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: 4YL4N

Calculation Name: 2D86-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D86

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UKW4

Base Structure: SolutionNMR

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 143
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1317838.118794
FMO2-HF: Nuclear repulsion 1260494.615989
FMO2-HF: Total energy -57343.502805
FMO2-MP2: Total energy -57506.520565


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:1:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
18.77119.638-0.007-0.256-0.6040
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.869 / q_NPA : 0.917
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].
3A3SER00.0300.0063.8233.5474.414-0.007-0.256-0.6040.000
4A4GLY00.0300.0226.2451.8811.8810.0000.0000.0000.000
5A5SER0-0.007-0.0039.359-0.205-0.2050.0000.0000.0000.000
6A6SER0-0.015-0.01111.8710.9630.9630.0000.0000.0000.000
7A7GLY00.0400.01815.6990.4420.4420.0000.0000.0000.000
8A8MET0-0.024-0.00317.018-0.281-0.2810.0000.0000.0000.000
9A9GLU-1-0.823-0.90711.994-25.694-25.6940.0000.0000.0000.000
10A10PRO00.0430.01015.0850.9180.9180.0000.0000.0000.000
11A11TRP0-0.051-0.04413.6231.6401.6400.0000.0000.0000.000
12A12LYS10.8840.96716.30919.32419.3240.0000.0000.0000.000
13A13GLN00.0130.00219.0611.3341.3340.0000.0000.0000.000
14A14CYS0-0.010-0.00119.7830.7350.7350.0000.0000.0000.000
15A15ALA00.0080.00619.9640.5970.5970.0000.0000.0000.000
16A16GLN00.0150.00721.8600.3730.3730.0000.0000.0000.000
17A17TRP00.0470.02225.0150.3460.3460.0000.0000.0000.000
18A18LEU00.0390.01321.6410.4690.4690.0000.0000.0000.000
19A19ILE0-0.0170.00024.9130.4350.4350.0000.0000.0000.000
20A20HIS0-0.032-0.01327.8590.6460.6460.0000.0000.0000.000
21A21CYS0-0.048-0.02828.5190.4990.4990.0000.0000.0000.000
22A22LYS10.8490.92730.5499.6339.6330.0000.0000.0000.000
23A23VAL00.0240.03526.0010.0810.0810.0000.0000.0000.000
24A24LEU0-0.021-0.01022.494-0.313-0.3130.0000.0000.0000.000
25A25PRO00.0260.01326.1100.3530.3530.0000.0000.0000.000
26A26THR00.031-0.01427.098-0.457-0.4570.0000.0000.0000.000
27A27ASN00.0130.01427.109-0.173-0.1730.0000.0000.0000.000
28A28HIS00.0240.02221.9260.0160.0160.0000.0000.0000.000
29A29ARG10.9200.94816.22617.48717.4870.0000.0000.0000.000
30A30VAL0-0.027-0.01918.081-0.478-0.4780.0000.0000.0000.000
31A31THR0-0.043-0.03219.376-0.388-0.3880.0000.0000.0000.000
32A32TRP0-0.0010.01819.6880.1000.1000.0000.0000.0000.000
33A33ASP-1-0.865-0.93018.596-16.788-16.7880.0000.0000.0000.000
34A34SER00.007-0.02715.861-1.151-1.1510.0000.0000.0000.000
35A35ALA0-0.0490.01514.598-1.205-1.2050.0000.0000.0000.000
36A36GLN00.003-0.0258.795-1.339-1.3390.0000.0000.0000.000
37A37VAL00.0370.0109.1971.3621.3620.0000.0000.0000.000
38A38PHE00.0320.0188.8041.3461.3460.0000.0000.0000.000
39A39ASP-1-0.786-0.88511.445-19.751-19.7510.0000.0000.0000.000
40A40LEU0-0.021-0.01714.9221.3771.3770.0000.0000.0000.000
41A41ALA00.0260.01513.1071.0731.0730.0000.0000.0000.000
42A42GLN0-0.032-0.02413.0031.8491.8490.0000.0000.0000.000
43A43THR0-0.063-0.02316.3271.0991.0990.0000.0000.0000.000
44A44LEU0-0.006-0.01218.6650.9950.9950.0000.0000.0000.000
45A45ARG10.9330.99515.45218.99618.9960.0000.0000.0000.000
46A46ASP-1-0.841-0.95118.542-14.166-14.1660.0000.0000.0000.000
47A47GLY00.005-0.00921.8070.6830.6830.0000.0000.0000.000
48A48VAL0-0.039-0.02123.6440.4570.4570.0000.0000.0000.000
49A49LEU00.0220.01423.0580.3600.3600.0000.0000.0000.000
50A50LEU00.0080.00221.5060.2960.2960.0000.0000.0000.000
51A51CYS0-0.044-0.01925.3770.3950.3950.0000.0000.0000.000
52A52GLN0-0.015-0.00428.6070.1260.1260.0000.0000.0000.000
53A53LEU00.0540.03225.8440.3050.3050.0000.0000.0000.000
54A54LEU00.009-0.00729.2900.2950.2950.0000.0000.0000.000
55A55ASN0-0.033-0.01131.7050.3920.3920.0000.0000.0000.000
56A56ASN0-0.046-0.01231.7730.0560.0560.0000.0000.0000.000
57A57LEU0-0.023-0.00130.3700.2060.2060.0000.0000.0000.000
58A58ARG10.9130.95534.5718.5598.5590.0000.0000.0000.000
59A59ALA00.0320.02036.901-0.127-0.1270.0000.0000.0000.000
60A60HIS0-0.027-0.03239.341-0.102-0.1020.0000.0000.0000.000
61A61SER0-0.014-0.00634.2660.0730.0730.0000.0000.0000.000
62A62ILE00.0340.02430.423-0.148-0.1480.0000.0000.0000.000
63A63ASN00.0510.04034.6930.0150.0150.0000.0000.0000.000
64A64LEU00.041-0.00233.234-0.185-0.1850.0000.0000.0000.000
65A65LYS10.9040.94534.6467.8347.8340.0000.0000.0000.000
66A66GLU-1-0.890-0.92234.567-8.687-8.6870.0000.0000.0000.000
67A67ILE0-0.045-0.02429.959-0.237-0.2370.0000.0000.0000.000
68A68ASN00.004-0.00929.0320.1270.1270.0000.0000.0000.000
69A69LEU00.0460.00628.959-0.398-0.3980.0000.0000.0000.000
70A70ARG10.9340.96828.70210.53310.5330.0000.0000.0000.000
71A71PRO00.0390.03025.2190.2720.2720.0000.0000.0000.000
72A72GLN0-0.050-0.03526.334-0.018-0.0180.0000.0000.0000.000
73A73MET00.0320.02620.605-0.291-0.2910.0000.0000.0000.000
74A74SER00.0120.01522.948-0.132-0.1320.0000.0000.0000.000
75A75GLN00.0340.01621.008-0.502-0.5020.0000.0000.0000.000
76A76PHE00.0200.00123.024-0.150-0.1500.0000.0000.0000.000
77A77LEU0-0.0120.00026.2230.1660.1660.0000.0000.0000.000
78A78CYS0-0.0160.01221.6970.0350.0350.0000.0000.0000.000
79A79LEU00.0250.00820.3300.0650.0650.0000.0000.0000.000
80A80LYS10.8700.95023.73510.25710.2570.0000.0000.0000.000
81A81ASN00.0190.01225.4290.6790.6790.0000.0000.0000.000
82A82ILE00.0170.01320.0420.2810.2810.0000.0000.0000.000
83A83ARG10.9430.96824.27611.65811.6580.0000.0000.0000.000
84A84THR0-0.0120.01326.7830.4500.4500.0000.0000.0000.000
85A85PHE00.0640.01424.6050.2350.2350.0000.0000.0000.000
86A86LEU0-0.019-0.00523.0720.3040.3040.0000.0000.0000.000
87A87THR0-0.012-0.01027.2570.2480.2480.0000.0000.0000.000
88A88ALA00.0500.02930.9420.2640.2640.0000.0000.0000.000
89A89CYS0-0.046-0.02728.2610.1390.1390.0000.0000.0000.000
90A90CYS0-0.108-0.05330.8110.0180.0180.0000.0000.0000.000
91A91GLU-1-0.882-0.94433.300-8.520-8.5200.0000.0000.0000.000
92A92THR0-0.071-0.02634.8210.3360.3360.0000.0000.0000.000
93A93PHE0-0.027-0.03633.1880.1920.1920.0000.0000.0000.000
94A94GLY00.0310.04635.0860.1690.1690.0000.0000.0000.000
95A95MET0-0.112-0.05027.792-0.030-0.0300.0000.0000.0000.000
96A96ARG10.9030.94829.44610.43910.4390.0000.0000.0000.000
97A97LYS10.9900.97428.64610.73710.7370.0000.0000.0000.000
98A98SER0-0.040-0.01525.644-0.031-0.0310.0000.0000.0000.000
99A99GLU-1-0.810-0.91623.980-11.855-11.8550.0000.0000.0000.000
100A100LEU0-0.064-0.01423.021-0.443-0.4430.0000.0000.0000.000
101A101PHE00.0110.00918.637-0.141-0.1410.0000.0000.0000.000
102A102GLU-1-0.893-0.94118.229-16.036-16.0360.0000.0000.0000.000
103A103ALA0-0.021-0.03518.742-0.698-0.6980.0000.0000.0000.000
104A104PHE00.0180.00114.905-0.027-0.0270.0000.0000.0000.000
105A105ASP-1-0.784-0.90014.398-21.626-21.6260.0000.0000.0000.000
106A106LEU0-0.044-0.01314.050-1.253-1.2530.0000.0000.0000.000
107A107PHE0-0.012-0.02315.602-0.486-0.4860.0000.0000.0000.000
108A108ASP-1-0.881-0.94812.446-25.038-25.0380.0000.0000.0000.000
109A109VAL0-0.080-0.03610.152-1.977-1.9770.0000.0000.0000.000
110A110ARG10.8910.9679.62423.00923.0090.0000.0000.0000.000
111A111ASP-1-0.807-0.8859.527-28.107-28.1070.0000.0000.0000.000
112A112PHE00.017-0.00911.6372.2512.2510.0000.0000.0000.000
113A113GLY00.0210.00512.9051.4651.4650.0000.0000.0000.000
114A114LYS10.8900.92914.70821.49121.4910.0000.0000.0000.000
115A115VAL0-0.046-0.01416.4651.2441.2440.0000.0000.0000.000
116A116ILE0-0.015-0.00815.5690.9800.9800.0000.0000.0000.000
117A117GLU-1-0.832-0.91219.112-13.556-13.5560.0000.0000.0000.000
118A118THR0-0.070-0.04321.1151.0891.0890.0000.0000.0000.000
119A119LEU0-0.038-0.02621.7290.7950.7950.0000.0000.0000.000
120A120SER00.0300.01022.7360.3800.3800.0000.0000.0000.000
121A121ARG10.9310.97024.92512.81412.8140.0000.0000.0000.000
122A122LEU0-0.010-0.00227.1330.4700.4700.0000.0000.0000.000
123A123SER0-0.022-0.01528.3870.5890.5890.0000.0000.0000.000
124A124ARG10.9971.00030.20010.23410.2340.0000.0000.0000.000
125A125THR0-0.042-0.02432.4030.4100.4100.0000.0000.0000.000
126A126PRO00.0330.00634.661-0.035-0.0350.0000.0000.0000.000
127A127ILE0-0.019-0.00535.6610.1410.1410.0000.0000.0000.000
128A128ALA00.0210.01732.2150.0200.0200.0000.0000.0000.000
129A129LEU0-0.0050.01033.8230.0260.0260.0000.0000.0000.000
130A130ALA0-0.0070.00736.2120.1110.1110.0000.0000.0000.000
131A131THR0-0.050-0.03835.1000.0860.0860.0000.0000.0000.000
132A132GLY00.0070.01137.3880.0630.0630.0000.0000.0000.000
133A133ILE0-0.072-0.03230.817-0.142-0.1420.0000.0000.0000.000
134A134ARG10.9380.95629.15310.68410.6840.0000.0000.0000.000
135A135PRO00.0360.02829.885-0.381-0.3810.0000.0000.0000.000
136A136PHE00.0280.01522.582-0.307-0.3070.0000.0000.0000.000
137A137PRO00.0180.01825.3770.4930.4930.0000.0000.0000.000
138A138SER0-0.022-0.01128.027-0.095-0.0950.0000.0000.0000.000
139A139GLY00.006-0.00729.7430.3560.3560.0000.0000.0000.000
140A140PRO0-0.027-0.02128.126-0.324-0.3240.0000.0000.0000.000
141A141SER0-0.0170.00326.908-0.251-0.2510.0000.0000.0000.000
142A142SER0-0.029-0.02021.860-0.105-0.1050.0000.0000.0000.000
143A143GLY-1-0.940-0.95323.110-13.172-13.1720.0000.0000.0000.000