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: 9RVV2

Calculation Name: 5DN6-I-Xray547

Preferred Name:

Target Type:

Ligand Name: adenosine-5'-triphosphate | adenosine-5'-diphosphate

Ligand 3-letter code: ATP | ADP

Ligand of Interest (LOI):

PDB ID: 5DN6

Chain ID: I

ChEMBL ID:

UniProt ID: A1B619

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 75
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -388334.321554
FMO2-HF: Nuclear repulsion 361547.639379
FMO2-HF: Total energy -26786.682176
FMO2-MP2: Total energy -26865.45568


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:9:VAL)


Summations of interaction energy for fragment #1(A:9:VAL)
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.
-183.967-175.47518.026-11.832-14.685-0.123
Interaction energy analysis for fragmet #1(A:9:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.768 / q_NPA : 0.883
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].
3A11PRO00.020-0.0052.949-0.4152.0430.259-1.166-1.551-0.005
4A12GLU-1-0.861-0.8905.154-23.204-23.101-0.001-0.004-0.0970.000
5A13ARG10.9540.9734.37434.86835.110-0.001-0.061-0.1810.000
6A14ASN00.018-0.0121.925-36.547-33.0796.637-5.265-4.840-0.040
7A15LEU0-0.025-0.0092.5838.8238.3470.3181.079-0.921-0.003
8A16VAL00.0440.0193.4767.7398.0830.010-0.089-0.2650.000
9A17SER0-0.039-0.0224.231-8.610-8.403-0.001-0.030-0.1750.000
69A77THR0-0.043-0.0153.889-3.469-3.2820.000-0.025-0.1620.000
70A78LEU00.0130.0124.0502.7403.359-0.001-0.273-0.346-0.001
71A79LEU0-0.038-0.0171.829-49.260-48.34610.780-6.085-5.609-0.074
72A80ALA00.0190.0033.40411.27511.7010.0260.087-0.5380.000
10A18VAL00.0030.0096.9403.6363.6360.0000.0000.0000.000
11A19PRO00.0320.0149.858-1.341-1.3410.0000.0000.0000.000
12A20VAL0-0.0150.0029.9830.3580.3580.0000.0000.0000.000
13A21ARG10.9450.98412.66616.00216.0020.0000.0000.0000.000
14A22GLU-1-0.875-0.96114.226-17.277-17.2770.0000.0000.0000.000
15A23VAL0-0.051-0.0078.813-1.091-1.0910.0000.0000.0000.000
16A24ARG10.8750.90412.01818.25318.2530.0000.0000.0000.000
17A25LEU0-0.017-0.0098.801-1.570-1.5700.0000.0000.0000.000
18A26PRO00.0100.00912.5911.3091.3090.0000.0000.0000.000
19A27GLY00.0500.01514.269-0.897-0.8970.0000.0000.0000.000
20A28ALA0-0.065-0.03815.2081.0271.0270.0000.0000.0000.000
21A29ASP-1-0.931-0.96717.469-15.739-15.7390.0000.0000.0000.000
22A30GLY0-0.035-0.02018.6301.0371.0370.0000.0000.0000.000
23A31ASP-1-0.894-0.91717.574-18.341-18.3410.0000.0000.0000.000
24A32LEU00.0090.01412.8580.5950.5950.0000.0000.0000.000
25A33THR0-0.0040.00314.848-1.060-1.0600.0000.0000.0000.000
26A34ALA0-0.024-0.00912.5290.6990.6990.0000.0000.0000.000
27A35MET00.0360.01314.177-0.697-0.6970.0000.0000.0000.000
28A36PRO0-0.011-0.02115.313-0.069-0.0690.0000.0000.0000.000
29A37GLY0-0.0070.00216.7601.0701.0700.0000.0000.0000.000
30A38HIS0-0.0160.00416.5180.6200.6200.0000.0000.0000.000
31A39ALA0-0.024-0.01717.020-0.354-0.3540.0000.0000.0000.000
32A40PRO0-0.040-0.03314.832-0.802-0.8020.0000.0000.0000.000
33A41ALA0-0.0250.00113.6951.2101.2100.0000.0000.0000.000
34A42ILE00.0090.00210.422-1.756-1.7560.0000.0000.0000.000
35A43VAL0-0.0100.00411.3641.8161.8160.0000.0000.0000.000
36A44ASN00.0100.00811.162-3.728-3.7280.0000.0000.0000.000
37A45LEU00.0010.0049.5031.1031.1030.0000.0000.0000.000
38A46ARG10.9360.97712.62716.62016.6200.0000.0000.0000.000
39A47PRO00.001-0.00413.695-0.917-0.9170.0000.0000.0000.000
40A48GLY0-0.048-0.02813.3551.8501.8500.0000.0000.0000.000
41A49LEU0-0.052-0.00512.818-1.510-1.5100.0000.0000.0000.000
42A50VAL0-0.001-0.0027.684-0.222-0.2220.0000.0000.0000.000
43A51THR00.0230.02510.9930.4460.4460.0000.0000.0000.000
44A52VAL0-0.008-0.0199.148-0.849-0.8490.0000.0000.0000.000
45A53VAL00.0210.02711.8980.9930.9930.0000.0000.0000.000
46A54ALA00.0400.00512.637-0.471-0.4710.0000.0000.0000.000
47A55GLY0-0.013-0.02313.9381.3721.3720.0000.0000.0000.000
48A56ASP-1-0.946-0.96616.428-14.757-14.7570.0000.0000.0000.000
49A57GLY0-0.060-0.03618.5970.7000.7000.0000.0000.0000.000
50A58SER0-0.036-0.01016.8790.5790.5790.0000.0000.0000.000
51A59GLU-1-0.922-0.96515.808-18.695-18.6950.0000.0000.0000.000
52A60THR0-0.080-0.03412.394-0.209-0.2090.0000.0000.0000.000
53A61GLU-1-0.865-0.94812.809-19.251-19.2510.0000.0000.0000.000
54A62PHE0-0.027-0.0157.3840.1390.1390.0000.0000.0000.000
55A63ALA00.0020.01111.273-0.028-0.0280.0000.0000.0000.000
56A64VAL0-0.028-0.0167.370-2.078-2.0780.0000.0000.0000.000
57A65THR0-0.029-0.05310.0201.2931.2930.0000.0000.0000.000
58A66GLY00.0690.03110.2242.4602.4600.0000.0000.0000.000
59A67GLY00.0160.0167.939-4.249-4.2490.0000.0000.0000.000
60A68PHE00.005-0.0077.1063.5343.5340.0000.0000.0000.000
61A69ALA00.0010.0046.402-6.986-6.9860.0000.0000.0000.000
62A70GLU-1-0.950-0.9717.105-25.052-25.0520.0000.0000.0000.000
63A71ILE00.0060.0018.414-2.776-2.7760.0000.0000.0000.000
64A72ASN00.012-0.01211.0412.9322.9320.0000.0000.0000.000
65A73ASN00.0140.00813.276-0.284-0.2840.0000.0000.0000.000
66A74GLU-1-0.951-0.95613.765-20.255-20.2550.0000.0000.0000.000
67A75SER0-0.017-0.0038.997-1.758-1.7580.0000.0000.0000.000
68A76VAL00.0460.0118.5111.2231.2230.0000.0000.0000.000
73A81GLU-1-0.940-0.9725.629-28.458-28.4580.0000.0000.0000.000
74A82ARG10.7740.8598.45524.29324.2930.0000.0000.0000.000
75A83GLY-1-0.819-0.87410.914-21.549-21.5490.0000.0000.0000.000