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: 4YL6N

Calculation Name: 2B6H-A-Xray547

Preferred Name: ADP-ribosylation factor 5

Target Type: SINGLE PROTEIN

Ligand Name: guanosine-5'-diphosphate | unknown atom or ion

Ligand 3-letter code: GDP | UNX

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2B6H

Chain ID: A

ChEMBL ID: CHEMBL5986

UniProt ID: P84085

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 176
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1964308.556207
FMO2-HF: Nuclear repulsion 1893358.527922
FMO2-HF: Total energy -70950.028285
FMO2-MP2: Total energy -71156.153713


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:5:ARG)


Summations of interaction energy for fragment #1(A:5:ARG)
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.
88.12691.010.006-1.238-1.653-0.003
Interaction energy analysis for fragmet #1(A:5:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.828 / q_NPA : 1.901
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].
3A7SER00.0540.0273.550-12.308-10.569-0.003-0.936-0.800-0.002
7A11ARG10.8310.8973.68079.30579.7430.003-0.172-0.270-0.001
54A58TYR0-0.048-0.0273.469-11.822-11.4200.003-0.065-0.3400.000
55A59LYS10.8650.9223.39688.15488.4590.003-0.065-0.2430.000
4A8LEU00.0280.0186.040-5.584-5.5840.0000.0000.0000.000
5A9PHE00.0970.0488.0990.3290.3290.0000.0000.0000.000
6A10SER0-0.097-0.0585.261-3.480-3.4800.0000.0000.0000.000
8A12ILE00.0310.0518.2742.1622.1620.0000.0000.0000.000
9A13PHE00.0820.06211.8182.2312.2310.0000.0000.0000.000
10A14GLY00.0030.01711.5212.0812.0810.0000.0000.0000.000
11A15LYS10.9200.9427.69158.18358.1830.0000.0000.0000.000
12A16LYS10.8470.91612.71928.95628.9560.0000.0000.0000.000
13A17GLN00.0310.01614.345-1.672-1.6720.0000.0000.0000.000
14A18MET0-0.0090.02015.6572.1592.1590.0000.0000.0000.000
15A19ARG10.8620.94317.12326.46926.4690.0000.0000.0000.000
16A20ILE00.0220.00417.6631.3031.3030.0000.0000.0000.000
17A21LEU00.0180.03121.029-0.567-0.5670.0000.0000.0000.000
18A22MET0-0.036-0.01420.4430.3500.3500.0000.0000.0000.000
19A23VAL00.0440.02124.1060.0160.0160.0000.0000.0000.000
20A24GLY00.0800.02827.573-0.325-0.3250.0000.0000.0000.000
21A25LEU00.0030.02130.097-0.235-0.2350.0000.0000.0000.000
22A26ASP-1-0.786-0.87230.417-19.070-19.0700.0000.0000.0000.000
23A27ALA00.0330.00730.3650.1670.1670.0000.0000.0000.000
24A28ALA00.0010.01429.188-0.257-0.2570.0000.0000.0000.000
25A29GLY00.0170.00426.130-0.352-0.3520.0000.0000.0000.000
26A30LYS10.7920.88723.70020.96920.9690.0000.0000.0000.000
27A31THR00.049-0.00521.277-0.983-0.9830.0000.0000.0000.000
28A32THR0-0.047-0.02820.131-1.158-1.1580.0000.0000.0000.000
29A33ILE00.0100.00319.336-1.507-1.5070.0000.0000.0000.000
30A34LEU00.0010.00617.058-2.189-2.1890.0000.0000.0000.000
31A35TYR00.0030.00715.410-3.109-3.1090.0000.0000.0000.000
32A36LYS10.7610.88015.16428.80128.8010.0000.0000.0000.000
33A37LEU00.0050.01813.206-2.789-2.7890.0000.0000.0000.000
34A38LYS10.9040.9479.69938.90638.9060.0000.0000.0000.000
35A39LEU0-0.023-0.0108.602-7.398-7.3980.0000.0000.0000.000
36A40GLY00.0120.0029.505-2.724-2.7240.0000.0000.0000.000
37A41GLU-1-0.940-0.96110.633-38.702-38.7020.0000.0000.0000.000
38A42ILE0-0.031-0.01913.976-0.165-0.1650.0000.0000.0000.000
39A43VAL00.0130.01615.6371.3151.3150.0000.0000.0000.000
40A44THR0-0.013-0.00618.3960.8630.8630.0000.0000.0000.000
41A45THR0-0.031-0.01521.4090.1830.1830.0000.0000.0000.000
42A46ILE00.010-0.00424.0610.3070.3070.0000.0000.0000.000
43A47PRO0-0.0270.00126.1650.5660.5660.0000.0000.0000.000
44A48THR00.002-0.00628.3200.6750.6750.0000.0000.0000.000
45A49ILE00.0410.02032.079-0.312-0.3120.0000.0000.0000.000
46A50GLY00.0310.01334.2330.2190.2190.0000.0000.0000.000
47A51PHE0-0.028-0.01529.2270.0540.0540.0000.0000.0000.000
48A52ASN00.0320.00827.968-0.264-0.2640.0000.0000.0000.000
49A53VAL0-0.027-0.00823.5060.1360.1360.0000.0000.0000.000
50A54GLU-1-0.792-0.87421.157-27.408-27.4080.0000.0000.0000.000
51A55THR0-0.042-0.03617.2850.3400.3400.0000.0000.0000.000
52A56VAL0-0.0180.00313.019-1.023-1.0230.0000.0000.0000.000
53A57GLU-1-0.848-0.91713.363-36.952-36.9520.0000.0000.0000.000
56A60ASN00.0030.00810.246-1.054-1.0540.0000.0000.0000.000
57A61ILE0-0.018-0.00110.2352.4512.4510.0000.0000.0000.000
58A62CYS0-0.021-0.02213.573-1.446-1.4460.0000.0000.0000.000
59A63PHE00.0070.00414.6921.3851.3850.0000.0000.0000.000
60A64THR00.0230.01018.180-0.120-0.1200.0000.0000.0000.000
61A65VAL0-0.018-0.01421.2550.3660.3660.0000.0000.0000.000
62A66TRP00.0480.01723.488-0.155-0.1550.0000.0000.0000.000
63A67ASP-1-0.830-0.89427.089-21.046-21.0460.0000.0000.0000.000
64A68VAL0-0.024-0.01030.2650.3180.3180.0000.0000.0000.000
65A69GLY00.0620.02033.269-0.139-0.1390.0000.0000.0000.000
66A70GLY00.0220.02835.7020.2910.2910.0000.0000.0000.000
67A71GLN0-0.050-0.03231.8170.2420.2420.0000.0000.0000.000
68A72ASP-1-0.830-0.90035.839-16.071-16.0710.0000.0000.0000.000
69A73LYS10.7530.87334.94416.31016.3100.0000.0000.0000.000
70A74ILE00.0430.02636.5630.1510.1510.0000.0000.0000.000
71A75ARG10.8130.89133.50417.79717.7970.0000.0000.0000.000
72A76PRO00.0500.02035.150-0.399-0.3990.0000.0000.0000.000
73A77LEU0-0.0080.00530.102-0.247-0.2470.0000.0000.0000.000
74A78TRP00.0100.00330.501-0.559-0.5590.0000.0000.0000.000
75A79ARG10.7640.85530.53717.05217.0520.0000.0000.0000.000
76A80HIS0-0.0090.01526.092-0.122-0.1220.0000.0000.0000.000
77A81TYR00.0550.01723.975-0.016-0.0160.0000.0000.0000.000
78A82PHE00.0060.00226.716-0.611-0.6110.0000.0000.0000.000
79A83GLN00.0100.02028.7390.1960.1960.0000.0000.0000.000
80A84ASN00.0190.01024.424-0.328-0.3280.0000.0000.0000.000
81A85THR0-0.007-0.01024.003-1.472-1.4720.0000.0000.0000.000
82A86GLN0-0.016-0.00320.724-0.195-0.1950.0000.0000.0000.000
83A87GLY00.0360.01422.3490.6230.6230.0000.0000.0000.000
84A88LEU00.0100.00623.339-0.377-0.3770.0000.0000.0000.000
85A89ILE0-0.025-0.02120.3760.0040.0040.0000.0000.0000.000
86A90PHE00.0280.01525.0270.2040.2040.0000.0000.0000.000
87A91VAL0-0.051-0.02624.842-0.072-0.0720.0000.0000.0000.000
88A92VAL00.0200.00127.6940.5800.5800.0000.0000.0000.000
89A93ASP-1-0.796-0.89230.140-19.509-19.5090.0000.0000.0000.000
90A94SER00.015-0.00330.9960.5380.5380.0000.0000.0000.000
91A95ASN0-0.005-0.00933.5020.6770.6770.0000.0000.0000.000
92A96ASP-1-0.889-0.94035.244-16.264-16.2640.0000.0000.0000.000
93A97ARG10.8360.90537.16015.50615.5060.0000.0000.0000.000
94A98GLU-1-0.916-0.95439.711-14.775-14.7750.0000.0000.0000.000
95A99ARG10.7760.87235.40517.37817.3780.0000.0000.0000.000
96A100VAL0-0.005-0.00936.578-0.315-0.3150.0000.0000.0000.000
97A101GLN0-0.039-0.02338.454-0.121-0.1210.0000.0000.0000.000
98A102GLU-1-0.809-0.90238.272-16.550-16.5500.0000.0000.0000.000
99A103SER0-0.032-0.03533.984-0.470-0.4700.0000.0000.0000.000
100A104ALA00.0130.01335.635-0.412-0.4120.0000.0000.0000.000
101A105ASP-1-0.839-0.91237.782-15.093-15.0930.0000.0000.0000.000
102A106GLU-1-0.805-0.90835.296-16.986-16.9860.0000.0000.0000.000
103A107LEU0-0.0090.00331.740-0.414-0.4140.0000.0000.0000.000
104A108GLN0-0.031-0.03334.826-0.049-0.0490.0000.0000.0000.000
105A109LYS10.8510.91637.16916.52216.5220.0000.0000.0000.000
106A110MET0-0.047-0.02930.201-0.045-0.0450.0000.0000.0000.000
107A111LEU0-0.035-0.02331.980-0.296-0.2960.0000.0000.0000.000
108A112GLN0-0.020-0.00635.0130.2430.2430.0000.0000.0000.000
109A113GLU-1-0.797-0.85334.547-17.082-17.0820.0000.0000.0000.000
110A114ASP-1-0.913-0.95035.085-17.095-17.0950.0000.0000.0000.000
111A115GLU0-0.006-0.03532.492-0.422-0.4220.0000.0000.0000.000
112A116LEU0-0.0310.00229.038-0.722-0.7220.0000.0000.0000.000
113A117ARG10.8610.93331.84317.14817.1480.0000.0000.0000.000
114A118ASP-1-0.888-0.95030.449-18.792-18.7920.0000.0000.0000.000
115A119ALA0-0.061-0.00927.354-0.628-0.6280.0000.0000.0000.000
116A120VAL0-0.009-0.00624.8940.7020.7020.0000.0000.0000.000
117A121LEU00.0050.00425.872-0.705-0.7050.0000.0000.0000.000
118A122LEU0-0.027-0.00921.5070.0500.0500.0000.0000.0000.000
119A123VAL00.0210.00625.559-0.232-0.2320.0000.0000.0000.000
120A124PHE0-0.006-0.01519.930-0.538-0.5380.0000.0000.0000.000
121A125ALA00.0430.02626.2270.4740.4740.0000.0000.0000.000
122A126ASN00.0200.00225.503-0.698-0.6980.0000.0000.0000.000
123A127LYS10.8040.89027.31220.99520.9950.0000.0000.0000.000
124A128GLN0-0.047-0.04128.4980.8180.8180.0000.0000.0000.000
125A129ASP-1-0.878-0.93028.012-21.104-21.1040.0000.0000.0000.000
126A130MET0-0.021-0.00430.0480.3380.3380.0000.0000.0000.000
127A131PRO00.006-0.01333.2090.2190.2190.0000.0000.0000.000
128A132ASN00.0120.01336.4820.4720.4720.0000.0000.0000.000
129A133ALA0-0.0040.01533.4950.1780.1780.0000.0000.0000.000
130A134MET0-0.0310.00335.4660.3090.3090.0000.0000.0000.000
131A135PRO00.0230.01134.828-0.572-0.5720.0000.0000.0000.000
132A136VAL00.0760.02930.6860.2000.2000.0000.0000.0000.000
133A137SER0-0.0070.01733.738-0.048-0.0480.0000.0000.0000.000
134A138GLU-1-0.773-0.89136.931-14.920-14.9200.0000.0000.0000.000
135A139LEU00.026-0.00332.6770.1780.1780.0000.0000.0000.000
136A140THR0-0.014-0.03234.294-0.179-0.1790.0000.0000.0000.000
137A141ASP-1-0.905-0.93935.901-14.604-14.6040.0000.0000.0000.000
138A142LYS10.8840.93539.13714.96714.9670.0000.0000.0000.000
139A143LEU0-0.026-0.00733.1190.0000.0000.0000.0000.0000.000
140A144GLY00.0260.01537.268-0.136-0.1360.0000.0000.0000.000
141A145LEU0-0.025-0.02132.7990.0820.0820.0000.0000.0000.000
142A146GLN0-0.061-0.04736.766-0.099-0.0990.0000.0000.0000.000
143A147HIS0-0.0110.00839.0470.3500.3500.0000.0000.0000.000
144A148LEU0-0.0400.00534.9490.1590.1590.0000.0000.0000.000
145A149ARG10.9680.97138.66814.16014.1600.0000.0000.0000.000
146A150SER0-0.062-0.02536.350-0.082-0.0820.0000.0000.0000.000
147A151ARG10.8850.94030.99818.95018.9500.0000.0000.0000.000
148A152THR00.0100.01227.8140.4910.4910.0000.0000.0000.000
149A153TRP00.008-0.00529.129-0.609-0.6090.0000.0000.0000.000
150A154TYR00.0010.00424.0430.5930.5930.0000.0000.0000.000
151A155VAL0-0.009-0.00228.089-0.336-0.3360.0000.0000.0000.000
152A156GLN0-0.036-0.00522.7570.0470.0470.0000.0000.0000.000
153A157ALA00.0330.01826.1780.1120.1120.0000.0000.0000.000
154A158THR0-0.030-0.03023.002-0.941-0.9410.0000.0000.0000.000
155A159CYS0-0.0280.00623.5690.6170.6170.0000.0000.0000.000
156A160ALA00.0200.00321.626-1.099-1.0990.0000.0000.0000.000
157A161THR00.0570.01721.032-1.489-1.4890.0000.0000.0000.000
158A162GLN00.0570.03421.402-1.349-1.3490.0000.0000.0000.000
159A163GLY0-0.034-0.02418.043-1.753-1.7530.0000.0000.0000.000
160A164THR0-0.006-0.01318.670-1.423-1.4230.0000.0000.0000.000
161A165GLY00.0810.03820.4990.7080.7080.0000.0000.0000.000
162A166LEU0-0.022-0.01017.630-0.188-0.1880.0000.0000.0000.000
163A167TYR0-0.029-0.03011.405-2.199-2.1990.0000.0000.0000.000
164A168ASP-1-0.863-0.91916.469-26.286-26.2860.0000.0000.0000.000
165A169GLY00.0780.03919.5540.2870.2870.0000.0000.0000.000
166A170LEU0-0.025-0.02415.9120.1000.1000.0000.0000.0000.000
167A171ASP-1-0.866-0.94316.654-33.486-33.4860.0000.0000.0000.000
168A172TRP0-0.0070.00317.6110.0200.0200.0000.0000.0000.000
169A173LEU00.0180.00719.7660.1790.1790.0000.0000.0000.000
170A174SER0-0.054-0.05715.4070.3930.3930.0000.0000.0000.000
171A175HIS0-0.061-0.03317.8880.7300.7300.0000.0000.0000.000
172A176GLU-1-0.871-0.91120.771-21.711-21.7110.0000.0000.0000.000
173A177LEU0-0.036-0.01320.5940.3890.3890.0000.0000.0000.000
174A178SER0-0.022-0.01119.566-0.845-0.8450.0000.0000.0000.000
175A179LYS10.8850.92720.61722.52822.5280.0000.0000.0000.000
176A180ARG0-0.031-0.00815.7426.6056.6050.0000.0000.0000.000