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: 5J8YZ

Calculation Name: 3BZB-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BZB

Chain ID: B

ChEMBL ID:

UniProt ID: D0VWS8

Base Structure: X-ray

Registration Date: 2023-09-23

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2272436.646674
FMO2-HF: Nuclear repulsion 2194999.590942
FMO2-HF: Total energy -77437.055732
FMO2-MP2: Total energy -77664.214269


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:29:ARG)


Summations of interaction energy for fragment #1(B:29:ARG)
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.
-107.148-96.9845.34-7.139-8.364-0.071
Interaction energy analysis for fragmet #1(B:29:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.932 / q_NPA : 0.953
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].
3B31GLU-1-0.920-0.9622.082-98.030-90.6473.562-5.361-5.584-0.063
4B32ARG10.9340.9665.11329.15629.209-0.001-0.002-0.0500.000
5B33TYR0-0.026-0.0418.656-2.213-2.2130.0000.0000.0000.000
6B34GLN00.0340.05211.1170.5840.5840.0000.0000.0000.000
7B35SER00.0570.04014.550-0.463-0.4630.0000.0000.0000.000
8B36PRO0-0.027-0.01116.9760.1990.1990.0000.0000.0000.000
9B37ALA00.0400.00718.5930.7010.7010.0000.0000.0000.000
10B38GLY0-0.031-0.01921.3990.1540.1540.0000.0000.0000.000
11B39ALA0-0.0130.00621.5930.4960.4960.0000.0000.0000.000
12B40PRO0-0.0130.01223.596-0.029-0.0290.0000.0000.0000.000
13B41LEU0-0.0040.01420.7490.2480.2480.0000.0000.0000.000
14B42GLN0-0.071-0.06921.059-1.055-1.0550.0000.0000.0000.000
15B43CYS0-0.041-0.02118.0160.0260.0260.0000.0000.0000.000
16B44SER0-0.017-0.03615.005-0.387-0.3870.0000.0000.0000.000
17B45VAL0-0.0120.01311.1250.4950.4950.0000.0000.0000.000
18B46GLN0-0.036-0.0288.754-2.941-2.9410.0000.0000.0000.000
19B47VAL00.0290.0206.1711.9671.9670.0000.0000.0000.000
20B48GLN00.007-0.0024.516-5.729-5.531-0.001-0.036-0.1610.000
21B49THR0-0.003-0.0072.3751.5052.5411.716-0.973-1.778-0.001
22B50THR00.0070.0123.125-6.414-4.9200.064-0.767-0.791-0.007
23B62SER0-0.026-0.0227.4180.1500.1500.0000.0000.0000.000
24B63GLY00.1190.0238.9311.9771.9770.0000.0000.0000.000
25B64ALA00.0200.0009.8451.5361.5360.0000.0000.0000.000
26B65ARG10.9010.9475.81438.58838.5880.0000.0000.0000.000
27B66ALA00.0370.03911.4531.5141.5140.0000.0000.0000.000
28B67LEU00.0210.01614.3351.2631.2630.0000.0000.0000.000
29B68ALA00.0270.01613.7291.1461.1460.0000.0000.0000.000
30B69ASP-1-0.807-0.91114.626-19.432-19.4320.0000.0000.0000.000
31B70THR0-0.095-0.06317.0071.1541.1540.0000.0000.0000.000
32B71LEU0-0.013-0.00918.8380.8480.8480.0000.0000.0000.000
33B72CYS0-0.024-0.00417.9610.5470.5470.0000.0000.0000.000
34B73TRP0-0.028-0.02020.1810.8450.8450.0000.0000.0000.000
35B74GLN0-0.042-0.00823.1090.2770.2770.0000.0000.0000.000
36B75PRO00.0950.05324.492-0.020-0.0200.0000.0000.0000.000
37B76GLU-1-0.872-0.95525.462-11.050-11.0500.0000.0000.0000.000
38B77LEU0-0.083-0.03823.7370.2530.2530.0000.0000.0000.000
39B78ILE0-0.080-0.01522.488-0.014-0.0140.0000.0000.0000.000
40B79ALA00.0290.03426.2010.1880.1880.0000.0000.0000.000
41B80GLY0-0.061-0.03728.3270.3130.3130.0000.0000.0000.000
42B81LYS10.8700.95228.33910.41010.4100.0000.0000.0000.000
43B82THR00.0470.03728.105-0.437-0.4370.0000.0000.0000.000
44B83VAL00.039-0.00822.339-0.021-0.0210.0000.0000.0000.000
45B84CYS0-0.0070.00223.038-0.220-0.2200.0000.0000.0000.000
46B85GLU-1-0.863-0.92315.765-19.494-19.4940.0000.0000.0000.000
47B86LEU0-0.012-0.00819.6690.1510.1510.0000.0000.0000.000
48B87GLY00.007-0.00416.678-0.431-0.4310.0000.0000.0000.000
49B88ALA00.0170.00814.668-1.189-1.1890.0000.0000.0000.000
50B89GLY00.0550.04011.244-1.471-1.4710.0000.0000.0000.000
51B90ALA0-0.035-0.0207.4180.4230.4230.0000.0000.0000.000
52B91GLY00.0640.0319.3420.9590.9590.0000.0000.0000.000
53B92LEU0-0.047-0.0119.5951.0761.0760.0000.0000.0000.000
54B93VAL00.017-0.00412.2131.2571.2570.0000.0000.0000.000
55B94SER00.020-0.00515.2631.5261.5260.0000.0000.0000.000
56B95ILE0-0.029-0.00612.5461.0541.0540.0000.0000.0000.000
57B96VAL0-0.015-0.01815.3810.8860.8860.0000.0000.0000.000
58B97ALA00.036-0.01117.9100.8850.8850.0000.0000.0000.000
59B98PHE0-0.005-0.00519.9060.7440.7440.0000.0000.0000.000
60B99LEU0-0.016-0.01117.5560.6330.6330.0000.0000.0000.000
61B100ALA0-0.008-0.00221.6520.3990.3990.0000.0000.0000.000
62B101GLY0-0.047-0.01423.8170.5460.5460.0000.0000.0000.000
63B102ALA0-0.0110.00624.4930.4770.4770.0000.0000.0000.000
64B103ASP-1-0.980-0.99226.392-10.127-10.1270.0000.0000.0000.000
65B104GLN0-0.017-0.02126.4620.0370.0370.0000.0000.0000.000
66B105VAL00.0070.01620.141-0.101-0.1010.0000.0000.0000.000
67B106VAL0-0.017-0.01122.3620.0380.0380.0000.0000.0000.000
68B107ALA00.0330.02516.804-0.233-0.2330.0000.0000.0000.000
69B108THR0-0.060-0.03218.7630.4770.4770.0000.0000.0000.000
70B109ASP-1-0.775-0.89714.243-21.107-21.1070.0000.0000.0000.000
71B110TYR00.016-0.00416.8541.5621.5620.0000.0000.0000.000
72B111PRO0-0.037-0.03017.173-0.402-0.4020.0000.0000.0000.000
73B112ASP-1-0.854-0.93413.520-18.228-18.2280.0000.0000.0000.000
74B113PRO0-0.0160.00314.911-0.480-0.4800.0000.0000.0000.000
75B114GLU-1-0.901-0.9539.397-19.811-19.8110.0000.0000.0000.000
76B115ILE0-0.044-0.01010.315-1.378-1.3780.0000.0000.0000.000
77B116LEU0-0.009-0.01911.673-0.285-0.2850.0000.0000.0000.000
78B117ASN00.0390.02112.2110.6810.6810.0000.0000.0000.000
79B118SER0-0.024-0.0047.794-0.176-0.1760.0000.0000.0000.000
80B119LEU00.0230.0319.753-0.114-0.1140.0000.0000.0000.000
81B120GLU-1-0.923-0.97912.047-14.231-14.2310.0000.0000.0000.000
82B121SER0-0.128-0.06410.2660.3750.3750.0000.0000.0000.000
83B122ASN00.016-0.0098.0520.0330.0330.0000.0000.0000.000
84B123ILE00.005-0.00411.6440.5550.5550.0000.0000.0000.000
85B124ARG10.9030.95114.84916.00216.0020.0000.0000.0000.000
86B125GLU-1-1.005-0.99411.628-19.197-19.1970.0000.0000.0000.000
87B126HIS0-0.052-0.01512.040-0.028-0.0280.0000.0000.0000.000
88B138ARG10.9740.98027.9239.2019.2010.0000.0000.0000.000
89B139ALA0-0.017-0.01927.016-0.248-0.2480.0000.0000.0000.000
90B140SER00.0390.02722.099-0.020-0.0200.0000.0000.0000.000
91B141PRO0-0.007-0.00319.4060.3160.3160.0000.0000.0000.000
92B142LYS10.9140.97320.87411.29411.2940.0000.0000.0000.000
93B143VAL00.0190.02016.298-0.269-0.2690.0000.0000.0000.000
94B144VAL0-0.036-0.02419.3900.6250.6250.0000.0000.0000.000
95B145PRO00.0060.00619.957-0.412-0.4120.0000.0000.0000.000
96B146TYR0-0.040-0.05020.7820.6200.6200.0000.0000.0000.000
97B147ARG10.8650.95021.58211.54611.5460.0000.0000.0000.000
98B148TRP00.0500.00418.1850.7210.7210.0000.0000.0000.000
99B149GLY0-0.035-0.01224.5050.1100.1100.0000.0000.0000.000
100B150ASP-1-0.822-0.89927.266-10.780-10.7800.0000.0000.0000.000
101B151SER0-0.024-0.01129.047-0.007-0.0070.0000.0000.0000.000
102B152PRO00.0700.01428.796-0.182-0.1820.0000.0000.0000.000
103B153ASP-1-0.859-0.91929.819-9.020-9.0200.0000.0000.0000.000
104B154SER0-0.088-0.05726.6080.0580.0580.0000.0000.0000.000
105B155LEU00.0870.03825.039-0.027-0.0270.0000.0000.0000.000
106B156GLN0-0.068-0.00727.6600.1590.1590.0000.0000.0000.000
107B157ARG10.9250.95031.0999.4009.4000.0000.0000.0000.000
108B158CYS0-0.074-0.02926.3930.0940.0940.0000.0000.0000.000
109B159THR0-0.058-0.05326.137-0.052-0.0520.0000.0000.0000.000
110B160GLY00.0110.03328.9240.1290.1290.0000.0000.0000.000
111B161LEU0-0.009-0.00828.9570.2150.2150.0000.0000.0000.000
112B162GLN00.0000.00331.514-0.290-0.2900.0000.0000.0000.000
113B163ARG10.8500.93331.0659.1589.1580.0000.0000.0000.000
114B164PHE00.0180.00726.8700.0810.0810.0000.0000.0000.000
115B165GLN0-0.035-0.01229.7070.0160.0160.0000.0000.0000.000
116B166VAL00.0150.01023.9990.0180.0180.0000.0000.0000.000
117B167VAL0-0.0110.00123.488-0.096-0.0960.0000.0000.0000.000
118B168LEU0-0.014-0.01819.0170.0290.0290.0000.0000.0000.000
119B169LEU00.019-0.00218.710-0.222-0.2220.0000.0000.0000.000
120B170ALA00.0400.01013.8690.2130.2130.0000.0000.0000.000
121B171ASP-1-0.829-0.91911.948-24.412-24.4120.0000.0000.0000.000
122B172LEU0-0.0060.02014.303-0.382-0.3820.0000.0000.0000.000
123B173LEU0-0.022-0.01217.0300.7970.7970.0000.0000.0000.000
124B174SER00.0110.01514.1240.9150.9150.0000.0000.0000.000
125B175PHE00.0300.01317.2750.3210.3210.0000.0000.0000.000
126B176HIS00.0860.01419.7520.1400.1400.0000.0000.0000.000
127B177GLN0-0.025-0.00323.3000.5320.5320.0000.0000.0000.000
128B178ALA0-0.0040.01021.7880.3610.3610.0000.0000.0000.000
129B179HIS0-0.039-0.02121.3840.5870.5870.0000.0000.0000.000
130B180ASP-1-0.811-0.90924.955-10.315-10.3150.0000.0000.0000.000
131B181ALA0-0.015-0.00425.2060.2430.2430.0000.0000.0000.000
132B182LEU00.0310.02820.6270.2870.2870.0000.0000.0000.000
133B183LEU00.0030.01624.9350.1220.1220.0000.0000.0000.000
134B184ARG10.8560.91928.05510.76710.7670.0000.0000.0000.000
135B185SER00.016-0.00325.6750.1500.1500.0000.0000.0000.000
136B186VAL00.0290.01725.2380.2300.2300.0000.0000.0000.000
137B187LYS10.8220.89227.7799.7219.7210.0000.0000.0000.000
138B188MET0-0.054-0.02930.6360.3930.3930.0000.0000.0000.000
139B189LEU00.0220.01025.6360.2140.2140.0000.0000.0000.000
140B190LEU00.0240.03728.455-0.001-0.0010.0000.0000.0000.000
141B191ALA0-0.008-0.02430.4250.3860.3860.0000.0000.0000.000
142B192LEU00.0050.00133.4090.0210.0210.0000.0000.0000.000
143B193PRO00.0540.01836.5800.0640.0640.0000.0000.0000.000
144B194ALA0-0.054-0.02638.4240.1080.1080.0000.0000.0000.000
145B195ASN0-0.048-0.02337.8920.2830.2830.0000.0000.0000.000
146B196ASP-1-0.771-0.91033.580-9.314-9.3140.0000.0000.0000.000
147B197PRO0-0.043-0.00735.654-0.179-0.1790.0000.0000.0000.000
148B198THR0-0.082-0.03733.493-0.164-0.1640.0000.0000.0000.000
149B199ALA0-0.0020.02531.215-0.302-0.3020.0000.0000.0000.000
150B200VAL0-0.043-0.02726.9850.0930.0930.0000.0000.0000.000
151B201ALA00.0190.00225.158-0.210-0.2100.0000.0000.0000.000
152B202LEU0-0.027-0.00921.9100.1780.1780.0000.0000.0000.000
153B203VAL0-0.005-0.00420.329-0.551-0.5510.0000.0000.0000.000
154B204THR0-0.0050.02614.8740.5670.5670.0000.0000.0000.000
155B205PHE0-0.018-0.01015.486-0.464-0.4640.0000.0000.0000.000
156B206THR00.003-0.00811.2510.2650.2650.0000.0000.0000.000
157B207HIS0-0.073-0.03714.1940.2650.2650.0000.0000.0000.000
158B208HIS00.0180.00310.3450.3420.3420.0000.0000.0000.000
159B209ARG10.8630.89615.80915.14615.1460.0000.0000.0000.000
160B210PRO0-0.0010.01419.557-0.052-0.0520.0000.0000.0000.000
161B211HIS00.0270.01121.8900.2480.2480.0000.0000.0000.000
162B212LEU0-0.032-0.00321.389-0.237-0.2370.0000.0000.0000.000
163B213ALA00.0110.00724.0550.5880.5880.0000.0000.0000.000
164B214GLU-1-0.888-0.96226.056-10.283-10.2830.0000.0000.0000.000
165B215ARG00.0230.01822.356-0.158-0.1580.0000.0000.0000.000
166B216ASP-1-0.812-0.90520.991-14.679-14.6790.0000.0000.0000.000
167B217LEU00.0190.01422.438-0.327-0.3270.0000.0000.0000.000
168B218ALA0-0.046-0.01925.0620.3800.3800.0000.0000.0000.000
169B219PHE00.0300.02023.5330.3590.3590.0000.0000.0000.000
170B220PHE00.0650.01522.0190.3800.3800.0000.0000.0000.000
171B221ARG10.8890.95627.33611.05611.0560.0000.0000.0000.000
172B222LEU00.0070.00728.0790.3620.3620.0000.0000.0000.000
173B223VAL0-0.042-0.02827.4830.2650.2650.0000.0000.0000.000
174B224ASN00.0060.00830.5580.2610.2610.0000.0000.0000.000
175B225ALA0-0.0440.00033.2870.2910.2910.0000.0000.0000.000
176B226ASP-1-0.845-0.89933.609-8.906-8.9060.0000.0000.0000.000
177B227GLY00.0480.02235.391-0.029-0.0290.0000.0000.0000.000
178B228ALA0-0.051-0.03035.004-0.024-0.0240.0000.0000.0000.000
179B229LEU0-0.024-0.01129.8760.0100.0100.0000.0000.0000.000
180B230ILE00.0100.01832.9620.1300.1300.0000.0000.0000.000
181B231ALA00.004-0.01027.888-0.320-0.3200.0000.0000.0000.000
182B232GLU-1-0.805-0.91128.432-9.509-9.5090.0000.0000.0000.000
183B233PRO0-0.020-0.00326.084-0.443-0.4430.0000.0000.0000.000
184B234TRP0-0.021-0.00621.0900.2830.2830.0000.0000.0000.000
185B235LEU00.006-0.00523.0240.2900.2900.0000.0000.0000.000
186B236SER00.0010.00623.983-0.194-0.1940.0000.0000.0000.000
187B237PRO00.0180.00420.095-0.387-0.3870.0000.0000.0000.000
188B238LEU00.0030.01916.6810.3480.3480.0000.0000.0000.000
189B239GLN00.0440.01116.602-0.296-0.2960.0000.0000.0000.000
190B240MET00.0010.01711.417-0.827-0.8270.0000.0000.0000.000
191B256GLN00.0020.00514.8040.3860.3860.0000.0000.0000.000
192B257VAL0-0.078-0.04212.865-0.555-0.5550.0000.0000.0000.000
193B258HIS00.007-0.00315.8501.2031.2030.0000.0000.0000.000
194B259ARG10.9170.94518.63814.10514.1050.0000.0000.0000.000
195B260TRP00.0160.00520.9490.8930.8930.0000.0000.0000.000
196B261ARG10.9020.95823.37210.20210.2020.0000.0000.0000.000
197B262LEU00.0020.00925.7350.2850.2850.0000.0000.0000.000
198B263ARG10.8850.93828.3389.3119.3110.0000.0000.0000.000
199B264TRP0-0.0020.00731.5370.1640.1640.0000.0000.0000.000
200B265ARG10.9200.96134.8968.3188.3180.0000.0000.0000.000