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: JLL99

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 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 174
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1903977.219197
FMO2-HF: Nuclear repulsion 1833652.118564
FMO2-HF: Total energy -70325.100633
FMO2-MP2: Total energy -70533.217155


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.
-337.292-336.3231.274-14.469-17.78-0.171
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 : 0.800 / q_NPA : 0.881
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].
3A127LEU00.0480.0222.421-4.733-1.1980.838-1.409-2.965-0.001
4A128LEU0-0.050-0.0024.5813.2043.388-0.001-0.016-0.1670.000
5A129ARG10.7750.8487.31121.47321.4730.0000.0000.0000.000
6A130ASN0-0.042-0.0359.4871.9611.9610.0000.0000.0000.000
7A131PRO00.0320.0098.4291.6491.6490.0000.0000.0000.000
8A132CYS0-0.069-0.04311.5390.8670.8670.0000.0000.0000.000
9A133GLY00.0710.05214.2971.0001.0000.0000.0000.0000.000
10A134GLU-1-0.849-0.92213.527-14.879-14.8790.0000.0000.0000.000
11A135GLU-1-0.895-0.92012.057-21.843-21.8430.0000.0000.0000.000
12A136ASP-1-0.861-0.94516.397-13.091-13.0910.0000.0000.0000.000
13A137LEU0-0.025-0.01818.152-0.634-0.6340.0000.0000.0000.000
14A138GLU-1-0.802-0.87416.164-18.576-18.5760.0000.0000.0000.000
15A139GLY0-0.002-0.01313.901-0.911-0.9110.0000.0000.0000.000
16A140TRP0-0.071-0.04313.164-0.739-0.7390.0000.0000.0000.000
17A141SER0-0.0180.00216.6850.7560.7560.0000.0000.0000.000
18A142LEU0-0.029-0.02319.4330.0960.0960.0000.0000.0000.000
19A143ASP-1-0.765-0.87422.648-11.651-11.6510.0000.0000.0000.000
20A144VAL00.022-0.01525.5370.0720.0720.0000.0000.0000.000
21A145ASN0-0.064-0.02928.2170.1390.1390.0000.0000.0000.000
22A146GLY00.0570.04426.0320.1830.1830.0000.0000.0000.000
23A147GLY00.021-0.01425.175-0.170-0.1700.0000.0000.0000.000
24A148ASP-1-0.890-0.93526.230-9.982-9.9820.0000.0000.0000.000
25A149GLY0-0.021-0.01827.0700.3060.3060.0000.0000.0000.000
26A150TRP0-0.049-0.02321.700-0.182-0.1820.0000.0000.0000.000
27A151LYS10.9550.98524.73910.58510.5850.0000.0000.0000.000
28A152VAL00.0130.02019.557-0.250-0.2500.0000.0000.0000.000
29A153GLU-1-0.943-0.96421.926-10.203-10.2030.0000.0000.0000.000
30A154GLU-1-0.916-0.96821.198-12.374-12.3740.0000.0000.0000.000
31A155LEU0-0.076-0.02018.1560.4740.4740.0000.0000.0000.000
32A156SER00.0270.01222.1210.0270.0270.0000.0000.0000.000
33A157ARG10.9650.95623.2759.7099.7090.0000.0000.0000.000
34A158ASP-1-0.827-0.91323.445-9.732-9.7320.0000.0000.0000.000
35A159GLN00.0860.04822.096-0.247-0.2470.0000.0000.0000.000
36A160ARG10.9290.96918.06712.06212.0620.0000.0000.0000.000
37A161LYS10.8070.90018.8779.4559.4550.0000.0000.0000.000
38A162GLU-1-0.865-0.93520.093-11.015-11.0150.0000.0000.0000.000
39A163PHE0-0.0020.00214.687-0.244-0.2440.0000.0000.0000.000
40A164PRO00.0210.01611.7910.2360.2360.0000.0000.0000.000
41A165ASN00.0060.0089.2330.9470.9470.0000.0000.0000.000
42A166ASP-1-0.856-0.92213.149-14.395-14.3950.0000.0000.0000.000
43A167GLN0-0.084-0.06110.663-0.136-0.1360.0000.0000.0000.000
44A168VAL00.0100.02212.352-0.474-0.4740.0000.0000.0000.000
45A169LYS10.8200.89014.27616.87016.8700.0000.0000.0000.000
46A170LYS10.9080.96116.49214.68214.6820.0000.0000.0000.000
47A171TYR0-0.0110.00117.172-0.291-0.2910.0000.0000.0000.000
48A172PHE00.0540.05015.4260.5620.5620.0000.0000.0000.000
49A173VAL0-0.032-0.02820.6170.1830.1830.0000.0000.0000.000
50A174THR00.0210.02224.1880.0270.0270.0000.0000.0000.000
51A175SER0-0.063-0.05726.1880.3190.3190.0000.0000.0000.000
52A176TYR00.0400.00529.1660.4880.4880.0000.0000.0000.000
53A177TYR0-0.052-0.04629.240-0.307-0.3070.0000.0000.0000.000
54A178THR00.0030.01329.508-0.089-0.0890.0000.0000.0000.000
55A179CYS0-0.0670.00925.797-0.126-0.1260.0000.0000.0000.000
56A180ARG10.7870.87022.20012.97212.9720.0000.0000.0000.000
57A181LYS10.8060.92616.33917.01217.0120.0000.0000.0000.000
58A182ALA00.000-0.01317.320-0.088-0.0880.0000.0000.0000.000
59A183GLN00.0160.02810.598-2.390-2.3900.0000.0000.0000.000
60A184VAL00.008-0.00713.3230.4090.4090.0000.0000.0000.000
61A185ILE00.0110.0147.070-0.443-0.4430.0000.0000.0000.000
62A186ASP-1-0.800-0.8998.825-28.306-28.3060.0000.0000.0000.000
63A187LEU0-0.005-0.0126.556-5.815-5.8150.0000.0000.0000.000
64A188GLN00.0440.0225.741-7.050-7.0500.0000.0000.0000.000
65A189ALA0-0.038-0.0156.621-3.018-3.0180.0000.0000.0000.000
66A190GLU-1-0.917-0.9551.998-100.058-98.9127.091-3.742-4.495-0.051
67A191GLY0-0.036-0.0141.799-50.146-54.36216.530-6.943-5.372-0.094
68A192TYR0-0.040-0.0262.088-9.552-9.8146.797-2.200-4.335-0.024
69A193TRP00.0490.0165.7133.0133.0130.0000.0000.0000.000
70A194GLU-1-0.819-0.9199.104-19.422-19.4220.0000.0000.0000.000
71A195GLU-1-0.914-0.92512.497-17.258-17.2580.0000.0000.0000.000
72A196LEU0-0.034-0.0057.2810.6750.6750.0000.0000.0000.000
73A197LEU00.0140.0088.5410.5250.5250.0000.0000.0000.000
74A198ASP-1-0.783-0.86111.814-18.516-18.5160.0000.0000.0000.000
75A199THR0-0.031-0.03315.0811.2361.2360.0000.0000.0000.000
76A200THR0-0.095-0.05112.0910.6570.6570.0000.0000.0000.000
77A201GLN0-0.070-0.01413.4091.5121.5120.0000.0000.0000.000
78A202PRO0-0.0020.0198.6690.5550.5550.0000.0000.0000.000
79A203ALA00.0520.02110.685-0.090-0.0900.0000.0000.0000.000
80A204ILE00.0230.0379.100-3.363-3.3630.0000.0000.0000.000
81A205VAL0-0.042-0.0077.8803.1443.1440.0000.0000.0000.000
82A206VAL0-0.014-0.0178.588-2.091-2.0910.0000.0000.0000.000
83A207LYS10.8460.9139.35820.21420.2140.0000.0000.0000.000
84A208ASP-1-0.733-0.81312.148-17.526-17.5260.0000.0000.0000.000
85A209TRP00.0040.00913.1931.1451.1450.0000.0000.0000.000
86A210TYR00.0560.02417.1350.2920.2920.0000.0000.0000.000
87A211SER0-0.024-0.02720.5950.2080.2080.0000.0000.0000.000
88A212GLY00.0310.02023.899-0.028-0.0280.0000.0000.0000.000
89A213ARG10.8500.90126.53710.00710.0070.0000.0000.0000.000
90A214PRO0-0.033-0.01429.0750.0890.0890.0000.0000.0000.000
91A215ASP-1-0.849-0.92331.976-7.893-7.8930.0000.0000.0000.000
92A216CYS0-0.109-0.05933.5530.2890.2890.0000.0000.0000.000
93A217GLY00.0100.00332.250-0.243-0.2430.0000.0000.0000.000
94A218SER0-0.024-0.01828.1420.1580.1580.0000.0000.0000.000
95A219LYS10.8170.91428.7489.2999.2990.0000.0000.0000.000
96A220TYR0-0.029-0.05218.3560.1000.1000.0000.0000.0000.000
97A221GLN0-0.012-0.01523.2890.7190.7190.0000.0000.0000.000
98A222LEU00.0140.02016.407-0.227-0.2270.0000.0000.0000.000
99A223THR0-0.036-0.01619.7240.7220.7220.0000.0000.0000.000
100A224VAL00.0170.01014.100-0.666-0.6660.0000.0000.0000.000
101A225ARG10.8210.88416.92915.00615.0060.0000.0000.0000.000
102A226LEU00.0130.02213.287-1.470-1.4700.0000.0000.0000.000
103A227LEU0-0.012-0.01415.3511.4411.4410.0000.0000.0000.000
104A228SER00.0410.00315.426-1.676-1.6760.0000.0000.0000.000
105A229GLU-1-0.842-0.94415.192-21.253-21.2530.0000.0000.0000.000
106A230ASN0-0.119-0.05717.744-0.007-0.0070.0000.0000.0000.000
107A231GLU-1-0.982-0.99518.525-15.299-15.2990.0000.0000.0000.000
108A232ASP-1-0.849-0.88120.313-13.436-13.4360.0000.0000.0000.000
109A233VAL0-0.047-0.04720.241-0.951-0.9510.0000.0000.0000.000
110A234LEU0-0.0080.01417.3570.6790.6790.0000.0000.0000.000
111A235ALA0-0.0050.00018.1350.3380.3380.0000.0000.0000.000
112A236GLU-1-0.800-0.89619.670-14.298-14.2980.0000.0000.0000.000
113A237PHE0-0.0080.01217.2810.6170.6170.0000.0000.0000.000
114A238GLN0-0.048-0.05219.878-0.100-0.1000.0000.0000.0000.000
115A239PRO0-0.0240.01520.6520.5730.5730.0000.0000.0000.000
116A240ASP-1-0.879-0.94023.549-10.560-10.5600.0000.0000.0000.000
117A241PRO0-0.012-0.00425.488-0.241-0.2410.0000.0000.0000.000
118A242ALA0-0.0020.01524.5090.2450.2450.0000.0000.0000.000
119A243THR0-0.034-0.02526.6100.2130.2130.0000.0000.0000.000
120A244ILE0-0.055-0.02025.6610.0620.0620.0000.0000.0000.000
121A245GLN00.011-0.01929.1730.2570.2570.0000.0000.0000.000
122A246GLN00.0570.05031.796-0.324-0.3240.0000.0000.0000.000
123A247LYS10.8650.92831.7388.5968.5960.0000.0000.0000.000
124A248SER00.0850.05633.717-0.056-0.0560.0000.0000.0000.000
125A249ASP-1-0.929-0.96529.787-9.150-9.1500.0000.0000.0000.000
126A250ALA0-0.031-0.02426.9940.0380.0380.0000.0000.0000.000
127A251LYS10.8360.92124.86710.00910.0090.0000.0000.0000.000
128A252TRP0-0.0190.00219.481-0.168-0.1680.0000.0000.0000.000
129A253ARG10.8440.93620.95810.98210.9820.0000.0000.0000.000
130A254GLU-1-0.795-0.88813.186-16.959-16.9590.0000.0000.0000.000
131A255ILE0-0.074-0.04016.4470.7150.7150.0000.0000.0000.000
132A256SER00.020-0.00113.487-1.105-1.1050.0000.0000.0000.000
133A257HIS0-0.0210.00313.6801.7861.7860.0000.0000.0000.000
134A258THR00.0080.00512.046-1.470-1.4700.0000.0000.0000.000
135A259PHE0-0.0110.00213.1731.4511.4510.0000.0000.0000.000
136A260ILE00.023-0.01313.822-1.669-1.6690.0000.0000.0000.000
137A261ASP-1-0.920-0.95816.294-14.963-14.9630.0000.0000.0000.000
138A262TYR0-0.067-0.05211.5020.7660.7660.0000.0000.0000.000
139A263GLY0-0.0060.01218.0940.5540.5540.0000.0000.0000.000
140A264PRO0-0.034-0.02917.113-0.991-0.9910.0000.0000.0000.000
141A265GLY00.013-0.00416.5980.5920.5920.0000.0000.0000.000
142A266VAL0-0.025-0.00912.179-0.230-0.2300.0000.0000.0000.000
143A267ARG10.7130.80811.78019.75619.7560.0000.0000.0000.000
144A268PHE00.0150.01111.041-2.865-2.8650.0000.0000.0000.000
145A269VAL0-0.0070.00510.4691.4571.4570.0000.0000.0000.000
146A270ARG10.9000.95612.73715.63915.6390.0000.0000.0000.000
147A271PHE0-0.006-0.01213.1340.6690.6690.0000.0000.0000.000
148A272GLU-1-0.795-0.88215.172-14.047-14.0470.0000.0000.0000.000
149A273HIS0-0.021-0.01216.5570.1760.1760.0000.0000.0000.000
150A274GLY00.0570.02920.0510.0410.0410.0000.0000.0000.000
151A275GLY00.000-0.00622.9190.1360.1360.0000.0000.0000.000
152A276VAL0-0.047-0.02026.308-0.289-0.2890.0000.0000.0000.000
153A277ASP-1-0.881-0.94928.519-9.903-9.9030.0000.0000.0000.000
154A278THR00.0250.00930.2740.1950.1950.0000.0000.0000.000
155A279HIS0-0.0140.00233.959-0.101-0.1010.0000.0000.0000.000
156A280TYR0-0.042-0.02836.8740.2970.2970.0000.0000.0000.000
157A281TRP00.0220.02334.868-0.165-0.1650.0000.0000.0000.000
158A282ALA00.014-0.00637.5900.2150.2150.0000.0000.0000.000
159A283GLY0-0.035-0.01238.1770.0880.0880.0000.0000.0000.000
160A284TRP0-0.008-0.01732.790-0.099-0.0990.0000.0000.0000.000
161A285TYR00.0730.03430.737-0.140-0.1400.0000.0000.0000.000
162A286GLY00.0640.03928.243-0.109-0.1090.0000.0000.0000.000
163A287PRO0-0.0250.00123.6130.3130.3130.0000.0000.0000.000
164A288ARG10.8500.94322.39810.93210.9320.0000.0000.0000.000
165A289VAL00.006-0.01118.1300.0610.0610.0000.0000.0000.000
166A290THR00.005-0.02515.733-0.290-0.2900.0000.0000.0000.000
167A291ASN0-0.025-0.03010.893-0.616-0.6160.0000.0000.0000.000
168A292SER0-0.0030.00411.449-0.239-0.2390.0000.0000.0000.000
169A293SER0-0.025-0.0317.031-1.166-1.1660.0000.0000.0000.000
170A294VAL00.0320.0217.4202.3482.3480.0000.0000.0000.000
171A295TRP0-0.041-0.0273.138-4.290-3.7710.020-0.156-0.384-0.001
172A296VAL00.0100.0104.8375.3365.3360.0000.0000.0000.000
173A297GLU-1-0.897-0.9585.179-31.584-31.518-0.001-0.003-0.0620.000
174A298PRO0-0.048-0.0135.5750.5870.5870.0000.0000.0000.000