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

tag_button

FMODB ID: G6R51

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2262738.755542
FMO2-HF: Nuclear repulsion 2182961.091502
FMO2-HF: Total energy -79777.66404
FMO2-MP2: Total energy -80012.991499


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.
-2.999-0.0350000000000010.248-1.669-1.544-0.009
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 : -0.019 / q_NPA : -0.013
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].
3B1SER00.016-0.0083.8000.4571.642-0.024-0.609-0.5530.000
4B2HIS00.0260.0196.9350.1770.1770.0000.0000.0000.000
5B3PRO00.0590.0089.841-0.147-0.1470.0000.0000.0000.000
6B4GLU-1-0.819-0.88612.187-0.064-0.0640.0000.0000.0000.000
7B5ILE0-0.0110.00411.062-0.027-0.0270.0000.0000.0000.000
8B6GLU-1-0.945-0.9719.463-0.672-0.6720.0000.0000.0000.000
9B7LYS10.8150.88912.2640.0450.0450.0000.0000.0000.000
10B8ALA0-0.0010.00215.7360.0090.0090.0000.0000.0000.000
11B9GLN0-0.002-0.00512.691-0.019-0.0190.0000.0000.0000.000
12B10ARG10.9390.96215.4590.2250.2250.0000.0000.0000.000
13B11GLU-1-0.839-0.89718.775-0.094-0.0940.0000.0000.0000.000
14B12ILE0-0.013-0.00614.8720.0130.0130.0000.0000.0000.000
15B13ILE0-0.020-0.01014.7440.0070.0070.0000.0000.0000.000
16B14GLU-1-0.957-0.96818.198-0.127-0.1270.0000.0000.0000.000
17B15ALA0-0.014-0.00820.9750.0150.0150.0000.0000.0000.000
18B16PHE0-0.026-0.02118.1030.0130.0130.0000.0000.0000.000
19B17ASN0-0.009-0.03419.6030.0060.0060.0000.0000.0000.000
20B18ALA0-0.0070.03322.2660.0110.0110.0000.0000.0000.000
21B19LYS10.9150.94124.0490.0770.0770.0000.0000.0000.000
22B20PRO00.1070.06220.8660.0030.0030.0000.0000.0000.000
23B21LYS10.8870.92220.6580.0470.0470.0000.0000.0000.000
24B22ASN0-0.039-0.00922.1600.0140.0140.0000.0000.0000.000
25B23GLY00.0640.03719.3960.0040.0040.0000.0000.0000.000
26B24ILE0-0.003-0.00916.134-0.006-0.0060.0000.0000.0000.000
27B25ASN0-0.019-0.02818.0820.0170.0170.0000.0000.0000.000
28B26LYS10.9440.98519.2980.0970.0970.0000.0000.0000.000
29B27ILE00.0040.01013.1190.0090.0090.0000.0000.0000.000
30B28LYS10.8400.90015.9690.0480.0480.0000.0000.0000.000
31B29GLU-1-0.904-0.94517.841-0.015-0.0150.0000.0000.0000.000
32B30ILE00.0000.00115.5740.0170.0170.0000.0000.0000.000
33B31CYS0-0.054-0.03013.9410.0300.0300.0000.0000.0000.000
34B32GLU-1-0.947-0.95916.0590.0840.0840.0000.0000.0000.000
35B33GLN0-0.0170.00119.5760.0080.0080.0000.0000.0000.000
36B34TYR0-0.132-0.09515.9860.0190.0190.0000.0000.0000.000
37B35LYS10.8640.94316.629-0.092-0.0920.0000.0000.0000.000
38B36ILE0-0.0040.01411.4990.0510.0510.0000.0000.0000.000
39B37SER0-0.008-0.03412.136-0.075-0.0750.0000.0000.0000.000
40B38PRO00.0610.01512.0120.0010.0010.0000.0000.0000.000
41B39ASN0-0.052-0.02212.644-0.035-0.0350.0000.0000.0000.000
42B40GLU-1-0.787-0.8938.1070.2060.2060.0000.0000.0000.000
43B41GLU-1-0.772-0.8658.137-0.226-0.2260.0000.0000.0000.000
44B42ILE0-0.038-0.0299.421-0.161-0.1610.0000.0000.0000.000
45B43ALA0-0.023-0.0018.948-0.088-0.0880.0000.0000.0000.000
46B44GLU-1-0.853-0.9283.187-4.994-3.3830.255-0.991-0.875-0.009
47B45PHE00.0200.0116.532-0.332-0.3320.0000.0000.0000.000
48B46PHE0-0.030-0.0209.425-0.039-0.0390.0000.0000.0000.000
49B47HIS10.8050.9096.4320.5480.5480.0000.0000.0000.000
50B48GLN0-0.045-0.0253.4810.9051.0730.017-0.069-0.1160.000
51B49GLN0-0.011-0.0087.7720.1900.1900.0000.0000.0000.000
52B50ARG10.9240.96110.8650.5230.5230.0000.0000.0000.000
53B51LYS10.8490.89912.7680.5250.5250.0000.0000.0000.000
54B52ASN0-0.033-0.00114.4480.0750.0750.0000.0000.0000.000
55B53LEU0-0.0020.01413.7230.0390.0390.0000.0000.0000.000
56B54ASP-1-0.809-0.89017.395-0.160-0.1600.0000.0000.0000.000
57B55LEU0-0.001-0.03715.9530.0080.0080.0000.0000.0000.000
58B56GLU-1-0.845-0.92318.930-0.120-0.1200.0000.0000.0000.000
59B57ALA00.0220.02520.9040.0120.0120.0000.0000.0000.000
60B58VAL0-0.033-0.01114.7480.0100.0100.0000.0000.0000.000
61B59GLY00.0190.01718.0370.0140.0140.0000.0000.0000.000
62B60ASP-1-0.852-0.89819.570-0.067-0.0670.0000.0000.0000.000
63B61TYR0-0.012-0.03316.5400.0140.0140.0000.0000.0000.000
64B62LEU00.0210.00614.0280.0210.0210.0000.0000.0000.000
65B63SER00.003-0.00218.0990.0200.0200.0000.0000.0000.000
66B64SER0-0.044-0.02921.3510.0130.0130.0000.0000.0000.000
67B65PRO0-0.012-0.01722.3300.0040.0040.0000.0000.0000.000
68B66GLU-1-0.910-0.94022.991-0.006-0.0060.0000.0000.0000.000
69B67ALA00.0360.01022.003-0.001-0.0010.0000.0000.0000.000
70B68GLU-1-0.761-0.85218.638-0.024-0.0240.0000.0000.0000.000
71B69ASN0-0.034-0.03617.7110.0100.0100.0000.0000.0000.000
72B70GLN00.0560.02717.476-0.014-0.0140.0000.0000.0000.000
73B71GLN00.0160.02315.4280.0180.0180.0000.0000.0000.000
74B72VAL0-0.025-0.00812.6920.0210.0210.0000.0000.0000.000
75B73LEU0-0.0040.01612.717-0.011-0.0110.0000.0000.0000.000
76B74LYS10.9040.95013.727-0.171-0.1710.0000.0000.0000.000
77B75ALA0-0.010-0.0059.8740.0190.0190.0000.0000.0000.000
78B76PHE0-0.011-0.0099.3000.0160.0160.0000.0000.0000.000
79B77THR00.025-0.0259.842-0.055-0.0550.0000.0000.0000.000
80B78SER0-0.064-0.02210.1910.0250.0250.0000.0000.0000.000
81B79GLN00.0180.0085.387-0.108-0.1080.0000.0000.0000.000
82B80MET0-0.087-0.0206.904-0.084-0.0840.0000.0000.0000.000
83B81ASN0-0.011-0.0049.4600.0990.0990.0000.0000.0000.000
84B82PHE0-0.031-0.04111.071-0.043-0.0430.0000.0000.0000.000
85B83ASN00.0090.02213.702-0.002-0.0020.0000.0000.0000.000
86B84GLY00.0010.00814.668-0.022-0.0220.0000.0000.0000.000
87B85GLN0-0.007-0.01914.411-0.040-0.0400.0000.0000.0000.000
88B86SER0-0.018-0.01618.2460.0120.0120.0000.0000.0000.000
89B87PHE00.0440.01220.189-0.010-0.0100.0000.0000.0000.000
90B88VAL0-0.0030.00321.220-0.008-0.0080.0000.0000.0000.000
91B89GLU-1-0.938-0.96319.146-0.098-0.0980.0000.0000.0000.000
92B90GLY00.0460.02416.899-0.019-0.0190.0000.0000.0000.000
93B91LEU0-0.005-0.00517.358-0.015-0.0150.0000.0000.0000.000
94B92ARG10.8070.89019.7060.0870.0870.0000.0000.0000.000
95B93THR0-0.030-0.01613.854-0.019-0.0190.0000.0000.0000.000
96B94PHE00.0040.00614.797-0.027-0.0270.0000.0000.0000.000
97B95LEU00.001-0.00816.242-0.015-0.0150.0000.0000.0000.000
98B96LYS10.7940.89317.7600.1930.1930.0000.0000.0000.000
99B97THR0-0.073-0.02612.607-0.040-0.0400.0000.0000.0000.000
100B98PHE0-0.017-0.01015.573-0.032-0.0320.0000.0000.0000.000
101B99LYS10.8820.96918.1420.1820.1820.0000.0000.0000.000
102B100LEU00.029-0.00121.2180.0050.0050.0000.0000.0000.000
103B101PRO00.0880.04622.4090.0020.0020.0000.0000.0000.000
104B102GLY00.0170.01825.5210.0040.0040.0000.0000.0000.000
105B103GLU-1-0.865-0.96428.104-0.053-0.0530.0000.0000.0000.000
106B104ALA00.0260.00828.012-0.002-0.0020.0000.0000.0000.000
107B105GLN00.0360.00628.3640.0000.0000.0000.0000.0000.000
108B106LYS10.7980.91124.5120.0740.0740.0000.0000.0000.000
109B107ILE00.0040.00123.684-0.003-0.0030.0000.0000.0000.000
110B108ASP-1-0.804-0.86823.843-0.022-0.0220.0000.0000.0000.000
111B109ARG10.8970.94822.3260.0390.0390.0000.0000.0000.000
112B110LEU0-0.032-0.00418.2660.0050.0050.0000.0000.0000.000
113B111VAL00.004-0.00619.6740.0020.0020.0000.0000.0000.000
114B112GLN0-0.036-0.02121.5870.0120.0120.0000.0000.0000.000
115B113SER00.0160.02516.2970.0140.0140.0000.0000.0000.000
116B114PHE0-0.0120.00016.9420.0150.0150.0000.0000.0000.000
117B115SER0-0.035-0.02018.1760.0120.0120.0000.0000.0000.000
118B116GLY00.0130.00019.3160.0090.0090.0000.0000.0000.000
119B117ALA0-0.020-0.01714.2510.0200.0200.0000.0000.0000.000
120B118TYR00.0470.01316.1910.0160.0160.0000.0000.0000.000
121B119PHE00.0260.01518.2360.0090.0090.0000.0000.0000.000
122B120GLN0-0.037-0.02016.3870.0220.0220.0000.0000.0000.000
123B121GLN0-0.016-0.00511.7330.0010.0010.0000.0000.0000.000
124B122ASN0-0.057-0.02116.299-0.006-0.0060.0000.0000.0000.000
125B123PRO0-0.015-0.00219.295-0.010-0.0100.0000.0000.0000.000
126B124ASP-1-0.914-0.96021.8850.0480.0480.0000.0000.0000.000
127B125VAL0-0.047-0.01022.427-0.008-0.0080.0000.0000.0000.000
128B126VAL0-0.065-0.03423.283-0.008-0.0080.0000.0000.0000.000
129B127SER0-0.0080.00125.1730.0070.0070.0000.0000.0000.000
130B128ASN00.036-0.00425.1190.0040.0040.0000.0000.0000.000
131B129ALA00.0600.02022.694-0.006-0.0060.0000.0000.0000.000
132B130ASP-1-0.886-0.94224.0410.0220.0220.0000.0000.0000.000
133B131ALA00.0030.01427.437-0.007-0.0070.0000.0000.0000.000
134B132ALA00.0070.00422.808-0.007-0.0070.0000.0000.0000.000
135B133TYR0-0.076-0.07224.906-0.008-0.0080.0000.0000.0000.000
136B134LEU0-0.0010.01725.843-0.007-0.0070.0000.0000.0000.000
137B135LEU00.0170.01326.437-0.005-0.0050.0000.0000.0000.000
138B136ALA00.0030.01323.907-0.007-0.0070.0000.0000.0000.000
139B137PHE00.0130.00625.785-0.007-0.0070.0000.0000.0000.000
140B138GLN00.0200.00828.784-0.001-0.0010.0000.0000.0000.000
141B139THR00.015-0.02226.111-0.003-0.0030.0000.0000.0000.000
142B140ILE0-0.004-0.00324.575-0.006-0.0060.0000.0000.0000.000
143B141MET0-0.020-0.00228.479-0.003-0.0030.0000.0000.0000.000
144B142LEU0-0.011-0.00531.155-0.001-0.0010.0000.0000.0000.000
145B143ASN00.0180.01128.482-0.004-0.0040.0000.0000.0000.000
146B144THR0-0.049-0.02130.596-0.004-0.0040.0000.0000.0000.000
147B145ASP-1-0.893-0.95733.021-0.034-0.0340.0000.0000.0000.000
148B146LEU0-0.076-0.04033.3310.0010.0010.0000.0000.0000.000
149B147HIS0-0.050-0.03031.5740.0010.0010.0000.0000.0000.000
150B148ASN00.0290.04635.665-0.002-0.0020.0000.0000.0000.000
151B149PRO00.022-0.00737.8920.0030.0030.0000.0000.0000.000
152B150SER0-0.102-0.04740.8900.0020.0020.0000.0000.0000.000
153B151ILE00.0120.00939.9130.0020.0020.0000.0000.0000.000
154B152PRO0-0.004-0.00443.268-0.001-0.0010.0000.0000.0000.000
155B153GLU-1-0.770-0.88340.890-0.035-0.0350.0000.0000.0000.000
156B154LYS10.9050.94843.5560.0200.0200.0000.0000.0000.000
157B155ASN0-0.037-0.02544.4310.0020.0020.0000.0000.0000.000
158B156LYS10.8120.92538.9280.0390.0390.0000.0000.0000.000
159B157MET00.0080.03436.9210.0010.0010.0000.0000.0000.000
160B158THR00.001-0.01438.645-0.002-0.0020.0000.0000.0000.000
161B159VAL00.0650.02635.8930.0010.0010.0000.0000.0000.000
162B160ASP-1-0.877-0.92838.079-0.013-0.0130.0000.0000.0000.000
163B161GLY0-0.053-0.02840.5570.0020.0020.0000.0000.0000.000
164B162LEU00.0680.02732.4970.0010.0010.0000.0000.0000.000
165B163LYS10.8110.88736.4030.0120.0120.0000.0000.0000.000
166B164ARG10.8890.94837.6960.0120.0120.0000.0000.0000.000
167B165ASN0-0.027-0.02236.2180.0020.0020.0000.0000.0000.000
168B166LEU00.0040.01131.9710.0000.0000.0000.0000.0000.000
169B167ARG10.7910.88535.4960.0000.0000.0000.0000.0000.000
170B168GLY00.0070.00337.2090.0000.0000.0000.0000.0000.000
171B169GLY0-0.001-0.00833.7990.0020.0020.0000.0000.0000.000
172B170ASN0-0.022-0.01829.4390.0030.0030.0000.0000.0000.000
173B171ASN0-0.033-0.02630.4940.0020.0020.0000.0000.0000.000
174B172GLY00.0260.02832.5260.0020.0020.0000.0000.0000.000
175B173GLY00.0030.01034.547-0.002-0.0020.0000.0000.0000.000
176B174ASP-1-0.798-0.87735.1160.0050.0050.0000.0000.0000.000
177B175PHE00.019-0.00128.4900.0030.0030.0000.0000.0000.000
178B176ASP-1-0.839-0.93231.3320.0010.0010.0000.0000.0000.000
179B177ALA0-0.010-0.01332.893-0.003-0.0030.0000.0000.0000.000
180B178LYS10.9981.00032.116-0.001-0.0010.0000.0000.0000.000
181B179PHE00.0460.02625.394-0.004-0.0040.0000.0000.0000.000
182B180LEU00.0150.00429.982-0.005-0.0050.0000.0000.0000.000
183B181GLU-1-0.857-0.92532.156-0.015-0.0150.0000.0000.0000.000
184B182GLU-1-0.963-0.96626.578-0.028-0.0280.0000.0000.0000.000
185B183LEU00.0210.01727.451-0.006-0.0060.0000.0000.0000.000
186B184TYR0-0.059-0.06729.022-0.006-0.0060.0000.0000.0000.000
187B185SER0-0.038-0.03931.413-0.003-0.0030.0000.0000.0000.000
188B186GLU-1-0.819-0.88124.544-0.061-0.0610.0000.0000.0000.000
189B187ILE0-0.043-0.00826.741-0.006-0.0060.0000.0000.0000.000
190B188LYS10.9640.99328.9890.0330.0330.0000.0000.0000.000
191B189ALA0-0.046-0.01530.210-0.001-0.0010.0000.0000.0000.000
192B190LYS10.9130.95423.1270.1090.1090.0000.0000.0000.000
193B191PRO00.1210.07627.120-0.002-0.0020.0000.0000.0000.000
194B192PHE0-0.029-0.03323.428-0.009-0.0090.0000.0000.0000.000
195B193GLU-1-0.835-0.89721.494-0.173-0.1730.0000.0000.0000.000
196B194LEU0-0.014-0.01122.606-0.009-0.0090.0000.0000.0000.000
197B195ASN0-0.0020.00622.4330.0000.0000.0000.0000.0000.000
198B196PHE00.019-0.00223.751-0.007-0.0070.0000.0000.0000.000
199B197VAL0-0.013-0.00224.609-0.002-0.0020.0000.0000.0000.000
200B198LYS10.8350.91127.0480.1250.1250.0000.0000.0000.000
201B199THR0-0.009-0.02330.6310.0000.0000.0000.0000.0000.000
202B200SER0-0.0050.00931.5030.0070.0070.0000.0000.0000.000
203B201PRO0-0.0080.02627.445-0.005-0.0050.0000.0000.0000.000