Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 8579Y

Calculation Name: 1XT0-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XT0

Chain ID: B

ChEMBL ID:

UniProt ID: Q8RT31

Base Structure: X-ray

Registration Date: 2023-06-22

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

DOI:


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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2268793.550965
FMO2-HF: Nuclear repulsion 2189015.485482
FMO2-HF: Total energy -79778.065483
FMO2-MP2: Total energy -80013.394901


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:-1:GLY)


Summations of interaction energy for fragment #1(B:-1: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.
-1.9540.4511.805-2.067-2.142-0.018
Interaction energy analysis for fragmet #1(B:-1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.009
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].
3B1SER0-0.002-0.0193.8551.1322.028-0.014-0.445-0.4360.001
4B2HIS00.0370.0216.7890.1240.1240.0000.0000.0000.000
5B3PRO00.0630.0139.699-0.149-0.1490.0000.0000.0000.000
6B4GLU-1-0.814-0.87512.226-0.042-0.0420.0000.0000.0000.000
7B5ILE00.0100.01510.798-0.027-0.0270.0000.0000.0000.000
8B6GLU-1-0.950-0.9729.741-0.672-0.6720.0000.0000.0000.000
9B7LYS10.8100.89212.2690.0150.0150.0000.0000.0000.000
10B8ALA00.0450.02015.703-0.005-0.0050.0000.0000.0000.000
11B9GLN0-0.035-0.01012.480-0.028-0.0280.0000.0000.0000.000
12B10ARG10.8920.93215.1250.2250.2250.0000.0000.0000.000
13B11GLU-1-0.819-0.88918.531-0.076-0.0760.0000.0000.0000.000
14B12ILE0-0.022-0.00514.5970.0130.0130.0000.0000.0000.000
15B13ILE0-0.015-0.01214.6380.0090.0090.0000.0000.0000.000
16B14GLU-1-0.956-0.96817.715-0.117-0.1170.0000.0000.0000.000
17B15ALA0-0.010-0.01120.3660.0140.0140.0000.0000.0000.000
18B16PHE0-0.033-0.02417.6220.0140.0140.0000.0000.0000.000
19B17ASN0-0.004-0.02619.1160.0090.0090.0000.0000.0000.000
20B18ALA00.0010.02621.8000.0100.0100.0000.0000.0000.000
21B19LYS10.9170.94923.4430.0590.0590.0000.0000.0000.000
22B20PRO00.0840.05620.4360.0080.0080.0000.0000.0000.000
23B21LYS10.8550.90120.0480.0060.0060.0000.0000.0000.000
24B22ASN0-0.053-0.01321.5710.0180.0180.0000.0000.0000.000
25B23GLY00.0500.02918.5560.0050.0050.0000.0000.0000.000
26B24ILE0-0.011-0.00415.651-0.001-0.0010.0000.0000.0000.000
27B25ASN0-0.021-0.00917.4550.0260.0260.0000.0000.0000.000
28B26LYS10.9570.98218.8450.0730.0730.0000.0000.0000.000
29B27ILE00.0030.00812.4720.0090.0090.0000.0000.0000.000
30B28LYS10.8480.90615.4800.0140.0140.0000.0000.0000.000
31B29GLU-1-0.895-0.94717.4170.0110.0110.0000.0000.0000.000
32B30ILE00.0120.00515.1240.0180.0180.0000.0000.0000.000
33B31CYS0-0.059-0.03013.5890.0370.0370.0000.0000.0000.000
34B32GLU-1-0.931-0.95015.7260.1190.1190.0000.0000.0000.000
35B33GLN0-0.025-0.00919.2230.0070.0070.0000.0000.0000.000
36B34TYR0-0.088-0.07215.8140.0060.0060.0000.0000.0000.000
37B35LYS10.7950.90216.441-0.109-0.1090.0000.0000.0000.000
38B36ILE00.0050.01310.9270.0590.0590.0000.0000.0000.000
39B37SER0-0.002-0.02711.825-0.089-0.0890.0000.0000.0000.000
40B38PRO00.0520.01011.7150.0200.0200.0000.0000.0000.000
41B39ASN0-0.052-0.03012.355-0.032-0.0320.0000.0000.0000.000
42B40GLU-1-0.738-0.8717.9800.3120.3120.0000.0000.0000.000
43B41GLU-1-0.772-0.8557.530-0.056-0.0560.0000.0000.0000.000
44B42ILE0-0.022-0.0198.653-0.182-0.1820.0000.0000.0000.000
45B43ALA0-0.0200.0028.667-0.103-0.1030.0000.0000.0000.000
46B44GLU-1-0.825-0.9102.769-4.683-3.3271.800-1.558-1.598-0.019
47B45PHE0-0.009-0.0055.849-0.397-0.3970.0000.0000.0000.000
48B46PHE0-0.015-0.0218.732-0.052-0.0520.0000.0000.0000.000
49B47HIS10.7880.9125.2660.4220.4220.0000.0000.0000.000
50B48GLN0-0.032-0.0213.3481.0681.2210.019-0.064-0.1080.000
51B49GLN0-0.004-0.0067.5210.2060.2060.0000.0000.0000.000
52B50ARG10.9050.95810.5040.5240.5240.0000.0000.0000.000
53B51LYS10.8830.92712.3620.5180.5180.0000.0000.0000.000
54B52ASN0-0.067-0.03514.0820.0670.0670.0000.0000.0000.000
55B53LEU00.0060.01713.4740.0380.0380.0000.0000.0000.000
56B54ASP-1-0.818-0.90817.113-0.155-0.1550.0000.0000.0000.000
57B55LEU00.016-0.01315.2690.0080.0080.0000.0000.0000.000
58B56GLU-1-0.841-0.90118.449-0.109-0.1090.0000.0000.0000.000
59B57ALA00.0300.02520.7340.0130.0130.0000.0000.0000.000
60B58VAL0-0.033-0.01714.4130.0140.0140.0000.0000.0000.000
61B59GLY00.0160.01817.5620.0140.0140.0000.0000.0000.000
62B60ASP-1-0.832-0.86919.350-0.046-0.0460.0000.0000.0000.000
63B61TYR00.013-0.02016.0780.0150.0150.0000.0000.0000.000
64B62LEU00.003-0.00113.4030.0240.0240.0000.0000.0000.000
65B63SER00.0450.01517.4460.0170.0170.0000.0000.0000.000
66B64SER0-0.036-0.02220.7980.0090.0090.0000.0000.0000.000
67B65PRO0-0.016-0.02121.8930.0060.0060.0000.0000.0000.000
68B66GLU-1-0.874-0.92522.4600.0180.0180.0000.0000.0000.000
69B67ALA00.0330.01221.4850.0030.0030.0000.0000.0000.000
70B68GLU-1-0.779-0.86518.1860.0210.0210.0000.0000.0000.000
71B69ASN00.003-0.02117.4140.0190.0190.0000.0000.0000.000
72B70GLN00.0580.02617.030-0.010-0.0100.0000.0000.0000.000
73B71GLN00.0410.03615.3300.0280.0280.0000.0000.0000.000
74B72VAL0-0.027-0.01012.2490.0370.0370.0000.0000.0000.000
75B73LEU0-0.0310.00212.4530.0040.0040.0000.0000.0000.000
76B74LYS10.8290.90812.894-0.273-0.2730.0000.0000.0000.000
77B75ALA0-0.027-0.0039.4910.0240.0240.0000.0000.0000.000
78B76PHE0-0.0010.0019.1290.0340.0340.0000.0000.0000.000
79B77THR00.033-0.0219.531-0.051-0.0510.0000.0000.0000.000
80B78SER0-0.063-0.0349.9830.0250.0250.0000.0000.0000.000
81B79GLN00.0080.0035.322-0.178-0.1780.0000.0000.0000.000
82B80MET0-0.078-0.0126.581-0.144-0.1440.0000.0000.0000.000
83B81ASN0-0.013-0.0069.1310.1020.1020.0000.0000.0000.000
84B82PHE0-0.041-0.04510.461-0.048-0.0480.0000.0000.0000.000
85B83ASN00.0470.04713.408-0.003-0.0030.0000.0000.0000.000
86B84GLY0-0.023-0.01214.623-0.031-0.0310.0000.0000.0000.000
87B85GLN0-0.026-0.00814.085-0.042-0.0420.0000.0000.0000.000
88B86SER00.012-0.02117.9200.0170.0170.0000.0000.0000.000
89B87PHE00.0290.00719.904-0.006-0.0060.0000.0000.0000.000
90B88VAL0-0.020-0.00721.275-0.006-0.0060.0000.0000.0000.000
91B89GLU-1-0.933-0.96518.771-0.113-0.1130.0000.0000.0000.000
92B90GLY00.0490.03316.650-0.018-0.0180.0000.0000.0000.000
93B91LEU00.0120.01017.006-0.014-0.0140.0000.0000.0000.000
94B92ARG10.8280.90219.3900.0920.0920.0000.0000.0000.000
95B93THR0-0.039-0.02413.416-0.020-0.0200.0000.0000.0000.000
96B94PHE00.0010.00914.486-0.029-0.0290.0000.0000.0000.000
97B95LEU0-0.011-0.01015.913-0.014-0.0140.0000.0000.0000.000
98B96LYS10.7950.88117.1320.2040.2040.0000.0000.0000.000
99B97THR0-0.050-0.02012.022-0.047-0.0470.0000.0000.0000.000
100B98PHE0-0.027-0.01414.872-0.030-0.0300.0000.0000.0000.000
101B99LYS10.8750.94617.5770.1680.1680.0000.0000.0000.000
102B100LEU00.0330.00820.8150.0080.0080.0000.0000.0000.000
103B101PRO00.0550.01721.9160.0030.0030.0000.0000.0000.000
104B102GLY00.0250.02225.1420.0040.0040.0000.0000.0000.000
105B103GLU-1-0.866-0.96027.548-0.036-0.0360.0000.0000.0000.000
106B104ALA00.0130.00327.487-0.001-0.0010.0000.0000.0000.000
107B105GLN00.0420.01727.7640.0030.0030.0000.0000.0000.000
108B106LYS10.7740.89923.8880.0550.0550.0000.0000.0000.000
109B107ILE00.0110.00023.004-0.001-0.0010.0000.0000.0000.000
110B108ASP-1-0.803-0.86623.277-0.006-0.0060.0000.0000.0000.000
111B109ARG10.8770.92521.8380.0160.0160.0000.0000.0000.000
112B110LEU0-0.0200.00417.6340.0080.0080.0000.0000.0000.000
113B111VAL00.002-0.00519.2480.0040.0040.0000.0000.0000.000
114B112GLN0-0.040-0.02521.4160.0130.0130.0000.0000.0000.000
115B113SER00.0190.03615.9250.0160.0160.0000.0000.0000.000
116B114PHE0-0.0090.00216.5810.0170.0170.0000.0000.0000.000
117B115SER0-0.038-0.02717.8860.0110.0110.0000.0000.0000.000
118B116GLY00.0230.00218.9160.0070.0070.0000.0000.0000.000
119B117ALA0-0.014-0.01113.7660.0190.0190.0000.0000.0000.000
120B118TYR00.0270.00815.4450.0150.0150.0000.0000.0000.000
121B119PHE00.0220.00817.5750.0090.0090.0000.0000.0000.000
122B120GLN0-0.073-0.04515.6270.0270.0270.0000.0000.0000.000
123B121GLN0-0.0070.00211.4740.0020.0020.0000.0000.0000.000
124B122ASN0-0.037-0.01215.797-0.011-0.0110.0000.0000.0000.000
125B123PRO00.0050.00819.032-0.011-0.0110.0000.0000.0000.000
126B124ASP-1-0.934-0.96621.6600.0500.0500.0000.0000.0000.000
127B125VAL0-0.034-0.01122.368-0.008-0.0080.0000.0000.0000.000
128B126VAL0-0.071-0.03822.421-0.008-0.0080.0000.0000.0000.000
129B127SER00.0060.00224.4320.0080.0080.0000.0000.0000.000
130B128ASN00.010-0.01324.6340.0040.0040.0000.0000.0000.000
131B129ALA00.0590.02722.115-0.006-0.0060.0000.0000.0000.000
132B130ASP-1-0.866-0.93323.5040.0380.0380.0000.0000.0000.000
133B131ALA00.0110.02026.980-0.008-0.0080.0000.0000.0000.000
134B132ALA00.0140.00322.364-0.008-0.0080.0000.0000.0000.000
135B133TYR0-0.082-0.07124.505-0.009-0.0090.0000.0000.0000.000
136B134LEU0-0.0090.01025.574-0.008-0.0080.0000.0000.0000.000
137B135LEU00.0050.00825.643-0.006-0.0060.0000.0000.0000.000
138B136ALA00.0140.01623.464-0.008-0.0080.0000.0000.0000.000
139B137PHE00.0230.00925.315-0.008-0.0080.0000.0000.0000.000
140B138GLN00.0240.01228.326-0.002-0.0020.0000.0000.0000.000
141B139THR00.011-0.02125.758-0.003-0.0030.0000.0000.0000.000
142B140ILE0-0.005-0.00824.173-0.007-0.0070.0000.0000.0000.000
143B141MET0-0.0260.00328.151-0.003-0.0030.0000.0000.0000.000
144B142LEU00.0050.00230.840-0.002-0.0020.0000.0000.0000.000
145B143ASN00.0270.01128.058-0.006-0.0060.0000.0000.0000.000
146B144THR0-0.044-0.01330.224-0.005-0.0050.0000.0000.0000.000
147B145ASP-1-0.895-0.96932.964-0.030-0.0300.0000.0000.0000.000
148B146LEU0-0.073-0.04332.9180.0010.0010.0000.0000.0000.000
149B147HIS0-0.038-0.02131.3070.0000.0000.0000.0000.0000.000
150B148ASN00.0330.05235.303-0.002-0.0020.0000.0000.0000.000
151B149PRO00.008-0.00937.3810.0030.0030.0000.0000.0000.000
152B150SER0-0.082-0.04740.4380.0030.0030.0000.0000.0000.000
153B151ILE0-0.0040.00839.1640.0030.0030.0000.0000.0000.000
154B152PRO00.008-0.00542.569-0.001-0.0010.0000.0000.0000.000
155B153GLU-1-0.755-0.87240.257-0.034-0.0340.0000.0000.0000.000
156B154LYS10.9110.95143.0740.0190.0190.0000.0000.0000.000
157B155ASN0-0.038-0.02644.3540.0030.0030.0000.0000.0000.000
158B156LYS10.8100.92938.5620.0380.0380.0000.0000.0000.000
159B157MET0-0.0090.02036.5540.0020.0020.0000.0000.0000.000
160B158THR00.0140.00438.225-0.002-0.0020.0000.0000.0000.000
161B159VAL00.0800.03535.4290.0010.0010.0000.0000.0000.000
162B160ASP-1-0.856-0.93637.613-0.011-0.0110.0000.0000.0000.000
163B161GLY0-0.044-0.01739.9920.0020.0020.0000.0000.0000.000
164B162LEU00.0700.03232.0380.0020.0020.0000.0000.0000.000
165B163LYS10.7670.88436.0420.0130.0130.0000.0000.0000.000
166B164ARG10.9010.95437.3780.0100.0100.0000.0000.0000.000
167B165ASN0-0.030-0.02935.7360.0030.0030.0000.0000.0000.000
168B166LEU00.0240.02131.6310.0000.0000.0000.0000.0000.000
169B167ARG10.7710.87234.899-0.003-0.0030.0000.0000.0000.000
170B168GLY00.0040.00936.6440.0000.0000.0000.0000.0000.000
171B169GLY00.003-0.00633.2070.0030.0030.0000.0000.0000.000
172B170ASN0-0.026-0.02528.8870.0050.0050.0000.0000.0000.000
173B171ASN0-0.040-0.03129.8030.0010.0010.0000.0000.0000.000
174B172GLY00.0260.02931.8500.0020.0020.0000.0000.0000.000
175B173GLY0-0.0090.00334.074-0.002-0.0020.0000.0000.0000.000
176B174ASP-1-0.810-0.89134.3860.0090.0090.0000.0000.0000.000
177B175PHE00.0490.01528.0040.0030.0030.0000.0000.0000.000
178B176ASP-1-0.822-0.90130.8870.0000.0000.0000.0000.0000.000
179B177ALA00.0100.00032.444-0.003-0.0030.0000.0000.0000.000
180B178LYS10.9390.95331.016-0.001-0.0010.0000.0000.0000.000
181B179PHE00.0490.02925.030-0.003-0.0030.0000.0000.0000.000
182B180LEU00.001-0.00429.686-0.005-0.0050.0000.0000.0000.000
183B181GLU-1-0.845-0.93331.857-0.015-0.0150.0000.0000.0000.000
184B182GLU-1-0.957-0.95126.246-0.029-0.0290.0000.0000.0000.000
185B183LEU00.0080.01327.029-0.006-0.0060.0000.0000.0000.000
186B184TYR0-0.025-0.05228.719-0.006-0.0060.0000.0000.0000.000
187B185SER0-0.039-0.03531.159-0.003-0.0030.0000.0000.0000.000
188B186GLU-1-0.823-0.89024.139-0.066-0.0660.0000.0000.0000.000
189B187ILE0-0.042-0.01326.467-0.007-0.0070.0000.0000.0000.000
190B188LYS10.8890.94928.8330.0340.0340.0000.0000.0000.000
191B189ALA0-0.029-0.00629.772-0.001-0.0010.0000.0000.0000.000
192B190LYS10.9190.95323.1880.1150.1150.0000.0000.0000.000
193B191PRO00.0980.06326.701-0.002-0.0020.0000.0000.0000.000
194B192PHE0-0.006-0.01722.946-0.011-0.0110.0000.0000.0000.000
195B193GLU-1-0.820-0.89121.124-0.177-0.1770.0000.0000.0000.000
196B194LEU00.002-0.00122.492-0.012-0.0120.0000.0000.0000.000
197B195ASN0-0.0100.00421.5730.0010.0010.0000.0000.0000.000
198B196PHE0-0.004-0.00123.237-0.005-0.0050.0000.0000.0000.000
199B197VAL0-0.0200.00624.010-0.006-0.0060.0000.0000.0000.000
200B198LYS10.8340.89626.4270.1210.1210.0000.0000.0000.000
201B199THR0-0.009-0.02529.8900.0000.0000.0000.0000.0000.000
202B200SER0-0.0200.00230.5630.0070.0070.0000.0000.0000.000
203B201PRO0-0.046-0.01526.084-0.005-0.0050.0000.0000.0000.000