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: VVN11

Calculation Name: 2BNM-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | zinc ion

Ligand 3-letter code: SO4 | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2BNM

Chain ID: A

ChEMBL ID:

UniProt ID: Q56185

Base Structure: X-ray

Registration Date: 2025-09-02

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 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1726625.481476
FMO2-HF: Nuclear repulsion 1653474.006852
FMO2-HF: Total energy -73151.474623
FMO2-MP2: Total energy -73365.611818


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:5:LYS)


Summations of interaction energy for fragment #1(A:5:LYS)
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.
-270.239-266.3630.036-1.669-2.244-0.008
Interaction energy analysis for fragmet #1(A:5:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.850 / q_NPA : 1.907
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].
3A7ALA00.0770.0383.8505.1166.584-0.006-0.584-0.878-0.001
4A8SER00.0030.0013.372-0.9240.3520.029-0.565-0.741-0.004
5A9THR00.000-0.0113.588-1.475-0.3430.013-0.520-0.625-0.003
6A10GLY00.0640.0275.4107.1327.1320.0000.0000.0000.000
7A11PHE0-0.013-0.0027.6465.1985.1980.0000.0000.0000.000
8A12ALA0-0.024-0.0038.0534.4654.4650.0000.0000.0000.000
9A13GLU-1-0.944-0.9739.683-43.481-43.4810.0000.0000.0000.000
10A14LEU00.0170.00911.7173.5223.5220.0000.0000.0000.000
11A15LEU0-0.043-0.01312.6733.2873.2870.0000.0000.0000.000
12A16LYS10.9280.98113.94236.98736.9870.0000.0000.0000.000
13A17ASP-1-0.885-0.93915.752-32.487-32.4870.0000.0000.0000.000
14A18ARG10.7760.87817.34728.21828.2180.0000.0000.0000.000
15A19ARG10.7290.81617.63732.65832.6580.0000.0000.0000.000
16A20GLU-1-0.863-0.93819.701-28.576-28.5760.0000.0000.0000.000
17A21GLN0-0.046-0.01221.5990.9170.9170.0000.0000.0000.000
18A22VAL0-0.068-0.04022.6291.2811.2810.0000.0000.0000.000
19A23LYS10.8760.94524.93322.93522.9350.0000.0000.0000.000
20A24MET00.0090.03022.7800.3620.3620.0000.0000.0000.000
21A25ASP-1-0.835-0.90622.771-24.411-24.4110.0000.0000.0000.000
22A26HIS0-0.015-0.04416.9600.9190.9190.0000.0000.0000.000
23A27ALA00.0220.01520.964-0.290-0.2900.0000.0000.0000.000
24A28ALA0-0.021-0.00124.1570.3150.3150.0000.0000.0000.000
25A29LEU00.0440.01018.0920.2950.2950.0000.0000.0000.000
26A30ALA00.0100.01021.001-0.159-0.1590.0000.0000.0000.000
27A31SER0-0.049-0.03022.0000.6170.6170.0000.0000.0000.000
28A32LEU0-0.032-0.02324.3760.6280.6280.0000.0000.0000.000
29A33LEU0-0.059-0.02818.966-0.059-0.0590.0000.0000.0000.000
30A34GLY0-0.056-0.01523.014-0.061-0.0610.0000.0000.0000.000
31A35GLU-1-0.944-0.96019.111-30.501-30.5010.0000.0000.0000.000
32A36THR0-0.025-0.02920.6090.5820.5820.0000.0000.0000.000
33A37PRO00.021-0.00719.905-1.183-1.1830.0000.0000.0000.000
34A38GLU-1-0.837-0.91718.641-28.734-28.7340.0000.0000.0000.000
35A39THR0-0.034-0.00716.155-2.405-2.4050.0000.0000.0000.000
36A40VAL0-0.0110.00014.838-2.294-2.2940.0000.0000.0000.000
37A41ALA0-0.004-0.00514.654-1.998-1.9980.0000.0000.0000.000
38A42ALA00.0360.01812.619-2.268-2.2680.0000.0000.0000.000
39A43TRP0-0.025-0.02710.521-4.406-4.4060.0000.0000.0000.000
40A44GLU-1-0.721-0.8419.840-38.955-38.9550.0000.0000.0000.000
41A45ASN0-0.087-0.03510.228-0.978-0.9780.0000.0000.0000.000
42A46GLY0-0.035-0.0116.093-5.811-5.8110.0000.0000.0000.000
43A47GLU-1-0.892-0.9465.555-61.117-61.1170.0000.0000.0000.000
44A48GLY0-0.005-0.0088.1803.1213.1210.0000.0000.0000.000
45A49GLY0-0.069-0.0396.090-0.114-0.1140.0000.0000.0000.000
46A50GLU-1-0.939-0.9656.719-54.704-54.7040.0000.0000.0000.000
47A51LEU0-0.0490.0009.8575.0845.0840.0000.0000.0000.000
48A52THR00.010-0.02411.482-0.033-0.0330.0000.0000.0000.000
49A53LEU00.0400.01114.1050.3090.3090.0000.0000.0000.000
50A54THR00.012-0.00415.3050.5680.5680.0000.0000.0000.000
51A55GLN00.0320.04115.4180.1050.1050.0000.0000.0000.000
52A56LEU00.0500.02810.8681.1791.1790.0000.0000.0000.000
53A57GLY00.0200.00915.2240.7990.7990.0000.0000.0000.000
54A58ARG10.9340.96618.69028.10928.1090.0000.0000.0000.000
55A59ILE00.0320.02414.9640.9830.9830.0000.0000.0000.000
56A60ALA0-0.005-0.00717.6880.5530.5530.0000.0000.0000.000
57A61HIS0-0.008-0.00519.2610.8050.8050.0000.0000.0000.000
58A62VAL0-0.013-0.00721.8930.9480.9480.0000.0000.0000.000
59A63LEU00.0010.01718.0430.6830.6830.0000.0000.0000.000
60A64GLY00.0190.01722.1550.1960.1960.0000.0000.0000.000
61A65THR0-0.051-0.03519.3690.6170.6170.0000.0000.0000.000
62A66SER00.0170.00819.711-0.289-0.2890.0000.0000.0000.000
63A67ILE00.0640.00713.831-0.588-0.5880.0000.0000.0000.000
64A68GLY0-0.0140.01514.648-2.073-2.0730.0000.0000.0000.000
65A69ALA0-0.020-0.00415.799-0.713-0.7130.0000.0000.0000.000
66A70LEU0-0.0040.00614.1820.0280.0280.0000.0000.0000.000
67A71THR0-0.020-0.03510.068-3.185-3.1850.0000.0000.0000.000
68A72PRO00.0050.0177.7562.0762.0760.0000.0000.0000.000
69A73PRO00.0190.01011.0670.7900.7900.0000.0000.0000.000
70A74ALA00.0250.01011.450-3.082-3.0820.0000.0000.0000.000
71A75GLY0-0.014-0.00111.232-3.144-3.1440.0000.0000.0000.000
72A76ASN0-0.031-0.05212.0284.0514.0510.0000.0000.0000.000
73A77ASP-1-0.789-0.85812.976-37.295-37.2950.0000.0000.0000.000
74A78LEU0-0.051-0.00515.4481.2011.2010.0000.0000.0000.000
75A79ASP-1-0.924-0.95517.768-29.607-29.6070.0000.0000.0000.000
76A80ASP-1-0.898-0.95520.090-26.116-26.1160.0000.0000.0000.000
77A81GLY0-0.075-0.03220.7421.0231.0230.0000.0000.0000.000
78A82VAL0-0.022-0.01522.1920.8630.8630.0000.0000.0000.000
79A83ILE0-0.009-0.00619.239-1.251-1.2510.0000.0000.0000.000
80A84ILE0-0.019-0.01122.9071.1261.1260.0000.0000.0000.000
81A85GLN0-0.017-0.02124.027-0.233-0.2330.0000.0000.0000.000
82A86MET0-0.025-0.00826.2631.0551.0550.0000.0000.0000.000
83A87PRO0-0.030-0.02528.541-0.364-0.3640.0000.0000.0000.000
84A88ASP-1-0.898-0.96030.006-19.122-19.1220.0000.0000.0000.000
85A89GLU-1-0.872-0.93524.146-24.696-24.6960.0000.0000.0000.000
86A90ARG10.8920.96625.26318.48418.4840.0000.0000.0000.000
87A91PRO0-0.022-0.01323.1640.3340.3340.0000.0000.0000.000
88A92ILE00.0280.02925.9690.3320.3320.0000.0000.0000.000
89A93LEU0-0.046-0.02724.816-0.244-0.2440.0000.0000.0000.000
90A94LYS10.9730.98129.20718.82918.8290.0000.0000.0000.000
91A95GLY00.0900.05330.6290.4620.4620.0000.0000.0000.000
92A96VAL0-0.053-0.04127.860-0.447-0.4470.0000.0000.0000.000
93A97ARG10.9130.94531.33318.05618.0560.0000.0000.0000.000
94A98ASP-1-0.874-0.93733.733-15.907-15.9070.0000.0000.0000.000
95A99ASN0-0.0310.00335.0800.6680.6680.0000.0000.0000.000
96A100VAL0-0.022-0.02633.600-0.569-0.5690.0000.0000.0000.000
97A101ASP-1-0.912-0.95835.747-15.939-15.9390.0000.0000.0000.000
98A102TYR0-0.022-0.01038.4710.2390.2390.0000.0000.0000.000
99A103TYR0-0.048-0.03836.1430.2250.2250.0000.0000.0000.000
100A104VAL0-0.0030.01333.759-0.462-0.4620.0000.0000.0000.000
101A105TYR0-0.0030.00130.0300.1170.1170.0000.0000.0000.000
102A106ASN0-0.053-0.03929.805-0.885-0.8850.0000.0000.0000.000
103A107CYS0-0.050-0.02225.058-0.169-0.1690.0000.0000.0000.000
104A108LEU00.0160.01626.864-0.139-0.1390.0000.0000.0000.000
105A109VAL00.0060.00422.796-0.795-0.7950.0000.0000.0000.000
106A110ARG10.9350.96220.62826.37326.3730.0000.0000.0000.000
107A111THR00.032-0.01218.218-0.611-0.6110.0000.0000.0000.000
108A112LYS10.8510.90510.06147.99047.9900.0000.0000.0000.000
109A113ARG10.9030.95116.30831.57931.5790.0000.0000.0000.000
110A114ALA0-0.0060.00218.7071.0451.0450.0000.0000.0000.000
111A115PRO0-0.021-0.01517.7240.6710.6710.0000.0000.0000.000
112A116SER00.0120.01120.172-0.290-0.2900.0000.0000.0000.000
113A117LEU0-0.0190.01523.3960.8090.8090.0000.0000.0000.000
114A118VAL0-0.038-0.03423.773-1.012-1.0120.0000.0000.0000.000
115A119PRO00.0060.02425.5740.9010.9010.0000.0000.0000.000
116A120LEU0-0.022-0.01727.777-0.631-0.6310.0000.0000.0000.000
117A121VAL00.010-0.00130.4650.5020.5020.0000.0000.0000.000
118A122VAL0-0.020-0.00533.279-0.343-0.3430.0000.0000.0000.000
119A123ASP-1-0.823-0.91035.309-16.115-16.1150.0000.0000.0000.000
120A124VAL0-0.045-0.01938.145-0.172-0.1720.0000.0000.0000.000
121A125LEU00.012-0.01139.5210.3540.3540.0000.0000.0000.000
122A126THR00.0080.02142.2960.3700.3700.0000.0000.0000.000
123A127ASP-1-0.817-0.90644.775-12.565-12.5650.0000.0000.0000.000
124A128ASN0-0.006-0.02347.8140.4660.4660.0000.0000.0000.000
125A129PRO00.0140.00048.009-0.178-0.1780.0000.0000.0000.000
126A130ASP-1-0.981-0.98148.628-11.784-11.7840.0000.0000.0000.000
127A131ASP-1-0.889-0.92746.576-12.604-12.6040.0000.0000.0000.000
128A132ALA0-0.039-0.01144.360-0.361-0.3610.0000.0000.0000.000
129A133LYS10.9150.96540.43514.54414.5440.0000.0000.0000.000
130A134PHE0-0.010-0.00640.722-0.281-0.2810.0000.0000.0000.000
131A135ASN00.0250.01635.8210.0630.0630.0000.0000.0000.000
132A136SER0-0.047-0.04934.6160.2920.2920.0000.0000.0000.000
133A137GLY00.0170.02436.075-0.067-0.0670.0000.0000.0000.000
134A138HIS0-0.063-0.02031.519-0.664-0.6640.0000.0000.0000.000
135A139ALA0-0.035-0.02927.9650.2450.2450.0000.0000.0000.000
136A140GLY00.0650.03629.300-0.011-0.0110.0000.0000.0000.000
137A141ASN00.0170.00430.1000.9780.9780.0000.0000.0000.000
138A142GLU-1-0.814-0.90931.577-18.296-18.2960.0000.0000.0000.000
139A143PHE0-0.023-0.00233.7530.5780.5780.0000.0000.0000.000
140A144LEU0-0.014-0.01134.906-0.366-0.3660.0000.0000.0000.000
141A145PHE0-0.001-0.00837.5010.3820.3820.0000.0000.0000.000
142A146VAL0-0.0020.01839.387-0.347-0.3470.0000.0000.0000.000
143A147LEU0-0.034-0.01836.8220.1950.1950.0000.0000.0000.000
144A148GLU-1-0.826-0.90441.473-14.574-14.5740.0000.0000.0000.000
145A149GLY00.0370.03244.113-0.112-0.1120.0000.0000.0000.000
146A150GLU-1-0.915-0.96947.003-11.993-11.9930.0000.0000.0000.000
147A151ILE00.0000.00242.142-0.067-0.0670.0000.0000.0000.000
148A152HIS0-0.034-0.03445.7430.2930.2930.0000.0000.0000.000
149A153MET0-0.026-0.00843.272-0.400-0.4000.0000.0000.0000.000
150A154LYS10.8700.93444.39812.88012.8800.0000.0000.0000.000
151A155TRP00.021-0.00842.694-0.343-0.3430.0000.0000.0000.000
152A156GLY0-0.0080.00443.3520.3710.3710.0000.0000.0000.000
153A157ASP-1-0.862-0.94944.264-12.895-12.8950.0000.0000.0000.000
154A158LYS10.8250.89044.36713.23813.2380.0000.0000.0000.000
155A159GLU-1-0.878-0.91046.669-12.415-12.4150.0000.0000.0000.000
156A160ASN0-0.077-0.03550.3480.3130.3130.0000.0000.0000.000
157A161PRO00.0170.02848.048-0.083-0.0830.0000.0000.0000.000
158A162LYS10.8710.94047.53712.26512.2650.0000.0000.0000.000
159A163GLU-1-0.799-0.90947.826-12.349-12.3490.0000.0000.0000.000
160A164ALA0-0.053-0.03147.6570.1560.1560.0000.0000.0000.000
161A165LEU00.0070.02548.419-0.166-0.1660.0000.0000.0000.000
162A166LEU0-0.016-0.01144.1240.0460.0460.0000.0000.0000.000
163A167PRO00.0440.02547.070-0.152-0.1520.0000.0000.0000.000
164A168THR00.000-0.03145.063-0.259-0.2590.0000.0000.0000.000
165A169GLY0-0.042-0.01544.6330.2810.2810.0000.0000.0000.000
166A170ALA0-0.039-0.00245.243-0.024-0.0240.0000.0000.0000.000
167A171SER0-0.039-0.02740.996-0.359-0.3590.0000.0000.0000.000
168A172MET0-0.032-0.00340.4750.3070.3070.0000.0000.0000.000
169A173PHE00.0090.00435.687-0.397-0.3970.0000.0000.0000.000
170A174VAL0-0.013-0.00836.7410.4810.4810.0000.0000.0000.000
171A175GLU-1-0.919-0.95636.271-15.828-15.8280.0000.0000.0000.000
172A176GLU-1-0.835-0.91232.384-18.203-18.2030.0000.0000.0000.000
173A177HIS10.7110.83531.82918.39518.3950.0000.0000.0000.000
174A178VAL00.0170.02835.8530.4100.4100.0000.0000.0000.000
175A179PRO0-0.021-0.00138.353-0.267-0.2670.0000.0000.0000.000
176A180HIS0-0.017-0.02635.9160.2110.2110.0000.0000.0000.000
177A181ALA00.0150.01539.909-0.289-0.2890.0000.0000.0000.000
178A182PHE00.0290.00337.7160.2780.2780.0000.0000.0000.000
179A183THR0-0.0110.00141.930-0.218-0.2180.0000.0000.0000.000
180A184ALA00.0380.02644.208-0.004-0.0040.0000.0000.0000.000
181A185ALA00.0070.01546.0800.1270.1270.0000.0000.0000.000
182A186LYS10.9920.99149.68011.17211.1720.0000.0000.0000.000
183A187GLY0-0.0300.00351.8510.2380.2380.0000.0000.0000.000
184A188THR0-0.067-0.04949.4060.0240.0240.0000.0000.0000.000
185A189GLY0-0.020-0.00748.952-0.102-0.1020.0000.0000.0000.000
186A190SER0-0.089-0.05243.784-0.317-0.3170.0000.0000.0000.000
187A191ALA00.0000.00543.5360.2590.2590.0000.0000.0000.000
188A192LYS10.8050.90038.71515.05815.0580.0000.0000.0000.000
189A193LEU00.0250.01337.5870.2640.2640.0000.0000.0000.000
190A194ILE0-0.037-0.00932.925-0.414-0.4140.0000.0000.0000.000
191A195ALA00.0050.00133.3550.4290.4290.0000.0000.0000.000
192A196VAL00.003-0.01729.556-0.673-0.6730.0000.0000.0000.000
193A197ASN00.018-0.00428.3050.2260.2260.0000.0000.0000.000
194A198PHE-1-0.895-0.95227.500-21.411-21.4110.0000.0000.0000.000