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

tag_button

FMODB ID: 7K2VK

Calculation Name: 1V6I-A-Xray547

Preferred Name:

Target Type:

Ligand Name: beta-d-galactopyranose | alpha-d-glucopyranose | calcium ion | manganese (ii) ion

Ligand 3-letter code: GAL | GLC | CA | MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1V6I

Chain ID: A

ChEMBL ID:

UniProt ID: P02872

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 232
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2738234.994666
FMO2-HF: Nuclear repulsion 2652660.836954
FMO2-HF: Total energy -85574.157712
FMO2-MP2: Total energy -85828.401533


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:1:ALA)


Summations of interaction energy for fragment #1(A:1: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.
-80.671-74.0855.268-5.418-6.438-0.058
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.802 / q_NPA : 0.898
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].
3A3THR0-0.020-0.0263.5152.2963.626-0.003-0.482-0.8450.001
228A228THR0-0.030-0.0312.480-1.075-0.7110.426-0.201-0.590-0.002
229A229LEU00.0150.0164.3643.8533.993-0.001-0.029-0.1100.000
230A230ILE00.0180.0052.658-21.432-18.7780.790-1.754-1.690-0.019
231A231THR0-0.045-0.0272.072-14.589-12.5864.056-2.913-3.146-0.038
232A232THR-1-0.856-0.9144.125-40.061-39.9660.000-0.039-0.0570.000
4A4VAL00.0180.0315.6401.8361.8360.0000.0000.0000.000
5A5SER0-0.017-0.0109.4180.8270.8270.0000.0000.0000.000
6A6PHE00.0020.00511.6300.4110.4110.0000.0000.0000.000
7A7ASN0-0.027-0.03715.426-0.006-0.0060.0000.0000.0000.000
8A8PHE0-0.0060.01418.4830.3040.3040.0000.0000.0000.000
9A9ASN00.020-0.00222.0260.0130.0130.0000.0000.0000.000
10A10SER00.0080.01724.6100.3270.3270.0000.0000.0000.000
11A11PHE0-0.024-0.01623.309-0.607-0.6070.0000.0000.0000.000
12A12SER00.007-0.00727.3910.2550.2550.0000.0000.0000.000
13A13GLU-1-0.878-0.94328.637-9.374-9.3740.0000.0000.0000.000
14A14GLY0-0.021-0.01530.315-0.010-0.0100.0000.0000.0000.000
15A15ASN0-0.0040.00523.496-0.550-0.5500.0000.0000.0000.000
16A16PRO00.0350.01423.689-0.112-0.1120.0000.0000.0000.000
17A17ALA0-0.014-0.00619.884-0.490-0.4900.0000.0000.0000.000
18A18ILE0-0.0150.00020.895-0.515-0.5150.0000.0000.0000.000
19A19ASN0-0.050-0.02323.6450.0360.0360.0000.0000.0000.000
20A20PHE00.0660.02325.717-0.136-0.1360.0000.0000.0000.000
21A21GLN0-0.015-0.01327.5240.0070.0070.0000.0000.0000.000
22A22GLY00.0570.02730.8940.0140.0140.0000.0000.0000.000
23A23ASP-1-0.814-0.88234.444-8.121-8.1210.0000.0000.0000.000
24A24VAL0-0.050-0.01630.1440.0600.0600.0000.0000.0000.000
25A25THR0-0.027-0.00633.5530.1520.1520.0000.0000.0000.000
26A26VAL00.003-0.00130.565-0.228-0.2280.0000.0000.0000.000
27A27LEU00.0020.01533.2170.2970.2970.0000.0000.0000.000
28A28SER00.010-0.00834.487-0.235-0.2350.0000.0000.0000.000
29A29ASN0-0.029-0.01834.604-0.147-0.1470.0000.0000.0000.000
30A30GLY00.0280.02231.060-0.183-0.1830.0000.0000.0000.000
31A31ASN00.0200.00129.781-0.592-0.5920.0000.0000.0000.000
32A32ILE0-0.0140.00326.8240.1650.1650.0000.0000.0000.000
33A33GLN0-0.007-0.01530.8120.0720.0720.0000.0000.0000.000
34A34LEU00.007-0.00928.653-0.034-0.0340.0000.0000.0000.000
35A35THR00.0570.05632.816-0.019-0.0190.0000.0000.0000.000
36A36ASN00.002-0.00136.4570.2330.2330.0000.0000.0000.000
37A37LEU00.0750.02739.8970.0960.0960.0000.0000.0000.000
38A38ASN0-0.0250.00042.5330.2720.2720.0000.0000.0000.000
39A39LYS10.7760.88539.8338.0098.0090.0000.0000.0000.000
40A40VAL00.0130.00543.558-0.036-0.0360.0000.0000.0000.000
41A41ASN0-0.027-0.01941.4620.0060.0060.0000.0000.0000.000
42A42SER0-0.050-0.02438.691-0.174-0.1740.0000.0000.0000.000
43A43VAL00.0640.02433.511-0.088-0.0880.0000.0000.0000.000
44A44GLY0-0.0140.00832.8280.0930.0930.0000.0000.0000.000
45A45ARG10.8070.89727.20010.92110.9210.0000.0000.0000.000
46A46VAL0-0.030-0.00624.6030.1040.1040.0000.0000.0000.000
47A47LEU00.0070.00622.164-0.294-0.2940.0000.0000.0000.000
48A48TYR00.010-0.00214.6870.3690.3690.0000.0000.0000.000
49A49ALA0-0.026-0.00919.912-0.061-0.0610.0000.0000.0000.000
50A50MET0-0.042-0.01614.402-0.379-0.3790.0000.0000.0000.000
51A51PRO0-0.025-0.00516.261-0.203-0.2030.0000.0000.0000.000
52A52VAL00.001-0.00911.240-1.539-1.5390.0000.0000.0000.000
53A53ARG10.8750.9308.11133.61633.6160.0000.0000.0000.000
54A54ILE00.0190.0119.732-2.633-2.6330.0000.0000.0000.000
55A55TRP0-0.041-0.03310.359-0.699-0.6990.0000.0000.0000.000
56A56SER0-0.028-0.0038.7700.4780.4780.0000.0000.0000.000
57A57SER0-0.026-0.04010.8630.5870.5870.0000.0000.0000.000
58A58ALA0-0.055-0.02211.4960.6530.6530.0000.0000.0000.000
59A59THR00.006-0.0058.2880.6920.6920.0000.0000.0000.000
60A60GLY0-0.0240.00811.3400.8210.8210.0000.0000.0000.000
61A61ASN0-0.006-0.0086.7214.2894.2890.0000.0000.0000.000
62A62VAL00.017-0.00510.0170.3980.3980.0000.0000.0000.000
63A63ALA0-0.001-0.0047.916-2.143-2.1430.0000.0000.0000.000
64A64SER00.0210.0267.9272.9812.9810.0000.0000.0000.000
65A65PHE0-0.015-0.0218.676-2.252-2.2520.0000.0000.0000.000
66A66LEU00.0170.02411.0781.3331.3330.0000.0000.0000.000
67A67THR0-0.050-0.04513.385-0.451-0.4510.0000.0000.0000.000
68A68SER00.0110.01416.1930.7620.7620.0000.0000.0000.000
69A69PHE00.0410.01119.610-0.227-0.2270.0000.0000.0000.000
70A70SER0-0.039-0.02022.7040.4340.4340.0000.0000.0000.000
71A71PHE00.0110.00226.469-0.146-0.1460.0000.0000.0000.000
72A72GLU-1-0.816-0.89529.307-8.405-8.4050.0000.0000.0000.000
73A73MET0-0.0280.01632.474-0.087-0.0870.0000.0000.0000.000
74A74LYS10.8920.94635.5737.9627.9620.0000.0000.0000.000
75A75ASP-1-0.753-0.85539.228-7.351-7.3510.0000.0000.0000.000
76A76ILE0-0.072-0.03742.3730.0180.0180.0000.0000.0000.000
77A77LYS10.8320.90944.9396.0056.0050.0000.0000.0000.000
78A78ASP-1-0.894-0.94748.687-6.017-6.0170.0000.0000.0000.000
79A79TYR0-0.065-0.03245.4660.0860.0860.0000.0000.0000.000
80A80ASP-1-0.850-0.91344.609-6.694-6.6940.0000.0000.0000.000
81A81PRO0-0.047-0.01840.920-0.076-0.0760.0000.0000.0000.000
82A82ALA00.0290.04639.822-0.024-0.0240.0000.0000.0000.000
83A83ASP-1-0.891-0.96337.013-7.842-7.8420.0000.0000.0000.000
84A84GLY00.0820.03533.960-0.009-0.0090.0000.0000.0000.000
85A85ILE0-0.066-0.03327.904-0.087-0.0870.0000.0000.0000.000
86A86ILE00.0030.01025.942-0.124-0.1240.0000.0000.0000.000
87A87PHE0-0.021-0.00617.802-0.287-0.2870.0000.0000.0000.000
88A88PHE0-0.026-0.02922.631-0.050-0.0500.0000.0000.0000.000
89A89ILE00.0240.00817.049-0.651-0.6510.0000.0000.0000.000
90A90ALA00.0280.01220.2750.5260.5260.0000.0000.0000.000
91A91PRO00.0560.02620.673-0.813-0.8130.0000.0000.0000.000
92A92GLU-1-0.849-0.92719.155-16.355-16.3550.0000.0000.0000.000
93A93ASP-1-0.931-0.96721.125-12.299-12.2990.0000.0000.0000.000
94A94THR0-0.0130.01023.7110.7840.7840.0000.0000.0000.000
95A95GLN00.0250.01226.1180.1710.1710.0000.0000.0000.000
96A96ILE0-0.0070.00329.556-0.070-0.0700.0000.0000.0000.000
97A97PRO0-0.0050.00631.4720.1460.1460.0000.0000.0000.000
98A98ALA00.018-0.00333.9900.2190.2190.0000.0000.0000.000
99A99GLY0-0.022-0.01437.1730.1040.1040.0000.0000.0000.000
100A100SER0-0.0180.00135.9670.1590.1590.0000.0000.0000.000
101A101ILE0-0.018-0.01738.0770.1300.1300.0000.0000.0000.000
102A102GLY00.0100.01437.4790.1520.1520.0000.0000.0000.000
103A103GLY00.0160.01338.391-0.031-0.0310.0000.0000.0000.000
104A104GLY00.1320.06236.716-0.238-0.2380.0000.0000.0000.000
105A105THR0-0.080-0.04635.093-0.228-0.2280.0000.0000.0000.000
106A106LEU00.0410.02331.180-0.395-0.3950.0000.0000.0000.000
107A107GLY00.0250.03531.078-0.336-0.3360.0000.0000.0000.000
108A108VAL0-0.058-0.03827.320-0.269-0.2690.0000.0000.0000.000
109A109SER0-0.035-0.01230.098-0.173-0.1730.0000.0000.0000.000
110A110ASP-1-0.845-0.92932.811-8.498-8.4980.0000.0000.0000.000
111A111THR00.033-0.00336.099-0.050-0.0500.0000.0000.0000.000
112A112LYS10.8690.94437.7407.8117.8110.0000.0000.0000.000
113A113GLY00.0930.07535.5500.0450.0450.0000.0000.0000.000
114A114ALA0-0.017-0.00732.761-0.314-0.3140.0000.0000.0000.000
115A115GLY00.023-0.00730.2180.1210.1210.0000.0000.0000.000
116A116HIS0-0.107-0.05623.2800.0940.0940.0000.0000.0000.000
117A117PHE00.002-0.01423.726-0.397-0.3970.0000.0000.0000.000
118A118VAL0-0.0030.00120.7190.1820.1820.0000.0000.0000.000
119A119GLY00.004-0.00722.618-0.268-0.2680.0000.0000.0000.000
120A120VAL0-0.029-0.00422.0290.0940.0940.0000.0000.0000.000
121A121GLU-1-0.824-0.87024.811-9.869-9.8690.0000.0000.0000.000
122A122PHE0-0.017-0.03225.036-0.136-0.1360.0000.0000.0000.000
123A123ASP-1-0.814-0.91630.733-8.581-8.5810.0000.0000.0000.000
124A124THR0-0.024-0.03334.0910.0720.0720.0000.0000.0000.000
125A125TYR00.0060.00037.5760.3120.3120.0000.0000.0000.000
126A126SER0-0.029-0.02238.753-0.099-0.0990.0000.0000.0000.000
127A127ASN0-0.028-0.03639.0460.1020.1020.0000.0000.0000.000
128A128SER0-0.031-0.00940.413-0.048-0.0480.0000.0000.0000.000
129A129GLU-1-0.884-0.94441.034-7.340-7.3400.0000.0000.0000.000
130A130TYR0-0.085-0.06536.661-0.087-0.0870.0000.0000.0000.000
131A131ASN0-0.086-0.05737.3020.0060.0060.0000.0000.0000.000
132A132ASP-1-0.783-0.87736.630-8.444-8.4440.0000.0000.0000.000
133A133PRO0-0.058-0.02535.9660.2140.2140.0000.0000.0000.000
134A134PRO0-0.038-0.00739.2090.0350.0350.0000.0000.0000.000
135A135THR0-0.049-0.03738.3730.1710.1710.0000.0000.0000.000
136A136ASP-1-0.719-0.84336.693-8.123-8.1230.0000.0000.0000.000
137A137HIS10.7820.90033.1478.7008.7000.0000.0000.0000.000
138A138VAL0-0.0100.01427.714-0.181-0.1810.0000.0000.0000.000
139A139GLY00.0480.01129.1950.1990.1990.0000.0000.0000.000
140A140ILE0-0.095-0.04323.608-0.503-0.5030.0000.0000.0000.000
141A141ASP00.024-0.03725.9930.3310.3310.0000.0000.0000.000
142A142VAL0-0.018-0.03524.037-0.659-0.6590.0000.0000.0000.000
143A143ASN0-0.040-0.02825.5320.0890.0890.0000.0000.0000.000
144A144SER00.0190.01328.1540.3670.3670.0000.0000.0000.000
145A145VAL0-0.0030.00130.058-0.357-0.3570.0000.0000.0000.000
146A146ASP-1-0.872-0.89432.263-8.462-8.4620.0000.0000.0000.000
147A147SER0-0.008-0.01030.495-0.196-0.1960.0000.0000.0000.000
148A148VAL0-0.075-0.02927.4980.1010.1010.0000.0000.0000.000
149A149LYS10.8510.91427.46610.78910.7890.0000.0000.0000.000
150A150THR00.0390.01729.901-0.173-0.1730.0000.0000.0000.000
151A151VAL0-0.050-0.01930.2440.0430.0430.0000.0000.0000.000
152A152PRO00.0130.00132.933-0.046-0.0460.0000.0000.0000.000
153A153TRP0-0.041-0.02732.528-0.242-0.2420.0000.0000.0000.000
154A154ASN00.003-0.01335.3760.3840.3840.0000.0000.0000.000
155A155SER0-0.0040.01535.887-0.237-0.2370.0000.0000.0000.000
156A156VAL0-0.024-0.01336.5600.2420.2420.0000.0000.0000.000
157A157SER00.007-0.01937.513-0.223-0.2230.0000.0000.0000.000
158A158GLY0-0.059-0.05137.9960.1460.1460.0000.0000.0000.000
159A159ALA0-0.0050.01935.174-0.049-0.0490.0000.0000.0000.000
160A160VAL0-0.089-0.04430.306-0.232-0.2320.0000.0000.0000.000
161A161VAL00.0440.03429.008-0.146-0.1460.0000.0000.0000.000
162A162LYS10.8990.94725.8389.9219.9210.0000.0000.0000.000
163A163VAL00.0200.01822.7410.2020.2020.0000.0000.0000.000
164A164THR0-0.017-0.00918.583-0.582-0.5820.0000.0000.0000.000
165A165VAL0-0.020-0.00917.9300.4590.4590.0000.0000.0000.000
166A166ILE00.011-0.00114.301-0.966-0.9660.0000.0000.0000.000
167A167TYR0-0.048-0.02712.8270.6260.6260.0000.0000.0000.000
168A168ASP-1-0.766-0.87212.647-21.756-21.7560.0000.0000.0000.000
169A169SER00.005-0.01210.0940.9400.9400.0000.0000.0000.000
170A170SER0-0.047-0.01912.6910.4070.4070.0000.0000.0000.000
171A171THR0-0.093-0.07614.3731.1411.1410.0000.0000.0000.000
172A172LYS10.8730.95915.97818.68018.6800.0000.0000.0000.000
173A173THR00.000-0.00517.3541.1081.1080.0000.0000.0000.000
174A174LEU00.0010.01117.338-0.949-0.9490.0000.0000.0000.000
175A175SER0-0.059-0.04118.4750.8500.8500.0000.0000.0000.000
176A176VAL00.0390.01519.915-0.583-0.5830.0000.0000.0000.000
177A177ALA00.001-0.00922.5700.4520.4520.0000.0000.0000.000
178A178VAL00.0460.02924.417-0.324-0.3240.0000.0000.0000.000
179A179THR0-0.060-0.03026.9470.1380.1380.0000.0000.0000.000
180A180ASN00.010-0.00529.109-0.050-0.0500.0000.0000.0000.000
181A181ASP-1-0.856-0.94532.663-8.592-8.5920.0000.0000.0000.000
182A182ASN0-0.068-0.03835.047-0.079-0.0790.0000.0000.0000.000
183A183GLY0-0.020-0.00433.0490.1100.1100.0000.0000.0000.000
184A184ASP-1-0.872-0.91532.544-8.538-8.5380.0000.0000.0000.000
185A185ILE0-0.037-0.02728.030-0.215-0.2150.0000.0000.0000.000
186A186THR00.0100.00829.4790.3040.3040.0000.0000.0000.000
187A187THR0-0.029-0.01626.018-0.260-0.2600.0000.0000.0000.000
188A188ILE00.0310.02425.4530.2800.2800.0000.0000.0000.000
189A189ALA00.0150.00122.973-0.561-0.5610.0000.0000.0000.000
190A190GLN0-0.008-0.00822.8540.8890.8890.0000.0000.0000.000
191A191VAL0-0.0020.01720.974-0.552-0.5520.0000.0000.0000.000
192A192VAL00.0300.00920.3550.6430.6430.0000.0000.0000.000
193A193ASP-1-0.825-0.91518.151-17.311-17.3110.0000.0000.0000.000
194A194LEU00.0360.00714.8810.5400.5400.0000.0000.0000.000
195A195LYS10.8680.94114.44519.40419.4040.0000.0000.0000.000
196A196ALA0-0.059-0.02417.0810.4910.4910.0000.0000.0000.000
197A197LYS10.8970.95420.16412.90512.9050.0000.0000.0000.000
198A198LEU00.0320.03118.4790.5780.5780.0000.0000.0000.000
199A199PRO00.0330.02818.412-0.498-0.4980.0000.0000.0000.000
200A200GLU-1-0.819-0.89413.674-21.236-21.2360.0000.0000.0000.000
201A201ARG10.8430.91813.57617.09517.0950.0000.0000.0000.000
202A202VAL00.0000.00215.4121.1581.1580.0000.0000.0000.000
203A203LYS10.8810.95516.98613.50413.5040.0000.0000.0000.000
204A204PHE00.0390.01513.9830.1940.1940.0000.0000.0000.000
205A205GLY00.028-0.00418.8450.0400.0400.0000.0000.0000.000
206A206PHE0-0.0210.00221.971-0.023-0.0230.0000.0000.0000.000
207A207SER0-0.059-0.05425.3140.1270.1270.0000.0000.0000.000
208A208ALA00.0560.03128.648-0.029-0.0290.0000.0000.0000.000
209A209SER0-0.041-0.03232.185-0.073-0.0730.0000.0000.0000.000
210A210GLY00.0490.04335.7810.0190.0190.0000.0000.0000.000
211A211SER00.0460.01339.4460.0280.0280.0000.0000.0000.000
212A212LEU0-0.021-0.02042.6970.0460.0460.0000.0000.0000.000
213A213GLY00.0370.00946.4120.0660.0660.0000.0000.0000.000
214A214GLY00.0570.04443.3600.0660.0660.0000.0000.0000.000
215A215ARG10.7610.86141.0786.7786.7780.0000.0000.0000.000
216A216GLN00.0550.02036.7700.2320.2320.0000.0000.0000.000
217A217ILE0-0.057-0.03136.684-0.122-0.1220.0000.0000.0000.000
218A218HIS00.0340.02033.035-0.129-0.1290.0000.0000.0000.000
219A219LEU0-0.040-0.02132.372-0.095-0.0950.0000.0000.0000.000
220A220ILE00.0000.00125.460-0.167-0.1670.0000.0000.0000.000
221A221ARG10.8470.91927.8729.5749.5740.0000.0000.0000.000
222A222SER00.0100.01724.0440.0130.0130.0000.0000.0000.000
223A223TRP0-0.021-0.02017.9280.1220.1220.0000.0000.0000.000
224A224SER0-0.0100.02117.076-0.450-0.4500.0000.0000.0000.000
225A225PHE00.0250.02311.6880.2090.2090.0000.0000.0000.000
226A226THR00.001-0.0208.504-0.933-0.9330.0000.0000.0000.000
227A227SER00.0130.0218.6551.5911.5910.0000.0000.0000.000