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: Y7YJ2

Calculation Name: 6UI3-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 1,2-ethanediol

Ligand 3-letter code: EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6UI3

Chain ID: A

ChEMBL ID:

UniProt ID:

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 337
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -5637971.654466
FMO2-HF: Nuclear repulsion 5504387.089134
FMO2-HF: Total energy -133584.565332
FMO2-MP2: Total energy -133973.492777


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:4:ASP)


Summations of interaction energy for fragment #1(A:4:ASP)
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.
-10.193-8.5260.013-0.886-0.7940.003
Interaction energy analysis for fragmet #1(A:4:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.095 / q_NPA : -0.065
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].
3A6THR0-0.016-0.0063.742-12.219-10.5520.013-0.886-0.7940.003
4A7HIS10.8530.9266.0885.5935.5930.0000.0000.0000.000
5A8PRO00.0240.0249.8560.0280.0280.0000.0000.0000.000
6A9THR00.030-0.00511.924-0.205-0.2050.0000.0000.0000.000
7A10GLU-1-0.955-0.97114.8981.3801.3800.0000.0000.0000.000
8A11MET0-0.024-0.00416.744-0.090-0.0900.0000.0000.0000.000
9A12ARG10.7960.85219.652-0.836-0.8360.0000.0000.0000.000
10A13GLY0-0.041-0.01722.323-0.015-0.0150.0000.0000.0000.000
11A14LEU0-0.031-0.00723.657-0.013-0.0130.0000.0000.0000.000
12A15SER00.0210.00726.738-0.073-0.0730.0000.0000.0000.000
13A16ALA00.0900.03528.8470.0350.0350.0000.0000.0000.000
14A17MET0-0.005-0.00529.8910.0120.0120.0000.0000.0000.000
15A18ASP-1-0.827-0.90027.6290.5010.5010.0000.0000.0000.000
16A19LEU0-0.029-0.00722.9740.0650.0650.0000.0000.0000.000
17A20VAL00.026-0.00425.7730.0370.0370.0000.0000.0000.000
18A21LYS10.8560.92828.158-0.532-0.5320.0000.0000.0000.000
19A22ASP-1-0.807-0.85621.9191.0151.0150.0000.0000.0000.000
20A23MET00.0020.02823.3690.0710.0710.0000.0000.0000.000
21A24LYS10.8210.91422.028-0.911-0.9110.0000.0000.0000.000
22A25ILE00.0450.03625.989-0.074-0.0740.0000.0000.0000.000
23A26GLY00.0300.00224.5610.0670.0670.0000.0000.0000.000
24A27TRP0-0.041-0.02322.250-0.032-0.0320.0000.0000.0000.000
25A28ASN00.000-0.02025.045-0.076-0.0760.0000.0000.0000.000
26A29LEU0-0.0030.00420.7790.0250.0250.0000.0000.0000.000
27A30GLY00.0360.02124.640-0.077-0.0770.0000.0000.0000.000
28A31ASN0-0.042-0.02927.8460.0030.0030.0000.0000.0000.000
29A32THR00.0010.00623.2250.0010.0010.0000.0000.0000.000
30A33LEU00.0420.03020.253-0.038-0.0380.0000.0000.0000.000
31A34GLU-1-0.732-0.85224.978-0.427-0.4270.0000.0000.0000.000
32A35SER0-0.032-0.02528.1990.0630.0630.0000.0000.0000.000
33A36VAL0-0.028-0.00630.163-0.033-0.0330.0000.0000.0000.000
34A37GLY00.003-0.01030.7450.0190.0190.0000.0000.0000.000
35A38GLY00.0190.01226.619-0.050-0.0500.0000.0000.0000.000
36A39GLU-1-0.769-0.84620.472-1.050-1.0500.0000.0000.0000.000
37A40THR0-0.010-0.00824.1830.0440.0440.0000.0000.0000.000
38A41GLY00.0090.02526.7820.0520.0520.0000.0000.0000.000
39A42TRP0-0.050-0.02829.8830.0460.0460.0000.0000.0000.000
40A43GLY00.0070.00730.5920.0450.0450.0000.0000.0000.000
41A44ASN0-0.024-0.01426.3360.0600.0600.0000.0000.0000.000
42A45PRO0-0.061-0.02723.504-0.065-0.0650.0000.0000.0000.000
43A46VAL00.0090.00118.6510.0050.0050.0000.0000.0000.000
44A47THR00.003-0.02118.0760.1220.1220.0000.0000.0000.000
45A48THR00.003-0.01215.374-0.173-0.1730.0000.0000.0000.000
46A49LYS10.8970.9268.895-2.377-2.3770.0000.0000.0000.000
47A50LYS10.9860.99813.639-0.140-0.1400.0000.0000.0000.000
48A51MET0-0.0310.02515.6230.1310.1310.0000.0000.0000.000
49A52PHE00.0650.02415.3580.0340.0340.0000.0000.0000.000
50A53ASP-1-0.788-0.86713.0951.7781.7780.0000.0000.0000.000
51A54THR0-0.025-0.02315.6670.1240.1240.0000.0000.0000.000
52A55LEU0-0.0060.00419.3600.0190.0190.0000.0000.0000.000
53A56LYS10.9210.95415.201-2.073-2.0730.0000.0000.0000.000
54A57ALA0-0.046-0.02218.3060.0530.0530.0000.0000.0000.000
55A58ALA0-0.022-0.00319.687-0.040-0.0400.0000.0000.0000.000
56A59GLY0-0.004-0.00421.745-0.071-0.0710.0000.0000.0000.000
57A60PHE0-0.044-0.01421.893-0.063-0.0630.0000.0000.0000.000
58A61ASN0-0.055-0.04620.1670.2900.2900.0000.0000.0000.000
59A62THR00.011-0.00320.2730.0080.0080.0000.0000.0000.000
60A63VAL0-0.045-0.02019.884-0.008-0.0080.0000.0000.0000.000
61A64ARG10.7440.86921.9130.1050.1050.0000.0000.0000.000
62A65ILE0-0.015-0.02018.7450.0080.0080.0000.0000.0000.000
63A66PRO0-0.0030.00023.223-0.043-0.0430.0000.0000.0000.000
64A67VAL0-0.038-0.01822.657-0.073-0.0730.0000.0000.0000.000
65A68ARG10.8430.94225.8410.5640.5640.0000.0000.0000.000
66A69TRP0-0.003-0.04921.800-0.133-0.1330.0000.0000.0000.000
67A70ASP-1-0.806-0.90728.050-0.606-0.6060.0000.0000.0000.000
68A71GLU-1-0.867-0.92929.550-0.627-0.6270.0000.0000.0000.000
69A72ASN0-0.058-0.02525.605-0.104-0.1040.0000.0000.0000.000
70A73TYR0-0.033-0.03527.100-0.073-0.0730.0000.0000.0000.000
71A74ILE00.003-0.00326.1650.0140.0140.0000.0000.0000.000
72A75ASP-1-0.831-0.88929.858-0.819-0.8190.0000.0000.0000.000
73A76ALA0-0.035-0.02532.9890.0190.0190.0000.0000.0000.000
74A77ASN0-0.065-0.03233.3690.0830.0830.0000.0000.0000.000
75A78TYR00.017-0.00331.858-0.001-0.0010.0000.0000.0000.000
76A79THR0-0.007-0.00827.069-0.038-0.0380.0000.0000.0000.000
77A80ILE0-0.051-0.03123.6920.0120.0120.0000.0000.0000.000
78A81ASP-1-0.834-0.91322.761-1.642-1.6420.0000.0000.0000.000
79A82PRO0-0.008-0.01919.855-0.074-0.0740.0000.0000.0000.000
80A83ALA00.0030.00418.291-0.244-0.2440.0000.0000.0000.000
81A84TYR0-0.037-0.02118.513-0.131-0.1310.0000.0000.0000.000
82A85MET00.0040.00518.6410.0260.0260.0000.0000.0000.000
83A86ALA00.0190.01314.628-0.053-0.0530.0000.0000.0000.000
84A87ARG10.7710.86314.7211.3181.3180.0000.0000.0000.000
85A88VAL00.0500.01516.4690.0570.0570.0000.0000.0000.000
86A89GLU-1-0.800-0.84612.541-3.259-3.2590.0000.0000.0000.000
87A90THR0-0.071-0.04211.498-0.232-0.2320.0000.0000.0000.000
88A91VAL0-0.022-0.01613.0240.2260.2260.0000.0000.0000.000
89A92VAL00.0230.01514.8620.3290.3290.0000.0000.0000.000
90A93ASN0-0.027-0.02810.0440.5300.5300.0000.0000.0000.000
91A94TYR0-0.0200.00711.5940.5050.5050.0000.0000.0000.000
92A95ALA00.0410.02713.4040.4960.4960.0000.0000.0000.000
93A96LEU00.0120.01112.6350.4040.4040.0000.0000.0000.000
94A97ALA0-0.018-0.0108.2830.6610.6610.0000.0000.0000.000
95A98ASN0-0.103-0.0699.5281.6201.6200.0000.0000.0000.000
96A99ASP-1-0.875-0.92112.2091.9081.9080.0000.0000.0000.000
97A100MET0-0.055-0.00413.943-0.178-0.1780.0000.0000.0000.000
98A101TYR0-0.007-0.03016.666-0.147-0.1470.0000.0000.0000.000
99A102ALA0-0.015-0.00317.819-0.038-0.0380.0000.0000.0000.000
100A103ILE00.0160.00619.858-0.019-0.0190.0000.0000.0000.000
101A104VAL00.0290.01920.157-0.043-0.0430.0000.0000.0000.000
102A105ASN00.029-0.00423.288-0.007-0.0070.0000.0000.0000.000
103A106ILE00.0100.03526.499-0.079-0.0790.0000.0000.0000.000
104A107HIS00.0380.00328.8350.0570.0570.0000.0000.0000.000
105A108HIS0-0.017-0.01530.679-0.035-0.0350.0000.0000.0000.000
106A109ASN00.0740.04830.795-0.020-0.0200.0000.0000.0000.000
107A110LYS10.9360.96633.6500.4100.4100.0000.0000.0000.000
108A111PHE00.0310.00333.0660.0380.0380.0000.0000.0000.000
109A112GLN00.0220.01934.5790.0260.0260.0000.0000.0000.000
110A113GLY00.0380.02637.3760.0290.0290.0000.0000.0000.000
111A114GLN0-0.059-0.02640.602-0.003-0.0030.0000.0000.0000.000
112A115PHE00.0420.00737.148-0.003-0.0030.0000.0000.0000.000
113A116ASP-1-0.785-0.86142.875-0.220-0.2200.0000.0000.0000.000
114A117GLU-1-0.755-0.90045.812-0.217-0.2170.0000.0000.0000.000
115A118ALA0-0.070-0.01647.902-0.010-0.0100.0000.0000.0000.000
116A119HIS10.8350.88843.2590.2600.2600.0000.0000.0000.000
117A120LYS10.8070.89543.1740.1860.1860.0000.0000.0000.000
118A121ALA00.0240.00141.967-0.014-0.0140.0000.0000.0000.000
119A122ALA0-0.0020.00240.905-0.021-0.0210.0000.0000.0000.000
120A123ILE00.0170.00538.395-0.031-0.0310.0000.0000.0000.000
121A124ILE00.0020.00837.031-0.022-0.0220.0000.0000.0000.000
122A125ASN0-0.0210.01436.459-0.027-0.0270.0000.0000.0000.000
123A126GLU-1-0.763-0.86633.656-0.575-0.5750.0000.0000.0000.000
124A127GLY00.0160.00832.769-0.044-0.0440.0000.0000.0000.000
125A128THR0-0.012-0.02731.646-0.023-0.0230.0000.0000.0000.000
126A129ILE0-0.0060.01530.836-0.042-0.0420.0000.0000.0000.000
127A130VAL00.0120.02327.722-0.079-0.0790.0000.0000.0000.000
128A131TRP0-0.020-0.03324.983-0.087-0.0870.0000.0000.0000.000
129A132THR0-0.023-0.02526.599-0.029-0.0290.0000.0000.0000.000
130A133GLN0-0.047-0.03024.546-0.147-0.1470.0000.0000.0000.000
131A134ILE00.0010.00422.243-0.140-0.1400.0000.0000.0000.000
132A135ALA00.000-0.00221.638-0.092-0.0920.0000.0000.0000.000
133A136ASN00.000-0.01821.818-0.038-0.0380.0000.0000.0000.000
134A137HIS10.7940.89715.4982.1942.1940.0000.0000.0000.000
135A138PHE0-0.005-0.00615.728-0.275-0.2750.0000.0000.0000.000
136A139LYS10.8800.94218.4831.2561.2560.0000.0000.0000.000
137A140ASP-1-0.790-0.88314.138-1.869-1.8690.0000.0000.0000.000
138A141TYR0-0.034-0.05212.4990.1700.1700.0000.0000.0000.000
139A142SER00.0220.01915.2850.0270.0270.0000.0000.0000.000
140A143ASP-1-0.791-0.88117.2730.4860.4860.0000.0000.0000.000
141A144LYS10.8710.92815.812-1.477-1.4770.0000.0000.0000.000
142A145LEU0-0.059-0.00617.497-0.043-0.0430.0000.0000.0000.000
143A146ILE00.0020.00419.822-0.007-0.0070.0000.0000.0000.000
144A147PHE00.0100.00021.327-0.087-0.0870.0000.0000.0000.000
145A148ASP-1-0.772-0.89525.696-0.147-0.1470.0000.0000.0000.000
146A149THR00.021-0.00128.803-0.044-0.0440.0000.0000.0000.000
147A150ILE0-0.053-0.01231.228-0.045-0.0450.0000.0000.0000.000
148A151ASN00.0330.02931.2240.0650.0650.0000.0000.0000.000
149A152GLN00.0030.01332.8910.0560.0560.0000.0000.0000.000
150A153PRO0-0.0360.00536.281-0.009-0.0090.0000.0000.0000.000
151A154ARG10.8370.87037.9530.2540.2540.0000.0000.0000.000
152A155HIS10.7910.89342.1900.1830.1830.0000.0000.0000.000
153A156GLU-1-0.882-0.96344.167-0.195-0.1950.0000.0000.0000.000
154A157GLU-1-0.792-0.86141.821-0.220-0.2200.0000.0000.0000.000
155A158ASP-1-0.818-0.89545.250-0.110-0.1100.0000.0000.0000.000
156A159TRP00.024-0.00939.0900.0030.0030.0000.0000.0000.000
157A160VAL0-0.075-0.02045.9960.0170.0170.0000.0000.0000.000
158A161GLY00.014-0.01147.5580.0060.0060.0000.0000.0000.000
159A162THR00.0110.00048.3800.0090.0090.0000.0000.0000.000
160A163SER00.043-0.00148.817-0.004-0.0040.0000.0000.0000.000
161A164GLU-1-0.846-0.90449.447-0.178-0.1780.0000.0000.0000.000
162A165TYR0-0.006-0.01045.675-0.007-0.0070.0000.0000.0000.000
163A166PHE0-0.029-0.01144.625-0.008-0.0080.0000.0000.0000.000
164A167ASN0-0.038-0.01144.5180.0040.0040.0000.0000.0000.000
165A168VAL0-0.0080.00442.731-0.010-0.0100.0000.0000.0000.000
166A169LEU0-0.0140.00137.935-0.021-0.0210.0000.0000.0000.000
167A170ASN00.0120.00540.059-0.008-0.0080.0000.0000.0000.000
168A171GLU-1-0.834-0.90341.049-0.209-0.2090.0000.0000.0000.000
169A172TYR0-0.012-0.02633.049-0.023-0.0230.0000.0000.0000.000
170A173ASN00.0730.03135.938-0.045-0.0450.0000.0000.0000.000
171A174ALA0-0.004-0.00236.225-0.006-0.0060.0000.0000.0000.000
172A175LYS10.8560.93136.9600.2520.2520.0000.0000.0000.000
173A176ILE00.0300.01231.241-0.020-0.0200.0000.0000.0000.000
174A177VAL00.0220.02031.687-0.028-0.0280.0000.0000.0000.000
175A178PRO0-0.004-0.01031.576-0.018-0.0180.0000.0000.0000.000
176A179VAL0-0.0090.00430.125-0.021-0.0210.0000.0000.0000.000
177A180ILE00.0200.01226.245-0.051-0.0510.0000.0000.0000.000
178A181ARG10.7110.81927.4000.1360.1360.0000.0000.0000.000
179A182ALA0-0.006-0.00228.718-0.011-0.0110.0000.0000.0000.000
180A183THR0-0.055-0.01924.860-0.044-0.0440.0000.0000.0000.000
181A184GLY00.0020.00824.946-0.070-0.0700.0000.0000.0000.000
182A185GLU-1-0.866-0.94719.916-1.039-1.0390.0000.0000.0000.000
183A186ASN0-0.007-0.00718.4650.1860.1860.0000.0000.0000.000
184A187ASN00.0050.00422.2770.1150.1150.0000.0000.0000.000
185A188ALA0-0.025-0.00924.4720.0610.0610.0000.0000.0000.000
186A189LYS10.9100.94924.9570.0130.0130.0000.0000.0000.000
187A190ARG10.7600.88619.5050.5490.5490.0000.0000.0000.000
188A191LEU00.0250.03825.350-0.013-0.0130.0000.0000.0000.000
189A192ILE0-0.015-0.01426.648-0.058-0.0580.0000.0000.0000.000
190A193MET0-0.031-0.01028.4260.0460.0460.0000.0000.0000.000
191A194VAL00.014-0.00131.047-0.051-0.0510.0000.0000.0000.000
192A195PRO0-0.0030.01734.0770.0390.0390.0000.0000.0000.000
193A196THR00.023-0.00836.501-0.011-0.0110.0000.0000.0000.000
194A197TYR00.029-0.00339.491-0.023-0.0230.0000.0000.0000.000
195A198CYS0-0.078-0.03539.9380.0180.0180.0000.0000.0000.000
196A199ALA00.0290.02636.2970.0030.0030.0000.0000.0000.000
197A200SER0-0.0020.00238.3120.0310.0310.0000.0000.0000.000
198A201SER00.0460.02440.883-0.003-0.0030.0000.0000.0000.000
199A202ASP-1-0.830-0.89242.551-0.021-0.0210.0000.0000.0000.000
200A203TYR00.010-0.01346.284-0.011-0.0110.0000.0000.0000.000
201A204PRO00.002-0.00948.164-0.003-0.0030.0000.0000.0000.000
202A205LYS10.8000.89543.8300.0630.0630.0000.0000.0000.000
203A206VAL0-0.040-0.01142.614-0.006-0.0060.0000.0000.0000.000
204A207ALA0-0.024-0.02244.7920.0010.0010.0000.0000.0000.000
205A208GLY0-0.0030.00947.364-0.003-0.0030.0000.0000.0000.000
206A209MET0-0.052-0.00338.402-0.019-0.0190.0000.0000.0000.000
207A210VAL0-0.032-0.01943.0440.0140.0140.0000.0000.0000.000
208A211VAL00.0050.00337.680-0.018-0.0180.0000.0000.0000.000
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