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: LRJR9

Calculation Name: 6T5K-C-Xray547

Preferred Name:

Target Type:

Ligand Name: 1,2-ethanediol

Ligand 3-letter code: EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6T5K

Chain ID: C

ChEMBL ID:

UniProt ID: L0FY79

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 224
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2776190.835993
FMO2-HF: Nuclear repulsion 2690568.384877
FMO2-HF: Total energy -85622.451115
FMO2-MP2: Total energy -85875.944015


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:29:SER)


Summations of interaction energy for fragment #1(A:29: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.
-75.838-74.3-0.003-0.758-0.776-0.002
Interaction energy analysis for fragmet #1(A:29:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.854 / q_NPA : 0.904
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].
3A31PHE00.0280.0283.585-8.119-6.581-0.003-0.758-0.776-0.002
4A32THR0-0.040-0.0216.3230.1170.1170.0000.0000.0000.000
5A33GLU-1-0.865-0.9208.267-22.769-22.7690.0000.0000.0000.000
6A34LYS10.9060.96411.67919.59319.5930.0000.0000.0000.000
7A35GLU-1-0.840-0.89214.656-14.690-14.6900.0000.0000.0000.000
8A36VAL0-0.048-0.03817.995-0.168-0.1680.0000.0000.0000.000
9A37TYR0-0.031-0.03420.5820.5670.5670.0000.0000.0000.000
10A38SER0-0.027-0.04023.329-0.325-0.3250.0000.0000.0000.000
11A39SER0-0.030-0.02325.5910.3080.3080.0000.0000.0000.000
12A40ASP-1-0.908-0.95528.808-9.883-9.8830.0000.0000.0000.000
13A41LYS10.7840.89231.2519.6139.6130.0000.0000.0000.000
14A42LEU0-0.014-0.00326.675-0.162-0.1620.0000.0000.0000.000
15A43ILE0-0.017-0.00421.794-0.158-0.1580.0000.0000.0000.000
16A44ILE00.0140.00320.582-0.151-0.1510.0000.0000.0000.000
17A45LYS10.8660.92316.46516.56616.5660.0000.0000.0000.000
18A46GLN00.0010.00813.5620.4670.4670.0000.0000.0000.000
19A48VAL0-0.010-0.01512.412-1.057-1.0570.0000.0000.0000.000
20A49SER0-0.071-0.05610.041-2.639-2.6390.0000.0000.0000.000
21A50PRO0-0.041-0.0309.0851.4161.4160.0000.0000.0000.000
22A51HIS0-0.017-0.02512.0072.1422.1420.0000.0000.0000.000
23A52THR0-0.034-0.02213.6311.5621.5620.0000.0000.0000.000
24A53TYR00.0460.01114.914-1.371-1.3710.0000.0000.0000.000
25A54VAL00.0000.00516.7970.5710.5710.0000.0000.0000.000
26A55HIS0-0.043-0.00719.353-0.043-0.0430.0000.0000.0000.000
27A56VAL00.0230.00221.898-0.070-0.0700.0000.0000.0000.000
28A57SER00.0520.03824.6800.4020.4020.0000.0000.0000.000
29A58PHE0-0.043-0.03525.935-0.253-0.2530.0000.0000.0000.000
30A59LEU00.0140.01230.7330.3060.3060.0000.0000.0000.000
31A60ASP-1-0.889-0.94833.604-9.373-9.3730.0000.0000.0000.000
32A61THR0-0.068-0.03534.6500.1570.1570.0000.0000.0000.000
33A62ASP-1-0.879-0.95137.482-8.045-8.0450.0000.0000.0000.000
34A63THR0-0.026-0.01037.3390.1190.1190.0000.0000.0000.000
35A64PHE0-0.051-0.03532.833-0.139-0.1390.0000.0000.0000.000
36A65GLY00.0260.03533.267-0.284-0.2840.0000.0000.0000.000
37A66LYS10.9580.98130.81510.18410.1840.0000.0000.0000.000
38A67VAL0-0.031-0.01429.358-0.434-0.4340.0000.0000.0000.000
39A68ALA00.0290.01825.4170.0980.0980.0000.0000.0000.000
40A69CYS0-0.063-0.01926.9930.0450.0450.0000.0000.0000.000
41A70ASN0-0.035-0.03021.7560.2130.2130.0000.0000.0000.000
42A71GLY00.0690.02623.8150.4110.4110.0000.0000.0000.000
43A72MET0-0.069-0.01618.816-1.089-1.0890.0000.0000.0000.000
44A73ILE0-0.009-0.00320.2670.8660.8660.0000.0000.0000.000
45A74VAL0-0.012-0.00318.249-1.081-1.0810.0000.0000.0000.000
46A75ILE00.008-0.00718.7490.9250.9250.0000.0000.0000.000
47A76SER00.007-0.03718.422-1.505-1.5050.0000.0000.0000.000
48A77ASP-1-0.863-0.88220.162-14.036-14.0360.0000.0000.0000.000
49A78GLY00.0410.03022.4460.5670.5670.0000.0000.0000.000
50A79GLU-1-0.818-0.88424.082-11.013-11.0130.0000.0000.0000.000
51A80ALA00.025-0.00723.234-0.756-0.7560.0000.0000.0000.000
52A81VAL0-0.049-0.01923.5790.6330.6330.0000.0000.0000.000
53A82VAL00.0040.01223.655-0.643-0.6430.0000.0000.0000.000
54A83PHE0-0.014-0.01823.4270.3830.3830.0000.0000.0000.000
55A84ASP-1-0.688-0.83825.356-11.973-11.9730.0000.0000.0000.000
56A85THR0-0.046-0.02927.737-0.110-0.1100.0000.0000.0000.000
57A86PRO00.0050.00928.5030.0470.0470.0000.0000.0000.000
58A87SER00.0080.00830.5510.2100.2100.0000.0000.0000.000
59A88THR0-0.018-0.01933.6640.4150.4150.0000.0000.0000.000
60A89SER00.0640.01734.715-0.201-0.2010.0000.0000.0000.000
61A90ASN0-0.0310.00236.3460.0200.0200.0000.0000.0000.000
62A91GLU-1-0.738-0.85131.253-9.914-9.9140.0000.0000.0000.000
63A92THR00.017-0.00531.145-0.446-0.4460.0000.0000.0000.000
64A93SER0-0.029-0.03032.126-0.069-0.0690.0000.0000.0000.000
65A94GLU-1-0.829-0.85030.343-10.410-10.4100.0000.0000.0000.000
66A95LEU0-0.005-0.01125.599-0.240-0.2400.0000.0000.0000.000
67A96LEU0-0.058-0.03328.349-0.292-0.2920.0000.0000.0000.000
68A97SER0-0.002-0.00430.576-0.114-0.1140.0000.0000.0000.000
69A98PHE00.0220.00322.267-0.168-0.1680.0000.0000.0000.000
70A99LEU0-0.015-0.02024.310-0.300-0.3000.0000.0000.0000.000
71A100GLU-1-0.810-0.86727.557-9.408-9.4080.0000.0000.0000.000
72A102GLU-1-0.874-0.92629.028-9.742-9.7420.0000.0000.0000.000
73A103GLU-1-1.000-1.00423.111-13.431-13.4310.0000.0000.0000.000
74A104LYS10.7990.90426.55610.59510.5950.0000.0000.0000.000
75A106LEU0-0.0170.00423.370-0.084-0.0840.0000.0000.0000.000
76A107GLN0-0.058-0.02827.3650.6280.6280.0000.0000.0000.000
77A109VAL00.012-0.00427.811-0.375-0.3750.0000.0000.0000.000
78A110ASN0-0.038-0.03427.1990.6560.6560.0000.0000.0000.000
79A111ALA0-0.048-0.03328.8700.3830.3830.0000.0000.0000.000
80A112VAL0-0.0070.01628.617-0.366-0.3660.0000.0000.0000.000
81A113VAL0-0.015-0.01526.9720.4040.4040.0000.0000.0000.000
82A114ALA00.0090.01428.721-0.252-0.2520.0000.0000.0000.000
83A115THR0-0.030-0.05325.5830.1950.1950.0000.0000.0000.000
84A116HIS00.026-0.00728.9790.2160.2160.0000.0000.0000.000
85A117PHE0-0.008-0.01332.251-0.042-0.0420.0000.0000.0000.000
86A118HIS10.8360.91033.1069.4819.4810.0000.0000.0000.000
87A119LEU00.0810.02634.161-0.181-0.1810.0000.0000.0000.000
88A120ASP-1-0.834-0.91830.498-10.449-10.4490.0000.0000.0000.000
89A121CYS0-0.067-0.02928.943-0.400-0.4000.0000.0000.0000.000
90A122LEU00.003-0.00331.096-0.105-0.1050.0000.0000.0000.000
91A123GLY00.0280.01634.2000.2650.2650.0000.0000.0000.000
92A124GLY00.0080.00334.4920.2510.2510.0000.0000.0000.000
93A125LEU0-0.046-0.03433.348-0.009-0.0090.0000.0000.0000.000
94A126GLU-1-0.882-0.94035.920-7.841-7.8410.0000.0000.0000.000
95A127ALA00.0150.01735.1330.0940.0940.0000.0000.0000.000
96A128PHE00.0490.01229.547-0.065-0.0650.0000.0000.0000.000
97A129HIS10.8340.91535.2878.4588.4580.0000.0000.0000.000
98A130ALA00.0340.02638.7050.1120.1120.0000.0000.0000.000
99A131ARG10.7570.84834.6129.3059.3050.0000.0000.0000.000
100A133ASN0-0.074-0.03737.5020.0400.0400.0000.0000.0000.000
101A134ILE00.0120.02831.742-0.067-0.0670.0000.0000.0000.000
102A135PRO0-0.072-0.02133.1630.1270.1270.0000.0000.0000.000
103A136SER00.0340.00433.130-0.260-0.2600.0000.0000.0000.000
104A137TYR0-0.008-0.02631.1650.4360.4360.0000.0000.0000.000
105A138ALA00.0550.03331.750-0.235-0.2350.0000.0000.0000.000
106A139PHE00.0460.02932.2700.1760.1760.0000.0000.0000.000
107A140LYS10.8840.92533.7198.4398.4390.0000.0000.0000.000
108A141ASN00.008-0.00137.1430.2000.2000.0000.0000.0000.000
109A142THR0-0.003-0.01834.0440.0770.0770.0000.0000.0000.000
110A143LEU0-0.051-0.01036.8060.0930.0930.0000.0000.0000.000
111A144SER00.0330.01839.5030.1070.1070.0000.0000.0000.000
112A145LEU0-0.017-0.00337.8840.1400.1400.0000.0000.0000.000
113A146ALA00.0200.01738.4970.0690.0690.0000.0000.0000.000
114A147SER00.0000.00140.4210.1800.1800.0000.0000.0000.000
115A148GLN0-0.054-0.04143.8490.0380.0380.0000.0000.0000.000
116A149HIS10.8020.89541.4907.8437.8430.0000.0000.0000.000
117A150ASP-1-0.924-0.93744.042-6.936-6.9360.0000.0000.0000.000
118A165PHE0-0.024-0.01039.100-0.135-0.1350.0000.0000.0000.000
119A166PRO00.003-0.00638.3600.0880.0880.0000.0000.0000.000
120A167GLN00.0490.02638.531-0.077-0.0770.0000.0000.0000.000
121A168PRO0-0.009-0.01135.237-0.004-0.0040.0000.0000.0000.000
122A169GLN00.0210.02237.2580.0010.0010.0000.0000.0000.000
123A170LYS10.9010.95835.7038.9308.9300.0000.0000.0000.000
124A171GLY00.0550.03235.629-0.211-0.2110.0000.0000.0000.000
125A172PHE0-0.023-0.00729.2070.1520.1520.0000.0000.0000.000
126A1173SER00.018-0.00634.7180.1760.1760.0000.0000.0000.000
127A173ASP-1-0.885-0.94432.153-9.307-9.3070.0000.0000.0000.000
128A174GLU-1-0.884-0.92725.200-12.445-12.4450.0000.0000.0000.000
129A175LEU0-0.0060.02228.5840.3340.3340.0000.0000.0000.000
130A176THR0-0.008-0.01025.630-0.553-0.5530.0000.0000.0000.000
131A177LEU0-0.012-0.00726.0330.4910.4910.0000.0000.0000.000
132A178LYS10.9170.96025.25711.01811.0180.0000.0000.0000.000
133A179VAL00.0030.00121.5690.1690.1690.0000.0000.0000.000
134A180GLY00.0600.04522.377-0.606-0.6060.0000.0000.0000.000
135A181THR0-0.145-0.11521.0740.3920.3920.0000.0000.0000.000
136A182LYS10.8380.92716.10917.73017.7300.0000.0000.0000.000
137A186ALA0-0.011-0.00921.1540.7400.7400.0000.0000.0000.000
138A187VAL0-0.018-0.00320.448-0.877-0.8770.0000.0000.0000.000
139A188PHE0-0.011-0.00321.0510.6240.6240.0000.0000.0000.000
140A189VAL00.0200.01123.238-0.419-0.4190.0000.0000.0000.000
141A190HIS10.8410.90124.79612.06712.0670.0000.0000.0000.000
142A191TYR0-0.005-0.00226.619-0.186-0.1860.0000.0000.0000.000
143A192PHE0-0.005-0.01823.5730.0110.0110.0000.0000.0000.000
144A193GLY00.0020.01928.6800.1410.1410.0000.0000.0000.000
145A194GLU-1-0.865-0.91831.018-8.665-8.6650.0000.0000.0000.000
146A195GLY00.014-0.00130.436-0.290-0.2900.0000.0000.0000.000
147A196HIS0-0.0180.00629.8110.3290.3290.0000.0000.0000.000
148A197THR0-0.032-0.03731.7410.1470.1470.0000.0000.0000.000
149A198GLN00.0850.02933.380-0.178-0.1780.0000.0000.0000.000
150A199ASP-1-0.763-0.85234.203-9.298-9.2980.0000.0000.0000.000
151A200ASN0-0.0140.00328.966-0.163-0.1630.0000.0000.0000.000
152A201VAL0-0.039-0.00927.813-0.032-0.0320.0000.0000.0000.000
153A202ILE0-0.046-0.00921.691-0.184-0.1840.0000.0000.0000.000
154A203GLY00.0740.02222.3300.4710.4710.0000.0000.0000.000
155A204TYR0-0.056-0.05215.349-0.467-0.4670.0000.0000.0000.000
156A205PHE00.0670.02114.5340.6290.6290.0000.0000.0000.000
157A209PRO00.0230.02015.214-1.339-1.3390.0000.0000.0000.000
158A210ASP-1-0.850-0.90813.744-19.379-19.3790.0000.0000.0000.000
159A211ASP-1-0.735-0.83810.765-26.598-26.5980.0000.0000.0000.000
160A215GLN0-0.052-0.00510.107-2.164-2.1640.0000.0000.0000.000
161A216VAL00.0390.01911.660-1.308-1.3080.0000.0000.0000.000
162A217LEU00.002-0.00614.0311.3281.3280.0000.0000.0000.000
163A218PHE00.0040.00717.198-0.587-0.5870.0000.0000.0000.000
164A219GLY00.024-0.00820.0160.6350.6350.0000.0000.0000.000
165A220GLY00.0970.05421.7650.6160.6160.0000.0000.0000.000
166A221CYS0-0.078-0.03724.384-0.465-0.4650.0000.0000.0000.000
167A222LEU00.0070.02525.5660.2280.2280.0000.0000.0000.000
168A223ILE0-0.045-0.01019.930-0.070-0.0700.0000.0000.0000.000
169A224LYS10.8600.94922.99211.53411.5340.0000.0000.0000.000
170A225ALA00.0690.03319.744-0.643-0.6430.0000.0000.0000.000
171A226ASN0-0.002-0.02217.0891.2741.2740.0000.0000.0000.000
172A227GLY00.0140.01219.825-0.083-0.0830.0000.0000.0000.000
173A228ALA0-0.0260.00623.0540.5230.5230.0000.0000.0000.000
174A229GLY00.0290.01725.0580.1560.1560.0000.0000.0000.000
175A231LYS10.9320.97028.1329.5909.5900.0000.0000.0000.000
176A232GLY0-0.013-0.00230.399-0.133-0.1330.0000.0000.0000.000
177A233ASN00.0560.02131.7990.3620.3620.0000.0000.0000.000
178A234LEU0-0.001-0.02132.765-0.271-0.2710.0000.0000.0000.000
179A235GLU-1-0.953-0.96235.963-7.989-7.9890.0000.0000.0000.000
180A236ASP-1-0.868-0.91536.889-8.085-8.0850.0000.0000.0000.000
181A237ALA0-0.058-0.02634.261-0.114-0.1140.0000.0000.0000.000
182A238ASN0-0.020-0.00834.9430.1540.1540.0000.0000.0000.000
183A239VAL0-0.004-0.02833.478-0.366-0.3660.0000.0000.0000.000
184A240GLU-1-0.874-0.93933.407-8.608-8.6080.0000.0000.0000.000
185A241ALA0-0.040-0.01933.369-0.141-0.1410.0000.0000.0000.000
186A242TRP00.0090.01726.864-0.169-0.1690.0000.0000.0000.000
187A243PRO00.0080.01427.779-0.532-0.5320.0000.0000.0000.000
188A244VAL00.0270.00727.448-0.393-0.3930.0000.0000.0000.000
189A245THR0-0.037-0.03827.131-0.270-0.2700.0000.0000.0000.000
190A246VAL00.0170.00122.575-0.431-0.4310.0000.0000.0000.000
191A247ASN0-0.029-0.00722.993-0.496-0.4960.0000.0000.0000.000
192A248LYS10.8630.92323.5959.9499.9490.0000.0000.0000.000
193A249ILE00.0070.01320.280-0.312-0.3120.0000.0000.0000.000
194A250SER0-0.043-0.04119.101-0.902-0.9020.0000.0000.0000.000
195A251THR0-0.072-0.04219.092-0.596-0.5960.0000.0000.0000.000
196A252ALA0-0.045-0.01121.137-0.055-0.0550.0000.0000.0000.000
197A253TYR00.0000.00116.731-0.119-0.1190.0000.0000.0000.000
198A254PRO00.0480.02515.723-1.167-1.1670.0000.0000.0000.000
199A255ASN0-0.056-0.04412.194-1.596-1.5960.0000.0000.0000.000
200A256LEU0-0.0230.00410.962-1.841-1.8410.0000.0000.0000.000
201A257ARG10.8210.9115.71130.70030.7000.0000.0000.0000.000
202A258LEU0-0.0310.0029.112-1.648-1.6480.0000.0000.0000.000
203A259VAL0-0.013-0.00611.6771.5341.5340.0000.0000.0000.000
204A260ILE00.0540.01415.371-0.268-0.2680.0000.0000.0000.000
205A261PRO0-0.0100.01517.9610.6650.6650.0000.0000.0000.000
206A262GLY00.0560.01321.247-0.119-0.1190.0000.0000.0000.000
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