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: N6JVQ

Calculation Name: 2BDT-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2BDT

Chain ID: A

ChEMBL ID:

UniProt ID: Q9K6P2

Base Structure: X-ray

Registration Date: 2025-10-06

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 176
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1908914.534214
FMO2-HF: Nuclear repulsion 1837865.19418
FMO2-HF: Total energy -71049.340034
FMO2-MP2: Total energy -71256.556258


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-217.086-209.6378.941-7.039-9.35-0.064
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.794 / q_NPA : 0.898
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].
3A3LYS10.8350.9143.34341.51244.0790.112-1.021-1.658-0.004
100A100ASP-1-0.942-0.9872.254-67.957-65.8263.660-2.826-2.965-0.023
101A101VAL0-0.003-0.0092.369-16.006-13.5772.405-2.325-2.509-0.034
102A102GLU-1-0.804-0.8882.808-30.541-30.1532.746-0.954-2.180-0.003
103A103ILE00.0030.0034.4160.020-0.0460.0180.087-0.0380.000
4A4LEU00.0260.0145.4612.0852.0850.0000.0000.0000.000
5A5TYR0-0.030-0.0227.9440.1490.1490.0000.0000.0000.000
6A6ILE00.0400.02111.6271.1211.1210.0000.0000.0000.000
7A7ILE0-0.036-0.02014.6900.4590.4590.0000.0000.0000.000
8A8THR00.026-0.02517.5250.6990.6990.0000.0000.0000.000
9A9GLY00.0490.02720.967-0.019-0.0190.0000.0000.0000.000
10A10PRO00.0180.01224.2670.0040.0040.0000.0000.0000.000
11A11ALA00.0080.00527.179-0.328-0.3280.0000.0000.0000.000
12A12GLY00.0270.00129.6860.1200.1200.0000.0000.0000.000
13A13VAL0-0.041-0.01124.6810.1040.1040.0000.0000.0000.000
14A14GLY00.0230.01625.506-0.274-0.2740.0000.0000.0000.000
15A15LYS10.8690.96421.66811.73611.7360.0000.0000.0000.000
16A16SER00.0920.06421.212-0.500-0.5000.0000.0000.0000.000
17A17THR0-0.024-0.02222.064-0.408-0.4080.0000.0000.0000.000
18A18THR00.001-0.01018.289-0.304-0.3040.0000.0000.0000.000
19A19CYS0-0.0270.00017.309-0.940-0.9400.0000.0000.0000.000
20A20LYS10.8580.93317.48712.12112.1210.0000.0000.0000.000
21A21ARG10.8630.93419.38514.74614.7460.0000.0000.0000.000
22A22LEU00.000-0.00712.099-0.377-0.3770.0000.0000.0000.000
23A23ALA00.0560.02413.958-1.028-1.0280.0000.0000.0000.000
24A24ALA0-0.021-0.00614.806-0.732-0.7320.0000.0000.0000.000
25A25GLN0-0.114-0.04714.640-0.360-0.3600.0000.0000.0000.000
26A26LEU0-0.036-0.0199.057-1.158-1.1580.0000.0000.0000.000
27A27ASP-1-0.918-0.94610.230-25.403-25.4030.0000.0000.0000.000
28A28ASN0-0.039-0.0199.1550.3670.3670.0000.0000.0000.000
29A29SER0-0.004-0.0039.954-2.407-2.4070.0000.0000.0000.000
30A30ALA00.0170.02612.4391.7531.7530.0000.0000.0000.000
31A31TYR0-0.087-0.06714.424-0.361-0.3610.0000.0000.0000.000
32A32ILE0-0.0050.00016.3300.7500.7500.0000.0000.0000.000
33A33GLU-1-0.819-0.90319.083-12.493-12.4930.0000.0000.0000.000
34A34GLY00.041-0.00722.2370.1710.1710.0000.0000.0000.000
35A35ASP-1-0.834-0.91823.300-10.538-10.5380.0000.0000.0000.000
36A36ILE0-0.047-0.01924.4100.4390.4390.0000.0000.0000.000
37A37ILE0-0.0060.00222.3380.2650.2650.0000.0000.0000.000
38A38ASN00.0000.00725.8380.6440.6440.0000.0000.0000.000
39A39HIS10.7900.87328.51610.42410.4240.0000.0000.0000.000
40A40MET00.0240.03226.5290.1780.1780.0000.0000.0000.000
41A41VAL0-0.0270.00130.7140.2300.2300.0000.0000.0000.000
42A42VAL00.0280.00933.1700.1370.1370.0000.0000.0000.000
43A43GLY0-0.014-0.01836.7740.2160.2160.0000.0000.0000.000
44A44GLY0-0.003-0.01037.977-0.113-0.1130.0000.0000.0000.000
45A45TYR0-0.062-0.02832.5290.0740.0740.0000.0000.0000.000
46A46ARG10.9230.94935.7958.1268.1260.0000.0000.0000.000
47A47PRO00.0100.03334.300-0.290-0.2900.0000.0000.0000.000
48A48PRO0-0.015-0.02229.9680.0860.0860.0000.0000.0000.000
49A49TRP00.0080.00332.007-0.222-0.2220.0000.0000.0000.000
50A50GLU-1-0.889-0.95334.420-7.696-7.6960.0000.0000.0000.000
51A51SER0-0.027-0.02734.4960.1330.1330.0000.0000.0000.000
52A52ASP-1-0.827-0.90431.514-9.471-9.4710.0000.0000.0000.000
53A53GLU-1-0.948-0.96630.404-9.545-9.5450.0000.0000.0000.000
54A54LEU0-0.021-0.01530.372-0.330-0.3300.0000.0000.0000.000
55A55LEU00.0090.03226.787-0.417-0.4170.0000.0000.0000.000
56A56ALA00.0490.01926.215-0.574-0.5740.0000.0000.0000.000
57A57LEU0-0.030-0.01325.457-0.523-0.5230.0000.0000.0000.000
58A58THR0-0.032-0.03224.643-0.360-0.3600.0000.0000.0000.000
59A59TRP00.0670.01518.481-0.831-0.8310.0000.0000.0000.000
60A60LYS10.8550.93820.83412.34512.3450.0000.0000.0000.000
61A61ASN0-0.003-0.01221.015-0.720-0.7200.0000.0000.0000.000
62A62ILE00.0170.01118.140-0.598-0.5980.0000.0000.0000.000
63A63THR0-0.009-0.00316.332-1.314-1.3140.0000.0000.0000.000
64A64ASP-1-0.843-0.91316.057-16.050-16.0500.0000.0000.0000.000
65A65LEU0-0.032-0.01516.859-0.663-0.6630.0000.0000.0000.000
66A66THR0-0.008-0.01212.208-1.194-1.1940.0000.0000.0000.000
67A67VAL00.0020.00012.205-1.929-1.9290.0000.0000.0000.000
68A68ASN0-0.002-0.00611.996-1.896-1.8960.0000.0000.0000.000
69A69PHE0-0.018-0.01712.541-0.393-0.3930.0000.0000.0000.000
70A70LEU00.0090.0107.107-1.851-1.8510.0000.0000.0000.000
71A71LEU0-0.011-0.0027.662-3.790-3.7900.0000.0000.0000.000
72A72ALA0-0.073-0.0289.905-0.652-0.6520.0000.0000.0000.000
73A73GLN0-0.043-0.0306.232-2.969-2.9690.0000.0000.0000.000
74A74ASN0-0.065-0.0197.785-0.677-0.6770.0000.0000.0000.000
75A75ASP-1-0.744-0.8756.063-46.460-46.4600.0000.0000.0000.000
76A76VAL0-0.033-0.0228.6773.3573.3570.0000.0000.0000.000
77A77VAL0-0.038-0.01211.195-0.345-0.3450.0000.0000.0000.000
78A78LEU00.0110.00513.8460.8480.8480.0000.0000.0000.000
79A79ASP-1-0.805-0.91916.609-13.348-13.3480.0000.0000.0000.000
80A80TYR00.0290.01719.9760.4710.4710.0000.0000.0000.000
81A81ILE0-0.0270.01222.402-0.139-0.1390.0000.0000.0000.000
82A82ALA00.0140.00219.975-0.073-0.0730.0000.0000.0000.000
83A83PHE00.008-0.00721.8880.0260.0260.0000.0000.0000.000
84A84PRO00.0340.00119.665-0.530-0.5300.0000.0000.0000.000
85A85ASP-1-0.863-0.91719.636-12.322-12.3220.0000.0000.0000.000
86A86GLU-1-0.844-0.93520.906-12.641-12.6410.0000.0000.0000.000
87A87ALA0-0.036-0.01316.177-0.708-0.7080.0000.0000.0000.000
88A88GLU-1-0.866-0.93615.815-17.122-17.1220.0000.0000.0000.000
89A89ALA0-0.033-0.00816.759-0.575-0.5750.0000.0000.0000.000
90A90LEU0-0.028-0.00614.048-0.509-0.5090.0000.0000.0000.000
91A91ALA00.0170.00012.495-1.147-1.1470.0000.0000.0000.000
92A92GLN0-0.005-0.01012.624-0.988-0.9880.0000.0000.0000.000
93A93THR0-0.056-0.03514.573-0.152-0.1520.0000.0000.0000.000
94A94VAL0-0.051-0.04010.049-0.397-0.3970.0000.0000.0000.000
95A95GLN00.0090.0118.986-2.299-2.2990.0000.0000.0000.000
96A96ALA0-0.029-0.00410.788-0.166-0.1660.0000.0000.0000.000
97A97LYS10.8670.93312.46217.86417.8640.0000.0000.0000.000
98A98VAL0-0.050-0.0277.102-0.329-0.3290.0000.0000.0000.000
99A99ASP-1-0.842-0.8997.034-29.955-29.9550.0000.0000.0000.000
104A104ARG10.7700.8677.00528.08228.0820.0000.0000.0000.000
105A105PHE00.0120.01410.6510.3900.3900.0000.0000.0000.000
106A106ILE0-0.030-0.02313.2320.3540.3540.0000.0000.0000.000
107A107ILE00.0140.01916.9490.2010.2010.0000.0000.0000.000
108A108LEU0-0.020-0.00719.7830.2860.2860.0000.0000.0000.000
109A109TRP00.0470.00322.4440.5110.5110.0000.0000.0000.000
110A110THR0-0.028-0.01525.9060.0450.0450.0000.0000.0000.000
111A111ASN00.0620.02629.0930.1610.1610.0000.0000.0000.000
112A112ARG10.8690.90232.5968.6388.6380.0000.0000.0000.000
113A113GLU-1-0.913-0.95335.285-7.419-7.4190.0000.0000.0000.000
114A114GLU-1-0.872-0.93632.690-8.904-8.9040.0000.0000.0000.000
115A115LEU0-0.033-0.02029.826-0.006-0.0060.0000.0000.0000.000
116A116LEU00.0150.02133.8610.0400.0400.0000.0000.0000.000
117A117ARG10.9250.95936.6157.6707.6700.0000.0000.0000.000
118A118ARG10.8480.91828.9789.7819.7810.0000.0000.0000.000
119A119ASP-1-0.765-0.88334.529-8.296-8.2960.0000.0000.0000.000
120A120ALA0-0.0050.00035.8700.1130.1130.0000.0000.0000.000
121A121LEU00.0120.01036.9290.1750.1750.0000.0000.0000.000
122A122ARG10.7300.86536.5747.7927.7920.0000.0000.0000.000
123A123LYS10.7490.83737.5517.3147.3140.0000.0000.0000.000
124A124LYS10.9410.97040.7326.9706.9700.0000.0000.0000.000
125A125ASP-1-0.818-0.88542.189-7.076-7.0760.0000.0000.0000.000
126A126GLU-1-0.807-0.89743.244-6.633-6.6330.0000.0000.0000.000
127A127GLN0-0.113-0.05145.2980.0060.0060.0000.0000.0000.000
128A128MET0-0.0020.01840.359-0.107-0.1070.0000.0000.0000.000
129A129GLY00.0370.01638.8050.1150.1150.0000.0000.0000.000
130A130GLU-1-0.882-0.94539.600-7.486-7.4860.0000.0000.0000.000
131A131ARG10.9400.97933.0108.6998.6990.0000.0000.0000.000
132A132CYS0-0.134-0.07133.947-0.343-0.3430.0000.0000.0000.000
133A133LEU00.008-0.00533.387-0.277-0.2770.0000.0000.0000.000
134A134GLU-1-0.824-0.91234.150-8.441-8.4410.0000.0000.0000.000
135A135LEU00.030-0.00228.455-0.156-0.1560.0000.0000.0000.000
136A136VAL0-0.107-0.03829.467-0.328-0.3280.0000.0000.0000.000
137A137GLU-1-0.851-0.93230.458-8.402-8.4020.0000.0000.0000.000
138A138GLU-1-0.923-0.93729.286-9.880-9.8800.0000.0000.0000.000
139A139PHE0-0.047-0.04022.872-0.188-0.1880.0000.0000.0000.000
140A140GLU-1-0.814-0.88426.921-9.268-9.2680.0000.0000.0000.000
141A141SER0-0.052-0.04629.444-0.071-0.0710.0000.0000.0000.000
142A142LYS10.8950.95725.82910.69810.6980.0000.0000.0000.000
143A143GLY0-0.0190.00726.204-0.260-0.2600.0000.0000.0000.000
144A144ILE0-0.033-0.01521.159-0.319-0.3190.0000.0000.0000.000
145A145ASP-1-0.774-0.87719.778-13.081-13.0810.0000.0000.0000.000
146A146GLU-1-0.862-0.94821.014-11.505-11.5050.0000.0000.0000.000
147A147ARG10.7450.86315.55814.95814.9580.0000.0000.0000.000
148A148TYR00.0280.01014.185-0.843-0.8430.0000.0000.0000.000
149A149PHE00.0230.03618.222-0.302-0.3020.0000.0000.0000.000
150A150TYR0-0.028-0.00918.496-0.398-0.3980.0000.0000.0000.000
151A151ASN00.0120.01221.5210.2540.2540.0000.0000.0000.000
152A152THR0-0.009-0.02223.290-0.075-0.0750.0000.0000.0000.000
153A153SER0-0.037-0.03726.0570.2350.2350.0000.0000.0000.000
154A154HIS00.0030.01629.2450.2530.2530.0000.0000.0000.000
155A155LEU0-0.042-0.01624.568-0.099-0.0990.0000.0000.0000.000
156A156GLN00.0460.02927.9500.1810.1810.0000.0000.0000.000
157A157PRO00.0360.01227.021-0.430-0.4300.0000.0000.0000.000
158A158THR0-0.032-0.02426.692-0.237-0.2370.0000.0000.0000.000
159A159ASN00.0370.02224.7050.0700.0700.0000.0000.0000.000
160A160LEU00.0120.01021.680-0.578-0.5780.0000.0000.0000.000
161A161ASN00.0450.00619.860-1.269-1.2690.0000.0000.0000.000
162A162ASP-1-0.857-0.93118.651-14.310-14.3100.0000.0000.0000.000
163A163ILE0-0.027-0.00618.584-0.694-0.6940.0000.0000.0000.000
164A164VAL00.011-0.00515.847-0.608-0.6080.0000.0000.0000.000
165A165LYS10.9300.97114.50117.38517.3850.0000.0000.0000.000
166A166ASN00.0330.02213.878-1.652-1.6520.0000.0000.0000.000
167A167LEU00.0110.01013.739-0.805-0.8050.0000.0000.0000.000
168A168LYS10.8280.9259.44822.18722.1870.0000.0000.0000.000
169A169THR0-0.022-0.0209.019-2.140-2.1400.0000.0000.0000.000
170A170ASN00.003-0.00410.456-0.669-0.6690.0000.0000.0000.000
171A171PRO00.0430.01510.756-0.338-0.3380.0000.0000.0000.000
172A172ARG10.8210.91211.77714.45514.4550.0000.0000.0000.000
173A173PHE00.0380.00512.5490.6490.6490.0000.0000.0000.000
174A174ILE0-0.088-0.0356.474-0.119-0.1190.0000.0000.0000.000
175A175PHE0-0.022-0.0229.402-0.783-0.7830.0000.0000.0000.000
176A176CYS-1-0.879-0.90211.255-17.332-17.3320.0000.0000.0000.000