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: 9QLY2

Calculation Name: 7QO6-5-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: 5

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 212
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2398476.146415
FMO2-HF: Nuclear repulsion 2316585.862743
FMO2-HF: Total energy -81890.283671
FMO2-MP2: Total energy -82128.921415


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:76:THR)


Summations of interaction energy for fragment #1(A:76: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.
-157.688-142.52321.882-17.717-19.331-0.171
Interaction energy analysis for fragmet #1(A:76:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.741 / q_NPA : 0.856
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].
3A78THR0-0.0190.0003.8225.5967.306-0.026-0.703-0.981-0.002
17A92ASP-1-0.757-0.8722.855-80.063-76.3310.610-2.390-1.953-0.023
19A94ARG10.8130.9024.38647.87747.992-0.001-0.009-0.1050.000
20A95ALA00.002-0.0043.910-6.614-6.0120.005-0.138-0.4690.000
21A96THR0-0.083-0.0414.4243.1663.290-0.001-0.009-0.1140.000
33A108LYS10.8550.9332.29651.00051.9951.081-0.567-1.5090.001
46A121ALA0-0.023-0.0143.302-6.919-6.3950.043-0.143-0.4240.000
47A122GLY00.0180.0153.4754.1644.2920.003-0.029-0.1030.000
48A123GLY00.019-0.0014.958-2.123-2.057-0.001-0.001-0.0640.000
130A205GLY00.014-0.0053.109-5.569-5.2110.106-0.175-0.2890.000
131A206SER0-0.104-0.0882.049-2.533-0.1042.802-2.187-3.044-0.023
132A207GLY00.0620.0363.7488.4528.696-0.001-0.050-0.1930.000
133A208GLN0-0.056-0.0305.2788.2588.338-0.001-0.002-0.0780.000
168A243ASP-1-0.732-0.8332.623-100.446-95.9350.679-3.095-2.094-0.035
169A244ALA00.0500.0255.163-2.243-2.201-0.0010.000-0.0400.000
170A245TYR0-0.013-0.0072.2516.1337.2231.491-1.140-1.441-0.004
171A246SER0-0.0130.0111.805-47.836-48.95514.869-7.599-6.151-0.085
172A247GLY00.0490.0292.79513.72313.2570.2250.520-0.2790.000
4A79LEU0-0.003-0.0046.0620.0460.0460.0000.0000.0000.000
5A80ALA00.0120.0079.5910.9110.9110.0000.0000.0000.000
6A81PHE00.0310.00812.9340.0210.0210.0000.0000.0000.000
7A82ARG10.7630.86416.47013.78713.7870.0000.0000.0000.000
8A83PHE00.0520.01220.017-0.065-0.0650.0000.0000.0000.000
9A84GLN00.000-0.01523.1310.0600.0600.0000.0000.0000.000
10A85GLY0-0.0200.00625.0100.3480.3480.0000.0000.0000.000
11A86GLY0-0.009-0.00723.1000.1520.1520.0000.0000.0000.000
12A87ILE0-0.070-0.04116.588-0.216-0.2160.0000.0000.0000.000
13A88ILE0-0.0220.02215.2100.1200.1200.0000.0000.0000.000
14A89VAL00.012-0.00511.523-0.807-0.8070.0000.0000.0000.000
15A90ALA0-0.0020.00211.3000.7100.7100.0000.0000.0000.000
16A91VAL0-0.007-0.0106.505-2.405-2.4050.0000.0000.0000.000
18A93SER00.005-0.0185.9122.0182.0180.0000.0000.0000.000
22A97ALA00.0430.0216.306-0.516-0.5160.0000.0000.0000.000
23A98GLY00.0090.0038.9931.3301.3300.0000.0000.0000.000
24A99ASN0-0.010-0.0059.747-3.087-3.0870.0000.0000.0000.000
25A100TRP00.0520.03310.688-0.191-0.1910.0000.0000.0000.000
26A101VAL0-0.003-0.0097.835-2.212-2.2120.0000.0000.0000.000
27A102ALA00.0350.0279.0392.0652.0650.0000.0000.0000.000
28A103SER0-0.023-0.0258.9572.6832.6830.0000.0000.0000.000
29A104GLN0-0.006-0.0088.430-4.640-4.6400.0000.0000.0000.000
30A105THR00.0440.02710.1050.3330.3330.0000.0000.0000.000
31A106VAL0-0.031-0.0037.0791.5561.5560.0000.0000.0000.000
32A107LYS10.9320.9577.99216.69416.6940.0000.0000.0000.000
34A109VAL00.0160.0337.285-0.048-0.0480.0000.0000.0000.000
35A110ILE00.0210.0069.7820.9790.9790.0000.0000.0000.000
36A111GLU-1-0.928-0.97012.855-13.461-13.4610.0000.0000.0000.000
37A112ILE0-0.026-0.00915.1310.3620.3620.0000.0000.0000.000
38A113ASN00.019-0.01718.2490.9850.9850.0000.0000.0000.000
39A114PRO00.0540.03620.262-0.521-0.5210.0000.0000.0000.000
40A115PHE0-0.015-0.00122.306-0.001-0.0010.0000.0000.0000.000
41A116LEU0-0.051-0.03418.8070.0140.0140.0000.0000.0000.000
42A117LEU00.0040.00813.982-0.137-0.1370.0000.0000.0000.000
43A118GLY00.0450.03412.7200.2860.2860.0000.0000.0000.000
44A119THR0-0.057-0.0647.789-0.390-0.3900.0000.0000.0000.000
45A120MET00.0060.0125.7660.4720.4720.0000.0000.0000.000
49A124ALA00.0250.0006.4521.2691.2690.0000.0000.0000.000
50A125ALA00.0140.0017.7061.2741.2740.0000.0000.0000.000
51A126ASP-1-0.850-0.93310.813-19.504-19.5040.0000.0000.0000.000
52A127CYS0-0.035-0.0168.5150.8720.8720.0000.0000.0000.000
53A128GLN00.0350.02010.6862.0822.0820.0000.0000.0000.000
54A129PHE0-0.0190.01212.4221.2921.2920.0000.0000.0000.000
55A130TRP00.0480.01014.7281.2981.2980.0000.0000.0000.000
56A131GLU-1-0.811-0.89311.451-20.580-20.5800.0000.0000.0000.000
57A132THR00.005-0.00815.6860.7790.7790.0000.0000.0000.000
58A133TRP0-0.018-0.01117.9720.7420.7420.0000.0000.0000.000
59A134LEU0-0.015-0.01217.7830.6720.6720.0000.0000.0000.000
60A135GLY00.0700.03719.4930.4950.4950.0000.0000.0000.000
61A136SER0-0.069-0.02921.0440.7010.7010.0000.0000.0000.000
62A137GLN0-0.020-0.01623.5110.7050.7050.0000.0000.0000.000
63A138CYS0-0.042-0.00222.8000.4360.4360.0000.0000.0000.000
64A139ARG10.9580.98224.73010.20510.2050.0000.0000.0000.000
65A140LEU0-0.007-0.01827.0490.4540.4540.0000.0000.0000.000
66A141HIS00.0090.00327.8990.2250.2250.0000.0000.0000.000
67A142GLU-1-0.870-0.94828.866-9.291-9.2910.0000.0000.0000.000
68A143LEU0-0.056-0.02430.6120.3340.3340.0000.0000.0000.000
69A144ARG10.8800.96932.7269.1109.1100.0000.0000.0000.000
70A145GLU-1-0.892-0.95832.914-8.248-8.2480.0000.0000.0000.000
71A146LYS10.7840.88934.4968.2448.2440.0000.0000.0000.000
72A147GLU-1-0.841-0.89631.875-8.836-8.8360.0000.0000.0000.000
73A148ARG10.8880.96824.97811.06911.0690.0000.0000.0000.000
74A149ILE0-0.029-0.01624.181-0.082-0.0820.0000.0000.0000.000
75A150SER00.0270.01625.467-0.301-0.3010.0000.0000.0000.000
76A151VAL00.0060.00319.707-0.166-0.1660.0000.0000.0000.000
77A152ALA00.0080.01321.417-0.398-0.3980.0000.0000.0000.000
78A153ALA0-0.023-0.00823.560-0.015-0.0150.0000.0000.0000.000
79A154ALA00.0460.01120.827-0.078-0.0780.0000.0000.0000.000
80A155SER00.0440.00018.730-0.195-0.1950.0000.0000.0000.000
81A156LYS10.8810.95319.71910.88210.8820.0000.0000.0000.000
82A157ILE0-0.018-0.00622.0990.1300.1300.0000.0000.0000.000
83A158LEU00.0410.02414.4720.1290.1290.0000.0000.0000.000
84A159SER00.0490.01718.386-0.106-0.1060.0000.0000.0000.000
85A160ASN0-0.043-0.02819.359-0.162-0.1620.0000.0000.0000.000
86A161LEU0-0.0180.00818.8170.1940.1940.0000.0000.0000.000
87A162VAL00.0270.01515.2980.0570.0570.0000.0000.0000.000
88A163TYR0-0.014-0.00718.123-0.029-0.0290.0000.0000.0000.000
89A164GLN0-0.068-0.03220.6410.6420.6420.0000.0000.0000.000
90A165TYR00.003-0.00118.1610.4220.4220.0000.0000.0000.000
91A166LYS10.8260.92618.79413.97013.9700.0000.0000.0000.000
92A167GLY0-0.013-0.00919.4890.5890.5890.0000.0000.0000.000
93A168ALA0-0.044-0.01820.4270.4240.4240.0000.0000.0000.000
94A169GLY0-0.041-0.00817.2550.0400.0400.0000.0000.0000.000
95A170LEU00.0010.01513.770-0.411-0.4110.0000.0000.0000.000
96A171SER0-0.033-0.0148.993-1.200-1.2000.0000.0000.0000.000
97A172MET00.022-0.0209.9290.4190.4190.0000.0000.0000.000
98A173GLY00.0190.0137.8070.1490.1490.0000.0000.0000.000
99A174THR0-0.026-0.0167.411-2.159-2.1590.0000.0000.0000.000
100A175MET00.0060.0158.4091.4491.4490.0000.0000.0000.000
101A176ILE0-0.0060.02812.1340.0750.0750.0000.0000.0000.000
102A177CYS0-0.043-0.01313.6150.4400.4400.0000.0000.0000.000
103A178GLY00.0430.00816.5160.1740.1740.0000.0000.0000.000
104A179TYR0-0.029-0.00320.2330.0510.0510.0000.0000.0000.000
105A180THR00.0430.01223.5420.3330.3330.0000.0000.0000.000
106A181ARG10.8940.93527.0599.7689.7680.0000.0000.0000.000
107A182LYS10.7920.86929.4009.3089.3080.0000.0000.0000.000
108A183GLU-1-0.825-0.91124.209-11.786-11.7860.0000.0000.0000.000
109A184GLY00.0370.03126.384-0.183-0.1830.0000.0000.0000.000
110A185PRO00.0670.02822.385-0.206-0.2060.0000.0000.0000.000
111A186THR0-0.067-0.02720.5960.0670.0670.0000.0000.0000.000
112A187ILE00.0720.03714.358-0.215-0.2150.0000.0000.0000.000
113A188TYR0-0.045-0.03816.8220.8110.8110.0000.0000.0000.000
114A189TYR0-0.044-0.0359.506-1.276-1.2760.0000.0000.0000.000
115A190VAL0-0.019-0.02212.6581.5481.5480.0000.0000.0000.000
116A191ASP-1-0.744-0.82311.963-21.783-21.7830.0000.0000.0000.000
117A192SER0-0.003-0.01512.4420.6970.6970.0000.0000.0000.000
118A193ASP-1-0.879-0.93514.078-16.046-16.0460.0000.0000.0000.000
119A194GLY00.0190.00116.7461.0391.0390.0000.0000.0000.000
120A195THR0-0.083-0.05815.7820.7930.7930.0000.0000.0000.000
121A196ARG10.8920.93516.68512.38512.3850.0000.0000.0000.000
122A197LEU0-0.0130.00516.0460.9180.9180.0000.0000.0000.000
123A198LYS10.9170.97817.29112.50812.5080.0000.0000.0000.000
124A199GLY00.0270.00018.0090.1520.1520.0000.0000.0000.000
125A200ASP-1-0.867-0.90918.700-13.668-13.6680.0000.0000.0000.000
126A201ILE00.0720.03115.267-0.223-0.2230.0000.0000.0000.000
127A202PHE0-0.029-0.00911.3820.4280.4280.0000.0000.0000.000
128A203CYS0-0.0180.0088.997-0.852-0.8520.0000.0000.0000.000
129A204VAL00.0270.0175.6680.3120.3120.0000.0000.0000.000
134A209THR00.0290.0118.2612.1782.1780.0000.0000.0000.000
135A210PHE0-0.009-0.0106.9843.0883.0880.0000.0000.0000.000
136A211ALA00.0080.0158.5141.8741.8740.0000.0000.0000.000
137A212TYR00.0330.00010.3962.2162.2160.0000.0000.0000.000
138A213GLY00.0080.01913.5911.5031.5030.0000.0000.0000.000
139A214VAL0-0.014-0.01013.5361.2381.2380.0000.0000.0000.000
140A215LEU00.0170.02013.3050.9170.9170.0000.0000.0000.000
141A216ASP-1-0.868-0.95615.919-17.187-17.1870.0000.0000.0000.000
142A217SER0-0.079-0.04418.5390.7890.7890.0000.0000.0000.000
143A218ASN0-0.074-0.04018.2941.3571.3570.0000.0000.0000.000
144A219TYR0-0.036-0.01719.8040.1810.1810.0000.0000.0000.000
145A220LYS10.8740.92021.68311.88611.8860.0000.0000.0000.000
146A221TRP00.0000.02523.082-0.275-0.2750.0000.0000.0000.000
147A222ASP-1-0.868-0.93425.546-10.477-10.4770.0000.0000.0000.000
148A223LEU0-0.0230.00322.2400.1640.1640.0000.0000.0000.000
149A224SER00.0340.01326.4300.0720.0720.0000.0000.0000.000
150A225VAL00.0500.00823.260-0.532-0.5320.0000.0000.0000.000
151A226GLU-1-0.913-0.96122.618-12.196-12.1960.0000.0000.0000.000
152A227ASP-1-0.901-0.94422.523-14.170-14.1700.0000.0000.0000.000
153A228ALA00.0400.02420.510-0.897-0.8970.0000.0000.0000.000
154A229LEU0-0.031-0.03118.247-1.286-1.2860.0000.0000.0000.000
155A230TYR0-0.095-0.06217.604-1.501-1.5010.0000.0000.0000.000
156A231LEU00.0550.03016.847-1.236-1.2360.0000.0000.0000.000
157A232GLY00.0060.00614.303-1.482-1.4820.0000.0000.0000.000
158A233LYS10.9250.96512.83414.29514.2950.0000.0000.0000.000
159A234ARG10.8070.88112.62716.71916.7190.0000.0000.0000.000
160A235SER00.0300.00112.222-0.506-0.5060.0000.0000.0000.000
161A236ILE0-0.045-0.0257.274-3.145-3.1450.0000.0000.0000.000
162A237LEU0-0.0040.0008.061-3.873-3.8730.0000.0000.0000.000
163A238ALA0-0.0120.00010.111-0.471-0.4710.0000.0000.0000.000
164A239ALA0-0.002-0.0045.698-0.540-0.5400.0000.0000.0000.000
165A240ALA0-0.038-0.0365.473-4.630-4.6300.0000.0000.0000.000
166A241HIS0-0.053-0.0096.4780.7930.7930.0000.0000.0000.000
167A242ARG10.9380.9677.85426.68626.6860.0000.0000.0000.000
173A248GLY0-0.004-0.0026.376-0.552-0.5520.0000.0000.0000.000
174A249SER00.0460.0318.9713.3233.3230.0000.0000.0000.000
175A250VAL0-0.0210.0068.664-3.640-3.6400.0000.0000.0000.000
176A251ASN0-0.027-0.01710.1114.1034.1030.0000.0000.0000.000
177A252LEU00.0290.01911.553-1.321-1.3210.0000.0000.0000.000
178A253TYR00.004-0.00614.3911.1581.1580.0000.0000.0000.000
179A254HIS00.0230.01816.229-0.454-0.4540.0000.0000.0000.000
180A255VAL0-0.032-0.02717.7610.5180.5180.0000.0000.0000.000
181A256THR00.011-0.00820.4690.1970.1970.0000.0000.0000.000
182A257GLU-1-0.772-0.87024.132-10.867-10.8670.0000.0000.0000.000
183A258ASP-1-0.918-0.97126.752-10.324-10.3240.0000.0000.0000.000
184A259GLY0-0.009-0.00123.6470.1050.1050.0000.0000.0000.000
185A260TRP0-0.083-0.03018.754-0.335-0.3350.0000.0000.0000.000
186A261ILE00.0280.02120.8160.3720.3720.0000.0000.0000.000
187A262TYR0-0.077-0.04915.040-0.351-0.3510.0000.0000.0000.000
188A263HIS00.014-0.00617.9810.6900.6900.0000.0000.0000.000
189A264GLY00.0050.01017.793-0.053-0.0530.0000.0000.0000.000
190A265ASN00.004-0.01013.018-2.216-2.2160.0000.0000.0000.000
191A266HIS0-0.021-0.02213.7851.4231.4230.0000.0000.0000.000
192A267ASP-1-0.861-0.91813.168-21.463-21.4630.0000.0000.0000.000
193A268VAL0-0.019-0.0268.8430.3240.3240.0000.0000.0000.000
194A269GLY00.0000.00412.2100.5600.5600.0000.0000.0000.000
195A270GLU-1-0.869-0.94214.788-14.768-14.7680.0000.0000.0000.000
196A271LEU0-0.080-0.04713.9150.8400.8400.0000.0000.0000.000
197A272PHE0-0.006-0.00314.1300.3210.3210.0000.0000.0000.000
198A273TRP00.0300.01715.9850.5230.5230.0000.0000.0000.000
199A274LYS10.9701.00119.31515.84015.8400.0000.0000.0000.000
200A275VAL00.0160.00916.8710.3690.3690.0000.0000.0000.000
201A276LYS10.8340.93519.40414.21514.2150.0000.0000.0000.000
202A277GLU-1-0.965-0.99320.810-12.496-12.4960.0000.0000.0000.000
203A278GLU-1-0.931-0.93822.633-13.406-13.4060.0000.0000.0000.000
204A279GLU-1-0.781-0.85219.741-15.983-15.9830.0000.0000.0000.000
205A280GLY00.0170.02323.1960.2910.2910.0000.0000.0000.000
206A281SER0-0.046-0.02419.439-0.048-0.0480.0000.0000.0000.000
207A282PHE0-0.015-0.03413.667-0.407-0.4070.0000.0000.0000.000
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