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: N9N1Q

Calculation Name: 5VYM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5VYM

Chain ID: A

ChEMBL ID:

UniProt ID: A1A399

Base Structure: X-ray

Registration Date: 2023-06-21

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2309060.605991
FMO2-HF: Nuclear repulsion 2224281.426944
FMO2-HF: Total energy -84779.179047
FMO2-MP2: Total energy -85030.256233


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:0:ALA)


Summations of interaction energy for fragment #1(A:0:ALA)
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.
-3.895-1.846-0.012-1.257-0.780.003
Interaction energy analysis for fragmet #1(A:0:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : 0.003
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].
3A2SER0-0.049-0.0493.734-1.7010.348-0.012-1.257-0.7800.003
4A3ASP-1-0.760-0.8636.479-0.891-0.8910.0000.0000.0000.000
5A4THR0-0.074-0.0378.1810.3350.3350.0000.0000.0000.000
6A5ALA00.0010.01510.594-0.197-0.1970.0000.0000.0000.000
7A6ILE0-0.020-0.01212.3250.1230.1230.0000.0000.0000.000
8A7LEU00.0250.00514.542-0.033-0.0330.0000.0000.0000.000
9A8PHE0-0.020-0.01117.2120.0540.0540.0000.0000.0000.000
10A9SER00.0440.02419.2780.0100.0100.0000.0000.0000.000
11A10ALA00.007-0.00822.2830.0110.0110.0000.0000.0000.000
12A11GLU-1-0.822-0.91624.019-0.166-0.1660.0000.0000.0000.000
13A12SER00.0230.01525.3940.0160.0160.0000.0000.0000.000
14A13GLU-1-0.816-0.88325.255-0.211-0.2110.0000.0000.0000.000
15A14TRP0-0.076-0.03127.2230.0110.0110.0000.0000.0000.000
16A15ALA00.0250.01229.9000.0100.0100.0000.0000.0000.000
17A16THR0-0.061-0.04229.2170.0040.0040.0000.0000.0000.000
18A17ARG10.8000.90427.2990.1920.1920.0000.0000.0000.000
19A18SER00.002-0.01332.5290.0110.0110.0000.0000.0000.000
20A19GLN00.0190.00835.9360.0040.0040.0000.0000.0000.000
21A20THR00.0770.04935.2270.0090.0090.0000.0000.0000.000
22A21LEU00.007-0.02438.652-0.002-0.0020.0000.0000.0000.000
23A22PRO0-0.0040.00940.527-0.001-0.0010.0000.0000.0000.000
24A23SER0-0.011-0.03135.841-0.001-0.0010.0000.0000.0000.000
25A24MET00.0170.02435.736-0.008-0.0080.0000.0000.0000.000
26A25LYS10.7850.91935.7800.1110.1110.0000.0000.0000.000
27A26LEU00.0350.02031.270-0.006-0.0060.0000.0000.0000.000
28A27ASN00.003-0.01628.241-0.007-0.0070.0000.0000.0000.000
29A28HIS00.0360.04521.940-0.024-0.0240.0000.0000.0000.000
30A29TRP00.0270.00219.417-0.028-0.0280.0000.0000.0000.000
31A30HIS0-0.022-0.01623.569-0.022-0.0220.0000.0000.0000.000
32A31ASP-1-0.774-0.86224.737-0.271-0.2710.0000.0000.0000.000
33A32VAL0-0.001-0.00118.831-0.025-0.0250.0000.0000.0000.000
34A33ARG10.7720.86019.9430.2190.2190.0000.0000.0000.000
35A34ASP-1-0.787-0.86721.065-0.283-0.2830.0000.0000.0000.000
36A35TRP00.0320.01519.691-0.010-0.0100.0000.0000.0000.000
37A36TYR0-0.027-0.01213.568-0.051-0.0510.0000.0000.0000.000
38A37ARG10.8380.90617.3920.2550.2550.0000.0000.0000.000
39A38ALA00.0420.03219.540-0.003-0.0030.0000.0000.0000.000
40A39PHE00.005-0.01014.9760.0050.0050.0000.0000.0000.000
41A40LEU0-0.078-0.03814.734-0.040-0.0400.0000.0000.0000.000
42A41ASP-1-0.907-0.95716.283-0.310-0.3100.0000.0000.0000.000
43A42ALA0-0.071-0.02317.8400.0340.0340.0000.0000.0000.000
44A43GLY0-0.023-0.01015.6390.0060.0060.0000.0000.0000.000
45A44SER0-0.066-0.03512.676-0.041-0.0410.0000.0000.0000.000
46A45ARG10.8260.8987.6891.6121.6120.0000.0000.0000.000
47A46ALA00.0450.06310.489-0.240-0.2400.0000.0000.0000.000
48A47ASP-1-0.741-0.8517.609-2.547-2.5470.0000.0000.0000.000
49A48ILE0-0.034-0.02011.1640.1560.1560.0000.0000.0000.000
50A49VAL0-0.0020.00410.551-0.061-0.0610.0000.0000.0000.000
51A50PRO0-0.017-0.00113.4850.0600.0600.0000.0000.0000.000
52A51LEU00.0390.01915.731-0.020-0.0200.0000.0000.0000.000
53A52ALA00.0690.03917.7680.0040.0040.0000.0000.0000.000
54A53TYR0-0.057-0.02412.2450.0200.0200.0000.0000.0000.000
55A54ASP-1-0.772-0.86211.781-0.306-0.3060.0000.0000.0000.000
56A55TRP0-0.042-0.05210.297-0.120-0.1200.0000.0000.0000.000
57A56SER0-0.053-0.04811.049-0.058-0.0580.0000.0000.0000.000
58A57SER0-0.021-0.0125.8780.1340.1340.0000.0000.0000.000
59A58TYR0-0.084-0.0557.556-0.103-0.1030.0000.0000.0000.000
60A59LYS10.8850.9208.6470.7200.7200.0000.0000.0000.000
61A60THR0-0.079-0.03111.8300.1260.1260.0000.0000.0000.000
62A61VAL00.0380.03812.898-0.132-0.1320.0000.0000.0000.000
63A62VAL00.0080.00315.2940.0640.0640.0000.0000.0000.000
64A63LEU00.0380.02018.202-0.024-0.0240.0000.0000.0000.000
65A64PRO0-0.0060.02720.2270.0350.0350.0000.0000.0000.000
66A65THR00.028-0.04123.3390.0030.0030.0000.0000.0000.000
67A66VAL0-0.047-0.01021.6490.0010.0010.0000.0000.0000.000
68A67LEU00.0340.00425.0620.0100.0100.0000.0000.0000.000
69A68ILE0-0.039-0.00827.3100.0110.0110.0000.0000.0000.000
70A69LEU0-0.015-0.02422.995-0.022-0.0220.0000.0000.0000.000
71A70SER00.0620.02224.6360.0160.0160.0000.0000.0000.000
72A71ALA00.0510.03026.478-0.007-0.0070.0000.0000.0000.000
73A72ALA00.0700.04424.556-0.002-0.0020.0000.0000.0000.000
74A73ASP-1-0.846-0.90621.152-0.222-0.2220.0000.0000.0000.000
75A74THR0-0.056-0.04722.030-0.017-0.0170.0000.0000.0000.000
76A75GLN0-0.025-0.02023.9770.0010.0010.0000.0000.0000.000
77A76ARG10.8610.91715.9540.2700.2700.0000.0000.0000.000
78A77LEU0-0.048-0.02918.528-0.020-0.0200.0000.0000.0000.000
79A78ALA00.0320.00320.425-0.005-0.0050.0000.0000.0000.000
80A79ASP-1-0.781-0.87120.043-0.113-0.1130.0000.0000.0000.000
81A80PHE0-0.069-0.03112.6410.0100.0100.0000.0000.0000.000
82A81ALA0-0.009-0.01017.780-0.002-0.0020.0000.0000.0000.000
83A82ALA0-0.042-0.01020.1630.0110.0110.0000.0000.0000.000
84A83ALA0-0.042-0.01517.0650.0200.0200.0000.0000.0000.000
85A84GLY0-0.037-0.01217.6960.0140.0140.0000.0000.0000.000
86A85GLY0-0.0240.00015.488-0.022-0.0220.0000.0000.0000.000
87A86ARG10.8730.90714.8660.4170.4170.0000.0000.0000.000
88A87VAL00.0560.02517.010-0.060-0.0600.0000.0000.0000.000
89A88VAL0-0.046-0.02318.8510.0250.0250.0000.0000.0000.000
90A89VAL00.0390.01521.074-0.021-0.0210.0000.0000.0000.000
91A90GLY0-0.0070.00223.8950.0100.0100.0000.0000.0000.000
92A91TYR00.026-0.00426.1520.0140.0140.0000.0000.0000.000
93A92ALA00.0210.01929.0190.0130.0130.0000.0000.0000.000
94A93THR0-0.058-0.03324.314-0.003-0.0030.0000.0000.0000.000
95A94GLY00.0090.00827.4770.0090.0090.0000.0000.0000.000
96A95LEU0-0.037-0.02628.4830.0120.0120.0000.0000.0000.000
97A96ILE0-0.035-0.00130.9290.0090.0090.0000.0000.0000.000
98A97ASP-1-0.756-0.86930.253-0.119-0.1190.0000.0000.0000.000
99A98GLU-1-0.841-0.95828.209-0.127-0.1270.0000.0000.0000.000
100A99HIS0-0.091-0.03430.0010.0030.0030.0000.0000.0000.000
101A100PHE0-0.105-0.05830.6900.0040.0040.0000.0000.0000.000
102A101HIS00.0180.01734.3660.0040.0040.0000.0000.0000.000
103A102THR0-0.056-0.03334.948-0.007-0.0070.0000.0000.0000.000
104A103TRP0-0.0130.00029.9680.0080.0080.0000.0000.0000.000
105A104LEU00.0020.00935.1440.0010.0010.0000.0000.0000.000
106A105GLY00.0380.01936.971-0.003-0.0030.0000.0000.0000.000
107A106GLY0-0.009-0.00337.9960.0010.0010.0000.0000.0000.000
108A107TYR0-0.056-0.02531.884-0.005-0.0050.0000.0000.0000.000
109A108PRO00.013-0.01829.8770.0040.0040.0000.0000.0000.000
110A109GLY00.0580.00732.2260.0060.0060.0000.0000.0000.000
111A110ALA0-0.0060.00327.9000.0050.0050.0000.0000.0000.000
112A111GLY00.0280.00529.4900.0000.0000.0000.0000.0000.000
113A112ASP-1-0.868-0.93030.290-0.079-0.0790.0000.0000.0000.000
114A113GLY0-0.010-0.01132.1440.0060.0060.0000.0000.0000.000
115A114LEU0-0.0230.01526.522-0.002-0.0020.0000.0000.0000.000
116A115LEU00.035-0.00424.649-0.007-0.0070.0000.0000.0000.000
117A116ARG10.7710.89827.9220.0960.0960.0000.0000.0000.000
118A117SER0-0.007-0.01730.664-0.002-0.0020.0000.0000.0000.000
119A118MET0-0.0460.00122.3550.0020.0020.0000.0000.0000.000
120A119LEU0-0.031-0.01225.168-0.007-0.0070.0000.0000.0000.000
121A120GLY0-0.0240.00028.1530.0020.0020.0000.0000.0000.000
122A121VAL0-0.076-0.03630.9070.0070.0070.0000.0000.0000.000
123A122ARG10.8530.87933.4360.0770.0770.0000.0000.0000.000
124A123GLY0-0.0200.00835.9190.0020.0020.0000.0000.0000.000
125A124GLU-1-0.817-0.88938.012-0.076-0.0760.0000.0000.0000.000
126A125GLU-1-0.822-0.88339.373-0.083-0.0830.0000.0000.0000.000
127A126PHE00.0080.00133.498-0.006-0.0060.0000.0000.0000.000
128A127ASN0-0.061-0.03437.293-0.002-0.0020.0000.0000.0000.000
129A128ILE0-0.044-0.00934.299-0.004-0.0040.0000.0000.0000.000
130A129LEU0-0.061-0.04938.1980.0010.0010.0000.0000.0000.000
131A130GLY00.0270.02941.0980.0040.0040.0000.0000.0000.000
132A131ALA00.1520.14641.559-0.002-0.0020.0000.0000.0000.000
133A132GLU-1-0.620-0.66739.734-0.093-0.0930.0000.0000.0000.000
134A133ALA0-0.0150.00741.4190.0080.0080.0000.0000.0000.000
135A134GLU-1-0.885-0.92242.305-0.049-0.0490.0000.0000.0000.000
136A135GLY0-0.034-0.01044.5640.0060.0060.0000.0000.0000.000
137A136GLU-1-1.162-1.24446.820-0.025-0.0250.0000.0000.0000.000
138A137PRO0-0.168-0.17449.6590.0020.0020.0000.0000.0000.000
139A138GLY0-0.098-0.12552.6010.0010.0010.0000.0000.0000.000
140A139GLU-1-0.856-0.91553.744-0.013-0.0130.0000.0000.0000.000
141A140ILE0-0.0020.01350.6200.0010.0010.0000.0000.0000.000
142A141ARG10.7800.85652.7760.0100.0100.0000.0000.0000.000
143A142LEU00.010-0.00546.795-0.001-0.0010.0000.0000.0000.000
144A143SER0-0.056-0.04446.8040.0020.0020.0000.0000.0000.000
145A144SER0-0.008-0.01442.995-0.002-0.0020.0000.0000.0000.000
146A145ALA0-0.024-0.00839.5870.0000.0000.0000.0000.0000.000
147A146ASP-1-0.794-0.86237.704-0.005-0.0050.0000.0000.0000.000
148A147ASP-1-0.926-0.97437.5330.0070.0070.0000.0000.0000.000
149A148SER0-0.114-0.08040.4320.0020.0020.0000.0000.0000.000
150A149ALA0-0.008-0.00342.2100.0010.0010.0000.0000.0000.000
151A150ALA0-0.020-0.00144.2170.0000.0000.0000.0000.0000.000
152A151LEU00.002-0.01843.9050.0000.0000.0000.0000.0000.000
153A152ASP-1-0.750-0.83047.075-0.005-0.0050.0000.0000.0000.000
154A153GLY0-0.085-0.05049.0820.0010.0010.0000.0000.0000.000
155A154THR0-0.068-0.02649.531-0.001-0.0010.0000.0000.0000.000
156A155THR0-0.035-0.01752.277-0.001-0.0010.0000.0000.0000.000
157A156THR00.004-0.01050.9620.0000.0000.0000.0000.0000.000
158A157ARG10.8040.84453.8150.0130.0130.0000.0000.0000.000
159A158LEU0-0.024-0.00653.7050.0000.0000.0000.0000.0000.000
160A159TRP0-0.0770.00949.7380.0020.0020.0000.0000.0000.000
161A160GLN0-0.0140.00645.7340.0010.0010.0000.0000.0000.000
162A161ASN00.0270.00747.7350.0020.0020.0000.0000.0000.000
163A162ASP-1-0.864-0.90044.817-0.044-0.0440.0000.0000.0000.000
164A163VAL0-0.015-0.01441.093-0.001-0.0010.0000.0000.0000.000
165A164ASN0-0.024-0.00839.2840.0020.0020.0000.0000.0000.000
166A165VAL0-0.003-0.00234.479-0.003-0.0030.0000.0000.0000.000
167A166THR0-0.007-0.01233.711-0.001-0.0010.0000.0000.0000.000
168A167GLY0-0.0170.00530.225-0.007-0.0070.0000.0000.0000.000
169A168GLU-1-0.941-0.98124.529-0.082-0.0820.0000.0000.0000.000
170A169HIS0-0.081-0.05323.1460.0180.0180.0000.0000.0000.000
171A170ALA0-0.017-0.00828.3280.0070.0070.0000.0000.0000.000
172A171GLN00.0180.03132.1640.0030.0030.0000.0000.0000.000
173A172VAL00.0320.00333.6640.0000.0000.0000.0000.0000.000
174A173LEU0-0.061-0.03236.4750.0030.0030.0000.0000.0000.000
175A174ALA0-0.003-0.00739.4810.0030.0030.0000.0000.0000.000
176A175THR0-0.015-0.00142.049-0.003-0.0030.0000.0000.0000.000
177A176TYR00.018-0.00644.5540.0030.0030.0000.0000.0000.000
178A177ALA00.002-0.00547.612-0.001-0.0010.0000.0000.0000.000
179A178GLY0-0.0080.00149.6230.0010.0010.0000.0000.0000.000
180A179GLU-1-0.936-0.97652.961-0.010-0.0100.0000.0000.0000.000
181A180GLU-1-0.784-0.86556.107-0.012-0.0120.0000.0000.0000.000
182A181ALA0-0.014-0.00450.784-0.001-0.0010.0000.0000.0000.000
183A182ASP-1-0.949-0.97352.413-0.019-0.0190.0000.0000.0000.000
184A183GLU-1-1.013-1.01153.446-0.015-0.0150.0000.0000.0000.000
185A184TRP0-0.085-0.04353.0280.0000.0000.0000.0000.0000.000
186A185GLU-1-1.005-0.99750.712-0.028-0.0280.0000.0000.0000.000
187A186LEU0-0.029-0.01547.663-0.002-0.0020.0000.0000.0000.000
188A187ASP-1-0.871-0.94447.910-0.016-0.0160.0000.0000.0000.000
189A188GLY0-0.012-0.00344.715-0.001-0.0010.0000.0000.0000.000
190A189THR0-0.040-0.01143.067-0.002-0.0020.0000.0000.0000.000
191A190ALA0-0.037-0.02540.2010.0020.0020.0000.0000.0000.000
192A191ALA00.0250.02642.237-0.001-0.0010.0000.0000.0000.000
193A192VAL0-0.034-0.02641.0450.0000.0000.0000.0000.0000.000
194A193THR0-0.0100.00036.8420.0010.0010.0000.0000.0000.000
195A194ARG10.8510.93233.5940.0150.0150.0000.0000.0000.000
196A195ASN00.0360.01129.877-0.002-0.0020.0000.0000.0000.000
197A196PRO00.0170.01227.021-0.001-0.0010.0000.0000.0000.000
198A197TYR00.000-0.00128.217-0.011-0.0110.0000.0000.0000.000
199A198GLY00.0180.01525.6320.0040.0040.0000.0000.0000.000
200A199SER0-0.038-0.03124.2370.0010.0010.0000.0000.0000.000
201A200GLY0-0.019-0.00826.3250.0100.0100.0000.0000.0000.000
202A201GLU-1-0.859-0.90129.244-0.028-0.0280.0000.0000.0000.000
203A202ALA0-0.035-0.00631.9440.0010.0010.0000.0000.0000.000
204A203TYR0-0.019-0.04634.7930.0020.0020.0000.0000.0000.000
205A204PHE0-0.0190.00437.910-0.002-0.0020.0000.0000.0000.000
206A205VAL00.000-0.00940.5250.0020.0020.0000.0000.0000.000
207A206GLY00.0180.01744.051-0.001-0.0010.0000.0000.0000.000
208A207CYS0-0.045-0.02345.6940.0000.0000.0000.0000.0000.000
209A208ASP-1-0.930-0.94749.109-0.015-0.0150.0000.0000.0000.000
210A209LEU00.0320.01148.3870.0010.0010.0000.0000.0000.000
211A210ASP-1-0.788-0.88652.590-0.007-0.0070.0000.0000.0000.000
212A211VAL0-0.009-0.00753.4020.0000.0000.0000.0000.0000.000
213A212ALA0-0.054-0.01853.4460.0010.0010.0000.0000.0000.000
214A213ASP-1-0.753-0.91451.302-0.006-0.0060.0000.0000.0000.000
215A214LEU0-0.0010.00748.7290.0000.0000.0000.0000.0000.000
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