FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: VV3G1

Calculation Name: 1X8H-A-Xray547

Preferred Name: Beta-lactamase

Target Type: SINGLE PROTEIN

Ligand Name: carbonate ion

Ligand 3-letter code: CO3

Ligand of Interest (LOI):

PDB ID: 1X8H

Chain ID: A

ChEMBL ID: CHEMBL1169593

UniProt ID: P26918

Base Structure: X-ray

Registration Date: 2025-10-03

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
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 -2874304.305961
FMO2-HF: Nuclear repulsion 2787086.384771
FMO2-HF: Total energy -87217.92119
FMO2-MP2: Total energy -87475.903071


3D Structure
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:41:ALA)


Summations of interaction energy for fragment #1(A:41:ALA)
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.
12.51616.3530.746-2.092-2.491-0.016
Interaction energy analysis for fragmet #1(A:41:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.855 / q_NPA : 0.919
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].
3A43MET00.0050.0183.0727.7289.3850.036-0.733-0.959-0.002
4A44SER0-0.063-0.0212.661-10.729-8.9260.712-1.248-1.268-0.014
5A45LEU00.0330.0054.6684.8594.890-0.001-0.010-0.0200.000
18A58ASN0-0.044-0.0333.7758.9569.302-0.001-0.101-0.2440.000
6A46THR00.0000.0058.051-0.011-0.0110.0000.0000.0000.000
7A47GLN0-0.055-0.02410.1491.0191.0190.0000.0000.0000.000
8A48VAL0-0.008-0.00513.945-0.446-0.4460.0000.0000.0000.000
9A49SER0-0.004-0.00616.2650.9370.9370.0000.0000.0000.000
10A50GLY00.0560.03419.6440.0950.0950.0000.0000.0000.000
11A51PRO00.0070.01519.062-0.847-0.8470.0000.0000.0000.000
12A52VAL0-0.0010.00717.568-0.558-0.5580.0000.0000.0000.000
13A53TYR00.007-0.01111.854-0.649-0.6490.0000.0000.0000.000
14A54VAL00.0400.01211.0831.0661.0660.0000.0000.0000.000
15A55VAL0-0.043-0.0268.993-1.756-1.7560.0000.0000.0000.000
16A56GLU-1-0.886-0.9476.427-36.236-36.2360.0000.0000.0000.000
17A57ASP-1-0.774-0.9166.558-37.395-37.3950.0000.0000.0000.000
19A59TYR0-0.0160.0006.485-1.472-1.4720.0000.0000.0000.000
20A60TYR0-0.006-0.0109.7091.8511.8510.0000.0000.0000.000
21A67VAL00.0120.01912.075-0.608-0.6080.0000.0000.0000.000
22A68GLN00.0300.0198.5880.9650.9650.0000.0000.0000.000
23A69GLU-1-0.859-0.89210.973-20.372-20.3720.0000.0000.0000.000
24A70ASN0-0.023-0.01610.697-4.897-4.8970.0000.0000.0000.000
25A71SER00.007-0.02212.5442.8732.8730.0000.0000.0000.000
26A72MET0-0.0330.00013.620-1.131-1.1310.0000.0000.0000.000
27A73VAL0-0.027-0.01513.2940.3020.3020.0000.0000.0000.000
28A74TYR00.0200.01416.0050.1050.1050.0000.0000.0000.000
29A75PHE0-0.010-0.02013.8340.4890.4890.0000.0000.0000.000
30A76GLY00.0570.03419.5810.4250.4250.0000.0000.0000.000
31A77ALA0-0.027-0.01923.351-0.033-0.0330.0000.0000.0000.000
32A78LYS10.8650.91126.4619.8809.8800.0000.0000.0000.000
33A79GLY00.0370.00223.2890.1180.1180.0000.0000.0000.000
34A80VAL0-0.041-0.00117.0240.0120.0120.0000.0000.0000.000
35A81THR00.0180.00420.2890.3710.3710.0000.0000.0000.000
36A82VAL0-0.012-0.00715.503-0.701-0.7010.0000.0000.0000.000
37A83VAL0-0.024-0.01017.3221.0851.0850.0000.0000.0000.000
38A84GLY00.0680.04717.075-0.870-0.8700.0000.0000.0000.000
39A85ALA0-0.037-0.02216.365-0.704-0.7040.0000.0000.0000.000
40A86THR00.0280.02311.617-0.964-0.9640.0000.0000.0000.000
41A87TRP00.0260.00812.3323.0153.0150.0000.0000.0000.000
42A88THR0-0.0340.00213.6121.3271.3270.0000.0000.0000.000
43A89PRO00.004-0.00714.921-0.693-0.6930.0000.0000.0000.000
44A90ASP-1-0.900-0.94211.243-24.150-24.1500.0000.0000.0000.000
45A91THR00.0470.0149.799-0.442-0.4420.0000.0000.0000.000
46A92ALA00.0120.02210.841-1.049-1.0490.0000.0000.0000.000
47A93ARG10.9750.99012.59019.95519.9550.0000.0000.0000.000
48A94GLU-1-0.822-0.8917.263-29.794-29.7940.0000.0000.0000.000
49A95LEU00.0630.0268.939-0.870-0.8700.0000.0000.0000.000
50A96HIS00.0360.02610.4840.5470.5470.0000.0000.0000.000
51A97LYS10.7250.8338.13828.94828.9480.0000.0000.0000.000
52A98LEU0-0.025-0.0015.4550.6560.6560.0000.0000.0000.000
53A99ILE00.0340.0109.6381.2781.2780.0000.0000.0000.000
54A100LYS10.8830.94213.13218.84418.8440.0000.0000.0000.000
55A102ARG10.9000.9599.50324.98824.9880.0000.0000.0000.000
56A103VAL0-0.0070.02312.1870.2330.2330.0000.0000.0000.000
57A104SER0-0.009-0.01414.9391.4821.4820.0000.0000.0000.000
58A105ARG10.9750.98917.92011.54511.5450.0000.0000.0000.000
59A106LYS10.8240.91520.56912.78012.7800.0000.0000.0000.000
60A108PRO00.0350.02420.582-0.616-0.6160.0000.0000.0000.000
61A109VAL00.0130.00417.711-0.105-0.1050.0000.0000.0000.000
62A110LEU0-0.056-0.00420.8800.4720.4720.0000.0000.0000.000
63A111GLU-1-0.870-0.93822.809-11.771-11.7710.0000.0000.0000.000
64A112VAL00.0210.01518.750-0.572-0.5720.0000.0000.0000.000
65A113ILE0-0.010-0.00321.1520.6130.6130.0000.0000.0000.000
66A114ASN0-0.019-0.01921.042-0.217-0.2170.0000.0000.0000.000
67A115THR00.028-0.01021.2060.4090.4090.0000.0000.0000.000
68A116ASN00.009-0.00423.0080.0060.0060.0000.0000.0000.000
69A117TYR00.000-0.01424.189-0.602-0.6020.0000.0000.0000.000
70A118HIS10.8350.93422.36512.92412.9240.0000.0000.0000.000
71A119THR00.0740.02019.897-0.296-0.2960.0000.0000.0000.000
72A120ASP-1-0.762-0.85716.632-17.486-17.4860.0000.0000.0000.000
73A121ARG10.7520.84615.57618.10818.1080.0000.0000.0000.000
74A122ALA00.0190.00319.4560.1850.1850.0000.0000.0000.000
75A123GLY00.0680.04418.7110.4460.4460.0000.0000.0000.000
76A124GLY0-0.029-0.01016.9600.1030.1030.0000.0000.0000.000
77A125ASN00.011-0.02517.570-0.255-0.2550.0000.0000.0000.000
78A126ALA00.0000.00120.7660.4510.4510.0000.0000.0000.000
79A127TYR00.003-0.00316.3400.3170.3170.0000.0000.0000.000
80A128TRP00.0070.00014.5400.5850.5850.0000.0000.0000.000
81A129LYS10.8870.94320.38811.93511.9350.0000.0000.0000.000
82A130SER0-0.079-0.03720.6890.3210.3210.0000.0000.0000.000
83A131ILE0-0.054-0.02618.3380.2350.2350.0000.0000.0000.000
84A133GLY00.0030.00622.2270.1650.1650.0000.0000.0000.000
85A134ALA0-0.0280.00421.9310.2980.2980.0000.0000.0000.000
86A135LYS10.9050.94723.88710.79310.7930.0000.0000.0000.000
87A136VAL00.0200.01022.967-0.485-0.4850.0000.0000.0000.000
88A137VAL0-0.001-0.00324.6880.5930.5930.0000.0000.0000.000
89A138SER00.007-0.01025.550-0.511-0.5110.0000.0000.0000.000
90A139THR00.0820.04927.9860.3850.3850.0000.0000.0000.000
91A140ARG10.8710.89131.1608.4658.4650.0000.0000.0000.000
92A141GLN00.0360.01832.886-0.069-0.0690.0000.0000.0000.000
93A142THR0-0.025-0.03126.666-0.004-0.0040.0000.0000.0000.000
94A143ARG10.8720.92229.6869.0619.0610.0000.0000.0000.000
95A144ASP-1-0.874-0.93830.964-8.959-8.9590.0000.0000.0000.000
96A145LEU00.0330.01931.1160.0720.0720.0000.0000.0000.000
97A146MET0-0.051-0.00125.180-0.168-0.1680.0000.0000.0000.000
98A147LYS10.9060.94329.7158.7258.7250.0000.0000.0000.000
99A148SER0-0.051-0.05132.8010.1220.1220.0000.0000.0000.000
100A149ASP-1-0.761-0.85530.827-9.873-9.8730.0000.0000.0000.000
101A150TRP0-0.090-0.04421.826-0.398-0.3980.0000.0000.0000.000
102A151ALA00.0300.00527.430-0.389-0.3890.0000.0000.0000.000
103A152GLU-1-0.901-0.93929.031-10.293-10.2930.0000.0000.0000.000
104A153ILE0-0.030-0.01323.718-0.313-0.3130.0000.0000.0000.000
105A154VAL00.0110.02723.581-0.725-0.7250.0000.0000.0000.000
106A155ALA00.0530.02224.567-0.364-0.3640.0000.0000.0000.000
107A156PHE0-0.071-0.02823.8520.0600.0600.0000.0000.0000.000
108A157THR0-0.002-0.01519.801-0.376-0.3760.0000.0000.0000.000
109A158ARG10.8970.94221.75113.04113.0410.0000.0000.0000.000
110A159LYS10.8680.93423.39811.65111.6510.0000.0000.0000.000
111A160GLY0-0.038-0.00621.5390.1560.1560.0000.0000.0000.000
112A161LEU0-0.024-0.00416.081-0.739-0.7390.0000.0000.0000.000
113A162PRO00.0070.00519.6360.0530.0530.0000.0000.0000.000
114A163GLU-1-0.877-0.95216.005-17.728-17.7280.0000.0000.0000.000
115A164TYR0-0.036-0.03516.773-0.166-0.1660.0000.0000.0000.000
116A165PRO0-0.029-0.01017.5851.0151.0150.0000.0000.0000.000
117A166ASP-1-0.910-0.96620.509-11.911-11.9110.0000.0000.0000.000
118A167LEU0-0.052-0.01019.0990.2180.2180.0000.0000.0000.000
119A168PRO00.0490.03023.4400.3730.3730.0000.0000.0000.000
120A169LEU00.002-0.00325.424-0.361-0.3610.0000.0000.0000.000
121A170VAL0-0.028-0.01624.3130.3060.3060.0000.0000.0000.000
122A171LEU00.0080.00425.743-0.333-0.3330.0000.0000.0000.000
123A172PRO00.011-0.00326.732-0.041-0.0410.0000.0000.0000.000
124A173ASN0-0.033-0.02128.1040.0540.0540.0000.0000.0000.000
125A174VAL0-0.0080.00629.0600.2830.2830.0000.0000.0000.000
126A175VAL0-0.016-0.00829.860-0.304-0.3040.0000.0000.0000.000
127A176HIS0-0.0070.00829.8960.4690.4690.0000.0000.0000.000
128A177ASP-1-0.793-0.87233.756-8.645-8.6450.0000.0000.0000.000
129A178GLY00.0210.01335.0870.2120.2120.0000.0000.0000.000
130A179ASP-1-0.844-0.91532.263-9.819-9.8190.0000.0000.0000.000
131A180PHE0-0.034-0.01926.9050.1580.1580.0000.0000.0000.000
132A181THR0-0.036-0.02429.143-0.205-0.2050.0000.0000.0000.000
133A182LEU0-0.004-0.00125.0600.2010.2010.0000.0000.0000.000
134A183GLN0-0.033-0.03923.2280.3860.3860.0000.0000.0000.000
135A184GLU-1-0.834-0.90127.269-9.817-9.8170.0000.0000.0000.000
136A185GLY00.0080.02030.0200.2300.2300.0000.0000.0000.000
137A186LYS10.8100.88826.45410.62210.6220.0000.0000.0000.000
138A187VAL00.0200.01622.985-0.476-0.4760.0000.0000.0000.000
139A188ARG10.8930.93725.55710.43710.4370.0000.0000.0000.000
140A189ALA00.0200.01826.349-0.331-0.3310.0000.0000.0000.000
141A190PHE0-0.009-0.01127.6820.3950.3950.0000.0000.0000.000
142A191TYR00.003-0.00929.242-0.280-0.2800.0000.0000.0000.000
143A192ALA00.0250.01331.1250.2370.2370.0000.0000.0000.000
144A193GLY00.0020.01232.9140.2350.2350.0000.0000.0000.000
145A194PRO00.0000.01531.795-0.356-0.3560.0000.0000.0000.000
146A195ALA00.0360.00528.2010.0490.0490.0000.0000.0000.000
147A196HIS0-0.020-0.00422.7240.1100.1100.0000.0000.0000.000
148A197THR0-0.016-0.02426.349-0.230-0.2300.0000.0000.0000.000
149A198PRO00.0430.00528.5670.0530.0530.0000.0000.0000.000
150A199ASP-1-0.736-0.83928.373-11.323-11.3230.0000.0000.0000.000
151A200GLY0-0.0230.00526.699-0.147-0.1470.0000.0000.0000.000
152A201ILE0-0.046-0.01625.5270.3150.3150.0000.0000.0000.000
153A202PHE00.0110.00424.792-0.676-0.6760.0000.0000.0000.000
154A203VAL0-0.020-0.02622.4220.3140.3140.0000.0000.0000.000
155A204TYR0-0.030-0.03423.550-0.289-0.2890.0000.0000.0000.000
156A205PHE00.0130.00320.1370.1200.1200.0000.0000.0000.000
157A209PRO00.0070.00224.793-0.064-0.0640.0000.0000.0000.000
158A210ASP-1-0.839-0.89126.285-10.676-10.6760.0000.0000.0000.000
159A211GLU-1-0.879-0.96521.818-12.854-12.8540.0000.0000.0000.000
160A215GLN0-0.027-0.00724.353-0.268-0.2680.0000.0000.0000.000
161A216VAL00.0390.02419.380-0.215-0.2150.0000.0000.0000.000
162A217LEU00.002-0.00122.4640.4460.4460.0000.0000.0000.000
163A218TYR0-0.024-0.02316.488-0.236-0.2360.0000.0000.0000.000
164A219GLY00.0690.03020.5720.7390.7390.0000.0000.0000.000
165A220GLY00.0270.01818.8560.3900.3900.0000.0000.0000.000
166A221CYS0-0.077-0.01319.493-0.270-0.2700.0000.0000.0000.000
167A222ILE0-0.0220.01320.7900.2100.2100.0000.0000.0000.000
168A223LEU00.0170.02821.4340.4670.4670.0000.0000.0000.000
169A224LYS10.8500.93718.23413.43713.4370.0000.0000.0000.000
170A225GLU-1-0.797-0.91016.315-18.758-18.7580.0000.0000.0000.000
171A226LYS10.9090.94116.01119.85719.8570.0000.0000.0000.000
172A231LEU00.0320.02721.024-0.158-0.1580.0000.0000.0000.000
173A232GLY00.0460.02722.629-0.146-0.1460.0000.0000.0000.000
174A233ASN00.014-0.01723.3020.4630.4630.0000.0000.0000.000
175A234LEU0-0.001-0.00626.0210.3780.3780.0000.0000.0000.000
176A235SER0-0.011-0.00427.3420.1390.1390.0000.0000.0000.000
177A236PHE00.0420.02326.0240.0610.0610.0000.0000.0000.000
178A237ALA0-0.0090.00328.2310.0680.0680.0000.0000.0000.000
179A238ASP-1-0.844-0.90930.211-8.746-8.7460.0000.0000.0000.000
180A239VAL0-0.008-0.01931.560-0.126-0.1260.0000.0000.0000.000
181A240LYS10.8470.92133.1888.3468.3460.0000.0000.0000.000
182A241ALA0-0.017-0.00634.9550.0610.0610.0000.0000.0000.000
183A242TYR0-0.005-0.02224.706-0.166-0.1660.0000.0000.0000.000
184A243PRO00.0200.00031.321-0.184-0.1840.0000.0000.0000.000
185A244GLN0-0.002-0.00432.7110.0600.0600.0000.0000.0000.000
186A245THR0-0.020-0.01930.2030.2350.2350.0000.0000.0000.000
187A246LEU0-0.0150.00127.167-0.141-0.1410.0000.0000.0000.000
188A247GLU-1-0.788-0.85430.961-9.280-9.2800.0000.0000.0000.000
189A248ARG10.8400.90634.4039.1279.1270.0000.0000.0000.000
190A249LEU0-0.003-0.00127.1880.0730.0730.0000.0000.0000.000
191A250LYS10.8350.91330.9509.8689.8680.0000.0000.0000.000
192A251ALA0-0.044-0.01833.0280.2200.2200.0000.0000.0000.000
193A252MET0-0.020-0.01532.4080.1510.1510.0000.0000.0000.000
194A253LYS10.8130.91834.0648.8008.8000.0000.0000.0000.000
195A254LEU00.0290.02729.2380.0430.0430.0000.0000.0000.000
196A255PRO0-0.0040.00230.634-0.198-0.1980.0000.0000.0000.000
197A256ILE0-0.0060.01224.811-0.343-0.3430.0000.0000.0000.000
198A257LYS10.9330.97324.42811.85111.8510.0000.0000.0000.000
199A258THR0-0.040-0.02318.659-0.396-0.3960.0000.0000.0000.000
200A259VAL0-0.021-0.00121.0160.3660.3660.0000.0000.0000.000
201A260ILE0-0.014-0.00615.215-0.715-0.7150.0000.0000.0000.000
202A261GLY00.0080.00517.0110.7710.7710.0000.0000.0000.000
203A262GLY00.0270.01415.361-1.443-1.4430.0000.0000.0000.000
204A263HIS10.7680.84514.26719.46519.4650.0000.0000.0000.000
205A264ASP-1-0.785-0.87113.627-17.809-17.8090.0000.0000.0000.000
206A265SER00.0630.04111.901-2.191-2.1910.0000.0000.0000.000
207A266PRO0-0.0160.00810.9852.1822.1820.0000.0000.0000.000
208A267LEU00.003-0.00912.9321.7201.7200.0000.0000.0000.000
209A289HIS10.8530.93515.69317.97617.9760.0000.0000.0000.000
210A290GLY00.1130.07019.414-0.083-0.0830.0000.0000.0000.000
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212A292GLU-1-0.845-0.92324.328-12.673-12.6730.0000.0000.0000.000
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