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: R4QJ8

Calculation Name: 7PXD-K-Other547

Preferred Name:

Target Type:

Ligand Name: adenosine-5'-triphosphate | magnesium ion

Ligand 3-letter code: ATP | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7PXD

Chain ID: K

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 227
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2657997.280703
FMO2-HF: Nuclear repulsion 2572613.196125
FMO2-HF: Total energy -85384.084578
FMO2-MP2: Total energy -85636.846044


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:8:SER)


Summations of interaction energy for fragment #1(A:8:SER)
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.
-53.178-55.28325.537-12.527-10.905-0.068
Interaction energy analysis for fragmet #1(A:8:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.848 / 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].
3A10GLU-1-0.752-0.8411.608-83.416-87.61617.708-8.198-5.310-0.080
4A11GLN0-0.066-0.0361.982-12.421-11.0017.784-4.218-4.9860.010
5A12ALA00.0380.0223.7017.6908.2460.046-0.105-0.4970.002
7A14ARG10.8910.9334.32045.54445.663-0.001-0.006-0.1120.000
6A13MET00.0110.0205.7186.1786.1780.0000.0000.0000.000
8A15GLU-1-0.868-0.9486.433-37.745-37.7450.0000.0000.0000.000
9A16ARG10.8410.9169.08629.29929.2990.0000.0000.0000.000
10A17SER00.0240.01511.3593.1093.1090.0000.0000.0000.000
11A18GLU-1-0.813-0.88311.720-18.318-18.3180.0000.0000.0000.000
12A19LEU0-0.0300.00113.3661.5151.5150.0000.0000.0000.000
13A20ALA00.0340.00515.1071.4311.4310.0000.0000.0000.000
14A21ARG10.8990.92016.03318.87618.8760.0000.0000.0000.000
15A22LYS10.8660.92914.59220.82920.8290.0000.0000.0000.000
16A23GLY00.007-0.00619.4610.7870.7870.0000.0000.0000.000
17A24ILE0-0.055-0.01720.7310.7840.7840.0000.0000.0000.000
18A25ALA00.0110.01122.4440.6230.6230.0000.0000.0000.000
19A26ARG10.8880.95120.52914.58314.5830.0000.0000.0000.000
20A27ALA0-0.060-0.00725.3270.4790.4790.0000.0000.0000.000
21A28LYS10.8320.92127.7079.4469.4460.0000.0000.0000.000
22A29SER00.0290.00430.235-0.168-0.1680.0000.0000.0000.000
23A30VAL0-0.107-0.06331.4190.3610.3610.0000.0000.0000.000
24A31VAL00.0130.01432.270-0.249-0.2490.0000.0000.0000.000
25A32ALA0-0.010-0.00534.6640.2050.2050.0000.0000.0000.000
26A33LEU00.0120.00835.814-0.155-0.1550.0000.0000.0000.000
27A34ALA00.0290.02738.4620.1630.1630.0000.0000.0000.000
28A35TYR0-0.017-0.00540.9440.1150.1150.0000.0000.0000.000
29A36ALA00.0230.01244.6010.0010.0010.0000.0000.0000.000
30A37GLY0-0.0140.00447.6090.1080.1080.0000.0000.0000.000
31A38GLY0-0.014-0.01144.8760.0210.0210.0000.0000.0000.000
32A39VAL00.000-0.00338.575-0.092-0.0920.0000.0000.0000.000
33A40LEU0-0.025-0.00641.2040.1560.1560.0000.0000.0000.000
34A41PHE0-0.001-0.00735.526-0.193-0.1930.0000.0000.0000.000
35A42VAL00.019-0.00538.0110.2530.2530.0000.0000.0000.000
36A43ALA00.0240.01135.654-0.284-0.2840.0000.0000.0000.000
37A44GLU-1-0.730-0.85134.388-8.972-8.9720.0000.0000.0000.000
38A45ASN0-0.085-0.07735.495-0.368-0.3680.0000.0000.0000.000
39A46PRO00.0370.02836.7050.2110.2110.0000.0000.0000.000
40A47SER0-0.0240.00437.7860.2580.2580.0000.0000.0000.000
41A48ARG10.9810.98539.7837.0167.0160.0000.0000.0000.000
42A49SER0-0.044-0.03040.8360.1670.1670.0000.0000.0000.000
43A50LEU0-0.048-0.00834.435-0.040-0.0400.0000.0000.0000.000
44A51GLN00.0020.01137.0430.0250.0250.0000.0000.0000.000
45A52LYS10.8970.94131.3099.7829.7820.0000.0000.0000.000
46A53ILE0-0.0110.00634.406-0.213-0.2130.0000.0000.0000.000
47A54SER0-0.055-0.03637.0130.1890.1890.0000.0000.0000.000
48A55GLU-1-0.797-0.84038.794-7.293-7.2930.0000.0000.0000.000
49A56LEU0-0.025-0.00634.149-0.144-0.1440.0000.0000.0000.000
50A57TYR00.038-0.00338.7860.0740.0740.0000.0000.0000.000
51A58ASP-1-0.790-0.84241.734-6.950-6.9500.0000.0000.0000.000
52A59ARG10.7990.86843.3546.9096.9090.0000.0000.0000.000
53A60VAL00.0280.01837.264-0.080-0.0800.0000.0000.0000.000
54A61GLY00.0100.00438.5440.1090.1090.0000.0000.0000.000
55A62PHE00.008-0.00330.740-0.186-0.1860.0000.0000.0000.000
56A63ALA00.0310.00533.5190.2910.2910.0000.0000.0000.000
57A64ALA0-0.0060.01129.238-0.312-0.3120.0000.0000.0000.000
58A65ALA00.0270.01927.6750.3310.3310.0000.0000.0000.000
59A66GLY00.0660.01825.495-0.397-0.3970.0000.0000.0000.000
60A67LYS10.8810.93623.19213.27413.2740.0000.0000.0000.000
61A68PHE00.0480.01226.346-0.065-0.0650.0000.0000.0000.000
62A69ASN00.0280.00625.6040.0110.0110.0000.0000.0000.000
63A70GLU-1-0.783-0.86222.179-14.359-14.3590.0000.0000.0000.000
64A71PHE00.0910.03626.3020.1320.1320.0000.0000.0000.000
65A72ASP-1-0.785-0.86228.584-9.017-9.0170.0000.0000.0000.000
66A73ASN0-0.035-0.02128.1100.3260.3260.0000.0000.0000.000
67A74LEU00.0450.02924.9610.2240.2240.0000.0000.0000.000
68A75ARG10.8270.92229.4009.1679.1670.0000.0000.0000.000
69A76ARG10.8380.90332.9859.2659.2650.0000.0000.0000.000
70A77GLY00.0400.02331.5520.2210.2210.0000.0000.0000.000
71A78GLY00.0200.00732.6340.0930.0930.0000.0000.0000.000
72A79ILE00.020-0.00533.9360.1970.1970.0000.0000.0000.000
73A80GLN0-0.0080.01035.3100.2380.2380.0000.0000.0000.000
74A81PHE00.0010.00934.0890.1720.1720.0000.0000.0000.000
75A82ALA00.0130.00636.2690.1760.1760.0000.0000.0000.000
76A83ASP-1-0.873-0.95138.870-7.359-7.3590.0000.0000.0000.000
77A84THR0-0.069-0.04738.7100.1900.1900.0000.0000.0000.000
78A85ARG10.9050.95236.0038.7748.7740.0000.0000.0000.000
79A86GLY00.010-0.00540.7470.1290.1290.0000.0000.0000.000
80A87TYR0-0.084-0.03043.8530.2050.2050.0000.0000.0000.000
81A88ALA0-0.021-0.00642.4680.1170.1170.0000.0000.0000.000
82A89TYR0-0.078-0.03540.473-0.058-0.0580.0000.0000.0000.000
83A90ASP-1-0.813-0.89145.496-6.500-6.5000.0000.0000.0000.000
84A91ARG10.8250.88345.0156.8596.8590.0000.0000.0000.000
85A92ARG10.8630.92144.7356.4466.4460.0000.0000.0000.000
86A93ASP-1-0.849-0.91242.302-7.308-7.3080.0000.0000.0000.000
87A94VAL0-0.092-0.03039.145-0.293-0.2930.0000.0000.0000.000
88A95THR00.0080.00037.8450.0060.0060.0000.0000.0000.000
89A96GLY00.007-0.01535.952-0.227-0.2270.0000.0000.0000.000
90A97ARG11.0051.01133.4068.9368.9360.0000.0000.0000.000
91A98GLN0-0.050-0.03132.600-0.338-0.3380.0000.0000.0000.000
92A99LEU0-0.0140.00032.237-0.327-0.3270.0000.0000.0000.000
93A100ALA00.0360.01829.708-0.360-0.3600.0000.0000.0000.000
94A101ASN0-0.023-0.00628.076-0.616-0.6160.0000.0000.0000.000
95A102VAL00.0460.02227.387-0.458-0.4580.0000.0000.0000.000
96A103TYR0-0.041-0.03726.949-0.309-0.3090.0000.0000.0000.000
97A104ALA00.0350.02923.859-0.532-0.5320.0000.0000.0000.000
98A105GLN00.0000.00422.630-0.574-0.5740.0000.0000.0000.000
99A106THR0-0.036-0.02422.524-0.517-0.5170.0000.0000.0000.000
100A107LEU0-0.026-0.02021.316-0.424-0.4240.0000.0000.0000.000
101A108GLY00.0730.05118.413-0.858-0.8580.0000.0000.0000.000
102A109THR0-0.044-0.02217.504-1.151-1.1510.0000.0000.0000.000
103A110ILE0-0.062-0.03418.010-0.759-0.7590.0000.0000.0000.000
104A111PHE0-0.037-0.03012.385-1.031-1.0310.0000.0000.0000.000
105A112THR0-0.048-0.01412.655-2.347-2.3470.0000.0000.0000.000
106A113GLU-1-0.899-0.95513.164-21.266-21.2660.0000.0000.0000.000
107A114GLN0-0.037-0.00815.6210.2300.2300.0000.0000.0000.000
108A115ALA0-0.014-0.00513.888-1.311-1.3110.0000.0000.0000.000
109A116LYS10.7460.85413.58214.78814.7880.0000.0000.0000.000
110A117PRO00.0320.03613.8350.8580.8580.0000.0000.0000.000
111A118TYR00.017-0.00316.6930.8430.8430.0000.0000.0000.000
112A119GLU-1-0.851-0.91319.483-15.519-15.5190.0000.0000.0000.000
113A120VAL0-0.080-0.04621.2000.8110.8110.0000.0000.0000.000
114A121GLU-1-0.817-0.93122.924-13.043-13.0430.0000.0000.0000.000
115A122LEU0-0.023-0.00925.2920.5350.5350.0000.0000.0000.000
116A123CYS00.0390.00728.208-0.061-0.0610.0000.0000.0000.000
117A124VAL0-0.051-0.01331.1320.2490.2490.0000.0000.0000.000
118A125ALA00.0020.00733.289-0.016-0.0160.0000.0000.0000.000
119A126GLU-1-0.804-0.91136.493-8.070-8.0700.0000.0000.0000.000
120A127VAL0-0.045-0.01039.4120.0380.0380.0000.0000.0000.000
121A128ALA00.0500.03442.993-0.043-0.0430.0000.0000.0000.000
122A129HIS0-0.025-0.01544.7500.1450.1450.0000.0000.0000.000
123A130TYR0-0.025-0.01148.2230.0750.0750.0000.0000.0000.000
124A131GLY0-0.011-0.00551.7010.0330.0330.0000.0000.0000.000
125A132GLU-1-0.839-0.91346.947-6.768-6.7680.0000.0000.0000.000
126A133THR0-0.020-0.01449.3280.0010.0010.0000.0000.0000.000
127A134LYS10.8460.91040.9067.6957.6950.0000.0000.0000.000
128A135ARG10.8710.94440.1157.5567.5560.0000.0000.0000.000
129A136PRO0-0.020-0.02140.715-0.092-0.0920.0000.0000.0000.000
130A137GLU-1-0.798-0.85436.326-8.411-8.4110.0000.0000.0000.000
131A138LEU0-0.023-0.02734.0570.0590.0590.0000.0000.0000.000
132A139TYR00.003-0.01530.265-0.274-0.2740.0000.0000.0000.000
133A140ARG10.8670.92625.32311.50111.5010.0000.0000.0000.000
134A141ILE0-0.049-0.02323.897-0.149-0.1490.0000.0000.0000.000
135A142THR00.003-0.01719.9660.4050.4050.0000.0000.0000.000
136A143TYR00.007-0.02415.3170.3680.3680.0000.0000.0000.000
137A144ASP-1-0.807-0.87815.933-17.430-17.4300.0000.0000.0000.000
138A145GLY0-0.012-0.00317.693-0.310-0.3100.0000.0000.0000.000
139A146SER0-0.063-0.04318.1160.6530.6530.0000.0000.0000.000
140A147ILE0-0.046-0.03320.9060.4080.4080.0000.0000.0000.000
141A148ALA0-0.026-0.00424.653-0.074-0.0740.0000.0000.0000.000
142A149ASP-1-0.932-0.96626.916-9.268-9.2680.0000.0000.0000.000
143A150GLU-1-0.840-0.90228.609-10.692-10.6920.0000.0000.0000.000
144A151PRO0-0.011-0.00532.4420.2830.2830.0000.0000.0000.000
145A152HIS10.8380.90835.4398.3798.3790.0000.0000.0000.000
146A153PHE00.0450.00533.1350.1970.1970.0000.0000.0000.000
147A154VAL00.0140.01929.746-0.249-0.2490.0000.0000.0000.000
148A155VAL0-0.016-0.01230.0360.2800.2800.0000.0000.0000.000
149A156MET0-0.0250.00127.463-0.398-0.3980.0000.0000.0000.000
150A157GLY00.0470.00626.1370.3310.3310.0000.0000.0000.000
151A158GLY00.0220.05627.0280.4100.4100.0000.0000.0000.000
152A159THR0-0.019-0.02226.388-0.451-0.4510.0000.0000.0000.000
153A160THR00.0270.00326.0100.3110.3110.0000.0000.0000.000
154A161GLU-1-0.887-0.94025.975-11.227-11.2270.0000.0000.0000.000
155A162PRO0-0.016-0.01129.0880.3020.3020.0000.0000.0000.000
156A163ILE00.0240.02231.8600.3020.3020.0000.0000.0000.000
157A164ALA00.021-0.00330.3920.2640.2640.0000.0000.0000.000
158A165ASN00.0060.00430.7520.1320.1320.0000.0000.0000.000
159A166ALA00.0240.02134.0240.2400.2400.0000.0000.0000.000
160A167LEU0-0.026-0.02334.7620.2510.2510.0000.0000.0000.000
161A168LYS10.8290.91029.85410.07810.0780.0000.0000.0000.000
162A169GLU-1-0.908-0.94936.604-8.090-8.0900.0000.0000.0000.000
163A170SER0-0.040-0.01339.7660.2640.2640.0000.0000.0000.000
164A171TYR0-0.065-0.04439.2090.1290.1290.0000.0000.0000.000
165A172ALA00.0180.01541.2310.0610.0610.0000.0000.0000.000
166A173GLU-1-0.825-0.92142.579-7.483-7.4830.0000.0000.0000.000
167A174ASN0-0.074-0.04944.4350.0500.0500.0000.0000.0000.000
168A175ALA00.0720.05245.5960.1540.1540.0000.0000.0000.000
169A176SER00.005-0.04747.584-0.036-0.0360.0000.0000.0000.000
170A177LEU00.018-0.00446.940-0.127-0.1270.0000.0000.0000.000
171A178THR00.0240.00947.708-0.138-0.1380.0000.0000.0000.000
172A179ASP-1-0.843-0.87548.162-6.401-6.4010.0000.0000.0000.000
173A180ALA00.0140.00843.945-0.142-0.1420.0000.0000.0000.000
174A181LEU0-0.010-0.00843.322-0.216-0.2160.0000.0000.0000.000
175A182ARG10.8140.88744.1286.2666.2660.0000.0000.0000.000
176A183ILE00.0140.01640.908-0.105-0.1050.0000.0000.0000.000
177A184ALA00.0020.00039.660-0.188-0.1880.0000.0000.0000.000
178A185VAL0-0.022-0.02539.553-0.201-0.2010.0000.0000.0000.000
179A186ALA0-0.033-0.01041.507-0.053-0.0530.0000.0000.0000.000
180A187ALA00.0180.00537.017-0.106-0.1060.0000.0000.0000.000
181A188LEU0-0.004-0.00935.229-0.216-0.2160.0000.0000.0000.000
182A189ARG10.8610.94636.9407.2207.2200.0000.0000.0000.000
183A190ALA0-0.016-0.00235.9870.0550.0550.0000.0000.0000.000
184A191GLY00.0080.00033.558-0.263-0.2630.0000.0000.0000.000
185A192SER0-0.055-0.04833.3170.1410.1410.0000.0000.0000.000
186A193ALA0-0.026-0.00328.403-0.186-0.1860.0000.0000.0000.000
187A194ASP-1-0.882-0.95124.766-12.326-12.3260.0000.0000.0000.000
188A195THR0-0.0010.01325.0370.0260.0260.0000.0000.0000.000
189A196SER0-0.047-0.04526.1160.2920.2920.0000.0000.0000.000
190A197GLY00.0050.00227.8790.2300.2300.0000.0000.0000.000
191A198GLY0-0.0110.01630.0540.1950.1950.0000.0000.0000.000
192A199ASP-1-0.855-0.91030.726-8.860-8.8600.0000.0000.0000.000
193A200GLN0-0.112-0.08629.8330.0160.0160.0000.0000.0000.000
194A201PRO00.0010.02635.3700.0950.0950.0000.0000.0000.000
195A202THR0-0.022-0.01638.8400.2470.2470.0000.0000.0000.000
196A203LEU00.0190.00240.7310.1760.1760.0000.0000.0000.000
197A204GLY00.0550.02144.3600.0860.0860.0000.0000.0000.000
198A205VAL0-0.007-0.01344.914-0.163-0.1630.0000.0000.0000.000
199A206ALA0-0.036-0.01445.247-0.093-0.0930.0000.0000.0000.000
200A207SER0-0.032-0.01441.067-0.117-0.1170.0000.0000.0000.000
201A208LEU00.0100.00840.131-0.205-0.2050.0000.0000.0000.000
202A209GLU-1-0.758-0.84238.214-8.308-8.3080.0000.0000.0000.000
203A210VAL00.0350.01340.331-0.141-0.1410.0000.0000.0000.000
204A211ALA0-0.043-0.02141.6360.1550.1550.0000.0000.0000.000
205A212VAL00.0070.00842.308-0.112-0.1120.0000.0000.0000.000
206A213LEU0-0.038-0.00739.7580.0240.0240.0000.0000.0000.000
207A214ASP-1-0.805-0.92043.959-6.381-6.3810.0000.0000.0000.000
208A215ALA00.0580.01147.0280.0430.0430.0000.0000.0000.000
209A216ASN00.0100.00748.4250.1220.1220.0000.0000.0000.000
210A217ARG10.8970.97049.5696.5556.5550.0000.0000.0000.000
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