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: KKQM3

Calculation Name: 1F6B-A-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate

Ligand 3-letter code: GDP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1F6B

Chain ID: A

ChEMBL ID:

UniProt ID: Q9QVY3

Base Structure: X-ray

Registration Date: 2025-09-02

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 -2090739.164182
FMO2-HF: Nuclear repulsion 2017026.708944
FMO2-HF: Total energy -73712.455238
FMO2-MP2: Total energy -73926.027967


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:13:SER)


Summations of interaction energy for fragment #1(A:13:SER)
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.
-124.803-112.32612.646-13.478-11.642-0.141
Interaction energy analysis for fragmet #1(A:13:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.792 / q_NPA : 0.874
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].
3A15VAL00.0420.0372.80410.45912.6770.241-0.972-1.486-0.001
4A16LEU00.0630.0202.6106.0197.5240.211-0.616-1.1010.002
5A17GLN0-0.034-0.0164.4241.2951.376-0.001-0.019-0.0600.000
10A22TYR0-0.031-0.0284.0090.7450.912-0.001-0.014-0.1510.000
35A47ASP-1-0.809-0.9271.867-141.291-133.13910.503-11.263-7.392-0.147
36A48ASP-1-0.822-0.8625.253-23.697-23.740-0.001-0.0020.0470.000
54A66ILE0-0.033-0.0152.496-3.697-3.3001.694-0.592-1.4990.005
6A18PHE00.0050.0076.5645.0715.0710.0000.0000.0000.000
7A19LEU0-0.0010.0017.5543.6373.6370.0000.0000.0000.000
8A20GLY00.0190.0128.9242.2892.2890.0000.0000.0000.000
9A21LEU00.0420.0197.6341.2671.2670.0000.0000.0000.000
11A23LYS10.8550.9166.58329.81029.8100.0000.0000.0000.000
12A24LYS10.8650.9578.67719.63419.6340.0000.0000.0000.000
13A25THR0-0.109-0.0819.414-1.581-1.5810.0000.0000.0000.000
14A26GLY00.0770.03212.0040.8860.8860.0000.0000.0000.000
15A27LYS10.8980.94512.55213.94613.9460.0000.0000.0000.000
16A28LEU0-0.0120.00912.0340.8280.8280.0000.0000.0000.000
17A29VAL00.0000.00415.182-0.277-0.2770.0000.0000.0000.000
18A30PHE0-0.021-0.02011.946-0.073-0.0730.0000.0000.0000.000
19A31LEU00.0310.00518.0490.3770.3770.0000.0000.0000.000
20A32GLY00.0960.05021.748-0.316-0.3160.0000.0000.0000.000
21A33LEU0-0.0040.01324.484-0.171-0.1710.0000.0000.0000.000
22A34ASP-1-0.802-0.89524.825-12.093-12.0930.0000.0000.0000.000
23A35ASN0-0.027-0.02124.907-0.050-0.0500.0000.0000.0000.000
24A36ALA00.0070.02423.341-0.294-0.2940.0000.0000.0000.000
25A37GLY00.009-0.00220.216-0.400-0.4000.0000.0000.0000.000
26A38LYS10.7910.88317.84812.33212.3320.0000.0000.0000.000
27A39THR00.0420.01216.103-0.999-0.9990.0000.0000.0000.000
28A40THR0-0.010-0.00515.081-1.384-1.3840.0000.0000.0000.000
29A41LEU00.0270.01112.764-1.223-1.2230.0000.0000.0000.000
30A42LEU00.015-0.00111.520-2.112-2.1120.0000.0000.0000.000
31A43HIS0-0.026-0.01510.448-3.726-3.7260.0000.0000.0000.000
32A44MET0-0.0550.00110.213-2.707-2.7070.0000.0000.0000.000
33A45LEU0-0.036-0.0036.977-3.094-3.0940.0000.0000.0000.000
34A46LYS10.8030.8985.71517.66617.6660.0000.0000.0000.000
37A49ARG10.8180.9058.96719.68619.6860.0000.0000.0000.000
38A50LEU00.0180.00712.6922.2252.2250.0000.0000.0000.000
39A51GLY00.0160.00815.033-0.068-0.0680.0000.0000.0000.000
40A52GLN00.0220.00218.2410.7560.7560.0000.0000.0000.000
41A53HIS00.0780.03419.033-1.308-1.3080.0000.0000.0000.000
42A54VAL00.0360.01220.664-0.395-0.3950.0000.0000.0000.000
43A55PRO0-0.0320.00218.7730.2380.2380.0000.0000.0000.000
44A56THR0-0.019-0.02016.069-1.069-1.0690.0000.0000.0000.000
45A57LEU00.0240.01519.3440.7460.7460.0000.0000.0000.000
46A58HIS00.0110.01518.353-1.148-1.1480.0000.0000.0000.000
47A59PRO00.0050.01219.0570.7610.7610.0000.0000.0000.000
48A60THR00.0390.01821.120-0.492-0.4920.0000.0000.0000.000
49A61SER0-0.077-0.05120.4400.1100.1100.0000.0000.0000.000
50A62GLU-1-0.852-0.93115.573-19.332-19.3320.0000.0000.0000.000
51A63GLU-1-0.922-0.96213.571-18.171-18.1710.0000.0000.0000.000
52A64LEU0-0.049-0.0157.078-0.749-0.7490.0000.0000.0000.000
53A65THR00.0360.0189.3290.5540.5540.0000.0000.0000.000
55A67ALA0-0.027-0.0245.5410.9510.9510.0000.0000.0000.000
56A68GLY00.0400.0257.0041.6661.6660.0000.0000.0000.000
57A69MET0-0.0310.0237.2151.9471.9470.0000.0000.0000.000
58A70THR0-0.021-0.0228.742-1.248-1.2480.0000.0000.0000.000
59A71PHE00.0200.0097.1130.5010.5010.0000.0000.0000.000
60A72THR00.0560.02112.502-0.399-0.3990.0000.0000.0000.000
61A73THR0-0.0140.00315.8660.6300.6300.0000.0000.0000.000
62A74PHE00.0230.00418.2840.4250.4250.0000.0000.0000.000
63A75ASP-1-0.813-0.90122.119-12.684-12.6840.0000.0000.0000.000
64A76LEU0-0.044-0.00924.8170.3520.3520.0000.0000.0000.000
65A77GLY00.0430.01027.414-0.082-0.0820.0000.0000.0000.000
66A78GLY0-0.025-0.01730.8370.0970.0970.0000.0000.0000.000
67A79HIS0-0.079-0.05130.0920.4050.4050.0000.0000.0000.000
68A80ILE0-0.0250.00928.071-0.017-0.0170.0000.0000.0000.000
69A81GLN0-0.038-0.01730.1880.1020.1020.0000.0000.0000.000
70A82ALA00.012-0.00932.1150.3140.3140.0000.0000.0000.000
71A83ARG10.9450.97231.7118.7988.7980.0000.0000.0000.000
72A84ARG10.9580.98929.9369.0109.0100.0000.0000.0000.000
73A85VAL00.004-0.00727.680-0.002-0.0020.0000.0000.0000.000
74A86TRP00.0890.03924.307-0.051-0.0510.0000.0000.0000.000
75A87LYS10.8790.93525.0179.5099.5090.0000.0000.0000.000
76A88ASN0-0.013-0.00827.0990.1840.1840.0000.0000.0000.000
77A89TYR0-0.010-0.00516.4360.1690.1690.0000.0000.0000.000
78A90LEU00.0070.00522.555-0.351-0.3510.0000.0000.0000.000
79A91PRO00.0130.00023.851-0.195-0.1950.0000.0000.0000.000
80A92ALA0-0.048-0.01220.7350.0090.0090.0000.0000.0000.000
81A93ILE0-0.051-0.01218.756-0.766-0.7660.0000.0000.0000.000
82A94ASN00.0240.00716.330-0.099-0.0990.0000.0000.0000.000
83A95GLY00.0600.01617.5750.1660.1660.0000.0000.0000.000
84A96ILE0-0.039-0.01018.109-0.381-0.3810.0000.0000.0000.000
85A97VAL00.0220.00715.3090.0590.0590.0000.0000.0000.000
86A98PHE00.0050.00718.748-0.175-0.1750.0000.0000.0000.000
87A99LEU0-0.054-0.02617.827-0.077-0.0770.0000.0000.0000.000
88A100VAL00.0040.00122.0090.4770.4770.0000.0000.0000.000
89A101ASP-1-0.799-0.89124.547-12.065-12.0650.0000.0000.0000.000
90A102CYS0-0.0120.00626.2300.2890.2890.0000.0000.0000.000
91A103ALA00.0000.00528.1940.3240.3240.0000.0000.0000.000
92A104ASP-1-0.877-0.94629.436-9.556-9.5560.0000.0000.0000.000
93A105HIS0-0.033-0.05431.2800.3030.3030.0000.0000.0000.000
94A106GLU-1-0.957-0.96134.177-8.183-8.1830.0000.0000.0000.000
95A107ARG10.8290.90229.36710.18810.1880.0000.0000.0000.000
96A108LEU0-0.016-0.00830.365-0.216-0.2160.0000.0000.0000.000
97A109LEU0-0.0150.00832.628-0.104-0.1040.0000.0000.0000.000
98A110GLU-1-0.695-0.83532.498-9.721-9.7210.0000.0000.0000.000
99A111SER0-0.029-0.03027.866-0.263-0.2630.0000.0000.0000.000
100A112LYS10.8570.94729.7518.4598.4590.0000.0000.0000.000
101A113GLU-1-0.896-0.94932.065-8.473-8.4730.0000.0000.0000.000
102A114GLU-1-0.907-0.96629.089-9.959-9.9590.0000.0000.0000.000
103A115LEU0-0.028-0.00726.562-0.210-0.2100.0000.0000.0000.000
104A116ASP-1-0.824-0.93429.316-9.199-9.1990.0000.0000.0000.000
105A117SER0-0.056-0.00831.3580.1610.1610.0000.0000.0000.000
106A118LEU0-0.022-0.02425.697-0.056-0.0560.0000.0000.0000.000
107A119MET0-0.052-0.04128.503-0.177-0.1770.0000.0000.0000.000
108A120THR0-0.052-0.03330.0400.1770.1770.0000.0000.0000.000
109A121ASP-1-0.839-0.88729.450-9.676-9.6760.0000.0000.0000.000
110A122GLU-1-0.885-0.95730.202-8.611-8.6110.0000.0000.0000.000
111A123THR0-0.107-0.06427.531-0.075-0.0750.0000.0000.0000.000
112A124ILE0-0.036-0.02624.827-0.385-0.3850.0000.0000.0000.000
113A125ALA00.0150.02426.521-0.286-0.2860.0000.0000.0000.000
114A126ASN0-0.005-0.01326.5990.1560.1560.0000.0000.0000.000
115A127VAL0-0.047-0.00321.073-0.307-0.3070.0000.0000.0000.000
116A128PRO00.0160.02619.4120.2860.2860.0000.0000.0000.000
117A129ILE00.000-0.01320.942-0.469-0.4690.0000.0000.0000.000
118A130LEU0-0.034-0.00316.5190.1290.1290.0000.0000.0000.000
119A131ILE00.0180.00520.471-0.195-0.1950.0000.0000.0000.000
120A132LEU0-0.017-0.01916.641-0.387-0.3870.0000.0000.0000.000
121A133GLY00.0850.02121.2980.3260.3260.0000.0000.0000.000
122A134ASN00.016-0.02219.723-0.599-0.5990.0000.0000.0000.000
123A135LYS10.8090.89021.99413.04513.0450.0000.0000.0000.000
124A136ILE00.0530.01722.7430.4660.4660.0000.0000.0000.000
125A137ASP-1-0.944-0.95023.230-13.114-13.1140.0000.0000.0000.000
126A138ARG10.8610.94425.40311.54111.5410.0000.0000.0000.000
127A139PRO0-0.020-0.00528.4890.0250.0250.0000.0000.0000.000
128A140GLU-1-0.821-0.92331.285-9.968-9.9680.0000.0000.0000.000
129A141ALA0-0.046-0.01228.2380.0820.0820.0000.0000.0000.000
130A142ILE0-0.041-0.01430.1080.2250.2250.0000.0000.0000.000
131A143SER00.0430.01429.570-0.368-0.3680.0000.0000.0000.000
132A144GLU-1-0.782-0.90526.416-11.740-11.7400.0000.0000.0000.000
133A145GLU-1-0.927-0.94829.350-8.839-8.8390.0000.0000.0000.000
134A146ARG10.9750.97633.0338.8548.8540.0000.0000.0000.000
135A147LEU0-0.004-0.00426.7340.0970.0970.0000.0000.0000.000
136A148ARG10.7960.86526.95810.98310.9830.0000.0000.0000.000
137A149GLU-1-0.940-0.96032.093-8.148-8.1480.0000.0000.0000.000
138A150MET0-0.024-0.00234.1480.1230.1230.0000.0000.0000.000
139A151PHE00.014-0.01828.4390.0800.0800.0000.0000.0000.000
140A152GLY0-0.0190.01033.3680.0390.0390.0000.0000.0000.000
141A153LEU0-0.002-0.02228.721-0.017-0.0170.0000.0000.0000.000
142A154TYR00.004-0.00132.125-0.243-0.2430.0000.0000.0000.000
143A155GLY0-0.025-0.01133.9120.2200.2200.0000.0000.0000.000
144A156GLN0-0.0090.00531.5890.1480.1480.0000.0000.0000.000
145A157THR0-0.048-0.00727.583-0.174-0.1740.0000.0000.0000.000
146A158THR00.0260.00125.3370.1640.1640.0000.0000.0000.000
147A159GLY00.0090.01926.8450.0820.0820.0000.0000.0000.000
148A160LYS10.8360.91722.88412.19812.1980.0000.0000.0000.000
149A161GLY0-0.0070.01122.092-0.513-0.5130.0000.0000.0000.000
150A162SER0-0.021-0.01820.142-0.371-0.3710.0000.0000.0000.000
151A163VAL00.0250.02522.4510.4490.4490.0000.0000.0000.000
152A164SER0-0.007-0.02424.124-0.265-0.2650.0000.0000.0000.000
153A165LEU00.032-0.00423.1650.3060.3060.0000.0000.0000.000
154A166LYS10.9090.95926.04310.86310.8630.0000.0000.0000.000
155A167GLU-1-0.862-0.89728.086-10.095-10.0950.0000.0000.0000.000
156A168LEU0-0.037-0.00725.5030.2820.2820.0000.0000.0000.000
157A169ASN0-0.032-0.01729.478-0.176-0.1760.0000.0000.0000.000
158A170ALA00.012-0.00629.7580.2310.2310.0000.0000.0000.000
159A171ARG10.8860.95725.55210.72710.7270.0000.0000.0000.000
160A172PRO0-0.0110.00622.5820.0880.0880.0000.0000.0000.000
161A173LEU00.0290.01024.111-0.292-0.2920.0000.0000.0000.000
162A174GLU-1-0.760-0.88622.698-11.290-11.2900.0000.0000.0000.000
163A175VAL0-0.0220.00623.633-0.297-0.2970.0000.0000.0000.000
164A176PHE0-0.014-0.01020.367-0.004-0.0040.0000.0000.0000.000
165A177MET0-0.0020.03022.159-0.083-0.0830.0000.0000.0000.000
166A178CYS0-0.052-0.02418.286-0.656-0.6560.0000.0000.0000.000
167A179SER0-0.024-0.02619.4150.4300.4300.0000.0000.0000.000
168A180VAL00.007-0.00414.663-0.771-0.7710.0000.0000.0000.000
169A181LEU00.0110.01315.715-1.109-1.1090.0000.0000.0000.000
170A182LYS10.9390.96717.25912.98412.9840.0000.0000.0000.000
171A183ARG10.7670.85511.95322.95622.9560.0000.0000.0000.000
172A184GLN0-0.003-0.01014.8410.0280.0280.0000.0000.0000.000
173A185GLY00.0540.02217.2860.3250.3250.0000.0000.0000.000
174A186TYR00.0560.01910.9110.7590.7590.0000.0000.0000.000
175A187GLY0-0.027-0.01512.828-0.210-0.2100.0000.0000.0000.000
176A188GLU-1-0.960-0.97513.580-15.648-15.6480.0000.0000.0000.000
177A189GLY00.0790.02716.6000.1420.1420.0000.0000.0000.000
178A190PHE0-0.003-0.01911.9290.0620.0620.0000.0000.0000.000
179A191ARG10.8420.92911.86022.85822.8580.0000.0000.0000.000
180A192TRP0-0.0230.00214.1620.0570.0570.0000.0000.0000.000
181A193MET00.0220.01415.3970.2150.2150.0000.0000.0000.000
182A194ALA0-0.012-0.00612.4170.4040.4040.0000.0000.0000.000
183A195GLN0-0.079-0.03614.2250.2990.2990.0000.0000.0000.000
184A196TYR0-0.053-0.04817.3700.6220.6220.0000.0000.0000.000
185A197ILE0-0.079-0.02913.2650.2370.2370.0000.0000.0000.000
186A198ASP-2-1.685-1.80913.825-34.398-34.3980.0000.0000.0000.000