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: LN4Y9

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 OptHSide
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 -1767119.674994
FMO2-HF: Nuclear repulsion 1700332.79405
FMO2-HF: Total energy -66786.880944
FMO2-MP2: Total energy -66980.69458


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.
-4.51-1.7542.962-3.105-2.614-0.011
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 : 0.022 / q_NPA : 0.009
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-1-0.876-0.9293.809-5.021-3.462-0.002-0.972-0.5860.005
4A4SER0-0.071-0.0365.4651.2621.2620.0000.0000.0000.000
5A5ARG10.9460.9517.0920.6170.6170.0000.0000.0000.000
6A6THR00.0220.0239.1220.0760.0760.0000.0000.0000.000
7A7VAL0-0.0100.0044.6370.1080.166-0.001-0.007-0.0500.000
8A8SER00.0650.0356.6690.2550.2550.0000.0000.0000.000
9A9GLU-1-0.897-0.9507.542-0.129-0.1290.0000.0000.0000.000
10A10LEU00.0230.0209.7850.1000.1000.0000.0000.0000.000
11A11VAL00.0070.0016.5430.1000.1000.0000.0000.0000.000
12A12THR0-0.025-0.0129.7940.0140.0140.0000.0000.0000.000
13A13ASN00.0340.01811.870-0.002-0.0020.0000.0000.0000.000
14A14THR0-0.067-0.03712.2820.0420.0420.0000.0000.0000.000
15A15ASN0-0.022-0.02211.3590.0220.0220.0000.0000.0000.000
16A16THR00.0280.01315.282-0.015-0.0150.0000.0000.0000.000
17A17ILE00.0250.01317.605-0.012-0.0120.0000.0000.0000.000
18A18ARG10.7980.90616.697-0.474-0.4740.0000.0000.0000.000
19A19VAL0-0.013-0.01019.199-0.014-0.0140.0000.0000.0000.000
20A20ALA00.0690.03821.541-0.014-0.0140.0000.0000.0000.000
21A21MET0-0.0130.00222.824-0.018-0.0180.0000.0000.0000.000
22A22LYS10.8230.90123.418-0.237-0.2370.0000.0000.0000.000
23A23ASP-1-0.838-0.90025.7220.0690.0690.0000.0000.0000.000
24A24ALA00.0020.00927.530-0.010-0.0100.0000.0000.0000.000
25A25TYR00.012-0.03627.344-0.007-0.0070.0000.0000.0000.000
26A26GLN00.0280.04227.8710.0150.0150.0000.0000.0000.000
27A27ARG10.8380.90629.923-0.092-0.0920.0000.0000.0000.000
28A28ASP-1-0.878-0.93333.2090.0940.0940.0000.0000.0000.000
29A29GLY0-0.051-0.01833.066-0.002-0.0020.0000.0000.0000.000
30A30LYS10.8640.93531.888-0.102-0.1020.0000.0000.0000.000
31A31TYR0-0.008-0.01326.907-0.006-0.0060.0000.0000.0000.000
32A32PRO0-0.009-0.00128.244-0.002-0.0020.0000.0000.0000.000
33A33ASP-1-0.869-0.92529.2000.1510.1510.0000.0000.0000.000
34A34TYR00.012-0.00825.1280.0000.0000.0000.0000.0000.000
35A35GLN0-0.0190.00528.457-0.011-0.0110.0000.0000.0000.000
36A36ALA00.0150.00527.1700.0070.0070.0000.0000.0000.000
37A37PRO00.018-0.00223.446-0.013-0.0130.0000.0000.0000.000
38A38LEU0-0.016-0.01023.107-0.011-0.0110.0000.0000.0000.000
39A39SER0-0.0070.00526.043-0.007-0.0070.0000.0000.0000.000
40A40LEU0-0.067-0.01626.255-0.010-0.0100.0000.0000.0000.000
41A41THR00.0470.01626.874-0.004-0.0040.0000.0000.0000.000
42A42ALA00.0540.01726.1120.0050.0050.0000.0000.0000.000
43A43ASP-1-0.863-0.92927.462-0.014-0.0140.0000.0000.0000.000
44A44SER00.0530.02730.7960.0030.0030.0000.0000.0000.000
45A45ILE0-0.0090.01024.7630.0060.0060.0000.0000.0000.000
46A46LYS10.8200.89828.8850.0120.0120.0000.0000.0000.000
47A47THR0-0.036-0.02931.4020.0000.0000.0000.0000.0000.000
48A48ASP-1-0.837-0.87831.7010.0680.0680.0000.0000.0000.000
49A49SER00.010-0.00133.2530.0040.0040.0000.0000.0000.000
50A50THR0-0.073-0.06133.2100.0040.0040.0000.0000.0000.000
51A51GLY00.0040.00132.7240.0040.0040.0000.0000.0000.000
52A52ILE0-0.0140.01526.8550.0110.0110.0000.0000.0000.000
53A53ALA00.0400.01825.371-0.007-0.0070.0000.0000.0000.000
54A54VAL00.0460.01021.830-0.008-0.0080.0000.0000.0000.000
55A55ALA00.0290.01525.053-0.014-0.0140.0000.0000.0000.000
56A56GLN00.0300.03628.375-0.002-0.0020.0000.0000.0000.000
57A57LEU0-0.007-0.01023.887-0.007-0.0070.0000.0000.0000.000
58A58VAL0-0.017-0.00825.456-0.011-0.0110.0000.0000.0000.000
59A59GLN0-0.103-0.05627.845-0.010-0.0100.0000.0000.0000.000
60A60LEU0-0.077-0.03529.956-0.004-0.0040.0000.0000.0000.000
61A61GLY0-0.030-0.00929.563-0.003-0.0030.0000.0000.0000.000
62A62LYS10.7400.85026.247-0.074-0.0740.0000.0000.0000.000
63A63LEU0-0.0080.00820.5240.0130.0130.0000.0000.0000.000
64A64THR0-0.015-0.02222.813-0.011-0.0110.0000.0000.0000.000
65A65PRO00.010-0.02522.6800.0100.0100.0000.0000.0000.000
66A66ASP-1-0.920-0.96019.294-0.058-0.0580.0000.0000.0000.000
67A67GLU-1-0.777-0.87118.1240.0160.0160.0000.0000.0000.000
68A68ALA0-0.011-0.00218.4050.0440.0440.0000.0000.0000.000
69A69ARG10.8650.94818.5330.0330.0330.0000.0000.0000.000
70A70ASN00.0430.02413.960-0.012-0.0120.0000.0000.0000.000
71A71GLY0-0.024-0.02514.468-0.016-0.0160.0000.0000.0000.000
72A72ILE0-0.050-0.0229.192-0.044-0.0440.0000.0000.0000.000
73A73SER0-0.031-0.01013.693-0.022-0.0220.0000.0000.0000.000
74A74GLY0-0.016-0.01316.926-0.020-0.0200.0000.0000.0000.000
75A75ASP-1-0.732-0.84318.7790.1200.1200.0000.0000.0000.000
76A76TYR0-0.031-0.03219.1990.0020.0020.0000.0000.0000.000
77A77ILE0-0.0020.00815.9300.0180.0180.0000.0000.0000.000
78A78GLY00.0290.03319.716-0.022-0.0220.0000.0000.0000.000
79A79ILE00.000-0.03420.7860.0380.0380.0000.0000.0000.000
80A80GLY00.0390.01423.210-0.026-0.0260.0000.0000.0000.000
81A81GLY00.0210.02725.6510.0120.0120.0000.0000.0000.000
82A82ALA0-0.012-0.00725.1300.0160.0160.0000.0000.0000.000
83A83ILE0-0.0050.00427.256-0.016-0.0160.0000.0000.0000.000
84A84THR00.021-0.01928.3820.0160.0160.0000.0000.0000.000
85A85SER0-0.005-0.01230.522-0.001-0.0010.0000.0000.0000.000
86A86SER00.0010.00033.6320.0010.0010.0000.0000.0000.000
87A87GLY00.0390.01835.195-0.008-0.0080.0000.0000.0000.000
88A88SER0-0.048-0.00534.112-0.013-0.0130.0000.0000.0000.000
89A89THR00.0260.00735.5740.0040.0040.0000.0000.0000.000
90A90ILE0-0.017-0.00934.174-0.005-0.0050.0000.0000.0000.000
91A91ASN0-0.003-0.00329.8830.0190.0190.0000.0000.0000.000
92A92LYS10.8840.92531.004-0.148-0.1480.0000.0000.0000.000
93A93GLY00.0060.00126.6660.0050.0050.0000.0000.0000.000
94A94PHE0-0.024-0.01320.937-0.014-0.0140.0000.0000.0000.000
95A95ALA00.011-0.00821.5550.0340.0340.0000.0000.0000.000
96A96MET0-0.0140.00816.818-0.023-0.0230.0000.0000.0000.000
97A97GLU-1-0.812-0.91817.7880.4000.4000.0000.0000.0000.000
98A98LEU0-0.036-0.01511.874-0.039-0.0390.0000.0000.0000.000
99A99ASN00.004-0.02815.0640.0770.0770.0000.0000.0000.000
100A100GLY00.0220.01315.108-0.005-0.0050.0000.0000.0000.000
101A101LEU0-0.049-0.01110.610-0.007-0.0070.0000.0000.0000.000
102A102SER00.0810.02510.4930.0680.0680.0000.0000.0000.000
103A103GLN00.0730.02910.7000.1980.1980.0000.0000.0000.000
104A104GLU-1-0.949-0.9696.9810.2220.2220.0000.0000.0000.000
105A105GLN00.0390.0176.0550.7110.7110.0000.0000.0000.000
106A106CYS0-0.059-0.0136.8100.5970.5970.0000.0000.0000.000
107A107ARG10.8930.9336.682-0.693-0.6930.0000.0000.0000.000
108A108SER00.0060.0092.3511.3551.7442.915-1.824-1.480-0.015
109A109ILE00.0340.0183.8871.4321.528-0.0010.026-0.1210.000
110A110LEU0-0.013-0.0096.550-0.055-0.0550.0000.0000.0000.000
111A111GLY0-0.015-0.0105.428-0.613-0.6130.0000.0000.0000.000
112A112GLN0-0.044-0.0173.315-3.348-2.6940.051-0.328-0.377-0.001
113A113VAL00.004-0.0106.338-0.917-0.9170.0000.0000.0000.000
114A114GLY00.0170.0189.781-0.366-0.3660.0000.0000.0000.000
115A115ASP-1-0.768-0.89911.8480.7340.7340.0000.0000.0000.000
116A116ASN0-0.057-0.01111.319-0.282-0.2820.0000.0000.0000.000
117A117TRP00.0250.00913.988-0.186-0.1860.0000.0000.0000.000
118A118GLU-1-0.758-0.82317.1790.3590.3590.0000.0000.0000.000
119A119TYR00.0010.00019.736-0.015-0.0150.0000.0000.0000.000
120A120VAL00.0060.00214.0200.0360.0360.0000.0000.0000.000
121A121ALA00.0020.00917.297-0.023-0.0230.0000.0000.0000.000
122A122VAL0-0.012-0.00713.9680.0610.0610.0000.0000.0000.000
123A123GLY00.006-0.00116.739-0.061-0.0610.0000.0000.0000.000
124A124THR0-0.015-0.02117.6250.0430.0430.0000.0000.0000.000
125A125SER00.0080.03419.207-0.045-0.0450.0000.0000.0000.000
126A126PRO00.0220.00318.5530.0310.0310.0000.0000.0000.000
127A127SER00.024-0.01918.0820.0170.0170.0000.0000.0000.000
128A128GLY0-0.036-0.00519.969-0.013-0.0130.0000.0000.0000.000
129A129SER0-0.033-0.01322.166-0.017-0.0170.0000.0000.0000.000
130A130TYR0-0.046-0.04318.7980.0300.0300.0000.0000.0000.000
131A131ASP-1-0.832-0.93522.8260.2080.2080.0000.0000.0000.000
132A132ALA0-0.030-0.01022.029-0.011-0.0110.0000.0000.0000.000
133A133LEU0-0.036-0.01621.804-0.015-0.0150.0000.0000.0000.000
134A134SER0-0.027-0.01625.225-0.021-0.0210.0000.0000.0000.000
135A135ALA0-0.050-0.00727.389-0.015-0.0150.0000.0000.0000.000
136A136GLY0-0.012-0.00428.577-0.011-0.0110.0000.0000.0000.000
137A137ALA0-0.036-0.00427.8960.0160.0160.0000.0000.0000.000
138A138VAL00.0320.01322.8910.0030.0030.0000.0000.0000.000
139A139ASN00.0230.00626.276-0.004-0.0040.0000.0000.0000.000
140A140MET0-0.018-0.00623.2910.0130.0130.0000.0000.0000.000
141A141LEU00.0010.00325.5470.0200.0200.0000.0000.0000.000
142A142ALA0-0.0180.01425.600-0.012-0.0120.0000.0000.0000.000
143A143ALA00.0110.00525.7570.0240.0240.0000.0000.0000.000
144A144THR0-0.0020.00721.650-0.009-0.0090.0000.0000.0000.000
145A145ASP-1-0.767-0.87021.6430.4010.4010.0000.0000.0000.000
146A146ASN0-0.066-0.05419.1600.0580.0580.0000.0000.0000.000
147A147THR00.0090.00117.6080.0460.0460.0000.0000.0000.000
148A148THR0-0.0180.01617.6560.0520.0520.0000.0000.0000.000
149A149ILE0-0.0110.00119.0490.0470.0470.0000.0000.0000.000
150A150LEU0-0.0060.00214.2290.0000.0000.0000.0000.0000.000
151A151ARG10.8400.92315.708-0.730-0.7300.0000.0000.0000.000
152A152SER00.009-0.01819.427-0.017-0.0170.0000.0000.0000.000
153A153LEU0-0.047-0.02522.768-0.002-0.0020.0000.0000.0000.000
154A154ALA0-0.0250.01125.815-0.030-0.0300.0000.0000.0000.000
155A155ALA00.015-0.00526.8090.0110.0110.0000.0000.0000.000
156A156ASN0-0.054-0.03925.9020.0060.0060.0000.0000.0000.000
157A157GLY00.0780.05623.4250.0220.0220.0000.0000.0000.000
158A158GLN0-0.080-0.05820.4750.0680.0680.0000.0000.0000.000
159A159VAL0-0.0020.00517.560-0.004-0.0040.0000.0000.0000.000
160A160SER0-0.010-0.01115.1960.0210.0210.0000.0000.0000.000
161A161LEU0-0.038-0.03012.226-0.052-0.0520.0000.0000.0000.000
162A162THR0-0.017-0.03510.9710.2700.2700.0000.0000.0000.000
163A163ALA00.0590.0288.3460.1240.1240.0000.0000.0000.000
164A164GLU-1-0.827-0.9119.5080.7680.7680.0000.0000.0000.000
165A165LYS10.8280.92012.813-0.774-0.7740.0000.0000.0000.000
166A166ILE00.0130.0197.810-0.130-0.1300.0000.0000.0000.000
167A167LEU0-0.024-0.0099.873-0.054-0.0540.0000.0000.0000.000
168A168LYS10.8500.93512.246-0.643-0.6430.0000.0000.0000.000
169A169THR00.0350.00212.369-0.057-0.0570.0000.0000.0000.000
170A171THR0-0.002-0.00813.033-0.019-0.0190.0000.0000.0000.000
171A172ALA00.0230.03615.485-0.079-0.0790.0000.0000.0000.000
172A173THR0-0.017-0.02615.6530.0430.0430.0000.0000.0000.000
173A174VAL0-0.0060.00816.193-0.011-0.0110.0000.0000.0000.000
174A175ASN0-0.052-0.04013.4110.0310.0310.0000.0000.0000.000
175A176SER0-0.024-0.00114.887-0.025-0.0250.0000.0000.0000.000
176A177ILE00.0220.00710.3340.0610.0610.0000.0000.0000.000
177A178THR0-0.0060.00414.833-0.091-0.0910.0000.0000.0000.000
178A179LEU0-0.0130.00213.1170.0580.0580.0000.0000.0000.000
179A180ALA00.0360.01017.442-0.071-0.0710.0000.0000.0000.000
180A181SER0-0.062-0.06220.5950.0260.0260.0000.0000.0000.000
181A182ARG10.8790.93922.513-0.330-0.3300.0000.0000.0000.000