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: 9Y652

Calculation Name: 3CUQ-B-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CUQ

Chain ID: B

ChEMBL ID:

UniProt ID: Q96H20

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 208
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2031572.105633
FMO2-HF: Nuclear repulsion 1948723.461952
FMO2-HF: Total energy -82848.643681
FMO2-MP2: Total energy -83081.682017


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:171:ACE )


Summations of interaction energy for fragment #1(B:171:ACE )
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.
2.1271.2546.499-3.27-2.355-0.012
Interaction energy analysis for fragmet #1(B:171:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.000
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].
3B173ASN 00.0820.0343.8930.5371.493-0.004-0.371-0.581-0.001
4B174ILE 00.0400.0582.3222.356-0.6386.371-2.252-1.124-0.005
5B175SER 0-0.020-0.0303.041-0.7960.3770.132-0.642-0.664-0.006
6B176GLU -1-0.881-0.9195.044-0.118-0.1260.000-0.0050.0140.000
7B177ALA 0-0.0040.0037.6250.0380.0380.0000.0000.0000.000
8B178PHE 0-0.047-0.0486.9930.0540.0540.0000.0000.0000.000
9B179GLU -1-0.906-0.9309.3190.3420.3420.0000.0000.0000.000
10B180ASP -1-0.876-0.94411.0760.0070.0070.0000.0000.0000.000
11B181LEU 0-0.041-0.01712.454-0.029-0.0290.0000.0000.0000.000
12B182SER 00.004-0.01313.728-0.022-0.0220.0000.0000.0000.000
13B183LYS 10.9180.95815.001-0.121-0.1210.0000.0000.0000.000
14B184LEU 0-0.011-0.00816.875-0.012-0.0120.0000.0000.0000.000
15B185MET 00.0020.00018.282-0.010-0.0100.0000.0000.0000.000
16B186ILE 0-0.0060.01319.775-0.006-0.0060.0000.0000.0000.000
17B187LYS 10.9580.97821.540-0.031-0.0310.0000.0000.0000.000
18B188ALA 00.0380.02623.265-0.005-0.0050.0000.0000.0000.000
19B189LYS 10.9600.96924.436-0.063-0.0630.0000.0000.0000.000
20B190GLU -1-0.847-0.91226.4500.0400.0400.0000.0000.0000.000
21B191MET 0-0.039-0.02127.095-0.004-0.0040.0000.0000.0000.000
22B192VAL 0-0.062-0.01027.918-0.002-0.0020.0000.0000.0000.000
23B193GLU -1-0.957-1.00129.3390.0430.0430.0000.0000.0000.000
24B194LEU 0-0.011-0.00332.302-0.002-0.0020.0000.0000.0000.000
25B195SER 0-0.062-0.06633.267-0.003-0.0030.0000.0000.0000.000
26B196LYS 10.9290.95732.821-0.034-0.0340.0000.0000.0000.000
27B197SER 00.0260.01137.3240.0000.0000.0000.0000.0000.000
28B198ILE 0-0.071-0.00138.137-0.001-0.0010.0000.0000.0000.000
29B199ALA 00.0130.01740.748-0.002-0.0020.0000.0000.0000.000
30B200ASN 0-0.044-0.01942.3910.0000.0000.0000.0000.0000.000
31B201LYS 10.9750.97745.582-0.007-0.0070.0000.0000.0000.000
32B202NME 00.0260.03348.7160.0000.0000.0000.0000.0000.000
33B211ACE 00.0210.00250.6930.0000.0000.0000.0000.0000.000
34B212ASP -1-0.906-0.99045.984-0.005-0.0050.0000.0000.0000.000
35B213GLU -1-0.898-0.92447.8170.0020.0020.0000.0000.0000.000
36B214THR 00.0130.00343.4350.0000.0000.0000.0000.0000.000
37B215ILE 0-0.0060.01042.9340.0000.0000.0000.0000.0000.000
38B216ARG 10.9160.93940.8680.0050.0050.0000.0000.0000.000
39B217PHE 00.0500.01738.081-0.001-0.0010.0000.0000.0000.000
40B218LYS 10.8440.93937.984-0.002-0.0020.0000.0000.0000.000
41B219SER 0-0.0200.00137.301-0.001-0.0010.0000.0000.0000.000
42B220TYR 0-0.0280.00933.473-0.002-0.0020.0000.0000.0000.000
43B221LEU 0-0.009-0.01533.5670.0010.0010.0000.0000.0000.000
44B222LEU 0-0.049-0.03133.0070.0010.0010.0000.0000.0000.000
45B223SER 0-0.021-0.01831.038-0.002-0.0020.0000.0000.0000.000
46B224MET 0-0.057-0.00827.1440.0000.0000.0000.0000.0000.000
47B225GLY 00.0560.03428.1640.0000.0000.0000.0000.0000.000
48B226ILE 0-0.052-0.01630.1930.0040.0040.0000.0000.0000.000
49B227ALA 00.0180.00432.082-0.002-0.0020.0000.0000.0000.000
50B228ASN 00.030-0.01335.1420.0020.0020.0000.0000.0000.000
51B229PRO 00.0750.04037.929-0.001-0.0010.0000.0000.0000.000
52B230VAL 00.0400.02541.142-0.001-0.0010.0000.0000.0000.000
53B231THR 00.013-0.01440.6340.0000.0000.0000.0000.0000.000
54B232ARG 10.8550.92837.817-0.006-0.0060.0000.0000.0000.000
55B233GLU -1-0.962-0.98342.4250.0020.0020.0000.0000.0000.000
56B234THR 0-0.0370.00745.1330.0000.0000.0000.0000.0000.000
57B235TYR 00.0180.00546.2800.0000.0000.0000.0000.0000.000
58B236GLY 00.0180.01445.6650.0000.0000.0000.0000.0000.000
59B237SER 0-0.031-0.01545.081-0.001-0.0010.0000.0000.0000.000
60B238GLY 00.1180.06242.4060.0010.0010.0000.0000.0000.000
61B239THR 0-0.038-0.00838.8010.0000.0000.0000.0000.0000.000
62B240GLN 00.0900.01341.815-0.001-0.0010.0000.0000.0000.000
63B241TYR 00.0000.01035.990-0.001-0.0010.0000.0000.0000.000
64B242HIS 00.0670.01637.5350.0000.0000.0000.0000.0000.000
65B243MET 00.0500.02241.7690.0000.0000.0000.0000.0000.000
66B244GLN 0-0.042-0.02742.4970.0000.0000.0000.0000.0000.000
67B245LEU 0-0.023-0.00639.062-0.001-0.0010.0000.0000.0000.000
68B246ALA 00.0280.01043.0450.0000.0000.0000.0000.0000.000
69B247LYS 10.9630.96446.0460.0110.0110.0000.0000.0000.000
70B248GLN 0-0.046-0.00141.2450.0000.0000.0000.0000.0000.000
71B249LEU 00.010-0.00842.224-0.001-0.0010.0000.0000.0000.000
72B250ALA 00.0110.00846.2510.0000.0000.0000.0000.0000.000
73B251GLY 00.0150.01149.4210.0000.0000.0000.0000.0000.000
74B252ILE 0-0.055-0.02243.7730.0000.0000.0000.0000.0000.000
75B253LEU 00.011-0.01245.2270.0000.0000.0000.0000.0000.000
76B254GLN 0-0.0220.01648.9570.0010.0010.0000.0000.0000.000
77B255VAL 00.0490.02352.3800.0010.0010.0000.0000.0000.000
78B256PRO 00.0160.01348.1830.0000.0000.0000.0000.0000.000
79B257LEU 0-0.010-0.01450.4830.0010.0010.0000.0000.0000.000
80B258GLU -1-0.888-0.93952.555-0.011-0.0110.0000.0000.0000.000
81B259GLU -1-0.970-0.99052.284-0.015-0.0150.0000.0000.0000.000
82B260ARG 10.8640.92947.3390.0140.0140.0000.0000.0000.000
83B261GLY 00.0190.02653.7960.0010.0010.0000.0000.0000.000
84B262GLY 0-0.057-0.04155.4400.0010.0010.0000.0000.0000.000
85B263ILE 0-0.044-0.03852.5110.0010.0010.0000.0000.0000.000
86B264MET 0-0.0110.01046.078-0.001-0.0010.0000.0000.0000.000
87B265SER 00.0490.02845.7190.0010.0010.0000.0000.0000.000
88B266LEU 00.047-0.00842.592-0.001-0.0010.0000.0000.0000.000
89B267THR 0-0.056-0.00940.461-0.002-0.0020.0000.0000.0000.000
90B268GLU -1-0.840-0.93741.241-0.011-0.0110.0000.0000.0000.000
91B269VAL 00.0230.00942.877-0.002-0.0020.0000.0000.0000.000
92B270TYR 0-0.037-0.02933.311-0.002-0.0020.0000.0000.0000.000
93B271CYS 0-0.049-0.02638.503-0.002-0.0020.0000.0000.0000.000
94B272LEU 0-0.059-0.02139.572-0.002-0.0020.0000.0000.0000.000
95B273VAL 00.008-0.00339.374-0.002-0.0020.0000.0000.0000.000
96B274ASN 00.0410.01934.829-0.003-0.0030.0000.0000.0000.000
97B275ARG 10.9881.00235.8430.0210.0210.0000.0000.0000.000
98B276ALA 0-0.044-0.00737.564-0.002-0.0020.0000.0000.0000.000
99B277ARG 10.9390.96335.5740.0280.0280.0000.0000.0000.000
100B278GLY 00.0070.02533.875-0.001-0.0010.0000.0000.0000.000
101B279MET 00.002-0.01126.273-0.003-0.0030.0000.0000.0000.000
102B280GLU -1-0.923-0.97030.942-0.043-0.0430.0000.0000.0000.000
103B281LEU 0-0.090-0.03231.4260.0040.0040.0000.0000.0000.000
104B282LEU 0-0.056-0.02733.4760.0010.0010.0000.0000.0000.000
105B283SER 00.0340.02332.4710.0010.0010.0000.0000.0000.000
106B284PRO 00.050-0.00133.1890.0000.0000.0000.0000.0000.000
107B285GLU -1-0.878-0.94033.8360.0010.0010.0000.0000.0000.000
108B286ASP -1-0.893-0.94235.383-0.013-0.0130.0000.0000.0000.000
109B287LEU 00.0090.00537.6860.0000.0000.0000.0000.0000.000
110B288VAL 00.0320.02239.7770.0010.0010.0000.0000.0000.000
111B289ASN 0-0.004-0.01738.8200.0020.0020.0000.0000.0000.000
112B290ALA 0-0.034-0.02341.6710.0000.0000.0000.0000.0000.000
113B291CYS 0-0.044-0.03043.5460.0000.0000.0000.0000.0000.000
114B292LYS 10.9400.97544.1380.0000.0000.0000.0000.0000.000
115B293MET 0-0.054-0.00844.4240.0000.0000.0000.0000.0000.000
116B294LEU 0-0.025-0.01747.9710.0000.0000.0000.0000.0000.000
117B295GLU -1-0.870-0.93350.305-0.004-0.0040.0000.0000.0000.000
118B296ALA 0-0.0050.00351.8810.0000.0000.0000.0000.0000.000
119B297LEU 0-0.049-0.03248.5330.0000.0000.0000.0000.0000.000
120B298LYS 10.8870.94553.0670.0060.0060.0000.0000.0000.000
121B299LEU 0-0.041-0.01750.462-0.001-0.0010.0000.0000.0000.000
122B300PRO 00.0210.00954.1380.0000.0000.0000.0000.0000.000
123B301LEU 00.0180.02749.4940.0000.0000.0000.0000.0000.000
124B302ARG 10.9981.00452.5190.0030.0030.0000.0000.0000.000
125B303LEU 0-0.011-0.00246.1910.0000.0000.0000.0000.0000.000
126B304ARG 10.8790.92850.2330.0040.0040.0000.0000.0000.000
127B305VAL 0-0.008-0.00748.5960.0000.0000.0000.0000.0000.000
128B306PHE 0-0.0010.00550.6560.0000.0000.0000.0000.0000.000
129B307ASP -1-0.851-0.93351.1670.0030.0030.0000.0000.0000.000
130B308SER 0-0.089-0.05250.0770.0010.0010.0000.0000.0000.000
131B309GLY 00.0060.00447.4200.0010.0010.0000.0000.0000.000
132B310VAL 0-0.047-0.01146.3480.0000.0000.0000.0000.0000.000
133B311MET 0-0.023-0.01344.7780.0000.0000.0000.0000.0000.000
134B312VAL 00.0050.00647.014-0.001-0.0010.0000.0000.0000.000
135B313ILE 0-0.039-0.01846.8000.0000.0000.0000.0000.0000.000
136B314GLU -1-0.810-0.92250.032-0.005-0.0050.0000.0000.0000.000
137B315LEU 0-0.0220.00253.5860.0000.0000.0000.0000.0000.000
138B316GLN 00.0390.02055.8250.0010.0010.0000.0000.0000.000
139B317SER 0-0.057-0.03758.4870.0000.0000.0000.0000.0000.000
140B318HIS 10.8200.91257.2930.0060.0060.0000.0000.0000.000
141B319LYS 11.0371.01259.1180.0030.0030.0000.0000.0000.000
142B320GLU -1-0.794-0.88957.009-0.004-0.0040.0000.0000.0000.000
143B321GLU -1-0.934-0.96260.150-0.002-0.0020.0000.0000.0000.000
144B322GLU -1-0.927-0.97263.398-0.004-0.0040.0000.0000.0000.000
145B323MET 0-0.087-0.03660.6040.0000.0000.0000.0000.0000.000
146B324VAL 0-0.0070.00363.2230.0000.0000.0000.0000.0000.000
147B325ALA 00.0200.02065.1190.0000.0000.0000.0000.0000.000
148B326SER 0-0.017-0.01265.1790.0000.0000.0000.0000.0000.000
149B327ALA 00.0330.00363.1600.0000.0000.0000.0000.0000.000
150B328LEU 0-0.012-0.00265.0060.0000.0000.0000.0000.0000.000
151B329GLU -1-0.892-0.95268.169-0.003-0.0030.0000.0000.0000.000
152B330THR 0-0.027-0.00563.9980.0000.0000.0000.0000.0000.000
153B331VAL 0-0.021-0.02265.0460.0000.0000.0000.0000.0000.000
154B332SER 0-0.027-0.03267.3820.0000.0000.0000.0000.0000.000
155B333GLU -1-0.982-0.96769.752-0.004-0.0040.0000.0000.0000.000
156B334LYS 10.8690.93366.1060.0040.0040.0000.0000.0000.000
157B335GLY 0-0.0200.02169.0550.0000.0000.0000.0000.0000.000
158B336SER 0-0.038-0.04067.0280.0000.0000.0000.0000.0000.000
159B337LEU 0-0.0140.00061.6790.0000.0000.0000.0000.0000.000
160B338THR 00.0460.02658.3930.0000.0000.0000.0000.0000.000
161B339SER 00.007-0.02755.5480.0000.0000.0000.0000.0000.000
162B340GLU -1-0.925-0.96852.358-0.005-0.0050.0000.0000.0000.000
163B341GLU -1-0.886-0.92855.961-0.003-0.0030.0000.0000.0000.000
164B342PHE 00.0160.01658.669-0.001-0.0010.0000.0000.0000.000
165B343ALA 00.007-0.00554.6290.0000.0000.0000.0000.0000.000
166B344LYS 10.9350.95455.5190.0070.0070.0000.0000.0000.000
167B345LEU 0-0.051-0.02057.4120.0000.0000.0000.0000.0000.000
168B346VAL 0-0.029-0.00959.5400.0000.0000.0000.0000.0000.000
169B347GLY 0-0.0160.01856.4380.0000.0000.0000.0000.0000.000
170B348MET 0-0.039-0.01954.2090.0000.0000.0000.0000.0000.000
171B349SER 00.0170.00249.6140.0000.0000.0000.0000.0000.000
172B350VAL 00.0950.02750.5140.0010.0010.0000.0000.0000.000
173B351LEU 0-0.036-0.01446.9380.0010.0010.0000.0000.0000.000
174B352LEU 00.015-0.00950.2860.0010.0010.0000.0000.0000.000
175B353ALA 00.0470.04053.1120.0000.0000.0000.0000.0000.000
176B354LYS 10.9710.97952.5980.0000.0000.0000.0000.0000.000
177B355GLU -1-0.880-0.92151.9680.0000.0000.0000.0000.0000.000
178B356ARG 10.9010.94755.7700.0050.0050.0000.0000.0000.000
179B357LEU 00.0230.00958.7240.0000.0000.0000.0000.0000.000
180B358LEU 00.0210.00955.7130.0000.0000.0000.0000.0000.000
181B359LEU 0-0.061-0.01259.5910.0000.0000.0000.0000.0000.000
182B360ALA 00.0600.01261.1720.0000.0000.0000.0000.0000.000
183B361GLU -1-0.816-0.84761.9030.0020.0020.0000.0000.0000.000
184B362LYS 10.9040.95359.293-0.001-0.0010.0000.0000.0000.000
185B363MET 0-0.095-0.03564.2110.0000.0000.0000.0000.0000.000
186B364GLY 00.0070.01267.0360.0000.0000.0000.0000.0000.000
187B365HIS 00.0240.01167.9160.0000.0000.0000.0000.0000.000
188B366LEU 0-0.027-0.00764.1900.0000.0000.0000.0000.0000.000
189B367CYS 0-0.046-0.00767.0930.0000.0000.0000.0000.0000.000
190B368ARG 10.8180.84659.230-0.002-0.0020.0000.0000.0000.000
191B369ASP -1-0.913-0.95564.5420.0010.0010.0000.0000.0000.000
192B370ASP -1-0.981-0.98159.8400.0030.0030.0000.0000.0000.000
193B371SER 00.0420.02461.9230.0000.0000.0000.0000.0000.000
194B372VAL 0-0.015-0.02459.8880.0000.0000.0000.0000.0000.000
195B373GLU -1-0.935-0.95959.4450.0000.0000.0000.0000.0000.000
196B374GLY 00.0020.01358.7280.0000.0000.0000.0000.0000.000
197B375LEU 0-0.047-0.01857.4100.0000.0000.0000.0000.0000.000
198B376ARG 10.8890.93360.1820.0000.0000.0000.0000.0000.000
199B377PHE 0-0.049-0.02359.3170.0000.0000.0000.0000.0000.000
200B378TYR 00.0740.02164.6540.0000.0000.0000.0000.0000.000
201B379PRO 00.0600.03368.3670.0000.0000.0000.0000.0000.000
202B380ASN 0-0.026-0.03570.5550.0000.0000.0000.0000.0000.000
203B381LEU 0-0.015-0.02571.9670.0000.0000.0000.0000.0000.000
204B382PHE 0-0.0020.00971.6080.0000.0000.0000.0000.0000.000
205B383MET 0-0.058-0.01473.5140.0000.0000.0000.0000.0000.000
206B384THR 0-0.033-0.02176.1570.0000.0000.0000.0000.0000.000
207B385GLN 0-0.040-0.02578.7810.0000.0000.0000.0000.0000.000
208B386NME 00.0370.03681.5990.0000.0000.0000.0000.0000.000