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: Q53JY

Calculation Name: 2A5L-B-Xray549

Preferred Name:

Target Type:

Ligand Name: magnesium ion

Ligand 3-letter code: MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2A5L

Chain ID: B

ChEMBL ID:

UniProt ID: Q9I509

Base Structure: X-ray

Registration Date: 2025-10-11

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1834178.160886
FMO2-HF: Nuclear repulsion 1765983.21709
FMO2-HF: Total energy -68194.943796
FMO2-MP2: Total energy -68393.582324


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(B:3:SER)


Summations of interaction energy for fragment #1(B:3: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.
-28.659-26.572.033-1.607-2.515-0.014
Interaction energy analysis for fragmet #1(B:3:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.860 / q_NPA : 0.924
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].
3B5TYR0-0.031-0.0263.499-4.362-2.8590.032-0.616-0.920-0.002
32B34GLU-1-0.904-0.9472.191-57.008-56.4252.002-0.989-1.596-0.012
33B35ALA00.0250.0075.0632.9172.920-0.001-0.0020.0010.000
4B6ILE00.0340.0365.7443.9493.9490.0000.0000.0000.000
5B7LEU0-0.051-0.0229.420-0.510-0.5100.0000.0000.0000.000
6B8VAL00.0090.00011.8311.7561.7560.0000.0000.0000.000
7B9LEU00.0330.02514.5150.2460.2460.0000.0000.0000.000
8B10TYR00.008-0.00417.2530.8110.8110.0000.0000.0000.000
9B11TYR00.0750.05420.7580.1890.1890.0000.0000.0000.000
10B12SER00.005-0.02724.0390.2600.2600.0000.0000.0000.000
11B13ARG10.8990.96926.1639.7659.7650.0000.0000.0000.000
12B14HIS00.0390.00329.2080.0310.0310.0000.0000.0000.000
13B15GLY00.0640.04626.2820.1890.1890.0000.0000.0000.000
14B16ALA00.0410.02725.294-0.526-0.5260.0000.0000.0000.000
15B17THR00.049-0.00723.425-0.214-0.2140.0000.0000.0000.000
16B18ALA0-0.0010.00321.134-0.666-0.6660.0000.0000.0000.000
17B19GLU-1-0.819-0.87220.327-14.954-14.9540.0000.0000.0000.000
18B20MET0-0.0100.00320.578-0.457-0.4570.0000.0000.0000.000
19B21ALA00.0130.01217.406-0.614-0.6140.0000.0000.0000.000
20B22ARG10.8630.91416.18413.62613.6260.0000.0000.0000.000
21B23GLN00.020-0.00216.174-1.223-1.2230.0000.0000.0000.000
22B24ILE00.0090.01414.841-0.320-0.3200.0000.0000.0000.000
23B25ALA00.002-0.00712.267-1.027-1.0270.0000.0000.0000.000
24B26ARG10.9610.97712.03016.75716.7570.0000.0000.0000.000
25B27GLY00.0220.01914.120-0.047-0.0470.0000.0000.0000.000
26B28VAL0-0.062-0.0308.732-0.108-0.1080.0000.0000.0000.000
27B29GLU-1-0.944-0.9639.462-25.605-25.6050.0000.0000.0000.000
28B30GLN0-0.045-0.03610.5170.1440.1440.0000.0000.0000.000
29B31GLY0-0.024-0.00212.0391.0821.0820.0000.0000.0000.000
30B32GLY0-0.0050.0058.933-0.483-0.4830.0000.0000.0000.000
31B33PHE0-0.039-0.0285.628-5.267-5.2670.0000.0000.0000.000
34B36ARG10.8250.9155.48139.95439.9540.0000.0000.0000.000
35B37VAL00.0260.02010.0551.9481.9480.0000.0000.0000.000
36B38ARG10.8350.91810.71824.58824.5880.0000.0000.0000.000
37B39THR0-0.025-0.01915.7130.9050.9050.0000.0000.0000.000
38B40VAL00.0240.00219.260-0.530-0.5300.0000.0000.0000.000
39B41PRO00.011-0.00122.0220.2860.2860.0000.0000.0000.000
40B42ALA0-0.037-0.01924.9500.1050.1050.0000.0000.0000.000
41B43VAL0-0.002-0.00728.317-0.134-0.1340.0000.0000.0000.000
42B44SER0-0.066-0.04030.8000.0720.0720.0000.0000.0000.000
43B45THR0-0.024-0.01334.360-0.159-0.1590.0000.0000.0000.000
44B46GLU-2-1.857-1.90636.308-16.977-16.9770.0000.0000.0000.000
45B59ALA10.8460.91618.72415.57615.5760.0000.0000.0000.000
46B60LEU00.1180.05414.2170.6490.6490.0000.0000.0000.000
47B61TYR00.0200.01217.360-0.240-0.2400.0000.0000.0000.000
48B62ALA0-0.0120.00315.447-0.992-0.9920.0000.0000.0000.000
49B63THR0-0.006-0.00513.8200.8130.8130.0000.0000.0000.000
50B64LEU00.0780.02315.735-0.538-0.5380.0000.0000.0000.000
51B65GLU-1-0.853-0.93712.116-20.102-20.1020.0000.0000.0000.000
52B66ASP-1-0.806-0.88410.658-28.225-28.2250.0000.0000.0000.000
53B67LEU00.0170.02611.117-1.984-1.9840.0000.0000.0000.000
54B68LYS10.9250.96813.25319.93619.9360.0000.0000.0000.000
55B69ASN0-0.013-0.0228.0841.6801.6800.0000.0000.0000.000
56B70CYS0-0.110-0.0248.053-3.890-3.8900.0000.0000.0000.000
57B71ALA00.0430.0057.4181.3571.3570.0000.0000.0000.000
58B72GLY00.0690.0289.4112.4302.4300.0000.0000.0000.000
59B73LEU0-0.050-0.02412.047-1.539-1.5390.0000.0000.0000.000
60B74ALA00.0310.02314.7181.0801.0800.0000.0000.0000.000
61B75LEU0-0.010-0.00716.787-0.383-0.3830.0000.0000.0000.000
62B76GLY00.0380.01019.8810.6490.6490.0000.0000.0000.000
63B77SER00.010-0.03022.0930.0660.0660.0000.0000.0000.000
64B78PRO0-0.079-0.02125.7730.2070.2070.0000.0000.0000.000
65B79THR00.0530.03128.9140.0400.0400.0000.0000.0000.000
66B80ARG10.8570.92131.68910.10710.1070.0000.0000.0000.000
67B81PHE00.0430.01833.976-0.055-0.0550.0000.0000.0000.000
68B82GLY00.0530.04434.6560.1260.1260.0000.0000.0000.000
69B83ASN0-0.023-0.00931.992-0.170-0.1700.0000.0000.0000.000
70B84MET00.0280.02426.232-0.146-0.1460.0000.0000.0000.000
71B85ALA0-0.044-0.02628.0000.3640.3640.0000.0000.0000.000
72B86SER00.0740.02428.395-0.416-0.4160.0000.0000.0000.000
73B87PRO00.0160.01326.543-0.131-0.1310.0000.0000.0000.000
74B88LEU0-0.018-0.00921.596-0.403-0.4030.0000.0000.0000.000
75B89LYS10.8330.89224.66410.72910.7290.0000.0000.0000.000
76B90TYR00.0550.02926.752-0.112-0.1120.0000.0000.0000.000
77B91PHE0-0.012-0.01117.697-0.143-0.1430.0000.0000.0000.000
78B92LEU0-0.004-0.01521.358-0.425-0.4250.0000.0000.0000.000
79B93ASP-1-0.791-0.84523.775-11.296-11.2960.0000.0000.0000.000
80B94GLY00.0110.01324.1330.1770.1770.0000.0000.0000.000
81B95THR0-0.090-0.07220.141-0.404-0.4040.0000.0000.0000.000
82B96SER00.0590.02422.202-0.253-0.2530.0000.0000.0000.000
83B97SER0-0.007-0.00321.665-0.016-0.0160.0000.0000.0000.000
84B98LEU0-0.003-0.01816.790-0.297-0.2970.0000.0000.0000.000
85B99TRP0-0.025-0.00719.835-0.277-0.2770.0000.0000.0000.000
86B100LEU0-0.011-0.00722.7120.0180.0180.0000.0000.0000.000
87B101THR0-0.045-0.00918.3180.1940.1940.0000.0000.0000.000
88B102GLY00.0500.03019.314-0.688-0.6880.0000.0000.0000.000
89B103SER0-0.053-0.03515.380-0.746-0.7460.0000.0000.0000.000
90B104LEU0-0.045-0.04115.212-1.739-1.7390.0000.0000.0000.000
91B105VAL00.0500.03417.210-0.048-0.0480.0000.0000.0000.000
92B106GLY0-0.019-0.00717.352-0.794-0.7940.0000.0000.0000.000
93B107LYS10.8390.93711.85324.92324.9230.0000.0000.0000.000
94B108PRO00.0020.01413.3561.2951.2950.0000.0000.0000.000
95B109ALA0-0.013-0.01715.294-1.264-1.2640.0000.0000.0000.000
96B110ALA00.0530.04217.8730.9460.9460.0000.0000.0000.000
97B111VAL0-0.016-0.00819.723-0.399-0.3990.0000.0000.0000.000
98B112PHE0-0.015-0.00318.4780.2480.2480.0000.0000.0000.000
99B113THR0-0.015-0.02023.3140.0180.0180.0000.0000.0000.000
100B114SER0-0.003-0.01926.5560.1000.1000.0000.0000.0000.000
101B115THR0-0.021-0.02028.7950.1900.1900.0000.0000.0000.000
102B116ALA00.0190.01832.593-0.021-0.0210.0000.0000.0000.000
103B117SER0-0.015-0.00635.4990.3610.3610.0000.0000.0000.000
104B118LEU00.0470.00837.213-0.177-0.1770.0000.0000.0000.000
105B119HIS0-0.0080.00539.7960.0400.0400.0000.0000.0000.000
106B120GLY00.0100.01936.6140.0110.0110.0000.0000.0000.000
107B121GLY00.0440.01635.690-0.041-0.0410.0000.0000.0000.000
108B122GLN0-0.0010.00629.777-0.552-0.5520.0000.0000.0000.000
109B123GLU-1-0.849-0.92130.636-9.789-9.7890.0000.0000.0000.000
110B124THR00.0230.00931.301-0.252-0.2520.0000.0000.0000.000
111B125THR0-0.019-0.01128.990-0.099-0.0990.0000.0000.0000.000
112B126GLN00.0300.01726.439-0.250-0.2500.0000.0000.0000.000
113B127LEU00.0550.02627.371-0.378-0.3780.0000.0000.0000.000
114B128SER0-0.049-0.04729.272-0.176-0.1760.0000.0000.0000.000
115B129MET0-0.065-0.03823.9030.0040.0040.0000.0000.0000.000
116B130LEU00.0290.01423.709-0.568-0.5680.0000.0000.0000.000
117B131LEU00.0160.02525.870-0.221-0.2210.0000.0000.0000.000
118B132PRO0-0.0010.00624.870-0.020-0.0200.0000.0000.0000.000
119B133LEU00.005-0.00320.290-0.421-0.4210.0000.0000.0000.000
120B134LEU00.0240.01122.766-0.328-0.3280.0000.0000.0000.000
121B135HIS0-0.046-0.02325.3860.3400.3400.0000.0000.0000.000
122B136HIS0-0.038-0.02320.760-0.180-0.1800.0000.0000.0000.000
123B137GLY00.0120.01721.235-0.610-0.6100.0000.0000.0000.000
124B138MET0-0.068-0.01616.078-0.370-0.3700.0000.0000.0000.000
125B139LEU00.0090.00917.7830.8960.8960.0000.0000.0000.000
126B140VAL0-0.017-0.01319.323-0.637-0.6370.0000.0000.0000.000
127B141LEU0-0.050-0.02016.9690.4670.4670.0000.0000.0000.000
128B142GLY00.0560.02221.558-0.193-0.1930.0000.0000.0000.000
129B143ILE0-0.043-0.01922.218-0.587-0.5870.0000.0000.0000.000
130B144PRO0-0.0190.00023.2170.5640.5640.0000.0000.0000.000
131B145TYR0-0.004-0.02526.2920.0210.0210.0000.0000.0000.000
132B146SER00.0020.00528.9940.1710.1710.0000.0000.0000.000
133B147GLU-1-0.898-0.95722.603-13.422-13.4220.0000.0000.0000.000
134B148PRO0-0.004-0.01026.9650.0590.0590.0000.0000.0000.000
135B149ALA0-0.015-0.00128.5700.1690.1690.0000.0000.0000.000
136B150LEU0-0.044-0.01827.9740.2570.2570.0000.0000.0000.000
137B151LEU0-0.036-0.00923.085-0.270-0.2700.0000.0000.0000.000
138B152GLU-1-0.924-0.93827.532-9.524-9.5240.0000.0000.0000.000
139B153THR0-0.016-0.02626.663-0.102-0.1020.0000.0000.0000.000
140B154ARG0-0.007-0.01429.951-0.009-0.0090.0000.0000.0000.000
141B155GLY00.0420.01731.122-0.280-0.2800.0000.0000.0000.000
142B156GLY00.0050.00031.7930.3390.3390.0000.0000.0000.000
143B157GLY0-0.006-0.00430.209-0.240-0.2400.0000.0000.0000.000
144B158THR00.0080.00527.9310.1680.1680.0000.0000.0000.000
145B159PRO00.0660.02327.869-0.386-0.3860.0000.0000.0000.000
146B160TYR0-0.031-0.01426.465-0.491-0.4910.0000.0000.0000.000
147B161GLY00.0280.00723.536-0.545-0.5450.0000.0000.0000.000
148B162ALA00.0030.02022.4040.2890.2890.0000.0000.0000.000
149B163SER0-0.043-0.04924.3110.3240.3240.0000.0000.0000.000
150B164HIS00.0330.03527.042-0.355-0.3550.0000.0000.0000.000
151B165PHE00.0060.01328.9330.1490.1490.0000.0000.0000.000
152B166ALA00.0110.00830.7210.0040.0040.0000.0000.0000.000
153B167GLY00.0330.02632.4370.1020.1020.0000.0000.0000.000
154B168ALA00.007-0.00935.878-0.160-0.1600.0000.0000.0000.000
155B169ASP-1-0.838-0.91336.292-8.786-8.7860.0000.0000.0000.000
156B170GLY0-0.064-0.04033.071-0.225-0.2250.0000.0000.0000.000
157B171LYS10.8160.90131.5809.4359.4350.0000.0000.0000.000
158B172ARG10.8010.89531.4669.6539.6530.0000.0000.0000.000
159B173SER00.022-0.00829.192-0.198-0.1980.0000.0000.0000.000
160B174LEU0-0.033-0.01123.8200.1410.1410.0000.0000.0000.000
161B175ASP-1-0.789-0.90027.976-10.179-10.1790.0000.0000.0000.000
162B176GLU-1-0.881-0.95327.703-10.687-10.6870.0000.0000.0000.000
163B177HIS10.8620.95926.77010.08210.0820.0000.0000.0000.000
164B178GLU-1-0.713-0.85026.469-10.852-10.8520.0000.0000.0000.000
165B179LEU0-0.023-0.01523.404-0.693-0.6930.0000.0000.0000.000
166B180THR0-0.019-0.02222.105-0.853-0.8530.0000.0000.0000.000
167B181LEU00.0060.00522.159-0.562-0.5620.0000.0000.0000.000
168B182CYS0-0.093-0.04520.167-0.427-0.4270.0000.0000.0000.000
169B183ARG10.8830.93817.69113.73613.7360.0000.0000.0000.000
170B184ALA00.0500.03017.468-0.929-0.9290.0000.0000.0000.000
171B185LEU00.0020.00018.558-0.500-0.5000.0000.0000.0000.000
172B186GLY0-0.009-0.01115.104-0.646-0.6460.0000.0000.0000.000
173B187LYS10.9070.97113.73615.77015.7700.0000.0000.0000.000
174B188ARG10.9480.97214.21613.45413.4540.0000.0000.0000.000
175B189LEU0-0.034-0.00613.571-0.071-0.0710.0000.0000.0000.000
176B190ALA0-0.0070.01410.038-0.828-0.8280.0000.0000.0000.000
177B191GLU-1-0.843-0.93910.777-19.285-19.2850.0000.0000.0000.000
178B192THR0-0.082-0.05313.0760.9180.9180.0000.0000.0000.000
179B193ALA00.005-0.0119.8420.2490.2490.0000.0000.0000.000
180B194GLY0-0.020-0.0139.298-1.190-1.1900.0000.0000.0000.000
181B195LYS10.9430.97510.25916.60516.6050.0000.0000.0000.000
182B196LEU0-0.036-0.01013.0301.0941.0940.0000.0000.0000.000
183B197GLY0-0.050-0.0069.8430.0010.0010.0000.0000.0000.000
184B198SER-1-0.991-0.99210.873-20.159-20.1590.0000.0000.0000.000