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: 1VKZZ

Calculation Name: 1M2X-A-Xray549

Preferred Name: Carbapenem-hydrolyzing beta-lactamase BlaB-1

Target Type: SINGLE PROTEIN

Ligand Name: 1-(3-mercapto-2-methyl-propionyl)-pyrrolidine-2-carboxylic acid | glycerol | zinc ion

Ligand 3-letter code: MCO | GOL | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1M2X

Chain ID: A

ChEMBL ID: CHEMBL1667692

UniProt ID: O08498

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 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2797697.814834
FMO2-HF: Nuclear repulsion 2711078.627132
FMO2-HF: Total energy -86619.187703
FMO2-MP2: Total energy -86875.599548


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:41:ASP)


Summations of interaction energy for fragment #1(A:41:ASP)
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.
-28.317-22.3951.278-2.66-4.5370.023
Interaction energy analysis for fragmet #1(A:41:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.065 / q_NPA : -0.051
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].
3A43LYS10.9170.9813.835-8.423-6.094-0.009-0.815-1.5050.001
4A44ILE0-0.019-0.0185.018-4.291-4.295-0.001-0.0060.0110.000
17A58TYR00.010-0.0122.685-1.8911.1051.290-1.666-2.6190.022
24A66LYS10.8970.9554.035-14.838-14.681-0.001-0.065-0.0900.000
49A91LYS10.7770.8703.62012.63512.9190.000-0.053-0.2300.000
52A94SER00.0580.0244.007-2.471-2.311-0.001-0.055-0.1040.000
5A45GLU-1-0.797-0.8678.5847.0447.0440.0000.0000.0000.000
6A47LYS10.8750.93311.672-2.006-2.0060.0000.0000.0000.000
7A48LEU00.0000.02715.3690.1440.1440.0000.0000.0000.000
8A49LYS10.8860.93317.825-1.436-1.4360.0000.0000.0000.000
9A50ASP-1-0.817-0.90220.8050.7370.7370.0000.0000.0000.000
10A51ASN0-0.025-0.01219.9280.1510.1510.0000.0000.0000.000
11A52LEU00.0250.02018.614-0.148-0.1480.0000.0000.0000.000
12A53TYR0-0.016-0.01313.3880.3090.3090.0000.0000.0000.000
13A54VAL00.0640.03511.373-0.469-0.4690.0000.0000.0000.000
14A55TYR0-0.089-0.0598.9880.6190.6190.0000.0000.0000.000
15A56THR0-0.005-0.0106.399-0.707-0.7070.0000.0000.0000.000
16A57THR0-0.030-0.0145.1321.3271.3270.0000.0000.0000.000
18A59ASN00.0020.0045.752-4.221-4.2210.0000.0000.0000.000
19A60THR0-0.017-0.0098.3351.6131.6130.0000.0000.0000.000
20A61PHE00.0310.02710.712-0.459-0.4590.0000.0000.0000.000
21A62ASN00.013-0.00214.4410.1960.1960.0000.0000.0000.000
22A63GLY00.0270.02014.7000.1290.1290.0000.0000.0000.000
23A64THR0-0.0060.00714.0740.4390.4390.0000.0000.0000.000
25A67TYR00.0500.03710.1520.8450.8450.0000.0000.0000.000
26A68ALA0-0.023-0.0228.2810.3360.3360.0000.0000.0000.000
27A69ALA0-0.024-0.0058.862-0.981-0.9810.0000.0000.0000.000
28A70ASN0-0.052-0.0309.5971.2781.2780.0000.0000.0000.000
29A71ALA00.0570.04511.832-0.579-0.5790.0000.0000.0000.000
30A72VAL00.0220.00513.5570.5080.5080.0000.0000.0000.000
31A73TYR0-0.028-0.03711.700-0.350-0.3500.0000.0000.0000.000
32A74LEU00.0130.01016.5270.2990.2990.0000.0000.0000.000
33A75VAL0-0.022-0.01117.885-0.218-0.2180.0000.0000.0000.000
34A76THR0-0.027-0.03020.4110.0830.0830.0000.0000.0000.000
35A77ASP-1-0.834-0.92623.997-0.043-0.0430.0000.0000.0000.000
36A78LYS10.9390.96825.8350.1680.1680.0000.0000.0000.000
37A79GLY00.0240.02621.924-0.099-0.0990.0000.0000.0000.000
38A80VAL0-0.029-0.00616.1510.1580.1580.0000.0000.0000.000
39A81VAL00.0160.01519.452-0.174-0.1740.0000.0000.0000.000
40A82VAL0-0.004-0.01014.1190.1900.1900.0000.0000.0000.000
41A83ILE00.0020.00616.991-0.097-0.0970.0000.0000.0000.000
42A84ASP-1-0.751-0.83315.172-0.312-0.3120.0000.0000.0000.000
43A85CYS0-0.042-0.00312.556-0.147-0.1470.0000.0000.0000.000
44A86PRO0-0.0200.0037.1630.1930.1930.0000.0000.0000.000
45A87TRP00.0570.0208.203-0.086-0.0860.0000.0000.0000.000
46A88GLY00.033-0.0057.868-0.516-0.5160.0000.0000.0000.000
47A89GLU-1-0.891-0.9408.414-5.291-5.2910.0000.0000.0000.000
48A90ASP-1-0.846-0.9096.030-14.306-14.3060.0000.0000.0000.000
50A92PHE00.0040.0135.8120.5600.5600.0000.0000.0000.000
51A93LYS10.8900.9488.8514.7334.7330.0000.0000.0000.000
53A95PHE00.0160.0106.1821.8181.8180.0000.0000.0000.000
54A96THR0-0.017-0.0107.5981.7261.7260.0000.0000.0000.000
55A97ASP-1-0.828-0.9038.772-4.025-4.0250.0000.0000.0000.000
56A98GLU-1-0.826-0.8917.1670.5940.5940.0000.0000.0000.000
57A99ILE0-0.028-0.0159.5411.0761.0760.0000.0000.0000.000
58A100TYR0-0.033-0.01512.7790.5100.5100.0000.0000.0000.000
59A102LYS10.8580.8968.0541.0991.0990.0000.0000.0000.000
60A103LYS10.9160.98210.042-2.109-2.1090.0000.0000.0000.000
61A104HIS0-0.0160.00714.1850.3120.3120.0000.0000.0000.000
62A105GLY00.0220.02616.9520.0200.0200.0000.0000.0000.000
63A106LYS10.8560.92517.7380.0900.0900.0000.0000.0000.000
64A107LYS11.0241.01017.2440.7620.7620.0000.0000.0000.000
65A109VAL00.0280.01714.7540.1900.1900.0000.0000.0000.000
66A110ILE0-0.011-0.00618.040-0.067-0.0670.0000.0000.0000.000
67A111MET0-0.058-0.01220.4060.0760.0760.0000.0000.0000.000
68A112ASN0-0.051-0.03116.535-0.119-0.1190.0000.0000.0000.000
69A113ILE0-0.014-0.01119.3220.0490.0490.0000.0000.0000.000
70A114ALA00.0340.03819.2050.0380.0380.0000.0000.0000.000
71A115THR0-0.065-0.07319.1840.1020.1020.0000.0000.0000.000
72A116HIS0-0.007-0.01719.1020.1620.1620.0000.0000.0000.000
73A117SER00.0380.01820.532-0.152-0.1520.0000.0000.0000.000
74A118HIS00.022-0.00417.879-0.114-0.1140.0000.0000.0000.000
75A119ASP-1-0.788-0.88914.374-1.850-1.8500.0000.0000.0000.000
76A120ASP-1-0.819-0.90812.550-1.045-1.0450.0000.0000.0000.000
77A121ARG10.6830.80213.5620.2860.2860.0000.0000.0000.000
78A122ALA00.0680.00816.382-0.035-0.0350.0000.0000.0000.000
79A123GLY00.0490.02914.754-0.029-0.0290.0000.0000.0000.000
80A124GLY0-0.006-0.01714.450-0.220-0.2200.0000.0000.0000.000
81A125LEU0-0.057-0.02315.0390.0610.0610.0000.0000.0000.000
82A126GLU-1-0.870-0.93518.126-2.038-2.0380.0000.0000.0000.000
83A127TYR00.003-0.02112.290-0.045-0.0450.0000.0000.0000.000
84A128PHE00.003-0.02712.5350.0030.0030.0000.0000.0000.000
85A129GLY00.0440.02417.3470.1540.1540.0000.0000.0000.000
86A130LYS10.9000.96416.0102.8222.8220.0000.0000.0000.000
87A131ILE0-0.093-0.04115.235-0.023-0.0230.0000.0000.0000.000
88A133GLY00.0000.00819.3650.1070.1070.0000.0000.0000.000
89A134ALA0-0.069-0.01919.2530.1600.1600.0000.0000.0000.000
90A135LYS10.9360.96521.2960.5530.5530.0000.0000.0000.000
91A136THR00.0150.00920.3750.0870.0870.0000.0000.0000.000
92A137TYR0-0.026-0.02622.6400.0930.0930.0000.0000.0000.000
93A138SER00.0540.02023.051-0.079-0.0790.0000.0000.0000.000
94A139THR00.0180.02625.1770.0330.0330.0000.0000.0000.000
95A140LYS10.9300.94427.9950.3190.3190.0000.0000.0000.000
96A141MET0-0.0040.02929.510-0.024-0.0240.0000.0000.0000.000
97A142THR00.008-0.03323.314-0.007-0.0070.0000.0000.0000.000
98A143ASP-1-0.834-0.88726.070-0.773-0.7730.0000.0000.0000.000
99A144SER0-0.0260.00127.503-0.052-0.0520.0000.0000.0000.000
100A145ILE00.0300.01325.217-0.018-0.0180.0000.0000.0000.000
101A146LEU0-0.036-0.01521.470-0.045-0.0450.0000.0000.0000.000
102A147ALA0-0.026-0.01625.152-0.066-0.0660.0000.0000.0000.000
103A148LYS10.8980.96928.3110.5650.5650.0000.0000.0000.000
104A149GLU-1-0.915-0.97224.517-0.754-0.7540.0000.0000.0000.000
105A150ASN0-0.089-0.03524.858-0.078-0.0780.0000.0000.0000.000
106A167LYS10.8940.94919.0011.2371.2370.0000.0000.0000.000
107A168PRO00.005-0.00319.7120.1190.1190.0000.0000.0000.000
108A169ARG10.8440.88722.2340.8080.8080.0000.0000.0000.000
109A170ALA0-0.023-0.00423.642-0.082-0.0820.0000.0000.0000.000
110A171GLN00.0270.01624.3510.0980.0980.0000.0000.0000.000
111A172TYR0-0.037-0.01926.7250.0790.0790.0000.0000.0000.000
112A173THR00.0650.03327.5270.0140.0140.0000.0000.0000.000
113A174PHE0-0.051-0.03126.6220.0280.0280.0000.0000.0000.000
114A175ASP-1-0.835-0.92331.246-0.199-0.1990.0000.0000.0000.000
115A176ASN00.0000.00030.5510.0280.0280.0000.0000.0000.000
116A177ASN00.007-0.00630.1640.0550.0550.0000.0000.0000.000
117A178LYS10.8830.94829.5050.1970.1970.0000.0000.0000.000
118A179SER00.0340.02829.8950.0240.0240.0000.0000.0000.000
119A180PHE0-0.028-0.02226.691-0.068-0.0680.0000.0000.0000.000
120A181LYS10.8720.92829.5540.0190.0190.0000.0000.0000.000
121A182VAL0-0.012-0.00724.633-0.061-0.0610.0000.0000.0000.000
122A183GLY00.0140.01027.5390.0500.0500.0000.0000.0000.000
123A184LYS10.8570.89728.645-0.146-0.1460.0000.0000.0000.000
124A185SER0-0.0080.00926.2650.0730.0730.0000.0000.0000.000
125A186GLU-1-0.834-0.90528.2360.0510.0510.0000.0000.0000.000
126A187PHE00.007-0.00224.5220.0570.0570.0000.0000.0000.000
127A188GLN0-0.028-0.01727.904-0.062-0.0620.0000.0000.0000.000
128A189VAL0-0.0020.00925.2250.0470.0470.0000.0000.0000.000
129A190TYR00.0380.00627.698-0.008-0.0080.0000.0000.0000.000
130A191TYR00.015-0.00828.3280.0280.0280.0000.0000.0000.000
131A192PRO0-0.037-0.00527.6780.0090.0090.0000.0000.0000.000
132A193GLY00.0490.03430.9620.0160.0160.0000.0000.0000.000
133A194LYS10.9040.96429.9050.0590.0590.0000.0000.0000.000
134A195GLY00.0610.01427.6500.0560.0560.0000.0000.0000.000
135A196HIS00.0100.03120.2820.0230.0230.0000.0000.0000.000
136A197THR0-0.033-0.02723.444-0.038-0.0380.0000.0000.0000.000
137A198ALA00.0350.00926.3050.0570.0570.0000.0000.0000.000
138A199ASP-1-0.707-0.84624.962-0.404-0.4040.0000.0000.0000.000
139A200ASN0-0.033-0.00624.3020.0080.0080.0000.0000.0000.000
140A201VAL0-0.038-0.00924.1890.0510.0510.0000.0000.0000.000
141A202VAL0-0.0040.01223.6220.0290.0290.0000.0000.0000.000
142A203VAL0-0.025-0.02622.380-0.084-0.0840.0000.0000.0000.000
143A204TRP00.0360.02723.6390.1210.1210.0000.0000.0000.000
144A205PHE00.018-0.00821.737-0.092-0.0920.0000.0000.0000.000
145A209PRO0-0.0070.00125.7650.0810.0810.0000.0000.0000.000
146A210LYS10.8520.92326.589-0.530-0.5300.0000.0000.0000.000
147A211GLU-1-0.885-0.96122.9290.6050.6050.0000.0000.0000.000
148A215LYS10.9240.98524.773-0.644-0.6440.0000.0000.0000.000
149A216VAL00.0240.01619.9490.0990.0990.0000.0000.0000.000
150A217LEU00.0090.01522.969-0.138-0.1380.0000.0000.0000.000
151A218VAL0-0.007-0.01818.1660.1540.1540.0000.0000.0000.000
152A219GLY00.0560.01220.084-0.158-0.1580.0000.0000.0000.000
153A220GLY00.0560.02818.640-0.099-0.0990.0000.0000.0000.000
154A221CYS0-0.060-0.03217.7890.2160.2160.0000.0000.0000.000
155A222ILE0-0.0010.02819.8270.0240.0240.0000.0000.0000.000
156A223ILE0-0.032-0.00220.7550.0320.0320.0000.0000.0000.000
157A224LYS10.8230.90819.027-0.725-0.7250.0000.0000.0000.000
158A225SER00.000-0.00616.007-0.095-0.0950.0000.0000.0000.000
159A226ALA00.007-0.01618.108-0.185-0.1850.0000.0000.0000.000
160A227ASP-1-0.844-0.90515.6802.4572.4570.0000.0000.0000.000
161A228SER0-0.036-0.02317.957-0.127-0.1270.0000.0000.0000.000
162A229LYS10.9690.98919.302-0.975-0.9750.0000.0000.0000.000
163A230ASP-1-0.839-0.91521.2090.5760.5760.0000.0000.0000.000
164A231LEU00.0670.01621.7080.0950.0950.0000.0000.0000.000
165A232GLY0-0.034-0.00119.901-0.004-0.0040.0000.0000.0000.000
166A233TYR0-0.089-0.06919.892-0.045-0.0450.0000.0000.0000.000
167A234ILE00.0490.00421.5070.0290.0290.0000.0000.0000.000
168A235GLY0-0.0050.01324.6590.0010.0010.0000.0000.0000.000
169A236GLU-1-0.822-0.87324.192-0.568-0.5680.0000.0000.0000.000
170A237ALA0-0.027-0.00526.0530.0130.0130.0000.0000.0000.000
171A238TYR0-0.018-0.01927.885-0.021-0.0210.0000.0000.0000.000
172A239VAL00.0140.00128.9780.0330.0330.0000.0000.0000.000
173A240ASN00.0300.01631.1660.0580.0580.0000.0000.0000.000
174A241ASP-1-0.902-0.94232.8750.0490.0490.0000.0000.0000.000
175A242TRP0-0.034-0.02323.6460.0030.0030.0000.0000.0000.000
176A243THR00.0450.01530.2360.0460.0460.0000.0000.0000.000
177A244GLN0-0.016-0.00132.1910.0260.0260.0000.0000.0000.000
178A245SER0-0.007-0.02430.0260.0090.0090.0000.0000.0000.000
179A246VAL00.005-0.00426.7470.0220.0220.0000.0000.0000.000
180A247HIS00.0350.01229.3850.0600.0600.0000.0000.0000.000
181A248ASN0-0.045-0.01832.3200.0240.0240.0000.0000.0000.000
182A249ILE0-0.036-0.02325.7870.0010.0010.0000.0000.0000.000
183A250GLN0-0.015-0.00529.6070.0640.0640.0000.0000.0000.000
184A251GLN0-0.014-0.00530.5070.0090.0090.0000.0000.0000.000
185A252LYS10.9040.97631.858-0.208-0.2080.0000.0000.0000.000
186A253PHE0-0.042-0.04228.315-0.028-0.0280.0000.0000.0000.000
187A254SER00.0250.02529.2180.0850.0850.0000.0000.0000.000
188A255GLY0-0.0010.00430.8190.0380.0380.0000.0000.0000.000
189A256ALA0-0.054-0.03025.3840.0200.0200.0000.0000.0000.000
190A257GLN0-0.053-0.02724.1540.0140.0140.0000.0000.0000.000
191A258TYR00.000-0.01820.0090.1080.1080.0000.0000.0000.000
192A259VAL00.0330.01921.234-0.154-0.1540.0000.0000.0000.000
193A260VAL0-0.042-0.02315.2850.1940.1940.0000.0000.0000.000
194A261ALA00.0450.02716.932-0.237-0.2370.0000.0000.0000.000
195A262GLY00.0360.02415.3220.3210.3210.0000.0000.0000.000
196A263HIS10.8070.87812.834-0.753-0.7530.0000.0000.0000.000
197A264ASP-1-0.801-0.89711.5862.5052.5050.0000.0000.0000.000
198A265ASP-1-0.843-0.91612.2993.7423.7420.0000.0000.0000.000
199A277TRP0-0.021-0.02111.883-0.756-0.7560.0000.0000.0000.000
200A278LYS10.8360.90712.700-4.987-4.9870.0000.0000.0000.000
201A279ASP-1-0.775-0.85317.0561.3791.3790.0000.0000.0000.000
202A280GLN0-0.005-0.01619.614-0.217-0.2170.0000.0000.0000.000
203A281ARG10.8760.91822.556-1.557-1.5570.0000.0000.0000.000
204A282SER00.0180.02119.990-0.140-0.1400.0000.0000.0000.000
205A283ILE00.0100.01621.934-0.099-0.0990.0000.0000.0000.000
206A284GLN00.0040.00525.184-0.021-0.0210.0000.0000.0000.000
207A285HIS10.8870.93821.847-1.133-1.1330.0000.0000.0000.000
208A286THR0-0.010-0.01723.459-0.044-0.0440.0000.0000.0000.000
209A287LEU0-0.001-0.00425.242-0.078-0.0780.0000.0000.0000.000
210A288ASP-1-0.875-0.93927.5590.7290.7290.0000.0000.0000.000
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