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: N99GQ

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 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 174
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1902456.121189
FMO2-HF: Nuclear repulsion 1832132.135398
FMO2-HF: Total energy -70323.985791
FMO2-MP2: Total energy -70532.132497


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.
-295.941-284.20311.572-9.93-13.381-0.106
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 : 0.872 / q_NPA : 0.922
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].
3A127LEU00.0360.0172.690-6.279-3.0510.956-1.264-2.9200.000
4A128LEU0-0.058-0.0054.6013.0123.183-0.001-0.014-0.1560.000
5A129ARG10.9260.9437.51421.32221.3220.0000.0000.0000.000
6A130ASN0-0.056-0.0439.6941.7801.7800.0000.0000.0000.000
7A131PRO00.0460.0098.5771.6171.6170.0000.0000.0000.000
8A132CYS0-0.073-0.03611.5131.2061.2060.0000.0000.0000.000
9A133GLY00.0650.04514.2750.9720.9720.0000.0000.0000.000
10A134GLU-1-0.954-0.99113.698-14.796-14.7960.0000.0000.0000.000
11A135GLU-1-0.922-0.93812.003-21.468-21.4680.0000.0000.0000.000
12A136ASP-1-0.870-0.94916.304-12.841-12.8410.0000.0000.0000.000
13A137LEU0-0.021-0.01518.058-0.610-0.6100.0000.0000.0000.000
14A138GLU-1-0.914-0.93716.309-16.033-16.0330.0000.0000.0000.000
15A139GLY0-0.032-0.03414.178-0.921-0.9210.0000.0000.0000.000
16A140TRP0-0.065-0.03313.424-0.705-0.7050.0000.0000.0000.000
17A141SER0-0.023-0.00916.8350.6650.6650.0000.0000.0000.000
18A142LEU0-0.028-0.02319.5860.0770.0770.0000.0000.0000.000
19A143ASP-1-0.786-0.89722.772-11.524-11.5240.0000.0000.0000.000
20A144VAL00.020-0.01425.6310.0730.0730.0000.0000.0000.000
21A145ASN0-0.052-0.02528.3210.0590.0590.0000.0000.0000.000
22A146GLY00.0550.04426.1830.1780.1780.0000.0000.0000.000
23A147GLY00.014-0.01525.371-0.172-0.1720.0000.0000.0000.000
24A148ASP-1-0.886-0.93326.424-9.902-9.9020.0000.0000.0000.000
25A149GLY0-0.050-0.04427.2320.2860.2860.0000.0000.0000.000
26A150TRP0-0.036-0.02021.823-0.205-0.2050.0000.0000.0000.000
27A151LYS10.9660.98924.70410.39310.3930.0000.0000.0000.000
28A152VAL00.0070.02219.714-0.236-0.2360.0000.0000.0000.000
29A153GLU-1-0.944-0.96621.895-10.091-10.0910.0000.0000.0000.000
30A154GLU-1-0.938-0.98221.181-11.980-11.9800.0000.0000.0000.000
31A155LEU0-0.065-0.01918.0700.4560.4560.0000.0000.0000.000
32A156SER00.0150.01122.1060.0560.0560.0000.0000.0000.000
33A157ARG10.9440.94623.2699.7069.7060.0000.0000.0000.000
34A158ASP-1-0.930-0.98123.438-9.748-9.7480.0000.0000.0000.000
35A159GLN00.0930.06122.284-0.416-0.4160.0000.0000.0000.000
36A160ARG10.9290.96218.52912.03012.0300.0000.0000.0000.000
37A161LYS10.8880.95718.8709.5089.5080.0000.0000.0000.000
38A162GLU-1-0.892-0.95320.093-11.107-11.1070.0000.0000.0000.000
39A163PHE0-0.0090.00014.645-0.290-0.2900.0000.0000.0000.000
40A164PRO00.0130.01411.8420.2190.2190.0000.0000.0000.000
41A165ASN00.0100.0079.3000.9850.9850.0000.0000.0000.000
42A166ASP-1-0.897-0.95213.149-14.182-14.1820.0000.0000.0000.000
43A167GLN0-0.071-0.04610.511-0.308-0.3080.0000.0000.0000.000
44A168VAL00.0310.03712.323-0.468-0.4680.0000.0000.0000.000
45A169LYS10.9010.92714.27816.43416.4340.0000.0000.0000.000
46A170LYS10.9520.99916.48214.33914.3390.0000.0000.0000.000
47A171TYR0-0.0170.00617.154-0.295-0.2950.0000.0000.0000.000
48A172PHE00.0430.05015.5030.5390.5390.0000.0000.0000.000
49A173VAL0-0.035-0.03320.5930.1880.1880.0000.0000.0000.000
50A174THR00.0070.01724.1640.1760.1760.0000.0000.0000.000
51A175SER0-0.034-0.02926.1620.3400.3400.0000.0000.0000.000
52A176TYR00.016-0.00529.2890.4810.4810.0000.0000.0000.000
53A177TYR0-0.025-0.03529.372-0.288-0.2880.0000.0000.0000.000
54A178THR00.0100.01529.584-0.073-0.0730.0000.0000.0000.000
55A179CYS0-0.0640.01925.918-0.123-0.1230.0000.0000.0000.000
56A180ARG10.8140.88422.19512.74512.7450.0000.0000.0000.000
57A181LYS10.8540.95816.71816.53816.5380.0000.0000.0000.000
58A182ALA0-0.005-0.01617.336-0.099-0.0990.0000.0000.0000.000
59A183GLN00.0300.04710.701-2.234-2.2340.0000.0000.0000.000
60A184VAL00.017-0.00412.9060.4510.4510.0000.0000.0000.000
61A185ILE00.0020.0087.069-0.313-0.3130.0000.0000.0000.000
62A186ASP-1-0.802-0.9048.616-27.598-27.5980.0000.0000.0000.000
63A187LEU0-0.005-0.0136.466-5.354-5.3540.0000.0000.0000.000
64A188GLN00.0450.0245.964-6.693-6.6930.0000.0000.0000.000
65A189ALA0-0.032-0.0076.858-3.014-3.0140.0000.0000.0000.000
66A190GLU-1-0.972-0.9742.186-73.637-71.3191.086-1.458-1.947-0.009
67A191GLY0-0.039-0.0311.977-48.964-45.4527.219-5.816-4.915-0.087
68A192TYR0-0.051-0.0362.664-1.5270.2562.285-1.187-2.881-0.009
69A193TRP00.0370.0135.7832.9932.9930.0000.0000.0000.000
70A194GLU-1-0.850-0.9389.138-19.098-19.0980.0000.0000.0000.000
71A195GLU-1-0.882-0.93012.584-17.372-17.3720.0000.0000.0000.000
72A196LEU0-0.054-0.0157.2120.7830.7830.0000.0000.0000.000
73A197LEU00.0220.0078.7040.5350.5350.0000.0000.0000.000
74A198ASP-1-0.778-0.88911.890-18.188-18.1880.0000.0000.0000.000
75A199THR0-0.053-0.01915.0971.2751.2750.0000.0000.0000.000
76A200THR0-0.091-0.05311.6330.6910.6910.0000.0000.0000.000
77A201GLN0-0.0340.01313.7861.4711.4710.0000.0000.0000.000
78A202PRO0-0.0040.0238.8670.6290.6290.0000.0000.0000.000
79A203ALA00.0500.01210.2840.0790.0790.0000.0000.0000.000
80A204ILE00.0190.0389.083-3.242-3.2420.0000.0000.0000.000
81A205VAL0-0.036-0.0057.7713.0173.0170.0000.0000.0000.000
82A206VAL0-0.012-0.0148.540-2.033-2.0330.0000.0000.0000.000
83A207LYS10.8580.9279.45920.64920.6490.0000.0000.0000.000
84A208ASP-1-0.717-0.79812.086-17.413-17.4130.0000.0000.0000.000
85A209TRP00.0360.02513.1841.0381.0380.0000.0000.0000.000
86A210TYR00.0360.00717.1190.3140.3140.0000.0000.0000.000
87A211SER0-0.009-0.01320.5740.1570.1570.0000.0000.0000.000
88A212GLY00.0320.01623.879-0.018-0.0180.0000.0000.0000.000
89A213ARG10.8460.89326.5179.8029.8020.0000.0000.0000.000
90A214PRO0-0.029-0.00729.0530.0820.0820.0000.0000.0000.000
91A215ASP-1-0.859-0.93131.958-7.860-7.8600.0000.0000.0000.000
92A216CYS0-0.081-0.02333.5270.2660.2660.0000.0000.0000.000
93A217GLY0-0.001-0.02132.229-0.241-0.2410.0000.0000.0000.000
94A218SER0-0.037-0.03928.0740.1550.1550.0000.0000.0000.000
95A219LYS10.9080.95828.7099.3109.3100.0000.0000.0000.000
96A220TYR0-0.023-0.04118.2800.0460.0460.0000.0000.0000.000
97A221GLN0-0.001-0.00323.5070.6950.6950.0000.0000.0000.000
98A222LEU00.0180.01816.309-0.200-0.2000.0000.0000.0000.000
99A223THR0-0.013-0.00319.6730.7380.7380.0000.0000.0000.000
100A224VAL00.0050.00314.197-0.642-0.6420.0000.0000.0000.000
101A225ARG10.8470.90816.80314.87214.8720.0000.0000.0000.000
102A226LEU00.0050.02013.651-1.383-1.3830.0000.0000.0000.000
103A227LEU0-0.011-0.01115.3741.3571.3570.0000.0000.0000.000
104A228SER00.0340.02015.586-1.616-1.6160.0000.0000.0000.000
105A229GLU-1-0.890-0.96015.587-20.316-20.3160.0000.0000.0000.000
106A230ASN0-0.066-0.03017.805-0.102-0.1020.0000.0000.0000.000
107A231GLU-1-0.974-0.99218.750-14.789-14.7890.0000.0000.0000.000
108A232ASP-1-0.877-0.91620.157-13.094-13.0940.0000.0000.0000.000
109A233VAL0-0.044-0.04620.355-0.922-0.9220.0000.0000.0000.000
110A234LEU0-0.0100.01017.5550.6430.6430.0000.0000.0000.000
111A235ALA00.0010.00718.5540.3150.3150.0000.0000.0000.000
112A236GLU-1-0.851-0.93219.886-13.827-13.8270.0000.0000.0000.000
113A237PHE0-0.0010.01317.1830.5740.5740.0000.0000.0000.000
114A238GLN0-0.047-0.05819.833-0.152-0.1520.0000.0000.0000.000
115A239PRO0-0.0280.01720.6240.5720.5720.0000.0000.0000.000
116A240ASP-1-0.879-0.95023.495-10.369-10.3690.0000.0000.0000.000
117A241PRO0-0.027-0.01325.430-0.249-0.2490.0000.0000.0000.000
118A242ALA00.0010.01724.4890.2310.2310.0000.0000.0000.000
119A243THR0-0.049-0.04326.5480.1860.1860.0000.0000.0000.000
120A244ILE0-0.069-0.02325.5480.0540.0540.0000.0000.0000.000
121A245GLN0-0.004-0.02829.1090.3730.3730.0000.0000.0000.000
122A246GLN00.0400.05031.754-0.281-0.2810.0000.0000.0000.000
123A247LYS10.9000.94531.7598.6528.6520.0000.0000.0000.000
124A248SER00.0830.04933.700-0.068-0.0680.0000.0000.0000.000
125A249ASP-1-0.918-0.95929.745-9.069-9.0690.0000.0000.0000.000
126A250ALA0-0.040-0.02226.9050.0430.0430.0000.0000.0000.000
127A251LYS10.9020.95625.1229.6229.6220.0000.0000.0000.000
128A252TRP0-0.004-0.00419.561-0.201-0.2010.0000.0000.0000.000
129A253ARG10.8380.94520.89510.99310.9930.0000.0000.0000.000
130A254GLU-1-0.853-0.93413.370-16.392-16.3920.0000.0000.0000.000
131A255ILE0-0.066-0.03616.3700.7210.7210.0000.0000.0000.000
132A256SER00.0420.00913.561-1.204-1.2040.0000.0000.0000.000
133A257HIS0-0.029-0.00413.6281.6091.6090.0000.0000.0000.000
134A258THR00.0000.00812.233-1.495-1.4950.0000.0000.0000.000
135A259PHE0-0.0090.00213.1421.4181.4180.0000.0000.0000.000
136A260ILE00.019-0.02213.804-1.619-1.6190.0000.0000.0000.000
137A261ASP-1-0.929-0.95816.280-14.692-14.6920.0000.0000.0000.000
138A262TYR0-0.054-0.04712.1390.7310.7310.0000.0000.0000.000
139A263GLY0-0.0200.00018.5310.5480.5480.0000.0000.0000.000
140A264PRO0-0.024-0.02317.256-0.978-0.9780.0000.0000.0000.000
141A265GLY0-0.019-0.02116.8000.5470.5470.0000.0000.0000.000
142A266VAL0-0.014-0.01112.286-0.211-0.2110.0000.0000.0000.000
143A267ARG10.7540.86112.00419.48119.4810.0000.0000.0000.000
144A268PHE00.0300.02011.055-2.656-2.6560.0000.0000.0000.000
145A269VAL0-0.0080.00010.4501.3541.3540.0000.0000.0000.000
146A270ARG10.9070.96912.64115.65115.6510.0000.0000.0000.000
147A271PHE0-0.010-0.00912.9580.6040.6040.0000.0000.0000.000
148A272GLU-1-0.825-0.91415.145-13.722-13.7220.0000.0000.0000.000
149A273HIS0-0.050-0.04716.7270.2160.2160.0000.0000.0000.000
150A274GLY00.0620.03420.0980.0390.0390.0000.0000.0000.000
151A275GLY00.003-0.00723.0020.1280.1280.0000.0000.0000.000
152A276VAL0-0.052-0.01326.360-0.291-0.2910.0000.0000.0000.000
153A277ASP-1-0.888-0.94928.557-9.847-9.8470.0000.0000.0000.000
154A278THR00.0160.00630.3160.1920.1920.0000.0000.0000.000
155A279HIS0-0.006-0.00233.994-0.098-0.0980.0000.0000.0000.000
156A280TYR0-0.038-0.02436.9430.2880.2880.0000.0000.0000.000
157A281TRP00.0090.01834.881-0.165-0.1650.0000.0000.0000.000
158A282ALA00.002-0.00937.5970.2100.2100.0000.0000.0000.000
159A283GLY0-0.029-0.00838.1530.0870.0870.0000.0000.0000.000
160A284TRP0-0.050-0.02632.732-0.081-0.0810.0000.0000.0000.000
161A285TYR00.0680.02930.645-0.080-0.0800.0000.0000.0000.000
162A286GLY00.1020.05328.216-0.096-0.0960.0000.0000.0000.000
163A287PRO0-0.055-0.00223.5740.2970.2970.0000.0000.0000.000
164A288ARG10.8970.95922.48110.80610.8060.0000.0000.0000.000
165A289VAL0-0.006-0.00918.1000.0500.0500.0000.0000.0000.000
166A290THR0-0.010-0.03815.774-0.263-0.2630.0000.0000.0000.000
167A291ASN00.006-0.01610.693-0.776-0.7760.0000.0000.0000.000
168A292SER0-0.023-0.00311.428-0.278-0.2780.0000.0000.0000.000
169A293SER0-0.035-0.0356.938-1.310-1.3100.0000.0000.0000.000
170A294VAL00.0500.0287.4152.2952.2950.0000.0000.0000.000
171A295TRP0-0.034-0.0153.077-4.309-3.6380.028-0.188-0.511-0.001
172A296VAL00.0170.0114.8025.2225.2220.0000.0000.0000.000
173A297GLU-1-0.908-0.9765.194-31.490-31.435-0.001-0.003-0.0510.000
174A298PRO0-0.062-0.0145.3770.8140.8140.0000.0000.0000.000