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: 989Z2

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1767815.082238
FMO2-HF: Nuclear repulsion 1701028.181503
FMO2-HF: Total energy -66786.900735
FMO2-MP2: Total energy -66980.737126


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.
-2.5060.7982.386-2.838-2.852-0.009
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 : 0.044 / q_NPA : 0.020
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-1-0.881-0.9373.854-4.002-2.396-0.002-0.912-0.6930.004
4A4SER0-0.101-0.0585.4991.1021.1020.0000.0000.0000.000
5A5ARG10.9700.9606.9990.6460.6460.0000.0000.0000.000
6A6THR00.0080.0049.4650.0810.0810.0000.0000.0000.000
7A7VAL0-0.0230.0004.6770.1160.166-0.001-0.005-0.0440.000
8A8SER00.0490.0216.2990.2460.2460.0000.0000.0000.000
9A9GLU-1-0.884-0.9137.270-0.101-0.1010.0000.0000.0000.000
10A10LEU00.0330.0209.8360.0780.0780.0000.0000.0000.000
11A11VAL0-0.003-0.0046.1500.0510.0510.0000.0000.0000.000
12A12THR0-0.016-0.0089.4840.0060.0060.0000.0000.0000.000
13A13ASN00.0290.01212.058-0.006-0.0060.0000.0000.0000.000
14A14THR0-0.065-0.03912.0690.0110.0110.0000.0000.0000.000
15A15ASN0-0.041-0.02512.004-0.032-0.0320.0000.0000.0000.000
16A16THR00.0370.02015.694-0.021-0.0210.0000.0000.0000.000
17A17ILE00.0370.02017.787-0.022-0.0220.0000.0000.0000.000
18A18ARG10.7890.89516.971-0.544-0.5440.0000.0000.0000.000
19A19VAL0-0.006-0.00819.712-0.019-0.0190.0000.0000.0000.000
20A20ALA00.0550.03221.912-0.019-0.0190.0000.0000.0000.000
21A21MET0-0.0020.00522.800-0.026-0.0260.0000.0000.0000.000
22A22LYS10.8040.90723.653-0.276-0.2760.0000.0000.0000.000
23A23ASP-1-0.817-0.89326.1280.1000.1000.0000.0000.0000.000
24A24ALA00.0200.01527.611-0.012-0.0120.0000.0000.0000.000
25A25TYR0-0.014-0.03327.353-0.009-0.0090.0000.0000.0000.000
26A26GLN00.0060.01627.9950.0140.0140.0000.0000.0000.000
27A27ARG10.8170.89130.091-0.118-0.1180.0000.0000.0000.000
28A28ASP-1-0.837-0.89733.4390.1110.1110.0000.0000.0000.000
29A29GLY0-0.023-0.00633.063-0.003-0.0030.0000.0000.0000.000
30A30LYS10.8360.91632.098-0.122-0.1220.0000.0000.0000.000
31A31TYR00.0120.00526.8650.0000.0000.0000.0000.0000.000
32A32PRO0-0.0080.00128.158-0.005-0.0050.0000.0000.0000.000
33A33ASP-1-0.857-0.93029.0330.1650.1650.0000.0000.0000.000
34A34TYR00.009-0.00725.1380.0040.0040.0000.0000.0000.000
35A35GLN0-0.0140.00228.418-0.014-0.0140.0000.0000.0000.000
36A36ALA00.0390.01927.3790.0080.0080.0000.0000.0000.000
37A37PRO00.0060.00123.665-0.014-0.0140.0000.0000.0000.000
38A38LEU0-0.021-0.00423.563-0.011-0.0110.0000.0000.0000.000
39A39SER0-0.038-0.02226.324-0.011-0.0110.0000.0000.0000.000
40A40LEU0-0.042-0.00226.220-0.009-0.0090.0000.0000.0000.000
41A41THR00.0380.01427.063-0.003-0.0030.0000.0000.0000.000
42A42ALA00.0580.01826.3320.0060.0060.0000.0000.0000.000
43A43ASP-1-0.877-0.91927.6010.0090.0090.0000.0000.0000.000
44A44SER00.0600.02930.9230.0030.0030.0000.0000.0000.000
45A45ILE00.0020.01824.8310.0050.0050.0000.0000.0000.000
46A46LYS10.8120.88029.080-0.015-0.0150.0000.0000.0000.000
47A47THR0-0.032-0.02431.593-0.001-0.0010.0000.0000.0000.000
48A48ASP-1-0.842-0.88731.6290.0840.0840.0000.0000.0000.000
49A49SER00.0310.01333.0130.0040.0040.0000.0000.0000.000
50A50THR0-0.091-0.06833.2440.0040.0040.0000.0000.0000.000
51A51GLY00.013-0.00332.8350.0020.0020.0000.0000.0000.000
52A52ILE0-0.0380.00027.1060.0120.0120.0000.0000.0000.000
53A53ALA00.0530.02725.778-0.006-0.0060.0000.0000.0000.000
54A54VAL00.0340.00921.967-0.006-0.0060.0000.0000.0000.000
55A55ALA00.0140.01125.051-0.011-0.0110.0000.0000.0000.000
56A56GLN00.0390.03228.416-0.002-0.0020.0000.0000.0000.000
57A57LEU0-0.017-0.01423.588-0.006-0.0060.0000.0000.0000.000
58A58VAL0-0.0100.00225.427-0.008-0.0080.0000.0000.0000.000
59A59GLN0-0.099-0.06027.718-0.010-0.0100.0000.0000.0000.000
60A60LEU0-0.064-0.03129.935-0.006-0.0060.0000.0000.0000.000
61A61GLY0-0.026-0.00629.727-0.001-0.0010.0000.0000.0000.000
62A62LYS10.7470.85826.431-0.103-0.1030.0000.0000.0000.000
63A63LEU0-0.0160.00020.3270.0200.0200.0000.0000.0000.000
64A64THR0-0.010-0.02522.291-0.018-0.0180.0000.0000.0000.000
65A65PRO00.007-0.02922.3700.0140.0140.0000.0000.0000.000
66A66ASP-1-0.908-0.95219.1180.0110.0110.0000.0000.0000.000
67A67GLU-1-0.783-0.87217.7370.1010.1010.0000.0000.0000.000
68A68ALA0-0.018-0.00518.1640.0460.0460.0000.0000.0000.000
69A69ARG10.8430.92818.567-0.022-0.0220.0000.0000.0000.000
70A70ASN00.027-0.00314.3580.0170.0170.0000.0000.0000.000
71A71GLY0-0.030-0.02414.903-0.025-0.0250.0000.0000.0000.000
72A72ILE0-0.035-0.0129.461-0.042-0.0420.0000.0000.0000.000
73A73SER0-0.045-0.03613.990-0.027-0.0270.0000.0000.0000.000
74A74GLY00.0220.00817.295-0.028-0.0280.0000.0000.0000.000
75A75ASP-1-0.744-0.82819.4310.1350.1350.0000.0000.0000.000
76A76TYR0-0.020-0.01719.6430.0020.0020.0000.0000.0000.000
77A77ILE0-0.0100.00416.0170.0130.0130.0000.0000.0000.000
78A78GLY00.0370.02819.861-0.021-0.0210.0000.0000.0000.000
79A79ILE0-0.009-0.03620.6880.0390.0390.0000.0000.0000.000
80A80GLY00.0260.01223.199-0.026-0.0260.0000.0000.0000.000
81A81GLY00.0220.03125.5100.0160.0160.0000.0000.0000.000
82A82ALA0-0.010-0.00925.1020.0150.0150.0000.0000.0000.000
83A83ILE0-0.021-0.00727.240-0.015-0.0150.0000.0000.0000.000
84A84THR00.026-0.01028.6760.0150.0150.0000.0000.0000.000
85A85SER00.003-0.01130.633-0.003-0.0030.0000.0000.0000.000
86A86SER0-0.0010.00433.6580.0030.0030.0000.0000.0000.000
87A87GLY00.0410.01535.128-0.007-0.0070.0000.0000.0000.000
88A88SER0-0.058-0.01633.929-0.012-0.0120.0000.0000.0000.000
89A89THR00.0200.00635.3630.0050.0050.0000.0000.0000.000
90A90ILE0-0.014-0.00934.267-0.004-0.0040.0000.0000.0000.000
91A91ASN00.0080.00729.9770.0180.0180.0000.0000.0000.000
92A92LYS10.8760.91530.956-0.157-0.1570.0000.0000.0000.000
93A93GLY0-0.006-0.00226.6120.0060.0060.0000.0000.0000.000
94A94PHE0-0.018-0.00420.927-0.016-0.0160.0000.0000.0000.000
95A95ALA00.006-0.01221.5030.0350.0350.0000.0000.0000.000
96A96MET0-0.0060.01016.652-0.016-0.0160.0000.0000.0000.000
97A97GLU-1-0.819-0.90517.7020.3920.3920.0000.0000.0000.000
98A98LEU0-0.033-0.00111.738-0.030-0.0300.0000.0000.0000.000
99A99ASN00.014-0.02115.1640.0750.0750.0000.0000.0000.000
100A100GLY00.0220.00915.454-0.004-0.0040.0000.0000.0000.000
101A101LEU0-0.055-0.00711.026-0.012-0.0120.0000.0000.0000.000
102A102SER00.0840.02310.5910.0440.0440.0000.0000.0000.000
103A103GLN00.0550.02410.8820.1530.1530.0000.0000.0000.000
104A104GLU-1-0.943-0.9636.917-0.006-0.0060.0000.0000.0000.000
105A105GLN00.0460.0225.9350.6010.6010.0000.0000.0000.000
106A106CYS0-0.044-0.0077.1900.5850.5850.0000.0000.0000.000
107A107ARG10.8890.9306.738-0.431-0.4310.0000.0000.0000.000
108A108SER0-0.0090.0012.6302.3222.8201.949-1.277-1.170-0.008
109A109ILE00.0370.0233.8451.7761.9850.0000.001-0.2100.000
110A110LEU0-0.009-0.0056.6530.1130.1130.0000.0000.0000.000
111A111GLY0-0.009-0.0115.142-0.685-0.662-0.001-0.006-0.0150.000
112A112GLN0-0.047-0.0252.790-3.064-2.1460.441-0.639-0.720-0.005
113A113VAL0-0.002-0.0036.419-0.996-0.9960.0000.0000.0000.000
114A114GLY00.0250.0089.830-0.371-0.3710.0000.0000.0000.000
115A115ASP-1-0.766-0.88011.8100.7470.7470.0000.0000.0000.000
116A116ASN0-0.054-0.00311.339-0.292-0.2920.0000.0000.0000.000
117A117TRP00.0120.00713.840-0.199-0.1990.0000.0000.0000.000
118A118GLU-1-0.732-0.82017.2000.3650.3650.0000.0000.0000.000
119A119TYR0-0.007-0.00719.780-0.032-0.0320.0000.0000.0000.000
120A120VAL0-0.011-0.00414.0960.0410.0410.0000.0000.0000.000
121A121ALA0-0.0060.00817.453-0.030-0.0300.0000.0000.0000.000
122A122VAL0-0.030-0.01514.0170.0700.0700.0000.0000.0000.000
123A123GLY00.0240.01516.952-0.058-0.0580.0000.0000.0000.000
124A124THR0-0.004-0.01417.6390.0380.0380.0000.0000.0000.000
125A125SER0-0.0070.03019.621-0.041-0.0410.0000.0000.0000.000
126A126PRO00.0240.00819.0230.0250.0250.0000.0000.0000.000
127A127SER00.026-0.00919.0080.0220.0220.0000.0000.0000.000
128A128GLY0-0.030-0.00520.702-0.014-0.0140.0000.0000.0000.000
129A129SER0-0.067-0.06322.600-0.013-0.0130.0000.0000.0000.000
130A130TYR0-0.015-0.03418.8890.0300.0300.0000.0000.0000.000
131A131ASP-1-0.818-0.89923.0940.2040.2040.0000.0000.0000.000
132A132ALA0-0.028-0.00122.037-0.011-0.0110.0000.0000.0000.000
133A133LEU0-0.037-0.02121.602-0.013-0.0130.0000.0000.0000.000
134A134SER0-0.039-0.02225.147-0.020-0.0200.0000.0000.0000.000
135A135ALA0-0.0230.00627.532-0.016-0.0160.0000.0000.0000.000
136A136GLY0-0.021-0.01228.583-0.014-0.0140.0000.0000.0000.000
137A137ALA0-0.0250.00227.9480.0160.0160.0000.0000.0000.000
138A138VAL00.0420.01722.8870.0000.0000.0000.0000.0000.000
139A139ASN00.0180.00026.2530.0020.0020.0000.0000.0000.000
140A140MET0-0.0090.00623.3040.0120.0120.0000.0000.0000.000
141A141LEU00.0010.00225.7830.0180.0180.0000.0000.0000.000
142A142ALA0-0.0180.01125.384-0.014-0.0140.0000.0000.0000.000
143A143ALA00.0070.00425.5860.0240.0240.0000.0000.0000.000
144A144THR00.0170.02021.603-0.009-0.0090.0000.0000.0000.000
145A145ASP-1-0.775-0.86521.5220.3750.3750.0000.0000.0000.000
146A146ASN0-0.073-0.04618.9510.0560.0560.0000.0000.0000.000
147A147THR0-0.038-0.02317.5820.0350.0350.0000.0000.0000.000
148A148THR00.0240.02517.4870.0470.0470.0000.0000.0000.000
149A149ILE0-0.027-0.01519.1410.0360.0360.0000.0000.0000.000
150A150LEU00.0180.00913.795-0.005-0.0050.0000.0000.0000.000
151A151ARG10.8240.89715.615-0.724-0.7240.0000.0000.0000.000
152A152SER0-0.012-0.02119.421-0.018-0.0180.0000.0000.0000.000
153A153LEU0-0.034-0.02022.895-0.001-0.0010.0000.0000.0000.000
154A154ALA0-0.0140.01425.881-0.029-0.0290.0000.0000.0000.000
155A155ALA00.021-0.00126.7370.0130.0130.0000.0000.0000.000
156A156ASN0-0.043-0.03325.3490.0020.0020.0000.0000.0000.000
157A157GLY00.0430.03823.4110.0250.0250.0000.0000.0000.000
158A158GLN0-0.063-0.04520.2980.0790.0790.0000.0000.0000.000
159A159VAL00.0210.01117.5010.0060.0060.0000.0000.0000.000
160A160SER00.014-0.01314.9530.0410.0410.0000.0000.0000.000
161A161LEU0-0.052-0.01211.983-0.062-0.0620.0000.0000.0000.000
162A162THR0-0.002-0.02510.6020.3040.3040.0000.0000.0000.000
163A163ALA00.0630.0277.6910.0220.0220.0000.0000.0000.000
164A164GLU-1-0.826-0.9079.3310.6720.6720.0000.0000.0000.000
165A165LYS10.7810.87812.860-0.830-0.8300.0000.0000.0000.000
166A166ILE00.0280.0257.564-0.134-0.1340.0000.0000.0000.000
167A167LEU0-0.024-0.01010.134-0.072-0.0720.0000.0000.0000.000
168A168LYS10.8490.93512.203-0.557-0.5570.0000.0000.0000.000
169A169THR00.0390.00512.334-0.048-0.0480.0000.0000.0000.000
170A171THR00.0070.00212.853-0.031-0.0310.0000.0000.0000.000
171A172ALA00.0260.03315.560-0.071-0.0710.0000.0000.0000.000
172A173THR0-0.023-0.03215.7180.0260.0260.0000.0000.0000.000
173A174VAL00.0000.01016.597-0.018-0.0180.0000.0000.0000.000
174A175ASN0-0.064-0.04613.6160.0350.0350.0000.0000.0000.000
175A176SER0-0.036-0.02715.372-0.023-0.0230.0000.0000.0000.000
176A177ILE00.0200.00310.5130.0520.0520.0000.0000.0000.000
177A178THR0-0.0160.00215.049-0.069-0.0690.0000.0000.0000.000
178A179LEU0-0.012-0.00112.9040.0690.0690.0000.0000.0000.000
179A180ALA00.0290.00417.354-0.069-0.0690.0000.0000.0000.000
180A181SER0-0.079-0.07420.5250.0370.0370.0000.0000.0000.000
181A182ARG10.8980.94822.446-0.343-0.3430.0000.0000.0000.000