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: 7KLVK

Calculation Name: 5O5L-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 3'-o-(n-methylanthraniloyl)-guanosine-5'-triphosphate | sulfate ion | manganese (ii) ion

Ligand 3-letter code: ONM | SO4 | MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5O5L

Chain ID: A

ChEMBL ID:

UniProt ID: X8CHM4

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 224
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2511711.854954
FMO2-HF: Nuclear repulsion 2424217.980761
FMO2-HF: Total energy -87493.874193
FMO2-MP2: Total energy -87746.018744


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:205:THR)


Summations of interaction energy for fragment #1(A:205:THR)
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.
-57.09-50.9294.382-4.504-6.038-0.048
Interaction energy analysis for fragmet #1(A:205:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.826 / q_NPA : 0.909
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].
3A207ARG10.9280.9703.29443.62745.767-0.005-0.941-1.194-0.004
4A208ALA0-0.014-0.0023.3676.3957.2280.020-0.306-0.5470.000
5A209GLU-1-0.814-0.9182.387-75.846-72.7544.368-3.249-4.210-0.044
6A210ALA00.0530.0235.0185.2085.304-0.001-0.008-0.0870.000
7A211VAL0-0.043-0.0187.9553.3643.3640.0000.0000.0000.000
8A212MET0-0.025-0.0097.2533.3813.3810.0000.0000.0000.000
9A213GLU-1-0.889-0.9458.968-23.147-23.1470.0000.0000.0000.000
10A214ALA00.0260.02211.2022.0022.0020.0000.0000.0000.000
11A215GLU-1-0.929-0.98612.638-16.132-16.1320.0000.0000.0000.000
12A216TYR0-0.063-0.02013.1761.4391.4390.0000.0000.0000.000
13A217GLU-1-0.907-0.96514.854-18.085-18.0850.0000.0000.0000.000
14A218ARG10.8480.93116.95416.29216.2920.0000.0000.0000.000
15A219SER00.002-0.00517.5641.1751.1750.0000.0000.0000.000
16A220GLU-1-0.801-0.88118.814-13.374-13.3740.0000.0000.0000.000
17A221ALA00.0030.00320.5960.7650.7650.0000.0000.0000.000
18A222LEU0-0.021-0.00822.4830.6930.6930.0000.0000.0000.000
19A223LEU0-0.045-0.02522.3710.6730.6730.0000.0000.0000.000
20A224ALA0-0.009-0.01424.6730.5090.5090.0000.0000.0000.000
21A225ASN0-0.060-0.01326.5910.4660.4660.0000.0000.0000.000
22A226MET0-0.046-0.01828.1730.2860.2860.0000.0000.0000.000
23A227LEU0-0.054-0.02727.3830.4350.4350.0000.0000.0000.000
24A228PRO00.0770.05129.518-0.252-0.2520.0000.0000.0000.000
25A229GLY00.0520.02228.336-0.103-0.1030.0000.0000.0000.000
26A230SER0-0.012-0.01328.417-0.254-0.2540.0000.0000.0000.000
27A231ILE0-0.003-0.00430.505-0.011-0.0110.0000.0000.0000.000
28A232ALA00.0480.02625.902-0.082-0.0820.0000.0000.0000.000
29A233GLU-1-0.809-0.89323.975-12.812-12.8120.0000.0000.0000.000
30A234ARG10.7850.89426.6918.6888.6880.0000.0000.0000.000
31A235LEU0-0.038-0.01827.8560.1040.1040.0000.0000.0000.000
32A236LYS10.8010.87520.95712.98612.9860.0000.0000.0000.000
33A237SER0-0.067-0.04923.993-0.211-0.2110.0000.0000.0000.000
34A238SER0-0.047-0.00824.4570.0540.0540.0000.0000.0000.000
35A239SER00.0130.01427.0480.3040.3040.0000.0000.0000.000
36A240ARG10.9400.95530.7328.6618.6610.0000.0000.0000.000
37A241SER0-0.042-0.01233.4440.3410.3410.0000.0000.0000.000
38A242VAL00.003-0.00134.756-0.178-0.1780.0000.0000.0000.000
39A243ILE00.0030.01032.1580.0780.0780.0000.0000.0000.000
40A244ALA00.001-0.01236.8060.0720.0720.0000.0000.0000.000
41A245ASP-1-0.815-0.88037.842-7.999-7.9990.0000.0000.0000.000
42A246LYS10.9310.95241.3346.5576.5570.0000.0000.0000.000
43A247TYR0-0.003-0.01139.304-0.095-0.0950.0000.0000.0000.000
44A248ASP-1-0.901-0.95246.026-6.274-6.2740.0000.0000.0000.000
45A249GLU-1-0.904-0.95848.928-5.778-5.7780.0000.0000.0000.000
46A250VAL0-0.0430.00245.125-0.134-0.1340.0000.0000.0000.000
47A251SER00.024-0.02247.5560.2250.2250.0000.0000.0000.000
48A252VAL0-0.039-0.02546.981-0.167-0.1670.0000.0000.0000.000
49A253LEU0-0.004-0.00147.0040.1900.1900.0000.0000.0000.000
50A254PHE0-0.007-0.01147.310-0.156-0.1560.0000.0000.0000.000
51A255ALA00.0460.01547.9180.1450.1450.0000.0000.0000.000
52A256ASP-1-0.784-0.86148.576-6.335-6.3350.0000.0000.0000.000
53A257ILE0-0.0070.01348.0080.1110.1110.0000.0000.0000.000
54A258VAL0-0.047-0.02552.2180.0830.0830.0000.0000.0000.000
55A259GLY00.0940.05555.744-0.023-0.0230.0000.0000.0000.000
56A260PHE0-0.0100.00147.522-0.043-0.0430.0000.0000.0000.000
57A261THR00.017-0.01653.150-0.049-0.0490.0000.0000.0000.000
58A262GLU-1-0.888-0.93554.087-5.412-5.4120.0000.0000.0000.000
59A263ARG10.8040.88652.5365.9805.9800.0000.0000.0000.000
60A264ALA0-0.029-0.01252.544-0.060-0.0600.0000.0000.0000.000
61A265SER0-0.067-0.03353.6750.0090.0090.0000.0000.0000.000
62A266THR00.001-0.00155.1460.0100.0100.0000.0000.0000.000
63A267THR0-0.025-0.01849.446-0.078-0.0780.0000.0000.0000.000
64A268THR00.007-0.00747.368-0.027-0.0270.0000.0000.0000.000
65A269PRO00.0730.01146.444-0.083-0.0830.0000.0000.0000.000
66A270ALA00.0190.01142.694-0.116-0.1160.0000.0000.0000.000
67A271ASP-1-0.811-0.86843.367-7.206-7.2060.0000.0000.0000.000
68A272LEU00.0070.00745.870-0.016-0.0160.0000.0000.0000.000
69A273VAL0-0.0040.00740.348-0.056-0.0560.0000.0000.0000.000
70A274ARG10.8490.89740.4047.4707.4700.0000.0000.0000.000
71A275PHE0-0.023-0.00842.300-0.068-0.0680.0000.0000.0000.000
72A276LEU00.0500.02242.657-0.019-0.0190.0000.0000.0000.000
73A277ASN0-0.021-0.00836.935-0.193-0.1930.0000.0000.0000.000
74A278ARG10.8750.94239.8116.9476.9470.0000.0000.0000.000
75A279LEU0-0.023-0.00341.967-0.001-0.0010.0000.0000.0000.000
76A280TYR0-0.010-0.04040.0700.0280.0280.0000.0000.0000.000
77A281GLY00.0330.02838.125-0.095-0.0950.0000.0000.0000.000
78A282ALA00.0340.02239.112-0.073-0.0730.0000.0000.0000.000
79A283PHE0-0.023-0.02541.9910.1340.1340.0000.0000.0000.000
80A284ASP-1-0.772-0.85036.713-8.336-8.3360.0000.0000.0000.000
81A285GLU-1-0.891-0.95137.746-8.197-8.1970.0000.0000.0000.000
82A286LEU0-0.043-0.01538.8760.0380.0380.0000.0000.0000.000
83A287VAL0-0.027-0.02137.8540.1230.1230.0000.0000.0000.000
84A288ASP-1-0.901-0.93834.812-9.020-9.0200.0000.0000.0000.000
85A289LYS10.7640.87037.7427.0707.0700.0000.0000.0000.000
86A290HIS0-0.064-0.04540.6080.1420.1420.0000.0000.0000.000
87A291GLY0-0.0270.00338.4920.0830.0830.0000.0000.0000.000
88A292LEU0-0.114-0.06539.5290.1260.1260.0000.0000.0000.000
89A293GLU-1-0.826-0.92735.828-8.823-8.8230.0000.0000.0000.000
90A294LYS10.8280.90136.7868.6358.6350.0000.0000.0000.000
91A295ILE0-0.054-0.01437.704-0.174-0.1740.0000.0000.0000.000
92A296LYS10.8120.87738.3797.0627.0620.0000.0000.0000.000
93A297VAL00.0250.02040.1420.1140.1140.0000.0000.0000.000
94A298SER0-0.113-0.06441.951-0.033-0.0330.0000.0000.0000.000
95A299GLY00.0070.01244.2480.1690.1690.0000.0000.0000.000
96A300ASP-1-0.834-0.93044.831-6.568-6.5680.0000.0000.0000.000
97A301SER00.0010.00147.1450.0240.0240.0000.0000.0000.000
98A302TYR0-0.050-0.06540.094-0.145-0.1450.0000.0000.0000.000
99A303MET0-0.030-0.00343.3910.1370.1370.0000.0000.0000.000
100A304VAL00.0260.01642.418-0.208-0.2080.0000.0000.0000.000
101A305VAL0-0.031-0.02542.4630.2230.2230.0000.0000.0000.000
102A306SER00.0070.00442.699-0.210-0.2100.0000.0000.0000.000
103A307GLY00.0330.00043.1390.1780.1780.0000.0000.0000.000
104A308VAL0-0.0130.01139.9510.0160.0160.0000.0000.0000.000
105A309PRO00.0460.02635.236-0.010-0.0100.0000.0000.0000.000
106A310ARG10.9220.96334.9468.4738.4730.0000.0000.0000.000
107A311ALA00.0420.02539.4300.0810.0810.0000.0000.0000.000
108A312ARG10.8460.91542.0857.1267.1260.0000.0000.0000.000
109A313PRO00.0250.00845.2490.0770.0770.0000.0000.0000.000
110A314ASP-1-0.811-0.89847.147-6.657-6.6570.0000.0000.0000.000
111A315HIS0-0.0280.00647.234-0.069-0.0690.0000.0000.0000.000
112A316ALA00.0580.02748.189-0.053-0.0530.0000.0000.0000.000
113A317PHE0-0.036-0.01751.0150.0220.0220.0000.0000.0000.000
114A318ALA00.0670.03645.9800.0080.0080.0000.0000.0000.000
115A319LEU00.006-0.00146.156-0.067-0.0670.0000.0000.0000.000
116A320ALA0-0.006-0.00448.5390.0260.0260.0000.0000.0000.000
117A321ASP-1-0.773-0.86649.180-6.184-6.1840.0000.0000.0000.000
118A322PHE00.0100.00043.3870.0250.0250.0000.0000.0000.000
119A323ALA00.0250.00147.914-0.013-0.0130.0000.0000.0000.000
120A324LEU0-0.019-0.00650.5730.0600.0600.0000.0000.0000.000
121A325ASP-1-0.800-0.86246.579-6.805-6.8050.0000.0000.0000.000
122A326MET0-0.008-0.00645.490-0.001-0.0010.0000.0000.0000.000
123A327ALA0-0.014-0.00448.7650.0110.0110.0000.0000.0000.000
124A328ASN0-0.019-0.01051.3280.1290.1290.0000.0000.0000.000
125A329VAL00.0000.00645.6330.0130.0130.0000.0000.0000.000
126A330ALA0-0.012-0.01549.024-0.021-0.0210.0000.0000.0000.000
127A331ALA0-0.042-0.01950.6480.0530.0530.0000.0000.0000.000
128A332ALA0-0.0080.00950.2110.0860.0860.0000.0000.0000.000
129A333LEU0-0.042-0.01546.084-0.067-0.0670.0000.0000.0000.000
130A334LYS10.9100.95649.7146.3466.3460.0000.0000.0000.000
131A335ASP-1-0.751-0.85349.397-6.240-6.2400.0000.0000.0000.000
132A336PRO0-0.123-0.09048.400-0.040-0.0400.0000.0000.0000.000
133A337HIS10.8410.92250.3955.9865.9860.0000.0000.0000.000
134A338GLY0-0.0230.00852.9200.0860.0860.0000.0000.0000.000
135A339ASP-1-0.872-0.92454.253-5.557-5.5570.0000.0000.0000.000
136A340PRO00.025-0.00354.107-0.143-0.1430.0000.0000.0000.000
137A341VAL00.0050.00550.007-0.006-0.0060.0000.0000.0000.000
138A342PRO0-0.0140.00153.082-0.028-0.0280.0000.0000.0000.000
139A343LEU00.0460.02449.812-0.038-0.0380.0000.0000.0000.000
140A344ARG10.7800.89053.8655.9815.9810.0000.0000.0000.000
141A345MET0-0.005-0.02051.353-0.199-0.1990.0000.0000.0000.000
142A346GLY0-0.0140.00552.7390.1490.1490.0000.0000.0000.000
143A347MET0-0.028-0.00751.396-0.184-0.1840.0000.0000.0000.000
144A348ALA0-0.031-0.03252.1070.1650.1650.0000.0000.0000.000
145A349CYS0-0.062-0.02251.614-0.096-0.0960.0000.0000.0000.000
146A350GLY00.004-0.00251.5110.1410.1410.0000.0000.0000.000
147A351PRO00.0080.01850.169-0.124-0.1240.0000.0000.0000.000
148A352VAL0-0.055-0.03444.8820.0430.0430.0000.0000.0000.000
149A353VAL0-0.040-0.01543.328-0.028-0.0280.0000.0000.0000.000
150A354ALA00.0430.01840.3900.0310.0310.0000.0000.0000.000
151A355GLY0-0.001-0.01338.100-0.045-0.0450.0000.0000.0000.000
152A356VAL0-0.0160.00733.119-0.048-0.0480.0000.0000.0000.000
153A357VAL0-0.0030.00036.5230.0760.0760.0000.0000.0000.000
154A358GLY00.0180.01136.878-0.057-0.0570.0000.0000.0000.000
155A359SER00.007-0.00932.858-0.146-0.1460.0000.0000.0000.000
156A360ARG10.9390.95531.0428.6628.6620.0000.0000.0000.000
157A361ARG10.9190.95330.3319.9289.9280.0000.0000.0000.000
158A362PHE00.0180.04028.6800.2220.2220.0000.0000.0000.000
159A363PHE00.0340.01332.760-0.238-0.2380.0000.0000.0000.000
160A364TYR00.0470.01134.4940.1170.1170.0000.0000.0000.000
161A365ASP-1-0.753-0.85636.178-7.307-7.3070.0000.0000.0000.000
162A366VAL00.005-0.01439.971-0.001-0.0010.0000.0000.0000.000
163A367TRP0-0.0120.00240.2670.1200.1200.0000.0000.0000.000
164A368GLY00.0560.01346.562-0.016-0.0160.0000.0000.0000.000
165A369ASP-1-0.832-0.89749.964-5.582-5.5820.0000.0000.0000.000
166A370ALA00.0530.03550.3440.0390.0390.0000.0000.0000.000
167A371VAL00.0610.02446.9940.0390.0390.0000.0000.0000.000
168A372ASN0-0.044-0.01350.1450.0550.0550.0000.0000.0000.000
169A373VAL0-0.004-0.01153.2240.0710.0710.0000.0000.0000.000
170A374ALA00.0220.02451.2510.0730.0730.0000.0000.0000.000
171A375SER00.0660.04151.3300.0630.0630.0000.0000.0000.000
172A376ARG10.8100.89853.0655.8285.8280.0000.0000.0000.000
173A377MET0-0.0280.01055.7520.1260.1260.0000.0000.0000.000
174A378GLU-1-0.782-0.88952.023-5.903-5.9030.0000.0000.0000.000
175A379SER0-0.046-0.00955.2280.1010.1010.0000.0000.0000.000
176A380THR0-0.023-0.03056.9570.0930.0930.0000.0000.0000.000
177A381ASP-1-0.759-0.87757.544-5.382-5.3820.0000.0000.0000.000
178A382SER0-0.102-0.03559.6310.0620.0620.0000.0000.0000.000
179A383VAL00.028-0.01058.533-0.040-0.0400.0000.0000.0000.000
180A384GLY0-0.0080.00456.9070.0730.0730.0000.0000.0000.000
181A385ARG10.8100.93057.9375.1475.1470.0000.0000.0000.000
182A386ILE00.1000.04954.118-0.095-0.0950.0000.0000.0000.000
183A387GLN0-0.0290.00756.6180.1950.1950.0000.0000.0000.000
184A388VAL00.0210.00755.901-0.117-0.1170.0000.0000.0000.000
185A389PRO00.0380.00857.2320.1270.1270.0000.0000.0000.000
186A390GLU-1-0.820-0.90260.118-4.888-4.8880.0000.0000.0000.000
187A391ALA0-0.0150.00058.755-0.014-0.0140.0000.0000.0000.000
188A392MET00.0510.02652.130-0.023-0.0230.0000.0000.0000.000
189A393TYR00.0500.02657.595-0.035-0.0350.0000.0000.0000.000
190A394GLU-1-0.881-0.94160.467-4.965-4.9650.0000.0000.0000.000
191A395ARG10.8660.93455.4475.4895.4890.0000.0000.0000.000
192A396LEU00.0430.01954.279-0.016-0.0160.0000.0000.0000.000
193A397LYS10.8110.91258.0375.0185.0180.0000.0000.0000.000
194A398ASN0-0.061-0.02758.6340.0240.0240.0000.0000.0000.000
195A399GLU-1-0.802-0.90555.962-5.536-5.5360.0000.0000.0000.000
196A400PHE0-0.034-0.01153.0640.0010.0010.0000.0000.0000.000
197A401VAL0-0.0050.00759.2980.1260.1260.0000.0000.0000.000
198A402LEU0-0.016-0.01959.085-0.079-0.0790.0000.0000.0000.000
199A403GLN00.0170.01362.8340.0510.0510.0000.0000.0000.000
200A404GLU-1-0.858-0.90864.872-4.653-4.6530.0000.0000.0000.000
201A405ARG10.8190.89062.2575.0785.0780.0000.0000.0000.000
202A406GLY00.0640.05467.1020.0650.0650.0000.0000.0000.000
203A407ARG10.8780.91867.4624.4744.4740.0000.0000.0000.000
204A408ILE00.0290.01962.5100.0180.0180.0000.0000.0000.000
205A409GLU-1-0.946-0.96965.681-4.718-4.7180.0000.0000.0000.000
206A410VAL0-0.005-0.01159.924-0.095-0.0950.0000.0000.0000.000
207A411LYS10.9930.97357.7235.4325.4320.0000.0000.0000.000
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209A413LYS10.8100.88057.7875.4055.4050.0000.0000.0000.000
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