Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 3JRLL

Calculation Name: 3VOR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VOR

Chain ID: A

ChEMBL ID:

UniProt ID: Q59393

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1766469.107654
FMO2-HF: Nuclear repulsion 1699682.611051
FMO2-HF: Total energy -66786.496603
FMO2-MP2: Total energy -66980.299962


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:1:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-2.63-0.7934.382-3.591-2.63-0.011
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.010
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].
3A3ASP-1-0.860-0.9183.809-5.147-3.568-0.002-1.015-0.5630.005
4A4SER0-0.080-0.0455.4361.2201.2200.0000.0000.0000.000
5A5ARG10.9520.9567.0730.6030.6030.0000.0000.0000.000
6A6THR00.0470.0239.1130.0560.0560.0000.0000.0000.000
7A7VAL00.0070.0154.3350.0710.151-0.001-0.018-0.0610.000
8A8SER00.0170.0106.5400.4480.4480.0000.0000.0000.000
9A9GLU-1-0.894-0.9467.572-0.062-0.0620.0000.0000.0000.000
10A10LEU00.0040.0109.8720.0910.0910.0000.0000.0000.000
11A11VAL0-0.005-0.0046.4690.0930.0930.0000.0000.0000.000
12A12THR00.0030.0109.7970.0180.0180.0000.0000.0000.000
13A13ASN00.0460.02511.920-0.014-0.0140.0000.0000.0000.000
14A14THR0-0.080-0.04812.3380.0370.0370.0000.0000.0000.000
15A15ASN0-0.025-0.02211.3490.0360.0360.0000.0000.0000.000
16A16THR00.0380.01615.338-0.018-0.0180.0000.0000.0000.000
17A17ILE00.0320.01817.566-0.017-0.0170.0000.0000.0000.000
18A18ARG10.7980.90216.472-0.496-0.4960.0000.0000.0000.000
19A19VAL0-0.019-0.01319.237-0.017-0.0170.0000.0000.0000.000
20A20ALA00.0640.03421.595-0.016-0.0160.0000.0000.0000.000
21A21MET0-0.021-0.00122.874-0.020-0.0200.0000.0000.0000.000
22A22LYS10.8290.91222.923-0.254-0.2540.0000.0000.0000.000
23A23ASP-1-0.868-0.93325.7770.0790.0790.0000.0000.0000.000
24A24ALA0-0.061-0.02527.588-0.011-0.0110.0000.0000.0000.000
25A25TYR00.012-0.04027.514-0.004-0.0040.0000.0000.0000.000
26A26GLN00.0330.03227.5270.0150.0150.0000.0000.0000.000
27A27ARG10.9230.95129.983-0.090-0.0900.0000.0000.0000.000
28A28ASP-1-0.914-0.94833.2730.1020.1020.0000.0000.0000.000
29A29GLY0-0.084-0.03933.126-0.003-0.0030.0000.0000.0000.000
30A30LYS10.8930.93231.911-0.109-0.1090.0000.0000.0000.000
31A31TYR00.0050.00726.979-0.005-0.0050.0000.0000.0000.000
32A32PRO0-0.0030.00328.279-0.003-0.0030.0000.0000.0000.000
33A33ASP-1-0.865-0.91929.2150.1560.1560.0000.0000.0000.000
34A34TYR00.007-0.01524.9830.0020.0020.0000.0000.0000.000
35A35GLN0-0.0060.01128.452-0.011-0.0110.0000.0000.0000.000
36A36ALA00.002-0.00327.1890.0080.0080.0000.0000.0000.000
37A37PRO00.012-0.00223.460-0.014-0.0140.0000.0000.0000.000
38A38LEU0-0.014-0.00923.045-0.011-0.0110.0000.0000.0000.000
39A39SER0-0.0050.00526.054-0.007-0.0070.0000.0000.0000.000
40A40LEU0-0.065-0.01526.070-0.011-0.0110.0000.0000.0000.000
41A41THR00.0570.02626.877-0.002-0.0020.0000.0000.0000.000
42A42ALA00.013-0.00526.0690.0050.0050.0000.0000.0000.000
43A43ASP-1-0.926-0.96527.456-0.001-0.0010.0000.0000.0000.000
44A44SER00.0340.00730.8060.0030.0030.0000.0000.0000.000
45A45ILE0-0.0020.01924.8000.0060.0060.0000.0000.0000.000
46A46LYS10.9240.95728.8850.0010.0010.0000.0000.0000.000
47A47THR0-0.033-0.02231.398-0.001-0.0010.0000.0000.0000.000
48A48ASP-1-0.857-0.89931.7240.0770.0770.0000.0000.0000.000
49A49SER00.013-0.00133.2570.0040.0040.0000.0000.0000.000
50A50THR0-0.053-0.04733.3670.0040.0040.0000.0000.0000.000
51A51GLY0-0.0060.00032.7330.0040.0040.0000.0000.0000.000
52A52ILE0-0.0010.01926.8640.0120.0120.0000.0000.0000.000
53A53ALA00.0430.02025.350-0.007-0.0070.0000.0000.0000.000
54A54VAL00.0560.01521.807-0.008-0.0080.0000.0000.0000.000
55A55ALA00.0280.01525.057-0.014-0.0140.0000.0000.0000.000
56A56GLN00.0240.04628.376-0.004-0.0040.0000.0000.0000.000
57A57LEU0-0.007-0.01223.930-0.008-0.0080.0000.0000.0000.000
58A58VAL0-0.013-0.00725.492-0.011-0.0110.0000.0000.0000.000
59A59GLN0-0.106-0.05627.841-0.012-0.0120.0000.0000.0000.000
60A60LEU0-0.075-0.03229.992-0.006-0.0060.0000.0000.0000.000
61A61GLY0-0.037-0.01429.611-0.003-0.0030.0000.0000.0000.000
62A62LYS10.7830.88726.276-0.082-0.0820.0000.0000.0000.000
63A63LEU00.0140.02120.6190.0140.0140.0000.0000.0000.000
64A64THR00.0160.01023.099-0.004-0.0040.0000.0000.0000.000
65A65PRO00.011-0.02322.6720.0100.0100.0000.0000.0000.000
66A66ASP-1-0.902-0.95819.251-0.037-0.0370.0000.0000.0000.000
67A67GLU-1-0.829-0.91018.1140.0430.0430.0000.0000.0000.000
68A68ALA0-0.027-0.00918.4010.0460.0460.0000.0000.0000.000
69A69ARG10.9190.96618.4310.0120.0120.0000.0000.0000.000
70A70ASN00.0510.03714.239-0.011-0.0110.0000.0000.0000.000
71A71GLY0-0.019-0.02514.482-0.021-0.0210.0000.0000.0000.000
72A72ILE0-0.066-0.0329.204-0.046-0.0460.0000.0000.0000.000
73A73SER0-0.032-0.02413.697-0.029-0.0290.0000.0000.0000.000
74A74GLY0-0.044-0.01716.935-0.024-0.0240.0000.0000.0000.000
75A75ASP-1-0.751-0.84718.7870.1360.1360.0000.0000.0000.000
76A76TYR0-0.052-0.04319.2050.0040.0040.0000.0000.0000.000
77A77ILE0-0.0050.00315.9900.0180.0180.0000.0000.0000.000
78A78GLY00.0250.03319.725-0.025-0.0250.0000.0000.0000.000
79A79ILE00.006-0.02920.8010.0400.0400.0000.0000.0000.000
80A80GLY00.0420.01223.224-0.027-0.0270.0000.0000.0000.000
81A81GLY00.0220.02825.6690.0120.0120.0000.0000.0000.000
82A82ALA0-0.013-0.00525.1590.0160.0160.0000.0000.0000.000
83A83ILE0-0.0140.00127.278-0.016-0.0160.0000.0000.0000.000
84A84THR00.016-0.02328.2690.0150.0150.0000.0000.0000.000
85A85SER0-0.020-0.01530.544-0.002-0.0020.0000.0000.0000.000
86A86SER00.0070.00633.6570.0010.0010.0000.0000.0000.000
87A87GLY00.0480.02135.223-0.008-0.0080.0000.0000.0000.000
88A88SER0-0.040-0.00334.153-0.013-0.0130.0000.0000.0000.000
89A89THR00.0260.00935.5980.0040.0040.0000.0000.0000.000
90A90ILE0-0.026-0.01334.154-0.005-0.0050.0000.0000.0000.000
91A91ASN0-0.026-0.02129.8290.0170.0170.0000.0000.0000.000
92A92LYS10.9000.94031.027-0.150-0.1500.0000.0000.0000.000
93A93GLY00.0120.00526.6850.0050.0050.0000.0000.0000.000
94A94PHE0-0.010-0.00620.688-0.015-0.0150.0000.0000.0000.000
95A95ALA00.013-0.00821.5750.0340.0340.0000.0000.0000.000
96A96MET0-0.0070.01116.860-0.027-0.0270.0000.0000.0000.000
97A97GLU-1-0.830-0.92717.8540.4000.4000.0000.0000.0000.000
98A98LEU0-0.036-0.01811.899-0.038-0.0380.0000.0000.0000.000
99A99ASN00.003-0.02115.0870.0850.0850.0000.0000.0000.000
100A100GLY00.0230.01215.1260.0000.0000.0000.0000.0000.000
101A101LEU0-0.048-0.01010.6950.0000.0000.0000.0000.0000.000
102A102SER00.0640.02010.3490.0370.0370.0000.0000.0000.000
103A103GLN00.0480.01210.7280.1960.1960.0000.0000.0000.000
104A104GLU-1-0.937-0.9636.9410.2670.2670.0000.0000.0000.000
105A105GLN00.0370.0136.0850.7300.7300.0000.0000.0000.000
106A106CYS0-0.061-0.0116.8370.6280.6280.0000.0000.0000.000
107A107ARG10.9120.9476.555-0.717-0.7170.0000.0000.0000.000
108A108SER00.0090.0102.2672.8092.4104.360-2.354-1.607-0.016
109A109ILE00.0330.0153.9221.4151.512-0.0010.028-0.1250.000
110A110LEU0-0.013-0.0106.574-0.083-0.0830.0000.0000.0000.000
111A111GLY0-0.015-0.0095.428-0.622-0.6220.0000.0000.0000.000
112A112GLN0-0.039-0.0123.379-2.975-2.4950.026-0.232-0.2740.000
113A113VAL0-0.005-0.0086.395-0.930-0.9300.0000.0000.0000.000
114A114GLY00.0130.0169.783-0.375-0.3750.0000.0000.0000.000
115A115ASP-1-0.808-0.91811.8480.8090.8090.0000.0000.0000.000
116A116ASN0-0.030-0.00211.542-0.245-0.2450.0000.0000.0000.000
117A117TRP00.0120.01213.970-0.190-0.1900.0000.0000.0000.000
118A118GLU-1-0.764-0.87217.1790.3610.3610.0000.0000.0000.000
119A119TYR0-0.003-0.00619.741-0.017-0.0170.0000.0000.0000.000
120A120VAL00.003-0.00114.1070.0390.0390.0000.0000.0000.000
121A121ALA00.0020.00917.326-0.026-0.0260.0000.0000.0000.000
122A122VAL0-0.016-0.01214.0350.0670.0670.0000.0000.0000.000
123A123GLY00.001-0.00116.773-0.064-0.0640.0000.0000.0000.000
124A124THR0-0.010-0.01817.6580.0440.0440.0000.0000.0000.000
125A125SER00.0080.02519.203-0.045-0.0450.0000.0000.0000.000
126A126PRO00.0350.01218.5780.0360.0360.0000.0000.0000.000
127A127SER00.026-0.01518.0000.0180.0180.0000.0000.0000.000
128A128GLY0-0.0150.00119.985-0.015-0.0150.0000.0000.0000.000
129A129SER0-0.071-0.03622.186-0.014-0.0140.0000.0000.0000.000
130A130TYR0-0.036-0.03618.9220.0320.0320.0000.0000.0000.000
131A131ASP-1-0.833-0.93522.8540.2180.2180.0000.0000.0000.000
132A132ALA0-0.039-0.01622.107-0.012-0.0120.0000.0000.0000.000
133A133LEU0-0.058-0.02921.918-0.017-0.0170.0000.0000.0000.000
134A134SER0-0.037-0.01825.248-0.022-0.0220.0000.0000.0000.000
135A135ALA0-0.043-0.00327.414-0.016-0.0160.0000.0000.0000.000
136A136GLY0-0.013-0.00528.594-0.012-0.0120.0000.0000.0000.000
137A137ALA0-0.038-0.00527.9210.0160.0160.0000.0000.0000.000
138A138VAL00.0320.01322.9730.0020.0020.0000.0000.0000.000
139A139ASN00.0330.01126.302-0.005-0.0050.0000.0000.0000.000
140A140MET0-0.028-0.01023.2130.0120.0120.0000.0000.0000.000
141A141LEU00.004-0.00125.5470.0190.0190.0000.0000.0000.000
142A142ALA0-0.0200.01225.621-0.013-0.0130.0000.0000.0000.000
143A143ALA00.0100.00025.7460.0230.0230.0000.0000.0000.000
144A144THR0-0.018-0.00121.679-0.009-0.0090.0000.0000.0000.000
145A145ASP-1-0.799-0.89821.5770.3900.3900.0000.0000.0000.000
146A146ASN0-0.087-0.07019.0650.0690.0690.0000.0000.0000.000
147A147THR0-0.0160.00217.5950.0410.0410.0000.0000.0000.000
148A148THR00.0230.04317.6380.0520.0520.0000.0000.0000.000
149A149ILE0-0.0010.00619.0320.0470.0470.0000.0000.0000.000
150A150LEU00.0060.00714.223-0.002-0.0020.0000.0000.0000.000
151A151ARG10.8250.90815.708-0.724-0.7240.0000.0000.0000.000
152A152SER00.012-0.00919.427-0.015-0.0150.0000.0000.0000.000
153A153LEU0-0.047-0.02122.768-0.003-0.0030.0000.0000.0000.000
154A154ALA0-0.0260.00725.815-0.030-0.0300.0000.0000.0000.000
155A155ALA00.016-0.00326.8090.0110.0110.0000.0000.0000.000
156A156ASN0-0.056-0.03925.8500.0070.0070.0000.0000.0000.000
157A157GLY00.0760.05423.4250.0220.0220.0000.0000.0000.000
158A158GLN0-0.078-0.05120.4800.0620.0620.0000.0000.0000.000
159A159VAL00.0060.00317.383-0.006-0.0060.0000.0000.0000.000
160A160SER00.0040.00615.1830.0250.0250.0000.0000.0000.000
161A161LEU0-0.016-0.02712.212-0.063-0.0630.0000.0000.0000.000
162A162THR00.0310.01310.9710.2750.2750.0000.0000.0000.000
163A163ALA00.0690.0298.2970.1280.1280.0000.0000.0000.000
164A164GLU-1-0.892-0.9629.5100.6510.6510.0000.0000.0000.000
165A165LYS10.8280.92712.815-0.741-0.7410.0000.0000.0000.000
166A166ILE00.0160.0207.925-0.116-0.1160.0000.0000.0000.000
167A167LEU0-0.024-0.00810.004-0.045-0.0450.0000.0000.0000.000
168A168LYS10.8810.95012.239-0.612-0.6120.0000.0000.0000.000
169A169THR00.0350.00012.379-0.058-0.0580.0000.0000.0000.000
170A171THR0-0.007-0.01213.014-0.017-0.0170.0000.0000.0000.000
171A172ALA00.0320.03915.468-0.079-0.0790.0000.0000.0000.000
172A173THR0-0.021-0.02915.6330.0450.0450.0000.0000.0000.000
173A174VAL00.0020.01416.219-0.007-0.0070.0000.0000.0000.000
174A175ASN0-0.047-0.03413.4380.0190.0190.0000.0000.0000.000
175A176SER00.0200.02614.936-0.024-0.0240.0000.0000.0000.000
176A177ILE00.0190.01110.4110.0550.0550.0000.0000.0000.000
177A178THR0-0.0100.00214.862-0.090-0.0900.0000.0000.0000.000
178A179LEU0-0.0110.00413.2290.0560.0560.0000.0000.0000.000
179A180ALA00.0410.01217.464-0.070-0.0700.0000.0000.0000.000
180A181SER0-0.052-0.02620.6580.0200.0200.0000.0000.0000.000
181A182ARG10.8720.94422.577-0.323-0.3230.0000.0000.0000.000