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: 4YYZN

Calculation Name: 2QQ1-D-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2QQ1

Chain ID: D

ChEMBL ID:

UniProt ID: O66472

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 175
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1771591.179671
FMO2-HF: Nuclear repulsion 1704750.964248
FMO2-HF: Total energy -66840.215423
FMO2-MP2: Total energy -67032.955541


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:4:LYS)


Summations of interaction energy for fragment #1(A:4: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.
-277.277-275.13122.777-12.718-12.206-0.157
Interaction energy analysis for fragmet #1(A:4:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.691 / q_NPA : 1.819
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].
3A6ALA00.0720.0273.078-7.824-5.0570.090-1.384-1.473-0.009
67A70SER00.003-0.0094.688-7.674-7.563-0.001-0.003-0.1070.000
125A128SER0-0.049-0.0274.2243.4333.531-0.001-0.014-0.0830.000
157A160GLY00.0180.0163.904-2.308-1.8520.002-0.249-0.209-0.001
158A161GLY00.0460.0221.814-48.973-50.26711.679-5.881-4.504-0.075
159A162ALA0-0.079-0.0421.851-46.827-46.14210.878-6.210-5.353-0.070
160A163TYR0-0.032-0.0202.94812.03211.3550.1301.023-0.477-0.002
4A7VAL00.0330.0105.4644.9744.9740.0000.0000.0000.000
5A8ILE00.0010.0018.059-2.089-2.0890.0000.0000.0000.000
6A9GLY00.0510.03111.2412.2662.2660.0000.0000.0000.000
7A10VAL0-0.058-0.03113.9720.5900.5900.0000.0000.0000.000
8A11VAL00.0260.01017.5540.8390.8390.0000.0000.0000.000
9A12THR0-0.035-0.04320.4240.2410.2410.0000.0000.0000.000
10A13ILE0-0.0060.00322.0550.4000.4000.0000.0000.0000.000
11A14SER0-0.009-0.01725.9390.9440.9440.0000.0000.0000.000
12A15ASP-1-0.774-0.85329.699-18.653-18.6530.0000.0000.0000.000
13A16ARG10.8750.93832.57016.96016.9600.0000.0000.0000.000
14A17ALA00.0510.02328.6640.2970.2970.0000.0000.0000.000
15A18SER00.0290.01729.4480.0370.0370.0000.0000.0000.000
16A19LYS10.8410.91930.37017.48117.4810.0000.0000.0000.000
17A20GLY00.0580.04031.8530.3180.3180.0000.0000.0000.000
18A21ILE0-0.075-0.03532.7520.2920.2920.0000.0000.0000.000
19A22TYR0-0.028-0.02533.9350.4760.4760.0000.0000.0000.000
20A23GLU-1-0.805-0.87630.040-20.255-20.2550.0000.0000.0000.000
21A24ASP-1-0.731-0.81725.106-23.603-23.6030.0000.0000.0000.000
22A25ILE00.010-0.01327.288-0.599-0.5990.0000.0000.0000.000
23A26SER0-0.051-0.02826.528-0.140-0.1400.0000.0000.0000.000
24A27GLY00.0540.00922.534-0.806-0.8060.0000.0000.0000.000
25A28LYS10.8290.89421.82920.72620.7260.0000.0000.0000.000
26A29ALA00.0280.02023.182-0.547-0.5470.0000.0000.0000.000
27A30ILE0-0.020-0.00518.485-0.525-0.5250.0000.0000.0000.000
28A31ILE00.000-0.00518.202-1.276-1.2760.0000.0000.0000.000
29A32ASP-1-0.868-0.94219.244-26.903-26.9030.0000.0000.0000.000
30A33TYR0-0.038-0.04319.131-0.554-0.5540.0000.0000.0000.000
31A34LEU0-0.025-0.01814.414-0.779-0.7790.0000.0000.0000.000
32A35LYS10.8740.93616.89027.44427.4440.0000.0000.0000.000
33A36ASP-1-0.864-0.89518.656-26.424-26.4240.0000.0000.0000.000
34A37VAL00.000-0.00216.8900.0160.0160.0000.0000.0000.000
35A38ILE0-0.045-0.01012.291-0.985-0.9850.0000.0000.0000.000
36A39ILE0-0.020-0.00213.9660.9210.9210.0000.0000.0000.000
37A40THR0-0.078-0.0138.321-0.569-0.5690.0000.0000.0000.000
38A41PRO00.010-0.0077.6201.5301.5300.0000.0000.0000.000
39A42PHE0-0.037-0.0348.445-6.911-6.9110.0000.0000.0000.000
40A43GLU-1-0.880-0.9319.187-41.013-41.0130.0000.0000.0000.000
41A44VAL0-0.036-0.03111.071-0.996-0.9960.0000.0000.0000.000
42A45GLU-1-0.797-0.89212.073-36.911-36.9110.0000.0000.0000.000
43A46TYR0-0.070-0.06214.5690.7640.7640.0000.0000.0000.000
44A47ARG10.7600.85115.91533.21533.2150.0000.0000.0000.000
45A48VAL0-0.012-0.00220.7580.1880.1880.0000.0000.0000.000
46A49ILE00.0080.01722.7360.1830.1830.0000.0000.0000.000
47A50PRO00.0110.00526.2510.2610.2610.0000.0000.0000.000
48A51ASP0-0.096-0.09227.726-0.654-0.6540.0000.0000.0000.000
49A52GLU-1-0.899-0.95428.591-19.180-19.1800.0000.0000.0000.000
50A53ARG10.8260.87026.09221.44921.4490.0000.0000.0000.000
51A54ASP-1-0.806-0.89325.384-23.015-23.0150.0000.0000.0000.000
52A55LEU00.0540.03624.389-1.037-1.0370.0000.0000.0000.000
53A56ILE0-0.0010.00921.880-1.186-1.1860.0000.0000.0000.000
54A57GLU-1-0.807-0.87920.755-25.459-25.4590.0000.0000.0000.000
55A58LYS10.8690.91919.51822.10322.1030.0000.0000.0000.000
56A59THR00.010-0.00218.657-1.251-1.2510.0000.0000.0000.000
57A60LEU0-0.042-0.03016.338-1.965-1.9650.0000.0000.0000.000
58A61ILE0-0.0010.00514.731-2.442-2.4420.0000.0000.0000.000
59A62GLU-1-0.852-0.90214.342-34.174-34.1740.0000.0000.0000.000
60A63LEU00.002-0.01213.232-2.632-2.6320.0000.0000.0000.000
61A64ALA00.0160.00110.177-4.171-4.1710.0000.0000.0000.000
62A65ASP-1-0.813-0.8759.437-44.339-44.3390.0000.0000.0000.000
63A66GLU-1-0.958-0.97511.137-35.617-35.6170.0000.0000.0000.000
64A67LYS10.8660.94110.70134.78834.7880.0000.0000.0000.000
65A68GLY00.0010.0187.015-5.016-5.0160.0000.0000.0000.000
66A69CYS0-0.094-0.0436.139-7.221-7.2210.0000.0000.0000.000
68A71LEU0-0.029-0.0047.0142.4552.4550.0000.0000.0000.000
69A72ILE00.0160.01110.7800.3420.3420.0000.0000.0000.000
70A73LEU0-0.0070.00313.9241.4261.4260.0000.0000.0000.000
71A74THR00.0480.03317.2840.5850.5850.0000.0000.0000.000
72A75THR0-0.033-0.02620.5040.7970.7970.0000.0000.0000.000
73A76GLY00.0380.02624.0890.2970.2970.0000.0000.0000.000
74A77GLY00.0700.04426.215-0.652-0.6520.0000.0000.0000.000
75A78THR00.002-0.00625.415-0.055-0.0550.0000.0000.0000.000
76A79GLY00.0130.01128.5660.0840.0840.0000.0000.0000.000
77A80PRO00.007-0.01732.305-0.202-0.2020.0000.0000.0000.000
78A81ALA0-0.035-0.00234.7750.4720.4720.0000.0000.0000.000
79A82PRO00.028-0.00634.334-0.432-0.4320.0000.0000.0000.000
80A83ARG10.9560.98833.23816.84416.8440.0000.0000.0000.000
81A84ASP-1-0.920-0.94830.476-19.563-19.5630.0000.0000.0000.000
82A85VAL00.0190.00627.941-0.074-0.0740.0000.0000.0000.000
83A86THR00.003-0.01622.896-0.505-0.5050.0000.0000.0000.000
84A87PRO0-0.0190.00623.439-1.026-1.0260.0000.0000.0000.000
85A88GLU-1-0.770-0.86123.861-21.517-21.5170.0000.0000.0000.000
86A89ALA00.0050.00122.803-0.232-0.2320.0000.0000.0000.000
87A90THR00.004-0.00918.569-1.433-1.4330.0000.0000.0000.000
88A91GLU-1-0.883-0.97419.651-26.050-26.0500.0000.0000.0000.000
89A92ALA0-0.045-0.00521.216-0.444-0.4440.0000.0000.0000.000
90A93VAL0-0.027-0.00217.147-0.345-0.3450.0000.0000.0000.000
91A94CYS0-0.059-0.01116.091-2.806-2.8060.0000.0000.0000.000
92A95GLU-1-0.868-0.91813.120-39.214-39.2140.0000.0000.0000.000
93A96LYS10.9080.93614.81534.09334.0930.0000.0000.0000.000
94A97MET00.0280.05016.875-1.790-1.7900.0000.0000.0000.000
95A98LEU0-0.032-0.02514.6230.0850.0850.0000.0000.0000.000
96A99PRO00.0190.01819.3050.1290.1290.0000.0000.0000.000
97A100GLY00.0660.02822.3810.5250.5250.0000.0000.0000.000
98A101PHE00.013-0.00515.5320.2380.2380.0000.0000.0000.000
99A102GLY00.0300.01521.5030.5690.5690.0000.0000.0000.000
100A103GLU-1-0.945-0.98024.476-21.684-21.6840.0000.0000.0000.000
101A104LEU00.0130.01822.2540.8980.8980.0000.0000.0000.000
102A105MET0-0.005-0.00322.0160.4790.4790.0000.0000.0000.000
103A106ARG10.8550.93925.88722.33222.3320.0000.0000.0000.000
104A107GLN00.000-0.00928.8930.6900.6900.0000.0000.0000.000
105A108VAL0-0.057-0.02826.6330.7460.7460.0000.0000.0000.000
106A109SER00.010-0.01028.9870.4600.4600.0000.0000.0000.000
107A110LEU0-0.027-0.01931.3610.6280.6280.0000.0000.0000.000
108A111LYS10.9120.96631.64619.63519.6350.0000.0000.0000.000
109A112GLN0-0.035-0.00731.786-0.085-0.0850.0000.0000.0000.000
110A113VAL00.003-0.00935.3280.5470.5470.0000.0000.0000.000
111A114PRO00.0720.02836.636-0.373-0.3730.0000.0000.0000.000
112A115THR00.004-0.00737.802-0.177-0.1770.0000.0000.0000.000
113A116ALA00.0050.02332.704-0.253-0.2530.0000.0000.0000.000
114A117ILE0-0.009-0.00932.803-0.587-0.5870.0000.0000.0000.000
115A118LEU0-0.028-0.01234.339-0.014-0.0140.0000.0000.0000.000
116A119SER0-0.054-0.01828.782-0.287-0.2870.0000.0000.0000.000
117A120ARG10.8360.88229.10319.80619.8060.0000.0000.0000.000
118A121GLN0-0.022-0.01624.3590.3770.3770.0000.0000.0000.000
119A122THR00.0150.01721.6920.2900.2900.0000.0000.0000.000
120A123ALA00.002-0.01217.518-0.537-0.5370.0000.0000.0000.000
121A124GLY00.0360.01716.5981.3891.3890.0000.0000.0000.000
122A125ILE0-0.046-0.01710.681-1.576-1.5760.0000.0000.0000.000
123A126ARG10.8280.86911.73239.55839.5580.0000.0000.0000.000
124A127GLY00.0410.0179.431-3.188-3.1880.0000.0000.0000.000
126A129CYS0-0.045-0.0076.291-5.350-5.3500.0000.0000.0000.000
127A130LEU0-0.016-0.0039.0024.1994.1990.0000.0000.0000.000
128A131ILE00.0350.00811.6510.0610.0610.0000.0000.0000.000
129A132VAL00.008-0.00515.0661.4371.4370.0000.0000.0000.000
130A133ASN0-0.021-0.02518.0860.9090.9090.0000.0000.0000.000
131A134LEU00.0410.01219.5580.6980.6980.0000.0000.0000.000
132A135PRO00.0000.00523.3970.7100.7100.0000.0000.0000.000
133A136GLY00.0670.03426.345-0.494-0.4940.0000.0000.0000.000
134A137LYS10.9590.98528.87117.56717.5670.0000.0000.0000.000
135A138PRO00.0900.04127.502-0.326-0.3260.0000.0000.0000.000
136A139GLN00.0410.02327.506-0.960-0.9600.0000.0000.0000.000
137A140SER0-0.045-0.02928.9660.0250.0250.0000.0000.0000.000
138A141ILE0-0.022-0.00622.968-0.409-0.4090.0000.0000.0000.000
139A142LYS10.9170.94723.96122.11622.1160.0000.0000.0000.000
140A143VAL00.0080.01124.524-0.637-0.6370.0000.0000.0000.000
141A144CYS0-0.036-0.01522.819-0.156-0.1560.0000.0000.0000.000
142A145LEU0-0.002-0.00118.592-0.912-0.9120.0000.0000.0000.000
143A146ASP-1-0.791-0.87020.797-25.517-25.5170.0000.0000.0000.000
144A147ALA0-0.042-0.00522.930-0.077-0.0770.0000.0000.0000.000
145A148VAL0-0.006-0.01118.767-0.509-0.5090.0000.0000.0000.000
146A149MET00.0060.00615.283-2.698-2.6980.0000.0000.0000.000
147A150PRO00.004-0.00116.169-2.090-2.0900.0000.0000.0000.000
148A151ALA00.0100.01015.949-0.929-0.9290.0000.0000.0000.000
149A152ILE0-0.016-0.00212.376-2.208-2.2080.0000.0000.0000.000
150A153PRO00.0210.00310.293-3.301-3.3010.0000.0000.0000.000
151A154TYR00.0800.0499.192-4.997-4.9970.0000.0000.0000.000
152A155CYS0-0.046-0.02010.217-1.812-1.8120.0000.0000.0000.000
153A156ILE00.0550.0235.886-2.080-2.0800.0000.0000.0000.000
154A157ASP-1-0.826-0.8855.594-72.333-72.3330.0000.0000.0000.000
155A158LEU0-0.096-0.0496.312-4.248-4.2480.0000.0000.0000.000
156A159ILE0-0.0440.0116.4381.6571.6570.0000.0000.0000.000
161A164ILE00.0400.0236.1293.0113.0110.0000.0000.0000.000
162A165ASP-1-0.815-0.9269.032-43.320-43.3200.0000.0000.0000.000
163A166THR0-0.006-0.02812.488-0.364-0.3640.0000.0000.0000.000
164A167ASP-1-0.758-0.87116.076-27.723-27.7230.0000.0000.0000.000
165A168PRO00.0060.00919.1991.1131.1130.0000.0000.0000.000
166A169ASN0-0.090-0.05321.4352.0962.0960.0000.0000.0000.000
167A170LYS10.7320.86521.78328.47028.4700.0000.0000.0000.000
168A171VAL00.0340.00318.5780.7030.7030.0000.0000.0000.000
169A172LYS10.8650.94019.30224.74624.7460.0000.0000.0000.000
170A173ALA00.0390.03113.7680.4560.4560.0000.0000.0000.000
171A174PHE0-0.015-0.01315.877-0.118-0.1180.0000.0000.0000.000
172A175ARG10.7820.8448.63452.57952.5790.0000.0000.0000.000
173A176PRO0-0.0220.01414.8350.4410.4410.0000.0000.0000.000
174A177LYS10.8370.90411.60643.87543.8750.0000.0000.0000.000
175A178LYS00.0560.04615.6966.0826.0820.0000.0000.0000.000