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: 4K95N

Calculation Name: 3JB9-M-Other549

Preferred Name:

Target Type:

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

Ligand 3-letter code: GDP | ADP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3JB9

Chain ID: M

ChEMBL ID:

UniProt ID: P39964

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 216
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1487196.243157
FMO2-HF: Nuclear repulsion 1402235.039359
FMO2-HF: Total energy -84961.203798
FMO2-MP2: Total energy -85210.92011


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(M:100:ALA)


Summations of interaction energy for fragment #1(M:100:ALA)
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.
59.263.2617.394-4.912-6.544-0.054
Interaction energy analysis for fragmet #1(M:100:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.833 / q_NPA : 0.910
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].
3M102ASP-1-0.809-0.9023.893-44.826-43.253-0.006-0.615-0.952-0.001
4M103TYR0-0.015-0.0192.369-14.773-13.4447.376-3.871-4.834-0.051
5M104ASN00.010-0.0013.4602.0913.1970.025-0.425-0.707-0.002
6M105ALA0-0.0130.0055.3505.9135.966-0.001-0.001-0.0510.000
7M106ILE00.0100.0136.7263.1543.1540.0000.0000.0000.000
8M107ALA0-0.002-0.0168.3412.8462.8460.0000.0000.0000.000
9M108ARG10.9600.9808.68131.50531.5050.0000.0000.0000.000
10M109GLN0-0.026-0.00111.1962.8682.8680.0000.0000.0000.000
11M110GLY00.0360.02614.3170.6180.6180.0000.0000.0000.000
12M111HIS0-0.016-0.01715.2180.4050.4050.0000.0000.0000.000
13M112GLU-1-0.970-0.98219.139-14.014-14.0140.0000.0000.0000.000
14M113HIS0-0.043-0.02719.6000.7680.7680.0000.0000.0000.000
15M114GLY00.0420.01315.564-0.009-0.0090.0000.0000.0000.000
16M115GLU-1-0.963-0.97914.278-19.821-19.8210.0000.0000.0000.000
17M116LEU0-0.016-0.00514.269-0.568-0.5680.0000.0000.0000.000
18M117VAL0-0.055-0.01212.1390.2820.2820.0000.0000.0000.000
19M118GLN0-0.028-0.01011.443-0.971-0.9710.0000.0000.0000.000
20M119ALA0-0.032-0.0296.647-0.907-0.9070.0000.0000.0000.000
21M120SER0-0.101-0.0655.458-3.656-3.6560.0000.0000.0000.000
22M121PHE00.0820.0246.8382.4572.4570.0000.0000.0000.000
23M122ARG10.9890.9916.95230.49630.4960.0000.0000.0000.000
24M123ASP-1-0.822-0.8979.215-25.201-25.2010.0000.0000.0000.000
25M124LEU00.0150.00911.9531.4071.4070.0000.0000.0000.000
26M125ILE0-0.0300.01612.3291.1101.1100.0000.0000.0000.000
27M126PRO00.0320.00815.2840.0650.0650.0000.0000.0000.000
28M127LEU00.0330.00318.224-0.365-0.3650.0000.0000.0000.000
29M128ARG10.9440.96719.38511.25211.2520.0000.0000.0000.000
30M129ALA00.0300.01418.6590.3380.3380.0000.0000.0000.000
31M130ARG10.8180.91813.99917.57817.5780.0000.0000.0000.000
32M131LEU00.0210.01714.069-1.134-1.1340.0000.0000.0000.000
33M132GLY00.0080.01614.621-1.052-1.0520.0000.0000.0000.000
34M133VAL0-0.047-0.03216.686-0.277-0.2770.0000.0000.0000.000
35M134GLY0-0.0080.00119.2470.2530.2530.0000.0000.0000.000
36M135GLU-1-0.838-0.91222.859-10.375-10.3750.0000.0000.0000.000
37M136ILE0-0.113-0.06622.710-0.589-0.5890.0000.0000.0000.000
38M137SER0-0.0060.00724.9350.2890.2890.0000.0000.0000.000
39M138LEU0-0.056-0.03826.220-0.269-0.2690.0000.0000.0000.000
40M139GLU-1-0.844-0.93329.198-9.891-9.8910.0000.0000.0000.000
41M140LYS10.8980.95430.9369.0939.0930.0000.0000.0000.000
42M141PRO0-0.002-0.00129.6850.2870.2870.0000.0000.0000.000
43M142SER00.0220.00032.4600.2380.2380.0000.0000.0000.000
44M143ASP-1-0.887-0.95835.854-7.744-7.7440.0000.0000.0000.000
45M144GLU-1-0.917-0.96137.662-7.813-7.8130.0000.0000.0000.000
46M145GLN00.0630.04630.2850.1120.1120.0000.0000.0000.000
47M146LYS10.9410.98435.0037.7787.7780.0000.0000.0000.000
48M147GLN00.000-0.01236.6650.0760.0760.0000.0000.0000.000
49M148GLU-1-0.844-0.90233.499-9.376-9.3760.0000.0000.0000.000
50M149VAL00.002-0.01132.4740.0260.0260.0000.0000.0000.000
51M150ALA00.0070.01435.3780.0350.0350.0000.0000.0000.000
52M151ASN0-0.026-0.00538.7540.2220.2220.0000.0000.0000.000
53M152LYS10.8900.93931.5079.7289.7280.0000.0000.0000.000
54M153THR0-0.030-0.03034.5380.0700.0700.0000.0000.0000.000
55M154LYS10.9600.99436.9747.2707.2700.0000.0000.0000.000
56M155LEU00.0470.02439.8950.1040.1040.0000.0000.0000.000
57M156ALA0-0.017-0.01436.6330.0790.0790.0000.0000.0000.000
58M157LEU00.0230.00437.6590.0780.0780.0000.0000.0000.000
59M158GLN00.0270.01140.2970.0500.0500.0000.0000.0000.000
60M159LYS10.9200.98139.5717.9987.9980.0000.0000.0000.000
61M160ILE0-0.0170.00336.9640.0230.0230.0000.0000.0000.000
62M161LEU00.0390.01541.5430.1190.1190.0000.0000.0000.000
63M162SER0-0.019-0.02944.6120.1330.1330.0000.0000.0000.000
64M163LYS10.9590.98041.4417.7027.7020.0000.0000.0000.000
65M164GLN00.009-0.00241.5160.1360.1360.0000.0000.0000.000
66M165ILE00.0190.00945.8310.1130.1130.0000.0000.0000.000
67M166ALA0-0.084-0.04348.1640.1550.1550.0000.0000.0000.000
68M167GLN0-0.0140.00544.702-0.029-0.0290.0000.0000.0000.000
69M168SER0-0.047-0.04348.7830.0440.0440.0000.0000.0000.000
70M169GLN00.0360.03550.4180.0490.0490.0000.0000.0000.000
71M170PRO00.004-0.00253.560-0.057-0.0570.0000.0000.0000.000
72M171LYS10.9080.95052.5626.0746.0740.0000.0000.0000.000
73M172SER00.0720.03457.2290.0040.0040.0000.0000.0000.000
74M173ALA00.0250.01660.4690.0480.0480.0000.0000.0000.000
75M174VAL0-0.073-0.01658.4530.0340.0340.0000.0000.0000.000
76M175VAL00.0320.01558.344-0.127-0.1270.0000.0000.0000.000
77M176GLN0-0.029-0.02354.400-0.005-0.0050.0000.0000.0000.000
78M177GLN00.0580.03857.108-0.090-0.0900.0000.0000.0000.000
79M178ARG10.8350.92250.4836.0996.0990.0000.0000.0000.000
80M179ASP-1-0.861-0.94056.139-5.435-5.4350.0000.0000.0000.000
81M180ASP-1-0.916-0.94255.397-5.657-5.6570.0000.0000.0000.000
82M181PRO0-0.078-0.04255.770-0.097-0.0970.0000.0000.0000.000
83M182VAL00.0260.01350.164-0.023-0.0230.0000.0000.0000.000
84M183TYR00.0280.01053.2030.0060.0060.0000.0000.0000.000
85M184ILE0-0.0020.00247.862-0.119-0.1190.0000.0000.0000.000
86M185ARG10.9130.95548.7576.4336.4330.0000.0000.0000.000
87M186TYR00.0020.00844.345-0.203-0.2030.0000.0000.0000.000
88M187THR00.011-0.00644.7190.1670.1670.0000.0000.0000.000
89M188PRO0-0.050-0.00844.400-0.183-0.1830.0000.0000.0000.000
90M189SER00.0210.00940.1250.0300.0300.0000.0000.0000.000
91M190ASN0-0.022-0.02841.8250.0540.0540.0000.0000.0000.000
92M191GLN00.0080.01042.6630.0610.0610.0000.0000.0000.000
93M192MET00.0220.02742.923-0.063-0.0630.0000.0000.0000.000
94M193GLY00.0670.02945.316-0.042-0.0420.0000.0000.0000.000
95M194GLN0-0.022-0.02746.8320.0740.0740.0000.0000.0000.000
96M195ALA00.0340.01550.5430.0240.0240.0000.0000.0000.000
97M196LEU0-0.004-0.00445.8080.0500.0500.0000.0000.0000.000
98M197SER00.0430.03347.8600.0290.0290.0000.0000.0000.000
99M198LYS10.9290.95349.1656.2526.2520.0000.0000.0000.000
100M199GLN0-0.012-0.00548.9160.0920.0920.0000.0000.0000.000
101M200ARG10.9750.97550.5356.2316.2310.0000.0000.0000.000
102M201ILE00.0330.02451.832-0.110-0.1100.0000.0000.0000.000
103M202ILE00.0020.01149.8520.0990.0990.0000.0000.0000.000
104M203LYS10.9310.96253.5125.3925.3920.0000.0000.0000.000
105M204MET0-0.027-0.00749.5250.0320.0320.0000.0000.0000.000
106M205VAL00.005-0.01753.8570.0730.0730.0000.0000.0000.000
107M206THR0-0.0170.00853.967-0.129-0.1290.0000.0000.0000.000
108M207ALA0-0.028-0.01355.5750.1140.1140.0000.0000.0000.000
109M208GLU-1-0.870-0.95657.027-5.672-5.6720.0000.0000.0000.000
110M209GLN0-0.047-0.01855.1170.0200.0200.0000.0000.0000.000
111M210ASP-1-0.827-0.92458.695-5.053-5.0530.0000.0000.0000.000
112M211PRO0-0.049-0.03560.521-0.075-0.0750.0000.0000.0000.000
113M212MET0-0.0240.00361.748-0.022-0.0220.0000.0000.0000.000
114M213GLU-1-0.852-0.90158.802-5.580-5.5800.0000.0000.0000.000
115M214PRO0-0.007-0.00658.043-0.104-0.1040.0000.0000.0000.000
116M215PRO0-0.018-0.01952.416-0.068-0.0680.0000.0000.0000.000
117M216LYS10.8510.92252.3825.7855.7850.0000.0000.0000.000
118M217PHE00.0070.00548.778-0.050-0.0500.0000.0000.0000.000
119M218ARG10.9540.97849.8966.2126.2120.0000.0000.0000.000
120M219HIS00.0500.02146.238-0.233-0.2330.0000.0000.0000.000
121M220LYS10.9600.98543.4907.0717.0710.0000.0000.0000.000
122M221LYS10.9600.97940.9587.2707.2700.0000.0000.0000.000
123M222VAL00.0140.00836.9980.0830.0830.0000.0000.0000.000
124M223PRO0-0.021-0.00635.162-0.013-0.0130.0000.0000.0000.000
125M224ARG10.9570.97831.5189.6139.6130.0000.0000.0000.000
126M225GLY00.0470.02129.954-0.026-0.0260.0000.0000.0000.000
127M226PRO0-0.003-0.00224.8530.1690.1690.0000.0000.0000.000
128M227PRO0-0.004-0.00223.5240.1220.1220.0000.0000.0000.000
129M228SER00.0320.01620.337-0.051-0.0510.0000.0000.0000.000
130M229PRO0-0.005-0.01116.6170.2620.2620.0000.0000.0000.000
131M230PRO00.0010.00116.893-0.043-0.0430.0000.0000.0000.000
132M231PRO00.0290.02814.269-1.081-1.0810.0000.0000.0000.000
133M232PRO0-0.024-0.02610.2560.4490.4490.0000.0000.0000.000
134M233VAL0-0.006-0.00212.8940.7040.7040.0000.0000.0000.000
135M234LEU0-0.037-0.01610.6560.5860.5860.0000.0000.0000.000
136M235HIS00.0640.03614.4180.5500.5500.0000.0000.0000.000
137M236SER0-0.0060.00316.425-0.522-0.5220.0000.0000.0000.000
138M237PRO00.000-0.01517.3720.0670.0670.0000.0000.0000.000
139M238PRO00.0070.01718.8230.6750.6750.0000.0000.0000.000
140M239ARG10.9760.97921.76311.44011.4400.0000.0000.0000.000
141M240LYS10.9410.96425.12411.04011.0400.0000.0000.0000.000
142M241VAL00.0690.04327.1780.1900.1900.0000.0000.0000.000
143M242SER0-0.033-0.01630.1620.4360.4360.0000.0000.0000.000
144M243ALA00.0510.00432.530-0.047-0.0470.0000.0000.0000.000
145M244GLN00.0080.01435.1080.0530.0530.0000.0000.0000.000
146M245GLU-1-0.859-0.92733.726-8.547-8.5470.0000.0000.0000.000
147M246GLN0-0.063-0.04232.180-0.126-0.1260.0000.0000.0000.000
148M247GLN0-0.055-0.02335.5160.1410.1410.0000.0000.0000.000
149M248ASP-1-0.865-0.93739.165-7.381-7.3810.0000.0000.0000.000
150M249TRP0-0.077-0.03236.5850.0550.0550.0000.0000.0000.000
151M250GLN0-0.053-0.01138.835-0.213-0.2130.0000.0000.0000.000
152M251ILE0-0.0010.00240.6400.1950.1950.0000.0000.0000.000
153M252PRO0-0.012-0.00242.8160.0000.0000.0000.0000.0000.000
154M253PRO0-0.021-0.03344.9930.0240.0240.0000.0000.0000.000
155M254SER00.0040.01947.0020.1940.1940.0000.0000.0000.000
156M255ILE0-0.022-0.01849.654-0.009-0.0090.0000.0000.0000.000
157M256SER0-0.027-0.02352.7870.0280.0280.0000.0000.0000.000
158M257ASN0-0.024-0.00155.609-0.005-0.0050.0000.0000.0000.000
159M258TRP00.0780.04157.1290.0550.0550.0000.0000.0000.000
160M259LYS10.9380.96852.4986.0216.0210.0000.0000.0000.000
161M260ASN00.0060.01454.856-0.232-0.2320.0000.0000.0000.000
162M261PRO0-0.010-0.01353.0640.0770.0770.0000.0000.0000.000
163M262LYS10.9280.97049.9066.2866.2860.0000.0000.0000.000
164M263GLY00.0620.02754.9840.1030.1030.0000.0000.0000.000
165M264TYR0-0.020-0.01448.4280.0190.0190.0000.0000.0000.000
166M265THR00.0440.02654.9400.0080.0080.0000.0000.0000.000
167M266ILE0-0.009-0.00153.775-0.071-0.0710.0000.0000.0000.000
168M267PRO00.0140.01457.1390.0720.0720.0000.0000.0000.000
169M268LEU00.0760.02959.668-0.069-0.0690.0000.0000.0000.000
170M269ASP-1-0.843-0.91760.825-5.151-5.1510.0000.0000.0000.000
171M270LYS10.7900.87355.0145.5535.5530.0000.0000.0000.000
172M271ARG10.8980.96556.2275.3985.3980.0000.0000.0000.000
173M272LEU00.0520.03158.4580.0750.0750.0000.0000.0000.000
174M273ALA0-0.013-0.01860.564-0.067-0.0670.0000.0000.0000.000
175M274ALA0-0.007-0.00462.7410.0210.0210.0000.0000.0000.000
176M275ASP-1-0.843-0.92060.320-5.195-5.1950.0000.0000.0000.000
177M276GLY0-0.0030.01461.418-0.022-0.0220.0000.0000.0000.000
178M277ARG10.8190.87760.4805.2635.2630.0000.0000.0000.000
179M278GLY00.0500.03364.227-0.045-0.0450.0000.0000.0000.000
180M279LEU00.000-0.00362.504-0.058-0.0580.0000.0000.0000.000
181M280ASN0-0.017-0.01266.465-0.019-0.0190.0000.0000.0000.000
182M281ASP-1-0.931-0.95264.323-4.939-4.9390.0000.0000.0000.000
183M282VAL0-0.053-0.03167.412-0.003-0.0030.0000.0000.0000.000
184M283GLU-1-0.867-0.91670.774-4.194-4.1940.0000.0000.0000.000
185M284ILE0-0.078-0.04274.292-0.014-0.0140.0000.0000.0000.000
186M285ASN00.0140.00576.6100.0080.0080.0000.0000.0000.000
187M286ASP-1-0.827-0.92378.005-4.012-4.0120.0000.0000.0000.000
188M287GLY0-0.062-0.04280.9540.0610.0610.0000.0000.0000.000
189M288PHE00.0090.00781.3210.0560.0560.0000.0000.0000.000
190M289ALA00.0540.03483.3610.0480.0480.0000.0000.0000.000
191M290LYS10.9720.98985.4143.7123.7120.0000.0000.0000.000
192M291PHE0-0.018-0.00986.1060.0550.0550.0000.0000.0000.000
193M292SER0-0.037-0.02987.5570.0450.0450.0000.0000.0000.000
194M293GLU-1-0.897-0.95389.342-3.500-3.5000.0000.0000.0000.000
195M294ALA00.0070.00491.2470.0510.0510.0000.0000.0000.000
196M295LEU00.0110.01290.6760.0540.0540.0000.0000.0000.000
197M296TYR00.0140.01091.8300.0450.0450.0000.0000.0000.000
198M297THR0-0.101-0.05295.9510.0510.0510.0000.0000.0000.000
199M298VAL00.0340.01896.5580.0440.0440.0000.0000.0000.000
200M299GLU-1-0.860-0.91698.279-3.239-3.2390.0000.0000.0000.000
201M300ARG10.9390.96399.4873.2493.2490.0000.0000.0000.000
202M301GLN00.0130.008101.8680.0060.0060.0000.0000.0000.000
203M302ALA00.0090.010102.6230.0400.0400.0000.0000.0000.000
204M303ARG10.8350.897101.2113.2243.2240.0000.0000.0000.000
205M304GLU-1-0.949-0.962106.230-2.996-2.9960.0000.0000.0000.000
206M305GLU-1-0.824-0.922106.396-3.000-3.0000.0000.0000.0000.000
207M306VAL0-0.048-0.028107.4540.0380.0380.0000.0000.0000.000
208M307ARG10.9550.977110.0402.9742.9740.0000.0000.0000.000
209M308TYR00.0440.024111.7020.0330.0330.0000.0000.0000.000
210M309ARG10.8750.939109.7662.9512.9510.0000.0000.0000.000
211M310ALA0-0.042-0.024114.2080.0250.0250.0000.0000.0000.000
212M311ILE00.0480.018115.7610.0280.0280.0000.0000.0000.000
213M312MET0-0.037-0.034117.4450.0230.0230.0000.0000.0000.000
214M313ARG10.9020.957116.2622.8012.8010.0000.0000.0000.000
215M314GLN0-0.055-0.025118.918-0.013-0.0130.0000.0000.0000.000
216M315LYS00.0070.040121.9190.0680.0680.0000.0000.0000.000