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: 2M9ZR

Calculation Name: 3VOF-A-Xray547

Preferred Name:

Target Type:

Ligand Name: beta-d-glucopyranose

Ligand 3-letter code: BGC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3VOF

Chain ID: A

ChEMBL ID:

UniProt ID: B7X9Z2

Base Structure: X-ray

Registration Date: 2025-10-05

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 370
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -6299948.994438
FMO2-HF: Nuclear repulsion 6157126.445653
FMO2-HF: Total energy -142822.548785
FMO2-MP2: Total energy -143245.202365


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:12:SER)


Summations of interaction energy for fragment #1(A:12: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.
-243.378-241.5197.802-4.021-5.6390.008
Interaction energy analysis for fragmet #1(A:12:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.858 / q_NPA : 0.932
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].
3A14ASN00.0530.0233.8590.3211.991-0.010-0.726-0.934-0.001
176A188ASP-1-0.864-0.9183.079-63.145-61.5590.027-0.847-0.765-0.008
215A227THR0-0.049-0.0413.9920.0860.201-0.001-0.024-0.0910.000
217A229ARG10.7290.8341.94331.27229.6947.787-2.410-3.7980.017
218A230GLY0-0.005-0.0144.0050.4850.551-0.001-0.014-0.0510.000
4A15PRO00.0190.0205.1191.0711.0710.0000.0000.0000.000
5A16TYR00.0430.0067.6191.8241.8240.0000.0000.0000.000
6A17ILE0-0.059-0.0259.9801.9691.9690.0000.0000.0000.000
7A18GLY0-0.029-0.02011.193-1.250-1.2500.0000.0000.0000.000
8A19ARG10.8430.9238.13429.78029.7800.0000.0000.0000.000
9A20SER00.011-0.01314.650-0.060-0.0600.0000.0000.0000.000
10A21PRO0-0.047-0.03114.697-0.195-0.1950.0000.0000.0000.000
11A22LEU00.0180.01416.5810.7270.7270.0000.0000.0000.000
12A23VAL00.0030.00419.165-0.027-0.0270.0000.0000.0000.000
13A24ILE0-0.0150.00319.8630.2030.2030.0000.0000.0000.000
14A25LYS10.9070.92723.73311.47011.4700.0000.0000.0000.000
15A26SER00.0490.02526.9000.1840.1840.0000.0000.0000.000
16A27TYR0-0.064-0.04925.6670.1570.1570.0000.0000.0000.000
17A28ALA00.0290.00427.8300.2950.2950.0000.0000.0000.000
18A29GLU-1-0.908-0.95829.696-9.266-9.2660.0000.0000.0000.000
19A30LYS10.8490.91928.67310.32410.3240.0000.0000.0000.000
20A31LEU0-0.002-0.00428.9580.2650.2650.0000.0000.0000.000
21A32GLU-1-0.848-0.91233.153-8.284-8.2840.0000.0000.0000.000
22A33GLU-1-0.931-0.96936.336-7.594-7.5940.0000.0000.0000.000
23A34THR0-0.018-0.02634.6510.0990.0990.0000.0000.0000.000
24A35ILE0-0.030-0.00834.9780.1230.1230.0000.0000.0000.000
25A36ALA00.0430.02738.3770.1860.1860.0000.0000.0000.000
26A37TYR0-0.041-0.01740.0820.2690.2690.0000.0000.0000.000
27A38PHE0-0.021-0.02336.6240.1700.1700.0000.0000.0000.000
28A39GLU-1-0.893-0.94541.968-7.130-7.1300.0000.0000.0000.000
29A40ALA0-0.070-0.02944.2380.1900.1900.0000.0000.0000.000
30A41GLN0-0.098-0.04744.6260.2510.2510.0000.0000.0000.000
31A42GLY0-0.0180.00746.7370.1140.1140.0000.0000.0000.000
32A43ASP-1-0.869-0.91542.138-7.344-7.3440.0000.0000.0000.000
33A44GLU-1-0.843-0.95641.939-7.116-7.1160.0000.0000.0000.000
34A45LEU0-0.058-0.00739.208-0.175-0.1750.0000.0000.0000.000
35A46ASN0-0.016-0.04237.695-0.453-0.4530.0000.0000.0000.000
36A47ALA00.0450.04637.057-0.255-0.2550.0000.0000.0000.000
37A48ALA00.0500.02136.915-0.223-0.2230.0000.0000.0000.000
38A49ARG10.8060.89734.1188.0288.0280.0000.0000.0000.000
39A50THR0-0.002-0.01632.656-0.360-0.3600.0000.0000.0000.000
40A51ARG10.8690.92132.2388.1568.1560.0000.0000.0000.000
41A52THR0-0.050-0.03429.322-0.177-0.1770.0000.0000.0000.000
42A53VAL0-0.055-0.02427.831-0.437-0.4370.0000.0000.0000.000
43A54GLN0-0.065-0.04427.428-0.371-0.3710.0000.0000.0000.000
44A55GLY0-0.0160.00126.994-0.177-0.1770.0000.0000.0000.000
45A56ILE0-0.070-0.03122.761-0.473-0.4730.0000.0000.0000.000
46A57PRO0-0.0310.00018.8870.1050.1050.0000.0000.0000.000
47A58THR0-0.008-0.01320.068-0.287-0.2870.0000.0000.0000.000
48A59PHE00.005-0.01213.023-0.532-0.5320.0000.0000.0000.000
49A60ALA00.0170.01318.7360.7330.7330.0000.0000.0000.000
50A61TRP0-0.051-0.04519.416-0.692-0.6920.0000.0000.0000.000
51A62ILE00.0130.00619.6790.5820.5820.0000.0000.0000.000
52A63SER00.0350.01122.198-0.260-0.2600.0000.0000.0000.000
53A64ASP-1-0.826-0.87424.681-10.096-10.0960.0000.0000.0000.000
54A65SER00.012-0.05225.759-0.476-0.4760.0000.0000.0000.000
55A66ALA0-0.036-0.00427.493-0.025-0.0250.0000.0000.0000.000
56A67THR0-0.007-0.01724.331-0.037-0.0370.0000.0000.0000.000
57A68ILE0-0.0300.00023.223-0.394-0.3940.0000.0000.0000.000
58A69ASP-1-0.869-0.91724.497-10.751-10.7510.0000.0000.0000.000
59A70THR0-0.080-0.05624.6220.0050.0050.0000.0000.0000.000
60A71ILE00.0080.00819.775-0.205-0.2050.0000.0000.0000.000
61A72GLN0-0.002-0.00321.994-0.507-0.5070.0000.0000.0000.000
62A73PRO0-0.023-0.01824.123-0.052-0.0520.0000.0000.0000.000
63A74LEU00.0150.01620.1550.0060.0060.0000.0000.0000.000
64A75ILE0-0.0070.00119.048-0.390-0.3900.0000.0000.0000.000
65A76ALA00.0290.00921.445-0.146-0.1460.0000.0000.0000.000
66A77ASP-1-0.844-0.90124.264-11.551-11.5510.0000.0000.0000.000
67A78ALA00.0140.00819.358-0.001-0.0010.0000.0000.0000.000
68A79VAL0-0.031-0.01620.534-0.305-0.3050.0000.0000.0000.000
69A80ALA0-0.017-0.00422.2360.1400.1400.0000.0000.0000.000
70A81HIS0-0.014-0.01121.6720.6110.6110.0000.0000.0000.000
71A82GLN00.0100.02317.410-0.427-0.4270.0000.0000.0000.000
72A83GLU-1-0.911-0.96321.663-12.849-12.8490.0000.0000.0000.000
73A84ALA0-0.056-0.01624.3070.4090.4090.0000.0000.0000.000
74A85SER0-0.040-0.03423.2020.1450.1450.0000.0000.0000.000
75A86GLY0-0.044-0.01622.3010.1350.1350.0000.0000.0000.000
76A87GLU-1-0.894-0.92519.586-14.521-14.5210.0000.0000.0000.000
77A88GLN0-0.039-0.02314.5270.4140.4140.0000.0000.0000.000
78A89VAL00.0300.01416.113-0.414-0.4140.0000.0000.0000.000
79A90LEU0-0.093-0.03510.132-1.355-1.3550.0000.0000.0000.000
80A91VAL00.0320.00613.9681.1041.1040.0000.0000.0000.000
81A92GLN00.0140.02113.815-2.089-2.0890.0000.0000.0000.000
82A93LEU00.0260.01714.3671.1351.1350.0000.0000.0000.000
83A94VAL0-0.015-0.00514.915-0.980-0.9800.0000.0000.0000.000
84A95ILE0-0.0070.01215.3390.6490.6490.0000.0000.0000.000
85A96TYR00.003-0.02918.143-0.308-0.3080.0000.0000.0000.000
86A97ASN0-0.057-0.04921.0960.8890.8890.0000.0000.0000.000
87A98LEU0-0.0050.02020.7160.2770.2770.0000.0000.0000.000
88A99PRO0-0.036-0.01324.0480.3610.3610.0000.0000.0000.000
89A100ASP-1-0.823-0.93927.504-9.441-9.4410.0000.0000.0000.000
90A101ARG10.7950.90524.28211.00711.0070.0000.0000.0000.000
91A102ALA00.0470.02626.0790.4030.4030.0000.0000.0000.000
92A103CYS0-0.049-0.00527.5300.0530.0530.0000.0000.0000.000
93A104ALA00.005-0.01029.1530.3410.3410.0000.0000.0000.000
94A105ALA0-0.039-0.00330.3810.2450.2450.0000.0000.0000.000
95A106LYS10.8880.94232.2447.7337.7330.0000.0000.0000.000
96A107ALA00.0060.00731.593-0.063-0.0630.0000.0000.0000.000
97A108SER00.0680.03127.342-0.024-0.0240.0000.0000.0000.000
98A109ASP-1-0.803-0.85028.534-9.590-9.5900.0000.0000.0000.000
99A110GLY00.0460.02028.7050.0000.0000.0000.0000.0000.000
100A111GLU-1-0.790-0.85628.407-9.981-9.9810.0000.0000.0000.000
101A112PHE0-0.022-0.00525.9470.3560.3560.0000.0000.0000.000
102A113HIS10.8580.90530.3158.9388.9380.0000.0000.0000.000
103A114LEU0-0.037-0.02428.637-0.055-0.0550.0000.0000.0000.000
104A115ASP-1-0.937-0.96032.464-8.297-8.2970.0000.0000.0000.000
105A116ASP-1-0.897-0.95135.119-8.281-8.2810.0000.0000.0000.000
106A117ASP-1-0.835-0.92233.301-9.552-9.5520.0000.0000.0000.000
107A118GLY00.0270.01530.361-0.278-0.2780.0000.0000.0000.000
108A119ALA00.0270.00727.052-0.375-0.3750.0000.0000.0000.000
109A120ASN0-0.075-0.05026.606-0.734-0.7340.0000.0000.0000.000
110A121LYS10.7930.90727.8318.6708.6700.0000.0000.0000.000
111A122TYR0-0.036-0.02819.811-0.304-0.3040.0000.0000.0000.000
112A123ARG10.9120.95823.17012.15212.1520.0000.0000.0000.000
113A124ALA00.0340.02423.562-0.386-0.3860.0000.0000.0000.000
114A125TYR0-0.039-0.03720.906-0.271-0.2710.0000.0000.0000.000
115A126VAL00.0040.00518.272-0.346-0.3460.0000.0000.0000.000
116A127ASP-1-0.839-0.89820.228-13.780-13.7800.0000.0000.0000.000
117A128ARG10.8200.89822.15710.96410.9640.0000.0000.0000.000
118A129ILE00.0360.02417.552-0.208-0.2080.0000.0000.0000.000
119A130VAL0-0.011-0.01116.796-0.589-0.5890.0000.0000.0000.000
120A131ALA0-0.0310.00818.563-0.462-0.4620.0000.0000.0000.000
121A132GLU-1-0.879-0.93120.942-12.629-12.6290.0000.0000.0000.000
122A133LEU0-0.014-0.00514.669-0.169-0.1690.0000.0000.0000.000
123A134SER0-0.058-0.05016.531-1.674-1.6740.0000.0000.0000.000
124A135THR0-0.002-0.00818.8430.3810.3810.0000.0000.0000.000
125A136ALA00.008-0.01019.673-0.592-0.5920.0000.0000.0000.000
126A137ASP-1-0.831-0.91720.617-13.296-13.2960.0000.0000.0000.000
127A138ALA00.0130.00417.383-0.502-0.5020.0000.0000.0000.000
128A139ASP-1-0.942-0.97915.447-19.258-19.2580.0000.0000.0000.000
129A140LYS10.7080.86515.49312.74012.7400.0000.0000.0000.000
130A141LEU0-0.0320.01615.376-0.262-0.2620.0000.0000.0000.000
131A142HIS0-0.046-0.0316.7221.2951.2950.0000.0000.0000.000
132A143PHE0-0.0040.00210.6851.8341.8340.0000.0000.0000.000
133A144SER0-0.020-0.0209.274-3.400-3.4000.0000.0000.0000.000
134A145ILE00.0210.0029.8211.9701.9700.0000.0000.0000.000
135A146VAL0-0.0030.00410.876-1.359-1.3590.0000.0000.0000.000
136A147LEU0-0.044-0.02811.7240.9130.9130.0000.0000.0000.000
137A148GLU-1-0.701-0.84314.776-13.649-13.6490.0000.0000.0000.000
138A149PRO00.0230.02417.7440.0910.0910.0000.0000.0000.000
139A150ASP-1-0.855-0.92119.697-10.817-10.8170.0000.0000.0000.000
140A151SER00.021-0.00419.0580.2960.2960.0000.0000.0000.000
141A152LEU00.021-0.01617.0980.5800.5800.0000.0000.0000.000
142A153GLY00.0480.02621.0620.2430.2430.0000.0000.0000.000
143A154ASN0-0.025-0.03522.6540.8230.8230.0000.0000.0000.000
144A155MET0-0.058-0.03323.6660.2700.2700.0000.0000.0000.000
145A156VAL0-0.057-0.00322.3490.1640.1640.0000.0000.0000.000
146A157THR0-0.007-0.00625.5460.2040.2040.0000.0000.0000.000
147A158ASN0-0.036-0.01828.3410.5530.5530.0000.0000.0000.000
148A159MET00.0240.02828.6110.1090.1090.0000.0000.0000.000
149A160HIS0-0.0170.00631.1110.1370.1370.0000.0000.0000.000
150A161VAL00.0030.00632.4390.3440.3440.0000.0000.0000.000
151A162PRO00.002-0.01333.235-0.221-0.2210.0000.0000.0000.000
152A163LYS10.8630.94930.8659.3329.3320.0000.0000.0000.000
153A165GLN0-0.014-0.01429.356-0.152-0.1520.0000.0000.0000.000
154A166GLY0-0.032-0.01631.260-0.088-0.0880.0000.0000.0000.000
155A167ALA00.0320.01227.618-0.127-0.1270.0000.0000.0000.000
156A168ALA00.0060.00025.870-0.453-0.4530.0000.0000.0000.000
157A169THR0-0.045-0.02124.639-0.487-0.4870.0000.0000.0000.000
158A170ALA00.0770.03624.129-0.485-0.4850.0000.0000.0000.000
159A171TYR0-0.021-0.03322.239-0.564-0.5640.0000.0000.0000.000
160A172LYS10.8400.91919.80412.11912.1190.0000.0000.0000.000
161A173GLU-1-0.927-0.97419.312-12.745-12.7450.0000.0000.0000.000
162A174GLY00.0180.00820.234-0.448-0.4480.0000.0000.0000.000
163A175ILE00.0360.02615.041-0.665-0.6650.0000.0000.0000.000
164A176ALA00.0070.00415.547-1.197-1.1970.0000.0000.0000.000
165A177TYR0-0.056-0.07515.751-0.951-0.9510.0000.0000.0000.000
166A178THR00.000-0.00514.820-0.344-0.3440.0000.0000.0000.000
167A179ILE0-0.018-0.01610.249-1.044-1.0440.0000.0000.0000.000
168A180ALA0-0.032-0.01212.122-1.705-1.7050.0000.0000.0000.000
169A181SER0-0.009-0.00714.127-0.201-0.2010.0000.0000.0000.000
170A182LEU0-0.0160.00111.9750.3040.3040.0000.0000.0000.000
171A183GLN0-0.057-0.0308.503-5.228-5.2280.0000.0000.0000.000
172A184LYS10.9300.9609.90021.53521.5350.0000.0000.0000.000
173A185PRO0-0.051-0.0277.228-2.869-2.8690.0000.0000.0000.000
174A186ASN0-0.004-0.0057.303-4.214-4.2140.0000.0000.0000.000
175A187ILE00.0260.0118.3812.5422.5420.0000.0000.0000.000
177A189LEU0-0.0040.0035.8554.2134.2130.0000.0000.0000.000
178A190TYR0-0.027-0.0556.837-2.961-2.9610.0000.0000.0000.000
179A191ILE00.0320.0149.5421.4181.4180.0000.0000.0000.000
180A192ASP-1-0.861-0.92912.586-15.287-15.2870.0000.0000.0000.000
181A193ALA00.0200.00015.2320.2080.2080.0000.0000.0000.000
182A194ALA00.0270.02216.9810.5110.5110.0000.0000.0000.000
183A195HIS00.0450.02519.472-0.489-0.4890.0000.0000.0000.000
184A196GLY00.0480.01121.5460.1490.1490.0000.0000.0000.000
185A197GLY00.020-0.02022.9180.2420.2420.0000.0000.0000.000
186A198TRP0-0.099-0.04223.8660.2340.2340.0000.0000.0000.000
187A199LEU00.003-0.01819.9430.3080.3080.0000.0000.0000.000
188A200GLY00.0150.00222.085-0.310-0.3100.0000.0000.0000.000
189A201TRP0-0.011-0.00122.9570.1740.1740.0000.0000.0000.000
190A202ASN00.026-0.00525.435-0.510-0.5100.0000.0000.0000.000
191A203ASP-1-0.925-0.95925.517-10.360-10.3600.0000.0000.0000.000
192A204ASN0-0.025-0.01724.1870.0630.0630.0000.0000.0000.000
193A205LEU0-0.0240.01720.644-0.592-0.5920.0000.0000.0000.000
194A206ARG10.8810.95219.01313.48113.4810.0000.0000.0000.000
195A207PRO00.0660.03921.002-0.586-0.5860.0000.0000.0000.000
196A208SER00.025-0.00819.087-0.256-0.2560.0000.0000.0000.000
197A209ALA0-0.019-0.01016.484-0.749-0.7490.0000.0000.0000.000
198A210GLU-1-0.945-0.97616.701-14.017-14.0170.0000.0000.0000.000
199A211ILE00.0170.01818.621-0.380-0.3800.0000.0000.0000.000
200A212PHE00.0200.01513.841-0.368-0.3680.0000.0000.0000.000
201A213LYS10.7930.90212.29819.26119.2610.0000.0000.0000.000
202A214GLU-1-0.826-0.89715.018-13.777-13.7770.0000.0000.0000.000
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