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: JL8K9

Calculation Name: 5BV0-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5BV0

Chain ID: B

ChEMBL ID:

UniProt ID: G0SCM5

Base Structure: X-ray

Registration Date: 2023-09-20

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2092447.387546
FMO2-HF: Nuclear repulsion 2010432.125615
FMO2-HF: Total energy -82015.261931
FMO2-MP2: Total energy -82256.54255


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:524:GLU)


Summations of interaction energy for fragment #1(B:524:GLU)
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.
52.98755.518-0.016-1.121-1.3930.004
Interaction energy analysis for fragmet #1(B:524:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.941 / q_NPA : -0.974
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].
3B526LEU0-0.0010.0243.794-3.157-0.626-0.016-1.121-1.3930.004
4B527ASN0-0.041-0.0415.366-10.885-10.8850.0000.0000.0000.000
5B528HIS0-0.007-0.0027.424-2.048-2.0480.0000.0000.0000.000
6B529GLU-1-0.993-0.9479.64826.03726.0370.0000.0000.0000.000
7B530PRO00.039-0.00410.4481.2081.2080.0000.0000.0000.000
8B531ARG10.9740.95613.889-15.987-15.9870.0000.0000.0000.000
9B532ALA00.0520.02714.930-0.007-0.0070.0000.0000.0000.000
10B533GLY00.0390.01915.907-1.034-1.0340.0000.0000.0000.000
11B534ARG10.8970.92117.392-15.566-15.5660.0000.0000.0000.000
12B535GLN00.0940.04511.042-1.717-1.7170.0000.0000.0000.000
13B536VAL00.0750.04613.0951.1761.1760.0000.0000.0000.000
14B537PRO0-0.040-0.02615.422-0.091-0.0910.0000.0000.0000.000
15B538LEU00.0090.02211.025-0.494-0.4940.0000.0000.0000.000
16B539LEU00.0530.0539.2030.3200.3200.0000.0000.0000.000
17B540LEU0-0.025-0.00212.665-0.084-0.0840.0000.0000.0000.000
18B541SER0-0.131-0.08914.593-0.430-0.4300.0000.0000.0000.000
19B542MET0-0.040-0.0248.4420.3240.3240.0000.0000.0000.000
20B543GLU-1-0.980-0.98812.43217.69317.6930.0000.0000.0000.000
21B544GLU-1-0.925-0.9518.80830.39430.3940.0000.0000.0000.000
22B545ASP-1-0.868-0.94812.31917.00217.0020.0000.0000.0000.000
23B546GLU-1-0.972-0.98713.64519.09919.0990.0000.0000.0000.000
24B547LEU00.0190.0167.773-0.195-0.1950.0000.0000.0000.000
25B548ALA0-0.014-0.02112.422-0.295-0.2950.0000.0000.0000.000
26B549LEU0-0.030-0.01714.626-0.776-0.7760.0000.0000.0000.000
27B550ASP-1-0.815-0.91113.92617.86017.8600.0000.0000.0000.000
28B551LYS10.8670.92811.113-23.923-23.9230.0000.0000.0000.000
29B552ALA0-0.017-0.00215.257-0.653-0.6530.0000.0000.0000.000
30B553ILE0-0.0250.00718.616-0.938-0.9380.0000.0000.0000.000
31B554GLU-1-0.921-0.96213.99920.25620.2560.0000.0000.0000.000
32B555SER0-0.073-0.04918.327-0.543-0.5430.0000.0000.0000.000
33B556GLY0-0.025-0.00620.110-0.492-0.4920.0000.0000.0000.000
34B557ASP-1-0.879-0.94722.95911.91411.9140.0000.0000.0000.000
35B558THR00.013-0.01924.2080.3790.3790.0000.0000.0000.000
36B559ASP-1-0.916-0.94626.54011.27311.2730.0000.0000.0000.000
37B560LEU0-0.060-0.02319.2520.2730.2730.0000.0000.0000.000
38B561ILE00.000-0.00622.0250.4330.4330.0000.0000.0000.000
39B562TYR00.0340.01423.1570.0600.0600.0000.0000.0000.000
40B563PHE0-0.041-0.00820.6780.0370.0370.0000.0000.0000.000
41B564VAL0-0.006-0.00418.6340.0680.0680.0000.0000.0000.000
42B565ILE00.0130.01121.5830.0160.0160.0000.0000.0000.000
43B566HIS0-0.024-0.02124.184-0.281-0.2810.0000.0000.0000.000
44B567GLN0-0.025-0.01920.5390.0720.0720.0000.0000.0000.000
45B568LEU00.0320.00918.846-0.177-0.1770.0000.0000.0000.000
46B569ARG10.9420.98522.932-10.080-10.0800.0000.0000.0000.000
47B570ARG10.8790.94426.506-10.604-10.6040.0000.0000.0000.000
48B571LYS10.9410.99217.854-16.744-16.7440.0000.0000.0000.000
49B572LEU0-0.009-0.00520.852-0.038-0.0380.0000.0000.0000.000
50B573PRO00.0130.00924.852-0.458-0.4580.0000.0000.0000.000
51B574LEU00.0500.02526.6000.3670.3670.0000.0000.0000.000
52B575ALA00.0760.03827.7220.1920.1920.0000.0000.0000.000
53B576SER0-0.043-0.01122.1070.3210.3210.0000.0000.0000.000
54B577PHE00.000-0.00323.2550.3920.3920.0000.0000.0000.000
55B578PHE00.020-0.01624.5090.1820.1820.0000.0000.0000.000
56B579ARG10.9610.98519.028-14.051-14.0510.0000.0000.0000.000
57B580VAL0-0.018-0.00919.2350.2840.2840.0000.0000.0000.000
58B581VAL0-0.020-0.01821.2850.3060.3060.0000.0000.0000.000
59B582SER0-0.0100.00323.6590.0470.0470.0000.0000.0000.000
60B583SER0-0.0220.00120.3750.1000.1000.0000.0000.0000.000
61B584ARG10.8540.93315.283-17.098-17.0980.0000.0000.0000.000
62B585PRO00.0580.01522.002-0.245-0.2450.0000.0000.0000.000
63B586THR00.0220.00523.341-0.428-0.4280.0000.0000.0000.000
64B587ALA00.0050.01322.599-0.249-0.2490.0000.0000.0000.000
65B588SER00.0500.02124.719-0.428-0.4280.0000.0000.0000.000
66B589ALA0-0.029-0.00527.482-0.396-0.3960.0000.0000.0000.000
67B590MET0-0.0240.00327.467-0.229-0.2290.0000.0000.0000.000
68B591VAL0-0.014-0.01827.245-0.262-0.2620.0000.0000.0000.000
69B592GLU-1-0.793-0.86729.9409.1049.1040.0000.0000.0000.000
70B593ALA0-0.055-0.02132.574-0.334-0.3340.0000.0000.0000.000
71B594LEU00.014-0.00430.562-0.255-0.2550.0000.0000.0000.000
72B595ALA0-0.0260.00334.428-0.182-0.1820.0000.0000.0000.000
73B596ARG10.9000.95335.903-8.682-8.6820.0000.0000.0000.000
74B597ASN0-0.007-0.01337.656-0.271-0.2710.0000.0000.0000.000
75B598SER0-0.047-0.00638.2550.2390.2390.0000.0000.0000.000
76B599ASP-1-0.819-0.88039.8356.9816.9810.0000.0000.0000.000
77B600GLY0-0.110-0.05541.649-0.033-0.0330.0000.0000.0000.000
78B601ASP-1-0.888-0.95541.6827.1477.1470.0000.0000.0000.000
79B602GLY0-0.049-0.04443.421-0.029-0.0290.0000.0000.0000.000
80B603ASN0-0.091-0.03344.353-0.039-0.0390.0000.0000.0000.000
81B604GLU-1-0.931-0.97441.2447.7297.7290.0000.0000.0000.000
82B605ASP-1-0.911-0.95136.8468.3878.3870.0000.0000.0000.000
83B606THR00.016-0.02738.2510.2200.2200.0000.0000.0000.000
84B607ALA0-0.043-0.02139.2580.0190.0190.0000.0000.0000.000
85B608LEU00.0260.02831.9710.1560.1560.0000.0000.0000.000
86B609LEU0-0.002-0.00234.7740.1860.1860.0000.0000.0000.000
87B610LYS10.8940.95436.092-7.171-7.1710.0000.0000.0000.000
88B611ASP-1-0.911-0.95134.2618.5308.5300.0000.0000.0000.000
89B612LEU0-0.037-0.01729.6120.1640.1640.0000.0000.0000.000
90B613TYR0-0.068-0.09332.0890.0380.0380.0000.0000.0000.000
91B614TYR0-0.058-0.01334.655-0.106-0.1060.0000.0000.0000.000
92B615GLN0-0.020-0.03030.2780.2700.2700.0000.0000.0000.000
93B616ASP-1-0.843-0.92428.83410.75810.7580.0000.0000.0000.000
94B617ASP-1-0.957-0.96231.2868.7858.7850.0000.0000.0000.000
95B618ARG10.8170.92730.692-9.696-9.6960.0000.0000.0000.000
96B619ARG10.9320.94035.380-8.167-8.1670.0000.0000.0000.000
97B620LEU00.0110.00538.800-0.177-0.1770.0000.0000.0000.000
98B621ASP-1-0.877-0.93636.0908.3238.3230.0000.0000.0000.000
99B622GLY00.0420.01038.594-0.064-0.0640.0000.0000.0000.000
100B623ALA0-0.022-0.01739.759-0.166-0.1660.0000.0000.0000.000
101B624SER0-0.025-0.02941.358-0.218-0.2180.0000.0000.0000.000
102B625VAL0-0.0230.01139.718-0.123-0.1230.0000.0000.0000.000
103B626PHE00.0130.00342.895-0.119-0.1190.0000.0000.0000.000
104B627ILE00.008-0.00646.079-0.170-0.1700.0000.0000.0000.000
105B628ARG10.9620.97240.271-7.620-7.6200.0000.0000.0000.000
106B629GLU-1-0.851-0.93845.6196.7276.7270.0000.0000.0000.000
107B630ALA0-0.043-0.02948.366-0.139-0.1390.0000.0000.0000.000
108B631LEU0-0.073-0.03148.909-0.140-0.1400.0000.0000.0000.000
109B632GLN00.0050.01148.994-0.092-0.0920.0000.0000.0000.000
110B633GLN0-0.102-0.03851.762-0.125-0.1250.0000.0000.0000.000
111B634PRO00.0160.02054.952-0.046-0.0460.0000.0000.0000.000
112B635GLU-1-0.915-0.95458.3115.0475.0470.0000.0000.0000.000
113B636THR00.0800.02958.4100.1360.1360.0000.0000.0000.000
114B637ARG10.9600.98258.873-5.215-5.2150.0000.0000.0000.000
115B638THR00.0200.01855.5130.0360.0360.0000.0000.0000.000
116B639ALA00.0240.00554.1980.1190.1190.0000.0000.0000.000
117B640SER0-0.032-0.04453.9650.0920.0920.0000.0000.0000.000
118B641ASP-1-0.868-0.92654.1985.6415.6410.0000.0000.0000.000
119B642LYS10.8620.94249.108-6.230-6.2300.0000.0000.0000.000
120B643LEU00.001-0.00649.6990.1370.1370.0000.0000.0000.000
121B644ASP-1-0.832-0.90750.9675.7745.7740.0000.0000.0000.000
122B645LEU0-0.063-0.02847.4350.0740.0740.0000.0000.0000.000
123B646ALA00.0200.00846.1800.1300.1300.0000.0000.0000.000
124B647ALA0-0.023-0.02046.3900.0990.0990.0000.0000.0000.000
125B648ASN0-0.011-0.01147.799-0.009-0.0090.0000.0000.0000.000
126B649LEU0-0.0300.00041.5330.0590.0590.0000.0000.0000.000
127B650LEU0-0.019-0.00343.1430.1030.1030.0000.0000.0000.000
128B651GLN0-0.075-0.02645.1580.0100.0100.0000.0000.0000.000
129B652GLY00.0540.01044.184-0.053-0.0530.0000.0000.0000.000
130B653ASN0-0.104-0.04539.9710.1690.1690.0000.0000.0000.000
131B654GLN00.1130.05443.608-0.092-0.0920.0000.0000.0000.000
132B655LYS10.9330.96641.822-7.250-7.2500.0000.0000.0000.000
133B656GLU-1-0.918-0.96440.5987.4547.4540.0000.0000.0000.000
134B657HIS00.0140.02340.8800.1170.1170.0000.0000.0000.000
135B658VAL0-0.014-0.00945.665-0.118-0.1180.0000.0000.0000.000
136B659PHE00.0100.00747.224-0.159-0.1590.0000.0000.0000.000
137B660GLU-1-0.787-0.90244.4536.7006.7000.0000.0000.0000.000
138B661LEU0-0.028-0.00748.191-0.110-0.1100.0000.0000.0000.000
139B662GLY0-0.013-0.00850.414-0.123-0.1230.0000.0000.0000.000
140B663ALA00.0050.00550.803-0.119-0.1190.0000.0000.0000.000
141B664LEU00.0170.00548.436-0.103-0.1030.0000.0000.0000.000
142B665LYS10.8700.93052.697-5.897-5.8970.0000.0000.0000.000
143B666GLU-1-0.927-0.96155.8245.3215.3210.0000.0000.0000.000
144B667ALA0-0.007-0.00154.826-0.107-0.1070.0000.0000.0000.000
145B668LYS10.8630.91855.597-5.645-5.6450.0000.0000.0000.000
146B669MET0-0.060-0.02758.168-0.069-0.0690.0000.0000.0000.000
147B670LEU0-0.023-0.01059.893-0.103-0.1030.0000.0000.0000.000
148B671LEU00.0390.02857.018-0.079-0.0790.0000.0000.0000.000
149B672ARG10.9660.98861.494-5.007-5.0070.0000.0000.0000.000
150B673MET0-0.050-0.03464.212-0.079-0.0790.0000.0000.0000.000
151B674GLN00.005-0.01261.912-0.048-0.0480.0000.0000.0000.000
152B675GLU-1-0.829-0.92164.4464.9074.9070.0000.0000.0000.000
153B676THR0-0.095-0.05167.048-0.094-0.0940.0000.0000.0000.000
154B677PHE0-0.028-0.02668.364-0.079-0.0790.0000.0000.0000.000
155B678GLU-1-0.765-0.88766.5494.7254.7250.0000.0000.0000.000
156B679ARG10.8850.96370.099-4.505-4.5050.0000.0000.0000.000
157B680ASP-1-0.932-0.97372.9624.2214.2210.0000.0000.0000.000
158B681LEU0-0.075-0.04873.185-0.057-0.0570.0000.0000.0000.000
159B682THR0-0.062-0.01174.242-0.050-0.0500.0000.0000.0000.000
160B683ASP-1-0.817-0.91971.9934.4144.4140.0000.0000.0000.000
161B684SER0-0.0040.00366.8250.0480.0480.0000.0000.0000.000
162B685PHE0-0.093-0.07866.575-0.039-0.0390.0000.0000.0000.000
163B686VAL00.0120.00861.6010.0580.0580.0000.0000.0000.000
164B687GLY00.0010.01559.4720.0230.0230.0000.0000.0000.000
165B688LEU0-0.073-0.01759.4080.0630.0630.0000.0000.0000.000
166B689SER00.0600.01858.947-0.004-0.0040.0000.0000.0000.000
167B690VAL00.1160.04260.068-0.100-0.1000.0000.0000.0000.000
168B691ASN0-0.005-0.02261.573-0.102-0.1020.0000.0000.0000.000
169B692GLN00.0490.03559.890-0.088-0.0880.0000.0000.0000.000
170B693THR00.0420.02763.912-0.079-0.0790.0000.0000.0000.000
171B694MET0-0.045-0.01866.265-0.073-0.0730.0000.0000.0000.000
172B695PHE00.0310.02067.564-0.087-0.0870.0000.0000.0000.000
173B696LYS10.8950.96668.599-4.691-4.6910.0000.0000.0000.000
174B697LEU0-0.012-0.00269.870-0.079-0.0790.0000.0000.0000.000
175B698ILE0-0.048-0.02971.501-0.078-0.0780.0000.0000.0000.000
176B699LYS10.9300.97571.927-4.473-4.4730.0000.0000.0000.000
177B700LEU0-0.033-0.00673.573-0.047-0.0470.0000.0000.0000.000
178B701GLY00.0100.01176.472-0.048-0.0480.0000.0000.0000.000
179B702TYR00.0230.01675.128-0.056-0.0560.0000.0000.0000.000
180B703HIS00.023-0.01075.1710.0990.0990.0000.0000.0000.000
181B704GLY0-0.022-0.00975.6960.0270.0270.0000.0000.0000.000
182B705ARG10.9170.96572.635-4.205-4.2050.0000.0000.0000.000
183B706ALA00.0270.01770.9800.0630.0630.0000.0000.0000.000
184B707LYS10.9130.95970.695-4.281-4.2810.0000.0000.0000.000
185B708LYS10.9790.99670.611-4.376-4.3760.0000.0000.0000.000
186B709ILE00.0680.03465.6440.0460.0460.0000.0000.0000.000
187B710GLN00.0850.04266.4640.0070.0070.0000.0000.0000.000
188B711SER0-0.095-0.05666.7560.0200.0200.0000.0000.0000.000
189B712GLU-1-0.950-0.96864.7434.7964.7960.0000.0000.0000.000
190B713PHE00.0100.00160.9490.0320.0320.0000.0000.0000.000
191B714LYS10.9260.97061.596-4.902-4.9020.0000.0000.0000.000
192B715VAL00.0150.02063.0360.0430.0430.0000.0000.0000.000
193B716PRO00.0170.00461.346-0.085-0.0850.0000.0000.0000.000
194B717GLU-1-0.881-0.94964.3034.4714.4710.0000.0000.0000.000
195B718ARG10.9650.97864.243-4.825-4.8250.0000.0000.0000.000
196B719VAL00.0420.02262.074-0.019-0.0190.0000.0000.0000.000
197B720ALA00.0440.02165.317-0.038-0.0380.0000.0000.0000.000
198B721TRP0-0.049-0.02468.213-0.037-0.0370.0000.0000.0000.000
199B722TRP00.022-0.00366.918-0.054-0.0540.0000.0000.0000.000
200B723ILE0-0.0250.00264.796-0.021-0.0210.0000.0000.0000.000
201B724ARG10.8670.92268.690-4.410-4.4100.0000.0000.0000.000
202B725LEU0-0.0030.00571.887-0.051-0.0510.0000.0000.0000.000
203B726GLN0-0.022-0.02266.406-0.017-0.0170.0000.0000.0000.000
204B727ALA0-0.012-0.00171.491-0.014-0.0140.0000.0000.0000.000
205B728LEU0-0.034-0.02272.835-0.037-0.0370.0000.0000.0000.000
206B729VAL0-0.0300.01074.060-0.050-0.0500.0000.0000.0000.000
207B730ALA0-0.022-0.00473.280-0.029-0.0290.0000.0000.0000.000