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: 1VY2Z

Calculation Name: 7QO6-f-Other547

Preferred Name:

Target Type:

Ligand Name: adenosine-5'-triphosphate | adenosine-5'-diphosphate | amino-acetaldehyde | magnesium ion

Ligand 3-letter code: ATP | ADP | GLZ | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7QO6

Chain ID: f

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2692606.044975
FMO2-HF: Nuclear repulsion 2605023.335847
FMO2-HF: Total energy -87582.709128
FMO2-MP2: Total energy -87840.991803


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:ASN)


Summations of interaction energy for fragment #1(A:4:ASN)
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.
-67.388-61.3647.964-6.502-7.485-0.011
Interaction energy analysis for fragmet #1(A:4:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.800 / q_NPA : 0.895
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].
3A6TYR00.0700.0093.7858.01510.063-0.027-0.798-1.222-0.003
4A7ASP-1-0.800-0.8831.969-68.303-65.4463.479-3.958-2.378-0.018
5A8GLY0-0.0080.0042.229-1.479-0.9444.310-2.095-2.7500.016
6A9ASP-1-0.805-0.8952.950-40.215-39.6310.2020.349-1.135-0.006
7A10THR0-0.035-0.0365.5390.9750.9750.0000.0000.0000.000
8A11VAL00.0150.0208.0291.3021.3020.0000.0000.0000.000
9A12THR0-0.062-0.0305.5240.2300.2300.0000.0000.0000.000
10A13PHE00.0300.0218.5750.5430.5430.0000.0000.0000.000
11A14SER0-0.071-0.0318.803-1.341-1.3410.0000.0000.0000.000
12A15PRO00.024-0.0079.8461.8251.8250.0000.0000.0000.000
13A16THR0-0.019-0.01311.8411.2041.2040.0000.0000.0000.000
14A17GLY00.0110.01014.0290.9160.9160.0000.0000.0000.000
15A18ARG10.8580.92311.56721.24321.2430.0000.0000.0000.000
16A19LEU00.0360.0227.555-0.428-0.4280.0000.0000.0000.000
17A20PHE00.0140.0196.3861.1511.1510.0000.0000.0000.000
18A21GLN00.012-0.0036.5042.9732.9730.0000.0000.0000.000
19A22VAL0-0.037-0.00610.0771.5301.5300.0000.0000.0000.000
20A23GLU-1-0.823-0.92111.421-21.507-21.5070.0000.0000.0000.000
21A24TYR00.0270.0136.018-0.529-0.5290.0000.0000.0000.000
22A25ALA0-0.027-0.00512.1281.1381.1380.0000.0000.0000.000
23A26LEU0-0.020-0.01915.2361.3281.3280.0000.0000.0000.000
24A27GLU-1-0.903-0.95212.181-22.774-22.7740.0000.0000.0000.000
25A28ALA00.0050.01516.5190.9020.9020.0000.0000.0000.000
26A29ILE0-0.029-0.01518.5390.9740.9740.0000.0000.0000.000
27A30LYS10.8140.91019.14714.55614.5560.0000.0000.0000.000
28A31GLN00.0360.01816.5520.8810.8810.0000.0000.0000.000
29A32GLY0-0.0270.00221.4210.5430.5430.0000.0000.0000.000
30A33SER00.0420.01424.411-0.045-0.0450.0000.0000.0000.000
31A34VAL0-0.0080.00927.999-0.123-0.1230.0000.0000.0000.000
32A35THR00.002-0.00329.3340.3770.3770.0000.0000.0000.000
33A36VAL00.0260.00731.266-0.304-0.3040.0000.0000.0000.000
34A37GLY00.0120.00834.1150.1230.1230.0000.0000.0000.000
35A38LEU0-0.019-0.01335.830-0.121-0.1210.0000.0000.0000.000
36A39ARG10.8170.91138.8097.6917.6910.0000.0000.0000.000
37A40SER00.0640.03741.378-0.049-0.0490.0000.0000.0000.000
38A41ASN0-0.081-0.06444.238-0.216-0.2160.0000.0000.0000.000
39A42THR0-0.131-0.10046.8110.0470.0470.0000.0000.0000.000
40A43HIS00.0490.02145.978-0.065-0.0650.0000.0000.0000.000
41A44ALA0-0.023-0.00740.339-0.108-0.1080.0000.0000.0000.000
42A45VAL00.0230.00540.5760.0880.0880.0000.0000.0000.000
43A46LEU0-0.038-0.02234.419-0.230-0.2300.0000.0000.0000.000
44A47VAL00.0310.01336.7030.2170.2170.0000.0000.0000.000
45A48ALA0-0.020-0.01433.318-0.304-0.3040.0000.0000.0000.000
46A49LEU00.0150.02132.2620.2170.2170.0000.0000.0000.000
47A50LYS10.7330.84632.3127.8647.8640.0000.0000.0000.000
48A51ARG10.9510.97324.47511.83411.8340.0000.0000.0000.000
49A52ASN00.0070.02032.450-0.222-0.2220.0000.0000.0000.000
50A53ALA0-0.074-0.03730.317-0.340-0.3400.0000.0000.0000.000
51A54ASP-1-0.827-0.92031.361-9.376-9.3760.0000.0000.0000.000
52A55GLU-1-0.839-0.94034.398-8.607-8.6070.0000.0000.0000.000
53A56LEU0-0.085-0.02637.4810.2800.2800.0000.0000.0000.000
54A57SER0-0.098-0.04134.015-0.012-0.0120.0000.0000.0000.000
55A58SER0-0.0070.00636.1820.1150.1150.0000.0000.0000.000
56A59TYR00.0360.00734.766-0.444-0.4440.0000.0000.0000.000
57A60GLN0-0.038-0.01329.6820.2410.2410.0000.0000.0000.000
58A61LYS10.8700.92932.9178.2328.2320.0000.0000.0000.000
59A62LYS10.8560.91928.54110.47210.4720.0000.0000.0000.000
60A63ILE0-0.011-0.01332.424-0.206-0.2060.0000.0000.0000.000
61A64ILE0-0.043-0.01931.3930.1430.1430.0000.0000.0000.000
62A65LYS10.8760.93435.2967.1927.1920.0000.0000.0000.000
63A66CYS0-0.089-0.04135.574-0.191-0.1910.0000.0000.0000.000
64A67ASP-1-0.767-0.87937.156-7.325-7.3250.0000.0000.0000.000
65A68GLU-1-0.824-0.91340.749-7.066-7.0660.0000.0000.0000.000
66A69HIS0-0.035-0.01041.2650.0680.0680.0000.0000.0000.000
67A70MET00.007-0.00435.238-0.039-0.0390.0000.0000.0000.000
68A71GLY00.0260.01236.7510.0500.0500.0000.0000.0000.000
69A72LEU0-0.0130.00730.365-0.093-0.0930.0000.0000.0000.000
70A73SER00.0190.02232.1810.0830.0830.0000.0000.0000.000
71A74LEU0-0.008-0.00126.462-0.220-0.2200.0000.0000.0000.000
72A75ALA00.0140.00625.5770.1840.1840.0000.0000.0000.000
73A76GLY00.0400.02522.061-0.388-0.3880.0000.0000.0000.000
74A77LEU0-0.019-0.01717.4040.6030.6030.0000.0000.0000.000
75A78ALA00.0610.01722.1160.2420.2420.0000.0000.0000.000
76A79PRO0-0.020-0.02021.9150.3660.3660.0000.0000.0000.000
77A80ASP-1-0.754-0.86719.385-15.060-15.0600.0000.0000.0000.000
78A81ALA00.0580.02722.5190.3780.3780.0000.0000.0000.000
79A82ARG10.9540.99625.99810.69310.6930.0000.0000.0000.000
80A83VAL0-0.0050.00822.7040.3700.3700.0000.0000.0000.000
81A84LEU0-0.017-0.01023.0120.3360.3360.0000.0000.0000.000
82A85SER00.022-0.00926.7870.4390.4390.0000.0000.0000.000
83A86ASN0-0.034-0.00529.2900.5050.5050.0000.0000.0000.000
84A87TYR00.0240.01328.0560.2590.2590.0000.0000.0000.000
85A88LEU00.0490.01730.1150.2500.2500.0000.0000.0000.000
86A89ARG10.9180.94732.1529.1519.1510.0000.0000.0000.000
87A90GLN0-0.0140.00430.7730.0880.0880.0000.0000.0000.000
88A91GLN0-0.0010.00231.9460.3240.3240.0000.0000.0000.000
89A92CYS0-0.071-0.03835.4390.2400.2400.0000.0000.0000.000
90A93ASN00.0120.00338.2290.1200.1200.0000.0000.0000.000
91A94TYR00.0320.01937.5430.2260.2260.0000.0000.0000.000
92A95SER0-0.035-0.03939.3070.1360.1360.0000.0000.0000.000
93A96SER0-0.034-0.02940.9670.2030.2030.0000.0000.0000.000
94A97LEU0-0.027-0.00742.7790.1590.1590.0000.0000.0000.000
95A98VAL0-0.031-0.01041.2210.1390.1390.0000.0000.0000.000
96A99PHE0-0.057-0.03240.2900.0900.0900.0000.0000.0000.000
97A100ASN00.0080.02045.6970.0830.0830.0000.0000.0000.000
98A101ARG10.8880.95141.1177.2257.2250.0000.0000.0000.000
99A102LYS11.0051.03743.0086.5686.5680.0000.0000.0000.000
100A103LEU00.0130.00135.2970.0460.0460.0000.0000.0000.000
101A104ALA0-0.0090.00039.3700.0330.0330.0000.0000.0000.000
102A105VAL00.0870.02836.305-0.186-0.1860.0000.0000.0000.000
103A106GLU-1-0.864-0.93534.870-8.221-8.2210.0000.0000.0000.000
104A107ARG10.8850.94134.5297.8677.8670.0000.0000.0000.000
105A108ALA00.013-0.00133.263-0.207-0.2070.0000.0000.0000.000
106A109GLY00.0340.01930.403-0.274-0.2740.0000.0000.0000.000
107A110HIS00.011-0.00128.872-0.570-0.5700.0000.0000.0000.000
108A111LEU00.0050.00328.327-0.237-0.2370.0000.0000.0000.000
109A112LEU0-0.056-0.01725.748-0.225-0.2250.0000.0000.0000.000
110A113CYS0-0.039-0.01224.579-0.546-0.5460.0000.0000.0000.000
111A114ASP-1-0.857-0.93323.353-11.117-11.1170.0000.0000.0000.000
112A115LYS10.8870.95322.97911.05611.0560.0000.0000.0000.000
113A116ALA00.0230.00120.301-0.432-0.4320.0000.0000.0000.000
114A117GLN00.0380.02818.776-0.538-0.5380.0000.0000.0000.000
115A118LYS10.9350.96118.30912.06112.0610.0000.0000.0000.000
116A119ASN0-0.070-0.03917.1070.5280.5280.0000.0000.0000.000
117A120THR0-0.003-0.00213.962-1.027-1.0270.0000.0000.0000.000
118A121GLN0-0.055-0.01513.767-1.223-1.2230.0000.0000.0000.000
119A122SER0-0.019-0.00714.628-0.319-0.3190.0000.0000.0000.000
120A123TYR0-0.025-0.0276.1770.7810.7810.0000.0000.0000.000
121A124GLY00.0060.00410.8420.9240.9240.0000.0000.0000.000
122A125GLY0-0.043-0.00512.3220.6650.6650.0000.0000.0000.000
123A126ARG10.8650.91511.90214.94714.9470.0000.0000.0000.000
124A127PRO00.0680.04412.5141.3961.3960.0000.0000.0000.000
125A128TYR0-0.051-0.03215.603-0.135-0.1350.0000.0000.0000.000
126A129GLY00.0610.03417.840-0.137-0.1370.0000.0000.0000.000
127A130VAL0-0.085-0.06418.4780.4080.4080.0000.0000.0000.000
128A131GLY00.0520.04022.125-0.158-0.1580.0000.0000.0000.000
129A132LEU0-0.081-0.05324.2480.2680.2680.0000.0000.0000.000
130A133LEU00.0230.03228.0010.0280.0280.0000.0000.0000.000
131A134ILE0-0.046-0.03529.8040.1630.1630.0000.0000.0000.000
132A135ILE00.0390.02833.7760.0500.0500.0000.0000.0000.000
133A136GLY00.003-0.01537.460-0.016-0.0160.0000.0000.0000.000
134A137TYR00.0190.03640.3360.0990.0990.0000.0000.0000.000
135A138ASP-1-0.779-0.90042.068-7.187-7.1870.0000.0000.0000.000
136A139LYS10.8700.91844.2066.8886.8880.0000.0000.0000.000
137A140SER0-0.077-0.04843.3090.1620.1620.0000.0000.0000.000
138A141GLY00.0220.02744.816-0.043-0.0430.0000.0000.0000.000
139A142ALA00.0290.02442.992-0.121-0.1210.0000.0000.0000.000
140A143HIS10.7770.88238.0847.8007.8000.0000.0000.0000.000
141A144LEU0-0.011-0.00134.0960.0110.0110.0000.0000.0000.000
142A145LEU0-0.034-0.01031.968-0.096-0.0960.0000.0000.0000.000
143A146GLU-1-0.800-0.90226.507-11.487-11.4870.0000.0000.0000.000
144A147PHE0-0.007-0.01822.8050.0380.0380.0000.0000.0000.000
145A148GLN00.010-0.01421.433-0.779-0.7790.0000.0000.0000.000
146A149PRO00.0180.00718.1240.1530.1530.0000.0000.0000.000
147A150SER0-0.014-0.01617.971-0.174-0.1740.0000.0000.0000.000
148A151GLY00.0020.00919.2540.0890.0890.0000.0000.0000.000
149A152ASN0-0.0040.00722.3620.7430.7430.0000.0000.0000.000
150A153VAL00.0130.01224.5890.0000.0000.0000.0000.0000.000
151A154THR0-0.055-0.03428.2440.0010.0010.0000.0000.0000.000
152A155GLU-1-0.740-0.85230.797-8.390-8.3900.0000.0000.0000.000
153A156LEU0-0.016-0.00930.987-0.063-0.0630.0000.0000.0000.000
154A157TYR00.0440.01235.3640.1560.1560.0000.0000.0000.000
155A158GLY00.0480.01136.4620.1860.1860.0000.0000.0000.000
156A159THR0-0.046-0.00830.014-0.220-0.2200.0000.0000.0000.000
157A160ALA00.0280.01030.6370.2060.2060.0000.0000.0000.000
158A161ILE0-0.048-0.00525.746-0.433-0.4330.0000.0000.0000.000
159A162GLY00.0810.03525.2590.3510.3510.0000.0000.0000.000
160A163ALA0-0.009-0.01024.813-0.239-0.2390.0000.0000.0000.000
161A164ARG10.7530.84425.68810.90510.9050.0000.0000.0000.000
162A165SER0-0.039-0.00726.4700.2670.2670.0000.0000.0000.000
163A166GLN00.0130.01528.0940.2540.2540.0000.0000.0000.000
164A167GLY00.0770.03729.8620.2560.2560.0000.0000.0000.000
165A168ALA00.0470.02932.5900.2720.2720.0000.0000.0000.000
166A169LYS10.8970.95228.10311.05111.0510.0000.0000.0000.000
167A170THR00.013-0.00233.4170.2250.2250.0000.0000.0000.000
168A171TYR0-0.056-0.05235.6080.1710.1710.0000.0000.0000.000
169A172LEU0-0.001-0.00335.0920.2500.2500.0000.0000.0000.000
170A173GLU-1-0.939-0.97136.443-8.326-8.3260.0000.0000.0000.000
171A174ARG10.8730.94638.4777.8887.8880.0000.0000.0000.000
172A175THR0-0.023-0.02141.3120.2530.2530.0000.0000.0000.000
173A176LEU00.0150.00939.2320.1240.1240.0000.0000.0000.000
174A177ASP-1-0.889-0.94942.221-6.956-6.9560.0000.0000.0000.000
175A178THR0-0.031-0.02045.7540.1650.1650.0000.0000.0000.000
176A179PHE00.0100.00139.4870.0950.0950.0000.0000.0000.000
177A180ILE0-0.024-0.01242.0790.0480.0480.0000.0000.0000.000
178A181LYS10.8760.94146.0086.5926.5920.0000.0000.0000.000
179A182ILE00.0150.02648.6820.1540.1540.0000.0000.0000.000
180A183ASP-1-0.728-0.83348.830-6.706-6.7060.0000.0000.0000.000
181A184GLY0-0.015-0.00851.0250.1220.1220.0000.0000.0000.000
182A185ASN0-0.013-0.00552.1270.0780.0780.0000.0000.0000.000
183A186PRO00.0420.02148.482-0.105-0.1050.0000.0000.0000.000
184A187ASP-1-0.848-0.92547.663-6.397-6.3970.0000.0000.0000.000
185A188GLU-1-0.891-0.95248.392-6.342-6.3420.0000.0000.0000.000
186A189LEU0-0.054-0.01344.321-0.149-0.1490.0000.0000.0000.000
187A190ILE0-0.019-0.00443.611-0.233-0.2330.0000.0000.0000.000
188A191LYS10.9420.98143.7326.2096.2090.0000.0000.0000.000
189A192ALA00.0630.03343.381-0.136-0.1360.0000.0000.0000.000
190A193GLY00.0150.00139.934-0.208-0.2080.0000.0000.0000.000
191A194VAL0-0.009-0.01039.380-0.286-0.2860.0000.0000.0000.000
192A195GLU-1-0.874-0.90140.624-7.225-7.2250.0000.0000.0000.000
193A196ALA0-0.018-0.01737.449-0.181-0.1810.0000.0000.0000.000
194A197ILE0-0.054-0.03134.193-0.300-0.3000.0000.0000.0000.000
195A198SER00.0390.01635.921-0.191-0.1910.0000.0000.0000.000
196A199GLN0-0.044-0.01736.350-0.051-0.0510.0000.0000.0000.000
197A200SER0-0.101-0.05131.729-0.316-0.3160.0000.0000.0000.000
198A201LEU00.0450.04332.270-0.360-0.3600.0000.0000.0000.000
199A202ARG10.8680.91325.84211.21011.2100.0000.0000.0000.000
200A203ASP-1-0.866-0.93332.745-8.444-8.4440.0000.0000.0000.000
201A204GLU-1-0.858-0.91130.607-10.319-10.3190.0000.0000.0000.000
202A205SER0-0.003-0.00835.5370.0830.0830.0000.0000.0000.000
203A206LEU00.002-0.00238.740-0.090-0.0900.0000.0000.0000.000
204A207THR00.0590.01340.8260.1300.1300.0000.0000.0000.000
205A208VAL00.010-0.01142.147-0.147-0.1470.0000.0000.0000.000
206A209ASP-1-0.846-0.90741.675-7.659-7.6590.0000.0000.0000.000
207A210ASN00.0010.01336.162-0.366-0.3660.0000.0000.0000.000
208A211LEU00.0230.01137.321-0.277-0.2770.0000.0000.0000.000
209A212SER0-0.030-0.01936.9240.1050.1050.0000.0000.0000.000
210A213ILE00.0190.01738.382-0.171-0.1710.0000.0000.0000.000
211A214ALA0-0.026-0.02139.1380.0330.0330.0000.0000.0000.000
212A215ILE00.0240.02341.053-0.091-0.0910.0000.0000.0000.000
213A216VAL0-0.040-0.01841.978-0.003-0.0030.0000.0000.0000.000
214A217GLY00.0880.04844.590-0.078-0.0780.0000.0000.0000.000
215A218LYS10.8160.91447.4466.2546.2540.0000.0000.0000.000
216A219ASP-1-0.880-0.95050.076-6.068-6.0680.0000.0000.0000.000
217A220THR0-0.0090.00248.8800.0260.0260.0000.0000.0000.000
218A221PRO00.002-0.00347.123-0.140-0.1400.0000.0000.0000.000
219A222PHE0-0.024-0.01538.527-0.056-0.0560.0000.0000.0000.000
220A223THR0-0.027-0.01343.9170.0480.0480.0000.0000.0000.000
221A224ILE0-0.048-0.03238.803-0.162-0.1620.0000.0000.0000.000
222A225TYR0-0.009-0.00142.5450.1680.1680.0000.0000.0000.000
223A226ASP-1-0.786-0.90540.015-8.193-8.1930.0000.0000.0000.000
224A227GLY00.0750.04843.2880.1850.1850.0000.0000.0000.000
225A228GLU-1-0.864-0.95145.576-6.524-6.5240.0000.0000.0000.000
226A229ALA0-0.099-0.04246.5490.1340.1340.0000.0000.0000.000
227A230VAL0-0.018-0.01242.6700.0470.0470.0000.0000.0000.000
228A231ALA00.0360.01946.085-0.003-0.0030.0000.0000.0000.000
229A232LYS10.8620.94748.7556.3196.3190.0000.0000.0000.000
230A233TYR0-0.128-0.09046.2180.0530.0530.0000.0000.0000.000
231A234ILE-1-0.908-0.92843.594-6.817-6.8170.0000.0000.0000.000