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: ZV92N

Calculation Name: 3RV1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RV1

Chain ID: A

ChEMBL ID:

UniProt ID: A7TR32

Base Structure: X-ray

Registration Date: 2023-09-23

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2341248.499021
FMO2-HF: Nuclear repulsion 2253464.314402
FMO2-HF: Total energy -87784.184619
FMO2-MP2: Total energy -88041.461782


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:15:SER)


Summations of interaction energy for fragment #1(A:15:SER)
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.
-14.124-8.9631.666-2.408-4.420.012
Interaction energy analysis for fragmet #1(A:15:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.013
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].
3A17GLU-1-0.852-0.9063.001-0.7861.4620.080-0.948-1.3800.004
4A18LEU00.0580.0172.566-4.638-2.8211.542-1.027-2.3330.006
5A19LYS10.9440.9743.293-8.272-7.1760.044-0.433-0.7070.002
6A20VAL00.0220.0245.957-0.381-0.3810.0000.0000.0000.000
7A21ARG10.7980.8887.247-1.221-1.2210.0000.0000.0000.000
8A22GLU-1-0.833-0.9128.3490.6860.6860.0000.0000.0000.000
9A23PHE0-0.0070.0079.827-0.166-0.1660.0000.0000.0000.000
10A24TYR0-0.005-0.03711.755-0.117-0.1170.0000.0000.0000.000
11A25ARG10.8520.93111.789-0.749-0.7490.0000.0000.0000.000
12A26LEU0-0.016-0.00414.190-0.077-0.0770.0000.0000.0000.000
13A27HIS00.001-0.00615.748-0.042-0.0420.0000.0000.0000.000
14A28ASN00.0100.00117.770-0.037-0.0370.0000.0000.0000.000
15A29ALA00.0130.01518.927-0.038-0.0380.0000.0000.0000.000
16A30CYS0-0.034-0.01419.168-0.032-0.0320.0000.0000.0000.000
17A31VAL00.0000.00021.855-0.028-0.0280.0000.0000.0000.000
18A32LYS10.9950.99723.226-0.253-0.2530.0000.0000.0000.000
19A33LEU0-0.0280.00324.463-0.019-0.0190.0000.0000.0000.000
20A34LYS10.8840.93326.031-0.213-0.2130.0000.0000.0000.000
21A35GLU-1-0.942-0.96827.9530.1510.1510.0000.0000.0000.000
22A36SER0-0.021-0.02228.756-0.014-0.0140.0000.0000.0000.000
23A37ILE00.009-0.00230.362-0.012-0.0120.0000.0000.0000.000
24A38LYS10.9030.95832.143-0.132-0.1320.0000.0000.0000.000
25A39LEU00.0010.00633.368-0.010-0.0100.0000.0000.0000.000
26A40ILE0-0.043-0.02633.036-0.008-0.0080.0000.0000.0000.000
27A41TYR0-0.040-0.03833.983-0.004-0.0040.0000.0000.0000.000
28A42GLU-1-0.877-0.94037.9770.1030.1030.0000.0000.0000.000
29A43ASN00.0090.01839.902-0.009-0.0090.0000.0000.0000.000
30A44PRO00.0410.00341.559-0.002-0.0020.0000.0000.0000.000
31A45LEU0-0.047-0.01643.760-0.003-0.0030.0000.0000.0000.000
32A46VAL0-0.078-0.04140.635-0.002-0.0020.0000.0000.0000.000
33A47THR0-0.0120.00443.010-0.001-0.0010.0000.0000.0000.000
34A48ASP-1-0.875-0.94245.2200.0740.0740.0000.0000.0000.000
35A49GLN0-0.069-0.04247.317-0.001-0.0010.0000.0000.0000.000
36A50ASN00.0270.02249.212-0.002-0.0020.0000.0000.0000.000
37A51VAL00.0200.00149.054-0.003-0.0030.0000.0000.0000.000
38A52LEU0-0.042-0.01748.261-0.002-0.0020.0000.0000.0000.000
39A53ASN0-0.072-0.03551.963-0.002-0.0020.0000.0000.0000.000
40A54LEU00.0440.02547.743-0.001-0.0010.0000.0000.0000.000
41A55GLY0-0.039-0.02951.9080.0010.0010.0000.0000.0000.000
42A56THR0-0.031-0.01754.093-0.002-0.0020.0000.0000.0000.000
43A57ALA0-0.0110.00056.275-0.002-0.0020.0000.0000.0000.000
44A58GLU-1-0.973-0.97057.1700.0420.0420.0000.0000.0000.000
45A59ASN0-0.016-0.01055.185-0.002-0.0020.0000.0000.0000.000
46A60THR00.023-0.01655.5190.0020.0020.0000.0000.0000.000
47A61ILE00.0380.01950.9000.0020.0020.0000.0000.0000.000
48A62ASP-1-0.776-0.86550.8500.0590.0590.0000.0000.0000.000
49A63TYR00.0010.00150.8750.0030.0030.0000.0000.0000.000
50A64THR0-0.050-0.03648.0690.0020.0020.0000.0000.0000.000
51A65ILE00.003-0.00645.7550.0030.0030.0000.0000.0000.000
52A66LEU0-0.001-0.01846.0160.0040.0040.0000.0000.0000.000
53A67ASN0-0.054-0.00746.8070.0020.0020.0000.0000.0000.000
54A68THR0-0.027-0.01242.6860.0020.0020.0000.0000.0000.000
55A69PRO00.028-0.00839.2450.0020.0020.0000.0000.0000.000
56A70THR00.0170.01338.3560.0040.0040.0000.0000.0000.000
57A71LEU00.0490.04639.4710.0040.0040.0000.0000.0000.000
58A72ASN00.0000.00641.4320.0000.0000.0000.0000.0000.000
59A73VAL0-0.024-0.01134.8470.0020.0020.0000.0000.0000.000
60A74ALA00.0260.00737.4080.0040.0040.0000.0000.0000.000
61A75LYS10.9790.98338.432-0.078-0.0780.0000.0000.0000.000
62A76THR0-0.029-0.00436.974-0.002-0.0020.0000.0000.0000.000
63A77LEU0-0.054-0.02632.8250.0030.0030.0000.0000.0000.000
64A78LEU0-0.0150.00036.4220.0040.0040.0000.0000.0000.000
65A79GLY00.0030.00739.050-0.001-0.0010.0000.0000.0000.000
66A80ASN0-0.023-0.02134.196-0.007-0.0070.0000.0000.0000.000
67A81ARG10.8540.91335.996-0.110-0.1100.0000.0000.0000.000
68A82TYR0-0.041-0.01836.7570.0020.0020.0000.0000.0000.000
69A83SER0-0.071-0.01135.2570.0020.0020.0000.0000.0000.000
70A84LEU0-0.003-0.01428.6220.0070.0070.0000.0000.0000.000
71A85ASP-1-0.726-0.83133.3310.1320.1320.0000.0000.0000.000
72A86LEU00.016-0.00728.4660.0080.0080.0000.0000.0000.000
73A87ILE0-0.016-0.00729.6670.0110.0110.0000.0000.0000.000
74A88ASP-1-0.876-0.94031.2360.1360.1360.0000.0000.0000.000
75A89LEU0-0.052-0.01925.8890.0060.0060.0000.0000.0000.000
76A90PHE0-0.023-0.02423.6900.0130.0130.0000.0000.0000.000
77A91GLN00.0180.01027.3480.0090.0090.0000.0000.0000.000
78A92SER0-0.088-0.03828.9650.0010.0010.0000.0000.0000.000
79A93HIS0-0.064-0.03624.2530.0030.0030.0000.0000.0000.000
80A94ASP-1-0.957-0.97425.1110.1920.1920.0000.0000.0000.000
81A95PHE0-0.042-0.00820.8740.0120.0120.0000.0000.0000.000
82A96LYS10.9340.95923.614-0.213-0.2130.0000.0000.0000.000
83A97ASP-1-0.800-0.89923.0710.2310.2310.0000.0000.0000.000
84A98SER0-0.047-0.03222.7370.0160.0160.0000.0000.0000.000
85A99ASN0-0.051-0.01621.777-0.009-0.0090.0000.0000.0000.000
86A100THR0-0.001-0.00417.0530.0290.0290.0000.0000.0000.000
87A101ASP-1-0.861-0.93516.9480.3080.3080.0000.0000.0000.000
88A102VAL0-0.049-0.02511.8040.0080.0080.0000.0000.0000.000
89A103ASP-1-0.758-0.85614.0230.3490.3490.0000.0000.0000.000
90A104MET0-0.054-0.02113.792-0.045-0.0450.0000.0000.0000.000
91A105PHE0-0.078-0.0448.536-0.024-0.0240.0000.0000.0000.000
92A106ILE0-0.068-0.02012.115-0.012-0.0120.0000.0000.0000.000
93A107LYS10.9380.96514.042-0.125-0.1250.0000.0000.0000.000
94A108TYR0-0.0020.00816.162-0.028-0.0280.0000.0000.0000.000
95A109PRO00.0350.02216.2700.0390.0390.0000.0000.0000.000
96A110VAL00.0800.05511.802-0.027-0.0270.0000.0000.0000.000
97A111VAL00.0050.02113.854-0.024-0.0240.0000.0000.0000.000
98A112TYR0-0.060-0.05612.0580.1020.1020.0000.0000.0000.000
99A113ASP-1-0.844-0.93310.9610.4750.4750.0000.0000.0000.000
100A114GLU-1-0.927-0.9737.0530.3160.3160.0000.0000.0000.000
101A115ASN0-0.017-0.01310.744-0.166-0.1660.0000.0000.0000.000
102A116LEU0-0.0080.00213.348-0.060-0.0600.0000.0000.0000.000
103A117GLU-1-0.782-0.89412.2230.2860.2860.0000.0000.0000.000
104A118ASN0-0.016-0.02411.264-0.047-0.0470.0000.0000.0000.000
105A119LEU0-0.0200.00615.131-0.031-0.0310.0000.0000.0000.000
106A120ALA00.0290.00918.027-0.016-0.0160.0000.0000.0000.000
107A121PHE0-0.052-0.03816.103-0.012-0.0120.0000.0000.0000.000
108A122MET0-0.045-0.00519.270-0.027-0.0270.0000.0000.0000.000
109A123HIS00.0380.00121.7410.0180.0180.0000.0000.0000.000
110A124LYS10.9821.00825.354-0.011-0.0110.0000.0000.0000.000
111A125SER0-0.035-0.01628.479-0.003-0.0030.0000.0000.0000.000
112A140GLN0-0.002-0.00224.861-0.013-0.0130.0000.0000.0000.000
113A141LEU0-0.036-0.02120.3700.0090.0090.0000.0000.0000.000
114A142SER0-0.006-0.01223.838-0.006-0.0060.0000.0000.0000.000
115A143ASN00.0050.01022.4810.0050.0050.0000.0000.0000.000
116A144GLU-1-0.851-0.93923.9500.0260.0260.0000.0000.0000.000
117A145ARG10.9690.97325.772-0.056-0.0560.0000.0000.0000.000
118A146LEU0-0.0090.00620.3520.0050.0050.0000.0000.0000.000
119A147GLU-1-0.899-0.95024.8280.0440.0440.0000.0000.0000.000
120A148PHE0-0.019-0.00527.0000.0020.0020.0000.0000.0000.000
121A149LEU0-0.025-0.00824.8010.0020.0020.0000.0000.0000.000
122A150GLY00.034-0.01026.0910.0050.0050.0000.0000.0000.000
123A151ASP-1-0.943-0.95926.9020.0600.0600.0000.0000.0000.000
124A152SER0-0.029-0.01530.1810.0010.0010.0000.0000.0000.000
125A153TRP00.0200.00027.6470.0050.0050.0000.0000.0000.000
126A154LEU0-0.0020.01328.4450.0040.0040.0000.0000.0000.000
127A155GLY00.0100.00029.739-0.002-0.0020.0000.0000.0000.000
128A156ALA00.0190.01632.000-0.002-0.0020.0000.0000.0000.000
129A157LEU00.0380.00927.0280.0000.0000.0000.0000.0000.000
130A158VAL00.0050.00831.307-0.001-0.0010.0000.0000.0000.000
131A159SER0-0.047-0.04333.382-0.006-0.0060.0000.0000.0000.000
132A160TYR00.0420.02733.145-0.005-0.0050.0000.0000.0000.000
133A161ILE0-0.011-0.00930.486-0.001-0.0010.0000.0000.0000.000
134A162VAL0-0.046-0.03034.909-0.003-0.0030.0000.0000.0000.000
135A163TYR00.0190.00638.335-0.004-0.0040.0000.0000.0000.000
136A164THR0-0.048-0.02236.491-0.001-0.0010.0000.0000.0000.000
137A165ARG10.9190.97834.909-0.078-0.0780.0000.0000.0000.000
138A166PHE0-0.068-0.04139.366-0.003-0.0030.0000.0000.0000.000
139A167PRO00.0630.03042.465-0.002-0.0020.0000.0000.0000.000
140A168SER0-0.017-0.01044.600-0.001-0.0010.0000.0000.0000.000
141A169ALA0-0.051-0.00444.905-0.003-0.0030.0000.0000.0000.000
142A170ASN00.0230.01547.0250.0010.0010.0000.0000.0000.000
143A171GLU-1-0.830-0.94045.8490.0430.0430.0000.0000.0000.000
144A172GLY00.0690.04445.7440.0010.0010.0000.0000.0000.000
145A173MET0-0.051-0.03446.0000.0000.0000.0000.0000.0000.000
146A174LEU00.0010.00841.5810.0010.0010.0000.0000.0000.000
147A175SER0-0.006-0.01241.3490.0030.0030.0000.0000.0000.000
148A176GLN00.0050.01641.830-0.001-0.0010.0000.0000.0000.000
149A177MET0-0.019-0.00938.6690.0000.0000.0000.0000.0000.000
150A178LYS10.9560.99336.102-0.062-0.0620.0000.0000.0000.000
151A179GLU-1-0.896-0.94637.0180.0400.0400.0000.0000.0000.000
152A180SER0-0.116-0.06838.290-0.002-0.0020.0000.0000.0000.000
153A181ILE0-0.039-0.02232.8400.0000.0000.0000.0000.0000.000
154A182VAL00.009-0.00732.7670.0020.0020.0000.0000.0000.000
155A183ASN00.0580.06634.043-0.004-0.0040.0000.0000.0000.000
156A184ASN00.040-0.02633.1230.0040.0040.0000.0000.0000.000
157A185ASN0-0.057-0.02633.0220.0000.0000.0000.0000.0000.000
158A186ASN00.0340.02032.851-0.004-0.0040.0000.0000.0000.000
159A187LEU0-0.0010.00129.1480.0030.0030.0000.0000.0000.000
160A188PHE0-0.038-0.01328.5900.0000.0000.0000.0000.0000.000
161A189ASP-1-0.862-0.93428.9700.0240.0240.0000.0000.0000.000
162A190TRP0-0.042-0.02826.4340.0040.0040.0000.0000.0000.000
163A191SER00.0280.01624.4440.0010.0010.0000.0000.0000.000
164A192THR0-0.042-0.01524.153-0.008-0.0080.0000.0000.0000.000
165A193LYS10.9320.97324.810-0.060-0.0600.0000.0000.0000.000
166A194LEU0-0.039-0.02321.0950.0020.0020.0000.0000.0000.000
167A195ASN0-0.046-0.04020.170-0.008-0.0080.0000.0000.0000.000
168A196PHE00.0300.00919.332-0.014-0.0140.0000.0000.0000.000
169A197THR00.0100.01720.857-0.017-0.0170.0000.0000.0000.000
170A198LYS10.9330.94519.5290.0360.0360.0000.0000.0000.000
171A199ARG10.8430.92013.324-0.116-0.1160.0000.0000.0000.000
172A200LEU00.0030.00917.962-0.017-0.0170.0000.0000.0000.000
173A201GLN0-0.0300.01720.700-0.003-0.0030.0000.0000.0000.000
174A202GLY00.0360.00120.645-0.009-0.0090.0000.0000.0000.000
175A203ASN0-0.052-0.01322.0890.0020.0020.0000.0000.0000.000
176A204ILE00.0070.00824.8170.0050.0050.0000.0000.0000.000
177A205ALA00.0180.01827.2310.0060.0060.0000.0000.0000.000
178A217LYS10.9320.95931.803-0.026-0.0260.0000.0000.0000.000
179A218ARG10.9790.99026.3450.0330.0330.0000.0000.0000.000
180A219TYR0-0.054-0.05124.7520.0030.0030.0000.0000.0000.000
181A220ALA00.0210.01425.9470.0080.0080.0000.0000.0000.000
182A221ASP-1-0.772-0.88527.3340.0340.0340.0000.0000.0000.000
183A222CYS0-0.048-0.00922.2160.0050.0050.0000.0000.0000.000
184A223VAL0-0.039-0.01222.5500.0160.0160.0000.0000.0000.000
185A224GLN00.0010.00023.8530.0120.0120.0000.0000.0000.000
186A225ALA00.0270.01922.5870.0120.0120.0000.0000.0000.000
187A226TYR0-0.061-0.04915.7460.0180.0180.0000.0000.0000.000
188A227ILE00.001-0.00120.3860.0270.0270.0000.0000.0000.000
189A228GLY00.0650.03022.8120.0120.0120.0000.0000.0000.000
190A229ALA0-0.017-0.00817.8770.0080.0080.0000.0000.0000.000
191A230LEU0-0.062-0.03117.6340.0270.0270.0000.0000.0000.000
192A231VAL0-0.003-0.00619.8120.0170.0170.0000.0000.0000.000
193A232ILE0-0.039-0.01719.9410.0010.0010.0000.0000.0000.000
194A233ASP-1-0.803-0.90615.6290.4020.4020.0000.0000.0000.000
195A234ARG10.8000.89916.824-0.325-0.3250.0000.0000.0000.000
196A235PHE0-0.057-0.00221.318-0.010-0.0100.0000.0000.0000.000
197A236GLY00.0230.00024.1250.0090.0090.0000.0000.0000.000
198A237THR0-0.008-0.03225.706-0.007-0.0070.0000.0000.0000.000
199A238GLU-1-0.979-0.96728.4440.1520.1520.0000.0000.0000.000
200A239PHE00.0300.00829.924-0.009-0.0090.0000.0000.0000.000
201A240LEU0-0.036-0.00729.721-0.005-0.0050.0000.0000.0000.000
202A241ASP-1-0.822-0.91132.3630.0940.0940.0000.0000.0000.000
203A242ILE00.000-0.00935.629-0.007-0.0070.0000.0000.0000.000
204A243LYS10.8640.94130.455-0.109-0.1090.0000.0000.0000.000
205A244GLU-1-0.914-0.97033.6650.0970.0970.0000.0000.0000.000
206A245TRP00.0110.02436.267-0.006-0.0060.0000.0000.0000.000
207A246LEU0-0.022-0.02436.784-0.005-0.0050.0000.0000.0000.000
208A247GLU-1-0.908-0.95434.4590.0770.0770.0000.0000.0000.000
209A248GLU-1-0.919-0.95937.9900.0570.0570.0000.0000.0000.000
210A249LEU0-0.073-0.03641.024-0.005-0.0050.0000.0000.0000.000
211A250SER0-0.100-0.04739.558-0.005-0.0050.0000.0000.0000.000
212A251GLU-1-0.857-0.91839.4890.0510.0510.0000.0000.0000.000
213A252LYS10.9320.95141.861-0.041-0.0410.0000.0000.0000.000
214A253LYS10.8710.91542.121-0.039-0.0390.0000.0000.0000.000
215A254LEU00.0520.03436.790-0.003-0.0030.0000.0000.0000.000
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