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: 535JZ

Calculation Name: 3CUQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CUQ

Chain ID: A

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2399559.960989
FMO2-HF: Nuclear repulsion 2313383.360974
FMO2-HF: Total energy -86176.600015
FMO2-MP2: Total energy -86428.700292


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(A:34:ALA)


Summations of interaction energy for fragment #1(A:34:ALA)
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.
-1.1380.682.066-1.574-2.3090
Interaction energy analysis for fragmet #1(A:34:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.001
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].
3A36MET00.0250.0083.642-2.314-0.696-0.002-0.757-0.8580.001
4A37SER00.010-0.0012.047-0.195-0.2822.070-0.790-1.193-0.001
5A38LYS10.9871.0053.9641.1691.388-0.001-0.025-0.1930.000
6A39GLN00.012-0.0255.3430.2900.358-0.001-0.002-0.0650.000
7A40LEU00.0120.0256.8870.1730.1730.0000.0000.0000.000
8A41ASP-1-0.897-0.9657.094-0.716-0.7160.0000.0000.0000.000
9A42MET0-0.080-0.0259.4570.0780.0780.0000.0000.0000.000
10A43PHE00.0410.02211.5980.0630.0630.0000.0000.0000.000
11A44LYS10.9310.97911.3500.3830.3830.0000.0000.0000.000
12A45THR00.0650.02514.2160.0210.0210.0000.0000.0000.000
13A46ASN0-0.045-0.01915.7920.0220.0220.0000.0000.0000.000
14A47LEU00.0130.01117.5810.0240.0240.0000.0000.0000.000
15A48GLU-1-0.900-0.95616.826-0.203-0.2030.0000.0000.0000.000
16A49GLU-1-0.939-0.94720.490-0.134-0.1340.0000.0000.0000.000
17A50PHE0-0.018-0.00522.0980.0160.0160.0000.0000.0000.000
18A51ALA00.0190.00023.1440.0130.0130.0000.0000.0000.000
19A52SER0-0.100-0.06324.6470.0100.0100.0000.0000.0000.000
20A53LYS10.9340.96126.5860.0830.0830.0000.0000.0000.000
21A54HIS0-0.015-0.00227.1770.0100.0100.0000.0000.0000.000
22A55LYS10.9640.99928.7590.0670.0670.0000.0000.0000.000
23A56GLN0-0.044-0.04929.6550.0020.0020.0000.0000.0000.000
24A57GLU-1-0.865-0.92832.223-0.039-0.0390.0000.0000.0000.000
25A58ILE00.0260.01628.1400.0050.0050.0000.0000.0000.000
26A59ARG10.9150.95229.5950.0560.0560.0000.0000.0000.000
27A60LYS10.9300.98934.3530.0340.0340.0000.0000.0000.000
28A61ASN0-0.035-0.03435.8060.0040.0040.0000.0000.0000.000
29A62PRO00.0830.03136.484-0.001-0.0010.0000.0000.0000.000
30A63GLU-1-0.899-0.95636.587-0.010-0.0100.0000.0000.0000.000
31A64PHE0-0.027-0.00930.0770.0000.0000.0000.0000.0000.000
32A65ARG10.8950.95831.9050.0200.0200.0000.0000.0000.000
33A66VAL00.0440.03331.5110.0000.0000.0000.0000.0000.000
34A67GLN00.0160.02831.9610.0040.0040.0000.0000.0000.000
35A68PHE0-0.008-0.00523.8980.0010.0010.0000.0000.0000.000
36A69GLN0-0.023-0.02627.4020.0050.0050.0000.0000.0000.000
37A70ASP-1-0.856-0.94228.1120.0110.0110.0000.0000.0000.000
38A71MET0-0.074-0.03326.8020.0020.0020.0000.0000.0000.000
39A72CYS0-0.060-0.02224.0620.0020.0020.0000.0000.0000.000
40A73ALA00.0320.00423.8820.0080.0080.0000.0000.0000.000
41A74THR0-0.046-0.00725.9920.0090.0090.0000.0000.0000.000
42A75ILE0-0.078-0.03619.9720.0070.0070.0000.0000.0000.000
43A76GLY00.0040.01721.1660.0140.0140.0000.0000.0000.000
44A77VAL0-0.091-0.04118.2990.0100.0100.0000.0000.0000.000
45A78ASP-1-0.795-0.93020.9780.0210.0210.0000.0000.0000.000
46A79PRO0-0.064-0.02721.988-0.003-0.0030.0000.0000.0000.000
47A80LEU00.0330.00023.414-0.007-0.0070.0000.0000.0000.000
48A81ALA0-0.0250.02921.6530.0020.0020.0000.0000.0000.000
49A82SER0-0.016-0.01619.9880.0000.0000.0000.0000.0000.000
50A83GLY00.0970.05222.273-0.008-0.0080.0000.0000.0000.000
51A84LYS10.9270.96714.1010.0240.0240.0000.0000.0000.000
52A85GLY00.0040.00617.214-0.007-0.0070.0000.0000.0000.000
53A86PHE00.0370.00512.072-0.014-0.0140.0000.0000.0000.000
54A87TRP00.0460.01217.968-0.009-0.0090.0000.0000.0000.000
55A88SER00.0440.01821.1890.0010.0010.0000.0000.0000.000
56A89GLU-1-0.960-0.96517.593-0.119-0.1190.0000.0000.0000.000
57A90MET0-0.019-0.01817.134-0.001-0.0010.0000.0000.0000.000
58A91LEU0-0.064-0.02922.3060.0030.0030.0000.0000.0000.000
59A92GLY0-0.040-0.00924.9780.0050.0050.0000.0000.0000.000
60A93VAL0-0.049-0.03325.5090.0050.0050.0000.0000.0000.000
61A94GLY00.0590.02126.3640.0060.0060.0000.0000.0000.000
62A95ASP-1-0.896-0.95527.228-0.033-0.0330.0000.0000.0000.000
63A96PHE0-0.092-0.01929.6520.0010.0010.0000.0000.0000.000
64A97TYR0-0.010-0.01330.0550.0030.0030.0000.0000.0000.000
65A98TYR0-0.080-0.07225.2410.0010.0010.0000.0000.0000.000
66A99GLU-1-0.893-0.93931.551-0.013-0.0130.0000.0000.0000.000
67A100LEU00.0020.01034.5040.0020.0020.0000.0000.0000.000
68A101GLY0-0.014-0.01834.9630.0020.0020.0000.0000.0000.000
69A102VAL00.0290.02535.3230.0020.0020.0000.0000.0000.000
70A103GLN00.1100.05937.8030.0000.0000.0000.0000.0000.000
71A104ILE0-0.061-0.02837.8300.0010.0010.0000.0000.0000.000
72A105ILE0-0.054-0.03037.0320.0020.0020.0000.0000.0000.000
73A106GLU-1-0.857-0.94441.274-0.005-0.0050.0000.0000.0000.000
74A107VAL0-0.023-0.00543.8820.0000.0000.0000.0000.0000.000
75A108CYS0-0.046-0.02543.9330.0010.0010.0000.0000.0000.000
76A109LEU0-0.018-0.00644.1140.0010.0010.0000.0000.0000.000
77A110ALA00.0220.02447.3740.0000.0000.0000.0000.0000.000
78A111LEU0-0.014-0.02649.4150.0000.0000.0000.0000.0000.000
79A112LYS10.9690.98947.825-0.009-0.0090.0000.0000.0000.000
80A113HIS0-0.0320.00150.9260.0000.0000.0000.0000.0000.000
81A114ARG10.8890.94554.527-0.001-0.0010.0000.0000.0000.000
82A115ASN00.047-0.00250.6830.0010.0010.0000.0000.0000.000
83A116GLY00.0570.04552.9790.0010.0010.0000.0000.0000.000
84A117GLY0-0.013-0.00848.7640.0010.0010.0000.0000.0000.000
85A118LEU0-0.016-0.01447.7740.0010.0010.0000.0000.0000.000
86A119ILE0-0.0130.00646.687-0.001-0.0010.0000.0000.0000.000
87A120THR00.0840.04648.0400.0010.0010.0000.0000.0000.000
88A121LEU0-0.017-0.02442.613-0.001-0.0010.0000.0000.0000.000
89A122GLU-1-0.956-0.98246.440-0.001-0.0010.0000.0000.0000.000
90A123GLU-1-0.878-0.94348.9760.0010.0010.0000.0000.0000.000
91A124LEU00.0400.01342.398-0.001-0.0010.0000.0000.0000.000
92A125HIS0-0.053-0.04343.6120.0000.0000.0000.0000.0000.000
93A126GLN0-0.003-0.00645.959-0.002-0.0020.0000.0000.0000.000
94A127GLN0-0.047-0.04547.847-0.001-0.0010.0000.0000.0000.000
95A128VAL00.0140.00641.627-0.001-0.0010.0000.0000.0000.000
96A129LEU0-0.034-0.01443.522-0.002-0.0020.0000.0000.0000.000
97A130LYS10.8940.96045.8660.0050.0050.0000.0000.0000.000
98A131GLY00.0170.01046.4230.0000.0000.0000.0000.0000.000
99A132ARG10.8240.92536.4580.0170.0170.0000.0000.0000.000
100A133GLY00.0000.01643.645-0.002-0.0020.0000.0000.0000.000
101A134LYS10.8970.91845.3140.0250.0250.0000.0000.0000.000
102A135PHE0-0.093-0.03539.702-0.002-0.0020.0000.0000.0000.000
103A136ALA00.0750.05242.9550.0010.0010.0000.0000.0000.000
104A137GLN0-0.028-0.04543.5980.0000.0000.0000.0000.0000.000
105A138ASP-1-0.840-0.92638.734-0.020-0.0200.0000.0000.0000.000
106A139VAL0-0.0230.00638.338-0.001-0.0010.0000.0000.0000.000
107A140SER0-0.013-0.01738.6590.0020.0020.0000.0000.0000.000
108A141GLN00.1030.01740.4330.0000.0000.0000.0000.0000.000
109A142ASP-1-0.833-0.91336.3980.0020.0020.0000.0000.0000.000
110A143ASP-1-0.790-0.88635.738-0.011-0.0110.0000.0000.0000.000
111A144LEU00.0320.02136.4130.0010.0010.0000.0000.0000.000
112A145ILE00.0290.01536.8780.0020.0020.0000.0000.0000.000
113A146ARG10.8200.90931.0160.0010.0010.0000.0000.0000.000
114A147ALA00.0290.01333.3840.0030.0030.0000.0000.0000.000
115A148ILE00.0100.01434.3460.0030.0030.0000.0000.0000.000
116A149LYS10.9230.95032.853-0.020-0.0200.0000.0000.0000.000
117A150LYS10.9140.95726.962-0.026-0.0260.0000.0000.0000.000
118A151LEU00.0440.04131.5720.0030.0030.0000.0000.0000.000
119A152LYS10.8920.95833.732-0.028-0.0280.0000.0000.0000.000
120A153ALA0-0.029-0.00629.6010.0040.0040.0000.0000.0000.000
121A154LEU0-0.070-0.02931.5550.0030.0030.0000.0000.0000.000
122A155GLY00.0000.00833.6970.0000.0000.0000.0000.0000.000
123A156THR0-0.049-0.04135.646-0.002-0.0020.0000.0000.0000.000
124A157GLY00.0680.02839.095-0.001-0.0010.0000.0000.0000.000
125A158PHE00.0320.02138.440-0.001-0.0010.0000.0000.0000.000
126A159GLY0-0.093-0.04839.6180.0040.0040.0000.0000.0000.000
127A160ILE0-0.0160.01038.205-0.002-0.0020.0000.0000.0000.000
128A161ILE0-0.004-0.00442.1290.0020.0020.0000.0000.0000.000
129A162PRO0-0.0010.01343.937-0.002-0.0020.0000.0000.0000.000
130A163VAL00.0420.01146.2890.0010.0010.0000.0000.0000.000
131A164GLY00.0580.01449.4260.0000.0000.0000.0000.0000.000
132A165GLY0-0.0310.00349.5930.0010.0010.0000.0000.0000.000
133A166THR0-0.019-0.01247.360-0.001-0.0010.0000.0000.0000.000
134A167TYR0-0.019-0.00942.4710.0010.0010.0000.0000.0000.000
135A168LEU00.0140.00446.162-0.002-0.0020.0000.0000.0000.000
136A169ILE0-0.050-0.03442.3370.0020.0020.0000.0000.0000.000
137A170GLN00.0120.01244.148-0.002-0.0020.0000.0000.0000.000
138A171SER0-0.018-0.01743.0680.0010.0010.0000.0000.0000.000
139A172VAL00.0160.01343.9790.0000.0000.0000.0000.0000.000
140A173PRO0-0.048-0.03243.1350.0010.0010.0000.0000.0000.000
141A174ALA00.0740.04545.128-0.001-0.0010.0000.0000.0000.000
142A175GLU-1-0.956-0.97945.6800.0280.0280.0000.0000.0000.000
143A176LEU0-0.015-0.02442.978-0.001-0.0010.0000.0000.0000.000
144A177ASN00.0250.03146.6770.0010.0010.0000.0000.0000.000
145A178MET00.0760.03548.796-0.001-0.0010.0000.0000.0000.000
146A179ASP-1-0.816-0.89549.7650.0210.0210.0000.0000.0000.000
147A180HIS0-0.016-0.01650.745-0.001-0.0010.0000.0000.0000.000
148A181THR00.0040.00547.741-0.001-0.0010.0000.0000.0000.000
149A182VAL00.017-0.00450.364-0.001-0.0010.0000.0000.0000.000
150A183VAL00.0120.01553.080-0.001-0.0010.0000.0000.0000.000
151A184LEU00.0160.02250.169-0.001-0.0010.0000.0000.0000.000
152A185GLN0-0.072-0.04948.810-0.001-0.0010.0000.0000.0000.000
153A186LEU0-0.046-0.01653.390-0.001-0.0010.0000.0000.0000.000
154A187ALA0-0.006-0.00756.042-0.001-0.0010.0000.0000.0000.000
155A188GLU-1-0.947-0.98252.7200.0070.0070.0000.0000.0000.000
156A189LYS10.9060.96855.946-0.008-0.0080.0000.0000.0000.000
157A190ASN0-0.046-0.02958.715-0.001-0.0010.0000.0000.0000.000
158A191GLY00.0150.01258.629-0.001-0.0010.0000.0000.0000.000
159A192TYR0-0.026-0.01859.6820.0000.0000.0000.0000.0000.000
160A193VAL00.0220.02259.4860.0000.0000.0000.0000.0000.000
161A194THR00.0290.01362.214-0.001-0.0010.0000.0000.0000.000
162A195VAL00.0450.02064.8210.0000.0000.0000.0000.0000.000
163A196SER0-0.016-0.04265.8670.0010.0010.0000.0000.0000.000
164A197GLU-1-0.905-0.96062.3880.0110.0110.0000.0000.0000.000
165A198ILE00.0030.01260.2530.0000.0000.0000.0000.0000.000
166A199LYN0-0.006-0.00262.4290.0010.0010.0000.0000.0000.000
167A200ALA0-0.0140.00464.6340.0000.0000.0000.0000.0000.000
168A201SER0-0.007-0.02061.2250.0000.0000.0000.0000.0000.000
169A202LEU0-0.016-0.01256.6530.0000.0000.0000.0000.0000.000
170A203LYS10.7910.90060.272-0.013-0.0130.0000.0000.0000.000
171A204TRP0-0.030-0.00355.8880.0010.0010.0000.0000.0000.000
172A205GLU-1-0.900-0.95862.5360.0160.0160.0000.0000.0000.000
173A206THR0-0.002-0.01163.9160.0000.0000.0000.0000.0000.000
174A207GLU-1-0.842-0.92763.6020.0160.0160.0000.0000.0000.000
175A208ARG10.8510.90455.862-0.021-0.0210.0000.0000.0000.000
176A209ALA00.0100.00760.2130.0000.0000.0000.0000.0000.000
177A210ARG10.9250.95961.441-0.015-0.0150.0000.0000.0000.000
178A211GLN00.0120.00958.7410.0000.0000.0000.0000.0000.000
179A212VAL0-0.0180.00055.6850.0000.0000.0000.0000.0000.000
180A213LEU0-0.032-0.01557.9460.0000.0000.0000.0000.0000.000
181A214GLU-1-0.955-0.98460.0200.0150.0150.0000.0000.0000.000
182A215HIS0-0.099-0.05952.4530.0000.0000.0000.0000.0000.000
183A216LEU00.0290.01854.7170.0000.0000.0000.0000.0000.000
184A217LEU0-0.048-0.02657.051-0.001-0.0010.0000.0000.0000.000
185A218LYS10.8980.94356.701-0.018-0.0180.0000.0000.0000.000
186A219GLU-1-0.862-0.91952.6080.0180.0180.0000.0000.0000.000
187A220GLY0-0.0280.00954.3100.0000.0000.0000.0000.0000.000
188A221LEU0-0.036-0.01251.454-0.001-0.0010.0000.0000.0000.000
189A222ALA0-0.027-0.02155.6260.0000.0000.0000.0000.0000.000
190A223TRP00.0060.00959.1250.0000.0000.0000.0000.0000.000
191A224LEU0-0.030-0.01662.5800.0000.0000.0000.0000.0000.000
192A225ASP-1-0.778-0.88965.8070.0060.0060.0000.0000.0000.000
193A226LEU0-0.046-0.04568.5980.0000.0000.0000.0000.0000.000
194A227GLN0-0.059-0.02971.8670.0000.0000.0000.0000.0000.000
195A228ALA00.0230.04070.2130.0000.0000.0000.0000.0000.000
196A229PRO00.001-0.01771.6020.0000.0000.0000.0000.0000.000
197A230GLY0-0.027-0.01372.4970.0000.0000.0000.0000.0000.000
198A231GLU-1-0.812-0.90069.6020.0100.0100.0000.0000.0000.000
199A232ALA00.0040.01868.9360.0000.0000.0000.0000.0000.000
200A233HIS10.8380.93666.003-0.007-0.0070.0000.0000.0000.000
201A234TYR0-0.007-0.01161.8270.0000.0000.0000.0000.0000.000
202A235TRP00.011-0.02061.6330.0000.0000.0000.0000.0000.000
203A236LEU0-0.004-0.00755.0050.0000.0000.0000.0000.0000.000
204A237PRO00.0070.00556.7630.0000.0000.0000.0000.0000.000
205A238ALA0-0.0120.01852.268-0.001-0.0010.0000.0000.0000.000
206A239LEU0-0.061-0.01253.8190.0000.0000.0000.0000.0000.000
207A240PHE0-0.026-0.01855.9600.0000.0000.0000.0000.0000.000
208A241THR0-0.005-0.00157.1130.0000.0000.0000.0000.0000.000
209A242ASP-1-0.905-0.94857.9630.0010.0010.0000.0000.0000.000
210A243LEU0-0.0010.00955.6500.0000.0000.0000.0000.0000.000
211A244TYR0-0.044-0.05057.651-0.001-0.0010.0000.0000.0000.000
212A245SER0-0.053-0.03657.3030.0000.0000.0000.0000.0000.000
213A246GLN00.0530.05351.184-0.001-0.0010.0000.0000.0000.000
214A247GLU-1-0.925-0.94753.167-0.007-0.0070.0000.0000.0000.000
215A248ILE0-0.076-0.04655.2450.0010.0010.0000.0000.0000.000
216A249THR00.0140.00552.0330.0000.0000.0000.0000.0000.000
217A250ALA0-0.018-0.01150.0490.0000.0000.0000.0000.0000.000
218A251GLU-1-0.996-0.98548.9330.0000.0000.0000.0000.0000.000
219A252GLU-1-0.965-0.97444.5640.0000.0000.0000.0000.0000.000