE0-0.038-0.01975.7080.0050.0050.0000.0000.0000.000
167A2330ARG10.9580.96878.8978.1518.1510.0000.0000.0000.000
168A2331ASN0-0.038-0.01281.9010.0770.0770.0000.0000.0000.000
169A2332VAL0-0.0230.00483.0850.0420.0420.0000.0000.0000.000
170A2333THR00.004-0.02585.6530.1390.1390.0000.0000.0000.000
171A2334PHE00.036-0.01387.643-0.058-0.0580.0000.0000.0000.000
172A2335GLU-1-0.945-0.95586.742-7.432-7.4320.0000.0000.0000.000
173A2336ASP-1-0.869-0.90783.379-7.826-7.8260.0000.0000.0000.000
174A2337ALA00.0620.04983.546-0.119-0.1190.0000.0000.0000.000
175A2338GLY0-0.023-0.01784.044-0.001-0.0010.0000.0000.0000.000
176A2339GLU-1-0.861-0.91478.032-8.388-8.3880.0000.0000.0000.000
177A2340TYR0-0.036-0.04976.146-0.036-0.0360.0000.0000.0000.000
178A2341THR0-0.032-0.01471.927-0.011-0.0110.0000.0000.0000.000
179A2342CYS00.0080.03268.287-0.068-0.0680.0000.0000.0000.000
180A2343LEU0-0.010-0.01767.461-0.026-0.0260.0000.0000.0000.000
181A2344ALA00.0490.02362.857-0.057-0.0570.0000.0000.0000.000
182A2345GLY0-0.008-0.01662.3740.0570.0570.0000.0000.0000.000
183A2346ASN00.029-0.00156.6510.0070.0070.0000.0000.0000.000
184A2347SER0-0.002-0.01153.5460.1430.1430.0000.0000.0000.000
185A2348ILE0-0.075-0.01853.275-0.094-0.0940.0000.0000.0000.000
186A2349GLY00.0180.00557.1220.1370.1370.0000.0000.0000.000
187A2350ILE00.008-0.00560.905-0.081-0.0810.0000.0000.0000.000
188A2351SER0-0.038-0.01763.8080.0700.0700.0000.0000.0000.000
189A2352PHE00.0240.00265.570-0.025-0.0250.0000.0000.0000.000
190A2353HIS0-0.046-0.00967.085-0.007-0.0070.0000.0000.0000.000
191A2354SER0-0.032-0.03870.958-0.050-0.0500.0000.0000.0000.000
192A2355ALA0-0.0030.03174.6470.0010.0010.0000.0000.0000.000
193A2356TRP00.006-0.01676.7520.0890.0890.0000.0000.0000.000
194A2357LEU0-0.0110.00780.505-0.045-0.0450.0000.0000.0000.000
195A2358THR0-0.032-0.01682.4110.0890.0890.0000.0000.0000.000
196A2359VAL0-0.007-0.01985.738-0.058-0.0580.0000.0000.0000.000
197A2360LEU-1-0.863-0.91788.220-7.008-7.0080.0000.0000.0000.000