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: M3MMZ

Calculation Name: 4D9O-A-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4D9O

Chain ID: A

ChEMBL ID:

UniProt ID: Q91DD5

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 207
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2336164.837438
FMO2-HF: Nuclear repulsion 2256012.207105
FMO2-HF: Total energy -80152.630333
FMO2-MP2: Total energy -80387.631959


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:9:ACE )


Summations of interaction energy for fragment #1(A:9:ACE )
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.
0.4181.712-0.007-0.618-0.669-0.002
Interaction energy analysis for fragmet #1(A:9:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / 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].
3A11VAL 00.0160.0193.8160.4431.656-0.007-0.613-0.593-0.002
4A12PRO 0-0.019-0.0025.0190.4360.5170.000-0.005-0.0760.000
5A13PRO 00.0570.0405.089-0.105-0.1050.0000.0000.0000.000
6A14LYS 11.0040.9887.217-0.318-0.3180.0000.0000.0000.000
7A15LYS 10.9530.96410.657-0.353-0.3530.0000.0000.0000.000
8A16ASP -1-0.813-0.9078.2350.5800.5800.0000.0000.0000.000
9A17MET 0-0.022-0.00710.625-0.072-0.0720.0000.0000.0000.000
10A18GLU -1-0.887-0.93413.1470.1610.1610.0000.0000.0000.000
11A19LYS 10.8630.92913.505-0.293-0.2930.0000.0000.0000.000
12A20GLY 0-0.0010.01015.021-0.020-0.0200.0000.0000.0000.000
13A21VAL 00.0230.00716.467-0.018-0.0180.0000.0000.0000.000
14A22ILE 0-0.025-0.01119.075-0.008-0.0080.0000.0000.0000.000
15A23PHE 00.004-0.01519.082-0.008-0.0080.0000.0000.0000.000
16A24SER 0-0.029-0.01320.672-0.012-0.0120.0000.0000.0000.000
17A25ASP -1-0.879-0.93522.4210.0320.0320.0000.0000.0000.000
18A26LEU 0-0.015-0.01224.115-0.003-0.0030.0000.0000.0000.000
19A27CYS 0-0.0410.00224.1260.0000.0000.0000.0000.0000.000
20A28ASN 0-0.024-0.00124.052-0.010-0.0100.0000.0000.0000.000
21A29PHE 00.0060.00527.8240.0010.0010.0000.0000.0000.000
22A30LEU 0-0.020-0.00429.390-0.003-0.0030.0000.0000.0000.000
23A31ILE 00.0190.00932.1090.0010.0010.0000.0000.0000.000
24A32THR 0-0.032-0.01434.912-0.003-0.0030.0000.0000.0000.000
25A33GLN 0-0.008-0.01437.5410.0020.0020.0000.0000.0000.000
26A34THR 00.0490.02940.839-0.001-0.0010.0000.0000.0000.000
27A35LEU 0-0.007-0.01543.1140.0000.0000.0000.0000.0000.000
28A36GLN 0-0.002-0.00844.3720.0000.0000.0000.0000.0000.000
29A37GLY 0-0.042-0.03645.3500.0010.0010.0000.0000.0000.000
30A38TRP 0-0.012-0.00640.0650.0000.0000.0000.0000.0000.000
31A39LYS 10.8710.94336.356-0.003-0.0030.0000.0000.0000.000
32A40VAL 0-0.030-0.02334.998-0.001-0.0010.0000.0000.0000.000
33A41TYR 00.0020.00627.6720.0010.0010.0000.0000.0000.000
34A42TRP 00.021-0.01729.264-0.001-0.0010.0000.0000.0000.000
35A43ALA 00.0260.01727.7690.0010.0010.0000.0000.0000.000
36A44GLY 00.0450.01828.3880.0030.0030.0000.0000.0000.000
37A45ILE 0-0.040-0.01428.998-0.001-0.0010.0000.0000.0000.000
38A46GLU -1-0.868-0.93532.7770.0050.0050.0000.0000.0000.000
39A47PHE 00.0280.00534.4920.0010.0010.0000.0000.0000.000
40A48ASP -1-0.852-0.91238.5870.0040.0040.0000.0000.0000.000
41A49VAL 00.0070.00640.7140.0010.0010.0000.0000.0000.000
42A50SER 00.0170.00943.420-0.002-0.0020.0000.0000.0000.000
43A51GLN 00.0710.02945.0840.0000.0000.0000.0000.0000.000
44A52LYS 10.9660.97947.857-0.007-0.0070.0000.0000.0000.000
45A53GLY 0-0.116-0.04950.8110.0010.0010.0000.0000.0000.000
46A54MET 00.1100.05049.8550.0000.0000.0000.0000.0000.000
47A55ALA 00.0340.03453.3200.0000.0000.0000.0000.0000.000
48A56LEU 0-0.0010.00056.6360.0000.0000.0000.0000.0000.000
49A57LEU 00.0340.01852.0290.0000.0000.0000.0000.0000.000
50A58THR 00.020-0.01555.1390.0000.0000.0000.0000.0000.000
51A59ARG 10.9270.97257.663-0.004-0.0040.0000.0000.0000.000
52A60LEU 0-0.022-0.01458.6040.0000.0000.0000.0000.0000.000
53A61LYS 10.8190.92955.916-0.008-0.0080.0000.0000.0000.000
54A62THR 0-0.043-0.02060.2630.0000.0000.0000.0000.0000.000
55A63NME 0-0.0260.00663.5020.0000.0000.0000.0000.0000.000
56A69ACE 00.039-0.00967.7100.0000.0000.0000.0000.0000.000
57A70ALA 0-0.029-0.01864.6240.0000.0000.0000.0000.0000.000
58A71MET 00.0780.04163.6750.0000.0000.0000.0000.0000.000
59A72THR 00.0350.01160.2550.0000.0000.0000.0000.0000.000
60A73ARG 10.9380.98761.102-0.007-0.0070.0000.0000.0000.000
61A74ASN 0-0.009-0.02562.5010.0000.0000.0000.0000.0000.000
62A75LEU 00.0300.03160.2500.0000.0000.0000.0000.0000.000
63A76PHE 0-0.018-0.00255.7560.0000.0000.0000.0000.0000.000
64A77PRO 00.0630.02459.168-0.001-0.0010.0000.0000.0000.000
65A78HIS 00.0150.01254.567-0.001-0.0010.0000.0000.0000.000
66A79LEU 00.0180.00953.1110.0000.0000.0000.0000.0000.000
67A80PHE 0-0.047-0.03556.534-0.001-0.0010.0000.0000.0000.000
68A81GLN 0-0.037-0.00259.569-0.001-0.0010.0000.0000.0000.000
69A82ASN 00.0560.03056.7830.0000.0000.0000.0000.0000.000
70A83PRO 0-0.043-0.02858.4030.0000.0000.0000.0000.0000.000
71A84ASN 0-0.019-0.01655.683-0.001-0.0010.0000.0000.0000.000
72A85SER 0-0.0400.00153.6920.0000.0000.0000.0000.0000.000
73A86VAL 0-0.016-0.02149.756-0.001-0.0010.0000.0000.0000.000
74A87ILE 0-0.019-0.00250.4200.0010.0010.0000.0000.0000.000
75A88GLN 0-0.021-0.00644.881-0.001-0.0010.0000.0000.0000.000
76A89SER 00.0190.02643.1990.0000.0000.0000.0000.0000.000
77A90PRO 00.0830.02145.1160.0010.0010.0000.0000.0000.000
78A91ILE 00.0100.01639.0990.0010.0010.0000.0000.0000.000
79A92TRP 00.006-0.00340.4740.0010.0010.0000.0000.0000.000
80A93ALA 00.0520.01841.7270.0020.0020.0000.0000.0000.000
81A94LEU 00.0020.01137.9500.0010.0010.0000.0000.0000.000
82A95ARG 10.7970.90234.010-0.018-0.0180.0000.0000.0000.000
83A96VAL 00.0190.01838.0700.0030.0030.0000.0000.0000.000
84A97ILE 00.0080.00340.3580.0020.0020.0000.0000.0000.000
85A98LEU 0-0.045-0.01634.8450.0020.0020.0000.0000.0000.000
86A99ALA 00.0090.00635.9670.0030.0030.0000.0000.0000.000
87A100ALA 00.0310.01137.0190.0030.0030.0000.0000.0000.000
88A101GLY 00.0490.02937.9320.0010.0010.0000.0000.0000.000
89A102LEU 0-0.061-0.03631.9270.0030.0030.0000.0000.0000.000
90A103GLN 0-0.006-0.01135.1270.0040.0040.0000.0000.0000.000
91A104ASP -1-0.923-0.96037.4440.0390.0390.0000.0000.0000.000
92A105GLN 00.0160.00131.1520.0000.0000.0000.0000.0000.000
93A106LEU 0-0.075-0.04433.7020.0040.0040.0000.0000.0000.000
94A107LEU 0-0.041-0.02334.9950.0020.0020.0000.0000.0000.000
95A108ASP -1-0.925-0.93737.0510.0500.0500.0000.0000.0000.000
96A109HIS 0-0.135-0.06031.6380.0010.0010.0000.0000.0000.000
97A110SER 00.0360.01133.601-0.004-0.0040.0000.0000.0000.000
98A111LEU 0-0.010-0.01631.3880.0040.0040.0000.0000.0000.000
99A112VAL 0-0.043-0.01529.8740.0050.0050.0000.0000.0000.000
100A113GLU -1-0.842-0.91427.4830.0970.0970.0000.0000.0000.000
101A114PRO 0-0.006-0.02023.160-0.004-0.0040.0000.0000.0000.000
102A115LEU 0-0.028-0.02125.310-0.004-0.0040.0000.0000.0000.000
103A116THR 00.0680.04127.188-0.007-0.0070.0000.0000.0000.000
104A117GLY 00.0140.01527.752-0.006-0.0060.0000.0000.0000.000
105A118ALA 0-0.046-0.03625.131-0.006-0.0060.0000.0000.0000.000
106A119LEU 0-0.014-0.00227.096-0.006-0.0060.0000.0000.0000.000
107A120GLY 00.0580.03430.409-0.006-0.0060.0000.0000.0000.000
108A121LEU 00.002-0.00326.736-0.004-0.0040.0000.0000.0000.000
109A122ILE 0-0.036-0.02126.159-0.005-0.0050.0000.0000.0000.000
110A123SER 0-0.008-0.00130.226-0.006-0.0060.0000.0000.0000.000
111A124ASP -1-0.834-0.92133.2350.0390.0390.0000.0000.0000.000
112A125TRP 0-0.085-0.03229.986-0.003-0.0030.0000.0000.0000.000
113A126LEU 0-0.044-0.02232.695-0.005-0.0050.0000.0000.0000.000
114A127LEU 00.0380.02034.935-0.004-0.0040.0000.0000.0000.000
115A128THR 0-0.062-0.03036.532-0.003-0.0030.0000.0000.0000.000
116A129THR 0-0.079-0.03234.447-0.003-0.0030.0000.0000.0000.000
117A130THR 00.002-0.02037.0440.0000.0000.0000.0000.0000.000
118A131SER 0-0.0150.00632.309-0.001-0.0010.0000.0000.0000.000
119A132THR 00.0540.01332.2030.0030.0030.0000.0000.0000.000
120A133HIS 0-0.017-0.00923.5130.0010.0010.0000.0000.0000.000
121A134PHE 00.0220.02327.1030.0000.0000.0000.0000.0000.000
122A135ASN 00.009-0.02124.6030.0050.0050.0000.0000.0000.000
123A136LEU 00.0200.03322.6760.0030.0030.0000.0000.0000.000
124A137ARG 10.9280.94221.525-0.018-0.0180.0000.0000.0000.000
125A138THR 00.0230.02422.4220.0000.0000.0000.0000.0000.000
126A139ARG 10.9630.96316.452-0.118-0.1180.0000.0000.0000.000
127A140SER 00.0380.02818.4140.0140.0140.0000.0000.0000.000
128A141VAL 00.0860.04720.1030.0110.0110.0000.0000.0000.000
129A142LYS 10.9120.95817.591-0.077-0.0770.0000.0000.0000.000
130A143ASP -1-0.866-0.93615.0950.2420.2420.0000.0000.0000.000
131A144GLN 0-0.038-0.02116.6360.0190.0190.0000.0000.0000.000
132A145LEU 00.0080.00718.960-0.016-0.0160.0000.0000.0000.000
133A146SER 0-0.034-0.03018.4590.0200.0200.0000.0000.0000.000
134A147LEU 00.0860.02319.991-0.015-0.0150.0000.0000.0000.000
135A148ARG 10.9710.98621.066-0.158-0.1580.0000.0000.0000.000
136A149MET 0-0.0470.00822.658-0.006-0.0060.0000.0000.0000.000
137A150LEU 00.0430.02324.083-0.008-0.0080.0000.0000.0000.000
138A151SER 0-0.012-0.00825.882-0.011-0.0110.0000.0000.0000.000
139A152LEU 00.0320.00727.830-0.006-0.0060.0000.0000.0000.000
140A153ILE 00.0170.02527.180-0.005-0.0050.0000.0000.0000.000
141A154ARG 10.8380.91828.264-0.046-0.0460.0000.0000.0000.000
142A155SER 0-0.013-0.00231.763-0.005-0.0050.0000.0000.0000.000
143A156ASN 0-0.005-0.01733.029-0.005-0.0050.0000.0000.0000.000
144A157ILE 00.0100.02433.807-0.003-0.0030.0000.0000.0000.000
145A158LEU 00.0080.00135.427-0.003-0.0030.0000.0000.0000.000
146A159GLN 00.0040.00937.821-0.002-0.0020.0000.0000.0000.000
147A160PHE 00.0180.00439.157-0.002-0.0020.0000.0000.0000.000
148A161ILE 00.000-0.01238.628-0.002-0.0020.0000.0000.0000.000
149A162ASN 0-0.006-0.01041.432-0.003-0.0030.0000.0000.0000.000
150A163LYS 10.9150.97242.717-0.034-0.0340.0000.0000.0000.000
151A164LEU 0-0.030-0.01543.540-0.002-0.0020.0000.0000.0000.000
152A165ASP -1-0.945-0.97646.1070.0160.0160.0000.0000.0000.000
153A166ALA 00.0090.02047.965-0.001-0.0010.0000.0000.0000.000
154A167LEU 0-0.088-0.01649.0660.0000.0000.0000.0000.0000.000
155A168HIS 00.0180.00251.896-0.002-0.0020.0000.0000.0000.000
156A169VAL 0-0.036-0.03055.2000.0000.0000.0000.0000.0000.000
157A170VAL 0-0.008-0.00556.6190.0000.0000.0000.0000.0000.000
158A171ASN 0-0.030-0.03158.6000.0000.0000.0000.0000.0000.000
159A172TYR 00.010-0.00661.9290.0000.0000.0000.0000.0000.000
160A173ASN 0-0.008-0.00263.8110.0000.0000.0000.0000.0000.000
161A174GLY 00.0120.01760.8490.0000.0000.0000.0000.0000.000
162A175LEU 0-0.0260.00558.3760.0010.0010.0000.0000.0000.000
163A176LEU 00.0140.00451.1650.0000.0000.0000.0000.0000.000
164A177SER 00.0460.02154.2660.0000.0000.0000.0000.0000.000
165A178SER 0-0.023-0.01751.2520.0000.0000.0000.0000.0000.000
166A179ILE 00.0190.01745.4640.0010.0010.0000.0000.0000.000
167A180GLU -1-0.952-0.97347.8930.0220.0220.0000.0000.0000.000
168A181ILE 0-0.028-0.01241.4060.0010.0010.0000.0000.0000.000
169A182GLY 00.0260.01644.766-0.001-0.0010.0000.0000.0000.000
170A183THR 0-0.003-0.00840.0980.0030.0030.0000.0000.0000.000
171A184SER 0-0.035-0.02841.410-0.002-0.0020.0000.0000.0000.000
172A185THR 0-0.044-0.02140.5260.0000.0000.0000.0000.0000.000
173A186HIS 00.0140.00440.982-0.001-0.0010.0000.0000.0000.000
174A187THR 00.0420.03544.3420.0020.0020.0000.0000.0000.000
175A188ILE 0-0.010-0.00341.334-0.002-0.0020.0000.0000.0000.000
176A189ILE 00.0360.02345.8610.0010.0010.0000.0000.0000.000
177A190ILE 0-0.023-0.01343.861-0.001-0.0010.0000.0000.0000.000
178A191THR 00.0330.00548.4250.0010.0010.0000.0000.0000.000
179A192ARG 10.8180.91351.147-0.016-0.0160.0000.0000.0000.000
180A193THR 0-0.023-0.03052.870-0.001-0.0010.0000.0000.0000.000
181A194ASN 00.043-0.00454.7940.0000.0000.0000.0000.0000.000
182A195MET 0-0.075-0.03154.623-0.001-0.0010.0000.0000.0000.000
183A196GLY 00.0060.01751.0410.0000.0000.0000.0000.0000.000
184A197PHE 00.0320.01447.6390.0000.0000.0000.0000.0000.000
185A198LEU 0-0.030-0.00549.239-0.001-0.0010.0000.0000.0000.000
186A199VAL 00.0030.00844.7020.0010.0010.0000.0000.0000.000
187A200GLU -1-0.845-0.94848.1240.0140.0140.0000.0000.0000.000
188A201VAL 00.0120.00443.8200.0010.0010.0000.0000.0000.000
189A202GLN 0-0.022-0.02247.094-0.001-0.0010.0000.0000.0000.000
190A203GLU -1-0.910-0.95144.6370.0220.0220.0000.0000.0000.000
191A204NME 00.0000.00848.0570.0010.0010.0000.0000.0000.000
192A216ACE 00.0130.00052.1170.0000.0000.0000.0000.0000.000
193A217VAL 0-0.039-0.00150.5140.0010.0010.0000.0000.0000.000
194A218LYS 10.9530.99444.196-0.016-0.0160.0000.0000.0000.000
195A219PHE 00.0490.00648.8750.0010.0010.0000.0000.0000.000
196A220SER 0-0.029-0.04147.240-0.001-0.0010.0000.0000.0000.000
197A221LEU 0-0.0180.00249.2500.0010.0010.0000.0000.0000.000
198A222LEU 0-0.0130.00543.196-0.001-0.0010.0000.0000.0000.000
199A223HIS 0-0.007-0.00847.3970.0010.0010.0000.0000.0000.000
200A224GLU -1-0.770-0.90147.2490.0120.0120.0000.0000.0000.000
201A225SER 0-0.054-0.03747.2050.0000.0000.0000.0000.0000.000
202A226ALA 00.0010.01042.6030.0000.0000.0000.0000.0000.000
203A227PHE 0-0.004-0.02740.8740.0010.0010.0000.0000.0000.000
204A228LYS 10.9210.97443.816-0.012-0.0120.0000.0000.0000.000
205A229PRO 0-0.0090.00040.9630.0000.0000.0000.0000.0000.000
206A230PHE 0-0.084-0.03836.9660.0010.0010.0000.0000.0000.000
207A231THR -1-0.928-0.93741.6020.0200.0200.0000.0000.0000.000