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: QY5ZY

Calculation Name: 3DMP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DMP

Chain ID: A

ChEMBL ID:

UniProt ID: Q63VS8

Base Structure: X-ray

Registration Date: 2023-06-26

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2486954.090103
FMO2-HF: Nuclear repulsion 2403794.068574
FMO2-HF: Total energy -83160.021529
FMO2-MP2: Total energy -83403.538498


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:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-15.999-9.9432.363-3.707-4.71-0.029
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.005
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].
3A2LYS10.9390.9973.8864.5346.299-0.017-0.894-0.8530.002
4A3GLN0-0.042-0.0316.1480.3190.3190.0000.0000.0000.000
5A4ASP-1-0.773-0.8629.910-0.994-0.9940.0000.0000.0000.000
6A5SER0-0.020-0.01213.2480.0470.0470.0000.0000.0000.000
7A6ARG10.8460.89716.2220.9320.9320.0000.0000.0000.000
8A7PHE0-0.0040.00415.2160.0530.0530.0000.0000.0000.000
9A8PRO00.0480.02314.684-0.157-0.1570.0000.0000.0000.000
10A9ASN00.003-0.01714.135-0.074-0.0740.0000.0000.0000.000
11A10LEU0-0.0100.01112.254-0.019-0.0190.0000.0000.0000.000
12A11PHE0-0.038-0.0208.271-0.062-0.0620.0000.0000.0000.000
13A12ILE00.004-0.0027.1410.1240.1240.0000.0000.0000.000
14A13LEU00.0040.0054.780-1.916-1.862-0.001-0.030-0.0230.000
15A14ASP-1-0.858-0.9412.452-16.713-14.7032.136-2.051-2.095-0.025
16A15HIS00.0580.0422.899-0.7500.6140.220-0.494-1.090-0.004
17A16PRO00.0450.0103.4710.3800.4940.0120.031-0.1560.000
18A17LEU0-0.006-0.0086.721-0.028-0.0280.0000.0000.0000.000
19A18ILE00.0120.0175.8300.1990.1990.0000.0000.0000.000
20A19GLN00.005-0.0155.3530.7450.7450.0000.0000.0000.000
21A20HIS0-0.0050.0199.0210.2160.2160.0000.0000.0000.000
22A21LYS10.8280.89311.5720.4050.4050.0000.0000.0000.000
23A22LEU00.0400.01711.3660.0900.0900.0000.0000.0000.000
24A23THR0-0.035-0.02812.7790.0930.0930.0000.0000.0000.000
25A24HIS0-0.054-0.03715.0680.1370.1370.0000.0000.0000.000
26A25MET0-0.0250.01515.4300.0700.0700.0000.0000.0000.000
27A26ARG10.7650.84513.4681.0421.0420.0000.0000.0000.000
28A27ASP-1-0.875-0.91518.806-0.285-0.2850.0000.0000.0000.000
29A28LYS10.8540.90821.5620.2510.2510.0000.0000.0000.000
30A29ASP-1-0.833-0.89624.866-0.215-0.2150.0000.0000.0000.000
31A30THR0-0.092-0.05420.7190.0420.0420.0000.0000.0000.000
32A31SER00.0390.01423.888-0.017-0.0170.0000.0000.0000.000
33A32THR00.0650.02224.982-0.007-0.0070.0000.0000.0000.000
34A33ARG10.9140.95925.5930.1270.1270.0000.0000.0000.000
35A34THR00.0180.00420.9710.0030.0030.0000.0000.0000.000
36A35PHE00.0240.01120.532-0.028-0.0280.0000.0000.0000.000
37A36ARG10.8480.91120.5020.2020.2020.0000.0000.0000.000
38A37GLU-1-0.872-0.91720.760-0.239-0.2390.0000.0000.0000.000
39A38LEU0-0.004-0.00416.484-0.012-0.0120.0000.0000.0000.000
40A39LEU00.0310.01615.689-0.097-0.0970.0000.0000.0000.000
41A40ARG10.8160.90816.1890.1780.1780.0000.0000.0000.000
42A41GLU-1-0.794-0.89014.676-0.277-0.2770.0000.0000.0000.000
43A42ILE00.000-0.00310.436-0.036-0.0360.0000.0000.0000.000
44A43THR0-0.021-0.03011.277-0.142-0.1420.0000.0000.0000.000
45A44LEU00.0030.02712.873-0.024-0.0240.0000.0000.0000.000
46A45LEU0-0.027-0.0218.5260.0530.0530.0000.0000.0000.000
47A46MET0-0.036-0.0167.919-0.153-0.1530.0000.0000.0000.000
48A47GLY00.0660.0268.976-0.060-0.0600.0000.0000.0000.000
49A48TYR0-0.0320.0027.3810.3060.3060.0000.0000.0000.000
50A49GLU-1-0.820-0.8883.6240.3130.9760.014-0.267-0.409-0.002
51A50ILE0-0.021-0.0106.5120.0840.0840.0000.0000.0000.000
52A51THR0-0.075-0.0609.3010.2570.2570.0000.0000.0000.000
53A52ARG10.8010.8704.659-1.558-1.472-0.001-0.002-0.0840.000
54A53ASN0-0.020-0.0028.8290.3100.3100.0000.0000.0000.000
55A54LEU0-0.0110.00112.115-0.054-0.0540.0000.0000.0000.000
56A55PRO0-0.019-0.01015.3280.0700.0700.0000.0000.0000.000
57A56ILE0-0.0210.00117.363-0.021-0.0210.0000.0000.0000.000
58A57THR0-0.046-0.02320.139-0.011-0.0110.0000.0000.0000.000
59A58THR0-0.013-0.02123.8300.0190.0190.0000.0000.0000.000
60A59LYS10.9340.96526.535-0.091-0.0910.0000.0000.0000.000
61A60ARG10.8070.88429.140-0.116-0.1160.0000.0000.0000.000
62A61VAL0-0.023-0.01728.826-0.011-0.0110.0000.0000.0000.000
63A62GLU-1-0.931-0.95132.0120.1030.1030.0000.0000.0000.000
64A63THR0-0.015-0.02330.7610.0000.0000.0000.0000.0000.000
65A64PRO0-0.013-0.03133.307-0.005-0.0050.0000.0000.0000.000
66A65LEU0-0.054-0.01433.895-0.002-0.0020.0000.0000.0000.000
67A66VAL0-0.0090.00333.815-0.004-0.0040.0000.0000.0000.000
68A67GLU-1-0.817-0.87634.3880.1170.1170.0000.0000.0000.000
69A68ILE0-0.016-0.01128.1390.0110.0110.0000.0000.0000.000
70A69ASP-1-0.795-0.88728.8820.1350.1350.0000.0000.0000.000
71A70ALA00.0030.01426.2700.0230.0230.0000.0000.0000.000
72A71PRO00.0270.00621.213-0.020-0.0200.0000.0000.0000.000
73A72VAL0-0.046-0.02222.384-0.009-0.0090.0000.0000.0000.000
74A73ILE00.0860.03516.8990.0060.0060.0000.0000.0000.000
75A74ALA00.0100.01021.012-0.018-0.0180.0000.0000.0000.000
76A75GLY00.0360.01121.268-0.026-0.0260.0000.0000.0000.000
77A76LYS10.9680.97922.3300.0020.0020.0000.0000.0000.000
78A77LYS10.8220.91422.6350.0370.0370.0000.0000.0000.000
79A78LEU00.0220.02317.015-0.020-0.0200.0000.0000.0000.000
80A79ALA0-0.022-0.01121.6340.0280.0280.0000.0000.0000.000
81A80ILE00.0220.02818.270-0.038-0.0380.0000.0000.0000.000
82A81VAL0-0.024-0.02621.1640.0440.0440.0000.0000.0000.000
83A82PRO00.0040.01822.413-0.043-0.0430.0000.0000.0000.000
84A83VAL00.0410.02122.9100.0430.0430.0000.0000.0000.000
85A84LEU0-0.060-0.01325.033-0.004-0.0040.0000.0000.0000.000
86A85ARG10.9610.96227.8950.2630.2630.0000.0000.0000.000
87A86ALA00.0450.01123.3800.0110.0110.0000.0000.0000.000
88A87GLY00.0770.04221.418-0.023-0.0230.0000.0000.0000.000
89A88VAL0-0.050-0.02921.591-0.008-0.0080.0000.0000.0000.000
90A89GLY00.0260.01221.9500.0110.0110.0000.0000.0000.000
91A90MET0-0.0280.00616.1030.0050.0050.0000.0000.0000.000
92A91SER00.008-0.00218.155-0.002-0.0020.0000.0000.0000.000
93A92ASP-1-0.846-0.90320.456-0.243-0.2430.0000.0000.0000.000
94A93GLY00.0870.05217.0650.0380.0380.0000.0000.0000.000
95A94LEU0-0.019-0.01814.0640.0270.0270.0000.0000.0000.000
96A95LEU0-0.066-0.03417.2850.0470.0470.0000.0000.0000.000
97A96GLU-1-0.940-0.97918.587-0.134-0.1340.0000.0000.0000.000
98A97LEU0-0.057-0.00713.0680.0490.0490.0000.0000.0000.000
99A98ILE0-0.035-0.02316.2060.0630.0630.0000.0000.0000.000
100A99PRO00.0490.03019.577-0.018-0.0180.0000.0000.0000.000
101A100SER0-0.115-0.05922.8310.0090.0090.0000.0000.0000.000
102A101ALA00.0060.01221.1350.0090.0090.0000.0000.0000.000
103A102ARG10.8040.89923.2980.1130.1130.0000.0000.0000.000
104A103VAL00.0360.01424.164-0.022-0.0220.0000.0000.0000.000
105A104GLY0-0.043-0.02125.5080.0230.0230.0000.0000.0000.000
106A105HIS00.003-0.00526.240-0.027-0.0270.0000.0000.0000.000
107A106ILE00.0240.00825.5690.0230.0230.0000.0000.0000.000
108A107GLY00.0220.01028.088-0.021-0.0210.0000.0000.0000.000
109A108VAL0-0.004-0.02728.7820.0210.0210.0000.0000.0000.000
110A109TYR00.0540.02029.282-0.010-0.0100.0000.0000.0000.000
111A110ARG10.8930.96630.2780.1890.1890.0000.0000.0000.000
112A111ALA0-0.075-0.03530.8320.0190.0190.0000.0000.0000.000
113A112ASP-1-0.848-0.91331.603-0.281-0.2810.0000.0000.0000.000
114A113ASP-1-0.858-0.92931.391-0.300-0.3000.0000.0000.0000.000
115A114HIS0-0.010-0.01133.379-0.009-0.0090.0000.0000.0000.000
116A115ARG10.8930.93634.6510.2070.2070.0000.0000.0000.000
117A116PRO00.0660.04331.519-0.005-0.0050.0000.0000.0000.000
118A117VAL0-0.065-0.03133.1700.0230.0230.0000.0000.0000.000
119A118GLU-1-0.703-0.81532.538-0.226-0.2260.0000.0000.0000.000
120A119TYR0-0.086-0.04330.8990.0210.0210.0000.0000.0000.000
121A120LEU0-0.020-0.01132.8800.0150.0150.0000.0000.0000.000
122A121VAL00.0420.04030.919-0.016-0.0160.0000.0000.0000.000
123A122ARG10.8420.91331.1000.1810.1810.0000.0000.0000.000
124A123LEU00.0500.02527.443-0.017-0.0170.0000.0000.0000.000
125A124PRO00.0110.00126.4720.0160.0160.0000.0000.0000.000
126A125ASP-1-0.800-0.88929.568-0.112-0.1120.0000.0000.0000.000
127A126LEU00.0400.03328.856-0.008-0.0080.0000.0000.0000.000
128A127GLU-1-0.895-0.95228.295-0.128-0.1280.0000.0000.0000.000
129A128ASP-1-0.873-0.92925.806-0.062-0.0620.0000.0000.0000.000
130A129ARG10.7890.90624.2400.1410.1410.0000.0000.0000.000
131A130ILE00.0320.02217.879-0.006-0.0060.0000.0000.0000.000
132A131PHE0-0.003-0.01621.3320.0160.0160.0000.0000.0000.000
133A132ILE00.0180.00415.536-0.037-0.0370.0000.0000.0000.000
134A133LEU00.0090.01218.7510.0320.0320.0000.0000.0000.000
135A134CYS0-0.055-0.02418.078-0.091-0.0910.0000.0000.0000.000
136A135ASP-1-0.779-0.92218.838-0.457-0.4570.0000.0000.0000.000
137A136PRO00.003-0.00217.562-0.084-0.0840.0000.0000.0000.000
138A137MET0-0.015-0.00117.513-0.122-0.1220.0000.0000.0000.000
139A138VAL00.0320.02118.2500.0720.0720.0000.0000.0000.000
140A139ALA00.0380.00420.084-0.042-0.0420.0000.0000.0000.000
141A140THR00.0720.02622.577-0.021-0.0210.0000.0000.0000.000
142A141GLY00.0490.03322.9410.0080.0080.0000.0000.0000.000
143A142TYR00.0080.00223.943-0.008-0.0080.0000.0000.0000.000
144A143SER00.0150.01025.5690.0060.0060.0000.0000.0000.000
145A144ALA00.0150.00721.4720.0140.0140.0000.0000.0000.000
146A145ALA00.0450.02023.5650.0060.0060.0000.0000.0000.000
147A146HIS0-0.017-0.02325.1870.0330.0330.0000.0000.0000.000
148A147ALA0-0.018-0.01224.5860.0310.0310.0000.0000.0000.000
149A148ILE00.0370.02020.9390.0230.0230.0000.0000.0000.000
150A149ASP-1-0.846-0.93425.129-0.287-0.2870.0000.0000.0000.000
151A150VAL0-0.131-0.05928.3840.0310.0310.0000.0000.0000.000
152A151LEU00.0140.01124.6100.0260.0260.0000.0000.0000.000
153A152LYS10.9720.98625.2440.3660.3660.0000.0000.0000.000
154A153ARG10.7850.88629.0790.2580.2580.0000.0000.0000.000
155A154ARG10.7180.82031.3110.2170.2170.0000.0000.0000.000
156A155GLY00.0260.02331.5330.0120.0120.0000.0000.0000.000
157A156VAL0-0.060-0.01926.1780.0100.0100.0000.0000.0000.000
158A157PRO00.0140.00425.064-0.017-0.0170.0000.0000.0000.000
159A158GLY00.0500.02523.084-0.012-0.0120.0000.0000.0000.000
160A159GLU-1-0.844-0.94020.145-0.298-0.2980.0000.0000.0000.000
161A160ARG10.7590.87419.6260.1920.1920.0000.0000.0000.000
162A161LEU0-0.032-0.01320.3730.0130.0130.0000.0000.0000.000
163A162MET0-0.017-0.00514.422-0.070-0.0700.0000.0000.0000.000
164A163PHE00.002-0.00216.1310.0950.0950.0000.0000.0000.000
165A164LEU00.0130.00611.264-0.150-0.1500.0000.0000.0000.000
166A165ALA00.0050.00313.9380.1510.1510.0000.0000.0000.000
167A166LEU0-0.029-0.02113.175-0.199-0.1990.0000.0000.0000.000
168A167VAL00.009-0.01312.961-0.197-0.1970.0000.0000.0000.000
169A168ALA0-0.0020.00615.1640.1010.1010.0000.0000.0000.000
170A169ALA00.0340.02916.706-0.065-0.0650.0000.0000.0000.000
171A170PRO0-0.015-0.00917.7780.0030.0030.0000.0000.0000.000
172A171GLU-1-0.795-0.90919.526-0.567-0.5670.0000.0000.0000.000
173A172GLY00.0500.02921.8780.0370.0370.0000.0000.0000.000
174A173VAL0-0.052-0.04116.5210.0030.0030.0000.0000.0000.000
175A174GLN0-0.040-0.01719.794-0.022-0.0220.0000.0000.0000.000
176A175VAL00.0190.01422.6020.0280.0280.0000.0000.0000.000
177A176PHE0-0.055-0.02518.7920.0200.0200.0000.0000.0000.000
178A177GLN0-0.042-0.05219.600-0.016-0.0160.0000.0000.0000.000
179A178ASP-1-0.862-0.92222.162-0.376-0.3760.0000.0000.0000.000
180A179ALA0-0.038-0.00125.5090.0360.0360.0000.0000.0000.000
181A180HIS0-0.095-0.06022.6370.0360.0360.0000.0000.0000.000
182A181PRO00.0740.05421.362-0.058-0.0580.0000.0000.0000.000
183A182ASP-1-0.931-0.96419.873-0.409-0.4090.0000.0000.0000.000
184A183VAL0-0.082-0.02219.023-0.006-0.0060.0000.0000.0000.000
185A184LYS10.9100.97112.9300.6070.6070.0000.0000.0000.000
186A185LEU0-0.0110.00814.7950.0330.0330.0000.0000.0000.000
187A186TYR00.017-0.0098.926-0.107-0.1070.0000.0000.0000.000
188A187VAL0-0.016-0.00810.2450.2750.2750.0000.0000.0000.000
189A188ALA00.0230.0108.519-0.635-0.6350.0000.0000.0000.000
190A189SER0-0.077-0.0618.906-0.348-0.3480.0000.0000.0000.000
191A190LEU0-0.033-0.00411.1500.1500.1500.0000.0000.0000.000
192A191ASP-1-0.745-0.82013.447-1.093-1.0930.0000.0000.0000.000
193A192SER0-0.036-0.05016.258-0.013-0.0130.0000.0000.0000.000
194A193HIS0-0.0220.00619.295-0.011-0.0110.0000.0000.0000.000
195A194LEU0-0.027-0.00522.235-0.031-0.0310.0000.0000.0000.000
196A195ASP-1-0.836-0.92824.801-0.351-0.3510.0000.0000.0000.000
197A196ASP-1-0.943-0.97727.795-0.291-0.2910.0000.0000.0000.000
198A197HIS0-0.089-0.03730.1130.0220.0220.0000.0000.0000.000
199A198ALA0-0.037-0.00827.584-0.003-0.0030.0000.0000.0000.000
200A199TYR0-0.039-0.04025.126-0.029-0.0290.0000.0000.0000.000
201A200ILE0-0.042-0.02918.794-0.003-0.0030.0000.0000.0000.000
202A201VAL0-0.0050.02021.6910.0200.0200.0000.0000.0000.000
203A202PRO0-0.002-0.03017.863-0.041-0.0410.0000.0000.0000.000
204A203GLY00.0130.02518.6920.0500.0500.0000.0000.0000.000
205A204LEU0-0.008-0.02416.556-0.032-0.0320.0000.0000.0000.000
206A205GLY00.0350.02820.4760.0490.0490.0000.0000.0000.000
207A206ASP-1-0.756-0.85523.588-0.388-0.3880.0000.0000.0000.000
208A207ALA00.019-0.00622.0760.0100.0100.0000.0000.0000.000
209A208GLY0-0.011-0.01023.8400.0120.0120.0000.0000.0000.000
210A209ASP-1-0.819-0.88227.181-0.246-0.2460.0000.0000.0000.000
211A210ARG10.7830.88721.7640.4290.4290.0000.0000.0000.000
212A211LEU0-0.0190.00822.2160.0110.0110.0000.0000.0000.000
213A212PHE0-0.098-0.05926.1070.0270.0270.0000.0000.0000.000
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