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: RQ4Q8

Calculation Name: 1EB6-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1EB6

Chain ID: A

ChEMBL ID:

UniProt ID: P46076

Base Structure: X-ray

Registration Date: 2025-09-02

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 174
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1794768.111503
FMO2-HF: Nuclear repulsion 1726921.448045
FMO2-HF: Total energy -67846.663458
FMO2-MP2: Total energy -68042.238158


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:THR)


Summations of interaction energy for fragment #1(A:1:THR)
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.
-372.118-366.56356.343-28.28-33.617-0.239
Interaction energy analysis for fragmet #1(A:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.725 / q_NPA : 0.843
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].
3A3VAL00.0120.0032.3386.4767.9861.263-0.748-2.0250.000
4A4THR00.0060.0033.9623.7343.8890.004-0.039-0.1200.000
14A14LEU00.0390.0304.574-0.515-0.423-0.001-0.004-0.0860.000
18A18LEU00.0010.0052.584-0.789-0.1500.605-0.210-1.034-0.001
65A65GLU-1-0.765-0.8382.284-111.793-109.0906.826-4.615-4.914-0.040
66A66ALA00.008-0.0022.066-35.350-34.6565.583-3.216-3.061-0.039
67A67GLY0-0.026-0.0104.5690.4040.514-0.001-0.014-0.0950.000
68A68SER0-0.067-0.0392.413-7.163-5.9162.316-1.591-1.972-0.016
69A69THR00.0320.0141.881-29.182-29.4788.101-4.112-3.693-0.047
70A70SER0-0.021-0.0184.2103.8364.117-0.001-0.063-0.2180.000
71A71GLY0-0.010-0.0013.24212.03412.7110.002-0.262-0.4180.000
72A72GLY0-0.0270.0051.873-35.382-38.3869.079-2.921-3.153-0.045
73A73SER0-0.052-0.0403.6947.3937.4930.000-0.012-0.0880.000
74A74THR0-0.046-0.0361.718-1.914-6.97114.786-5.662-4.067-0.046
75A75THR0-0.044-0.0082.443-10.082-8.3673.355-2.241-2.829-0.016
76A76TYR00.012-0.0132.400-0.6671.3583.378-1.713-3.6900.011
77A77HIS10.7740.8493.96524.78025.0020.014-0.095-0.1400.001
98A99GLU-1-0.708-0.7885.185-29.115-29.061-0.001-0.001-0.0510.000
99A100ILE00.0290.0194.1652.0752.201-0.001-0.010-0.1150.000
128A130PHE0-0.004-0.0072.443-3.276-1.7141.036-0.751-1.848-0.001
5A5ASP-1-0.847-0.9117.513-21.694-21.6940.0000.0000.0000.000
6A6CYS0-0.0130.0177.6630.2550.2550.0000.0000.0000.000
7A7LYS10.9580.94910.99717.74317.7430.0000.0000.0000.000
8A8GLY00.0110.01214.5400.2050.2050.0000.0000.0000.000
9A9ASP-1-0.854-0.92514.166-17.441-17.4410.0000.0000.0000.000
10A10ALA00.0430.03412.617-0.459-0.4590.0000.0000.0000.000
11A11GLU-1-0.897-0.9579.016-24.650-24.6500.0000.0000.0000.000
12A12SER0-0.006-0.0079.684-2.395-2.3950.0000.0000.0000.000
13A13SER0-0.050-0.00511.530-0.387-0.3870.0000.0000.0000.000
15A15THR0-0.014-0.0326.675-2.122-2.1220.0000.0000.0000.000
16A16THR0-0.042-0.0227.875-0.763-0.7630.0000.0000.0000.000
17A17ALA00.0030.0018.2780.0010.0010.0000.0000.0000.000
19A19SER0-0.020-0.0226.412-0.324-0.3240.0000.0000.0000.000
20A20ASN0-0.056-0.0319.1021.7111.7110.0000.0000.0000.000
21A21ALA00.0280.0217.9271.2851.2850.0000.0000.0000.000
22A22ALA00.0240.0108.1811.0811.0810.0000.0000.0000.000
23A23LYS10.9010.9579.93822.50922.5090.0000.0000.0000.000
24A24LEU00.0310.01413.2461.0131.0130.0000.0000.0000.000
25A25ALA00.0330.01611.2231.2391.2390.0000.0000.0000.000
26A26ASN0-0.019-0.01211.8791.7451.7450.0000.0000.0000.000
27A27GLN0-0.019-0.01314.6181.5221.5220.0000.0000.0000.000
28A28ALA00.0240.01516.3901.0301.0300.0000.0000.0000.000
29A29ALA0-0.006-0.00515.5200.7890.7890.0000.0000.0000.000
30A30GLU-1-0.933-0.96117.599-14.299-14.2990.0000.0000.0000.000
31A31ALA0-0.017-0.00820.2690.9060.9060.0000.0000.0000.000
32A32ALA00.0060.01320.2190.6510.6510.0000.0000.0000.000
33A33GLU-1-0.810-0.88018.479-16.299-16.2990.0000.0000.0000.000
34A34SER0-0.114-0.06022.9210.6920.6920.0000.0000.0000.000
35A35GLY00.0110.02024.8120.4520.4520.0000.0000.0000.000
36A36ASP-1-0.837-0.90726.312-10.188-10.1880.0000.0000.0000.000
37A37GLU-1-0.926-0.96027.572-10.364-10.3640.0000.0000.0000.000
38A38SER0-0.053-0.04229.316-0.090-0.0900.0000.0000.0000.000
39A39LYS10.7890.85525.44911.22611.2260.0000.0000.0000.000
40A40PHE00.0270.02021.942-0.476-0.4760.0000.0000.0000.000
41A41GLU-1-0.943-0.97725.649-10.049-10.0490.0000.0000.0000.000
42A42GLU-1-0.799-0.86427.208-11.204-11.2040.0000.0000.0000.000
43A43TYR0-0.059-0.03922.448-0.151-0.1510.0000.0000.0000.000
44A44PHE00.017-0.00818.863-0.320-0.3200.0000.0000.0000.000
45A45LYS10.7690.87924.71210.78810.7880.0000.0000.0000.000
46A46THR0-0.024-0.03227.2490.5250.5250.0000.0000.0000.000
47A47THR00.0370.02328.211-0.382-0.3820.0000.0000.0000.000
48A48ASP-1-0.826-0.86128.097-11.638-11.6380.0000.0000.0000.000
49A49GLN00.0590.00825.925-0.755-0.7550.0000.0000.0000.000
50A50GLN0-0.0440.00323.204-0.099-0.0990.0000.0000.0000.000
51A51THR0-0.003-0.03823.579-0.788-0.7880.0000.0000.0000.000
52A52ARG10.8290.90822.33411.34311.3430.0000.0000.0000.000
53A53THR0-0.013-0.01421.184-0.716-0.7160.0000.0000.0000.000
54A54THR0-0.018-0.01019.260-0.557-0.5570.0000.0000.0000.000
55A55VAL0-0.0100.00517.685-1.165-1.1650.0000.0000.0000.000
56A56ALA00.0190.01016.545-1.333-1.3330.0000.0000.0000.000
57A57GLU-1-0.915-0.94015.419-18.398-18.3980.0000.0000.0000.000
58A58ARG10.8870.94613.05917.14417.1440.0000.0000.0000.000
59A59LEU00.0010.00511.629-2.721-2.7210.0000.0000.0000.000
60A60ARG10.7690.83111.31516.71716.7170.0000.0000.0000.000
61A61ALA0-0.063-0.0179.486-2.017-2.0170.0000.0000.0000.000
62A62VAL00.0400.0067.426-5.553-5.5530.0000.0000.0000.000
63A63ALA0-0.011-0.0066.693-5.360-5.3600.0000.0000.0000.000
64A64LYS10.8970.9476.72125.70225.7020.0000.0000.0000.000
78A79ASN0-0.0020.0148.8151.6751.6750.0000.0000.0000.000
79A80ASP-1-0.669-0.82811.689-18.055-18.0550.0000.0000.0000.000
80A81PRO0-0.069-0.02111.2750.9190.9190.0000.0000.0000.000
81A82TYR0-0.148-0.11111.3541.0471.0470.0000.0000.0000.000
82A83GLY0-0.0270.00316.3880.8450.8450.0000.0000.0000.000
83A84TYR0-0.064-0.04914.3320.8550.8550.0000.0000.0000.000
84A85CYS0-0.049-0.00610.5310.1440.1440.0000.0000.0000.000
85A86GLU-1-0.914-0.94117.551-12.231-12.2310.0000.0000.0000.000
86A87PRO0-0.026-0.03920.245-0.262-0.2620.0000.0000.0000.000
87A88ASN0-0.046-0.03221.2520.3070.3070.0000.0000.0000.000
88A89VAL00.0040.02915.701-0.244-0.2440.0000.0000.0000.000
89A90LEU00.0300.00914.480-0.166-0.1660.0000.0000.0000.000
90A91ALA00.008-0.01210.199-0.705-0.7050.0000.0000.0000.000
91A92TYR0-0.002-0.02111.1540.7260.7260.0000.0000.0000.000
92A93THR00.022-0.0247.954-2.934-2.9340.0000.0000.0000.000
93A94LEU0-0.039-0.0119.4282.1192.1190.0000.0000.0000.000
94A95PRO00.0530.02010.060-1.620-1.6200.0000.0000.0000.000
95A96SER0-0.051-0.03411.328-0.996-0.9960.0000.0000.0000.000
96A97LYS10.8200.89010.11421.77621.7760.0000.0000.0000.000
97A98ASN00.0090.0206.361-2.132-2.1320.0000.0000.0000.000
100A101ALA0-0.018-0.0086.618-0.510-0.5100.0000.0000.0000.000
101A102ASN00.0350.0358.276-0.104-0.1040.0000.0000.0000.000
102A104ASP-1-0.895-0.95514.337-15.329-15.3290.0000.0000.0000.000
103A105ILE0-0.0010.00916.386-0.163-0.1630.0000.0000.0000.000
104A106TYR0-0.012-0.0138.5360.3930.3930.0000.0000.0000.000
105A107TYR0-0.070-0.07010.232-0.683-0.6830.0000.0000.0000.000
106A108SER0-0.036-0.01415.7970.3560.3560.0000.0000.0000.000
107A109GLU-1-0.965-0.98618.590-12.199-12.1990.0000.0000.0000.000
108A110LEU0-0.0490.00314.0060.1880.1880.0000.0000.0000.000
109A111PRO0-0.032-0.00517.198-0.045-0.0450.0000.0000.0000.000
110A112PRO00.0580.00514.416-0.615-0.6150.0000.0000.0000.000
111A113LEU0-0.016-0.01514.492-1.018-1.0180.0000.0000.0000.000
112A114ALA0-0.0070.00117.2260.9460.9460.0000.0000.0000.000
113A115GLN0-0.066-0.04220.0460.4040.4040.0000.0000.0000.000
114A116LYS10.9260.95922.97211.10411.1040.0000.0000.0000.000
115A177CYS-1-0.799-0.88523.085-11.699-11.6990.0000.0000.0000.000
116A118HIS10.8860.94222.28012.27412.2740.0000.0000.0000.000
117A119ALA0-0.0320.00521.8820.0580.0580.0000.0000.0000.000
118A120GLN00.0400.01417.233-0.008-0.0080.0000.0000.0000.000
119A121ASP-1-0.779-0.85714.691-17.510-17.5100.0000.0000.0000.000
120A122GLN00.0180.01911.336-1.384-1.3840.0000.0000.0000.000
121A123ALA00.0100.01010.133-1.761-1.7610.0000.0000.0000.000
122A124THR0-0.038-0.05810.493-1.653-1.6530.0000.0000.0000.000
123A125THR00.009-0.00211.179-0.110-0.1100.0000.0000.0000.000
124A126THR00.005-0.0015.427-0.122-0.1220.0000.0000.0000.000
125A127LEU0-0.051-0.0227.714-2.812-2.8120.0000.0000.0000.000
126A128HIS0-0.014-0.0199.958-0.643-0.6430.0000.0000.0000.000
127A129GLU-1-0.761-0.8378.176-23.068-23.0680.0000.0000.0000.000
129A131THR0-0.050-0.0267.3950.6810.6810.0000.0000.0000.000
130A132HIS10.7990.88910.10221.85421.8540.0000.0000.0000.000
131A133ALA00.0090.0056.9201.0691.0690.0000.0000.0000.000
132A134PRO0-0.020-0.0228.870-0.632-0.6320.0000.0000.0000.000
133A135GLY0-0.032-0.0199.2591.0981.0980.0000.0000.0000.000
134A136VAL0-0.047-0.0076.070-2.602-2.6020.0000.0000.0000.000
135A137TYR0-0.031-0.0608.6751.4431.4430.0000.0000.0000.000
136A138GLN0-0.0420.01612.3770.6320.6320.0000.0000.0000.000
137A139PRO00.005-0.00315.0640.6060.6060.0000.0000.0000.000
138A140GLY00.0040.01212.973-0.724-0.7240.0000.0000.0000.000
139A141THR0-0.052-0.05013.4851.1651.1650.0000.0000.0000.000
140A142GLU-1-0.925-0.96515.108-14.613-14.6130.0000.0000.0000.000
141A143ASP-1-0.875-0.93416.513-17.580-17.5800.0000.0000.0000.000
142A144LEU0-0.042-0.01419.1130.6830.6830.0000.0000.0000.000
143A145GLY0-0.010-0.01521.8290.7340.7340.0000.0000.0000.000
144A146TYR0-0.0030.01917.351-0.764-0.7640.0000.0000.0000.000
145A147GLY00.0500.01921.3210.6180.6180.0000.0000.0000.000
146A148TYR0-0.087-0.08123.1310.1330.1330.0000.0000.0000.000
147A149ASP-1-0.872-0.92325.249-10.282-10.2820.0000.0000.0000.000
148A150ALA0-0.026-0.01625.4470.1180.1180.0000.0000.0000.000
149A151ALA00.0110.01222.321-0.022-0.0220.0000.0000.0000.000
150A152THR00.000-0.00624.1930.0650.0650.0000.0000.0000.000
151A153GLN0-0.061-0.03726.8160.3730.3730.0000.0000.0000.000
152A154LEU0-0.0290.01723.4220.3240.3240.0000.0000.0000.000
153A155SER0-0.045-0.04727.7270.2150.2150.0000.0000.0000.000
154A156ALA00.0630.02826.566-0.380-0.3800.0000.0000.0000.000
155A157GLN0-0.015-0.00924.976-0.245-0.2450.0000.0000.0000.000
156A158ASP-1-0.802-0.87623.558-12.128-12.1280.0000.0000.0000.000
157A159ALA00.0160.00022.124-0.669-0.6690.0000.0000.0000.000
158A160LEU0-0.023-0.00520.182-0.783-0.7830.0000.0000.0000.000
159A161ASN0-0.065-0.04218.580-1.628-1.6280.0000.0000.0000.000
160A162ASN00.0580.02918.432-0.458-0.4580.0000.0000.0000.000
161A163ALA00.0130.01114.164-0.179-0.1790.0000.0000.0000.000
162A164ASP-1-0.798-0.90315.691-16.318-16.3180.0000.0000.0000.000
163A165SER00.0180.01817.7920.1600.1600.0000.0000.0000.000
164A166TYR0-0.049-0.03414.937-0.021-0.0210.0000.0000.0000.000
165A167ALA0-0.0030.00914.664-0.169-0.1690.0000.0000.0000.000
166A168LEU0-0.042-0.01916.1570.4820.4820.0000.0000.0000.000
167A169TYR00.0230.01518.8580.6610.6610.0000.0000.0000.000
168A170ALA00.0150.00216.2180.3430.3430.0000.0000.0000.000
169A171ASN00.0000.00318.1000.8980.8980.0000.0000.0000.000
170A172ALA00.0130.01219.5170.4690.4690.0000.0000.0000.000
171A173ILE0-0.016-0.01020.7010.5700.5700.0000.0000.0000.000
172A174GLU-1-0.936-0.95119.232-15.297-15.2970.0000.0000.0000.000
173A175LEU0-0.080-0.04921.4000.6270.6270.0000.0000.0000.000
174A176LYS10.8350.93124.15413.37913.3790.0000.0000.0000.000