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: 3GN6L

Calculation Name: 1S5E-A-Xray547

Preferred Name:

Target Type:

Ligand Name: beta-d-galactopyranose

Ligand 3-letter code: GAL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1S5E

Chain ID: A

ChEMBL ID:

UniProt ID: P01555

Base Structure: X-ray

Registration Date: 2025-10-06

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 235
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2967412.567215
FMO2-HF: Nuclear repulsion 2873645.62507
FMO2-HF: Total energy -93766.942144
FMO2-MP2: Total energy -94041.775056


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:ASN)


Summations of interaction energy for fragment #1(A:1:ASN)
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.
-212.649-211.58743.908-23.153-21.819-0.178
Interaction energy analysis for fragmet #1(A:1:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.734 / q_NPA : 0.855
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].
3A3ASP-1-0.807-0.8721.778-70.225-70.10118.785-9.763-9.147-0.033
4A4LYS10.7650.8703.67736.89837.0800.0270.029-0.2380.002
90A90THR00.0190.0203.2565.6446.3010.034-0.256-0.436-0.001
91A91ALA00.000-0.0095.052-4.173-4.181-0.001-0.0030.0120.000
151A151SER00.0290.0073.897-8.836-8.5090.001-0.157-0.1710.000
152A152ASN0-0.090-0.0342.575-14.779-13.4181.305-1.117-1.550-0.014
153A153LEU0-0.064-0.0223.0096.7107.4930.040-0.265-0.559-0.002
154A154ASP-1-0.800-0.9011.914-150.613-153.21623.706-11.563-9.539-0.130
155A155ILE0-0.020-0.0193.7568.6288.8670.011-0.058-0.1910.000
5A5LEU00.0390.0247.2860.8810.8810.0000.0000.0000.000
6A6TYR00.006-0.0049.7161.4971.4970.0000.0000.0000.000
7A7ARG10.7720.86713.43115.34815.3480.0000.0000.0000.000
8A8ALA0-0.0030.01716.7590.2250.2250.0000.0000.0000.000
9A9ASP-1-0.727-0.85820.315-13.344-13.3440.0000.0000.0000.000
10A10SER00.0370.01022.542-0.080-0.0800.0000.0000.0000.000
11A11ARG10.8100.91322.61313.17113.1710.0000.0000.0000.000
12A12PRO00.0110.01824.493-0.545-0.5450.0000.0000.0000.000
13A13PRO00.0390.00322.577-0.023-0.0230.0000.0000.0000.000
14A14ASP-1-0.847-0.90823.689-11.512-11.5120.0000.0000.0000.000
15A15GLU-1-0.816-0.91426.372-11.134-11.1340.0000.0000.0000.000
16A16ILE0-0.0250.00719.962-0.215-0.2150.0000.0000.0000.000
17A17LYS10.7870.87322.05511.19411.1940.0000.0000.0000.000
18A18GLN0-0.039-0.01623.057-0.105-0.1050.0000.0000.0000.000
19A19SER00.0100.00523.4630.2360.2360.0000.0000.0000.000
20A20GLY00.0110.00721.448-0.267-0.2670.0000.0000.0000.000
21A21GLY0-0.012-0.03218.706-1.047-1.0470.0000.0000.0000.000
22A22LEU0-0.046-0.01316.7180.7480.7480.0000.0000.0000.000
23A23MET00.0100.04119.350-0.588-0.5880.0000.0000.0000.000
24A24PRO00.0490.00820.9790.2310.2310.0000.0000.0000.000
25A25ARG10.8400.90023.54710.96110.9610.0000.0000.0000.000
26A26GLY0-0.030-0.01627.3230.0430.0430.0000.0000.0000.000
27A27GLN0-0.034-0.01023.6830.4120.4120.0000.0000.0000.000
28A28SER00.007-0.00226.134-0.217-0.2170.0000.0000.0000.000
29A29GLU-1-0.937-0.97524.990-11.060-11.0600.0000.0000.0000.000
30A30TYR00.007-0.01016.496-0.363-0.3630.0000.0000.0000.000
31A31PHE0-0.045-0.05018.271-0.158-0.1580.0000.0000.0000.000
32A32ASP-1-0.863-0.91623.272-10.311-10.3110.0000.0000.0000.000
33A33ARG10.7870.85622.98212.47412.4740.0000.0000.0000.000
34A34GLY00.0070.02327.7280.1900.1900.0000.0000.0000.000
35A35THR0-0.073-0.03630.6920.3180.3180.0000.0000.0000.000
36A36GLN00.0230.00725.048-0.501-0.5010.0000.0000.0000.000
37A37MET00.0210.03922.5740.1840.1840.0000.0000.0000.000
38A38ASN00.002-0.00927.434-0.174-0.1740.0000.0000.0000.000
39A39ILE0-0.035-0.01521.974-0.445-0.4450.0000.0000.0000.000
40A40ASN00.0270.00324.317-0.314-0.3140.0000.0000.0000.000
41A41LEU00.0480.02618.072-0.013-0.0130.0000.0000.0000.000
42A42TYR00.0230.01421.9150.0040.0040.0000.0000.0000.000
43A43ASP-1-0.908-0.96024.692-10.786-10.7860.0000.0000.0000.000
44A44HIS0-0.033-0.01320.048-0.557-0.5570.0000.0000.0000.000
45A45ALA0-0.006-0.01221.2980.0270.0270.0000.0000.0000.000
46A46ARG10.9010.94222.78810.75010.7500.0000.0000.0000.000
47A47GLY00.0040.02925.9180.4110.4110.0000.0000.0000.000
48A48THR0-0.041-0.02826.164-0.350-0.3500.0000.0000.0000.000
49A49GLN00.0910.07121.6520.0300.0300.0000.0000.0000.000
50A50THR0-0.061-0.06026.9010.4920.4920.0000.0000.0000.000
51A51GLY00.0360.03729.6250.0180.0180.0000.0000.0000.000
52A52PHE0-0.055-0.04424.100-0.023-0.0230.0000.0000.0000.000
53A53VAL00.0470.03420.1990.1580.1580.0000.0000.0000.000
54A54ARG10.8360.89221.35813.07213.0720.0000.0000.0000.000
55A55HIS0-0.013-0.01321.105-0.905-0.9050.0000.0000.0000.000
56A56ASP-1-0.733-0.83823.010-10.737-10.7370.0000.0000.0000.000
57A57ASP-1-0.828-0.90123.925-11.792-11.7920.0000.0000.0000.000
58A58GLY00.0570.02223.149-0.341-0.3410.0000.0000.0000.000
59A59TYR0-0.014-0.00516.957-0.601-0.6010.0000.0000.0000.000
60A60VAL0-0.059-0.03217.3950.6980.6980.0000.0000.0000.000
61A61SER0-0.013-0.01616.829-1.450-1.4500.0000.0000.0000.000
62A62THR0-0.088-0.05312.600-0.161-0.1610.0000.0000.0000.000
63A63SER00.0840.03514.1450.2070.2070.0000.0000.0000.000
64A64ILE00.0310.0129.392-0.949-0.9490.0000.0000.0000.000
65A65SER00.004-0.00910.089-0.614-0.6140.0000.0000.0000.000
66A66LEU00.0380.02612.5440.8810.8810.0000.0000.0000.000
67A67ARG10.9320.96415.18913.87413.8740.0000.0000.0000.000
68A68SER00.0530.02915.4750.5640.5640.0000.0000.0000.000
69A69ALA00.0570.02916.2590.7350.7350.0000.0000.0000.000
70A70HIS0-0.014-0.01218.0500.4080.4080.0000.0000.0000.000
71A71LEU0-0.050-0.02020.1560.7250.7250.0000.0000.0000.000
72A72VAL00.0830.05219.8540.6290.6290.0000.0000.0000.000
73A73GLY00.0320.00122.0420.4790.4790.0000.0000.0000.000
74A74GLN0-0.022-0.00623.8140.3420.3420.0000.0000.0000.000
75A75THR0-0.030-0.01325.3920.5670.5670.0000.0000.0000.000
76A76ILE0-0.045-0.01025.0550.2810.2810.0000.0000.0000.000
77A77LEU0-0.064-0.02123.8800.1520.1520.0000.0000.0000.000
78A78SER00.000-0.00327.7180.2420.2420.0000.0000.0000.000
79A79GLY0-0.005-0.00430.4270.1320.1320.0000.0000.0000.000
80A80HIS0-0.0230.00029.2140.2770.2770.0000.0000.0000.000
81A81SER0-0.018-0.00830.988-0.198-0.1980.0000.0000.0000.000
82A82THR0-0.034-0.02727.951-0.033-0.0330.0000.0000.0000.000
83A83TYR00.000-0.00422.842-0.145-0.1450.0000.0000.0000.000
84A84TYR0-0.004-0.00421.7280.0680.0680.0000.0000.0000.000
85A85ILE00.0010.00716.740-0.046-0.0460.0000.0000.0000.000
86A86TYR0-0.006-0.02516.393-0.437-0.4370.0000.0000.0000.000
87A87VAL00.0010.00411.335-0.482-0.4820.0000.0000.0000.000
88A88ILE0-0.032-0.02510.4080.4560.4560.0000.0000.0000.000
89A89ALA00.0230.0176.415-0.905-0.9050.0000.0000.0000.000
92A92PRO00.011-0.0026.9143.0833.0830.0000.0000.0000.000
93A93ASN00.0330.0199.5600.2600.2600.0000.0000.0000.000
94A94MET0-0.0560.0039.1182.4512.4510.0000.0000.0000.000
95A95PHE00.0700.03010.778-1.546-1.5460.0000.0000.0000.000
96A96ASN00.011-0.00311.2051.7621.7620.0000.0000.0000.000
97A97VAL00.0310.00813.1310.7620.7620.0000.0000.0000.000
98A98ASN0-0.008-0.00815.3961.4151.4150.0000.0000.0000.000
99A99ASP-1-0.876-0.92412.295-21.638-21.6380.0000.0000.0000.000
100A100VAL0-0.039-0.01615.5020.7040.7040.0000.0000.0000.000
101A101LEU00.0000.00618.1310.8890.8890.0000.0000.0000.000
102A102GLY00.0360.02319.5300.7730.7730.0000.0000.0000.000
103A103ALA0-0.047-0.03420.8730.0330.0330.0000.0000.0000.000
104A104TYR0-0.113-0.09123.6540.6920.6920.0000.0000.0000.000
105A105SER00.013-0.00419.3830.1930.1930.0000.0000.0000.000
106A106PRO0-0.055-0.02122.1510.3060.3060.0000.0000.0000.000
107A107HIS0-0.006-0.00822.0310.4460.4460.0000.0000.0000.000
108A108PRO00.0140.02019.568-0.624-0.6240.0000.0000.0000.000
109A109ASP-1-0.885-0.94618.328-13.779-13.7790.0000.0000.0000.000
110A110GLU-1-0.958-0.97918.653-13.890-13.8900.0000.0000.0000.000
111A111GLN0-0.114-0.05813.550-0.847-0.8470.0000.0000.0000.000
112A112GLU-1-0.758-0.82513.639-16.084-16.0840.0000.0000.0000.000
113A113VAL0-0.003-0.0059.847-0.639-0.6390.0000.0000.0000.000
114A114SER00.0170.00513.1810.0540.0540.0000.0000.0000.000
115A115ALA0-0.023-0.01313.874-0.882-0.8820.0000.0000.0000.000
116A116LEU0-0.004-0.00114.9201.3111.3110.0000.0000.0000.000
117A117GLY00.005-0.01716.740-0.486-0.4860.0000.0000.0000.000
118A118GLY0-0.025-0.00717.8350.6110.6110.0000.0000.0000.000
119A119ILE0-0.043-0.01312.929-0.917-0.9170.0000.0000.0000.000
120A120PRO00.0330.02713.5100.9600.9600.0000.0000.0000.000
121A121TYR00.0660.00114.746-1.217-1.2170.0000.0000.0000.000
122A122SER0-0.015-0.01114.113-0.731-0.7310.0000.0000.0000.000
123A123GLN00.004-0.0029.0550.7900.7900.0000.0000.0000.000
124A124ILE0-0.0080.00911.014-1.557-1.5570.0000.0000.0000.000
125A125TYR00.0560.01610.9530.6330.6330.0000.0000.0000.000
126A126GLY00.010-0.01113.1791.0401.0400.0000.0000.0000.000
127A127TRP0-0.0070.00416.326-0.681-0.6810.0000.0000.0000.000
128A128TYR00.0610.03515.6690.4140.4140.0000.0000.0000.000
129A129ARG10.8480.91820.40610.80510.8050.0000.0000.0000.000
130A130VAL00.0070.00922.884-0.109-0.1090.0000.0000.0000.000
131A131HIS0-0.031-0.03125.5380.4520.4520.0000.0000.0000.000
132A132PHE00.025-0.00829.3580.0970.0970.0000.0000.0000.000
133A133GLY00.0120.01127.6970.1460.1460.0000.0000.0000.000
134A134VAL0-0.0170.00126.864-0.371-0.3710.0000.0000.0000.000
135A135LEU0-0.015-0.01120.100-0.087-0.0870.0000.0000.0000.000
136A136ASP-1-0.871-0.92524.450-11.101-11.1010.0000.0000.0000.000
137A137GLU-1-0.923-0.96522.843-12.701-12.7010.0000.0000.0000.000
138A138GLN0-0.035-0.01521.666-0.660-0.6600.0000.0000.0000.000
139A139LEU0-0.039-0.00914.772-0.085-0.0850.0000.0000.0000.000
140A140HIS0-0.022-0.00519.487-0.028-0.0280.0000.0000.0000.000
141A141ARG10.9290.96312.79520.27920.2790.0000.0000.0000.000
142A142ASN00.0050.00716.0221.8751.8750.0000.0000.0000.000
143A143ARG10.9600.97017.11412.20412.2040.0000.0000.0000.000
144A144GLY0-0.008-0.00117.8340.0670.0670.0000.0000.0000.000
145A145TYR0-0.040-0.0098.745-0.582-0.5820.0000.0000.0000.000
146A146ARG10.8210.90211.88419.16919.1690.0000.0000.0000.000
147A147ASP-1-0.800-0.8828.795-32.950-32.9500.0000.0000.0000.000
148A148ARG10.9570.9687.87718.07818.0780.0000.0000.0000.000
149A149TYR0-0.0130.0088.134-1.218-1.2180.0000.0000.0000.000
150A150TYR00.010-0.0256.058-2.514-2.5140.0000.0000.0000.000
156A156ALA0-0.0140.0107.075-0.943-0.9430.0000.0000.0000.000
157A157PRO0-0.0080.00610.2430.1420.1420.0000.0000.0000.000
158A158ALA00.0420.00211.7191.4981.4980.0000.0000.0000.000
159A159ALA0-0.031-0.02114.9381.1981.1980.0000.0000.0000.000
160A160ASP-1-0.898-0.95113.808-20.353-20.3530.0000.0000.0000.000
161A161GLY0-0.005-0.00816.1310.6270.6270.0000.0000.0000.000
162A162TYR0-0.038-0.02517.2890.8210.8210.0000.0000.0000.000
163A163GLY00.0260.00720.4960.7030.7030.0000.0000.0000.000
164A164LEU0-0.054-0.02617.9550.5950.5950.0000.0000.0000.000
165A165ALA0-0.0080.00521.3350.0740.0740.0000.0000.0000.000
166A166GLY00.0190.00022.2090.1350.1350.0000.0000.0000.000
167A167PHE0-0.015-0.00123.9860.3540.3540.0000.0000.0000.000
168A168PRO00.0890.05127.8660.0740.0740.0000.0000.0000.000
169A169PRO00.0210.02231.580-0.096-0.0960.0000.0000.0000.000
170A170GLU-1-0.870-0.96233.127-9.027-9.0270.0000.0000.0000.000
171A171HIS0-0.045-0.00428.7820.2430.2430.0000.0000.0000.000
172A172ARG10.8450.89831.0669.9219.9210.0000.0000.0000.000
173A173ALA00.0940.05426.675-0.004-0.0040.0000.0000.0000.000
174A174TRP0-0.041-0.02225.059-0.305-0.3050.0000.0000.0000.000
175A175ARG10.8580.92429.6819.2539.2530.0000.0000.0000.000
176A176GLU-1-0.765-0.83128.494-10.215-10.2150.0000.0000.0000.000
177A177GLU-1-0.885-0.90225.939-11.801-11.8010.0000.0000.0000.000
178A178PRO00.0290.01321.1550.0870.0870.0000.0000.0000.000
179A179TRP00.008-0.02321.8070.3530.3530.0000.0000.0000.000
180A180ILE0-0.0250.00225.0850.1410.1410.0000.0000.0000.000
181A181HIS10.7530.84624.84112.09812.0980.0000.0000.0000.000
182A182HIS0-0.029-0.01720.422-0.130-0.1300.0000.0000.0000.000
183A183ALA00.0200.02524.737-0.172-0.1720.0000.0000.0000.000
184A184PRO00.0170.01326.0920.2110.2110.0000.0000.0000.000
185A185PRO0-0.049-0.04028.4820.3540.3540.0000.0000.0000.000
186A186GLY00.0180.00832.1120.0530.0530.0000.0000.0000.000
187A187CYS00.0370.05130.297-0.225-0.2250.0000.0000.0000.000
188A188GLY00.0330.00132.584-0.029-0.0290.0000.0000.0000.000
189A189ASN0-0.046-0.03433.6080.3950.3950.0000.0000.0000.000
190A190ALA0-0.0130.02934.0060.1920.1920.0000.0000.0000.000
191A191PRO00.008-0.01236.1130.2100.2100.0000.0000.0000.000
192A192ARG10.9380.95939.3967.5317.5310.0000.0000.0000.000
193A193SER00.0730.01039.485-0.147-0.1470.0000.0000.0000.000
194A194SER00.0270.03540.1030.0610.0610.0000.0000.0000.000
195A195MET0-0.0160.03235.291-0.111-0.1110.0000.0000.0000.000
196A196SER0-0.053-0.05135.258-0.205-0.2050.0000.0000.0000.000
197A197ASN00.0030.02536.0020.1090.1090.0000.0000.0000.000
198A198THR0-0.047-0.04734.717-0.154-0.1540.0000.0000.0000.000
199A200ASP-1-0.838-0.91130.222-10.398-10.3980.0000.0000.0000.000
200A201GLU-1-0.908-0.96230.131-9.096-9.0960.0000.0000.0000.000
201A202LYS10.8810.95129.2309.6009.6000.0000.0000.0000.000
202A203THR00.0310.01225.242-0.459-0.4590.0000.0000.0000.000
203A204GLN00.0350.02025.370-0.745-0.7450.0000.0000.0000.000
204A205SER0-0.061-0.05926.080-0.354-0.3540.0000.0000.0000.000
205A206LEU0-0.034-0.01623.406-0.270-0.2700.0000.0000.0000.000
206A207GLY00.0520.02121.486-0.680-0.6800.0000.0000.0000.000
207A208VAL0-0.026-0.01721.486-0.530-0.5300.0000.0000.0000.000
208A209LYS10.8820.94021.23913.97213.9720.0000.0000.0000.000
209A210PHE00.0010.00213.869-0.312-0.3120.0000.0000.0000.000
210A211LEU0-0.0080.00717.863-1.022-1.0220.0000.0000.0000.000
211A212ASP-1-0.800-0.88519.267-13.145-13.1450.0000.0000.0000.000
212A213GLU-1-0.876-0.92417.978-15.373-15.3730.0000.0000.0000.000
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215A216SER0-0.030-0.02618.1170.3680.3680.0000.0000.0000.000
216A217LYS10.9150.96312.49722.27722.2770.0000.0000.0000.000
217A218VAL0-0.0010.01113.266-0.254-0.2540.0000.0000.0000.000
218A219LYS10.9700.99015.38813.43613.4360.0000.0000.0000.000
219A220ARG10.9690.99416.92817.35317.3530.0000.0000.0000.000
220A221GLN00.0010.01412.4640.4340.4340.0000.0000.0000.000
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222A223PHE00.017-0.00717.8570.5260.5260.0000.0000.0000.000
223A224SER0-0.012-0.00818.8030.7940.7940.0000.0000.0000.000
224A225GLY0-0.0150.00019.1840.2950.2950.0000.0000.0000.000
225A226TYR0-0.072-0.05420.0220.1840.1840.0000.0000.0000.000
226A227GLN00.0060.00923.1850.8750.8750.0000.0000.0000.000
227A228SER0-0.095-0.05122.2200.1580.1580.0000.0000.0000.000
228A229ASP-1-0.891-0.94924.345-11.072-11.0720.0000.0000.0000.000
229A230ILE0-0.059-0.02627.6660.5100.5100.0000.0000.0000.000
230A231ASP-1-0.818-0.90329.781-9.354-9.3540.0000.0000.0000.000
231A232THR0-0.056-0.04832.2610.1880.1880.0000.0000.0000.000
232A233HIS00.0260.01634.4680.1410.1410.0000.0000.0000.000
233A234ASN0-0.046-0.03436.5530.3690.3690.0000.0000.0000.000
234A235ARG10.8290.91633.6119.1089.1080.0000.0000.0000.000
235A236ILE-1-0.946-0.93738.471-7.405-7.4050.0000.0000.0000.000