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: LQ929

Calculation Name: 1MQO-A-Xray547

Preferred Name: Metallo-beta-lactamase type 2

Target Type: SINGLE PROTEIN

Ligand Name: citric acid | cadmium ion

Ligand 3-letter code: CIT | CD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1MQO

Chain ID: A

ChEMBL ID: CHEMBL4295695

UniProt ID: P04190

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
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 221
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2700656.941817
FMO2-HF: Nuclear repulsion 2616738.76743
FMO2-HF: Total energy -83918.174387
FMO2-MP2: Total energy -84167.511225


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:33:THR)


Summations of interaction energy for fragment #1(A:33: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.
28.99235.1517.232-5.298-8.092-0.047
Interaction energy analysis for fragmet #1(A:33:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.834 / q_NPA : 0.906
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].
3A35ILE0-0.016-0.0032.9881.6733.9470.040-0.894-1.420-0.004
13A45SER00.015-0.0064.663-7.789-7.683-0.001-0.025-0.0800.000
14A47GLN0-0.085-0.0402.015-17.485-15.2945.927-3.459-4.659-0.037
15A48LEU00.0250.0213.768-4.377-3.9660.001-0.227-0.185-0.001
20A53TRP00.012-0.0052.491-11.820-10.7031.266-0.690-1.692-0.005
68A103LYS10.8630.9604.43238.25038.310-0.001-0.003-0.0560.000
4A36LYS10.9760.9935.49726.28126.2810.0000.0000.0000.000
5A37ASN00.0400.0219.372-0.602-0.6020.0000.0000.0000.000
6A38GLU-1-0.918-0.96312.505-16.910-16.9100.0000.0000.0000.000
7A39THR0-0.012-0.00115.3140.8370.8370.0000.0000.0000.000
8A40GLY0-0.037-0.01213.3650.2990.2990.0000.0000.0000.000
9A41THR00.0180.01314.442-0.771-0.7710.0000.0000.0000.000
10A42ILE00.0070.01111.851-0.192-0.1920.0000.0000.0000.000
11A43SER0-0.007-0.0108.568-0.783-0.7830.0000.0000.0000.000
12A44ILE0-0.016-0.0095.7561.1671.1670.0000.0000.0000.000
16A49ASN00.012-0.0046.4652.1052.1050.0000.0000.0000.000
17A50LYS10.9480.9726.62821.90421.9040.0000.0000.0000.000
18A51ASN00.0140.0037.695-1.569-1.5690.0000.0000.0000.000
19A52VAL00.0180.0278.8302.1862.1860.0000.0000.0000.000
21A54VAL00.0670.0357.6163.9233.9230.0000.0000.0000.000
22A55HIS10.7310.8528.73717.18217.1820.0000.0000.0000.000
23A56THR00.024-0.00511.3810.1470.1470.0000.0000.0000.000
24A57GLU-1-0.742-0.83213.322-21.428-21.4280.0000.0000.0000.000
25A58LEU0-0.027-0.01216.2490.4760.4760.0000.0000.0000.000
26A59GLY00.0540.03318.7510.4620.4620.0000.0000.0000.000
27A60SER0-0.066-0.04822.0880.2330.2330.0000.0000.0000.000
28A61PHE00.0140.00225.5800.1530.1530.0000.0000.0000.000
29A62ASN0-0.026-0.02327.7440.2940.2940.0000.0000.0000.000
30A63GLY00.0280.02930.1960.2560.2560.0000.0000.0000.000
31A64GLU-1-0.929-0.94525.552-12.159-12.1590.0000.0000.0000.000
32A66ALA0-0.0060.00123.221-0.174-0.1740.0000.0000.0000.000
33A67VAL00.017-0.00321.482-0.318-0.3180.0000.0000.0000.000
34A68PRO00.0090.01916.353-0.306-0.3060.0000.0000.0000.000
35A69SER0-0.025-0.00317.7540.3800.3800.0000.0000.0000.000
36A70ASN0-0.021-0.01513.825-1.739-1.7390.0000.0000.0000.000
37A71GLY00.0460.02914.0651.8251.8250.0000.0000.0000.000
38A72LEU0-0.052-0.01711.430-2.291-2.2910.0000.0000.0000.000
39A73VAL00.0100.00310.0181.6641.6640.0000.0000.0000.000
40A74LEU0-0.020-0.00810.899-2.060-2.0600.0000.0000.0000.000
41A75ASN00.0630.0309.7163.2473.2470.0000.0000.0000.000
42A76THR0-0.023-0.02012.5140.3310.3310.0000.0000.0000.000
43A77SER0-0.003-0.01716.015-0.156-0.1560.0000.0000.0000.000
44A78LYS10.9240.95318.33313.29113.2910.0000.0000.0000.000
45A79GLY00.0690.05218.4150.7220.7220.0000.0000.0000.000
46A80LEU0-0.0450.00913.065-1.054-1.0540.0000.0000.0000.000
47A81VAL00.0090.00415.7201.0131.0130.0000.0000.0000.000
48A82LEU00.0100.00514.567-1.483-1.4830.0000.0000.0000.000
49A83VAL0-0.040-0.01815.9891.1051.1050.0000.0000.0000.000
50A84ASP-1-0.685-0.83016.932-16.145-16.1450.0000.0000.0000.000
51A85SER0-0.0150.00117.872-0.916-0.9160.0000.0000.0000.000
52A86SER0-0.017-0.05918.243-0.715-0.7150.0000.0000.0000.000
53A87TRP00.0200.01019.6391.1211.1210.0000.0000.0000.000
54A88ASP-1-0.777-0.87022.870-12.601-12.6010.0000.0000.0000.000
55A89ASP-1-0.757-0.85223.044-12.223-12.2230.0000.0000.0000.000
56A90LYS10.8910.96522.11112.77512.7750.0000.0000.0000.000
57A91LEU00.0290.00618.280-0.604-0.6040.0000.0000.0000.000
58A92THR0-0.019-0.02418.348-1.122-1.1220.0000.0000.0000.000
59A93LYS10.7970.88019.30211.45611.4560.0000.0000.0000.000
60A94GLU-1-0.888-0.95916.811-16.223-16.2230.0000.0000.0000.000
61A95LEU0-0.033-0.00813.306-1.226-1.2260.0000.0000.0000.000
62A96ILE0-0.026-0.01414.406-1.131-1.1310.0000.0000.0000.000
63A97GLU-1-0.749-0.84615.661-15.208-15.2080.0000.0000.0000.000
64A98MET0-0.040-0.00310.224-1.404-1.4040.0000.0000.0000.000
65A99VAL0-0.017-0.01710.662-1.476-1.4760.0000.0000.0000.000
66A100GLU-1-0.752-0.85612.132-15.654-15.6540.0000.0000.0000.000
67A102LYS10.9600.98713.55618.60418.6040.0000.0000.0000.000
69A104PHE0-0.048-0.0457.200-1.564-1.5640.0000.0000.0000.000
70A105GLN0-0.052-0.01811.4631.6101.6100.0000.0000.0000.000
71A106LYS10.8230.90813.54020.70420.7040.0000.0000.0000.000
72A107ARG10.9020.92616.77813.54413.5440.0000.0000.0000.000
73A109VAL0-0.005-0.00716.702-0.468-0.4680.0000.0000.0000.000
74A110THR0-0.033-0.02619.1500.5210.5210.0000.0000.0000.000
75A111ASP-1-0.822-0.87520.701-12.090-12.0900.0000.0000.0000.000
76A112VAL00.0220.01219.785-0.914-0.9140.0000.0000.0000.000
77A113ILE0-0.026-0.00820.5310.7610.7610.0000.0000.0000.000
78A114ILE00.0030.00321.458-0.714-0.7140.0000.0000.0000.000
79A115THR0-0.039-0.05321.0210.6750.6750.0000.0000.0000.000
80A116HIS10.8490.88424.18312.77812.7780.0000.0000.0000.000
81A117ALA00.0130.00727.180-0.292-0.2920.0000.0000.0000.000
82A118HIS0-0.029-0.02227.791-0.149-0.1490.0000.0000.0000.000
83A119ALA00.0380.01527.669-0.357-0.3570.0000.0000.0000.000
84A120ASP-1-0.844-0.94023.827-13.033-13.0330.0000.0000.0000.000
85A121ARG10.6930.80818.64714.84814.8480.0000.0000.0000.000
86A122ILE0-0.007-0.00424.156-0.216-0.2160.0000.0000.0000.000
87A123GLY00.0470.02526.3670.2590.2590.0000.0000.0000.000
88A124GLY0-0.019-0.00623.7640.1450.1450.0000.0000.0000.000
89A125ILE0-0.020-0.02024.793-0.153-0.1530.0000.0000.0000.000
90A126LYS10.9760.99327.1999.7569.7560.0000.0000.0000.000
91A127THR0-0.025-0.04822.7770.1040.1040.0000.0000.0000.000
92A128LEU0-0.059-0.02821.822-0.188-0.1880.0000.0000.0000.000
93A129LYS10.8350.92025.5349.9089.9080.0000.0000.0000.000
94A130GLU-1-0.858-0.93027.921-10.586-10.5860.0000.0000.0000.000
95A131ARG10.7660.85120.84813.41613.4160.0000.0000.0000.000
96A133GLY0-0.0030.01326.415-0.167-0.1670.0000.0000.0000.000
97A134ILE0-0.063-0.02221.501-0.178-0.1780.0000.0000.0000.000
98A135LYS10.8420.90225.04812.40112.4010.0000.0000.0000.000
99A136ALA00.0380.02424.664-0.534-0.5340.0000.0000.0000.000
100A137HIS10.7600.83924.13412.54612.5460.0000.0000.0000.000
101A138SER00.0560.01225.895-0.424-0.4240.0000.0000.0000.000
102A139THR00.0370.03528.2570.3650.3650.0000.0000.0000.000
103A140ALA00.0770.03131.083-0.005-0.0050.0000.0000.0000.000
104A141LEU00.0130.01734.0140.1040.1040.0000.0000.0000.000
105A142THR0-0.014-0.03828.2970.0210.0210.0000.0000.0000.000
106A143ALA0-0.013-0.00531.778-0.061-0.0610.0000.0000.0000.000
107A144GLU-1-0.895-0.94933.386-8.299-8.2990.0000.0000.0000.000
108A145LEU00.0280.01533.5020.0910.0910.0000.0000.0000.000
109A146ALA0-0.0080.00231.5140.0230.0230.0000.0000.0000.000
110A147LYS10.8500.91033.4628.3988.3980.0000.0000.0000.000
111A148LYS10.9150.96436.7368.5178.5170.0000.0000.0000.000
112A149ASN0-0.099-0.05534.8320.2910.2910.0000.0000.0000.000
113A150GLY00.0070.00936.159-0.098-0.0980.0000.0000.0000.000
114A167TYR0-0.041-0.01830.563-0.228-0.2280.0000.0000.0000.000
115A168GLU-1-0.903-0.96331.672-8.985-8.9850.0000.0000.0000.000
116A169GLU-1-0.824-0.89332.079-8.818-8.8180.0000.0000.0000.000
117A170PRO0-0.019-0.00528.489-0.117-0.1170.0000.0000.0000.000
118A171LEU0-0.038-0.04228.2640.2850.2850.0000.0000.0000.000
119A172GLY0-0.0190.01231.2880.2720.2720.0000.0000.0000.000
120A173ASP-1-0.769-0.87229.097-10.839-10.8390.0000.0000.0000.000
121A174LEU0-0.092-0.03225.9430.0190.0190.0000.0000.0000.000
122A175GLN00.019-0.01030.4370.4230.4230.0000.0000.0000.000
123A176THR00.019-0.00230.985-0.341-0.3410.0000.0000.0000.000
124A177VAL00.0020.00328.683-0.323-0.3230.0000.0000.0000.000
125A178THR00.0060.02128.0690.4420.4420.0000.0000.0000.000
126A179ASN0-0.077-0.04926.088-0.883-0.8830.0000.0000.0000.000
127A180LEU00.0360.02623.5530.3630.3630.0000.0000.0000.000
128A181LYS10.9390.95322.70711.50211.5020.0000.0000.0000.000
129A182PHE00.0650.04919.6670.4020.4020.0000.0000.0000.000
130A183GLY00.012-0.01019.827-0.751-0.7510.0000.0000.0000.000
131A184ASN0-0.052-0.03218.9440.9710.9710.0000.0000.0000.000
132A185MET00.0000.02213.535-0.245-0.2450.0000.0000.0000.000
133A186LYS10.9190.95818.60914.51914.5190.0000.0000.0000.000
134A187VAL00.0200.00118.492-0.889-0.8890.0000.0000.0000.000
135A188GLU-1-0.770-0.82221.034-11.387-11.3870.0000.0000.0000.000
136A189THR0-0.037-0.01122.685-0.513-0.5130.0000.0000.0000.000
137A190PHE00.038-0.00425.0650.4950.4950.0000.0000.0000.000
138A191TYR00.001-0.00526.778-0.264-0.2640.0000.0000.0000.000
139A192PRO0-0.064-0.01727.2630.3140.3140.0000.0000.0000.000
140A193GLY00.0500.02630.0980.3410.3410.0000.0000.0000.000
141A194LYS10.8500.93231.1968.1988.1980.0000.0000.0000.000
142A195GLY00.0360.00329.965-0.041-0.0410.0000.0000.0000.000
143A196HIS0-0.0030.02627.2930.1680.1680.0000.0000.0000.000
144A197THR0-0.015-0.02729.2920.0220.0220.0000.0000.0000.000
145A198GLU-1-0.823-0.91931.419-8.685-8.6850.0000.0000.0000.000
146A199ASP-1-0.740-0.82730.388-10.673-10.6730.0000.0000.0000.000
147A200ASN0-0.026-0.00426.637-0.278-0.2780.0000.0000.0000.000
148A201ILE0-0.035-0.00924.6790.2030.2030.0000.0000.0000.000
149A202VAL0-0.0190.00622.231-0.538-0.5380.0000.0000.0000.000
150A203VAL0-0.003-0.01719.5760.3590.3590.0000.0000.0000.000
151A204TRP00.0310.02419.155-1.025-1.0250.0000.0000.0000.000
152A205LEU00.0340.01614.1320.2740.2740.0000.0000.0000.000
153A209PRO0-0.004-0.00917.927-0.485-0.4850.0000.0000.0000.000
154A210GLN0-0.051-0.03417.3350.5020.5020.0000.0000.0000.000
155A211TYR0-0.014-0.02413.582-0.724-0.7240.0000.0000.0000.000
156A215ASN0-0.0160.00615.379-0.697-0.6970.0000.0000.0000.000
157A216ILE00.0250.02111.333-0.383-0.3830.0000.0000.0000.000
158A217LEU0-0.004-0.00315.4090.7890.7890.0000.0000.0000.000
159A218VAL0-0.013-0.01315.461-0.987-0.9870.0000.0000.0000.000
160A219GLY00.0370.00217.5900.9800.9800.0000.0000.0000.000
161A220GLY00.0790.03619.1820.7370.7370.0000.0000.0000.000
162A221CYS-1-0.833-0.79120.823-14.537-14.5370.0000.0000.0000.000
163A222LEU00.0010.02023.0330.3630.3630.0000.0000.0000.000
164A223VAL0-0.034-0.00520.3140.2540.2540.0000.0000.0000.000
165A224LYS10.8860.95821.04112.03612.0360.0000.0000.0000.000
166A225SER00.0410.01117.162-0.068-0.0680.0000.0000.0000.000
167A226THR00.031-0.00218.1930.4810.4810.0000.0000.0000.000
168A227SER0-0.071-0.03018.4900.7470.7470.0000.0000.0000.000
169A228ALA00.0300.02020.5040.5500.5500.0000.0000.0000.000
170A229LYS10.8940.93023.21413.25213.2520.0000.0000.0000.000
171A230ASP-1-0.816-0.89626.841-11.224-11.2240.0000.0000.0000.000
172A231LEU00.0430.00426.957-0.512-0.5120.0000.0000.0000.000
173A232GLY0-0.028-0.00727.173-0.295-0.2950.0000.0000.0000.000
174A233ASN0-0.053-0.03028.0910.6580.6580.0000.0000.0000.000
175A234VAL00.031-0.00130.127-0.173-0.1730.0000.0000.0000.000
176A235ALA0-0.0090.00332.8840.2370.2370.0000.0000.0000.000
177A236ASP-1-0.848-0.90233.104-9.217-9.2170.0000.0000.0000.000
178A237ALA0-0.034-0.01332.078-0.121-0.1210.0000.0000.0000.000
179A238TYR00.000-0.00633.5310.2750.2750.0000.0000.0000.000
180A239VAL00.0400.00433.214-0.169-0.1690.0000.0000.0000.000
181A240ASN00.0190.02034.575-0.146-0.1460.0000.0000.0000.000
182A241GLU-1-0.878-0.95935.203-8.621-8.6210.0000.0000.0000.000
183A242TRP0-0.003-0.00126.780-0.148-0.1480.0000.0000.0000.000
184A243SER00.0550.02630.579-0.432-0.4320.0000.0000.0000.000
185A244THR0-0.011-0.00831.703-0.118-0.1180.0000.0000.0000.000
186A245SER0-0.030-0.02829.811-0.046-0.0460.0000.0000.0000.000
187A246ILE0-0.009-0.00225.278-0.418-0.4180.0000.0000.0000.000
188A247GLU-1-0.844-0.93327.849-10.596-10.5960.0000.0000.0000.000
189A248ASN0-0.075-0.03930.4700.1370.1370.0000.0000.0000.000
190A249VAL0-0.029-0.01323.685-0.159-0.1590.0000.0000.0000.000
191A250LEU0-0.0060.00125.045-0.363-0.3630.0000.0000.0000.000
192A251LYS10.8300.90427.0229.7069.7060.0000.0000.0000.000
193A252ARG10.8030.90326.88411.46311.4630.0000.0000.0000.000
194A253TYR0-0.063-0.06622.502-0.129-0.1290.0000.0000.0000.000
195A254ARG10.9570.98323.99010.29210.2920.0000.0000.0000.000
196A255ASN0-0.024-0.01121.489-0.260-0.2600.0000.0000.0000.000
197A256ILE0-0.024-0.01117.433-0.233-0.2330.0000.0000.0000.000
198A257ASN0-0.036-0.01614.3880.6240.6240.0000.0000.0000.000
199A258ALA00.004-0.00112.300-1.168-1.1680.0000.0000.0000.000
200A259VAL0-0.025-0.01214.2970.8500.8500.0000.0000.0000.000
201A260VAL00.0220.00311.943-1.059-1.0590.0000.0000.0000.000
202A261PRO00.0260.03114.5661.1181.1180.0000.0000.0000.000
203A262GLY00.0100.00916.441-0.992-0.9920.0000.0000.0000.000
204A263HIS10.8540.84017.62615.16015.1600.0000.0000.0000.000
205A264GLY00.0320.04215.8030.6810.6810.0000.0000.0000.000
206A265GLU-1-0.906-0.95510.897-27.989-27.9890.0000.0000.0000.000
207A277VAL0-0.033-0.0249.8771.3371.3370.0000.0000.0000.000
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