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: 5R9YZ

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 OptAll
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 -544200.533604
FMO2-HF: Nuclear repulsion 506549.928379
FMO2-HF: Total energy -37650.605225
FMO2-MP2: Total energy -37758.183802


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.
-10.145-25.75636.83-11.199-10.019-0.068
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 : 0.007 / q_NPA : 0.015
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].
4B5ASN0-0.1350.0654.079-0.835-0.5310.000-0.108-0.1950.000
5B6THR00.061-0.0723.872-0.4530.918-0.012-0.779-0.5800.003
6B6THR0-0.0260.0777.575-0.018-0.0180.0000.0000.0000.000
7B7LEU00.035-0.0996.834-0.083-0.0830.0000.0000.0000.000
8B7LEU0-0.0690.1206.6020.0070.0070.0000.0000.0000.000
9B8THR0-0.060-0.0908.2000.0460.0460.0000.0000.0000.000
10B8THR00.0440.09012.433-0.058-0.0580.0000.0000.0000.000
11B9VAL00.015-0.08011.9870.0230.0230.0000.0000.0000.000
12B9VAL0-0.0190.09411.7680.0200.0200.0000.0000.0000.000
13B10GLN00.180-0.09514.342-0.025-0.0250.0000.0000.0000.000
14B10GLN0-0.1650.07018.3000.0100.0100.0000.0000.0000.000
15B11ILE00.078-0.10418.1390.0250.0250.0000.0000.0000.000
16B11ILE0-0.0960.08515.8300.0050.0050.0000.0000.0000.000
17B12LEU00.091-0.08519.982-0.014-0.0140.0000.0000.0000.000
18B12LEU0-0.1100.08023.7310.0030.0030.0000.0000.0000.000
19B13ASP00.039-0.09423.382-0.005-0.0050.0000.0000.0000.000
20B13ASP-1-0.863-0.78525.891-0.036-0.0360.0000.0000.0000.000
21B14LYS00.081-0.10221.784-0.009-0.0090.0000.0000.0000.000
22B14LYS10.8671.04521.3290.0820.0820.0000.0000.0000.000
23B15GLU00.136-0.07817.9880.0350.0350.0000.0000.0000.000
24B15GLU-1-0.931-0.79916.511-0.329-0.3290.0000.0000.0000.000
25B16TYR0-0.018-0.11815.287-0.005-0.0050.0000.0000.0000.000
26B16TYR0-0.1550.05714.7810.0200.0200.0000.0000.0000.000
27B17CYS00.196-0.09411.8660.0370.0370.0000.0000.0000.000
28B17CYS0-0.1370.10211.621-0.002-0.0020.0000.0000.0000.000
29B18ILE00.040-0.1149.3770.0120.0120.0000.0000.0000.000
30B18ILE0-0.0860.0928.2240.0420.0420.0000.0000.0000.000
31B19ASN00.105-0.0425.573-0.249-0.2490.0000.0000.0000.000
32B19ASN0-0.0790.0704.673-0.268-0.266-0.001-0.0050.0040.000
33B20CYS00.121-0.1174.1040.6811.2010.001-0.283-0.2380.000
34B20CYS0-0.1450.1134.5060.0150.082-0.001-0.024-0.0420.000
35B21PRO00.046-0.0741.885-4.692-10.49815.432-5.930-3.697-0.023
36B22ASP00.1070.0342.361-3.559-6.9003.6361.616-1.9110.005
37B22ASP-1-0.821-0.7901.779-4.707-13.61317.728-5.643-3.179-0.053
38B23ASP00.027-0.1453.590-1.490-1.3920.048-0.027-0.1180.000
39B23ASP-1-0.923-0.8245.9924.4444.4440.0000.0000.0000.000
40B24GLU00.067-0.1175.631-0.705-0.7050.0000.0000.0000.000
41B24GLU-1-0.926-0.8155.8621.5501.5500.0000.0000.0000.000
42B25ARG00.033-0.1166.301-0.340-0.3400.0000.0000.0000.000
43B25ARG10.7040.9694.0871.7681.848-0.001-0.016-0.0630.000
44B26ALA00.164-0.0717.434-0.157-0.1570.0000.0000.0000.000
45B26ALA0-0.0360.11911.5270.0010.0010.0000.0000.0000.000
46B27ASN00.031-0.10110.295-0.163-0.1630.0000.0000.0000.000
47B27ASN0-0.1210.07510.560-0.158-0.1580.0000.0000.0000.000
48B28LEU00.141-0.0879.524-0.087-0.0870.0000.0000.0000.000
49B28LEU0-0.0770.1077.858-0.011-0.0110.0000.0000.0000.000
50B29GLU00.089-0.15310.842-0.089-0.0890.0000.0000.0000.000
51B29GLU-1-0.953-0.80711.1670.0300.0300.0000.0000.0000.000
52B30SER00.001-0.07612.737-0.062-0.0620.0000.0000.0000.000
53B30SER0-0.0490.07414.565-0.019-0.0190.0000.0000.0000.000
54B31ALA00.085-0.09414.378-0.050-0.0500.0000.0000.0000.000
55B31ALA0-0.0750.10614.0220.0130.0130.0000.0000.0000.000
56B32ALA00.048-0.12414.603-0.013-0.0130.0000.0000.0000.000
57B32ALA0-0.0580.11314.252-0.011-0.0110.0000.0000.0000.000
58B33ARG00.142-0.05216.102-0.032-0.0320.0000.0000.0000.000
59B33ARG10.7270.99015.101-0.113-0.1130.0000.0000.0000.000
60B34TYR00.088-0.11018.520-0.025-0.0250.0000.0000.0000.000
61B34TYR0-0.1650.04919.5600.0080.0080.0000.0000.0000.000
62B35LEU00.076-0.10819.238-0.011-0.0110.0000.0000.0000.000
63B35LEU0-0.0760.09717.444-0.003-0.0030.0000.0000.0000.000
64B36ASP00.073-0.10220.141-0.007-0.0070.0000.0000.0000.000
65B36ASP-1-0.851-0.75520.151-0.013-0.0130.0000.0000.0000.000
66B37GLY0-0.018-0.11021.861-0.011-0.0110.0000.0000.0000.000
67B38LYS00.1390.00223.857-0.012-0.0120.0000.0000.0000.000
68B38LYS10.6811.02523.863-0.109-0.1090.0000.0000.0000.000
69B39MET00.102-0.11424.3600.0000.0000.0000.0000.0000.000
70B39MET0-0.1130.09621.028-0.009-0.0090.0000.0000.0000.000
71B40ARG00.037-0.10225.856-0.007-0.0070.0000.0000.0000.000
72B40ARG10.6910.96123.5100.0150.0150.0000.0000.0000.000
73B41GLU00.099-0.07928.030-0.009-0.0090.0000.0000.0000.000
74B41GLU-1-0.916-0.81928.4830.0830.0830.0000.0000.0000.000
75B42ILE00.075-0.10029.229-0.004-0.0040.0000.0000.0000.000
76B42ILE0-0.0920.10627.6250.0000.0000.0000.0000.0000.000
77B43ARG00.101-0.07429.799-0.001-0.0010.0000.0000.0000.000
78B43ARG10.7460.97828.0350.0170.0170.0000.0000.0000.000
79B44SER0-0.001-0.10731.431-0.005-0.0050.0000.0000.0000.000
80B44SER0-0.0230.08032.617-0.001-0.0010.0000.0000.0000.000
81B45SER0-0.049-0.10633.741-0.003-0.0030.0000.0000.0000.000
82B45SER0-0.0610.05733.9260.0020.0020.0000.0000.0000.000
83B46GLY0-0.019-0.09635.3070.0000.0000.0000.0000.0000.000
84B47LYS00.0610.00336.127-0.003-0.0030.0000.0000.0000.000
85B47LYS10.8731.08035.652-0.038-0.0380.0000.0000.0000.000
86B48VAL00.002-0.13633.7080.0020.0020.0000.0000.0000.000
87B48VAL0-0.0600.09631.6880.0010.0010.0000.0000.0000.000
88B49ILE00.100-0.09134.177-0.002-0.0020.0000.0000.0000.000
89B49ILE0-0.0340.13135.275-0.001-0.0010.0000.0000.0000.000
90B50GLY00.019-0.09931.6250.0030.0030.0000.0000.0000.000
91B51ALA00.1250.00827.6400.0100.0100.0000.0000.0000.000
92B51ALA0-0.0780.09426.701-0.003-0.0030.0000.0000.0000.000
93B52ASP00.036-0.08725.7720.0050.0050.0000.0000.0000.000
94B52ASP-1-0.865-0.84227.1310.0130.0130.0000.0000.0000.000
95B53ARG00.093-0.08526.5610.0140.0140.0000.0000.0000.000
96B53ARG10.8481.07330.356-0.029-0.0290.0000.0000.0000.000
97B54VAL00.061-0.09128.2010.0130.0130.0000.0000.0000.000
98B54VAL0-0.0720.09726.501-0.002-0.0020.0000.0000.0000.000
99B55ALA00.148-0.09623.7820.0110.0110.0000.0000.0000.000
100B55ALA0-0.0820.11022.773-0.002-0.0020.0000.0000.0000.000
101B56VAL00.068-0.10024.0830.0200.0200.0000.0000.0000.000
102B56VAL0-0.1060.08925.2910.0000.0000.0000.0000.0000.000
103B57MET00.090-0.11525.9030.0180.0180.0000.0000.0000.000
104B57MET0-0.0890.09829.274-0.001-0.0010.0000.0000.0000.000
105B58ALA00.102-0.08424.6250.0080.0080.0000.0000.0000.000
106B58ALA0-0.0580.09624.001-0.002-0.0020.0000.0000.0000.000
107B59ALA00.116-0.08722.7450.0120.0120.0000.0000.0000.000
108B59ALA0-0.0710.10322.2290.0020.0020.0000.0000.0000.000
109B60LEU00.035-0.10623.5350.0240.0240.0000.0000.0000.000
110B60LEU0-0.0920.10026.330-0.002-0.0020.0000.0000.0000.000
111B61ASN00.160-0.05426.9840.0100.0100.0000.0000.0000.000
112B61ASN0-0.1080.05527.637-0.002-0.0020.0000.0000.0000.000
113B62ILE00.108-0.07623.287-0.004-0.0040.0000.0000.0000.000
114B62ILE0-0.0750.10321.1480.0020.0020.0000.0000.0000.000
115B63THR00.007-0.10124.7270.0170.0170.0000.0000.0000.000
116B63THR0-0.0690.04924.4810.0070.0070.0000.0000.0000.000
117B64HIS00.076-0.07725.5790.0090.0090.0000.0000.0000.000
118B64HIS0-0.1050.07329.578-0.006-0.0060.0000.0000.0000.000
119B65ASP00.058-0.10527.246-0.001-0.0010.0000.0000.0000.000
120B65ASP-1-0.856-0.79426.2430.1320.1320.0000.0000.0000.000
121B66LEU00.099-0.10424.929-0.006-0.0060.0000.0000.0000.000
122B66LEU0-0.1080.11323.2580.0030.0030.0000.0000.0000.000
123B67LEU00.055-0.12326.2380.0070.0070.0000.0000.0000.000
124B67LEU0-0.0700.11027.616-0.001-0.0010.0000.0000.0000.000
125B68HIS00.145-0.07529.098-0.002-0.0020.0000.0000.0000.000
126B68HIS0-0.1450.07631.367-0.004-0.0040.0000.0000.0000.000
127B69ARG00.073-0.09828.579-0.012-0.0120.0000.0000.0000.000
128B69ARG10.8521.06526.281-0.181-0.1810.0000.0000.0000.000
129B70LYS00.085-0.06929.593-0.004-0.0040.0000.0000.0000.000
130B70LYS10.7630.98228.929-0.189-0.1890.0000.0000.0000.000
131B71GLU00.127-0.09330.6340.0000.0000.0000.0000.0000.000
132B71GLU-1-0.956-0.81334.0090.1290.1290.0000.0000.0000.000
133B72ARG00.038-0.11733.619-0.008-0.0080.0000.0000.0000.000
134B72ARG10.7761.01333.369-0.113-0.1130.0000.0000.0000.000
135B73LEU00.103-0.10132.592-0.012-0.0120.0000.0000.0000.000
136B73LEU0-0.0880.10930.3320.0030.0030.0000.0000.0000.000
137B74ASP00.117-0.10634.046-0.003-0.0030.0000.0000.0000.000
138B74ASP-1-0.922-0.79133.4780.1740.1740.0000.0000.0000.000
139B75GLN00.079-0.10035.789-0.004-0.0040.0000.0000.0000.000
140B75GLN0-0.1270.07138.267-0.005-0.0050.0000.0000.0000.000
141B76GLU00.074-0.08537.654-0.008-0.0080.0000.0000.0000.000
142B76GLU-1-0.941-0.82036.9210.1270.1270.0000.0000.0000.000
143B77SER00.134-0.04437.202-0.008-0.0080.0000.0000.0000.000
144B77SER0-0.0360.09636.3270.0030.0030.0000.0000.0000.000
145B78SER0-0.060-0.12338.461-0.002-0.0020.0000.0000.0000.000
146B78SER0-0.0310.07140.4720.0010.0010.0000.0000.0000.000
147B79SER00.083-0.05741.273-0.003-0.0030.0000.0000.0000.000
148B79SER0-0.0880.05441.825-0.002-0.0020.0000.0000.0000.000
149B80THR0-0.011-0.09741.639-0.007-0.0070.0000.0000.0000.000
150B80THR0-0.0800.05440.750-0.002-0.0020.0000.0000.0000.000
151B81ARG00.111-0.10242.322-0.003-0.0030.0000.0000.0000.000
152B81ARG10.8331.00740.284-0.120-0.1200.0000.0000.0000.000
153B82GLU00.011-0.12543.781-0.002-0.0020.0000.0000.0000.000
154B82GLU-1-0.916-0.78744.6850.0950.0950.0000.0000.0000.000
155B83ARG00.119-0.07346.375-0.004-0.0040.0000.0000.0000.000
156B83ARG10.8811.06645.553-0.082-0.0820.0000.0000.0000.000
157B84VAL00.084-0.08946.110-0.005-0.0050.0000.0000.0000.000
158B84VAL0-0.1010.09944.2400.0010.0010.0000.0000.0000.000
159B85ARG00.064-0.11547.390-0.002-0.0020.0000.0000.0000.000
160B85ARG10.8561.06547.058-0.095-0.0950.0000.0000.0000.000
161B86GLU00.139-0.09349.835-0.003-0.0030.0000.0000.0000.000
162B86GLU-1-0.961-0.79550.9110.0690.0690.0000.0000.0000.000
163B87LEU00.072-0.09050.847-0.005-0.0050.0000.0000.0000.000
164B87LEU0-0.1040.09149.3960.0000.0000.0000.0000.0000.000
165B88LEU00.066-0.10051.265-0.003-0.0030.0000.0000.0000.000
166B88LEU0-0.0860.06948.6140.0010.0010.0000.0000.0000.000
167B89ASP00.123-0.06552.672-0.002-0.0020.0000.0000.0000.000
168B89ASP-1-0.938-0.81154.6600.0630.0630.0000.0000.0000.000
169B90ARG00.085-0.09155.453-0.002-0.0020.0000.0000.0000.000
170B90ARG10.7300.95754.444-0.064-0.0640.0000.0000.0000.000
171B91VAL00.010-0.09955.878-0.003-0.0030.0000.0000.0000.000
172B91VAL0-0.1040.08254.2790.0000.0000.0000.0000.0000.000
173B92ASP00.133-0.08156.933-0.002-0.0020.0000.0000.0000.000
174B92ASP-1-0.999-0.85456.7420.0640.0640.0000.0000.0000.000
175B93ARG0-0.009-0.12658.500-0.002-0.0020.0000.0000.0000.000
176B93ARG10.7500.97258.432-0.059-0.0590.0000.0000.0000.000
177B94ALA00.105-0.07560.928-0.002-0.0020.0000.0000.0000.000
178B94ALA0-0.0980.08561.1770.0000.0000.0000.0000.0000.000
179B95LEU00.003-0.12462.3850.0000.0000.0000.0000.0000.000
180B95LEU0-0.0760.10261.8490.0000.0000.0000.0000.0000.000
181B96ALA0-0.113-0.15363.093-0.001-0.0010.0000.0000.0000.000
182B96ALA00.0710.04265.2630.0000.0000.0000.0000.0000.000