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: 672KZ

Calculation Name: 6A8D-A-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate | sulfate ion | magnesium ion

Ligand 3-letter code: GDP | SO4 | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6A8D

Chain ID: A

ChEMBL ID:

UniProt ID: A8ILA3

Base Structure: X-ray

Registration Date: 2025-10-04

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 181
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2008052.170217
FMO2-HF: Nuclear repulsion 1935684.380045
FMO2-HF: Total energy -72367.790172
FMO2-MP2: Total energy -72577.643722


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:-1:HIS)


Summations of interaction energy for fragment #1(A:-1:HIS)
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.
21.51223.1210.003-0.775-0.837-0.001
Interaction energy analysis for fragmet #1(A:-1:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.874 / q_NPA : 0.926
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].
3A1MET00.0130.0083.469-6.021-4.4120.003-0.775-0.837-0.001
4A2GLY00.0360.0286.0293.7883.7880.0000.0000.0000.000
5A3GLN0-0.031-0.0249.5560.8720.8720.0000.0000.0000.000
6A4ALA00.0440.02212.6710.5970.5970.0000.0000.0000.000
7A5PHE00.0550.02015.3070.3040.3040.0000.0000.0000.000
8A6THR00.0540.03118.3730.5180.5180.0000.0000.0000.000
9A7LYS10.9680.97413.90620.69320.6930.0000.0000.0000.000
10A8LEU0-0.0390.00415.8030.0410.0410.0000.0000.0000.000
11A9PHE00.0720.02619.6660.6460.6460.0000.0000.0000.000
12A10ASP-1-0.833-0.87921.928-12.634-12.6340.0000.0000.0000.000
13A11ARG10.9230.96417.50516.77616.7760.0000.0000.0000.000
14A12TRP0-0.059-0.04019.3930.4380.4380.0000.0000.0000.000
15A13PHE00.0610.01624.7490.4890.4890.0000.0000.0000.000
16A14GLY0-0.0030.00726.3680.4120.4120.0000.0000.0000.000
17A15ASN0-0.070-0.06327.6630.0850.0850.0000.0000.0000.000
18A16ARG10.9140.97128.52010.87310.8730.0000.0000.0000.000
19A17GLU-1-0.883-0.92532.497-9.089-9.0890.0000.0000.0000.000
20A18MET0-0.013-0.00330.765-0.102-0.1020.0000.0000.0000.000
21A19ARG10.8650.94133.6508.6968.6960.0000.0000.0000.000
22A20VAL00.0000.00429.5440.0430.0430.0000.0000.0000.000
23A21VAL00.0170.01632.9660.0040.0040.0000.0000.0000.000
24A22MET0-0.041-0.01527.297-0.267-0.2670.0000.0000.0000.000
25A23LEU00.0320.01232.1550.1500.1500.0000.0000.0000.000
26A24GLY00.0610.02032.865-0.303-0.3030.0000.0000.0000.000
27A25LEU00.0030.01334.5530.0720.0720.0000.0000.0000.000
28A26ASP-1-0.791-0.88033.991-8.751-8.7510.0000.0000.0000.000
29A27ALA00.0180.00231.894-0.063-0.0630.0000.0000.0000.000
30A28ALA0-0.0160.01030.470-0.357-0.3570.0000.0000.0000.000
31A29GLY00.0310.00626.989-0.392-0.3920.0000.0000.0000.000
32A30LYS10.7730.87426.5358.9198.9190.0000.0000.0000.000
33A31THR00.038-0.00727.379-0.347-0.3470.0000.0000.0000.000
34A32THR0-0.050-0.02822.732-0.176-0.1760.0000.0000.0000.000
35A33ILE00.0190.00722.841-0.636-0.6360.0000.0000.0000.000
36A34LEU0-0.027-0.00723.097-0.491-0.4910.0000.0000.0000.000
37A35TYR00.0350.00923.520-0.347-0.3470.0000.0000.0000.000
38A36LYS10.8200.91316.25916.73716.7370.0000.0000.0000.000
39A37LEU0-0.013-0.01318.681-0.951-0.9510.0000.0000.0000.000
40A38HIS0-0.064-0.02718.045-0.171-0.1710.0000.0000.0000.000
41A39ILE0-0.0120.00221.140-0.167-0.1670.0000.0000.0000.000
42A40GLY00.013-0.00523.4630.3660.3660.0000.0000.0000.000
43A41GLU-1-0.941-0.95626.485-10.176-10.1760.0000.0000.0000.000
44A42VAL0-0.030-0.02028.1610.0900.0900.0000.0000.0000.000
45A43LEU0-0.0140.00530.7400.2200.2200.0000.0000.0000.000
46A44THR00.007-0.00634.524-0.060-0.0600.0000.0000.0000.000
47A45THR0-0.047-0.03336.7970.2100.2100.0000.0000.0000.000
48A46VAL00.0370.03140.360-0.094-0.0940.0000.0000.0000.000
49A47PRO0-0.032-0.00842.4190.1750.1750.0000.0000.0000.000
50A48THR0-0.019-0.02745.5960.2180.2180.0000.0000.0000.000
51A49ILE00.0040.00445.834-0.142-0.1420.0000.0000.0000.000
52A50GLY00.0300.02544.629-0.045-0.0450.0000.0000.0000.000
53A51PHE0-0.055-0.01341.081-0.148-0.1480.0000.0000.0000.000
54A52ASN00.026-0.00536.6160.1470.1470.0000.0000.0000.000
55A53VAL0-0.013-0.00637.348-0.101-0.1010.0000.0000.0000.000
56A54GLU-1-0.841-0.89931.789-9.956-9.9560.0000.0000.0000.000
57A55LYS10.9330.96133.2739.0149.0140.0000.0000.0000.000
58A56VAL00.0290.02827.028-0.068-0.0680.0000.0000.0000.000
59A57GLN0-0.063-0.04730.1570.4020.4020.0000.0000.0000.000
60A58TYR0-0.019-0.02023.961-0.233-0.2330.0000.0000.0000.000
61A59LYS10.8320.90325.70112.12112.1210.0000.0000.0000.000
62A60ASN00.0160.00930.2090.1490.1490.0000.0000.0000.000
63A61VAL0-0.0010.00527.6940.2200.2200.0000.0000.0000.000
64A62VAL0-0.038-0.02330.751-0.134-0.1340.0000.0000.0000.000
65A63PHE00.0210.01326.332-0.041-0.0410.0000.0000.0000.000
66A64THR00.0070.00031.1770.0780.0780.0000.0000.0000.000
67A65VAL00.000-0.00430.552-0.033-0.0330.0000.0000.0000.000
68A66TRP00.0520.02233.9490.1190.1190.0000.0000.0000.000
69A67ASP-1-0.830-0.89335.139-9.039-9.0390.0000.0000.0000.000
70A68VAL0-0.045-0.01937.1940.2450.2450.0000.0000.0000.000
71A69GLY00.0270.00839.294-0.092-0.0920.0000.0000.0000.000
72A70GLY0-0.031-0.02342.073-0.062-0.0620.0000.0000.0000.000
73A71GLN0-0.004-0.01540.9460.1500.1500.0000.0000.0000.000
74A72GLU-1-0.858-0.91845.303-6.152-6.1520.0000.0000.0000.000
75A73LYS10.9220.94648.1356.3716.3710.0000.0000.0000.000
76A74LEU00.0790.04345.2760.0610.0610.0000.0000.0000.000
77A75ARG10.7970.89144.6526.9606.9600.0000.0000.0000.000
78A76PRO0-0.033-0.03046.467-0.092-0.0920.0000.0000.0000.000
79A77LEU00.0160.01145.998-0.018-0.0180.0000.0000.0000.000
80A78TRP0-0.0060.00342.265-0.135-0.1350.0000.0000.0000.000
81A79ARG10.8360.88542.9766.6006.6000.0000.0000.0000.000
82A80HIS0-0.0020.01743.3860.0320.0320.0000.0000.0000.000
83A81TYR00.011-0.01139.390-0.071-0.0710.0000.0000.0000.000
84A82PHE00.0130.00039.122-0.181-0.1810.0000.0000.0000.000
85A83ASN0-0.067-0.02141.1850.0570.0570.0000.0000.0000.000
86A84ASN0-0.023-0.02040.773-0.054-0.0540.0000.0000.0000.000
87A85THR00.0070.01135.974-0.218-0.2180.0000.0000.0000.000
88A86ASP-1-0.798-0.89134.183-8.743-8.7430.0000.0000.0000.000
89A87GLY0-0.009-0.01232.590-0.043-0.0430.0000.0000.0000.000
90A88LEU0-0.008-0.00233.6410.0950.0950.0000.0000.0000.000
91A89ILE0-0.018-0.00927.742-0.242-0.2420.0000.0000.0000.000
92A90PHE00.0240.00330.8210.2620.2620.0000.0000.0000.000
93A91VAL0-0.025-0.01127.543-0.274-0.2740.0000.0000.0000.000
94A92VAL00.017-0.00329.8090.3690.3690.0000.0000.0000.000
95A93ASP-1-0.816-0.89629.384-10.529-10.5290.0000.0000.0000.000
96A94SER00.0260.00528.0410.3230.3230.0000.0000.0000.000
97A95GLN0-0.001-0.01129.5810.0670.0670.0000.0000.0000.000
98A96ASP-1-0.829-0.88131.375-8.291-8.2910.0000.0000.0000.000
99A97ARG10.8000.86932.5529.3109.3100.0000.0000.0000.000
100A98ASP-1-0.899-0.92336.582-7.621-7.6210.0000.0000.0000.000
101A99ARG10.7510.83935.6878.5898.5890.0000.0000.0000.000
102A100ILE00.0340.02134.1940.0290.0290.0000.0000.0000.000
103A101GLY00.0360.02437.5070.0520.0520.0000.0000.0000.000
104A102LYS10.8100.89440.6647.2767.2760.0000.0000.0000.000
105A103ALA00.017-0.00635.9690.0260.0260.0000.0000.0000.000
106A104ALA00.0480.01838.114-0.037-0.0370.0000.0000.0000.000
107A105GLN0-0.022-0.00439.7290.0830.0830.0000.0000.0000.000
108A106GLU-1-0.821-0.92139.528-7.204-7.2040.0000.0000.0000.000
109A107PHE00.0070.00835.021-0.007-0.0070.0000.0000.0000.000
110A108GLN00.0400.02038.8240.0900.0900.0000.0000.0000.000
111A109ALA00.0240.01141.8100.1310.1310.0000.0000.0000.000
112A110ILE0-0.0270.00237.7050.1170.1170.0000.0000.0000.000
113A111LEU00.0190.00837.5650.0770.0770.0000.0000.0000.000
114A112GLN0-0.011-0.00141.2650.1390.1390.0000.0000.0000.000
115A113ASP-1-0.740-0.82743.482-6.768-6.7680.0000.0000.0000.000
116A114PRO00.001-0.01344.399-0.114-0.1140.0000.0000.0000.000
117A115LEU0-0.028-0.01443.459-0.009-0.0090.0000.0000.0000.000
118A116MET00.0240.02238.923-0.239-0.2390.0000.0000.0000.000
119A117LEU0-0.079-0.00740.623-0.153-0.1530.0000.0000.0000.000
120A118HIS00.017-0.01840.884-0.117-0.1170.0000.0000.0000.000
121A119SER0-0.0060.02036.333-0.083-0.0830.0000.0000.0000.000
122A120ALA0-0.0180.00232.4670.0430.0430.0000.0000.0000.000
123A121ILE0-0.032-0.02533.247-0.063-0.0630.0000.0000.0000.000
124A122LEU0-0.0100.00925.266-0.184-0.1840.0000.0000.0000.000
125A123VAL00.0050.00729.7600.0950.0950.0000.0000.0000.000
126A124PHE00.008-0.01022.654-0.372-0.3720.0000.0000.0000.000
127A125ALA00.0240.01526.7270.3650.3650.0000.0000.0000.000
128A126ASN00.0140.00723.883-1.087-1.0870.0000.0000.0000.000
129A127LYS10.8110.89124.05511.04211.0420.0000.0000.0000.000
130A128GLN00.004-0.01622.4820.5160.5160.0000.0000.0000.000
131A129ASP-1-0.879-0.94520.649-13.751-13.7510.0000.0000.0000.000
132A130MET0-0.0220.00322.4970.1020.1020.0000.0000.0000.000
133A131LYS10.9730.97126.11510.27610.2760.0000.0000.0000.000
134A132GLY00.0140.00827.9780.2970.2970.0000.0000.0000.000
135A133CYS0-0.025-0.00527.2590.2280.2280.0000.0000.0000.000
136A134LEU0-0.043-0.01529.8260.0990.0990.0000.0000.0000.000
137A135THR00.0090.01728.352-0.545-0.5450.0000.0000.0000.000
138A136PRO00.0650.00425.7360.3210.3210.0000.0000.0000.000
139A137ALA00.0300.01428.8680.2410.2410.0000.0000.0000.000
140A138GLU-1-0.792-0.88032.045-9.019-9.0190.0000.0000.0000.000
141A139VAL00.0310.01230.3270.2690.2690.0000.0000.0000.000
142A140CYS0-0.062-0.01932.1640.2670.2670.0000.0000.0000.000
143A141THR0-0.018-0.01633.9430.2770.2770.0000.0000.0000.000
144A142ALA0-0.022-0.01236.5330.2160.2160.0000.0000.0000.000
145A143LEU0-0.044-0.02333.8930.1850.1850.0000.0000.0000.000
146A144GLY00.0180.01637.6620.1020.1020.0000.0000.0000.000
147A145LEU0-0.001-0.01433.0870.0380.0380.0000.0000.0000.000
148A146SER0-0.013-0.01337.244-0.020-0.0200.0000.0000.0000.000
149A147ASP-1-0.847-0.89738.958-7.378-7.3780.0000.0000.0000.000
150A148MET0-0.052-0.02337.3130.2600.2600.0000.0000.0000.000
151A149ARG10.7770.87540.6537.2877.2870.0000.0000.0000.000
152A150THR00.0360.02541.3880.0240.0240.0000.0000.0000.000
153A151ARG10.8070.89937.6947.6277.6270.0000.0000.0000.000
154A152LYS10.9730.98833.2888.5618.5610.0000.0000.0000.000
155A153TRP00.0400.00632.467-0.168-0.1680.0000.0000.0000.000
156A154HIS00.0090.00824.2030.2700.2700.0000.0000.0000.000
157A155VAL0-0.001-0.00828.6230.1610.1610.0000.0000.0000.000
158A156GLN0-0.026-0.00221.010-0.023-0.0230.0000.0000.0000.000
159A157SER00.0160.01221.8290.2220.2220.0000.0000.0000.000
160A158SER00.0490.00120.773-0.434-0.4340.0000.0000.0000.000
161A159VAL0-0.0020.01218.6690.5660.5660.0000.0000.0000.000
162A160ALA00.0300.01719.147-0.784-0.7840.0000.0000.0000.000
163A161THR00.0250.00620.271-0.451-0.4510.0000.0000.0000.000
164A162ARG10.8280.90115.26716.39016.3900.0000.0000.0000.000
165A163GLY0-0.012-0.00515.069-1.150-1.1500.0000.0000.0000.000
166A164GLU-1-0.851-0.90614.726-18.609-18.6090.0000.0000.0000.000
167A165GLY00.0660.02616.6811.0271.0270.0000.0000.0000.000
168A166LEU0-0.035-0.02518.3770.6650.6650.0000.0000.0000.000
169A167TYR0-0.026-0.00415.757-0.106-0.1060.0000.0000.0000.000
170A168GLU-1-0.869-0.94316.455-17.130-17.1300.0000.0000.0000.000
171A169GLY00.0310.00920.1410.6530.6530.0000.0000.0000.000
172A170LEU0-0.005-0.01321.4260.6600.6600.0000.0000.0000.000
173A171ASP-1-0.852-0.91320.314-14.534-14.5340.0000.0000.0000.000
174A172TRP00.0320.02822.4610.4660.4660.0000.0000.0000.000
175A173LEU00.0090.01025.3880.4830.4830.0000.0000.0000.000
176A174ALA0-0.025-0.01624.7910.4400.4400.0000.0000.0000.000
177A175THR0-0.068-0.03525.1740.2860.2860.0000.0000.0000.000
178A176THR0-0.051-0.04227.8190.4910.4910.0000.0000.0000.000
179A177LEU0-0.023-0.02130.2760.3510.3510.0000.0000.0000.000
180A178LYS10.7890.91327.21711.51911.5190.0000.0000.0000.000
181A179ASN-1-0.934-0.94432.336-9.177-9.1770.0000.0000.0000.000