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: 43YJN

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2027201.92001
FMO2-HF: Nuclear repulsion 1944691.719349
FMO2-HF: Total energy -82510.20066
FMO2-MP2: Total energy -82742.059706


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.
-31.373-26.8260.934-2.581-2.899-0.002
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 : 0.954 / q_NPA : 0.948
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].
3B174ILE00.0660.0362.638-1.2213.0780.934-2.526-2.707-0.002
4B175SER0-0.005-0.0153.8631.0631.3110.000-0.055-0.1920.000
5B176GLU-1-0.873-0.9115.669-25.085-25.0850.0000.0000.0000.000
6B177ALA00.0190.0137.7422.0842.0840.0000.0000.0000.000
7B178PHE0-0.037-0.0387.3221.4691.4690.0000.0000.0000.000
8B179GLU-1-0.856-0.9079.868-16.185-16.1850.0000.0000.0000.000
9B180ASP-1-0.808-0.91011.631-16.487-16.4870.0000.0000.0000.000
10B181LEU0-0.022-0.00313.0071.1931.1930.0000.0000.0000.000
11B182SER00.0040.00214.6071.2661.2660.0000.0000.0000.000
12B183LYS10.8050.88514.27817.73417.7340.0000.0000.0000.000
13B184LEU0-0.013-0.00317.4080.7810.7810.0000.0000.0000.000
14B185MET0-0.004-0.00718.5970.8110.8110.0000.0000.0000.000
15B186ILE0-0.023-0.00820.9210.5980.5980.0000.0000.0000.000
16B187LYS10.8400.90821.71311.58611.5860.0000.0000.0000.000
17B188ALA00.0360.02523.4930.3990.3990.0000.0000.0000.000
18B189LYS10.8480.91625.18410.09010.0900.0000.0000.0000.000
19B190GLU-1-0.805-0.90026.594-9.956-9.9560.0000.0000.0000.000
20B191MET00.0000.01326.9430.4150.4150.0000.0000.0000.000
21B192VAL00.0340.04228.7480.3150.3150.0000.0000.0000.000
22B193GLU-1-0.882-0.93330.763-8.796-8.7960.0000.0000.0000.000
23B194LEU0-0.018-0.01533.1310.2700.2700.0000.0000.0000.000
24B195SER0-0.046-0.04133.5700.1750.1750.0000.0000.0000.000
25B196LYS10.9260.95133.6508.5198.5190.0000.0000.0000.000
26B197SER00.0170.00337.4740.1510.1510.0000.0000.0000.000
27B198ILE0-0.035-0.00438.8990.1680.1680.0000.0000.0000.000
28B199ALA0-0.0190.00041.4010.1300.1300.0000.0000.0000.000
29B200ASN0-0.061-0.02443.2190.0320.0320.0000.0000.0000.000
30B201LYS10.8740.93246.2076.1586.1580.0000.0000.0000.000
31B212ASP-1-0.782-0.87245.326-6.492-6.4920.0000.0000.0000.000
32B213GLU-1-0.805-0.90246.992-6.165-6.1650.0000.0000.0000.000
33B214THR00.0240.02043.867-0.134-0.1340.0000.0000.0000.000
34B215ILE0-0.014-0.00443.051-0.141-0.1410.0000.0000.0000.000
35B216ARG10.8590.88440.5566.5596.5590.0000.0000.0000.000
36B217PHE00.0410.01837.488-0.191-0.1910.0000.0000.0000.000
37B218LYS10.8580.95338.2106.5896.5890.0000.0000.0000.000
38B219SER00.0290.01136.335-0.138-0.1380.0000.0000.0000.000
39B220TYR0-0.057-0.01832.860-0.223-0.2230.0000.0000.0000.000
40B221LEU00.005-0.00233.354-0.227-0.2270.0000.0000.0000.000
41B222LEU0-0.035-0.01433.179-0.172-0.1720.0000.0000.0000.000
42B223SER0-0.038-0.03530.986-0.216-0.2160.0000.0000.0000.000
43B224MET0-0.040-0.01427.645-0.366-0.3660.0000.0000.0000.000
44B225GLY00.0270.02728.814-0.226-0.2260.0000.0000.0000.000
45B226ILE0-0.041-0.01230.6080.0720.0720.0000.0000.0000.000
46B227ALA00.002-0.00332.6800.2980.2980.0000.0000.0000.000
47B228ASN00.0420.01735.3500.1330.1330.0000.0000.0000.000
48B229PRO00.0390.00638.3550.1520.1520.0000.0000.0000.000
49B230VAL00.0430.02441.4440.1200.1200.0000.0000.0000.000
50B231THR0-0.016-0.00741.0690.1020.1020.0000.0000.0000.000
51B232ARG10.8210.89438.0807.3597.3590.0000.0000.0000.000
52B233GLU-1-0.810-0.87642.459-6.769-6.7690.0000.0000.0000.000
53B234THR0-0.027-0.01645.3940.1200.1200.0000.0000.0000.000
54B235TYR00.0300.02046.5650.1590.1590.0000.0000.0000.000
55B236GLY00.0320.00746.099-0.111-0.1110.0000.0000.0000.000
56B237SER0-0.0320.01346.021-0.064-0.0640.0000.0000.0000.000
57B238GLY00.024-0.00942.573-0.100-0.1000.0000.0000.0000.000
58B239THR00.006-0.01638.572-0.041-0.0410.0000.0000.0000.000
59B240GLN00.0470.00941.818-0.088-0.0880.0000.0000.0000.000
60B241TYR0-0.041-0.02935.1910.1500.1500.0000.0000.0000.000
61B242HIS00.0260.00737.2560.1820.1820.0000.0000.0000.000
62B243MET00.0610.03741.5350.1490.1490.0000.0000.0000.000
63B244GLN0-0.018-0.01441.7290.2340.2340.0000.0000.0000.000
64B245LEU00.0130.01838.4890.0470.0470.0000.0000.0000.000
65B246ALA00.0240.01241.8900.0410.0410.0000.0000.0000.000
66B247LYS10.8740.91745.1766.3436.3430.0000.0000.0000.000
67B248GLN0-0.023-0.00339.5170.0510.0510.0000.0000.0000.000
68B249LEU0-0.004-0.00641.1750.0400.0400.0000.0000.0000.000
69B250ALA00.009-0.00244.8320.0610.0610.0000.0000.0000.000
70B251GLY0-0.0050.01047.5840.1120.1120.0000.0000.0000.000
71B252ILE0-0.049-0.03342.4260.0330.0330.0000.0000.0000.000
72B253LEU00.014-0.00943.916-0.022-0.0220.0000.0000.0000.000
73B254GLN0-0.028-0.01247.4850.0180.0180.0000.0000.0000.000
74B255VAL00.0490.02750.3920.0530.0530.0000.0000.0000.000
75B256PRO0-0.006-0.00146.4560.0440.0440.0000.0000.0000.000
76B257LEU00.0400.02249.1470.0070.0070.0000.0000.0000.000
77B258GLU-1-0.873-0.92151.483-5.415-5.4150.0000.0000.0000.000
78B259GLU-1-0.885-0.94449.419-6.105-6.1050.0000.0000.0000.000
79B260ARG10.7430.85747.8316.2106.2100.0000.0000.0000.000
80B261GLY00.0420.03453.0680.0100.0100.0000.0000.0000.000
81B262GLY0-0.025-0.02954.7480.0900.0900.0000.0000.0000.000
82B263ILE0-0.048-0.03552.4650.0000.0000.0000.0000.0000.000
83B264MET00.0070.02345.558-0.026-0.0260.0000.0000.0000.000
84B265SER00.004-0.02745.654-0.062-0.0620.0000.0000.0000.000
85B266LEU00.024-0.01742.512-0.086-0.0860.0000.0000.0000.000
86B267THR0-0.036-0.01040.861-0.167-0.1670.0000.0000.0000.000
87B268GLU-1-0.749-0.83341.037-6.527-6.5270.0000.0000.0000.000
88B269VAL00.0210.01542.355-0.060-0.0600.0000.0000.0000.000
89B270TYR0-0.044-0.03233.308-0.123-0.1230.0000.0000.0000.000
90B271CYS0-0.042-0.02737.901-0.226-0.2260.0000.0000.0000.000
91B272LEU0-0.039-0.00138.981-0.053-0.0530.0000.0000.0000.000
92B273VAL00.013-0.01237.830-0.092-0.0920.0000.0000.0000.000
93B274ASN00.008-0.01433.838-0.029-0.0290.0000.0000.0000.000
94B275ARG10.8970.96034.2827.2937.2930.0000.0000.0000.000
95B276ALA0-0.0190.00536.194-0.010-0.0100.0000.0000.0000.000
96B277ARG10.8510.92733.6388.3268.3260.0000.0000.0000.000
97B278GLY00.0200.02231.604-0.061-0.0610.0000.0000.0000.000
98B279MET00.003-0.01023.795-0.415-0.4150.0000.0000.0000.000
99B280GLU-1-0.892-0.95328.954-9.115-9.1150.0000.0000.0000.000
100B281LEU0-0.0340.00229.1420.3460.3460.0000.0000.0000.000
101B282LEU0-0.020-0.00531.797-0.031-0.0310.0000.0000.0000.000
102B283SER00.0840.05632.295-0.014-0.0140.0000.0000.0000.000
103B284PRO00.0370.00133.3770.2450.2450.0000.0000.0000.000
104B285GLU-1-0.841-0.93033.309-8.325-8.3250.0000.0000.0000.000
105B286ASP-1-0.790-0.86734.904-8.035-8.0350.0000.0000.0000.000
106B287LEU00.0070.00637.7030.2060.2060.0000.0000.0000.000
107B288VAL00.0390.02239.9580.2230.2230.0000.0000.0000.000
108B289ASN0-0.038-0.04739.1270.3470.3470.0000.0000.0000.000
109B290ALA00.0070.00641.7830.1380.1380.0000.0000.0000.000
110B291CYS0-0.036-0.02643.5080.1820.1820.0000.0000.0000.000
111B292LYS10.8180.89443.2496.8826.8820.0000.0000.0000.000
112B293MET0-0.059-0.01444.1730.1000.1000.0000.0000.0000.000
113B294LEU0-0.0210.00047.1590.0820.0820.0000.0000.0000.000
114B295GLU-1-0.796-0.88449.558-5.408-5.4080.0000.0000.0000.000
115B296ALA0-0.0040.00051.3750.1020.1020.0000.0000.0000.000
116B297LEU0-0.071-0.03647.7150.0440.0440.0000.0000.0000.000
117B298LYS10.8920.93852.3395.3245.3240.0000.0000.0000.000
118B299LEU0-0.0220.01049.1060.0690.0690.0000.0000.0000.000
119B300PRO00.0170.00052.8730.0350.0350.0000.0000.0000.000
120B301LEU0-0.0200.01548.8320.0250.0250.0000.0000.0000.000
121B302ARG10.8820.93052.2855.4015.4010.0000.0000.0000.000
122B303LEU0-0.010-0.00246.838-0.067-0.0670.0000.0000.0000.000
123B304ARG10.7940.86650.3765.6335.6330.0000.0000.0000.000
124B305VAL0-0.021-0.01548.790-0.153-0.1530.0000.0000.0000.000
125B306PHE00.0400.02751.1310.1360.1360.0000.0000.0000.000
126B307ASP-1-0.805-0.90152.100-5.438-5.4380.0000.0000.0000.000
127B308SER0-0.060-0.04551.073-0.054-0.0540.0000.0000.0000.000
128B309GLY00.0050.00948.168-0.118-0.1180.0000.0000.0000.000
129B310VAL0-0.029-0.01647.272-0.152-0.1520.0000.0000.0000.000
130B311MET00.0050.00444.6460.0640.0640.0000.0000.0000.000
131B312VAL0-0.041-0.01947.004-0.097-0.0970.0000.0000.0000.000
132B313ILE00.0060.00346.5680.0170.0170.0000.0000.0000.000
133B314GLU-1-0.744-0.85349.706-5.434-5.4340.0000.0000.0000.000
134B315LEU00.0060.00953.194-0.035-0.0350.0000.0000.0000.000
135B316GLN0-0.024-0.02355.1630.0540.0540.0000.0000.0000.000
136B317SER0-0.040-0.01557.7750.0560.0560.0000.0000.0000.000
137B318HIS10.7930.89256.8765.3915.3910.0000.0000.0000.000
138B319LYS10.8020.88858.4344.8134.8130.0000.0000.0000.000
139B320GLU-1-0.766-0.87257.274-5.337-5.3370.0000.0000.0000.000
140B321GLU-1-0.792-0.90460.409-4.933-4.9330.0000.0000.0000.000
141B322GLU-1-0.808-0.89563.962-4.722-4.7220.0000.0000.0000.000
142B323MET0-0.053-0.01660.2040.0150.0150.0000.0000.0000.000
143B324VAL00.0110.01963.2600.0050.0050.0000.0000.0000.000
144B325ALA00.0160.01965.0080.0320.0320.0000.0000.0000.000
145B326SER0-0.032-0.02764.3280.0090.0090.0000.0000.0000.000
146B327ALA00.0050.00963.183-0.008-0.0080.0000.0000.0000.000
147B328LEU00.0350.01464.941-0.002-0.0020.0000.0000.0000.000
148B329GLU-1-0.901-0.93268.421-4.280-4.2800.0000.0000.0000.000
149B330THR0-0.049-0.04763.5900.0040.0040.0000.0000.0000.000
150B331VAL0-0.029-0.01765.274-0.008-0.0080.0000.0000.0000.000
151B332SER0-0.017-0.03067.4740.0450.0450.0000.0000.0000.000
152B333GLU-1-0.883-0.92668.924-4.490-4.4900.0000.0000.0000.000
153B334LYS10.7690.87766.0934.6214.6210.0000.0000.0000.000
154B335GLY0-0.0200.01569.459-0.004-0.0040.0000.0000.0000.000
155B336SER0-0.049-0.03567.6010.0000.0000.0000.0000.0000.000
156B337LEU0-0.034-0.01162.260-0.030-0.0300.0000.0000.0000.000
157B338THR00.037-0.00759.072-0.041-0.0410.0000.0000.0000.000
158B339SER00.009-0.02956.250-0.003-0.0030.0000.0000.0000.000
159B340GLU-1-0.891-0.94552.348-5.901-5.9010.0000.0000.0000.000
160B341GLU-1-0.809-0.86256.413-5.041-5.0410.0000.0000.0000.000
161B342PHE00.0170.01158.5920.0260.0260.0000.0000.0000.000
162B343ALA00.013-0.00254.3200.0060.0060.0000.0000.0000.000
163B344LYS10.8750.93054.9885.5415.5410.0000.0000.0000.000
164B345LEU0-0.022-0.00657.3410.0130.0130.0000.0000.0000.000
165B346VAL0-0.0090.00158.8450.0450.0450.0000.0000.0000.000
166B347GLY0-0.0330.00655.854-0.009-0.0090.0000.0000.0000.000
167B348MET0-0.050-0.01953.554-0.025-0.0250.0000.0000.0000.000
168B349SER0-0.008-0.01949.2640.0280.0280.0000.0000.0000.000
169B350VAL00.0520.00750.8840.0650.0650.0000.0000.0000.000
170B351LEU0-0.032-0.00547.0370.0740.0740.0000.0000.0000.000
171B352LEU00.0510.00850.4300.0680.0680.0000.0000.0000.000
172B353ALA0-0.0010.01453.4500.1100.1100.0000.0000.0000.000
173B354LYS10.9090.95152.7855.8345.8340.0000.0000.0000.000
174B355GLU-1-0.838-0.90353.094-5.639-5.6390.0000.0000.0000.000
175B356ARG10.8800.93756.1965.2915.2910.0000.0000.0000.000
176B357LEU00.0110.01059.0410.0920.0920.0000.0000.0000.000
177B358LEU00.0350.01356.4610.0610.0610.0000.0000.0000.000
178B359LEU0-0.048-0.01659.9080.0590.0590.0000.0000.0000.000
179B360ALA00.0410.00261.5760.0820.0820.0000.0000.0000.000
180B361GLU-1-0.806-0.86362.694-4.850-4.8500.0000.0000.0000.000
181B362LYS10.8120.89359.1025.2255.2250.0000.0000.0000.000
182B363MET0-0.092-0.03364.6910.0240.0240.0000.0000.0000.000
183B364GLY00.0150.01667.3260.0710.0710.0000.0000.0000.000
184B365HIS00.0240.01268.1400.0760.0760.0000.0000.0000.000
185B366LEU0-0.032-0.01164.5260.0320.0320.0000.0000.0000.000
186B367CYS0-0.031-0.00568.0430.0220.0220.0000.0000.0000.000
187B368ARG10.7290.81760.1734.9954.9950.0000.0000.0000.000
188B369ASP-1-0.843-0.91665.511-4.583-4.5830.0000.0000.0000.000
189B370ASP-1-0.837-0.90861.029-5.162-5.1620.0000.0000.0000.000
190B371SER0-0.0050.00863.2210.0420.0420.0000.0000.0000.000
191B372VAL0-0.016-0.03061.586-0.083-0.0830.0000.0000.0000.000
192B373GLU-1-0.883-0.91861.102-4.835-4.8350.0000.0000.0000.000
193B374GLY0-0.029-0.00959.561-0.076-0.0760.0000.0000.0000.000
194B375LEU0-0.048-0.01758.4780.0700.0700.0000.0000.0000.000
195B376ARG10.8070.89360.9994.8094.8090.0000.0000.0000.000
196B377PHE0-0.035-0.02959.9360.0080.0080.0000.0000.0000.000
197B378TYR00.003-0.02165.3520.0310.0310.0000.0000.0000.000
198B379PRO00.0590.02269.009-0.026-0.0260.0000.0000.0000.000
199B380ASN0-0.016-0.02071.0270.0500.0500.0000.0000.0000.000
200B381LEU00.001-0.01772.5530.0550.0550.0000.0000.0000.000
201B382PHE0-0.009-0.00172.4130.0660.0660.0000.0000.0000.000
202B383MET0-0.072-0.01974.0420.0430.0430.0000.0000.0000.000
203B384THR0-0.044-0.03077.0630.0110.0110.0000.0000.0000.000
204B385GLN0-0.0140.01179.3990.0290.0290.0000.0000.0000.000