FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 89MVY

Calculation Name: 4AE7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AE7

Chain ID: A

ChEMBL ID:

UniProt ID: Q8N1Q8

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:

Apendix: None


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 186
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2044087.276381
FMO2-HF: Nuclear repulsion 1969307.005874
FMO2-HF: Total energy -74780.270507
FMO2-MP2: Total energy -74994.722048


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:52:LEU)


Summations of interaction energy for fragment #1(A:52:LEU)
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.
-6.26-3.2351.681-1.688-3.018-0.004
Interaction energy analysis for fragmet #1(A:52:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.014
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].
3A54ASP-1-0.711-0.8413.6270.3011.9000.004-0.618-0.9850.004
4A55TYR0-0.030-0.0545.746-0.227-0.2270.0000.0000.0000.000
5A56ALA0-0.0090.0198.951-0.032-0.0320.0000.0000.0000.000
6A57LEU0-0.036-0.0159.055-0.144-0.1440.0000.0000.0000.000
7A58PRO00.0260.01112.3180.0620.0620.0000.0000.0000.000
8A59ASN0-0.041-0.00313.505-0.034-0.0340.0000.0000.0000.000
9A60ALA00.0110.00315.466-0.003-0.0030.0000.0000.0000.000
10A61SER0-0.014-0.00717.3540.0070.0070.0000.0000.0000.000
11A62TRP0-0.065-0.03314.486-0.030-0.0300.0000.0000.0000.000
12A63CYS0-0.0010.01320.468-0.020-0.0200.0000.0000.0000.000
13A64SER00.045-0.00623.771-0.007-0.0070.0000.0000.0000.000
14A65ASP-1-0.815-0.91625.6360.0070.0070.0000.0000.0000.000
15A66MET0-0.0200.00017.735-0.005-0.0050.0000.0000.0000.000
16A67LEU00.0100.00819.893-0.013-0.0130.0000.0000.0000.000
17A68SER0-0.031-0.00722.028-0.016-0.0160.0000.0000.0000.000
18A69LEU00.0250.00723.161-0.010-0.0100.0000.0000.0000.000
19A70TYR00.0360.00114.713-0.012-0.0120.0000.0000.0000.000
20A71GLN00.0220.00519.962-0.030-0.0300.0000.0000.0000.000
21A72GLU-1-0.827-0.88821.774-0.035-0.0350.0000.0000.0000.000
22A73PHE00.020-0.01719.760-0.003-0.0030.0000.0000.0000.000
23A74LEU0-0.0130.00615.686-0.018-0.0180.0000.0000.0000.000
24A75GLU-1-0.802-0.87619.431-0.167-0.1670.0000.0000.0000.000
25A76LYS10.8460.92622.2290.0370.0370.0000.0000.0000.000
26A77THR0-0.123-0.08416.859-0.009-0.0090.0000.0000.0000.000
27A78LYS10.7770.89419.6250.1650.1650.0000.0000.0000.000
28A79SER0-0.015-0.00722.0990.0020.0020.0000.0000.0000.000
29A80SER0-0.041-0.02123.8900.0130.0130.0000.0000.0000.000
30A81GLY00.0140.01322.3720.0120.0120.0000.0000.0000.000
31A82TRP0-0.016-0.00519.8650.0040.0040.0000.0000.0000.000
32A83ILE00.0070.00614.638-0.028-0.0280.0000.0000.0000.000
33A84LYS10.7770.8689.5030.2910.2910.0000.0000.0000.000
34A85LEU0-0.017-0.00111.462-0.068-0.0680.0000.0000.0000.000
35A86PRO0-0.0100.0115.9660.0000.0000.0000.0000.0000.000
36A87SER0-0.0020.0067.4850.2280.2280.0000.0000.0000.000
37A88PHE00.0340.0142.472-1.2630.0571.678-1.063-1.935-0.008
38A89LYS11.0140.9984.860-3.096-3.0960.0000.0000.0000.000
39A90SER00.0230.0057.134-0.586-0.5860.0000.0000.0000.000
40A91ASN00.1030.0447.9280.3960.3960.0000.0000.0000.000
41A92ARG10.9170.9749.150-1.018-1.0180.0000.0000.0000.000
42A93ASP-1-0.888-0.9497.3481.1441.1440.0000.0000.0000.000
43A94HIS10.7870.8834.101-2.555-2.449-0.001-0.007-0.0980.000
44A95ILE00.0330.0238.989-0.061-0.0610.0000.0000.0000.000
45A96ARG10.9420.96312.7290.0700.0700.0000.0000.0000.000
46A97GLY00.0460.02413.995-0.019-0.0190.0000.0000.0000.000
47A98LEU0-0.0100.01715.795-0.005-0.0050.0000.0000.0000.000
48A99LYS10.8430.90017.667-0.091-0.0910.0000.0000.0000.000
49A100LEU0-0.010-0.00417.7320.0020.0020.0000.0000.0000.000
50A101PRO0-0.020-0.00921.647-0.008-0.0080.0000.0000.0000.000
51A112ASP-1-0.858-0.91910.9320.9870.9870.0000.0000.0000.000
52A113CYS0-0.045-0.03311.776-0.113-0.1130.0000.0000.0000.000
53A114ARG10.8350.90710.329-0.635-0.6350.0000.0000.0000.000
54A115ILE0-0.019-0.00710.685-0.151-0.1510.0000.0000.0000.000
55A116PHE00.0670.03313.0000.0100.0100.0000.0000.0000.000
56A117THR00.0800.04214.4380.0300.0300.0000.0000.0000.000
57A118ARG10.8360.91310.125-0.627-0.6270.0000.0000.0000.000
58A119CYS0-0.039-0.01912.1250.0850.0850.0000.0000.0000.000
59A120ILE00.0180.02114.665-0.003-0.0030.0000.0000.0000.000
60A121GLN0-0.014-0.0198.2460.1710.1710.0000.0000.0000.000
61A122VAL0-0.0180.00012.580-0.025-0.0250.0000.0000.0000.000
62A123GLU-1-0.848-0.93414.1590.0930.0930.0000.0000.0000.000
63A124GLY00.026-0.00715.675-0.028-0.0280.0000.0000.0000.000
64A125GLN0-0.0160.00118.427-0.017-0.0170.0000.0000.0000.000
65A126GLY00.0290.00717.686-0.002-0.0020.0000.0000.0000.000
66A127PHE0-0.035-0.02216.339-0.037-0.0370.0000.0000.0000.000
67A128GLU-1-0.770-0.84415.5200.3220.3220.0000.0000.0000.000
68A129TYR0-0.015-0.04512.607-0.006-0.0060.0000.0000.0000.000
69A130VAL0-0.001-0.00113.4440.0290.0290.0000.0000.0000.000
70A131ILE00.0190.01913.940-0.004-0.0040.0000.0000.0000.000
71A132PHE00.0030.00414.739-0.039-0.0390.0000.0000.0000.000
72A133PHE00.0650.00916.8750.0280.0280.0000.0000.0000.000
73A134GLN00.0400.01918.555-0.023-0.0230.0000.0000.0000.000
74A135PRO00.0310.00319.1280.0150.0150.0000.0000.0000.000
75A136THR0-0.040-0.01921.7800.0060.0060.0000.0000.0000.000
76A137GLN0-0.031-0.02225.1470.0120.0120.0000.0000.0000.000
77A138LYS10.8700.94323.349-0.005-0.0050.0000.0000.0000.000
78A139LYS10.8820.93123.475-0.012-0.0120.0000.0000.0000.000
79A140SER0-0.053-0.05019.256-0.011-0.0110.0000.0000.0000.000
80A141VAL00.0150.01820.1290.0020.0020.0000.0000.0000.000
81A142CYS0-0.061-0.01318.2850.0010.0010.0000.0000.0000.000
82A143LEU0-0.024-0.00118.585-0.009-0.0090.0000.0000.0000.000
83A144PHE00.067-0.00118.4920.0260.0260.0000.0000.0000.000
84A145GLN00.0950.05219.909-0.036-0.0360.0000.0000.0000.000
85A146PRO0-0.061-0.01920.7870.0260.0260.0000.0000.0000.000
86A147GLY00.1230.06621.398-0.022-0.0220.0000.0000.0000.000
87A148SER00.0330.00622.6010.0080.0080.0000.0000.0000.000
88A149TYR0-0.076-0.04019.9130.0090.0090.0000.0000.0000.000
89A150LEU0-0.087-0.03820.2260.0170.0170.0000.0000.0000.000
90A151GLU-1-0.798-0.88824.1910.1170.1170.0000.0000.0000.000
91A152GLY0-0.031-0.02927.9230.0100.0100.0000.0000.0000.000
92A153PRO0-0.081-0.01930.873-0.003-0.0030.0000.0000.0000.000
93A154PRO00.043-0.00432.5930.0030.0030.0000.0000.0000.000
94A155GLY00.0090.01631.607-0.008-0.0080.0000.0000.0000.000
95A156PHE0-0.027-0.02630.715-0.005-0.0050.0000.0000.0000.000
96A157ALA00.0250.01926.3230.0090.0090.0000.0000.0000.000
97A158HIS00.0360.02026.990-0.010-0.0100.0000.0000.0000.000
98A159GLY00.0410.02727.4580.0070.0070.0000.0000.0000.000
99A160GLY00.001-0.01727.1410.0030.0030.0000.0000.0000.000
100A161SER0-0.040-0.02823.1570.0190.0190.0000.0000.0000.000
101A162LEU00.0560.01922.8160.0150.0150.0000.0000.0000.000
102A163ALA0-0.007-0.01124.1380.0020.0020.0000.0000.0000.000
103A164ALA00.0050.00920.6870.0060.0060.0000.0000.0000.000
104A165MET0-0.0030.01116.1220.0270.0270.0000.0000.0000.000
105A166MET0-0.0170.02919.971-0.005-0.0050.0000.0000.0000.000
106A167ASP-1-0.835-0.89821.3440.2520.2520.0000.0000.0000.000
107A168GLU-1-0.801-0.88013.5700.5440.5440.0000.0000.0000.000
108A169THR0-0.019-0.03217.1790.0000.0000.0000.0000.0000.000
109A170PHE0-0.022-0.00318.644-0.023-0.0230.0000.0000.0000.000
110A171SER00.0120.01917.429-0.010-0.0100.0000.0000.0000.000
111A172LYS10.7980.87311.619-0.577-0.5770.0000.0000.0000.000
112A173THR00.002-0.00316.157-0.042-0.0420.0000.0000.0000.000
113A174ALA00.0230.00219.140-0.025-0.0250.0000.0000.0000.000
114A175PHE0-0.0200.00714.352-0.011-0.0110.0000.0000.0000.000
115A176LEU0-0.010-0.01013.982-0.027-0.0270.0000.0000.0000.000
116A177ALA0-0.054-0.01918.000-0.025-0.0250.0000.0000.0000.000
117A178GLY00.0200.00321.530-0.016-0.0160.0000.0000.0000.000
118A179GLU-1-0.912-0.93119.7520.0660.0660.0000.0000.0000.000
119A180GLY00.0080.00020.9620.0060.0060.0000.0000.0000.000
120A181LEU0-0.050-0.03716.5980.0230.0230.0000.0000.0000.000
121A182PHE00.0000.00220.5330.0190.0190.0000.0000.0000.000
122A183THR00.012-0.00322.961-0.018-0.0180.0000.0000.0000.000
123A184LEU0-0.042-0.01724.756-0.002-0.0020.0000.0000.0000.000
124A185SER0-0.043-0.03228.287-0.007-0.0070.0000.0000.0000.000
125A186LEU00.0560.02825.3130.0010.0010.0000.0000.0000.000
126A187ASN0-0.031-0.00628.888-0.002-0.0020.0000.0000.0000.000
127A188ILE00.0520.01627.426-0.004-0.0040.0000.0000.0000.000
128A189ARG10.8490.93631.611-0.087-0.0870.0000.0000.0000.000
129A190PHE00.0480.01029.344-0.002-0.0020.0000.0000.0000.000
130A191LYS10.8430.91233.916-0.070-0.0700.0000.0000.0000.000
131A192ASN00.0030.00034.135-0.006-0.0060.0000.0000.0000.000
132A193LEU00.0100.01632.7800.0060.0060.0000.0000.0000.000
133A194ILE00.0180.00526.747-0.006-0.0060.0000.0000.0000.000
134A195PRO00.0120.01730.0240.0080.0080.0000.0000.0000.000
135A196VAL0-0.0010.01825.8770.0040.0040.0000.0000.0000.000
136A197ASP-1-0.896-0.95024.1590.1160.1160.0000.0000.0000.000
137A198SER0-0.101-0.05725.739-0.016-0.0160.0000.0000.0000.000
138A199LEU0-0.013-0.02122.7550.0120.0120.0000.0000.0000.000
139A200VAL0-0.052-0.02824.007-0.008-0.0080.0000.0000.0000.000
140A201VAL00.004-0.00423.3820.0070.0070.0000.0000.0000.000
141A202MET0-0.051-0.02822.3790.0050.0050.0000.0000.0000.000
142A203ASP-1-0.786-0.86623.1510.0430.0430.0000.0000.0000.000
143A204VAL00.002-0.01522.3720.0080.0080.0000.0000.0000.000
144A205GLU-1-0.870-0.91424.6580.0240.0240.0000.0000.0000.000
145A206VAL0-0.001-0.01224.3370.0100.0100.0000.0000.0000.000
146A207ASP-1-0.889-0.92327.0280.0490.0490.0000.0000.0000.000
147A208LYS10.7900.87330.161-0.059-0.0590.0000.0000.0000.000
148A209ILE0-0.002-0.00626.4020.0080.0080.0000.0000.0000.000
149A210GLU-1-0.772-0.85130.3020.0450.0450.0000.0000.0000.000
150A211ASP-1-0.894-0.95132.4690.0580.0580.0000.0000.0000.000
151A212GLN00.0050.01029.4750.0090.0090.0000.0000.0000.000
152A213LYS10.8770.94828.425-0.063-0.0630.0000.0000.0000.000
153A214LEU0-0.0030.01023.802-0.010-0.0100.0000.0000.0000.000
154A215TYR0-0.089-0.06527.5220.0140.0140.0000.0000.0000.000
155A216MET0-0.0040.01623.042-0.007-0.0070.0000.0000.0000.000
156A217SER0-0.019-0.01727.6540.0050.0050.0000.0000.0000.000
157A218CYS0-0.018-0.00625.4130.0030.0030.0000.0000.0000.000
158A219ILE0-0.045-0.01927.632-0.001-0.0010.0000.0000.0000.000
159A220ALA00.0340.02126.7260.0000.0000.0000.0000.0000.000
160A221HIS10.7930.86227.872-0.048-0.0480.0000.0000.0000.000
161A222SER00.0680.01928.1980.0050.0050.0000.0000.0000.000
162A223ARG10.8800.93027.3220.0030.0030.0000.0000.0000.000
163A224ASP-1-0.812-0.87729.3820.0280.0280.0000.0000.0000.000
164A225GLN0-0.077-0.04631.6640.0000.0000.0000.0000.0000.000
165A226GLN0-0.040-0.01733.6130.0000.0000.0000.0000.0000.000
166A227THR0-0.0120.00533.3500.0020.0020.0000.0000.0000.000
167A228VAL0-0.015-0.00332.6110.0020.0020.0000.0000.0000.000
168A229TYR00.0460.01428.8700.0000.0000.0000.0000.0000.000
169A230ALA00.0080.00129.5120.0040.0040.0000.0000.0000.000
170A231LYS10.9260.97530.675-0.060-0.0600.0000.0000.0000.000
171A232SER0-0.014-0.05527.2330.0010.0010.0000.0000.0000.000
172A233SER00.0110.00229.504-0.009-0.0090.0000.0000.0000.000
173A234GLY00.0230.02026.7680.0090.0090.0000.0000.0000.000
174A235VAL0-0.045-0.01027.833-0.011-0.0110.0000.0000.0000.000
175A236PHE00.0280.01021.1820.0060.0060.0000.0000.0000.000
176A237LEU00.0030.00325.551-0.016-0.0160.0000.0000.0000.000
177A238GLN0-0.026-0.03124.3260.0100.0100.0000.0000.0000.000
178A239LEU0-0.042-0.02419.0700.0070.0070.0000.0000.0000.000
179A240GLN00.0150.01223.717-0.018-0.0180.0000.0000.0000.000
180A241LEU0-0.0110.00123.0240.0070.0070.0000.0000.0000.000
181A242GLU-1-0.888-0.94025.0350.0990.0990.0000.0000.0000.000
182A243GLU-1-0.972-0.97825.8060.0180.0180.0000.0000.0000.000
183A244GLU-1-0.886-0.92224.7710.0920.0920.0000.0000.0000.000
184A245SER0-0.031-0.02028.101-0.009-0.0090.0000.0000.0000.000
185A246PRO0-0.025-0.01026.9680.0050.0050.0000.0000.0000.000
186A247GLN00.0130.00522.3750.0050.0050.0000.0000.0000.000