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: ZZ78N

Calculation Name: 2GF0-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: 2GF0

Chain ID: A

ChEMBL ID:

UniProt ID: O95057

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 173
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1845894.97866
FMO2-HF: Nuclear repulsion 1776532.422761
FMO2-HF: Total energy -69362.555899
FMO2-MP2: Total energy -69561.22009


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:GLN)


Summations of interaction energy for fragment #1(A:4:GLN)
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.
-5.465-5.5888.308-3.928-4.257-0.042
Interaction energy analysis for fragmet #1(A:4:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.859 / q_NPA : 0.918
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].
3A6ASN00.0590.0201.900-15.419-15.7118.309-3.900-4.117-0.042
4A7ASP-1-0.783-0.8744.385-31.021-30.852-0.001-0.028-0.1400.000
5A8TYR00.019-0.0156.517-0.499-0.4990.0000.0000.0000.000
6A9ARG10.8400.9125.86431.44531.4450.0000.0000.0000.000
7A10VAL00.0690.04311.6320.7920.7920.0000.0000.0000.000
8A11VAL0-0.024-0.00615.445-0.204-0.2040.0000.0000.0000.000
9A12VAL00.0180.01617.9080.4910.4910.0000.0000.0000.000
10A13PHE00.0040.01420.2310.1710.1710.0000.0000.0000.000
11A14GLY00.0850.02324.1280.1410.1410.0000.0000.0000.000
12A15ALA00.0520.04927.931-0.154-0.1540.0000.0000.0000.000
13A16GLY00.006-0.00230.355-0.279-0.2790.0000.0000.0000.000
14A17GLY00.0210.00232.3460.1590.1590.0000.0000.0000.000
15A18VAL0-0.0060.00329.4880.1540.1540.0000.0000.0000.000
16A19GLY00.0250.02130.3040.0000.0000.0000.0000.0000.000
17A20LYS10.8380.93824.93610.78310.7830.0000.0000.0000.000
18A21SER00.056-0.01524.826-0.082-0.0820.0000.0000.0000.000
19A22SER0-0.054-0.02625.889-0.147-0.1470.0000.0000.0000.000
20A23LEU00.0150.01625.324-0.029-0.0290.0000.0000.0000.000
21A24VAL00.0230.01820.203-0.280-0.2800.0000.0000.0000.000
22A25LEU0-0.022-0.01322.581-0.430-0.4300.0000.0000.0000.000
23A26ARG10.8360.93024.78710.10410.1040.0000.0000.0000.000
24A27PHE0-0.043-0.02618.5880.0730.0730.0000.0000.0000.000
25A28VAL00.0250.01118.863-0.015-0.0150.0000.0000.0000.000
26A29LYS10.9240.95821.48113.73613.7360.0000.0000.0000.000
27A30GLY00.0220.03724.2890.3820.3820.0000.0000.0000.000
28A31THR0-0.048-0.01526.8280.6640.6640.0000.0000.0000.000
29A32PHE00.005-0.00328.768-0.090-0.0900.0000.0000.0000.000
30A33ARG10.8140.87327.38310.35110.3510.0000.0000.0000.000
31A34ASP-1-0.829-0.92530.014-8.926-8.9260.0000.0000.0000.000
32A35THR0-0.029-0.01231.642-0.299-0.2990.0000.0000.0000.000
33A36TYR00.001-0.00334.1240.0740.0740.0000.0000.0000.000
34A37ILE0-0.0150.01627.725-0.066-0.0660.0000.0000.0000.000
35A38PRO00.0420.02428.3570.0550.0550.0000.0000.0000.000
36A39THR0-0.021-0.00428.254-0.316-0.3160.0000.0000.0000.000
37A40ILE0-0.011-0.01123.2290.2460.2460.0000.0000.0000.000
38A41GLU-1-0.910-0.94218.455-14.433-14.4330.0000.0000.0000.000
39A42ASP-1-0.842-0.90419.568-14.004-14.0040.0000.0000.0000.000
40A43THR0-0.054-0.03813.270-0.370-0.3700.0000.0000.0000.000
41A44TYR0-0.052-0.01616.235-0.357-0.3570.0000.0000.0000.000
42A45ARG10.9060.9519.57526.78726.7870.0000.0000.0000.000
43A46GLN00.0380.01914.1021.2931.2930.0000.0000.0000.000
44A47VAL0-0.049-0.02112.815-1.677-1.6770.0000.0000.0000.000
45A48ILE00.0180.00512.4621.6281.6280.0000.0000.0000.000
46A49SER00.020-0.00912.952-2.608-2.6080.0000.0000.0000.000
47A50CYS0-0.056-0.03410.4490.1630.1630.0000.0000.0000.000
48A51ASP-1-0.803-0.89910.617-26.148-26.1480.0000.0000.0000.000
49A52LYS10.8850.93312.27116.65816.6580.0000.0000.0000.000
50A53SER00.0110.0178.9770.4020.4020.0000.0000.0000.000
51A54VAL00.0380.0279.8951.8021.8020.0000.0000.0000.000
52A55CYS0-0.083-0.0367.589-4.106-4.1060.0000.0000.0000.000
53A56THR0-0.050-0.0208.0803.0883.0880.0000.0000.0000.000
54A57LEU00.0520.0439.724-1.148-1.1480.0000.0000.0000.000
55A58GLN0-0.058-0.0678.6372.3582.3580.0000.0000.0000.000
56A59ILE00.0310.01312.4770.4300.4300.0000.0000.0000.000
57A60THR0-0.016-0.01815.4160.1040.1040.0000.0000.0000.000
58A61ASP-1-0.805-0.88617.324-11.816-11.8160.0000.0000.0000.000
59A62THR0-0.002-0.01420.7470.3240.3240.0000.0000.0000.000
60A63THR00.009-0.00922.7640.2910.2910.0000.0000.0000.000
61A64GLY00.002-0.00125.5180.4440.4440.0000.0000.0000.000
62A65SER00.0140.00327.361-0.213-0.2130.0000.0000.0000.000
63A66HIS0-0.0010.00428.8040.1490.1490.0000.0000.0000.000
64A67GLN0-0.068-0.03820.5260.1520.1520.0000.0000.0000.000
65A68PHE00.0650.02124.8890.1270.1270.0000.0000.0000.000
66A69PRO00.0830.02624.510-0.492-0.4920.0000.0000.0000.000
67A70ALA0-0.030-0.00822.967-0.301-0.3010.0000.0000.0000.000
68A71MET00.0190.00918.697-0.535-0.5350.0000.0000.0000.000
69A72GLN00.0380.04519.879-0.581-0.5810.0000.0000.0000.000
70A73ARG10.9910.99820.45611.05911.0590.0000.0000.0000.000
71A74LEU0-0.035-0.02416.289-0.673-0.6730.0000.0000.0000.000
72A75SER0-0.013-0.01915.748-1.165-1.1650.0000.0000.0000.000
73A76ILE00.0130.00816.088-0.827-0.8270.0000.0000.0000.000
74A77SER0-0.063-0.02715.165-0.747-0.7470.0000.0000.0000.000
75A78LYS10.9330.95111.58517.63117.6310.0000.0000.0000.000
76A79GLY00.0090.02011.412-1.627-1.6270.0000.0000.0000.000
77A80HIS0-0.057-0.0297.7200.3320.3320.0000.0000.0000.000
78A81ALA00.0720.04813.3900.6260.6260.0000.0000.0000.000
79A82PHE0-0.025-0.02216.625-0.261-0.2610.0000.0000.0000.000
80A83ILE00.0220.02019.7600.4030.4030.0000.0000.0000.000
81A84LEU0-0.017-0.01122.553-0.010-0.0100.0000.0000.0000.000
82A85VAL00.004-0.00425.5350.2990.2990.0000.0000.0000.000
83A86PHE00.0430.02328.1090.0860.0860.0000.0000.0000.000
84A87SER0-0.031-0.01631.849-0.041-0.0410.0000.0000.0000.000
85A88VAL00.0300.01834.6690.1320.1320.0000.0000.0000.000
86A89THR0-0.017-0.01337.4920.1980.1980.0000.0000.0000.000
87A90SER0-0.019-0.00337.2810.0780.0780.0000.0000.0000.000
88A91LYS11.0011.01137.3306.8966.8960.0000.0000.0000.000
89A92GLN00.0020.00437.4080.0170.0170.0000.0000.0000.000
90A93SER0-0.054-0.04933.710-0.289-0.2890.0000.0000.0000.000
91A94LEU00.0090.00032.832-0.329-0.3290.0000.0000.0000.000
92A95GLU-1-0.883-0.94733.548-7.728-7.7280.0000.0000.0000.000
93A96GLU-1-0.925-0.97932.284-8.859-8.8590.0000.0000.0000.000
94A97LEU0-0.051-0.01527.730-0.339-0.3390.0000.0000.0000.000
95A98GLY00.0190.02229.388-0.257-0.2570.0000.0000.0000.000
96A99PRO0-0.059-0.04530.186-0.154-0.1540.0000.0000.0000.000
97A100ILE0-0.0050.00123.696-0.205-0.2050.0000.0000.0000.000
98A101TYR00.0130.00725.253-0.375-0.3750.0000.0000.0000.000
99A102LYS10.9670.98726.1348.7728.7720.0000.0000.0000.000
100A103LEU0-0.035-0.01623.566-0.150-0.1500.0000.0000.0000.000
101A104ILE00.016-0.00220.800-0.427-0.4270.0000.0000.0000.000
102A105VAL00.0180.01622.046-0.389-0.3890.0000.0000.0000.000
103A106GLN0-0.045-0.03324.171-0.107-0.1070.0000.0000.0000.000
104A107ILE0-0.087-0.04318.799-0.064-0.0640.0000.0000.0000.000
105A108LYS10.8140.91514.70616.49516.4950.0000.0000.0000.000
106A109GLY00.0080.03620.194-0.211-0.2110.0000.0000.0000.000
107A110SER00.0460.01122.6270.7020.7020.0000.0000.0000.000
108A111VAL0-0.047-0.03222.619-0.534-0.5340.0000.0000.0000.000
109A112GLU-1-0.937-0.97623.504-10.661-10.6610.0000.0000.0000.000
110A113ASP-1-0.906-0.93719.732-13.180-13.1800.0000.0000.0000.000
111A114ILE0-0.122-0.07016.806-1.133-1.1330.0000.0000.0000.000
112A115PRO00.0110.02517.0280.7140.7140.0000.0000.0000.000
113A116VAL00.0090.00119.714-0.281-0.2810.0000.0000.0000.000
114A117MET00.0010.02122.5520.5020.5020.0000.0000.0000.000
115A118LEU0-0.0190.00024.790-0.109-0.1090.0000.0000.0000.000
116A119VAL00.000-0.02226.0780.0330.0330.0000.0000.0000.000
117A120GLY00.0610.03229.0460.1120.1120.0000.0000.0000.000
118A121ASN0-0.009-0.02330.3830.0630.0630.0000.0000.0000.000
119A122LYS10.8840.94332.4218.7368.7360.0000.0000.0000.000
120A123CYS00.0240.01635.1330.1360.1360.0000.0000.0000.000
121A124ASP-1-0.866-0.90736.688-8.326-8.3260.0000.0000.0000.000
122A125GLU-1-0.964-0.97639.151-7.403-7.4030.0000.0000.0000.000
123A126THR0-0.010-0.01541.156-0.035-0.0350.0000.0000.0000.000
124A127GLN0-0.049-0.01944.2330.0870.0870.0000.0000.0000.000
125A128ARG10.7780.83638.1597.6977.6970.0000.0000.0000.000
126A129GLU-1-0.859-0.92141.142-7.076-7.0760.0000.0000.0000.000
127A130VAL0-0.022-0.00337.345-0.019-0.0190.0000.0000.0000.000
128A131ASP-1-0.877-0.92540.134-7.122-7.1220.0000.0000.0000.000
129A132THR0-0.059-0.07136.914-0.073-0.0730.0000.0000.0000.000
130A133ARG10.9430.96837.8036.9796.9790.0000.0000.0000.000
131A134GLU-1-0.851-0.90939.601-7.324-7.3240.0000.0000.0000.000
132A135ALA00.0040.00134.509-0.123-0.1230.0000.0000.0000.000
133A136GLN0-0.020-0.01234.447-0.042-0.0420.0000.0000.0000.000
134A137ALA00.0260.01935.275-0.144-0.1440.0000.0000.0000.000
135A138VAL00.000-0.00332.903-0.083-0.0830.0000.0000.0000.000
136A139ALA00.005-0.00930.831-0.161-0.1610.0000.0000.0000.000
137A140GLN0-0.029-0.01431.378-0.220-0.2200.0000.0000.0000.000
138A141GLU-1-0.915-0.95133.401-8.170-8.1700.0000.0000.0000.000
139A142TRP0-0.075-0.05629.245-0.235-0.2350.0000.0000.0000.000
140A143LYS10.9190.98129.0629.2619.2610.0000.0000.0000.000
141A144CYS0-0.059-0.00626.150-0.307-0.3070.0000.0000.0000.000
142A145ALA00.0460.03025.5320.3220.3220.0000.0000.0000.000
143A146PHE00.012-0.02727.4590.0800.0800.0000.0000.0000.000
144A147MET0-0.0110.00627.499-0.107-0.1070.0000.0000.0000.000
145A148GLU-1-0.738-0.80630.484-8.241-8.2410.0000.0000.0000.000
146A149THR00.019-0.01228.266-0.186-0.1860.0000.0000.0000.000
147A150SER0-0.023-0.03731.7330.2040.2040.0000.0000.0000.000
148A151ALA00.0180.00229.763-0.129-0.1290.0000.0000.0000.000
149A152LYS10.9000.96430.8998.0948.0940.0000.0000.0000.000
150A153MET00.0370.00234.218-0.033-0.0330.0000.0000.0000.000
151A154ASN0-0.022-0.01628.952-0.331-0.3310.0000.0000.0000.000
152A155TYR00.0470.03130.946-0.188-0.1880.0000.0000.0000.000
153A156ASN00.035-0.00229.642-0.104-0.1040.0000.0000.0000.000
154A157VAL0-0.0120.00525.745-0.356-0.3560.0000.0000.0000.000
155A158LYS10.8460.92524.30311.85211.8520.0000.0000.0000.000
156A159GLU-1-0.836-0.92323.809-11.493-11.4930.0000.0000.0000.000
157A160LEU00.0010.00723.234-0.274-0.2740.0000.0000.0000.000
158A161PHE0-0.002-0.01518.610-0.342-0.3420.0000.0000.0000.000
159A162GLN00.0370.02619.826-0.964-0.9640.0000.0000.0000.000
160A163GLU-1-0.869-0.92621.389-12.381-12.3810.0000.0000.0000.000
161A164LEU0-0.042-0.03218.359-0.265-0.2650.0000.0000.0000.000
162A165LEU0-0.049-0.04014.963-0.673-0.6730.0000.0000.0000.000
163A166THR0-0.025-0.03018.054-0.523-0.5230.0000.0000.0000.000
164A167LEU00.0000.00620.8570.2220.2220.0000.0000.0000.000
165A168GLU-1-0.807-0.83014.234-18.565-18.5650.0000.0000.0000.000
166A169THR00.0280.01117.723-0.180-0.1800.0000.0000.0000.000
167A170ARG10.7770.85113.76218.23518.2350.0000.0000.0000.000
168A171ARG10.8270.8917.25728.97228.9720.0000.0000.0000.000
169A172ASN0-0.0220.00313.7611.3411.3410.0000.0000.0000.000
170A173MET0-0.001-0.00212.936-2.174-2.1740.0000.0000.0000.000
171A174SER0-0.026-0.01815.7381.3051.3050.0000.0000.0000.000
172A175LEU0-0.017-0.02817.080-1.114-1.1140.0000.0000.0000.000
173A176ASN-1-0.903-0.89519.128-16.496-16.4960.0000.0000.0000.000