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

tag_button

FMODB ID: 89J5Y

Calculation Name: 3F5C-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F5C

Chain ID: C

ChEMBL ID:

UniProt ID: Q61066

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2008000.563324
FMO2-HF: Nuclear repulsion 1932649.667115
FMO2-HF: Total energy -75350.896209
FMO2-MP2: Total energy -75563.184764


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(C:252:ASP)


Summations of interaction energy for fragment #1(C:252: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.
-1.248.34.585-5.959-8.1690.05
Interaction energy analysis for fragmet #1(C:252:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.840 / q_NPA : -0.942
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].
3C254GLN00.0600.0073.831-3.076-1.282-0.013-0.644-1.1370.003
4C255VAL0-0.0180.0152.438-6.161-5.5272.380-1.320-1.6950.001
5C256VAL00.0290.0063.037-6.670-5.7850.062-0.287-0.6610.000
6C257CYS0-0.0120.0045.546-5.275-5.2750.0000.0000.0000.000
7C258GLU-1-0.917-0.9477.62522.62822.6280.0000.0000.0000.000
8C259ALA0-0.029-0.0288.765-2.864-2.8640.0000.0000.0000.000
9C260ALA0-0.017-0.0089.392-1.882-1.8820.0000.0000.0000.000
10C261SER00.0240.00211.107-2.252-2.2520.0000.0000.0000.000
11C262ALA0-0.030-0.00513.444-1.634-1.6340.0000.0000.0000.000
12C263GLY00.0560.03514.307-1.160-1.1600.0000.0000.0000.000
13C264LEU00.0330.01915.519-1.301-1.3010.0000.0000.0000.000
14C265LEU0-0.018-0.01417.449-1.264-1.2640.0000.0000.0000.000
15C266LYS10.8960.95418.348-16.003-16.0030.0000.0000.0000.000
16C267THR00.0320.01018.932-0.770-0.7700.0000.0000.0000.000
17C268LEU00.000-0.01121.276-0.826-0.8260.0000.0000.0000.000
18C269ARG10.9090.97123.201-13.213-13.2130.0000.0000.0000.000
19C270PHE00.0010.00224.062-0.612-0.6120.0000.0000.0000.000
20C271VAL00.0080.00925.258-0.440-0.4400.0000.0000.0000.000
21C272LYS10.8840.94727.386-10.447-10.4470.0000.0000.0000.000
22C273TYR0-0.081-0.04628.044-0.255-0.2550.0000.0000.0000.000
23C274LEU00.0340.02629.888-0.295-0.2950.0000.0000.0000.000
24C275PRO00.0410.02132.410-0.125-0.1250.0000.0000.0000.000
25C276CYS0-0.046-0.03035.362-0.087-0.0870.0000.0000.0000.000
26C277PHE00.003-0.00130.020-0.047-0.0470.0000.0000.0000.000
27C278GLN00.0520.01433.633-0.001-0.0010.0000.0000.0000.000
28C279ILE0-0.091-0.02136.218-0.160-0.1600.0000.0000.0000.000
29C280LEU0-0.009-0.02234.563-0.021-0.0210.0000.0000.0000.000
30C281PRO00.0000.02437.4760.1090.1090.0000.0000.0000.000
31C282LEU00.010-0.00732.8260.0150.0150.0000.0000.0000.000
32C283ASP-1-0.773-0.92734.0168.6438.6430.0000.0000.0000.000
33C284GLN0-0.011-0.01434.5320.2440.2440.0000.0000.0000.000
34C285GLN0-0.044-0.00131.9240.3940.3940.0000.0000.0000.000
35C286LEU00.0020.01428.6710.3730.3730.0000.0000.0000.000
36C287VAL0-0.0010.00629.5040.4220.4220.0000.0000.0000.000
37C288LEU0-0.0080.00429.7560.2470.2470.0000.0000.0000.000
38C289VAL00.0550.01524.8780.4130.4130.0000.0000.0000.000
39C290ARG10.8080.91025.046-11.146-11.1460.0000.0000.0000.000
40C291SER0-0.006-0.00824.9620.2600.2600.0000.0000.0000.000
41C292CYS0-0.039-0.01323.6660.4030.4030.0000.0000.0000.000
42C293TRP00.0100.01416.9660.5900.5900.0000.0000.0000.000
43C294ALA00.0600.03718.3130.6230.6230.0000.0000.0000.000
44C295PRO0-0.002-0.00718.2330.7270.7270.0000.0000.0000.000
45C296LEU0-0.019-0.01819.3460.4080.4080.0000.0000.0000.000
46C297LEU0-0.0010.02214.3350.1120.1120.0000.0000.0000.000
47C298MET0-0.012-0.00613.3890.9700.9700.0000.0000.0000.000
48C299LEU0-0.006-0.01816.2200.2120.2120.0000.0000.0000.000
49C300GLU-1-0.908-0.95216.80714.77314.7730.0000.0000.0000.000
50C301LEU00.0000.00911.2930.2540.2540.0000.0000.0000.000
51C302ALA0-0.011-0.01113.6550.6450.6450.0000.0000.0000.000
52C303GLN0-0.0060.01715.542-0.461-0.4610.0000.0000.0000.000
53C304ASP-1-0.936-0.95714.15916.61416.6140.0000.0000.0000.000
54C305HIS0-0.107-0.05113.6120.2010.2010.0000.0000.0000.000
55C306LEU00.0250.0057.1640.8980.8980.0000.0000.0000.000
56C307HIS0-0.021-0.0066.304-1.646-1.6460.0000.0000.0000.000
57C308PHE0-0.048-0.0354.2151.4981.638-0.001-0.030-0.1100.000
58C309GLU-1-0.941-0.9583.99430.95031.1750.000-0.115-0.1100.001
59C310MET0-0.061-0.0463.6027.2537.8530.038-0.173-0.4650.000
60C311MET00.0080.0123.762-3.093-2.7170.007-0.120-0.2630.001
61C312GLU-1-0.930-0.9477.18028.26228.2620.0000.0000.0000.000
62C353HIS0-0.001-0.0122.451-30.704-25.8182.112-3.270-3.7280.044
63C354LEU0-0.038-0.0307.588-4.102-4.1020.0000.0000.0000.000
64C355LEU00.0160.01811.1080.1660.1660.0000.0000.0000.000
65C356PRO00.002-0.00713.617-0.720-0.7200.0000.0000.0000.000
66C357ALA00.0730.04413.6031.1681.1680.0000.0000.0000.000
67C358ALA0-0.008-0.01115.0390.4470.4470.0000.0000.0000.000
68C359ALA00.0130.00514.640-0.134-0.1340.0000.0000.0000.000
69C360VAL00.0780.03910.3060.1000.1000.0000.0000.0000.000
70C361GLN0-0.005-0.01412.5591.5931.5930.0000.0000.0000.000
71C362ALA0-0.0040.01414.759-0.601-0.6010.0000.0000.0000.000
72C363ILE00.0460.02111.468-0.668-0.6680.0000.0000.0000.000
73C364LYS10.9660.9929.840-28.940-28.9400.0000.0000.0000.000
74C365SER0-0.029-0.03813.238-0.894-0.8940.0000.0000.0000.000
75C366PHE0-0.029-0.01116.051-1.116-1.1160.0000.0000.0000.000
76C367PHE00.0600.01512.632-0.814-0.8140.0000.0000.0000.000
77C368PHE00.0090.01113.244-0.522-0.5220.0000.0000.0000.000
78C369LYS10.9260.97717.144-13.572-13.5720.0000.0000.0000.000
79C370CYS0-0.004-0.00518.228-0.938-0.9380.0000.0000.0000.000
80C371TRP0-0.037-0.02111.578-0.679-0.6790.0000.0000.0000.000
81C372SER0-0.070-0.02519.183-0.646-0.6460.0000.0000.0000.000
82C373LEU0-0.062-0.02521.856-0.635-0.6350.0000.0000.0000.000
83C374ASN0-0.004-0.00523.016-0.079-0.0790.0000.0000.0000.000
84C375ILE0-0.0160.01121.754-0.462-0.4620.0000.0000.0000.000
85C376ASP-1-0.774-0.88523.36110.95410.9540.0000.0000.0000.000
86C377THR00.027-0.02024.3250.2710.2710.0000.0000.0000.000
87C378LYS10.9300.96925.560-9.026-9.0260.0000.0000.0000.000
88C379GLU-1-0.805-0.90326.81510.72910.7290.0000.0000.0000.000
89C380TYR00.0830.02719.1620.0650.0650.0000.0000.0000.000
90C381ALA0-0.081-0.02524.4820.1770.1770.0000.0000.0000.000
91C382TYR00.016-0.02226.559-0.075-0.0750.0000.0000.0000.000
92C383LEU00.0020.01723.995-0.169-0.1690.0000.0000.0000.000
93C384LYS10.8910.94321.134-13.499-13.4990.0000.0000.0000.000
94C385GLY0-0.0050.00325.453-0.054-0.0540.0000.0000.0000.000
95C386THR0-0.008-0.01228.581-0.267-0.2670.0000.0000.0000.000
96C387VAL0-0.057-0.01524.126-0.090-0.0900.0000.0000.0000.000
97C388LEU0-0.045-0.03327.246-0.049-0.0490.0000.0000.0000.000
98C389PHE0-0.016-0.01028.377-0.200-0.2000.0000.0000.0000.000
99C390ASN00.0360.00729.855-0.302-0.3020.0000.0000.0000.000
100C391PRO00.001-0.02632.9810.0760.0760.0000.0000.0000.000
101C392ASP-1-0.899-0.93633.3308.8738.8730.0000.0000.0000.000
102C393LEU0-0.060-0.01429.259-0.032-0.0320.0000.0000.0000.000
103C394PRO00.0480.01032.449-0.289-0.2890.0000.0000.0000.000
104C395GLY00.0070.00334.3470.1970.1970.0000.0000.0000.000
105C396LEU0-0.031-0.00534.422-0.115-0.1150.0000.0000.0000.000
106C397GLN0-0.016-0.00537.600-0.353-0.3530.0000.0000.0000.000
107C398CYS0-0.052-0.02338.438-0.173-0.1730.0000.0000.0000.000
108C399VAL00.1010.05139.1970.0690.0690.0000.0000.0000.000
109C400LYS10.9870.97640.017-6.621-6.6210.0000.0000.0000.000
110C401TYR0-0.083-0.02738.156-0.111-0.1110.0000.0000.0000.000
111C402ILE00.0530.01435.3140.0350.0350.0000.0000.0000.000
112C403GLU-1-0.856-0.92636.9727.8227.8220.0000.0000.0000.000
113C404GLY00.0010.01138.969-0.001-0.0010.0000.0000.0000.000
114C405LEU0-0.051-0.01535.399-0.013-0.0130.0000.0000.0000.000
115C406GLN00.001-0.00632.3880.1190.1190.0000.0000.0000.000
116C407TRP00.0060.00435.5670.0830.0830.0000.0000.0000.000
117C408ARG10.9180.92637.844-7.511-7.5110.0000.0000.0000.000
118C409THR0-0.0150.00131.5150.0680.0680.0000.0000.0000.000
119C410GLN00.0540.01133.5420.2330.2330.0000.0000.0000.000
120C411GLN0-0.0330.00935.261-0.032-0.0320.0000.0000.0000.000
121C412ILE0-0.054-0.03834.400-0.090-0.0900.0000.0000.0000.000
122C413LEU00.0020.01731.1080.0520.0520.0000.0000.0000.000
123C414THR0-0.014-0.01634.3720.0440.0440.0000.0000.0000.000
124C415GLU-1-0.930-0.95937.0657.4427.4420.0000.0000.0000.000
125C416HIS0-0.049-0.02731.001-0.298-0.2980.0000.0000.0000.000
126C417ILE00.0200.00533.036-0.014-0.0140.0000.0000.0000.000
127C418ARG10.9320.96435.658-7.545-7.5450.0000.0000.0000.000
128C419MET0-0.088-0.03737.270-0.192-0.1920.0000.0000.0000.000
129C420MET0-0.061-0.01633.7780.0820.0820.0000.0000.0000.000
130C421GLN0-0.0070.00730.143-0.110-0.1100.0000.0000.0000.000
131C422ARG10.9680.97635.773-7.407-7.4070.0000.0000.0000.000
132C423GLU-1-0.896-0.95637.1167.9517.9510.0000.0000.0000.000
133C424TYR00.017-0.00836.9610.2130.2130.0000.0000.0000.000
134C425GLN00.017-0.01336.1710.2090.2090.0000.0000.0000.000
135C426ILE00.0090.02433.8010.1950.1950.0000.0000.0000.000
136C427ARG10.8890.96226.948-10.470-10.4700.0000.0000.0000.000
137C428SER0-0.042-0.01231.1980.3890.3890.0000.0000.0000.000
138C429ALA00.020-0.00631.6750.2860.2860.0000.0000.0000.000
139C430GLU-1-0.899-0.94028.32710.67210.6720.0000.0000.0000.000
140C431LEU00.0090.00226.4970.4940.4940.0000.0000.0000.000
141C432ASN0-0.054-0.03326.9740.3030.3030.0000.0000.0000.000
142C433SER0-0.039-0.02026.7440.1400.1400.0000.0000.0000.000
143C434ALA00.0290.00922.7080.3950.3950.0000.0000.0000.000
144C435LEU00.0220.00222.9980.5250.5250.0000.0000.0000.000
145C436PHE0-0.056-0.02424.9150.1000.1000.0000.0000.0000.000
146C437LEU0-0.012-0.01520.5080.0580.0580.0000.0000.0000.000
147C438LEU00.0210.01819.5030.3620.3620.0000.0000.0000.000
148C439ARG10.9100.95521.513-10.800-10.8000.0000.0000.0000.000
149C440PHE0-0.085-0.01720.607-0.345-0.3450.0000.0000.0000.000
150C441ILE00.1020.03616.7800.7690.7690.0000.0000.0000.000
151C442ASN0-0.0130.01717.8500.4380.4380.0000.0000.0000.000
152C443SER0-0.008-0.04417.934-0.586-0.5860.0000.0000.0000.000
153C444ASP-1-0.894-0.92918.35515.13115.1310.0000.0000.0000.000
154C445VAL0-0.003-0.02213.0160.7330.7330.0000.0000.0000.000
155C446VAL00.0400.02513.0671.5551.5550.0000.0000.0000.000
156C447THR00.005-0.00612.6821.4581.4580.0000.0000.0000.000
157C448GLU-1-0.905-0.98812.99921.21821.2180.0000.0000.0000.000
158C449LEU0-0.062-0.0207.8861.4821.4820.0000.0000.0000.000
159C450PHE0-0.021-0.0067.9543.9823.9820.0000.0000.0000.000
160C451PHE00.0330.0069.898-0.632-0.6320.0000.0000.0000.000
161C452ARG10.9020.99812.433-19.099-19.0990.0000.0000.0000.000
162C453PRO00.010-0.0088.555-1.535-1.5350.0000.0000.0000.000
163C454ILE0-0.006-0.0039.657-0.225-0.2250.0000.0000.0000.000
164C455ILE0-0.081-0.01913.108-1.405-1.4050.0000.0000.0000.000
165C456GLY00.006-0.00515.782-1.013-1.0130.0000.0000.0000.000
166C457ALA0-0.067-0.05417.571-0.868-0.8680.0000.0000.0000.000
167C458VAL00.0300.02920.200-0.602-0.6020.0000.0000.0000.000
168C459SER00.0300.01420.692-0.495-0.4950.0000.0000.0000.000
169C460MET0-0.046-0.02717.6740.6320.6320.0000.0000.0000.000
170C461ASP-1-0.838-0.91220.89812.63712.6370.0000.0000.0000.000
171C462ASP-1-0.870-0.96024.49411.90511.9050.0000.0000.0000.000
172C463MET0-0.051-0.01319.068-0.248-0.2480.0000.0000.0000.000
173C464MET00.017-0.01120.558-0.391-0.3910.0000.0000.0000.000
174C465LEU00.0090.00224.723-0.280-0.2800.0000.0000.0000.000
175C466GLU-1-0.846-0.89825.38110.99710.9970.0000.0000.0000.000
176C467MET0-0.019-0.00720.756-0.297-0.2970.0000.0000.0000.000
177C468LEU0-0.049-0.03025.776-0.244-0.2440.0000.0000.0000.000
178C469CYS0-0.026-0.02728.753-0.422-0.4220.0000.0000.0000.000
179C470ALA00.0220.03127.260-0.256-0.2560.0000.0000.0000.000
180C471LYS10.8420.93124.916-12.081-12.0810.0000.0000.0000.000
181C472LEU0-0.0100.00429.437-0.130-0.1300.0000.0000.0000.000