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: MNYMZ

Calculation Name: 3EXV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EXV

Chain ID: A

ChEMBL ID:

UniProt ID: P35774

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2220922.657391
FMO2-HF: Nuclear repulsion 2142447.281828
FMO2-HF: Total energy -78475.375563
FMO2-MP2: Total energy -78700.960198


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:129:ASP)


Summations of interaction energy for fragment #1(A:129:ASP)
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.
-88.537-89.30915.54-7.83-6.9380.054
Interaction energy analysis for fragmet #1(A:129:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.839 / q_NPA : -0.924
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].
3A131ILE0-0.004-0.0103.149-7.994-5.6020.020-1.002-1.4100.003
4A132ASN0-0.008-0.0151.740-37.373-40.91215.522-6.807-5.1760.051
5A133THR0-0.0070.0084.910-4.338-4.126-0.001-0.012-0.1990.000
6A134LEU0-0.0330.0107.287-1.735-1.7350.0000.0000.0000.000
7A135TRP0-0.025-0.02510.4590.4360.4360.0000.0000.0000.000
8A136THR00.0510.02012.643-0.468-0.4680.0000.0000.0000.000
9A137GLY0-0.0460.00113.360-1.025-1.0250.0000.0000.0000.000
10A138VAL0-0.007-0.02413.102-0.625-0.6250.0000.0000.0000.000
11A139ASN0-0.015-0.00915.748-0.989-0.9890.0000.0000.0000.000
12A140PRO00.0640.05118.826-0.269-0.2690.0000.0000.0000.000
13A141THR00.009-0.00520.958-0.209-0.2090.0000.0000.0000.000
14A142GLU-1-0.888-0.93824.41410.72710.7270.0000.0000.0000.000
15A143ALA0-0.021-0.00224.5080.6010.6010.0000.0000.0000.000
16A144ASN00.0010.00720.232-0.702-0.7020.0000.0000.0000.000
17A145CYS0-0.020-0.01523.9210.2560.2560.0000.0000.0000.000
18A146GLN0-0.0250.00825.876-0.170-0.1700.0000.0000.0000.000
19A147ILE0-0.059-0.04625.9790.0460.0460.0000.0000.0000.000
20A148MET0-0.0290.01529.357-0.187-0.1870.0000.0000.0000.000
21A149ASN00.017-0.01433.1470.1730.1730.0000.0000.0000.000
22A150SER0-0.008-0.00535.357-0.119-0.1190.0000.0000.0000.000
23A151SER0-0.072-0.03133.497-0.284-0.2840.0000.0000.0000.000
24A152GLU-1-0.914-0.95736.0518.2628.2620.0000.0000.0000.000
25A153SER0-0.027-0.01432.797-0.076-0.0760.0000.0000.0000.000
26A154ASN0-0.061-0.03327.335-0.110-0.1100.0000.0000.0000.000
27A155ASP-1-0.743-0.86929.59510.58010.5800.0000.0000.0000.000
28A156CYS0-0.029-0.01326.4400.0570.0570.0000.0000.0000.000
29A157LYS10.8710.92022.108-13.006-13.0060.0000.0000.0000.000
30A158LEU00.0180.00620.1570.0360.0360.0000.0000.0000.000
31A159ILE0-0.047-0.01415.8120.6350.6350.0000.0000.0000.000
32A160LEU00.0500.00915.604-0.242-0.2420.0000.0000.0000.000
33A161THR0-0.041-0.0369.7191.3731.3730.0000.0000.0000.000
34A162LEU00.0110.01911.600-0.648-0.6480.0000.0000.0000.000
35A163VAL00.014-0.0025.6942.6782.6780.0000.0000.0000.000
36A164LYS10.8070.9266.949-32.009-32.0090.0000.0000.0000.000
37A165THR00.004-0.0046.6797.0127.0120.0000.0000.0000.000
38A166GLY00.0300.0219.113-3.380-3.3800.0000.0000.0000.000
39A167ALA00.004-0.00711.2230.3540.3540.0000.0000.0000.000
40A168LEU00.0060.00712.917-1.435-1.4350.0000.0000.0000.000
41A169VAL0-0.0060.00811.4682.6852.6850.0000.0000.0000.000
42A170THR0-0.033-0.02010.550-2.300-2.3000.0000.0000.0000.000
43A171ALA0-0.010-0.00711.8721.9341.9340.0000.0000.0000.000
44A172PHE00.0000.00712.945-1.070-1.0700.0000.0000.0000.000
45A173VAL0-0.001-0.01014.9620.4060.4060.0000.0000.0000.000
46A174TYR0-0.0120.00216.596-0.656-0.6560.0000.0000.0000.000
47A175VAL00.0330.01620.7970.3280.3280.0000.0000.0000.000
48A176ILE00.000-0.00320.923-0.171-0.1710.0000.0000.0000.000
49A177GLY00.0270.00924.8850.0090.0090.0000.0000.0000.000
50A178VAL0-0.038-0.02327.3970.0600.0600.0000.0000.0000.000
51A179SER00.0220.01430.146-0.375-0.3750.0000.0000.0000.000
52A180ASN00.0480.01133.4800.1150.1150.0000.0000.0000.000
53A181ASN00.018-0.00636.362-0.113-0.1130.0000.0000.0000.000
54A182PHE00.0550.03628.471-0.048-0.0480.0000.0000.0000.000
55A183ASN00.0520.02031.4160.3260.3260.0000.0000.0000.000
56A184MET0-0.0030.00733.756-0.123-0.1230.0000.0000.0000.000
57A185LEU00.0210.02033.184-0.226-0.2260.0000.0000.0000.000
58A186THR00.000-0.00533.323-0.153-0.1530.0000.0000.0000.000
59A187THR0-0.027-0.01735.861-0.175-0.1750.0000.0000.0000.000
60A188HIS0-0.076-0.03538.477-0.290-0.2900.0000.0000.0000.000
61A189ARG10.9390.96838.724-7.214-7.2140.0000.0000.0000.000
62A190ASN0-0.088-0.04738.6350.1860.1860.0000.0000.0000.000
63A191ILE00.0130.02333.449-0.086-0.0860.0000.0000.0000.000
64A192ASN0-0.036-0.03133.3150.2190.2190.0000.0000.0000.000
65A193PHE00.0280.02427.395-0.149-0.1490.0000.0000.0000.000
66A194THR00.014-0.02028.3530.1690.1690.0000.0000.0000.000
67A195ALA0-0.0040.01224.259-0.132-0.1320.0000.0000.0000.000
68A196GLU-1-0.812-0.91625.45310.96410.9640.0000.0000.0000.000
69A197LEU0-0.023-0.01020.1990.0840.0840.0000.0000.0000.000
70A198PHE00.0280.00523.8710.0630.0630.0000.0000.0000.000
71A199PHE00.013-0.00318.5400.3880.3880.0000.0000.0000.000
72A200ASP-1-0.687-0.82821.84913.60913.6090.0000.0000.0000.000
73A201SER00.0000.01222.0940.6250.6250.0000.0000.0000.000
74A202THR0-0.048-0.05119.3930.5960.5960.0000.0000.0000.000
75A203GLY00.017-0.00717.6571.0351.0350.0000.0000.0000.000
76A204ASN0-0.072-0.04817.7061.5191.5190.0000.0000.0000.000
77A205LEU0-0.015-0.00419.649-0.547-0.5470.0000.0000.0000.000
78A206LEU00.0360.01721.469-0.271-0.2710.0000.0000.0000.000
79A207THR0-0.006-0.00623.820-0.428-0.4280.0000.0000.0000.000
80A208ARG10.9220.95126.145-10.714-10.7140.0000.0000.0000.000
81A209LEU00.0050.01528.667-0.354-0.3540.0000.0000.0000.000
82A210SER0-0.0070.01525.2770.0340.0340.0000.0000.0000.000
83A211SER00.0340.02626.159-0.181-0.1810.0000.0000.0000.000
84A212LEU0-0.0220.00019.493-0.120-0.1200.0000.0000.0000.000
85A213LYS10.9000.93824.155-11.185-11.1850.0000.0000.0000.000
86A214THR0-0.016-0.01820.412-0.206-0.2060.0000.0000.0000.000
87A215PRO0-0.013-0.00819.1880.5770.5770.0000.0000.0000.000
88A216LEU00.0330.03014.7660.3250.3250.0000.0000.0000.000
89A217ASN00.0210.00012.4271.0351.0350.0000.0000.0000.000
90A218HIS10.8510.9117.750-30.164-30.1640.0000.0000.0000.000
91A219LYS10.8970.9665.146-41.854-41.691-0.001-0.009-0.1530.000
92A220SER00.0170.0067.9552.0932.0930.0000.0000.0000.000
93A221GLY00.0550.0328.836-2.652-2.6520.0000.0000.0000.000
94A222GLN00.010-0.0069.9374.0634.0630.0000.0000.0000.000
95A223ASN00.0340.01912.501-1.343-1.3430.0000.0000.0000.000
96A224MET0-0.0150.01112.0332.3122.3120.0000.0000.0000.000
97A225ALA0-0.020-0.01410.198-0.893-0.8930.0000.0000.0000.000
98A226THR00.0120.00612.357-1.216-1.2160.0000.0000.0000.000
99A227GLY00.008-0.00413.8000.2690.2690.0000.0000.0000.000
100A228ALA00.0290.01113.2720.7880.7880.0000.0000.0000.000
101A229ILE0-0.0090.00411.8311.0901.0900.0000.0000.0000.000
102A230THR00.001-0.06113.127-0.301-0.3010.0000.0000.0000.000
103A231ASN00.0260.0337.584-1.756-1.7560.0000.0000.0000.000
104A232ALA0-0.0140.04011.9281.0851.0850.0000.0000.0000.000
105A233LYS10.9430.97013.711-14.947-14.9470.0000.0000.0000.000
106A234GLY0-0.0020.00512.895-0.417-0.4170.0000.0000.0000.000
107A235PHE0-0.058-0.0547.8161.0391.0390.0000.0000.0000.000
108A236MET0-0.0460.02313.482-0.780-0.7800.0000.0000.0000.000
109A237PRO00.0120.01617.1980.4650.4650.0000.0000.0000.000
110A238SER00.0290.00319.361-0.903-0.9030.0000.0000.0000.000
111A239THR0-0.024-0.04220.843-0.591-0.5910.0000.0000.0000.000
112A240THR0-0.045-0.00823.589-0.710-0.7100.0000.0000.0000.000
113A241ALA0-0.014-0.01522.309-0.465-0.4650.0000.0000.0000.000
114A242TYR0-0.0170.00320.1700.0910.0910.0000.0000.0000.000
115A243PRO00.0640.04825.4440.1520.1520.0000.0000.0000.000
116A244PHE00.038-0.00126.1460.0330.0330.0000.0000.0000.000
117A245ASN0-0.081-0.06230.556-0.151-0.1510.0000.0000.0000.000
118A246ASP-1-0.771-0.86632.6179.0529.0520.0000.0000.0000.000
119A247ASN00.026-0.00834.1210.3370.3370.0000.0000.0000.000
120A248SER0-0.108-0.05636.140-0.034-0.0340.0000.0000.0000.000
121A249ARG10.8260.88527.449-10.957-10.9570.0000.0000.0000.000
122A250GLU-1-0.836-0.88831.3029.2879.2870.0000.0000.0000.000
123A251LYS10.8580.90431.154-8.659-8.6590.0000.0000.0000.000
124A252GLU-1-0.800-0.85927.62111.13511.1350.0000.0000.0000.000
125A253ASN0-0.086-0.05826.4650.2320.2320.0000.0000.0000.000
126A254TYR0-0.024-0.00526.4290.2040.2040.0000.0000.0000.000
127A255ILE0-0.0050.00420.9190.1640.1640.0000.0000.0000.000
128A256TYR00.004-0.00425.110-0.232-0.2320.0000.0000.0000.000
129A257GLY0-0.003-0.00324.8610.4470.4470.0000.0000.0000.000
130A258THR0-0.0030.00625.362-0.440-0.4400.0000.0000.0000.000
131A259CYS0-0.091-0.01623.7400.5650.5650.0000.0000.0000.000
132A260TYR00.0510.00525.364-0.429-0.4290.0000.0000.0000.000
133A261TYR0-0.060-0.03526.5270.5260.5260.0000.0000.0000.000
134A262THR0-0.061-0.03327.499-0.149-0.1490.0000.0000.0000.000
135A263ALA00.0590.03329.904-0.005-0.0050.0000.0000.0000.000
136A264SER0-0.027-0.04333.4770.0630.0630.0000.0000.0000.000
137A265ASP-1-0.867-0.91435.6898.7088.7080.0000.0000.0000.000
138A266ARG10.8360.90131.938-9.463-9.4630.0000.0000.0000.000
139A267THR0-0.051-0.02532.4400.2890.2890.0000.0000.0000.000
140A268ALA0-0.022-0.01429.4220.1860.1860.0000.0000.0000.000
141A269PHE00.0400.00931.152-0.174-0.1740.0000.0000.0000.000
142A270PRO0-0.026-0.01130.1700.3880.3880.0000.0000.0000.000
143A271ILE0-0.035-0.02228.416-0.263-0.2630.0000.0000.0000.000
144A272ASP-1-0.901-0.94428.46510.44610.4460.0000.0000.0000.000
145A273ILE0-0.025-0.02323.1100.0800.0800.0000.0000.0000.000
146A274SER0-0.042-0.02127.204-0.055-0.0550.0000.0000.0000.000
147A275VAL00.005-0.00821.7580.0700.0700.0000.0000.0000.000
148A276MET0-0.0230.00625.094-0.367-0.3670.0000.0000.0000.000
149A277LEU0-0.026-0.01120.9430.3620.3620.0000.0000.0000.000
150A278ASN0-0.010-0.02122.943-0.335-0.3350.0000.0000.0000.000
151A279ARG10.9070.96126.149-9.870-9.8700.0000.0000.0000.000
152A280ARG10.9150.95529.731-10.300-10.3000.0000.0000.0000.000
153A281ALA00.0460.03530.1580.3340.3340.0000.0000.0000.000
154A282ILE0-0.062-0.02530.642-0.344-0.3440.0000.0000.0000.000
155A283ASN00.011-0.00931.431-0.136-0.1360.0000.0000.0000.000
156A284ASP-1-0.879-0.94931.5329.4809.4800.0000.0000.0000.000
157A285GLU-1-0.957-0.97128.15510.96910.9690.0000.0000.0000.000
158A286THR0-0.055-0.02926.9120.4700.4700.0000.0000.0000.000
159A287SER0-0.018-0.00724.082-0.182-0.1820.0000.0000.0000.000
160A288TYR0-0.044-0.03021.5200.2510.2510.0000.0000.0000.000
161A289CYS0-0.068-0.02523.718-0.387-0.3870.0000.0000.0000.000
162A290ILE00.0110.01718.4510.2100.2100.0000.0000.0000.000
163A291ARG10.7720.88122.907-11.221-11.2210.0000.0000.0000.000
164A292ILE00.0150.01320.5750.0280.0280.0000.0000.0000.000
165A293THR00.0240.01325.108-0.125-0.1250.0000.0000.0000.000
166A294TRP00.0420.02722.4720.2120.2120.0000.0000.0000.000
167A295SER0-0.017-0.02328.792-0.353-0.3530.0000.0000.0000.000
168A296TRP00.0250.01131.3260.3580.3580.0000.0000.0000.000
169A297ASN00.0220.00634.731-0.310-0.3100.0000.0000.0000.000
170A298THR00.0080.00736.933-0.044-0.0440.0000.0000.0000.000
171A299GLY0-0.023-0.02039.778-0.157-0.1570.0000.0000.0000.000
172A300ASP-1-0.894-0.95941.3737.1557.1550.0000.0000.0000.000
173A301ALA0-0.044-0.00539.1910.2240.2240.0000.0000.0000.000
174A302PRO0-0.0180.00134.822-0.104-0.1040.0000.0000.0000.000
175A303GLU-1-0.718-0.76735.5818.8958.8950.0000.0000.0000.000
176A304VAL00.0240.00638.922-0.176-0.1760.0000.0000.0000.000
177A305GLN00.022-0.01140.8720.0430.0430.0000.0000.0000.000
178A306THR0-0.051-0.03541.7530.1090.1090.0000.0000.0000.000
179A307SER0-0.029-0.03339.205-0.069-0.0690.0000.0000.0000.000
180A308ALA00.0070.02236.8620.2410.2410.0000.0000.0000.000
181A309THR0-0.003-0.00933.8110.0440.0440.0000.0000.0000.000
182A310THR0-0.047-0.02428.772-0.003-0.0030.0000.0000.0000.000
183A311LEU0-0.0090.01329.3660.0840.0840.0000.0000.0000.000
184A312VAL0-0.011-0.01324.3010.3560.3560.0000.0000.0000.000
185A313THR00.0310.01823.179-0.289-0.2890.0000.0000.0000.000
186A314SER00.0210.00522.5410.3400.3400.0000.0000.0000.000
187A315PRO0-0.055-0.03417.311-0.092-0.0920.0000.0000.0000.000
188A316PHE00.0400.03519.436-0.171-0.1710.0000.0000.0000.000
189A317THR0-0.015-0.02614.7091.3211.3210.0000.0000.0000.000
190A318PHE0-0.023-0.00217.144-0.838-0.8380.0000.0000.0000.000
191A319TYR00.026-0.00113.3290.8520.8520.0000.0000.0000.000
192A320TYR0-0.038-0.02415.572-1.288-1.2880.0000.0000.0000.000
193A321ILE00.0360.01116.1151.3941.3940.0000.0000.0000.000
194A322ARG10.7700.88112.080-23.256-23.2560.0000.0000.0000.000
195A323GLU-1-0.743-0.83616.21113.89113.8910.0000.0000.0000.000
196A324ASP-1-0.838-0.90515.62220.63520.6350.0000.0000.0000.000
197A325ASP-1-0.832-0.92712.39322.12922.1290.0000.0000.0000.000