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

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FMODB ID: 98Y42

Calculation Name: 3F5C-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F5C

Chain ID: B

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2057182.844941
FMO2-HF: Nuclear repulsion 1981048.121543
FMO2-HF: Total energy -76134.723398
FMO2-MP2: Total energy -76349.261409


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(B:251:LYS)


Summations of interaction energy for fragment #1(B:251:LYS)
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.
-135.863-140.37928.012-12.126-11.371-0.113
Interaction energy analysis for fragmet #1(B:251:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.841 / q_NPA : 0.905
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].
3B253PRO00.0000.0212.6866.0918.9070.176-1.249-1.743-0.001
4B254GLN00.0700.0154.4060.0330.185-0.001-0.018-0.1330.000
5B255VAL00.0380.0273.6793.2053.4810.002-0.061-0.2180.000
6B256VAL00.008-0.0096.2393.4653.4650.0000.0000.0000.000
7B257CYS0-0.0320.0048.4833.1763.1760.0000.0000.0000.000
8B258GLU-1-0.956-0.9689.775-19.472-19.4720.0000.0000.0000.000
9B259ALA00.004-0.00210.0751.9401.9400.0000.0000.0000.000
10B260ALA00.0230.01011.8581.6851.6850.0000.0000.0000.000
11B261SER00.0180.00314.2441.8941.8940.0000.0000.0000.000
12B262ALA0-0.009-0.00614.9621.2611.2610.0000.0000.0000.000
13B263GLY00.0260.01116.0430.9890.9890.0000.0000.0000.000
14B264LEU00.0180.01717.8311.0201.0200.0000.0000.0000.000
15B265LEU0-0.012-0.01519.3250.9840.9840.0000.0000.0000.000
16B266LYS10.8060.89816.98016.35616.3560.0000.0000.0000.000
17B267THR00.0340.00121.4040.6290.6290.0000.0000.0000.000
18B268LEU00.019-0.00923.8160.5810.5810.0000.0000.0000.000
19B269ARG10.9060.97022.45912.26812.2680.0000.0000.0000.000
20B270PHE0-0.006-0.00826.3430.4430.4430.0000.0000.0000.000
21B271VAL00.0140.00128.0620.3710.3710.0000.0000.0000.000
22B272LYS10.8240.92329.7889.8789.8780.0000.0000.0000.000
23B273TYR0-0.012-0.01429.6130.2000.2000.0000.0000.0000.000
24B274LEU00.0210.03331.8380.2830.2830.0000.0000.0000.000
25B275PRO00.0290.00734.6600.0960.0960.0000.0000.0000.000
26B276CYS0-0.061-0.02537.6540.0540.0540.0000.0000.0000.000
27B277PHE00.0630.04333.3350.0650.0650.0000.0000.0000.000
28B278GLN0-0.023-0.02535.4580.2800.2800.0000.0000.0000.000
29B279ILE0-0.041-0.00637.5910.1320.1320.0000.0000.0000.000
30B280LEU0-0.029-0.00437.8740.1950.1950.0000.0000.0000.000
31B281PRO00.0340.01840.370-0.078-0.0780.0000.0000.0000.000
32B282LEU00.0520.02235.732-0.158-0.1580.0000.0000.0000.000
33B283ASP-1-0.785-0.89237.468-7.903-7.9030.0000.0000.0000.000
34B284GLN00.0280.01837.962-0.186-0.1860.0000.0000.0000.000
35B285GLN0-0.028-0.02234.997-0.439-0.4390.0000.0000.0000.000
36B286LEU00.0130.00332.289-0.345-0.3450.0000.0000.0000.000
37B287VAL0-0.0030.00433.181-0.326-0.3260.0000.0000.0000.000
38B288LEU00.0090.01833.608-0.261-0.2610.0000.0000.0000.000
39B289VAL00.0140.00528.409-0.377-0.3770.0000.0000.0000.000
40B290ARG10.8300.89228.8349.5429.5420.0000.0000.0000.000
41B291SER0-0.0220.00228.780-0.289-0.2890.0000.0000.0000.000
42B292CYS0-0.054-0.02728.516-0.310-0.3100.0000.0000.0000.000
43B293TRP00.006-0.00120.466-0.686-0.6860.0000.0000.0000.000
44B294ALA00.0450.03722.490-0.471-0.4710.0000.0000.0000.000
45B295PRO00.013-0.00322.350-0.633-0.6330.0000.0000.0000.000
46B296LEU00.003-0.00423.869-0.233-0.2330.0000.0000.0000.000
47B297LEU0-0.0070.01117.576-0.198-0.1980.0000.0000.0000.000
48B298MET0-0.021-0.00817.039-1.023-1.0230.0000.0000.0000.000
49B299LEU00.0070.00219.803-0.393-0.3930.0000.0000.0000.000
50B300GLU-1-0.848-0.91920.130-13.011-13.0110.0000.0000.0000.000
51B301LEU0-0.025-0.01314.462-0.337-0.3370.0000.0000.0000.000
52B302ALA0-0.0150.00916.522-0.822-0.8220.0000.0000.0000.000
53B303GLN0-0.012-0.00319.0050.5810.5810.0000.0000.0000.000
54B304ASP-1-0.867-0.92416.142-15.051-15.0510.0000.0000.0000.000
55B305HIS0-0.055-0.01715.366-0.194-0.1940.0000.0000.0000.000
56B306LEU00.0310.02010.067-1.271-1.2710.0000.0000.0000.000
57B307HIS0-0.058-0.04010.255-0.163-0.1630.0000.0000.0000.000
58B308PHE0-0.047-0.0257.772-1.531-1.5310.0000.0000.0000.000
59B309GLU-1-0.918-0.9491.764-122.588-124.26513.380-6.757-4.946-0.087
60B310MET00.0340.0104.819-5.140-5.1400.0000.0000.0000.000
61B311MET0-0.0410.0092.354-9.437-15.56814.456-4.041-4.283-0.025
62B312GLU-1-0.876-0.9445.388-30.625-30.577-0.0010.000-0.0480.000
63B313ILE0-0.070-0.0375.8734.2594.2590.0000.0000.0000.000
64B353HIS0-0.094-0.06417.4510.1000.1000.0000.0000.0000.000
65B354LEU00.0480.01510.9480.0250.0250.0000.0000.0000.000
66B355LEU00.0360.04012.753-1.060-1.0600.0000.0000.0000.000
67B356PRO0-0.0010.01114.1581.4231.4230.0000.0000.0000.000
68B357ALA00.015-0.01215.209-0.366-0.3660.0000.0000.0000.000
69B358ALA00.0260.00615.538-0.769-0.7690.0000.0000.0000.000
70B359ALA00.0230.01517.7650.0500.0500.0000.0000.0000.000
71B360VAL00.0780.03311.2660.2430.2430.0000.0000.0000.000
72B361GLN00.003-0.00114.287-2.278-2.2780.0000.0000.0000.000
73B362ALA00.0210.02815.7100.3610.3610.0000.0000.0000.000
74B363ILE00.0360.01715.0580.4750.4750.0000.0000.0000.000
75B364LYS10.9240.97910.82326.90726.9070.0000.0000.0000.000
76B365SER0-0.034-0.03615.1200.6130.6130.0000.0000.0000.000
77B366PHE00.007-0.00418.4970.8510.8510.0000.0000.0000.000
78B367PHE00.0180.01314.0220.7950.7950.0000.0000.0000.000
79B368PHE00.0400.01213.2950.5710.5710.0000.0000.0000.000
80B369LYS10.8740.95718.64712.84812.8480.0000.0000.0000.000
81B370CYS0-0.005-0.00621.3210.8430.8430.0000.0000.0000.000
82B371TRP0-0.063-0.04213.8370.2600.2600.0000.0000.0000.000
83B372SER0-0.077-0.04621.3510.6190.6190.0000.0000.0000.000
84B373LEU0-0.026-0.01323.4660.5270.5270.0000.0000.0000.000
85B374ASN0-0.054-0.01325.0290.4010.4010.0000.0000.0000.000
86B375ILE0-0.0080.01325.3000.5290.5290.0000.0000.0000.000
87B376ASP-1-0.713-0.83425.907-10.390-10.3900.0000.0000.0000.000
88B377THR00.036-0.01224.6870.0250.0250.0000.0000.0000.000
89B378LYS10.8160.90627.1718.7808.7800.0000.0000.0000.000
90B379GLU-1-0.794-0.91029.692-10.010-10.0100.0000.0000.0000.000
91B380TYR00.0690.02322.2850.0140.0140.0000.0000.0000.000
92B381ALA0-0.031-0.00527.544-0.073-0.0730.0000.0000.0000.000
93B382TYR00.0490.02329.5980.1970.1970.0000.0000.0000.000
94B383LEU0-0.0090.01327.5860.1560.1560.0000.0000.0000.000
95B384LYS10.8250.88524.48812.18212.1820.0000.0000.0000.000
96B385GLY00.0110.00629.0360.1050.1050.0000.0000.0000.000
97B386THR0-0.044-0.04032.6760.3190.3190.0000.0000.0000.000
98B387VAL0-0.052-0.01528.2540.1250.1250.0000.0000.0000.000
99B388LEU0-0.016-0.01530.6850.0880.0880.0000.0000.0000.000
100B389PHE0-0.037-0.03532.2610.2030.2030.0000.0000.0000.000
101B390ASN0-0.010-0.02134.4530.1640.1640.0000.0000.0000.000
102B391PRO00.010-0.01236.3990.0030.0030.0000.0000.0000.000
103B392ASP-1-0.881-0.92637.403-8.327-8.3270.0000.0000.0000.000
104B393LEU0-0.016-0.00133.267-0.039-0.0390.0000.0000.0000.000
105B394PRO00.010-0.01035.9390.2420.2420.0000.0000.0000.000
106B395GLY00.0280.01837.474-0.180-0.1800.0000.0000.0000.000
107B396LEU0-0.049-0.01538.1420.1340.1340.0000.0000.0000.000
108B397GLN0-0.040-0.02341.1030.3050.3050.0000.0000.0000.000
109B398CYS0-0.098-0.05541.7800.1370.1370.0000.0000.0000.000
110B399VAL00.0530.02842.7980.0040.0040.0000.0000.0000.000
111B400LYS10.9990.99043.6506.3356.3350.0000.0000.0000.000
112B401TYR0-0.091-0.04640.8770.1270.1270.0000.0000.0000.000
113B402ILE00.0360.01838.627-0.056-0.0560.0000.0000.0000.000
114B403GLU-1-0.839-0.92640.829-7.251-7.2510.0000.0000.0000.000
115B404GLY00.0080.00842.919-0.028-0.0280.0000.0000.0000.000
116B405LEU0-0.065-0.03238.5930.0400.0400.0000.0000.0000.000
117B406GLN00.0530.03637.2040.0500.0500.0000.0000.0000.000
118B407TRP0-0.006-0.00239.318-0.112-0.1120.0000.0000.0000.000
119B408ARG10.8920.94441.6157.3637.3630.0000.0000.0000.000
120B409THR0-0.031-0.01734.892-0.067-0.0670.0000.0000.0000.000
121B410GLN00.015-0.00635.552-0.042-0.0420.0000.0000.0000.000
122B411GLN0-0.0120.00938.8990.1380.1380.0000.0000.0000.000
123B412ILE0-0.016-0.01637.2790.0660.0660.0000.0000.0000.000
124B413LEU00.0150.01733.774-0.091-0.0910.0000.0000.0000.000
125B414THR0-0.014-0.01437.185-0.075-0.0750.0000.0000.0000.000
126B415GLU-1-0.817-0.87340.159-7.193-7.1930.0000.0000.0000.000
127B416HIS0-0.026-0.01932.9920.3160.3160.0000.0000.0000.000
128B417ILE00.0260.01035.288-0.003-0.0030.0000.0000.0000.000
129B418ARG10.7600.83737.7357.2837.2830.0000.0000.0000.000
130B419MET0-0.054-0.01039.6680.2680.2680.0000.0000.0000.000
131B420MET0-0.037-0.00533.1140.1170.1170.0000.0000.0000.000
132B421GLN0-0.010-0.00734.3130.0250.0250.0000.0000.0000.000
133B422ARG10.9480.96838.8347.4477.4470.0000.0000.0000.000
134B423GLU-1-0.850-0.93139.963-8.139-8.1390.0000.0000.0000.000
135B424TYR00.0000.00038.4790.1830.1830.0000.0000.0000.000
136B425GLN0-0.022-0.01238.820-0.267-0.2670.0000.0000.0000.000
137B426ILE00.0290.02535.361-0.183-0.1830.0000.0000.0000.000
138B427ARG10.8200.89029.80210.19210.1920.0000.0000.0000.000
139B428SER00.0200.01533.895-0.380-0.3800.0000.0000.0000.000
140B429ALA00.0090.01034.459-0.229-0.2290.0000.0000.0000.000
141B430GLU-1-0.860-0.93830.670-10.501-10.5010.0000.0000.0000.000
142B431LEU00.0030.00429.445-0.473-0.4730.0000.0000.0000.000
143B432ASN0-0.011-0.02129.886-0.395-0.3950.0000.0000.0000.000
144B433SER0-0.0300.00428.581-0.293-0.2930.0000.0000.0000.000
145B434ALA00.0140.00425.609-0.396-0.3960.0000.0000.0000.000
146B435LEU00.010-0.00326.213-0.398-0.3980.0000.0000.0000.000
147B436PHE0-0.073-0.03928.601-0.040-0.0400.0000.0000.0000.000
148B437LEU0-0.005-0.00422.054-0.063-0.0630.0000.0000.0000.000
149B438LEU0-0.0180.00223.114-0.390-0.3900.0000.0000.0000.000
150B439ARG10.9410.97424.81910.23510.2350.0000.0000.0000.000
151B440PHE0-0.049-0.01924.3310.1980.1980.0000.0000.0000.000
152B441ILE00.0020.00619.554-0.495-0.4950.0000.0000.0000.000
153B442ASN0-0.043-0.02621.328-0.158-0.1580.0000.0000.0000.000
154B443SER00.0430.02922.4090.2300.2300.0000.0000.0000.000
155B444ASP-1-0.857-0.92421.487-13.566-13.5660.0000.0000.0000.000
156B445VAL00.010-0.00216.685-0.631-0.6310.0000.0000.0000.000
157B446VAL00.0010.01316.687-1.198-1.1980.0000.0000.0000.000
158B447THR0-0.042-0.04016.716-0.625-0.6250.0000.0000.0000.000
159B448GLU-1-0.796-0.90316.475-16.811-16.8110.0000.0000.0000.000
160B449LEU0-0.049-0.01610.322-0.843-0.8430.0000.0000.0000.000
161B450PHE0-0.003-0.01611.186-1.684-1.6840.0000.0000.0000.000
162B451PHE00.006-0.00213.4520.2580.2580.0000.0000.0000.000
163B452ARG10.8420.93515.12315.59115.5910.0000.0000.0000.000
164B453PRO0-0.016-0.01810.8640.7840.7840.0000.0000.0000.000
165B454ILE0-0.045-0.01612.3390.1250.1250.0000.0000.0000.000
166B455ILE0-0.026-0.01915.3400.8740.8740.0000.0000.0000.000
167B456GLY00.0320.02717.5890.8730.8730.0000.0000.0000.000
168B457ALA0-0.018-0.02019.062-0.073-0.0730.0000.0000.0000.000
169B458VAL0-0.0140.00622.2950.5670.5670.0000.0000.0000.000
170B459SER00.015-0.02323.200-0.621-0.6210.0000.0000.0000.000
171B460MET00.0110.00321.558-0.039-0.0390.0000.0000.0000.000
172B461ASP-1-0.829-0.93424.406-11.047-11.0470.0000.0000.0000.000
173B462ASP-1-0.845-0.89128.005-9.869-9.8690.0000.0000.0000.000
174B463MET00.0250.01722.2910.3050.3050.0000.0000.0000.000
175B464MET0-0.040-0.01325.381-0.034-0.0340.0000.0000.0000.000
176B465LEU00.0150.01428.0120.2310.2310.0000.0000.0000.000
177B466GLU-1-0.842-0.92228.326-9.499-9.4990.0000.0000.0000.000
178B467MET0-0.107-0.04322.0170.0410.0410.0000.0000.0000.000
179B468LEU00.0110.00627.7020.0210.0210.0000.0000.0000.000
180B469CYS0-0.059-0.00531.1260.3810.3810.0000.0000.0000.000
181B470ALA00.0470.01628.4280.1680.1680.0000.0000.0000.000
182B471LYS10.8280.90725.17611.16211.1620.0000.0000.0000.000
183B472LEU00.0210.02828.6220.2640.2640.0000.0000.0000.000