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: VR371

Calculation Name: 4D9O-A-Xray372

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: 2023-06-20

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 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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2315767.190952
FMO2-HF: Nuclear repulsion 2236106.544433
FMO2-HF: Total energy -79660.646519
FMO2-MP2: Total energy -79894.063014


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:10:MET)


Summations of interaction energy for fragment #1(A:10:MET)
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.
1.4743.255-0.017-0.857-0.9080.002
Interaction energy analysis for fragmet #1(A:10:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.012
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].
3A12PRO00.0060.0053.8091.6153.396-0.017-0.857-0.9080.002
4A13PRO00.0700.0455.4070.2950.2950.0000.0000.0000.000
5A14LYS11.0060.9887.472-0.552-0.5520.0000.0000.0000.000
6A15LYS10.8640.91211.123-0.232-0.2320.0000.0000.0000.000
7A16ASP-1-0.816-0.9148.782-0.139-0.1390.0000.0000.0000.000
8A17MET0-0.0170.0028.632-0.093-0.0930.0000.0000.0000.000
9A18GLU-1-0.845-0.91012.4040.0290.0290.0000.0000.0000.000
10A19LYS10.8860.93613.3920.0140.0140.0000.0000.0000.000
11A20GLY0-0.0070.00414.533-0.012-0.0120.0000.0000.0000.000
12A21VAL00.0210.00715.8140.0000.0000.0000.0000.0000.000
13A22ILE0-0.016-0.00718.3470.0090.0090.0000.0000.0000.000
14A23PHE00.0430.00118.526-0.002-0.0020.0000.0000.0000.000
15A24SER0-0.021-0.01119.888-0.001-0.0010.0000.0000.0000.000
16A25ASP-1-0.840-0.93621.588-0.110-0.1100.0000.0000.0000.000
17A26LEU0-0.018-0.00723.8270.0100.0100.0000.0000.0000.000
18A27CYS0-0.041-0.00223.5320.0090.0090.0000.0000.0000.000
19A28ASN0-0.0160.01123.052-0.010-0.0100.0000.0000.0000.000
20A29PHE00.0070.00426.9740.0080.0080.0000.0000.0000.000
21A30LEU0-0.011-0.00128.421-0.001-0.0010.0000.0000.0000.000
22A31ILE00.0100.00331.0140.0090.0090.0000.0000.0000.000
23A32THR0-0.026-0.00933.196-0.004-0.0040.0000.0000.0000.000
24A33GLN00.000-0.00936.1250.0030.0030.0000.0000.0000.000
25A34THR00.0310.00938.646-0.001-0.0010.0000.0000.0000.000
26A35LEU00.0160.00541.0690.0010.0010.0000.0000.0000.000
27A36GLN00.007-0.00442.9330.0000.0000.0000.0000.0000.000
28A37GLY0-0.053-0.04543.7940.0030.0030.0000.0000.0000.000
29A38TRP0-0.015-0.00638.9680.0000.0000.0000.0000.0000.000
30A39LYS10.8690.94535.0160.0730.0730.0000.0000.0000.000
31A40VAL0-0.037-0.02634.036-0.006-0.0060.0000.0000.0000.000
32A41TYR0-0.0170.00025.9560.0060.0060.0000.0000.0000.000
33A42TRP00.019-0.01428.874-0.004-0.0040.0000.0000.0000.000
34A43ALA00.0100.01227.1700.0080.0080.0000.0000.0000.000
35A44GLY00.0870.04527.6340.0090.0090.0000.0000.0000.000
36A45ILE0-0.076-0.03028.2110.0080.0080.0000.0000.0000.000
37A46GLU-1-0.848-0.91932.011-0.080-0.0800.0000.0000.0000.000
38A47PHE00.018-0.00733.5890.0060.0060.0000.0000.0000.000
39A48ASP-1-0.859-0.92237.688-0.066-0.0660.0000.0000.0000.000
40A49VAL00.0030.00439.8220.0040.0040.0000.0000.0000.000
41A50SER00.0190.00242.450-0.001-0.0010.0000.0000.0000.000
42A51GLN00.0790.04444.231-0.003-0.0030.0000.0000.0000.000
43A52LYS10.9530.98346.7850.0420.0420.0000.0000.0000.000
44A53GLY0-0.068-0.03849.8720.0000.0000.0000.0000.0000.000
45A54MET00.0780.04449.1070.0010.0010.0000.0000.0000.000
46A55ALA00.0350.03452.4200.0010.0010.0000.0000.0000.000
47A56LEU0-0.008-0.00255.8290.0010.0010.0000.0000.0000.000
48A57LEU00.0350.01551.3680.0010.0010.0000.0000.0000.000
49A58THR00.020-0.01454.2700.0010.0010.0000.0000.0000.000
50A59ARG10.9370.98456.8580.0310.0310.0000.0000.0000.000
51A60LEU0-0.0220.00457.9370.0010.0010.0000.0000.0000.000
52A61LYS10.8600.94755.2050.0380.0380.0000.0000.0000.000
53A62THR0-0.074-0.04059.6170.0010.0010.0000.0000.0000.000
54A70ALA00.013-0.00664.0860.0000.0000.0000.0000.0000.000
55A71MET00.0640.03063.5890.0000.0000.0000.0000.0000.000
56A72THR00.0370.01059.7860.0000.0000.0000.0000.0000.000
57A73ARG10.8900.93860.6620.0270.0270.0000.0000.0000.000
58A74ASN0-0.007-0.02562.086-0.001-0.0010.0000.0000.0000.000
59A75LEU00.0230.03060.0130.0000.0000.0000.0000.0000.000
60A76PHE0-0.022-0.00555.2040.0000.0000.0000.0000.0000.000
61A77PRO00.0550.03558.832-0.001-0.0010.0000.0000.0000.000
62A78HIS00.012-0.01054.1890.0000.0000.0000.0000.0000.000
63A79LEU00.0150.01052.791-0.002-0.0020.0000.0000.0000.000
64A80PHE0-0.051-0.02556.123-0.001-0.0010.0000.0000.0000.000
65A81GLN0-0.0220.00559.0720.0000.0000.0000.0000.0000.000
66A82ASN00.0720.02956.1300.0010.0010.0000.0000.0000.000
67A83PRO0-0.042-0.02057.936-0.001-0.0010.0000.0000.0000.000
68A84ASN0-0.024-0.01855.438-0.002-0.0020.0000.0000.0000.000
69A85SER0-0.0310.00153.275-0.002-0.0020.0000.0000.0000.000
70A86VAL0-0.028-0.02649.1290.0000.0000.0000.0000.0000.000
71A87ILE0-0.016-0.00249.8590.0000.0000.0000.0000.0000.000
72A88GLN0-0.030-0.00944.732-0.001-0.0010.0000.0000.0000.000
73A89SER00.0390.02342.4490.0020.0020.0000.0000.0000.000
74A90PRO00.0600.01244.2950.0000.0000.0000.0000.0000.000
75A91ILE00.0020.00938.1680.0000.0000.0000.0000.0000.000
76A92TRP00.0060.00439.752-0.001-0.0010.0000.0000.0000.000
77A93ALA00.0510.02041.1610.0010.0010.0000.0000.0000.000
78A94LEU0-0.0030.00737.2530.0020.0020.0000.0000.0000.000
79A95ARG10.7900.90133.4020.0900.0900.0000.0000.0000.000
80A96VAL00.0050.01337.6670.0000.0000.0000.0000.0000.000
81A97ILE00.0060.00040.1040.0020.0020.0000.0000.0000.000
82A98LEU0-0.034-0.01434.3240.0020.0020.0000.0000.0000.000
83A99ALA00.0150.00835.7930.0010.0010.0000.0000.0000.000
84A100ALA00.0320.01736.8270.0020.0020.0000.0000.0000.000
85A101GLY00.0490.02637.8190.0030.0030.0000.0000.0000.000
86A102LEU0-0.058-0.03631.5240.0020.0020.0000.0000.0000.000
87A103GLN00.009-0.00635.1630.0050.0050.0000.0000.0000.000
88A104ASP-1-0.846-0.92237.624-0.023-0.0230.0000.0000.0000.000
89A105GLN0-0.014-0.01231.230-0.001-0.0010.0000.0000.0000.000
90A106LEU0-0.071-0.04134.1070.0030.0030.0000.0000.0000.000
91A107LEU0-0.035-0.02135.4220.0020.0020.0000.0000.0000.000
92A108ASP-1-0.939-0.94537.551-0.010-0.0100.0000.0000.0000.000
93A109HIS0-0.094-0.05532.0560.0020.0020.0000.0000.0000.000
94A110SER00.0360.02034.4520.0000.0000.0000.0000.0000.000
95A111LEU0-0.002-0.01832.364-0.001-0.0010.0000.0000.0000.000
96A112VAL0-0.042-0.01631.229-0.003-0.0030.0000.0000.0000.000
97A113GLU-1-0.844-0.90228.432-0.006-0.0060.0000.0000.0000.000
98A114PRO0-0.006-0.02223.927-0.006-0.0060.0000.0000.0000.000
99A115LEU0-0.049-0.02726.066-0.010-0.0100.0000.0000.0000.000
100A116THR00.0680.03327.717-0.005-0.0050.0000.0000.0000.000
101A117GLY00.0280.02628.325-0.004-0.0040.0000.0000.0000.000
102A118ALA0-0.052-0.03825.457-0.007-0.0070.0000.0000.0000.000
103A119LEU0-0.0120.00027.376-0.006-0.0060.0000.0000.0000.000
104A120GLY00.0540.03230.610-0.002-0.0020.0000.0000.0000.000
105A121LEU00.002-0.00527.203-0.005-0.0050.0000.0000.0000.000
106A122ILE0-0.030-0.02026.145-0.005-0.0050.0000.0000.0000.000
107A123SER0-0.0070.00030.111-0.002-0.0020.0000.0000.0000.000
108A124ASP-1-0.838-0.92233.319-0.064-0.0640.0000.0000.0000.000
109A125TRP0-0.087-0.02929.303-0.001-0.0010.0000.0000.0000.000
110A126LEU0-0.043-0.02432.143-0.001-0.0010.0000.0000.0000.000
111A127LEU00.0290.01834.5390.0010.0010.0000.0000.0000.000
112A128THR0-0.054-0.04036.2870.0010.0010.0000.0000.0000.000
113A129THR0-0.077-0.02734.003-0.004-0.0040.0000.0000.0000.000
114A130THR00.014-0.01136.5630.0010.0010.0000.0000.0000.000
115A131SER0-0.0220.00731.551-0.005-0.0050.0000.0000.0000.000
116A132THR00.0700.02131.0890.0030.0030.0000.0000.0000.000
117A133HIS0-0.035-0.02122.741-0.011-0.0110.0000.0000.0000.000
118A134PHE00.0300.03026.5620.0040.0040.0000.0000.0000.000
119A135ASN00.0530.00824.200-0.025-0.0250.0000.0000.0000.000
120A136LEU00.0090.02122.6840.0050.0050.0000.0000.0000.000
121A137ARG10.8850.91621.4550.1840.1840.0000.0000.0000.000
122A138THR00.0340.02722.505-0.003-0.0030.0000.0000.0000.000
123A139ARG10.9850.97916.4770.2710.2710.0000.0000.0000.000
124A140SER00.0600.03218.9460.0090.0090.0000.0000.0000.000
125A141VAL00.0280.01920.8100.0090.0090.0000.0000.0000.000
126A142LYS10.8800.95217.2810.2660.2660.0000.0000.0000.000
127A143ASP-1-0.887-0.94115.734-0.177-0.1770.0000.0000.0000.000
128A144GLN0-0.042-0.02017.2500.0280.0280.0000.0000.0000.000
129A145LEU0-0.0030.02519.2490.0110.0110.0000.0000.0000.000
130A146SER0-0.016-0.02618.6630.0100.0100.0000.0000.0000.000
131A147LEU00.0650.01520.158-0.008-0.0080.0000.0000.0000.000
132A148ARG10.9620.98421.956-0.018-0.0180.0000.0000.0000.000
133A149MET0-0.0120.00923.395-0.002-0.0020.0000.0000.0000.000
134A150LEU00.0360.02223.702-0.001-0.0010.0000.0000.0000.000
135A151SER00.0300.00825.801-0.002-0.0020.0000.0000.0000.000
136A152LEU0-0.0170.00127.8740.0000.0000.0000.0000.0000.000
137A153ILE00.0370.02827.106-0.001-0.0010.0000.0000.0000.000
138A154ARG10.8250.90727.7980.0550.0550.0000.0000.0000.000
139A155SER0-0.036-0.02831.5240.0020.0020.0000.0000.0000.000
140A156ASN00.0130.00233.3080.0030.0030.0000.0000.0000.000
141A157ILE00.0090.02033.3410.0000.0000.0000.0000.0000.000
142A158LEU00.0150.00834.9180.0000.0000.0000.0000.0000.000
143A159GLN00.0030.00737.6820.0010.0010.0000.0000.0000.000
144A160PHE00.0250.00839.0490.0010.0010.0000.0000.0000.000
145A161ILE0-0.005-0.01238.1410.0000.0000.0000.0000.0000.000
146A162ASN0-0.048-0.03941.1260.0020.0020.0000.0000.0000.000
147A163LYS10.8370.94041.6680.0240.0240.0000.0000.0000.000
148A164LEU0-0.012-0.00742.9890.0000.0000.0000.0000.0000.000
149A165ASP-1-0.855-0.93345.791-0.026-0.0260.0000.0000.0000.000
150A166ALA0-0.0040.01647.6010.0010.0010.0000.0000.0000.000
151A167LEU0-0.066-0.00448.9390.0010.0010.0000.0000.0000.000
152A168HIS00.0310.01151.6710.0000.0000.0000.0000.0000.000
153A169VAL0-0.040-0.03054.922-0.001-0.0010.0000.0000.0000.000
154A170VAL00.010-0.00156.1880.0010.0010.0000.0000.0000.000
155A171ASN0-0.046-0.03958.3070.0000.0000.0000.0000.0000.000
156A172TYR00.0180.00061.6680.0000.0000.0000.0000.0000.000
157A173ASN0-0.0040.00363.8130.0000.0000.0000.0000.0000.000
158A174GLY00.0140.01860.7760.0010.0010.0000.0000.0000.000
159A175LEU0-0.0220.00858.3080.0000.0000.0000.0000.0000.000
160A176LEU00.0220.00751.287-0.001-0.0010.0000.0000.0000.000
161A177SER00.0500.01954.040-0.001-0.0010.0000.0000.0000.000
162A178SER0-0.035-0.02051.082-0.001-0.0010.0000.0000.0000.000
163A179ILE00.0080.01045.4640.0010.0010.0000.0000.0000.000
164A180GLU-1-0.943-0.97047.907-0.029-0.0290.0000.0000.0000.000
165A181ILE0-0.027-0.01141.4820.0010.0010.0000.0000.0000.000
166A182GLY00.0220.01544.853-0.002-0.0020.0000.0000.0000.000
167A183THR0-0.038-0.02239.8130.0000.0000.0000.0000.0000.000
168A184SER0-0.006-0.01541.9650.0010.0010.0000.0000.0000.000
169A185THR0-0.040-0.02640.6020.0010.0010.0000.0000.0000.000
170A186HIS0-0.020-0.01340.904-0.001-0.0010.0000.0000.0000.000
171A187THR00.0310.02644.4100.0020.0020.0000.0000.0000.000
172A188ILE0-0.013-0.00441.173-0.002-0.0020.0000.0000.0000.000
173A189ILE00.0240.02045.7730.0020.0020.0000.0000.0000.000
174A190ILE0-0.026-0.01343.508-0.002-0.0020.0000.0000.0000.000
175A191THR00.0280.00348.1740.0030.0030.0000.0000.0000.000
176A192ARG10.7700.88050.1080.0250.0250.0000.0000.0000.000
177A193THR0-0.008-0.02552.4890.0010.0010.0000.0000.0000.000
178A194ASN00.0560.00554.2440.0000.0000.0000.0000.0000.000
179A195MET0-0.081-0.03554.026-0.001-0.0010.0000.0000.0000.000
180A196GLY0-0.0040.00950.383-0.002-0.0020.0000.0000.0000.000
181A197PHE00.0290.01247.0970.0010.0010.0000.0000.0000.000
182A198LEU0-0.028-0.00348.686-0.002-0.0020.0000.0000.0000.000
183A199VAL0-0.010-0.00144.2490.0010.0010.0000.0000.0000.000
184A200GLU-1-0.798-0.89947.717-0.034-0.0340.0000.0000.0000.000
185A201VAL00.0270.01243.5620.0000.0000.0000.0000.0000.000
186A202GLN0-0.009-0.02746.872-0.002-0.0020.0000.0000.0000.000
187A203GLU-1-0.874-0.91944.411-0.050-0.0500.0000.0000.0000.000
188A217VAL00.0100.02650.2270.0010.0010.0000.0000.0000.000
189A218LYS10.9150.95943.7930.0560.0560.0000.0000.0000.000
190A219PHE00.0490.00648.4320.0010.0010.0000.0000.0000.000
191A220SER0-0.023-0.03146.593-0.001-0.0010.0000.0000.0000.000
192A221LEU0-0.024-0.00348.5510.0020.0020.0000.0000.0000.000
193A222LEU00.0000.01142.574-0.002-0.0020.0000.0000.0000.000
194A223HIS0-0.0110.00646.6970.0010.0010.0000.0000.0000.000
195A224GLU-1-0.726-0.87146.484-0.031-0.0310.0000.0000.0000.000
196A225SER0-0.031-0.03246.4930.0000.0000.0000.0000.0000.000
197A226ALA0-0.0080.00641.8890.0000.0000.0000.0000.0000.000
198A227PHE0-0.013-0.03140.451-0.002-0.0020.0000.0000.0000.000
199A228LYS10.8250.91543.1550.0300.0300.0000.0000.0000.000
200A229PRO0-0.0040.00540.2450.0020.0020.0000.0000.0000.000
201A230PHE0-0.026-0.00336.5610.0010.0010.0000.0000.0000.000
202A231THR0-0.044-0.00141.1150.0030.0030.0000.0000.0000.000