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: 17YNZ

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 OptH
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 -2260938.355452
FMO2-HF: Nuclear repulsion 2181162.067884
FMO2-HF: Total energy -79776.287567
FMO2-MP2: Total energy -80011.720872


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.
-3.136-0.0750000000000010.19-1.709-1.544-0.009
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 : -0.018 / q_NPA : -0.014
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].
3B1SER00.0180.0133.8000.4021.582-0.023-0.603-0.5540.000
4B2HIS00.0420.0306.9320.1910.1910.0000.0000.0000.000
5B3PRO00.0560.0079.838-0.145-0.1450.0000.0000.0000.000
6B4GLU-1-0.914-0.97612.187-0.065-0.0650.0000.0000.0000.000
7B5ILE0-0.027-0.00711.002-0.028-0.0280.0000.0000.0000.000
8B6GLU-1-0.955-0.9769.481-0.637-0.6370.0000.0000.0000.000
9B7LYS10.8910.94112.2640.0900.0900.0000.0000.0000.000
10B8ALA0-0.0100.00315.7400.0110.0110.0000.0000.0000.000
11B9GLN00.005-0.00113.204-0.032-0.0320.0000.0000.0000.000
12B10ARG10.9690.96915.4580.2260.2260.0000.0000.0000.000
13B11GLU-1-0.842-0.90018.775-0.104-0.1040.0000.0000.0000.000
14B12ILE0-0.013-0.00614.8160.0130.0130.0000.0000.0000.000
15B13ILE0-0.020-0.00914.7410.0070.0070.0000.0000.0000.000
16B14GLU-1-0.955-0.96718.197-0.128-0.1280.0000.0000.0000.000
17B15ALA0-0.022-0.01420.9780.0160.0160.0000.0000.0000.000
18B16PHE0-0.036-0.02418.1990.0130.0130.0000.0000.0000.000
19B17ASN00.004-0.02519.7230.0060.0060.0000.0000.0000.000
20B18ALA0-0.0090.03222.2660.0110.0110.0000.0000.0000.000
21B19LYS10.9110.94124.0490.0840.0840.0000.0000.0000.000
22B20PRO00.1070.06320.9610.0030.0030.0000.0000.0000.000
23B21LYS10.9650.95820.6570.0620.0620.0000.0000.0000.000
24B22ASN0-0.031-0.00822.1590.0140.0140.0000.0000.0000.000
25B23GLY00.0650.03919.3950.0030.0030.0000.0000.0000.000
26B24ILE00.003-0.00416.396-0.008-0.0080.0000.0000.0000.000
27B25ASN0-0.031-0.03318.0810.0170.0170.0000.0000.0000.000
28B26LYS10.9260.97719.0360.1110.1110.0000.0000.0000.000
29B27ILE00.0110.01713.1650.0080.0080.0000.0000.0000.000
30B28LYS10.8560.91215.9660.0500.0500.0000.0000.0000.000
31B29GLU-1-0.919-0.95217.840-0.022-0.0220.0000.0000.0000.000
32B30ILE00.0140.01215.6060.0160.0160.0000.0000.0000.000
33B31CYS0-0.061-0.03113.9240.0290.0290.0000.0000.0000.000
34B32GLU-1-0.953-0.96016.0570.0710.0710.0000.0000.0000.000
35B33GLN0-0.018-0.00419.5740.0080.0080.0000.0000.0000.000
36B34TYR0-0.101-0.05515.9290.0190.0190.0000.0000.0000.000
37B35LYS10.8870.95116.626-0.094-0.0940.0000.0000.0000.000
38B36ILE0-0.0050.01211.4050.0480.0480.0000.0000.0000.000
39B37SER0-0.039-0.07412.153-0.071-0.0710.0000.0000.0000.000
40B38PRO00.0660.01012.010-0.005-0.0050.0000.0000.0000.000
41B39ASN0-0.035-0.01712.643-0.038-0.0380.0000.0000.0000.000
42B40GLU-1-0.770-0.8578.0620.1830.1830.0000.0000.0000.000
43B41GLU-1-0.780-0.8808.136-0.235-0.2350.0000.0000.0000.000
44B42ILE0-0.044-0.0329.420-0.165-0.1650.0000.0000.0000.000
45B43ALA0-0.022-0.0038.944-0.084-0.0840.0000.0000.0000.000
46B44GLU-1-0.876-0.9463.227-4.671-2.9060.205-1.049-0.922-0.009
47B45PHE00.0070.0046.532-0.317-0.3170.0000.0000.0000.000
48B46PHE0-0.034-0.0229.425-0.028-0.0280.0000.0000.0000.000
49B47HIS10.8010.8916.3540.6030.6030.0000.0000.0000.000
50B48GLN0-0.028-0.0063.5640.4500.5660.008-0.057-0.0680.000
51B49GLN00.005-0.0027.7730.1760.1760.0000.0000.0000.000
52B50ARG10.9080.95010.8650.5150.5150.0000.0000.0000.000
53B51LYS10.8420.90612.7690.5340.5340.0000.0000.0000.000
54B52ASN0-0.0150.00114.4690.0860.0860.0000.0000.0000.000
55B53LEU0-0.0140.00913.6940.0390.0390.0000.0000.0000.000
56B54ASP-1-0.801-0.88017.395-0.164-0.1640.0000.0000.0000.000
57B55LEU0-0.001-0.04216.0730.0080.0080.0000.0000.0000.000
58B56GLU-1-0.919-0.95718.930-0.125-0.1250.0000.0000.0000.000
59B57ALA00.0090.01320.7000.0110.0110.0000.0000.0000.000
60B58VAL0-0.042-0.01414.7850.0090.0090.0000.0000.0000.000
61B59GLY00.0090.00918.0380.0130.0130.0000.0000.0000.000
62B60ASP-1-0.883-0.94119.568-0.075-0.0750.0000.0000.0000.000
63B61TYR0-0.034-0.03616.3940.0140.0140.0000.0000.0000.000
64B62LEU00.0220.00613.8650.0200.0200.0000.0000.0000.000
65B63SER00.0080.01718.1000.0200.0200.0000.0000.0000.000
66B64SER0-0.064-0.04121.3400.0140.0140.0000.0000.0000.000
67B65PRO0-0.023-0.02722.3310.0030.0030.0000.0000.0000.000
68B66GLU-1-0.905-0.93023.142-0.015-0.0150.0000.0000.0000.000
69B67ALA00.0290.00422.004-0.002-0.0020.0000.0000.0000.000
70B68GLU-1-0.815-0.89318.444-0.034-0.0340.0000.0000.0000.000
71B69ASN0-0.032-0.03017.7110.0090.0090.0000.0000.0000.000
72B70GLN00.0470.01817.477-0.015-0.0150.0000.0000.0000.000
73B71GLN0-0.027-0.00315.4270.0240.0240.0000.0000.0000.000
74B72VAL0-0.013-0.00112.6610.0160.0160.0000.0000.0000.000
75B73LEU00.0150.01512.718-0.019-0.0190.0000.0000.0000.000
76B74LYS10.9530.98513.729-0.146-0.1460.0000.0000.0000.000
77B75ALA00.0150.0089.8210.0180.0180.0000.0000.0000.000
78B76PHE0-0.016-0.0189.3020.0090.0090.0000.0000.0000.000
79B77THR00.0370.0139.845-0.053-0.0530.0000.0000.0000.000
80B78SER0-0.062-0.02410.4630.0250.0250.0000.0000.0000.000
81B79GLN00.0080.0105.624-0.187-0.1870.0000.0000.0000.000
82B80MET0-0.089-0.0246.901-0.077-0.0770.0000.0000.0000.000
83B81ASN0-0.025-0.0099.4740.0990.0990.0000.0000.0000.000
84B82PHE0-0.039-0.05111.070-0.041-0.0410.0000.0000.0000.000
85B83ASN00.0910.06313.706-0.011-0.0110.0000.0000.0000.000
86B84GLY0-0.059-0.02314.667-0.019-0.0190.0000.0000.0000.000
87B85GLN0-0.014-0.03114.444-0.042-0.0420.0000.0000.0000.000
88B86SER00.0270.01718.2460.0090.0090.0000.0000.0000.000
89B87PHE00.0240.00720.187-0.010-0.0100.0000.0000.0000.000
90B88VAL0-0.0040.00221.218-0.009-0.0090.0000.0000.0000.000
91B89GLU-1-0.921-0.95419.156-0.084-0.0840.0000.0000.0000.000
92B90GLY00.0480.02516.897-0.019-0.0190.0000.0000.0000.000
93B91LEU00.001-0.00417.356-0.016-0.0160.0000.0000.0000.000
94B92ARG10.8120.89019.7040.0850.0850.0000.0000.0000.000
95B93THR0-0.034-0.01713.771-0.019-0.0190.0000.0000.0000.000
96B94PHE00.0080.00715.077-0.028-0.0280.0000.0000.0000.000
97B95LEU00.001-0.00716.240-0.017-0.0170.0000.0000.0000.000
98B96LYS10.8530.93217.7080.1960.1960.0000.0000.0000.000
99B97THR0-0.069-0.01712.701-0.039-0.0390.0000.0000.0000.000
100B98PHE0-0.026-0.01415.572-0.034-0.0340.0000.0000.0000.000
101B99LYS10.9120.99218.1410.1920.1920.0000.0000.0000.000
102B100LEU00.031-0.00221.2170.0040.0040.0000.0000.0000.000
103B101PRO00.0840.04522.3870.0030.0030.0000.0000.0000.000
104B102GLY00.0290.02325.5190.0040.0040.0000.0000.0000.000
105B103GLU-1-0.880-0.97228.103-0.059-0.0590.0000.0000.0000.000
106B104ALA00.0280.01028.014-0.002-0.0020.0000.0000.0000.000
107B105GLN00.021-0.00228.367-0.001-0.0010.0000.0000.0000.000
108B106LYS10.8710.95824.5830.0780.0780.0000.0000.0000.000
109B107ILE00.0220.00823.686-0.003-0.0030.0000.0000.0000.000
110B108ASP-1-0.800-0.84823.846-0.026-0.0260.0000.0000.0000.000
111B109ARG10.9140.95322.3120.0450.0450.0000.0000.0000.000
112B110LEU0-0.029-0.00118.5120.0040.0040.0000.0000.0000.000
113B111VAL00.008-0.00219.6770.0010.0010.0000.0000.0000.000
114B112GLN0-0.049-0.02521.5890.0120.0120.0000.0000.0000.000
115B113SER0-0.012-0.00515.9540.0200.0200.0000.0000.0000.000
116B114PHE0-0.021-0.00817.0700.0150.0150.0000.0000.0000.000
117B115SER0-0.039-0.01818.1780.0140.0140.0000.0000.0000.000
118B116GLY00.0160.00219.3190.0100.0100.0000.0000.0000.000
119B117ALA0-0.030-0.02114.2410.0200.0200.0000.0000.0000.000
120B118TYR00.0470.01516.1940.0130.0130.0000.0000.0000.000
121B119PHE00.0180.01318.2390.0100.0100.0000.0000.0000.000
122B120GLN0-0.036-0.02416.3360.0250.0250.0000.0000.0000.000
123B121GLN0-0.018-0.00611.838-0.001-0.0010.0000.0000.0000.000
124B122ASN0-0.048-0.01116.297-0.002-0.0020.0000.0000.0000.000
125B123PRO0-0.032-0.01119.328-0.011-0.0110.0000.0000.0000.000
126B124ASP-1-0.894-0.95422.1940.0500.0500.0000.0000.0000.000
127B125VAL0-0.060-0.01022.361-0.009-0.0090.0000.0000.0000.000
128B126VAL0-0.070-0.03823.301-0.008-0.0080.0000.0000.0000.000
129B127SER0-0.022-0.01025.1700.0060.0060.0000.0000.0000.000
130B128ASN00.0450.00525.0930.0030.0030.0000.0000.0000.000
131B129ALA00.0650.02022.699-0.005-0.0050.0000.0000.0000.000
132B130ASP-1-0.880-0.93824.0430.0140.0140.0000.0000.0000.000
133B131ALA0-0.0150.00627.408-0.007-0.0070.0000.0000.0000.000
134B132ALA00.0070.00422.812-0.006-0.0060.0000.0000.0000.000
135B133TYR0-0.089-0.10124.871-0.008-0.0080.0000.0000.0000.000
136B134LEU00.0030.02025.845-0.007-0.0070.0000.0000.0000.000
137B135LEU00.0220.01126.211-0.005-0.0050.0000.0000.0000.000
138B136ALA00.0030.02823.914-0.007-0.0070.0000.0000.0000.000
139B137PHE00.0160.00725.783-0.007-0.0070.0000.0000.0000.000
140B138GLN00.017-0.00228.7820.0000.0000.0000.0000.0000.000
141B139THR00.009-0.03625.897-0.002-0.0020.0000.0000.0000.000
142B140ILE0-0.008-0.00124.882-0.005-0.0050.0000.0000.0000.000
143B141MET0-0.031-0.00928.477-0.003-0.0030.0000.0000.0000.000
144B142LEU00.004-0.00431.195-0.001-0.0010.0000.0000.0000.000
145B143ASN00.0310.01728.459-0.003-0.0030.0000.0000.0000.000
146B144THR0-0.042-0.01130.595-0.004-0.0040.0000.0000.0000.000
147B145ASP-1-0.897-0.96033.019-0.035-0.0350.0000.0000.0000.000
148B146LEU0-0.045-0.02833.4230.0010.0010.0000.0000.0000.000
149B147HIS0-0.055-0.00831.4820.0010.0010.0000.0000.0000.000
150B148ASN00.0330.05335.664-0.001-0.0010.0000.0000.0000.000
151B149PRO00.024-0.01237.8700.0030.0030.0000.0000.0000.000
152B150SER0-0.100-0.04840.8890.0020.0020.0000.0000.0000.000
153B151ILE00.0090.01039.8210.0020.0020.0000.0000.0000.000
154B152PRO0-0.013-0.01143.2660.0000.0000.0000.0000.0000.000
155B153GLU-1-0.814-0.92141.301-0.033-0.0330.0000.0000.0000.000
156B154LYS10.8930.94443.5550.0190.0190.0000.0000.0000.000
157B155ASN0-0.021-0.01644.4250.0030.0030.0000.0000.0000.000
158B156LYS10.8180.93038.5990.0380.0380.0000.0000.0000.000
159B157MET00.0070.03336.7010.0010.0010.0000.0000.0000.000
160B158THR00.0440.04038.626-0.002-0.0020.0000.0000.0000.000
161B159VAL00.0780.03336.3260.0010.0010.0000.0000.0000.000
162B160ASP-1-0.931-0.97838.077-0.012-0.0120.0000.0000.0000.000
163B161GLY0-0.049-0.03140.5550.0020.0020.0000.0000.0000.000
164B162LEU00.0690.03132.4530.0010.0010.0000.0000.0000.000
165B163LYS10.9250.95836.4960.0090.0090.0000.0000.0000.000
166B164ARG10.8960.94737.6940.0120.0120.0000.0000.0000.000
167B165ASN0-0.016-0.01036.4840.0020.0020.0000.0000.0000.000
168B166LEU0-0.0070.01032.1480.0000.0000.0000.0000.0000.000
169B167ARG10.8100.91535.4930.0010.0010.0000.0000.0000.000
170B168GLY00.0180.01037.206-0.001-0.0010.0000.0000.0000.000
171B169GLY0-0.008-0.01033.8010.0010.0010.0000.0000.0000.000
172B170ASN0-0.0020.00029.3210.0020.0020.0000.0000.0000.000
173B171ASN0-0.027-0.02230.5520.0030.0030.0000.0000.0000.000
174B172GLY00.0160.02232.5280.0020.0020.0000.0000.0000.000
175B173GLY00.0010.00934.543-0.001-0.0010.0000.0000.0000.000
176B174ASP-1-0.820-0.91335.1130.0060.0060.0000.0000.0000.000
177B175PHE00.0170.00028.4310.0020.0020.0000.0000.0000.000
178B176ASP-1-0.855-0.93931.3930.0030.0030.0000.0000.0000.000
179B177ALA0-0.015-0.02532.892-0.003-0.0030.0000.0000.0000.000
180B178LYS11.0241.01232.169-0.002-0.0020.0000.0000.0000.000
181B179PHE00.0400.02625.421-0.003-0.0030.0000.0000.0000.000
182B180LEU00.008-0.00129.980-0.005-0.0050.0000.0000.0000.000
183B181GLU-1-0.992-0.99632.155-0.015-0.0150.0000.0000.0000.000
184B182GLU-1-0.953-0.97226.410-0.027-0.0270.0000.0000.0000.000
185B183LEU00.0180.01827.435-0.005-0.0050.0000.0000.0000.000
186B184TYR0-0.062-0.07829.020-0.006-0.0060.0000.0000.0000.000
187B185SER0-0.031-0.03031.527-0.003-0.0030.0000.0000.0000.000
188B186GLU-1-0.819-0.89124.523-0.056-0.0560.0000.0000.0000.000
189B187ILE0-0.041-0.00327.456-0.006-0.0060.0000.0000.0000.000
190B188LYS10.9550.98228.9870.0330.0330.0000.0000.0000.000
191B189ALA0-0.052-0.01630.196-0.001-0.0010.0000.0000.0000.000
192B190LYS10.9060.95522.7730.1060.1060.0000.0000.0000.000
193B191PRO00.1210.06427.119-0.002-0.0020.0000.0000.0000.000
194B192PHE0-0.038-0.03423.263-0.009-0.0090.0000.0000.0000.000
195B193GLU-1-0.897-0.93621.556-0.162-0.1620.0000.0000.0000.000
196B194LEU0-0.021-0.01922.605-0.009-0.0090.0000.0000.0000.000
197B195ASN0-0.027-0.01421.5600.0090.0090.0000.0000.0000.000
198B196PHE00.005-0.00723.750-0.007-0.0070.0000.0000.0000.000
199B197VAL00.0070.01124.638-0.001-0.0010.0000.0000.0000.000
200B198LYS10.9170.95327.0470.1120.1120.0000.0000.0000.000
201B199THR0-0.016-0.03330.6300.0000.0000.0000.0000.0000.000
202B200SER00.0000.00931.2420.0070.0070.0000.0000.0000.000
203B201PRO0-0.0180.02927.446-0.004-0.0040.0000.0000.0000.000