FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: 4QN6N

Calculation Name: 1T3U-B-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T3U

Chain ID: B

ChEMBL ID:

UniProt ID: Q9HTW3

Base Structure: X-ray

Registration Date: 2025-07-11

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 OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 182
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -542648.835267
FMO2-HF: Nuclear repulsion 504998.351674
FMO2-HF: Total energy -37650.483593
FMO2-MP2: Total energy -37758.07492


3D Structure
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(B:4:SER)


Summations of interaction energy for fragment #1(B:4: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.
-13.449-12.1812.631-5.998-7.9-0.031
Interaction energy analysis for fragmet #1(B:4:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.060
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].
4B5ASN0-0.1320.0333.164-2.120-1.1690.048-0.481-0.518-0.003
5B6THR00.094-0.0873.827-0.2731.714-0.018-1.188-0.7820.006
6B6THR0-0.0240.0867.703-0.123-0.1230.0000.0000.0000.000
7B7LEU00.050-0.1136.953-0.191-0.1910.0000.0000.0000.000
8B7LEU0-0.0870.1226.7500.0350.0350.0000.0000.0000.000
9B8THR0-0.044-0.0958.3190.0720.0720.0000.0000.0000.000
10B8THR00.0360.09212.345-0.036-0.0360.0000.0000.0000.000
11B9VAL00.020-0.09112.087-0.003-0.0030.0000.0000.0000.000
12B9VAL0-0.0200.10212.0870.0150.0150.0000.0000.0000.000
13B10GLN00.149-0.09314.592-0.016-0.0160.0000.0000.0000.000
14B10GLN0-0.1530.06718.0510.0010.0010.0000.0000.0000.000
15B11ILE00.080-0.10518.3540.0210.0210.0000.0000.0000.000
16B11ILE0-0.1030.08416.1020.0060.0060.0000.0000.0000.000
17B12LEU00.109-0.08420.111-0.014-0.0140.0000.0000.0000.000
18B12LEU0-0.1300.07323.7930.0010.0010.0000.0000.0000.000
19B13ASP00.005-0.08623.538-0.005-0.0050.0000.0000.0000.000
20B13ASP-1-0.887-0.82625.7500.0430.0430.0000.0000.0000.000
21B14LYS00.115-0.09621.564-0.020-0.0200.0000.0000.0000.000
22B14LYS10.8631.05520.833-0.022-0.0220.0000.0000.0000.000
23B15GLU00.142-0.08617.9390.0370.0370.0000.0000.0000.000
24B15GLU-1-0.935-0.80216.287-0.145-0.1450.0000.0000.0000.000
25B16TYR0-0.027-0.11814.942-0.016-0.0160.0000.0000.0000.000
26B16TYR0-0.1370.06914.2530.0150.0150.0000.0000.0000.000
27B17CYS00.168-0.10411.6480.0610.0610.0000.0000.0000.000
28B17CYS0-0.1440.10311.367-0.021-0.0210.0000.0000.0000.000
29B18ILE00.068-0.1008.969-0.085-0.0850.0000.0000.0000.000
30B18ILE0-0.0880.0857.7020.0200.0200.0000.0000.0000.000
31B19ASN00.101-0.0325.242-0.219-0.2190.0000.0000.0000.000
32B19ASN0-0.1040.0484.621-0.288-0.298-0.001-0.0040.0150.000
33B20CYS00.118-0.1164.3010.4410.6770.000-0.074-0.1610.000
34B20CYS0-0.1560.0954.715-0.317-0.275-0.001-0.013-0.0270.000
35B21PRO00.060-0.0872.136-4.143-4.3288.189-4.758-3.246-0.011
36B22ASP00.2170.0712.601-3.254-5.7781.1672.608-1.2500.001
37B22ASP-1-0.927-0.8212.227-5.633-4.9813.240-2.033-1.859-0.024
38B23ASP0-0.035-0.1773.916-1.236-1.1740.008-0.049-0.0210.000
39B23ASP-1-0.953-0.8316.6293.6173.6170.0000.0000.0000.000
40B24GLU00.050-0.1395.929-0.477-0.4770.0000.0000.0000.000
41B24GLU-1-0.913-0.8046.0111.8161.8160.0000.0000.0000.000
42B25ARG00.036-0.1056.359-0.317-0.3170.0000.0000.0000.000
43B25ARG10.7681.0274.3800.7460.804-0.001-0.006-0.0510.000
44B26ALA00.187-0.0617.653-0.124-0.1240.0000.0000.0000.000
45B26ALA0-0.0620.10711.682-0.010-0.0100.0000.0000.0000.000
46B27ASN00.026-0.11310.477-0.182-0.1820.0000.0000.0000.000
47B27ASN0-0.1150.07110.688-0.183-0.1830.0000.0000.0000.000
48B28LEU00.133-0.0909.968-0.144-0.1440.0000.0000.0000.000
49B28LEU0-0.0740.1098.233-0.002-0.0020.0000.0000.0000.000
50B29GLU00.106-0.12611.222-0.096-0.0960.0000.0000.0000.000
51B29GLU-1-1.019-0.85611.0130.2290.2290.0000.0000.0000.000
52B30SER0-0.014-0.08813.176-0.088-0.0880.0000.0000.0000.000
53B30SER0-0.0650.06014.683-0.027-0.0270.0000.0000.0000.000
54B31ALA00.086-0.08714.629-0.083-0.0830.0000.0000.0000.000
55B31ALA0-0.0700.10714.2650.0150.0150.0000.0000.0000.000
56B32ALA00.053-0.12114.869-0.040-0.0400.0000.0000.0000.000
57B32ALA0-0.0500.11614.532-0.005-0.0050.0000.0000.0000.000
58B33ARG00.166-0.03816.388-0.046-0.0460.0000.0000.0000.000
59B33ARG10.8091.04715.773-0.258-0.2580.0000.0000.0000.000
60B34TYR00.069-0.11818.867-0.039-0.0390.0000.0000.0000.000
61B34TYR0-0.1500.06619.6720.0070.0070.0000.0000.0000.000
62B35LEU00.071-0.11219.383-0.026-0.0260.0000.0000.0000.000
63B35LEU0-0.0960.08518.107-0.001-0.0010.0000.0000.0000.000
64B36ASP00.080-0.10620.281-0.018-0.0180.0000.0000.0000.000
65B36ASP-1-0.868-0.77220.5400.1040.1040.0000.0000.0000.000
66B37GLY0-0.018-0.10722.097-0.020-0.0200.0000.0000.0000.000
67B38LYS00.1660.00424.089-0.020-0.0200.0000.0000.0000.000
68B38LYS10.7111.03924.382-0.166-0.1660.0000.0000.0000.000
69B39MET00.086-0.12124.635-0.010-0.0100.0000.0000.0000.000
70B39MET0-0.0880.09321.226-0.008-0.0080.0000.0000.0000.000
71B40ARG00.025-0.10126.121-0.013-0.0130.0000.0000.0000.000
72B40ARG10.7000.98724.150-0.079-0.0790.0000.0000.0000.000
73B41GLU00.073-0.11827.998-0.014-0.0140.0000.0000.0000.000
74B41GLU-1-0.890-0.80528.7710.1360.1360.0000.0000.0000.000
75B42ILE00.036-0.10729.493-0.008-0.0080.0000.0000.0000.000
76B42ILE0-0.0790.10628.0420.0000.0000.0000.0000.0000.000
77B43ARG00.117-0.07630.286-0.005-0.0050.0000.0000.0000.000
78B43ARG10.7590.99728.178-0.055-0.0550.0000.0000.0000.000
79B44SER0-0.008-0.10131.788-0.008-0.0080.0000.0000.0000.000
80B44SER0-0.0090.08532.9130.0000.0000.0000.0000.0000.000
81B45SER0-0.054-0.10334.137-0.006-0.0060.0000.0000.0000.000
82B45SER0-0.0510.07134.2170.0010.0010.0000.0000.0000.000
83B46GLY0-0.014-0.08835.344-0.004-0.0040.0000.0000.0000.000
84B47LYS00.088-0.00136.373-0.005-0.0050.0000.0000.0000.000
85B47LYS10.8721.08135.854-0.070-0.0700.0000.0000.0000.000
86B48VAL00.005-0.13833.478-0.002-0.0020.0000.0000.0000.000
87B48VAL0-0.0820.11131.6360.0010.0010.0000.0000.0000.000
88B49ILE00.105-0.09933.8900.0010.0010.0000.0000.0000.000
89B49ILE0-0.0480.13335.059-0.001-0.0010.0000.0000.0000.000
90B50GLY00.040-0.09831.4260.0000.0000.0000.0000.0000.000
91B51ALA00.1360.01927.4390.0100.0100.0000.0000.0000.000
92B51ALA0-0.0830.09726.466-0.002-0.0020.0000.0000.0000.000
93B52ASP00.047-0.10225.4400.0130.0130.0000.0000.0000.000
94B52ASP-1-0.881-0.84326.4010.0760.0760.0000.0000.0000.000
95B53ARG00.072-0.09326.3080.0170.0170.0000.0000.0000.000
96B53ARG10.8711.07230.487-0.080-0.0800.0000.0000.0000.000
97B54VAL00.055-0.10228.2120.0100.0100.0000.0000.0000.000
98B54VAL0-0.0730.09426.803-0.001-0.0010.0000.0000.0000.000
99B55ALA00.141-0.08823.6040.0090.0090.0000.0000.0000.000
100B55ALA0-0.0880.10822.5950.0000.0000.0000.0000.0000.000
101B56VAL00.075-0.09924.1660.0250.0250.0000.0000.0000.000
102B56VAL0-0.0990.09725.002-0.001-0.0010.0000.0000.0000.000
103B57MET00.094-0.11625.7340.0170.0170.0000.0000.0000.000
104B57MET0-0.0800.10129.357-0.002-0.0020.0000.0000.0000.000
105B58ALA00.062-0.09025.2510.0010.0010.0000.0000.0000.000
106B58ALA0-0.0370.10524.4910.0000.0000.0000.0000.0000.000
107B59ALA00.105-0.09523.1250.0100.0100.0000.0000.0000.000
108B59ALA0-0.0650.10722.4530.0030.0030.0000.0000.0000.000
109B60LEU00.031-0.10523.8830.0230.0230.0000.0000.0000.000
110B60LEU0-0.1050.10326.434-0.003-0.0030.0000.0000.0000.000
111B61ASN00.167-0.05027.1800.0070.0070.0000.0000.0000.000
112B61ASN0-0.1010.05728.078-0.003-0.0030.0000.0000.0000.000
113B62ILE00.126-0.07523.856-0.010-0.0100.0000.0000.0000.000
114B62ILE0-0.0720.10821.7740.0020.0020.0000.0000.0000.000
115B63THR0-0.013-0.09925.0780.0160.0160.0000.0000.0000.000
116B63THR0-0.0600.05024.6410.0080.0080.0000.0000.0000.000
117B64HIS00.058-0.10325.8550.0060.0060.0000.0000.0000.000
118B64HIS0-0.1110.07429.980-0.010-0.0100.0000.0000.0000.000
119B65ASP00.056-0.10027.756-0.010-0.0100.0000.0000.0000.000
120B65ASP-1-0.918-0.83826.7240.1860.1860.0000.0000.0000.000
121B66LEU00.140-0.09225.485-0.011-0.0110.0000.0000.0000.000
122B66LEU0-0.1090.11323.8880.0030.0030.0000.0000.0000.000
123B67LEU00.041-0.11226.7990.0000.0000.0000.0000.0000.000
124B67LEU0-0.0680.10828.178-0.001-0.0010.0000.0000.0000.000
125B68HIS00.143-0.08129.664-0.005-0.0050.0000.0000.0000.000
126B68HIS0-0.0960.09831.771-0.006-0.0060.0000.0000.0000.000
127B69ARG00.066-0.08329.156-0.016-0.0160.0000.0000.0000.000
128B69ARG10.8451.05726.889-0.216-0.2160.0000.0000.0000.000
129B70LYS00.093-0.08830.056-0.007-0.0070.0000.0000.0000.000
130B70LYS10.7650.99229.162-0.199-0.1990.0000.0000.0000.000
131B71GLU00.137-0.08130.969-0.003-0.0030.0000.0000.0000.000
132B71GLU-1-0.986-0.82434.3220.1450.1450.0000.0000.0000.000
133B72ARG00.052-0.12534.071-0.009-0.0090.0000.0000.0000.000
134B72ARG10.8021.04133.869-0.131-0.1310.0000.0000.0000.000
135B73LEU00.088-0.10432.776-0.012-0.0120.0000.0000.0000.000
136B73LEU0-0.0950.10630.4030.0030.0030.0000.0000.0000.000
137B74ASP00.107-0.11734.238-0.005-0.0050.0000.0000.0000.000
138B74ASP-1-0.925-0.79233.9010.1840.1840.0000.0000.0000.000
139B75GLN00.085-0.09736.134-0.006-0.0060.0000.0000.0000.000
140B75GLN0-0.1270.06338.549-0.004-0.0040.0000.0000.0000.000
141B76GLU00.069-0.10537.738-0.010-0.0100.0000.0000.0000.000
142B76GLU-1-0.943-0.83137.0850.1330.1330.0000.0000.0000.000
143B77SER00.074-0.07537.527-0.007-0.0070.0000.0000.0000.000
144B77SER0-0.0480.08636.5920.0020.0020.0000.0000.0000.000
145B78SER0-0.057-0.15038.709-0.003-0.0030.0000.0000.0000.000
146B78SER0-0.0160.08740.8550.0000.0000.0000.0000.0000.000
147B79SER00.050-0.05041.605-0.004-0.0040.0000.0000.0000.000
148B79SER0-0.0700.08042.108-0.001-0.0010.0000.0000.0000.000
149B80THR0-0.001-0.10341.891-0.007-0.0070.0000.0000.0000.000
150B80THR0-0.0540.08940.961-0.002-0.0020.0000.0000.0000.000
151B81ARG00.099-0.09242.897-0.004-0.0040.0000.0000.0000.000
152B81ARG10.8591.04241.221-0.121-0.1210.0000.0000.0000.000
153B82GLU0-0.002-0.15344.252-0.003-0.0030.0000.0000.0000.000
154B82GLU-1-0.929-0.81545.6390.0970.0970.0000.0000.0000.000
155B83ARG00.128-0.07046.745-0.005-0.0050.0000.0000.0000.000
156B83ARG10.8781.06545.860-0.087-0.0870.0000.0000.0000.000
157B84VAL00.082-0.09146.593-0.005-0.0050.0000.0000.0000.000
158B84VAL0-0.1050.10244.7040.0000.0000.0000.0000.0000.000
159B85ARG00.062-0.12547.867-0.002-0.0020.0000.0000.0000.000
160B85ARG10.8821.07147.208-0.094-0.0940.0000.0000.0000.000
161B86GLU00.111-0.08450.258-0.003-0.0030.0000.0000.0000.000
162B86GLU-1-0.960-0.79451.6700.0720.0720.0000.0000.0000.000
163B87LEU00.089-0.10151.147-0.004-0.0040.0000.0000.0000.000
164B87LEU0-0.1110.09249.6490.0000.0000.0000.0000.0000.000
165B88LEU00.028-0.10951.736-0.003-0.0030.0000.0000.0000.000
166B88LEU0-0.0750.06949.2760.0010.0010.0000.0000.0000.000
167B89ASP00.139-0.07053.107-0.002-0.0020.0000.0000.0000.000
168B89ASP-1-0.930-0.80855.1260.0640.0640.0000.0000.0000.000
169B90ARG00.076-0.08255.562-0.003-0.0030.0000.0000.0000.000
170B90ARG10.7630.98055.581-0.064-0.0640.0000.0000.0000.000
171B91VAL0-0.043-0.11356.084-0.003-0.0030.0000.0000.0000.000
172B91VAL0-0.0980.08654.5740.0000.0000.0000.0000.0000.000
173B92ASP00.127-0.10157.507-0.001-0.0010.0000.0000.0000.000
174B92ASP-1-0.989-0.85057.1260.0620.0620.0000.0000.0000.000
175B93ARG00.031-0.12358.986-0.002-0.0020.0000.0000.0000.000
176B93ARG10.7610.97958.810-0.059-0.0590.0000.0000.0000.000
177B94ALA00.057-0.06661.360-0.002-0.0020.0000.0000.0000.000
178B94ALA0-0.1070.08361.7580.0000.0000.0000.0000.0000.000
179B95LEU00.035-0.11862.8180.0000.0000.0000.0000.0000.000
180B95LEU0-0.0780.09562.4980.0000.0000.0000.0000.0000.000
181B96ALA0-0.098-0.14063.632-0.001-0.0010.0000.0000.0000.000
182B96ALA00.0660.03965.1720.0000.0000.0000.0000.0000.000