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: Q1LVY

Calculation Name: 3CUQ-B-Xray372

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: 2023-03-14

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2018537.463336
FMO2-HF: Nuclear repulsion 1936030.664182
FMO2-HF: Total energy -82506.799154
FMO2-MP2: Total energy -82738.764657


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:172:LYS)


Summations of interaction energy for fragment #1(B:172: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.
-35.212-29.4970.717-2.973-3.459-0.001
Interaction energy analysis for fragmet #1(B:172:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.946 / q_NPA : 0.947
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].
3B174ILE00.0460.0402.851-2.0533.2510.717-2.890-3.131-0.001
4B175SER0-0.026-0.0283.7190.0480.3670.001-0.079-0.2410.000
5B176GLU-1-0.885-0.9225.376-25.054-24.962-0.001-0.004-0.0870.000
6B177ALA0-0.0060.0027.3592.1762.1760.0000.0000.0000.000
7B178PHE0-0.045-0.0487.8021.3061.3060.0000.0000.0000.000
8B179GLU-1-0.908-0.9309.729-17.295-17.2950.0000.0000.0000.000
9B180ASP-1-0.877-0.94511.150-17.724-17.7240.0000.0000.0000.000
10B181LEU0-0.041-0.01712.6331.1711.1710.0000.0000.0000.000
11B182SER00.001-0.01514.1971.3181.3180.0000.0000.0000.000
12B183LYS10.9180.95915.12817.13617.1360.0000.0000.0000.000
13B184LEU0-0.010-0.00816.8050.8490.8490.0000.0000.0000.000
14B185MET00.0020.00018.5770.8630.8630.0000.0000.0000.000
15B186ILE0-0.0070.01320.2980.5490.5490.0000.0000.0000.000
16B187LYS10.9580.97721.35212.33112.3310.0000.0000.0000.000
17B188ALA00.0380.02623.3740.4100.4100.0000.0000.0000.000
18B189LYS10.9600.96924.96610.55910.5590.0000.0000.0000.000
19B190GLU-1-0.848-0.91226.581-9.779-9.7790.0000.0000.0000.000
20B191MET0-0.039-0.02126.9050.3190.3190.0000.0000.0000.000
21B192VAL0-0.061-0.00928.2900.3180.3180.0000.0000.0000.000
22B193GLU-1-0.956-1.00129.810-9.011-9.0110.0000.0000.0000.000
23B194LEU0-0.012-0.00532.7300.3380.3380.0000.0000.0000.000
24B195SER0-0.061-0.06433.4880.1010.1010.0000.0000.0000.000
25B196LYS10.9290.95733.4768.4728.4720.0000.0000.0000.000
26B197SER00.0270.01137.7190.1540.1540.0000.0000.0000.000
27B198ILE0-0.072-0.00138.2300.1650.1650.0000.0000.0000.000
28B199ALA00.0110.01540.9600.0990.0990.0000.0000.0000.000
29B200ASN0-0.035-0.01442.6960.0040.0040.0000.0000.0000.000
30B201LYS10.9981.01045.9316.0846.0840.0000.0000.0000.000
31B212ASP-1-0.900-0.98545.647-6.417-6.4170.0000.0000.0000.000
32B213GLU-1-0.900-0.93447.621-6.044-6.0440.0000.0000.0000.000
33B214THR00.0150.00443.406-0.132-0.1320.0000.0000.0000.000
34B215ILE0-0.0040.00842.824-0.141-0.1410.0000.0000.0000.000
35B216ARG10.9220.94140.4906.6806.6800.0000.0000.0000.000
36B217PHE00.0520.01838.144-0.187-0.1870.0000.0000.0000.000
37B218LYS10.8460.93937.9076.6636.6630.0000.0000.0000.000
38B219SER0-0.0240.00136.971-0.235-0.2350.0000.0000.0000.000
39B220TYR0-0.0250.01033.264-0.244-0.2440.0000.0000.0000.000
40B221LEU0-0.001-0.01233.414-0.200-0.2000.0000.0000.0000.000
41B222LEU0-0.058-0.03532.999-0.193-0.1930.0000.0000.0000.000
42B223SER0-0.019-0.01730.553-0.185-0.1850.0000.0000.0000.000
43B224MET0-0.056-0.00826.968-0.342-0.3420.0000.0000.0000.000
44B225GLY00.0550.03328.188-0.294-0.2940.0000.0000.0000.000
45B226ILE0-0.051-0.01530.4620.0210.0210.0000.0000.0000.000
46B227ALA00.0170.00332.3380.2660.2660.0000.0000.0000.000
47B228ASN00.030-0.01235.4470.1730.1730.0000.0000.0000.000
48B229PRO00.0750.04038.3590.1300.1300.0000.0000.0000.000
49B230VAL00.0390.02441.5310.1170.1170.0000.0000.0000.000
50B231THR00.011-0.01341.0140.0740.0740.0000.0000.0000.000
51B232ARG10.8570.92937.9877.5637.5630.0000.0000.0000.000
52B233GLU-1-0.962-0.98442.629-6.661-6.6610.0000.0000.0000.000
53B234THR0-0.0420.00445.3700.1100.1100.0000.0000.0000.000
54B235TYR00.0250.00846.4840.1740.1740.0000.0000.0000.000
55B236GLY00.0160.01345.703-0.147-0.1470.0000.0000.0000.000
56B237SER0-0.030-0.01545.054-0.098-0.0980.0000.0000.0000.000
57B238GLY00.1140.06142.415-0.102-0.1020.0000.0000.0000.000
58B239THR0-0.038-0.00738.267-0.044-0.0440.0000.0000.0000.000
59B240GLN00.0860.01141.395-0.061-0.0610.0000.0000.0000.000
60B241TYR00.0010.01134.6960.1340.1340.0000.0000.0000.000
61B242HIS00.0690.01637.0480.1820.1820.0000.0000.0000.000
62B243MET00.0490.02240.8560.0850.0850.0000.0000.0000.000
63B244GLN0-0.045-0.02940.9290.1810.1810.0000.0000.0000.000
64B245LEU0-0.017-0.00337.6550.0430.0430.0000.0000.0000.000
65B246ALA00.0230.00941.5170.0350.0350.0000.0000.0000.000
66B247LYS10.9650.96644.7286.2856.2850.0000.0000.0000.000
67B248GLN0-0.047-0.00239.1440.1910.1910.0000.0000.0000.000
68B249LEU00.010-0.00840.7430.0380.0380.0000.0000.0000.000
69B250ALA00.0110.00744.5250.0670.0670.0000.0000.0000.000
70B251GLY00.0150.01047.4120.0930.0930.0000.0000.0000.000
71B252ILE0-0.056-0.02241.5650.0310.0310.0000.0000.0000.000
72B253LEU00.016-0.00943.819-0.006-0.0060.0000.0000.0000.000
73B254GLN0-0.0220.01547.2740.0280.0280.0000.0000.0000.000
74B255VAL00.0470.02350.3170.0590.0590.0000.0000.0000.000
75B256PRO00.0170.01346.3650.0360.0360.0000.0000.0000.000
76B257LEU0-0.011-0.01449.1580.0330.0330.0000.0000.0000.000
77B258GLU-1-0.888-0.93951.220-5.401-5.4010.0000.0000.0000.000
78B259GLU-1-0.970-0.99150.371-5.954-5.9540.0000.0000.0000.000
79B260ARG10.8610.92845.9136.2706.2700.0000.0000.0000.000
80B261GLY00.0210.02652.5790.0080.0080.0000.0000.0000.000
81B262GLY0-0.056-0.04054.2680.0740.0740.0000.0000.0000.000
82B263ILE0-0.046-0.03951.8860.0040.0040.0000.0000.0000.000
83B264MET0-0.0090.01244.922-0.039-0.0390.0000.0000.0000.000
84B265SER00.0490.02845.234-0.048-0.0480.0000.0000.0000.000
85B266LEU00.054-0.00742.173-0.085-0.0850.0000.0000.0000.000
86B267THR0-0.063-0.01140.144-0.149-0.1490.0000.0000.0000.000
87B268GLU-1-0.842-0.93840.496-6.527-6.5270.0000.0000.0000.000
88B269VAL00.0270.01141.855-0.064-0.0640.0000.0000.0000.000
89B270TYR0-0.037-0.03032.537-0.122-0.1220.0000.0000.0000.000
90B271CYS0-0.053-0.02737.325-0.225-0.2250.0000.0000.0000.000
91B272LEU0-0.058-0.02138.335-0.095-0.0950.0000.0000.0000.000
92B273VAL00.011-0.00237.717-0.031-0.0310.0000.0000.0000.000
93B274ASN00.0390.01933.366-0.124-0.1240.0000.0000.0000.000
94B275ARG10.9891.00233.9677.3137.3130.0000.0000.0000.000
95B276ALA0-0.044-0.00835.569-0.084-0.0840.0000.0000.0000.000
96B277ARG10.9360.96333.1778.3318.3310.0000.0000.0000.000
97B278GLY00.0090.02631.009-0.124-0.1240.0000.0000.0000.000
98B279MET00.003-0.01123.787-0.291-0.2910.0000.0000.0000.000
99B280GLU-1-0.923-0.97028.421-9.154-9.1540.0000.0000.0000.000
100B281LEU0-0.089-0.03229.5430.3260.3260.0000.0000.0000.000
101B282LEU0-0.055-0.02631.6850.0310.0310.0000.0000.0000.000
102B283SER00.0310.02231.838-0.017-0.0170.0000.0000.0000.000
103B284PRO00.049-0.00232.8590.2270.2270.0000.0000.0000.000
104B285GLU-1-0.877-0.94033.869-8.298-8.2980.0000.0000.0000.000
105B286ASP-1-0.895-0.94234.401-8.153-8.1530.0000.0000.0000.000
106B287LEU00.0090.00537.0760.2120.2120.0000.0000.0000.000
107B288VAL00.0330.02139.3170.2340.2340.0000.0000.0000.000
108B289ASN0-0.006-0.01738.7490.3460.3460.0000.0000.0000.000
109B290ALA0-0.032-0.02341.0330.1560.1560.0000.0000.0000.000
110B291CYS0-0.044-0.03042.7680.1860.1860.0000.0000.0000.000
111B292LYS10.9420.97544.2106.6886.6880.0000.0000.0000.000
112B293MET0-0.055-0.00844.0120.1190.1190.0000.0000.0000.000
113B294LEU0-0.027-0.01746.8940.0720.0720.0000.0000.0000.000
114B295GLU-1-0.871-0.93449.446-5.424-5.4240.0000.0000.0000.000
115B296ALA0-0.0020.00451.3770.0920.0920.0000.0000.0000.000
116B297LEU0-0.052-0.03347.5150.0420.0420.0000.0000.0000.000
117B298LYS10.8880.94652.0865.2475.2470.0000.0000.0000.000
118B299LEU0-0.039-0.01648.9920.0540.0540.0000.0000.0000.000
119B300PRO00.0200.00952.5430.0180.0180.0000.0000.0000.000
120B301LEU00.0180.02648.1560.0360.0360.0000.0000.0000.000
121B302ARG10.9981.00451.7045.4715.4710.0000.0000.0000.000
122B303LEU0-0.009-0.00245.844-0.037-0.0370.0000.0000.0000.000
123B304ARG10.8780.92849.7765.5395.5390.0000.0000.0000.000
124B305VAL0-0.008-0.00748.691-0.143-0.1430.0000.0000.0000.000
125B306PHE00.0000.00750.7690.1260.1260.0000.0000.0000.000
126B307ASP-1-0.853-0.93451.589-5.499-5.4990.0000.0000.0000.000
127B308SER0-0.088-0.05250.626-0.072-0.0720.0000.0000.0000.000
128B309GLY00.0040.00348.044-0.105-0.1050.0000.0000.0000.000
129B310VAL0-0.047-0.01146.739-0.173-0.1730.0000.0000.0000.000
130B311MET0-0.023-0.01344.8540.0690.0690.0000.0000.0000.000
131B312VAL00.0080.00746.787-0.090-0.0900.0000.0000.0000.000
132B313ILE0-0.039-0.01846.041-0.002-0.0020.0000.0000.0000.000
133B314GLU-1-0.816-0.92349.350-5.440-5.4400.0000.0000.0000.000
134B315LEU0-0.0230.00252.772-0.028-0.0280.0000.0000.0000.000
135B316GLN00.0420.02154.759-0.012-0.0120.0000.0000.0000.000
136B317SER0-0.057-0.03857.4270.0360.0360.0000.0000.0000.000
137B318HIS10.8200.91256.6585.3815.3810.0000.0000.0000.000
138B319LYS11.0331.01258.4344.7744.7740.0000.0000.0000.000
139B320GLU-1-0.791-0.88856.740-5.267-5.2670.0000.0000.0000.000
140B321GLU-1-0.933-0.96259.761-4.820-4.8200.0000.0000.0000.000
141B322GLU-1-0.930-0.97463.130-4.655-4.6550.0000.0000.0000.000
142B323MET0-0.087-0.03659.9940.0230.0230.0000.0000.0000.000
143B324VAL0-0.0090.00263.0140.0080.0080.0000.0000.0000.000
144B325ALA00.0250.02264.8300.0300.0300.0000.0000.0000.000
145B326SER0-0.020-0.01364.556-0.001-0.0010.0000.0000.0000.000
146B327ALA00.0350.00362.823-0.008-0.0080.0000.0000.0000.000
147B328LEU0-0.015-0.00264.643-0.003-0.0030.0000.0000.0000.000
148B329GLU-1-0.890-0.95167.942-4.287-4.2870.0000.0000.0000.000
149B330THR0-0.029-0.00563.490-0.016-0.0160.0000.0000.0000.000
150B331VAL0-0.018-0.02164.9070.0100.0100.0000.0000.0000.000
151B332SER0-0.029-0.03267.1830.0410.0410.0000.0000.0000.000
152B333GLU-1-0.981-0.96769.244-4.405-4.4050.0000.0000.0000.000
153B334LYS10.8690.93365.6304.6514.6510.0000.0000.0000.000
154B335GLY0-0.0220.01968.904-0.014-0.0140.0000.0000.0000.000
155B336SER0-0.035-0.03967.231-0.002-0.0020.0000.0000.0000.000
156B337LEU0-0.0140.00061.557-0.031-0.0310.0000.0000.0000.000
157B338THR00.0460.02758.603-0.054-0.0540.0000.0000.0000.000
158B339SER00.008-0.02655.678-0.007-0.0070.0000.0000.0000.000
159B340GLU-1-0.923-0.96752.317-5.822-5.8220.0000.0000.0000.000
160B341GLU-1-0.889-0.93055.850-5.004-5.0040.0000.0000.0000.000
161B342PHE00.0160.01658.3640.0110.0110.0000.0000.0000.000
162B343ALA00.009-0.00454.1700.0140.0140.0000.0000.0000.000
163B344LYS10.9310.95354.9135.4475.4470.0000.0000.0000.000
164B345LEU0-0.050-0.02056.7910.0170.0170.0000.0000.0000.000
165B346VAL0-0.024-0.00758.8840.0380.0380.0000.0000.0000.000
166B347GLY0-0.0200.01655.538-0.012-0.0120.0000.0000.0000.000
167B348MET0-0.041-0.01953.390-0.011-0.0110.0000.0000.0000.000
168B349SER00.0180.00349.1090.0140.0140.0000.0000.0000.000
169B350VAL00.0990.02950.3470.0730.0730.0000.0000.0000.000
170B351LEU0-0.039-0.01546.7680.0770.0770.0000.0000.0000.000
171B352LEU00.014-0.00949.9320.0640.0640.0000.0000.0000.000
172B353ALA00.0470.04052.8400.1050.1050.0000.0000.0000.000
173B354LYS10.9720.97953.0405.7015.7010.0000.0000.0000.000
174B355GLU-1-0.883-0.92252.224-5.649-5.6490.0000.0000.0000.000
175B356ARG10.9010.94755.8495.2995.2990.0000.0000.0000.000
176B357LEU00.0260.01058.6460.0920.0920.0000.0000.0000.000
177B358LEU00.0190.00856.1460.0740.0740.0000.0000.0000.000
178B359LEU0-0.061-0.01259.6950.0630.0630.0000.0000.0000.000
179B360ALA00.0580.01261.3550.0750.0750.0000.0000.0000.000
180B361GLU-1-0.816-0.84962.478-4.831-4.8310.0000.0000.0000.000
181B362LYS10.9040.95359.6915.1345.1340.0000.0000.0000.000
182B363MET0-0.093-0.03464.6590.0260.0260.0000.0000.0000.000
183B364GLY00.0080.01267.3060.0720.0720.0000.0000.0000.000
184B365HIS00.0220.01067.9660.0840.0840.0000.0000.0000.000
185B366LEU0-0.023-0.00564.2930.0300.0300.0000.0000.0000.000
186B367CYS0-0.048-0.00867.488-0.012-0.0120.0000.0000.0000.000
187B368ARG10.8170.84560.0884.9454.9450.0000.0000.0000.000
188B369ASP-1-0.912-0.95465.130-4.578-4.5780.0000.0000.0000.000
189B370ASP-1-0.978-0.98060.792-5.153-5.1530.0000.0000.0000.000
190B371SER00.0380.02362.7340.0510.0510.0000.0000.0000.000
191B372VAL0-0.014-0.02460.856-0.078-0.0780.0000.0000.0000.000
192B373GLU-1-0.935-0.96060.232-4.778-4.7780.0000.0000.0000.000
193B374GLY00.0020.01359.404-0.063-0.0630.0000.0000.0000.000
194B375LEU0-0.048-0.01858.0270.0610.0610.0000.0000.0000.000
195B376ARG10.8910.93460.6294.7214.7210.0000.0000.0000.000
196B377PHE0-0.048-0.02359.6240.0110.0110.0000.0000.0000.000
197B378TYR00.0740.02264.9340.0030.0030.0000.0000.0000.000
198B379PRO00.0570.03168.609-0.024-0.0240.0000.0000.0000.000
199B380ASN0-0.024-0.03570.8710.0410.0410.0000.0000.0000.000
200B381LEU0-0.015-0.02472.2960.0480.0480.0000.0000.0000.000
201B382PHE0-0.0050.00772.2810.0590.0590.0000.0000.0000.000
202B383MET0-0.058-0.01573.9480.0540.0540.0000.0000.0000.000
203B384THR0-0.027-0.01176.5830.0220.0220.0000.0000.0000.000
204B385GLN0-0.0040.00479.081-0.001-0.0010.0000.0000.0000.000