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: LNL99

Calculation Name: 3VPR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VPR

Chain ID: A

ChEMBL ID:

UniProt ID: Q53WD9

Base Structure: X-ray

Registration Date: 2023-09-20

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2048813.954665
FMO2-HF: Nuclear repulsion 1973898.141264
FMO2-HF: Total energy -74915.813401
FMO2-MP2: Total energy -75136.394816


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:VAL)


Summations of interaction energy for fragment #1(A:1:VAL)
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.
-2.7220.2530.218-1.309-1.8830.002
Interaction energy analysis for fragmet #1(A:1:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / 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].
3A3THR0-0.022-0.0412.789-0.4282.3590.219-1.267-1.7390.002
4A4THR00.001-0.0194.370-0.178-0.1340.000-0.015-0.0280.000
5A5ARG10.7960.8697.5940.6430.6430.0000.0000.0000.000
6A6ASP-1-0.797-0.8714.315-2.845-2.701-0.001-0.027-0.1160.000
7A7ARG10.9510.9756.3411.1541.1540.0000.0000.0000.000
8A8ILE0-0.0090.0029.4080.1630.1630.0000.0000.0000.000
9A9LEU0-0.034-0.01310.3160.1000.1000.0000.0000.0000.000
10A10GLU-1-0.874-0.9229.165-1.217-1.2170.0000.0000.0000.000
11A11GLU-1-0.830-0.91912.533-0.613-0.6130.0000.0000.0000.000
12A12ALA0-0.018-0.00215.0440.0940.0940.0000.0000.0000.000
13A13ALA0-0.0060.00215.4030.0680.0680.0000.0000.0000.000
14A14LYS10.7900.89212.2670.8030.8030.0000.0000.0000.000
15A15LEU00.0760.03518.1550.0540.0540.0000.0000.0000.000
16A16PHE0-0.040-0.04419.4800.0450.0450.0000.0000.0000.000
17A17THR0-0.043-0.02720.1530.0310.0310.0000.0000.0000.000
18A18GLU-1-0.961-0.98520.234-0.306-0.3060.0000.0000.0000.000
19A19LYS10.8080.90424.1720.2250.2250.0000.0000.0000.000
20A20GLY00.0180.02725.5450.0200.0200.0000.0000.0000.000
21A21TYR00.000-0.01122.604-0.006-0.0060.0000.0000.0000.000
22A22GLU-1-0.782-0.88225.376-0.198-0.1980.0000.0000.0000.000
23A23ALA0-0.018-0.00628.6320.0040.0040.0000.0000.0000.000
24A24THR00.0210.01622.7100.0100.0100.0000.0000.0000.000
25A25SER0-0.047-0.04925.394-0.005-0.0050.0000.0000.0000.000
26A26VAL00.056-0.00121.189-0.014-0.0140.0000.0000.0000.000
27A27GLN0-0.009-0.00922.128-0.007-0.0070.0000.0000.0000.000
28A28ASP-1-0.767-0.85323.355-0.200-0.2000.0000.0000.0000.000
29A29LEU00.0310.02318.446-0.006-0.0060.0000.0000.0000.000
30A30ALA0-0.024-0.01118.604-0.022-0.0220.0000.0000.0000.000
31A31GLN00.0130.00619.1240.0020.0020.0000.0000.0000.000
32A32ALA0-0.0050.00619.4100.0090.0090.0000.0000.0000.000
33A33LEU0-0.0200.00113.072-0.021-0.0210.0000.0000.0000.000
34A34GLY0-0.0200.01315.302-0.004-0.0040.0000.0000.0000.000
35A35LEU0-0.038-0.01813.2670.0190.0190.0000.0000.0000.000
36A36SER00.0270.00617.7440.0110.0110.0000.0000.0000.000
37A37LYS10.9370.94219.2750.1340.1340.0000.0000.0000.000
38A38ALA00.0120.01220.589-0.013-0.0130.0000.0000.0000.000
39A39ALA00.0330.02715.851-0.004-0.0040.0000.0000.0000.000
40A40LEU00.0270.02615.603-0.029-0.0290.0000.0000.0000.000
41A41TYR0-0.014-0.02317.252-0.015-0.0150.0000.0000.0000.000
42A42HIS00.0210.00417.045-0.008-0.0080.0000.0000.0000.000
43A43HIS0-0.061-0.01410.928-0.038-0.0380.0000.0000.0000.000
44A44PHE00.0260.00311.993-0.020-0.0200.0000.0000.0000.000
45A45GLY00.0290.03117.1190.0160.0160.0000.0000.0000.000
46A46SER0-0.069-0.05220.4220.0210.0210.0000.0000.0000.000
47A47LYS10.8480.90920.3120.2070.2070.0000.0000.0000.000
48A48GLU-1-0.758-0.84621.307-0.273-0.2730.0000.0000.0000.000
49A49GLU-1-0.815-0.91317.971-0.333-0.3330.0000.0000.0000.000
50A50ILE0-0.0150.00115.869-0.037-0.0370.0000.0000.0000.000
51A51LEU00.0060.01117.314-0.048-0.0480.0000.0000.0000.000
52A52TYR0-0.0080.01019.811-0.018-0.0180.0000.0000.0000.000
53A53GLU-1-0.738-0.86212.921-0.654-0.6540.0000.0000.0000.000
54A54ILE0-0.0060.00715.392-0.063-0.0630.0000.0000.0000.000
55A55SER0-0.023-0.03116.451-0.001-0.0010.0000.0000.0000.000
56A56LEU0-0.048-0.02416.1990.0160.0160.0000.0000.0000.000
57A57LEU0-0.0020.00910.1780.0260.0260.0000.0000.0000.000
58A58ALA00.0230.01514.1940.0000.0000.0000.0000.0000.000
59A59LEU00.009-0.01516.6100.0340.0340.0000.0000.0000.000
60A60LYS10.9210.96415.1530.5100.5100.0000.0000.0000.000
61A61GLY00.0320.02814.5800.0300.0300.0000.0000.0000.000
62A62LEU00.0030.00615.2370.0480.0480.0000.0000.0000.000
63A63VAL0-0.017-0.00818.7920.0390.0390.0000.0000.0000.000
64A64ALA0-0.0250.00115.9560.0340.0340.0000.0000.0000.000
65A65ALA00.0330.01117.5910.0400.0400.0000.0000.0000.000
66A66GLY00.0250.00518.8740.0310.0310.0000.0000.0000.000
67A67GLU-1-0.844-0.94020.174-0.176-0.1760.0000.0000.0000.000
68A68LYS10.7970.90517.4570.2060.2060.0000.0000.0000.000
69A69ALA0-0.0100.00522.0460.0170.0170.0000.0000.0000.000
70A70LEU0-0.044-0.01325.2070.0100.0100.0000.0000.0000.000
71A71GLU-1-0.896-0.95624.402-0.058-0.0580.0000.0000.0000.000
72A72VAL0-0.062-0.01026.4750.0120.0120.0000.0000.0000.000
73A73ALA00.0510.03029.025-0.003-0.0030.0000.0000.0000.000
74A74ASP-1-0.803-0.88832.690-0.041-0.0410.0000.0000.0000.000
75A75PRO00.0670.02332.609-0.005-0.0050.0000.0000.0000.000
76A76LYS10.8870.93433.1750.0340.0340.0000.0000.0000.000
77A77GLU-1-0.771-0.85228.537-0.062-0.0620.0000.0000.0000.000
78A78ALA0-0.0090.00528.501-0.008-0.0080.0000.0000.0000.000
79A79LEU00.0100.00228.165-0.012-0.0120.0000.0000.0000.000
80A80ARG10.7610.83727.0160.0580.0580.0000.0000.0000.000
81A81ARG10.9580.97021.4020.0660.0660.0000.0000.0000.000
82A82PHE00.0110.01823.928-0.018-0.0180.0000.0000.0000.000
83A83MET0-0.060-0.01924.402-0.016-0.0160.0000.0000.0000.000
84A84GLU-1-0.737-0.84523.913-0.107-0.1070.0000.0000.0000.000
85A85ALA00.0100.00819.939-0.019-0.0190.0000.0000.0000.000
86A86HIS00.0110.02019.767-0.032-0.0320.0000.0000.0000.000
87A87ALA00.006-0.00821.004-0.028-0.0280.0000.0000.0000.000
88A88ARG10.7820.87116.3380.1890.1890.0000.0000.0000.000
89A89TYR00.0060.01012.625-0.056-0.0560.0000.0000.0000.000
90A90PHE0-0.013-0.01416.822-0.056-0.0560.0000.0000.0000.000
91A91GLU-1-0.822-0.91218.734-0.245-0.2450.0000.0000.0000.000
92A92GLU-1-0.883-0.94313.525-0.384-0.3840.0000.0000.0000.000
93A93ASN0-0.048-0.02412.590-0.211-0.2110.0000.0000.0000.000
94A94TYR00.0020.00715.1920.0020.0020.0000.0000.0000.000
95A95PRO00.0440.01315.6980.0290.0290.0000.0000.0000.000
96A96PHE00.0310.01611.5720.0400.0400.0000.0000.0000.000
97A97PHE00.0110.00517.3450.0460.0460.0000.0000.0000.000
98A98VAL00.0160.01220.4670.0350.0350.0000.0000.0000.000
99A99THR0-0.034-0.00819.8600.0350.0350.0000.0000.0000.000
100A100MET0-0.013-0.00820.5690.0250.0250.0000.0000.0000.000
101A101LEU0-0.050-0.02522.4000.0300.0300.0000.0000.0000.000
102A102GLN0-0.021-0.00324.6070.0380.0380.0000.0000.0000.000
103A103GLY00.0410.02225.1420.0180.0180.0000.0000.0000.000
104A104ILE00.0260.02026.1750.0080.0080.0000.0000.0000.000
105A105LYS10.8100.88927.3910.2000.2000.0000.0000.0000.000
106A106SER0-0.059-0.04627.0250.0120.0120.0000.0000.0000.000
107A107LEU00.0000.02422.870-0.001-0.0010.0000.0000.0000.000
108A108SER0-0.018-0.01625.4880.0240.0240.0000.0000.0000.000
109A109PRO0-0.017-0.03227.754-0.007-0.0070.0000.0000.0000.000
110A110GLU-1-0.826-0.88926.609-0.176-0.1760.0000.0000.0000.000
111A111ASN00.0220.00722.3680.0020.0020.0000.0000.0000.000
112A112ARG10.8290.91424.6500.1680.1680.0000.0000.0000.000
113A113LEU00.0010.00827.238-0.002-0.0020.0000.0000.0000.000
114A114LYS10.8730.90922.6350.2030.2030.0000.0000.0000.000
115A115THR0-0.002-0.01222.896-0.019-0.0190.0000.0000.0000.000
116A116ILE0-0.033-0.02523.932-0.001-0.0010.0000.0000.0000.000
117A117ALA00.0060.00525.7450.0070.0070.0000.0000.0000.000
118A118LEU0-0.013-0.00219.5660.0060.0060.0000.0000.0000.000
119A119ARG10.8560.90223.6340.1700.1700.0000.0000.0000.000
120A120ASP-1-0.803-0.88125.641-0.147-0.1470.0000.0000.0000.000
121A121ARG10.8500.92522.5740.1830.1830.0000.0000.0000.000
122A122HIS0-0.011-0.01722.6900.0090.0090.0000.0000.0000.000
123A123GLU-1-0.771-0.85525.332-0.120-0.1200.0000.0000.0000.000
124A124GLU-1-0.800-0.88528.981-0.087-0.0870.0000.0000.0000.000
125A125ASN00.0220.00924.2670.0200.0200.0000.0000.0000.000
126A126LEU00.0000.01728.2260.0100.0100.0000.0000.0000.000
127A127ARG10.8240.88229.7190.1210.1210.0000.0000.0000.000
128A128ALA0-0.0020.00130.9210.0080.0080.0000.0000.0000.000
129A129ILE0-0.021-0.00127.7290.0080.0080.0000.0000.0000.000
130A130LEU0-0.024-0.02132.3120.0070.0070.0000.0000.0000.000
131A131ARG10.8250.90434.1710.0840.0840.0000.0000.0000.000
132A132ARG10.8850.92930.7740.0640.0640.0000.0000.0000.000
133A133GLY00.000-0.00636.4300.0050.0050.0000.0000.0000.000
134A134VAL0-0.030-0.00237.9100.0040.0040.0000.0000.0000.000
135A135GLU-1-0.924-0.96838.537-0.052-0.0520.0000.0000.0000.000
136A136GLN0-0.057-0.03536.4570.0000.0000.0000.0000.0000.000
137A137GLY00.0060.01041.1620.0030.0030.0000.0000.0000.000
138A138VAL0-0.087-0.03737.9170.0020.0020.0000.0000.0000.000
139A139PHE0-0.062-0.02635.052-0.002-0.0020.0000.0000.0000.000
140A140ARG10.9650.98541.2670.0530.0530.0000.0000.0000.000
141A141GLU-1-0.838-0.93243.095-0.054-0.0540.0000.0000.0000.000
142A142VAL0-0.069-0.04640.0550.0000.0000.0000.0000.0000.000
143A143ASP-1-0.816-0.89540.914-0.076-0.0760.0000.0000.0000.000
144A144VAL00.0430.01636.304-0.004-0.0040.0000.0000.0000.000
145A145ALA0-0.0020.00936.539-0.007-0.0070.0000.0000.0000.000
146A146LEU0-0.021-0.00736.655-0.007-0.0070.0000.0000.0000.000
147A147ALA00.0140.00537.054-0.004-0.0040.0000.0000.0000.000
148A148GLY00.0460.01233.150-0.005-0.0050.0000.0000.0000.000
149A149ARG10.8100.88232.0370.1160.1160.0000.0000.0000.000
150A150ALA00.0240.02533.819-0.007-0.0070.0000.0000.0000.000
151A151VAL00.0470.01729.967-0.005-0.0050.0000.0000.0000.000
152A152LEU00.011-0.00427.209-0.011-0.0110.0000.0000.0000.000
153A153SER0-0.091-0.05429.577-0.012-0.0120.0000.0000.0000.000
154A154MET0-0.046-0.01731.418-0.004-0.0040.0000.0000.0000.000
155A155LEU00.0100.00925.990-0.004-0.0040.0000.0000.0000.000
156A156ASN0-0.024-0.02325.490-0.031-0.0310.0000.0000.0000.000
157A157TRP00.0140.00827.402-0.011-0.0110.0000.0000.0000.000
158A158MET0-0.0180.01225.7520.0010.0010.0000.0000.0000.000
159A159ILE00.008-0.00523.756-0.004-0.0040.0000.0000.0000.000
160A160ARG10.8580.92926.0090.1680.1680.0000.0000.0000.000
161A161TRP0-0.023-0.00128.8480.0080.0080.0000.0000.0000.000
162A162PHE0-0.0150.01122.3430.0060.0060.0000.0000.0000.000
163A163ARG10.8950.93725.6410.1200.1200.0000.0000.0000.000
164A164PRO00.0170.00120.4010.0100.0100.0000.0000.0000.000
165A165ASP-1-0.873-0.92522.420-0.146-0.1460.0000.0000.0000.000
166A166GLY00.0230.02824.9920.0150.0150.0000.0000.0000.000
167A167PRO0-0.023-0.02224.992-0.009-0.0090.0000.0000.0000.000
168A168MET0-0.045-0.02526.1150.0030.0030.0000.0000.0000.000
169A169ARG10.8340.90619.1670.1690.1690.0000.0000.0000.000
170A170ALA00.0390.01022.4110.0130.0130.0000.0000.0000.000
171A171GLU-1-0.789-0.86721.278-0.141-0.1410.0000.0000.0000.000
172A172GLU-1-0.810-0.89024.240-0.076-0.0760.0000.0000.0000.000
173A173VAL0-0.018-0.00327.4080.0090.0090.0000.0000.0000.000
174A174ALA00.0140.00826.2780.0060.0060.0000.0000.0000.000
175A175ARG10.7600.83725.8910.0930.0930.0000.0000.0000.000
176A176ALA0-0.015-0.00229.9080.0080.0080.0000.0000.0000.000
177A177TYR00.004-0.02329.8720.0020.0020.0000.0000.0000.000
178A178HIS0-0.024-0.01230.7800.0040.0040.0000.0000.0000.000
179A179ASP-1-0.822-0.90032.802-0.050-0.0500.0000.0000.0000.000
180A180LEU0-0.002-0.00335.7880.0040.0040.0000.0000.0000.000
181A181ILE0-0.061-0.03734.0380.0030.0030.0000.0000.0000.000
182A182LEU0-0.045-0.01335.7390.0030.0030.0000.0000.0000.000
183A183ARG10.8120.88937.8980.0520.0520.0000.0000.0000.000
184A184GLY00.0220.02940.5010.0030.0030.0000.0000.0000.000
185A185LEU0-0.021-0.02741.8000.0000.0000.0000.0000.0000.000
186A186GLU-1-0.956-0.95944.229-0.043-0.0430.0000.0000.0000.000
187A187ARG10.9380.96346.8460.0310.0310.0000.0000.0000.000
188A188GLY00.0190.01148.0970.0020.0020.0000.0000.0000.000
189A189SER0-0.036-0.01445.8280.0030.0030.0000.0000.0000.000