Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 399VL

Calculation Name: 5B4N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5B4N

Chain ID: A

ChEMBL ID:

UniProt ID: Q80UW2

Base Structure: X-ray

Registration Date: 2023-06-21

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 174
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1905494.405299
FMO2-HF: Nuclear repulsion 1835168.689113
FMO2-HF: Total energy -70325.716186
FMO2-MP2: Total energy -70533.783991


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(A:125:ARG)


Summations of interaction energy for fragment #1(A:125: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.
-356.012-354.57436.513-17.015-20.937-0.193
Interaction energy analysis for fragmet #1(A:125:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.781 / q_NPA : 0.866
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].
3A127LEU00.0200.0072.224-7.217-3.4452.007-1.893-3.887-0.009
4A128LEU0-0.060-0.0094.0573.7643.9830.001-0.023-0.1970.000
5A129ARG10.7800.8517.14122.94322.9430.0000.0000.0000.000
6A130ASN0-0.026-0.0299.1021.7551.7550.0000.0000.0000.000
7A131PRO00.0240.0108.2601.6311.6310.0000.0000.0000.000
8A132CYS0-0.079-0.04211.3610.8530.8530.0000.0000.0000.000
9A133GLY00.0660.05014.3451.0581.0580.0000.0000.0000.000
10A134GLU-1-0.874-0.94713.040-15.374-15.3740.0000.0000.0000.000
11A135GLU-1-0.873-0.91811.482-22.757-22.7570.0000.0000.0000.000
12A136ASP-1-0.860-0.92915.896-13.264-13.2640.0000.0000.0000.000
13A137LEU0-0.012-0.02017.906-0.666-0.6660.0000.0000.0000.000
14A138GLU-1-0.797-0.86015.667-19.440-19.4400.0000.0000.0000.000
15A139GLY00.000-0.02413.489-0.854-0.8540.0000.0000.0000.000
16A140TRP0-0.084-0.04312.545-0.856-0.8560.0000.0000.0000.000
17A141SER0-0.0170.00116.3270.9690.9690.0000.0000.0000.000
18A142LEU00.0020.00019.1000.0480.0480.0000.0000.0000.000
19A143ASP-1-0.762-0.88322.012-11.888-11.8880.0000.0000.0000.000
20A144VAL0-0.001-0.01225.2340.1170.1170.0000.0000.0000.000
21A145ASN0-0.048-0.01728.1130.2320.2320.0000.0000.0000.000
22A146GLY00.0220.02025.8210.1570.1570.0000.0000.0000.000
23A147GLY00.017-0.00924.785-0.255-0.2550.0000.0000.0000.000
24A148ASP-1-0.881-0.93325.854-10.149-10.1490.0000.0000.0000.000
25A149GLY0-0.011-0.00226.7560.2480.2480.0000.0000.0000.000
26A150TRP0-0.057-0.03821.378-0.143-0.1430.0000.0000.0000.000
27A151LYS10.9130.95724.26610.84710.8470.0000.0000.0000.000
28A152VAL00.0000.00819.687-0.414-0.4140.0000.0000.0000.000
29A153GLU-1-0.920-0.94621.843-10.255-10.2550.0000.0000.0000.000
30A154GLU-1-0.899-0.96520.741-12.804-12.8040.0000.0000.0000.000
31A155LEU0-0.085-0.02118.0150.5920.5920.0000.0000.0000.000
32A156SER00.0280.00921.959-0.025-0.0250.0000.0000.0000.000
33A157ARG10.9790.96223.4699.7079.7070.0000.0000.0000.000
34A158ASP-1-0.833-0.90523.797-9.682-9.6820.0000.0000.0000.000
35A159GLN00.0720.02822.519-0.160-0.1600.0000.0000.0000.000
36A160ARG10.8930.95918.11712.17312.1730.0000.0000.0000.000
37A161LYS10.7970.89119.3219.4169.4160.0000.0000.0000.000
38A162GLU-1-0.839-0.91020.632-11.024-11.0240.0000.0000.0000.000
39A163PHE00.0360.02515.125-0.273-0.2730.0000.0000.0000.000
40A164PRO00.0020.00512.2640.3680.3680.0000.0000.0000.000
41A165ASN0-0.014-0.0159.9330.1680.1680.0000.0000.0000.000
42A166ASP-1-0.852-0.92513.680-14.686-14.6860.0000.0000.0000.000
43A167GLN0-0.015-0.01910.8980.0350.0350.0000.0000.0000.000
44A168VAL00.0450.03812.394-0.352-0.3520.0000.0000.0000.000
45A169LYS10.7870.88813.82817.40817.4080.0000.0000.0000.000
46A170LYS10.8750.95116.41015.16115.1610.0000.0000.0000.000
47A171TYR0-0.0020.00417.122-0.307-0.3070.0000.0000.0000.000
48A172PHE00.0710.04815.1220.6330.6330.0000.0000.0000.000
49A173VAL0-0.037-0.03420.5560.2630.2630.0000.0000.0000.000
50A174THR00.0080.01524.2110.0080.0080.0000.0000.0000.000
51A175SER0-0.031-0.04726.0740.3420.3420.0000.0000.0000.000
52A176TYR00.014-0.00129.0350.5110.5110.0000.0000.0000.000
53A177TYR0-0.042-0.03929.067-0.294-0.2940.0000.0000.0000.000
54A178THR0-0.0020.00629.124-0.200-0.2000.0000.0000.0000.000
55A179CYS0-0.0570.00425.758-0.174-0.1740.0000.0000.0000.000
56A180ARG10.7940.86521.78813.20713.2070.0000.0000.0000.000
57A181LYS10.8210.94015.97117.48617.4860.0000.0000.0000.000
58A182ALA00.004-0.00816.938-0.166-0.1660.0000.0000.0000.000
59A183GLN00.0070.0089.989-2.621-2.6210.0000.0000.0000.000
60A184VAL00.007-0.00813.1520.6800.6800.0000.0000.0000.000
61A185ILE00.0080.0166.916-0.589-0.5890.0000.0000.0000.000
62A186ASP-1-0.800-0.9008.755-29.368-29.3680.0000.0000.0000.000
63A187LEU0-0.005-0.0146.408-6.323-6.3230.0000.0000.0000.000
64A188GLN00.0290.0125.787-6.691-6.6910.0000.0000.0000.000
65A189ALA0-0.051-0.0256.788-2.390-2.3900.0000.0000.0000.000
66A190GLU-1-0.888-0.9381.921-114.883-113.40812.072-6.393-7.154-0.072
67A191GLY0-0.019-0.0051.832-47.019-51.29115.972-6.470-5.231-0.089
68A192TYR0-0.056-0.0342.077-11.141-11.1656.461-2.144-4.292-0.023
69A193TRP00.0350.0135.8653.1073.1070.0000.0000.0000.000
70A194GLU-1-0.818-0.9079.230-19.006-19.0060.0000.0000.0000.000
71A195GLU-1-0.899-0.92712.625-17.358-17.3580.0000.0000.0000.000
72A196LEU0-0.048-0.0057.3340.4990.4990.0000.0000.0000.000
73A197LEU00.005-0.0068.4950.4350.4350.0000.0000.0000.000
74A198ASP-1-0.759-0.84611.848-18.303-18.3030.0000.0000.0000.000
75A199THR0-0.051-0.04515.1731.4091.4090.0000.0000.0000.000
76A200THR0-0.081-0.04212.2750.7500.7500.0000.0000.0000.000
77A201GLN0-0.081-0.02313.7121.1261.1260.0000.0000.0000.000
78A202PRO0-0.0020.0269.0630.4750.4750.0000.0000.0000.000
79A203ALA00.0390.00811.037-0.561-0.5610.0000.0000.0000.000
80A204ILE00.0240.0199.391-2.627-2.6270.0000.0000.0000.000
81A205VAL0-0.0350.0028.3102.9872.9870.0000.0000.0000.000
82A206VAL0-0.017-0.0179.380-2.405-2.4050.0000.0000.0000.000
83A207LYS10.8540.9129.90820.91720.9170.0000.0000.0000.000
84A208ASP-1-0.709-0.79612.733-17.998-17.9980.0000.0000.0000.000
85A209TRP0-0.027-0.01113.9241.1761.1760.0000.0000.0000.000
86A210TYR00.0090.00017.0890.3180.3180.0000.0000.0000.000
87A211SER0-0.004-0.01520.6310.2310.2310.0000.0000.0000.000
88A212GLY00.0360.02024.138-0.073-0.0730.0000.0000.0000.000
89A213ARG10.8260.88826.88710.24110.2410.0000.0000.0000.000
90A214PRO00.001-0.00229.3810.0990.0990.0000.0000.0000.000
91A215ASP-1-0.894-0.94632.228-7.923-7.9230.0000.0000.0000.000
92A216CYS0-0.089-0.03433.9320.2640.2640.0000.0000.0000.000
93A217GLY00.0370.01732.643-0.202-0.2020.0000.0000.0000.000
94A218SER0-0.037-0.02928.5860.1290.1290.0000.0000.0000.000
95A219LYS10.8050.90828.7929.4229.4220.0000.0000.0000.000
96A220TYR0-0.043-0.06018.4020.0660.0660.0000.0000.0000.000
97A221GLN0-0.026-0.02623.4390.7120.7120.0000.0000.0000.000
98A222LEU00.0410.03716.214-0.209-0.2090.0000.0000.0000.000
99A223THR0-0.034-0.01518.9920.9710.9710.0000.0000.0000.000
100A224VAL0-0.0040.00413.809-0.703-0.7030.0000.0000.0000.000
101A225ARG10.8340.88716.39315.27215.2720.0000.0000.0000.000
102A226LEU00.0150.02412.991-1.346-1.3460.0000.0000.0000.000
103A227LEU0-0.019-0.01915.1191.4901.4900.0000.0000.0000.000
104A228SER00.060-0.00215.356-1.602-1.6020.0000.0000.0000.000
105A229GLU-1-0.830-0.92914.814-22.131-22.1310.0000.0000.0000.000
106A230ASN0-0.127-0.07217.3230.2850.2850.0000.0000.0000.000
107A231GLU-1-0.971-0.98318.553-15.672-15.6720.0000.0000.0000.000
108A232ASP-1-0.847-0.87420.099-13.659-13.6590.0000.0000.0000.000
109A233VAL0-0.040-0.04220.008-0.969-0.9690.0000.0000.0000.000
110A234LEU0-0.0150.01217.4600.6470.6470.0000.0000.0000.000
111A235ALA00.0060.00617.9570.4250.4250.0000.0000.0000.000
112A236GLU-1-0.807-0.89519.102-14.728-14.7280.0000.0000.0000.000
113A237PHE0-0.020-0.00518.1230.4980.4980.0000.0000.0000.000
114A238GLN0-0.027-0.03019.936-0.079-0.0790.0000.0000.0000.000
115A239PRO0-0.0230.00821.5650.5490.5490.0000.0000.0000.000
116A240ASP-1-0.879-0.94024.486-10.655-10.6550.0000.0000.0000.000
117A241PRO0-0.008-0.00826.473-0.228-0.2280.0000.0000.0000.000
118A242ALA00.0150.03524.9730.3910.3910.0000.0000.0000.000
119A243THR0-0.033-0.02027.0850.2310.2310.0000.0000.0000.000
120A244ILE0-0.050-0.02026.0330.0410.0410.0000.0000.0000.000
121A245GLN00.016-0.00929.7800.2500.2500.0000.0000.0000.000
122A246GLN00.0690.05632.230-0.348-0.3480.0000.0000.0000.000
123A247LYS10.8500.92131.7598.5828.5820.0000.0000.0000.000
124A248SER00.0770.04934.094-0.022-0.0220.0000.0000.0000.000
125A249ASP-1-0.927-0.97429.748-9.291-9.2910.0000.0000.0000.000
126A250ALA0-0.007-0.00927.0490.0430.0430.0000.0000.0000.000
127A251LYS10.8280.91925.30010.02110.0210.0000.0000.0000.000
128A252TRP0-0.0250.00119.519-0.154-0.1540.0000.0000.0000.000
129A253ARG10.8490.92521.30511.16011.1600.0000.0000.0000.000
130A254GLU-1-0.783-0.86613.698-17.426-17.4260.0000.0000.0000.000
131A255ILE0-0.050-0.03017.1260.8220.8220.0000.0000.0000.000
132A256SER00.011-0.00214.010-1.217-1.2170.0000.0000.0000.000
133A257HIS0-0.041-0.00714.4171.7991.7990.0000.0000.0000.000
134A258THR00.0210.00012.260-1.363-1.3630.0000.0000.0000.000
135A259PHE0-0.0130.01313.9491.3791.3790.0000.0000.0000.000
136A260ILE00.026-0.00114.227-1.664-1.6640.0000.0000.0000.000
137A261ASP-1-0.921-0.96816.502-15.076-15.0760.0000.0000.0000.000
138A262TYR0-0.063-0.04611.5510.8710.8710.0000.0000.0000.000
139A263GLY00.0090.02118.2240.2900.2900.0000.0000.0000.000
140A264PRO0-0.034-0.02217.149-0.999-0.9990.0000.0000.0000.000
141A265GLY00.012-0.00516.6350.7100.7100.0000.0000.0000.000
142A266VAL0-0.037-0.01912.434-0.106-0.1060.0000.0000.0000.000
143A267ARG10.7010.80611.65920.01820.0180.0000.0000.0000.000
144A268PHE00.0130.01310.853-3.024-3.0240.0000.0000.0000.000
145A269VAL00.001-0.00210.6091.3291.3290.0000.0000.0000.000
146A270ARG10.8790.95112.65315.55015.5500.0000.0000.0000.000
147A271PHE00.019-0.00212.5460.3770.3770.0000.0000.0000.000
148A272GLU-1-0.785-0.87614.565-14.458-14.4580.0000.0000.0000.000
149A273HIS0-0.038-0.02816.2300.2510.2510.0000.0000.0000.000
150A274GLY00.0530.02119.3700.0780.0780.0000.0000.0000.000
151A275GLY00.012-0.00422.3690.1390.1390.0000.0000.0000.000
152A276VAL0-0.041-0.00925.814-0.296-0.2960.0000.0000.0000.000
153A277ASP-1-0.850-0.94128.086-9.960-9.9600.0000.0000.0000.000
154A278THR00.004-0.00829.8340.2140.2140.0000.0000.0000.000
155A279HIS00.0010.01733.607-0.102-0.1020.0000.0000.0000.000
156A280TYR0-0.040-0.01936.6200.3310.3310.0000.0000.0000.000
157A281TRP00.0180.02534.901-0.162-0.1620.0000.0000.0000.000
158A282ALA00.017-0.00737.1430.2130.2130.0000.0000.0000.000
159A283GLY0-0.037-0.01038.0120.0440.0440.0000.0000.0000.000
160A284TRP0-0.008-0.01832.778-0.136-0.1360.0000.0000.0000.000
161A285TYR00.0600.02130.921-0.095-0.0950.0000.0000.0000.000
162A286GLY00.0690.04328.145-0.121-0.1210.0000.0000.0000.000
163A287PRO0-0.027-0.00323.5750.2860.2860.0000.0000.0000.000
164A288ARG10.8230.93722.40811.26511.2650.0000.0000.0000.000
165A289VAL00.009-0.01318.1670.0690.0690.0000.0000.0000.000
166A290THR00.020-0.01615.648-0.262-0.2620.0000.0000.0000.000
167A291ASN0-0.019-0.02310.921-0.648-0.6480.0000.0000.0000.000
168A292SER0-0.029-0.00611.446-0.357-0.3570.0000.0000.0000.000
169A293SER0-0.037-0.0387.788-1.384-1.3840.0000.0000.0000.000
170A294VAL00.0210.0127.1862.5712.5710.0000.0000.0000.000
171A295TRP0-0.055-0.0373.859-4.795-4.5270.000-0.092-0.1760.000
172A296VAL00.0150.0075.0404.8614.8610.0000.0000.0000.000
173A297GLU-1-0.885-0.9345.792-31.184-31.1840.0000.0000.0000.000
174A298PRO0-0.049-0.0146.1320.3130.3130.0000.0000.0000.000