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: GY2J1

Calculation Name: 3UEB-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3UEB

Chain ID: A

ChEMBL ID:

UniProt ID: B6YTZ3

Base Structure: X-ray

Registration Date: 2025-07-09

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -779597.992395
FMO2-HF: Nuclear repulsion 738679.855195
FMO2-HF: Total energy -40918.1372
FMO2-MP2: Total energy -41039.188366


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:GLY)


Summations of interaction energy for fragment #1(A:4:GLY)
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.
-1.4970.7730.092-0.991-1.37-0.002
Interaction energy analysis for fragmet #1(A:4:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.017
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].
3A5SER0-0.0230.0764.3420.9541.182-0.001-0.081-0.1460.000
4A6SER0-0.030-0.1012.986-0.4990.8510.060-0.585-0.8250.000
5A6SER0-0.0440.0665.5010.4860.4860.0000.0000.0000.000
6A7GLY00.035-0.0723.401-1.601-0.9090.033-0.325-0.399-0.002
7A8LYS00.1220.0106.0980.1280.1280.0000.0000.0000.000
8A8LYS10.7200.9978.756-0.036-0.0360.0000.0000.0000.000
9A9ARG00.048-0.1179.5300.0320.0320.0000.0000.0000.000
10A9ARG10.7651.00611.9220.2320.2320.0000.0000.0000.000
11A10VAL00.072-0.11512.7320.0020.0020.0000.0000.0000.000
12A10VAL0-0.0620.10214.8700.0070.0070.0000.0000.0000.000
13A11ILE0-0.007-0.10016.3850.0000.0000.0000.0000.0000.000
14A11ILE0-0.0540.10517.233-0.003-0.0030.0000.0000.0000.000
15A12HIS00.159-0.09519.4360.0040.0040.0000.0000.0000.000
16A12HIS0-0.1490.07222.510-0.001-0.0010.0000.0000.0000.000
17A13ILE00.031-0.11023.196-0.005-0.0050.0000.0000.0000.000
18A13ILE0-0.0570.11022.953-0.001-0.0010.0000.0000.0000.000
19A14GLY0-0.002-0.09226.0080.0060.0060.0000.0000.0000.000
20A15LEU0-0.048-0.03729.752-0.005-0.0050.0000.0000.0000.000
21A15LEU0-0.0360.11628.778-0.001-0.0010.0000.0000.0000.000
22A16PRO00.076-0.10932.3040.0010.0010.0000.0000.0000.000
23A17GLU00.057-0.02435.7730.0040.0040.0000.0000.0000.000
24A17GLU-1-1.022-0.86336.448-0.038-0.0380.0000.0000.0000.000
25A18LEU00.005-0.11535.3060.0000.0000.0000.0000.0000.000
26A18LEU0-0.0460.11532.771-0.001-0.0010.0000.0000.0000.000
27A19SER00.053-0.05336.7520.0030.0030.0000.0000.0000.000
28A19SER0-0.0520.01238.515-0.001-0.0010.0000.0000.0000.000
29A20GLU00.127-0.09935.369-0.004-0.0040.0000.0000.0000.000
30A20GLU-1-0.990-0.85435.913-0.011-0.0110.0000.0000.0000.000
31A21GLU00.016-0.10634.7630.0000.0000.0000.0000.0000.000
32A21GLU-1-0.952-0.82137.524-0.025-0.0250.0000.0000.0000.000
33A22GLN00.133-0.08834.479-0.002-0.0020.0000.0000.0000.000
34A22GLN0-0.0340.11435.0560.0020.0020.0000.0000.0000.000
35A23LEU00.068-0.09531.425-0.007-0.0070.0000.0000.0000.000
36A23LEU0-0.1320.08731.1490.0000.0000.0000.0000.0000.000
37A24ILE00.077-0.08429.957-0.004-0.0040.0000.0000.0000.000
38A24ILE0-0.1260.08130.9870.0010.0010.0000.0000.0000.000
39A25GLU00.186-0.06929.744-0.005-0.0050.0000.0000.0000.000
40A25GLU-1-1.010-0.86332.336-0.050-0.0500.0000.0000.0000.000
41A26ILE00.006-0.11729.120-0.007-0.0070.0000.0000.0000.000
42A26ILE0-0.0720.10727.8120.0000.0000.0000.0000.0000.000
43A27GLY00.027-0.11925.943-0.009-0.0090.0000.0000.0000.000
44A28GLU00.065-0.03125.036-0.010-0.0100.0000.0000.0000.000
45A28GLU-1-0.966-0.83928.499-0.046-0.0460.0000.0000.0000.000
46A29LEU00.140-0.07625.525-0.011-0.0110.0000.0000.0000.000
47A29LEU0-0.0920.10227.0880.0000.0000.0000.0000.0000.000
48A30ALA00.086-0.09223.534-0.016-0.0160.0000.0000.0000.000
49A30ALA0-0.0760.09922.6940.0010.0010.0000.0000.0000.000
50A31GLN00.105-0.10020.993-0.024-0.0240.0000.0000.0000.000
51A31GLN0-0.1660.05521.1640.0040.0040.0000.0000.0000.000
52A32GLU00.049-0.14520.886-0.023-0.0230.0000.0000.0000.000
53A32GLU-1-0.993-0.82224.891-0.081-0.0810.0000.0000.0000.000
54A33THR0-0.005-0.08522.186-0.015-0.0150.0000.0000.0000.000
55A33THR0-0.0560.03421.4820.0000.0000.0000.0000.0000.000
56A34ILE00.065-0.07718.161-0.023-0.0230.0000.0000.0000.000
57A34ILE0-0.0910.07916.061-0.004-0.0040.0000.0000.0000.000
58A35ILE00.068-0.10217.424-0.050-0.0500.0000.0000.0000.000
59A35ILE0-0.1060.08019.0410.0010.0010.0000.0000.0000.000
60A36ASP00.083-0.13218.727-0.033-0.0330.0000.0000.0000.000
61A36ASP-1-0.999-0.82822.494-0.142-0.1420.0000.0000.0000.000
62A37TYR00.113-0.06418.962-0.013-0.0130.0000.0000.0000.000
63A37TYR0-0.1200.03516.5620.0250.0250.0000.0000.0000.000
64A38VAL00.049-0.09915.275-0.031-0.0310.0000.0000.0000.000
65A38VAL0-0.0570.10413.694-0.016-0.0160.0000.0000.0000.000
66A39PHE00.041-0.09216.071-0.050-0.0500.0000.0000.0000.000
67A39PHE0-0.1070.06417.9290.0010.0010.0000.0000.0000.000
68A40ASP00.092-0.12618.5800.0030.0030.0000.0000.0000.000
69A40ASP-1-1.029-0.86320.110-0.205-0.2050.0000.0000.0000.000
70A41HIS0-0.080-0.13416.2770.0180.0180.0000.0000.0000.000
71A41HIS10.7501.00615.4250.3320.3320.0000.0000.0000.000
72A42LEU00.093-0.09714.287-0.058-0.0580.0000.0000.0000.000
73A42LEU0-0.0420.10811.117-0.029-0.0290.0000.0000.0000.000
74A43THR00.1110.00115.4850.0470.0470.0000.0000.0000.000
75A43THR0-0.1070.00916.8140.0160.0160.0000.0000.0000.000
76A44ARG00.051-0.10516.519-0.037-0.0370.0000.0000.0000.000
77A44ARG10.8641.06619.9360.1540.1540.0000.0000.0000.000
78A45SER00.068-0.06816.9920.0240.0240.0000.0000.0000.000
79A45SER0-0.0550.05017.1240.0090.0090.0000.0000.0000.000
80A46GLU00.017-0.15213.0600.0460.0460.0000.0000.0000.000
81A46GLU-1-0.929-0.82112.491-0.549-0.5490.0000.0000.0000.000
82A47VAL00.104-0.08811.786-0.130-0.1300.0000.0000.0000.000
83A47VAL0-0.0900.12913.602-0.002-0.0020.0000.0000.0000.000
84A48LYS00.130-0.06911.9600.0670.0670.0000.0000.0000.000
85A48LYS10.6730.94510.802-0.295-0.2950.0000.0000.0000.000
86A49ASP00.049-0.13312.2250.0580.0580.0000.0000.0000.000
87A49ASP-1-0.962-0.83412.2430.0280.0280.0000.0000.0000.000
88A50ILE00.041-0.10112.138-0.102-0.1020.0000.0000.0000.000
89A50ILE0-0.0930.07913.844-0.010-0.0100.0000.0000.0000.000
90A51GLU00.064-0.12413.9080.0210.0210.0000.0000.0000.000
91A51GLU-1-0.997-0.83814.8590.0620.0620.0000.0000.0000.000
92A52VAL00.058-0.11015.086-0.027-0.0270.0000.0000.0000.000
93A52VAL0-0.0840.11116.050-0.003-0.0030.0000.0000.0000.000
94A53THR00.051-0.04817.7410.0080.0080.0000.0000.0000.000
95A53THR0-0.0480.05318.8090.0000.0000.0000.0000.0000.000
96A54MET00.120-0.08820.213-0.010-0.0100.0000.0000.0000.000
97A54MET0-0.0380.12223.5850.0010.0010.0000.0000.0000.000
98A55ARG00.086-0.10123.2490.0080.0080.0000.0000.0000.000
99A55ARG10.6940.97624.397-0.012-0.0120.0000.0000.0000.000
100A56ILE00.067-0.10325.664-0.002-0.0020.0000.0000.0000.000
101A56ILE0-0.0700.12727.3520.0000.0000.0000.0000.0000.000
102A57ASN00.108-0.09428.9850.0040.0040.0000.0000.0000.000
103A57ASN0-0.1710.03429.2390.0000.0000.0000.0000.0000.000
104A58ARG00.144-0.04230.8370.0010.0010.0000.0000.0000.000
105A58ARG10.7190.96234.1280.0210.0210.0000.0000.0000.000
106A59GLU00.025-0.12533.419-0.001-0.0010.0000.0000.0000.000
107A59GLU-1-1.038-0.87235.1980.0040.0040.0000.0000.0000.000
108A60GLU00.002-0.13031.1170.0010.0010.0000.0000.0000.000
109A60GLU-1-0.930-0.83530.4780.0220.0220.0000.0000.0000.000
110A61THR0-0.080-0.09528.0530.0060.0060.0000.0000.0000.000
111A61THR0-0.0630.02127.014-0.002-0.0020.0000.0000.0000.000
112A62LEU00.101-0.07127.8520.0020.0020.0000.0000.0000.000
113A62LEU0-0.0910.07026.3600.0000.0000.0000.0000.0000.000
114A63ASP00.144-0.06729.020-0.001-0.0010.0000.0000.0000.000
115A63ASP-1-0.829-0.77230.267-0.024-0.0240.0000.0000.0000.000
116A64LEU00.091-0.08326.9150.0050.0050.0000.0000.0000.000
117A64LEU0-0.0950.11325.011-0.002-0.0020.0000.0000.0000.000
118A65GLU00.037-0.11023.075-0.005-0.0050.0000.0000.0000.000
119A65GLU-1-0.884-0.81122.2040.0100.0100.0000.0000.0000.000
120A66ILE00.038-0.10320.4980.0080.0080.0000.0000.0000.000
121A66ILE0-0.0510.11118.623-0.003-0.0030.0000.0000.0000.000
122A67GLU00.088-0.09716.635-0.008-0.0080.0000.0000.0000.000
123A67GLU-1-0.941-0.82715.2590.0500.0500.0000.0000.0000.000
124A68VAL00.052-0.12013.9960.0140.0140.0000.0000.0000.000
125A68VAL0-0.0620.10212.811-0.009-0.0090.0000.0000.0000.000
126A69TYR00.100-0.08310.636-0.008-0.0080.0000.0000.0000.000
127A69TYR0-0.0850.0667.7780.0730.0730.0000.0000.0000.000
128A70LEU00.125-0.0819.2870.0830.0830.0000.0000.0000.000
129A70LEU0-0.1130.0999.448-0.016-0.0160.0000.0000.0000.000
130A71GLU00.113-0.0917.503-0.309-0.3090.0000.0000.0000.000
131A71GLU-1-0.910-0.7677.4580.5590.5590.0000.0000.0000.000
132A72VAL00.009-0.1007.4700.2060.2060.0000.0000.0000.000
133A72VAL0-0.0840.1006.450-0.028-0.0280.0000.0000.0000.000
134A73PRO0-0.009-0.1318.3340.2040.2040.0000.0000.0000.000
135A74ILE00.0930.0096.581-0.337-0.3370.0000.0000.0000.000
136A74ILE0-0.0680.1026.6800.0250.0250.0000.0000.0000.000
137A75PHE00.081-0.0767.135-0.087-0.0870.0000.0000.0000.000
138A75PHE0-0.0890.07311.1010.0180.0180.0000.0000.0000.000
139A76VAL00.012-0.1289.2000.0500.0500.0000.0000.0000.000
140A76VAL0-0.0220.1379.3590.0140.0140.0000.0000.0000.000
141A77LYS00.065-0.0677.272-0.367-0.3670.0000.0000.0000.000
142A77LYS10.7530.9878.0270.6400.6400.0000.0000.0000.000
143A78VAL00.060-0.1296.7500.3500.3500.0000.0000.0000.000
144A78VAL0-0.0180.1357.8420.0260.0260.0000.0000.0000.000
145A79ASP00.176-0.0615.574-0.982-0.9820.0000.0000.0000.000
146A79ASP-1-0.986-0.8177.575-0.884-0.8840.0000.0000.0000.000
147A80VAL00.068-0.1235.4890.6190.6190.0000.0000.0000.000
148A80VAL0-0.0830.1095.0560.0290.0290.0000.0000.0000.000
149A81ASP00.154-0.0746.0620.3020.3020.0000.0000.0000.000
150A81ASP-1-0.955-0.8425.462-0.822-0.8220.0000.0000.0000.000
151A82LYS00.149-0.0657.8620.1830.1830.0000.0000.0000.000
152A82LYS10.7140.9949.8140.6480.6480.0000.0000.0000.000
153A83LEU00.072-0.1089.9080.1500.1500.0000.0000.0000.000
154A83LEU0-0.0960.09810.409-0.024-0.0240.0000.0000.0000.000
155A84ILE00.091-0.09410.5040.0970.0970.0000.0000.0000.000
156A84ILE0-0.0970.1008.8210.0110.0110.0000.0000.0000.000
157A85ASP00.075-0.10712.0380.0840.0840.0000.0000.0000.000
158A85ASP-1-0.921-0.81512.317-0.349-0.3490.0000.0000.0000.000
159A86GLU00.030-0.13014.0870.0610.0610.0000.0000.0000.000
160A86GLU-1-0.931-0.81714.863-0.429-0.4290.0000.0000.0000.000
161A87ALA00.112-0.07215.2580.0490.0490.0000.0000.0000.000
162A87ALA0-0.0700.11115.191-0.005-0.0050.0000.0000.0000.000
163A88VAL00.050-0.08916.1330.0350.0350.0000.0000.0000.000
164A88VAL0-0.1070.08715.6660.0040.0040.0000.0000.0000.000
165A89GLU00.097-0.10617.8160.0310.0310.0000.0000.0000.000
166A89GLU-1-0.990-0.86117.919-0.169-0.1690.0000.0000.0000.000
167A90ARG00.074-0.10819.6990.0270.0270.0000.0000.0000.000
168A90ARG10.7541.01620.1850.1810.1810.0000.0000.0000.000
169A91ALA00.145-0.09520.5220.0170.0170.0000.0000.0000.000
170A91ALA0-0.0660.11620.5630.0000.0000.0000.0000.0000.000
171A92TYR00.036-0.13021.9170.0170.0170.0000.0000.0000.000
172A92TYR0-0.0850.08920.1710.0060.0060.0000.0000.0000.000
173A93GLU00.118-0.07923.8430.0160.0160.0000.0000.0000.000
174A93GLU-1-0.909-0.77824.594-0.144-0.1440.0000.0000.0000.000
175A94ILE00.013-0.11525.2730.0120.0120.0000.0000.0000.000
176A94ILE0-0.0540.11224.766-0.001-0.0010.0000.0000.0000.000
177A95VAL00.124-0.09126.1930.0080.0080.0000.0000.0000.000
178A95VAL0-0.0870.10325.5880.0010.0010.0000.0000.0000.000
179A96GLU00.148-0.08227.8250.0090.0090.0000.0000.0000.000
180A96GLU-1-0.934-0.80928.628-0.069-0.0690.0000.0000.0000.000
181A97ARG0-0.002-0.12429.6690.0070.0070.0000.0000.0000.000
182A97ARG10.7150.96728.7080.1070.1070.0000.0000.0000.000
183A98LYS00.124-0.07331.0060.0050.0050.0000.0000.0000.000
184A98LYS10.7721.03831.0950.0590.0590.0000.0000.0000.000
185A99LEU00.035-0.11031.9650.0050.0050.0000.0000.0000.000
186A99LEU0-0.0460.09730.2390.0010.0010.0000.0000.0000.000
187A100ARG00.139-0.05833.6420.0060.0060.0000.0000.0000.000
188A100ARG10.7330.97232.1110.0710.0710.0000.0000.0000.000
189A101GLU00.081-0.09735.4990.0040.0040.0000.0000.0000.000
190A101GLU-1-0.968-0.82535.352-0.062-0.0620.0000.0000.0000.000
191A102ILE00.119-0.08036.5190.0030.0030.0000.0000.0000.000
192A102ILE0-0.0750.09634.7790.0000.0000.0000.0000.0000.000
193A103ALA00.113-0.08837.8690.0040.0040.0000.0000.0000.000
194A103ALA0-0.0920.09738.1930.0000.0000.0000.0000.0000.000
195A104ASN0-0.057-0.14639.7530.0030.0030.0000.0000.0000.000
196A104ASN0-0.1600.04840.446-0.002-0.0020.0000.0000.0000.000
197A105GLU0-0.178-0.17941.2560.0050.0050.0000.0000.0000.000
198A105GLU-1-0.908-0.93440.261-0.042-0.0420.0000.0000.0000.000