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

tag_button

FMODB ID: KV2M3

Calculation Name: 2CDN-A-Xray547

Preferred Name:

Target Type:

Ligand Name: adenosine-5'-diphosphate

Ligand 3-letter code: ADP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2CDN

Chain ID: A

ChEMBL ID:

UniProt ID: P9WKF5

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 186
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2006173.861816
FMO2-HF: Nuclear repulsion 1934080.953292
FMO2-HF: Total energy -72092.908524
FMO2-MP2: Total energy -72304.804373


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:PRO)


Summations of interaction energy for fragment #1(A:-4:PRO)
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.
-76.977-72.841-0.019-1.987-2.13-0.012
Interaction energy analysis for fragmet #1(A:-4:PRO)
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 : 0.901
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].
3A-2GLY00.0650.0573.5873.9407.931-0.018-1.981-1.992-0.012
186A181LYS0-0.094-0.0564.1875.6805.825-0.001-0.006-0.1380.000
4A-1SER0-0.057-0.0505.538-2.592-2.5920.0000.0000.0000.000
5A0HIS00.0180.0318.7101.0151.0150.0000.0000.0000.000
6A1MET0-0.028-0.0058.2860.5580.5580.0000.0000.0000.000
7A2ARG10.9210.97912.17119.47219.4720.0000.0000.0000.000
8A3VAL00.001-0.00613.624-0.339-0.3390.0000.0000.0000.000
9A4LEU00.0270.02216.3010.8620.8620.0000.0000.0000.000
10A5LEU0-0.046-0.01618.101-0.445-0.4450.0000.0000.0000.000
11A6LEU00.0550.02721.2690.7150.7150.0000.0000.0000.000
12A7GLY00.0670.02023.788-0.292-0.2920.0000.0000.0000.000
13A8PRO00.0280.04126.5030.1140.1140.0000.0000.0000.000
14A9PRO0-0.024-0.02229.166-0.368-0.3680.0000.0000.0000.000
15A10GLY00.0780.02730.3620.1610.1610.0000.0000.0000.000
16A11ALA0-0.014-0.01026.291-0.111-0.1110.0000.0000.0000.000
17A12GLY00.0420.01024.885-0.310-0.3100.0000.0000.0000.000
18A13LYS10.8160.91322.78611.01311.0130.0000.0000.0000.000
19A14GLY00.1020.05222.473-0.459-0.4590.0000.0000.0000.000
20A15THR0-0.039-0.02423.461-0.141-0.1410.0000.0000.0000.000
21A16GLN00.006-0.01718.807-0.739-0.7390.0000.0000.0000.000
22A17ALA00.0180.01718.659-0.777-0.7770.0000.0000.0000.000
23A18VAL00.0080.00619.105-0.513-0.5130.0000.0000.0000.000
24A19LYS10.8470.93217.77813.97313.9730.0000.0000.0000.000
25A20LEU0-0.020-0.02213.603-0.905-0.9050.0000.0000.0000.000
26A21ALA00.0250.01614.462-1.138-1.1380.0000.0000.0000.000
27A22GLU-1-0.921-0.95215.915-16.163-16.1630.0000.0000.0000.000
28A23LYS10.8560.93510.61620.67420.6740.0000.0000.0000.000
29A24LEU0-0.025-0.0279.518-2.322-2.3220.0000.0000.0000.000
30A25GLY00.0140.03111.905-1.155-1.1550.0000.0000.0000.000
31A26ILE0-0.058-0.01113.3610.2170.2170.0000.0000.0000.000
32A27PRO00.0200.02316.4440.3310.3310.0000.0000.0000.000
33A28GLN0-0.029-0.01719.449-0.292-0.2920.0000.0000.0000.000
34A29ILE00.0090.00221.2530.5900.5900.0000.0000.0000.000
35A30SER0-0.011-0.01024.3770.0930.0930.0000.0000.0000.000
36A31THR00.0640.02326.9590.3200.3200.0000.0000.0000.000
37A32GLY0-0.003-0.00129.9360.3420.3420.0000.0000.0000.000
38A33GLU-1-0.818-0.90429.704-9.109-9.1090.0000.0000.0000.000
39A34LEU00.0280.01928.7940.2430.2430.0000.0000.0000.000
40A35PHE00.0570.01532.4990.2720.2720.0000.0000.0000.000
41A36ARG10.8500.91731.2789.5259.5250.0000.0000.0000.000
42A37ARG10.8400.90832.5409.1729.1720.0000.0000.0000.000
43A38ASN00.0370.02035.7890.3750.3750.0000.0000.0000.000
44A39ILE0-0.043-0.00938.5830.2370.2370.0000.0000.0000.000
45A40GLU-1-0.937-0.94837.638-8.020-8.0200.0000.0000.0000.000
46A41GLU-1-0.941-0.96738.644-7.702-7.7020.0000.0000.0000.000
47A42GLY0-0.042-0.00741.5990.1360.1360.0000.0000.0000.000
48A43THR0-0.018-0.02940.1920.1910.1910.0000.0000.0000.000
49A44LYS10.9500.95343.2546.6666.6660.0000.0000.0000.000
50A45LEU00.0600.04237.0560.0820.0820.0000.0000.0000.000
51A46GLY00.0480.02440.626-0.087-0.0870.0000.0000.0000.000
52A47VAL0-0.045-0.03241.5250.0480.0480.0000.0000.0000.000
53A48GLU-1-0.892-0.93142.879-6.942-6.9420.0000.0000.0000.000
54A49ALA00.0270.00438.9560.0080.0080.0000.0000.0000.000
55A50LYS10.8580.89841.0056.9956.9950.0000.0000.0000.000
56A51ARG10.8440.91542.7796.8476.8470.0000.0000.0000.000
57A52TYR00.0380.02440.3300.1110.1110.0000.0000.0000.000
58A53LEU0-0.027-0.02536.137-0.108-0.1080.0000.0000.0000.000
59A54ASP-1-0.874-0.91339.791-7.199-7.1990.0000.0000.0000.000
60A55ALA00.0130.01742.8340.0690.0690.0000.0000.0000.000
61A56GLY0-0.040-0.02638.939-0.004-0.0040.0000.0000.0000.000
62A57ASP-1-0.890-0.92338.520-7.569-7.5690.0000.0000.0000.000
63A58LEU0-0.056-0.03734.112-0.229-0.2290.0000.0000.0000.000
64A59VAL0-0.010-0.00136.7330.2470.2470.0000.0000.0000.000
65A60PRO00.0100.01237.199-0.186-0.1860.0000.0000.0000.000
66A61SER00.026-0.00934.525-0.181-0.1810.0000.0000.0000.000
67A62ASP-1-0.906-0.94335.155-8.149-8.1490.0000.0000.0000.000
68A63LEU00.0210.00336.410-0.188-0.1880.0000.0000.0000.000
69A64THR0-0.076-0.04831.856-0.182-0.1820.0000.0000.0000.000
70A65ASN00.008-0.00231.439-0.571-0.5710.0000.0000.0000.000
71A66GLU-1-0.943-0.95931.670-9.015-9.0150.0000.0000.0000.000
72A67LEU00.0390.02532.355-0.211-0.2110.0000.0000.0000.000
73A68VAL0-0.050-0.03626.899-0.282-0.2820.0000.0000.0000.000
74A69ASP-1-0.740-0.84428.188-10.902-10.9020.0000.0000.0000.000
75A70ASP-1-0.896-0.94829.283-9.711-9.7110.0000.0000.0000.000
76A71ARG10.7460.83524.56811.73811.7380.0000.0000.0000.000
77A72LEU0-0.022-0.01622.995-0.453-0.4530.0000.0000.0000.000
78A73ASN0-0.052-0.00725.832-0.529-0.5290.0000.0000.0000.000
79A74ASN0-0.0020.00326.3940.0200.0200.0000.0000.0000.000
80A75PRO00.021-0.00724.206-0.461-0.4610.0000.0000.0000.000
81A76ASP-1-0.798-0.85821.963-13.355-13.3550.0000.0000.0000.000
82A77ALA00.0210.01320.243-0.782-0.7820.0000.0000.0000.000
83A78ALA0-0.0130.00619.930-0.505-0.5050.0000.0000.0000.000
84A79ASN0-0.048-0.03514.968-0.294-0.2940.0000.0000.0000.000
85A80GLY00.0130.00714.709-1.579-1.5790.0000.0000.0000.000
86A81PHE00.033-0.00116.3150.8260.8260.0000.0000.0000.000
87A82ILE0-0.022-0.00315.458-0.708-0.7080.0000.0000.0000.000
88A83LEU00.0150.01518.6010.6880.6880.0000.0000.0000.000
89A84ASP-1-0.885-0.95522.022-11.814-11.8140.0000.0000.0000.000
90A85GLY0-0.021-0.02724.2550.4890.4890.0000.0000.0000.000
91A86TYR00.000-0.00825.5910.4270.4270.0000.0000.0000.000
92A87PRO00.0600.03824.138-0.493-0.4930.0000.0000.0000.000
93A88ARG10.8760.91327.1849.9599.9590.0000.0000.0000.000
94A89SER00.0880.06529.9950.1240.1240.0000.0000.0000.000
95A90VAL00.037-0.00229.761-0.259-0.2590.0000.0000.0000.000
96A91GLU-1-0.870-0.89930.580-9.369-9.3690.0000.0000.0000.000
97A92GLN00.0720.02929.774-0.498-0.4980.0000.0000.0000.000
98A93ALA00.009-0.00326.113-0.299-0.2990.0000.0000.0000.000
99A94LYS10.8840.96626.3539.3249.3240.0000.0000.0000.000
100A95ALA00.0840.04728.437-0.186-0.1860.0000.0000.0000.000
101A96LEU00.000-0.00922.754-0.168-0.1680.0000.0000.0000.000
102A97HIS0-0.0040.01123.209-0.688-0.6880.0000.0000.0000.000
103A98GLU-1-0.915-0.95725.112-10.147-10.1470.0000.0000.0000.000
104A99MET0-0.089-0.02526.217-0.140-0.1400.0000.0000.0000.000
105A100LEU0-0.039-0.00920.265-0.227-0.2270.0000.0000.0000.000
106A101GLU-1-0.864-0.92923.090-11.972-11.9720.0000.0000.0000.000
107A102ARG10.7980.86224.75810.37310.3730.0000.0000.0000.000
108A103ARG10.7040.83223.11811.88811.8880.0000.0000.0000.000
109A104GLY0-0.0260.00222.236-0.526-0.5260.0000.0000.0000.000
110A105THR0-0.099-0.06117.183-1.148-1.1480.0000.0000.0000.000
111A106ASP-1-0.793-0.89917.858-14.226-14.2260.0000.0000.0000.000
112A107ILE0-0.088-0.05416.986-0.899-0.8990.0000.0000.0000.000
113A108ASP-1-0.819-0.89711.541-24.428-24.4280.0000.0000.0000.000
114A109ALA0-0.024-0.02012.333-0.772-0.7720.0000.0000.0000.000
115A110VAL00.0280.01814.4320.7930.7930.0000.0000.0000.000
116A111LEU0-0.0130.00114.514-0.078-0.0780.0000.0000.0000.000
117A112GLU-1-0.836-0.90018.415-11.649-11.6490.0000.0000.0000.000
118A113PHE0-0.082-0.04518.834-0.243-0.2430.0000.0000.0000.000
119A114ARG11.0020.99523.36711.71311.7130.0000.0000.0000.000
120A115VAL0-0.036-0.02725.783-0.163-0.1630.0000.0000.0000.000
121A116SER0-0.027-0.02528.736-0.006-0.0060.0000.0000.0000.000
122A117GLU-1-0.870-0.95032.442-8.201-8.2010.0000.0000.0000.000
123A118GLU-1-0.814-0.90235.240-8.665-8.6650.0000.0000.0000.000
124A119VAL00.0160.00630.4790.0260.0260.0000.0000.0000.000
125A120LEU0-0.053-0.02529.905-0.159-0.1590.0000.0000.0000.000
126A121LEU0-0.013-0.01133.3450.0890.0890.0000.0000.0000.000
127A122GLU-1-0.930-0.95233.624-8.775-8.7750.0000.0000.0000.000
128A123ARG10.8300.91426.77510.73710.7370.0000.0000.0000.000
129A124LEU0-0.071-0.03633.381-0.029-0.0290.0000.0000.0000.000
130A125LYS10.8700.93735.6077.7387.7380.0000.0000.0000.000
131A126GLY0-0.0060.00936.2460.1520.1520.0000.0000.0000.000
132A127ARG10.7460.85331.1609.1569.1560.0000.0000.0000.000
133A128GLY00.0280.02135.7880.0560.0560.0000.0000.0000.000
134A129ARG10.7980.86332.1629.0489.0480.0000.0000.0000.000
135A130ALA00.0300.00938.3650.0830.0830.0000.0000.0000.000
136A131ASP-1-0.697-0.80436.459-8.432-8.4320.0000.0000.0000.000
137A132ASP-1-0.798-0.86836.194-8.778-8.7780.0000.0000.0000.000
138A133THR00.0690.02439.1220.0840.0840.0000.0000.0000.000
139A134ASP-1-0.841-0.92642.058-7.252-7.2520.0000.0000.0000.000
140A135ASP-1-0.902-0.94842.870-6.741-6.7410.0000.0000.0000.000
141A136VAL00.0200.01640.303-0.101-0.1010.0000.0000.0000.000
142A137ILE0-0.041-0.02337.370-0.251-0.2510.0000.0000.0000.000
143A138LEU0-0.016-0.00638.889-0.167-0.1670.0000.0000.0000.000
144A139ASN0-0.058-0.04140.881-0.056-0.0560.0000.0000.0000.000
145A140ARG10.7780.88035.2468.2378.2370.0000.0000.0000.000
146A141MET0-0.051-0.01933.970-0.409-0.4090.0000.0000.0000.000
147A142LYS10.9220.97436.1907.0437.0430.0000.0000.0000.000
148A143VAL00.0720.03935.060-0.136-0.1360.0000.0000.0000.000
149A144TYR00.016-0.00127.986-0.310-0.3100.0000.0000.0000.000
150A145ARG10.8080.86832.6017.7307.7300.0000.0000.0000.000
151A146ASP-1-0.835-0.89734.571-8.074-8.0740.0000.0000.0000.000
152A147GLU-1-0.926-0.96234.043-8.596-8.5960.0000.0000.0000.000
153A148THR0-0.065-0.05428.390-0.228-0.2280.0000.0000.0000.000
154A149ALA0-0.0200.00328.975-0.393-0.3930.0000.0000.0000.000
155A150PRO00.009-0.00128.896-0.343-0.3430.0000.0000.0000.000
156A151LEU0-0.018-0.01125.758-0.223-0.2230.0000.0000.0000.000
157A152LEU0-0.060-0.02424.267-0.533-0.5330.0000.0000.0000.000
158A153GLU-1-0.862-0.93124.367-11.543-11.5430.0000.0000.0000.000
159A154TYR0-0.066-0.03424.7510.1540.1540.0000.0000.0000.000
160A155TYR00.0410.00520.7900.0080.0080.0000.0000.0000.000
161A156ARG10.9160.96320.60811.02211.0220.0000.0000.0000.000
162A157ASP-1-0.920-0.96319.235-14.362-14.3620.0000.0000.0000.000
163A158GLN0-0.048-0.03116.159-0.440-0.4400.0000.0000.0000.000
164A159LEU0-0.0390.00716.540-0.666-0.6660.0000.0000.0000.000
165A160LYS10.8680.93114.12018.62318.6230.0000.0000.0000.000
166A161THR00.004-0.01317.6220.1200.1200.0000.0000.0000.000
167A162VAL0-0.043-0.02317.488-0.510-0.5100.0000.0000.0000.000
168A163ASP-1-0.900-0.95720.146-11.567-11.5670.0000.0000.0000.000
169A164ALA00.0110.00422.207-0.385-0.3850.0000.0000.0000.000
170A165VAL00.0020.00923.7740.3700.3700.0000.0000.0000.000
171A166GLY00.0500.02224.466-0.191-0.1910.0000.0000.0000.000
172A167THR0-0.009-0.00423.5990.0620.0620.0000.0000.0000.000
173A168MET00.028-0.00122.968-0.333-0.3330.0000.0000.0000.000
174A169ASP-1-0.828-0.90619.736-14.155-14.1550.0000.0000.0000.000
175A170GLU-1-0.894-0.93918.584-13.320-13.3200.0000.0000.0000.000
176A171VAL0-0.023-0.00918.728-0.787-0.7870.0000.0000.0000.000
177A172PHE00.0120.01714.813-0.710-0.7100.0000.0000.0000.000
178A173ALA00.0440.01114.316-1.175-1.1750.0000.0000.0000.000
179A174ARG10.7820.88414.17712.30012.3000.0000.0000.0000.000
180A175ALA00.0440.01715.046-0.711-0.7110.0000.0000.0000.000
181A176LEU0-0.019-0.00310.312-0.802-0.8020.0000.0000.0000.000
182A177ARG10.9590.98010.24117.27017.2700.0000.0000.0000.000
183A178ALA0-0.053-0.01511.205-1.089-1.0890.0000.0000.0000.000
184A179LEU00.0090.00410.0160.0850.0850.0000.0000.0000.000
185A180GLY0-0.054-0.0126.825-2.556-2.5560.0000.0000.0000.000