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: 141ZZ

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 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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2317391.485414
FMO2-HF: Nuclear repulsion 2237730.39147
FMO2-HF: Total energy -79661.093945
FMO2-MP2: Total energy -79894.45846


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.
1.6893.158-0.011-0.698-0.7610.002
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 : 0.011 / q_NPA : -0.008
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].
3A12PRO00.0140.0103.8851.6443.113-0.011-0.698-0.7610.002
4A13PRO00.0730.0496.0040.1610.1610.0000.0000.0000.000
5A14LYS11.0060.9897.985-0.368-0.3680.0000.0000.0000.000
6A15LYS10.8530.89811.649-0.133-0.1330.0000.0000.0000.000
7A16ASP-1-0.827-0.9179.413-0.078-0.0780.0000.0000.0000.000
8A17MET0-0.037-0.0128.623-0.081-0.0810.0000.0000.0000.000
9A18GLU-1-0.817-0.88812.588-0.006-0.0060.0000.0000.0000.000
10A19LYS10.8500.92613.6590.0370.0370.0000.0000.0000.000
11A20GLY00.0060.00914.586-0.006-0.0060.0000.0000.0000.000
12A21VAL00.0140.00615.7980.0040.0040.0000.0000.0000.000
13A22ILE00.004-0.00718.5180.0110.0110.0000.0000.0000.000
14A23PHE00.0540.00918.6720.0040.0040.0000.0000.0000.000
15A24SER0-0.023-0.01419.8540.0030.0030.0000.0000.0000.000
16A25ASP-1-0.808-0.89721.585-0.102-0.1020.0000.0000.0000.000
17A26LEU00.0130.00823.8910.0120.0120.0000.0000.0000.000
18A27CYS0-0.048-0.01023.4400.0090.0090.0000.0000.0000.000
19A28ASN0-0.042-0.00823.173-0.008-0.0080.0000.0000.0000.000
20A29PHE00.0280.01027.0480.0070.0070.0000.0000.0000.000
21A30LEU00.0070.01128.5200.0010.0010.0000.0000.0000.000
22A31ILE00.011-0.00131.1420.0080.0080.0000.0000.0000.000
23A32THR0-0.027-0.00833.228-0.004-0.0040.0000.0000.0000.000
24A33GLN00.011-0.00435.9200.0030.0030.0000.0000.0000.000
25A34THR00.0180.00038.780-0.001-0.0010.0000.0000.0000.000
26A35LEU00.0170.00941.2020.0010.0010.0000.0000.0000.000
27A36GLN00.0300.01743.0670.0010.0010.0000.0000.0000.000
28A37GLY0-0.066-0.06143.9790.0020.0020.0000.0000.0000.000
29A38TRP00.0030.00639.2900.0000.0000.0000.0000.0000.000
30A39LYS10.8490.92234.7900.0700.0700.0000.0000.0000.000
31A40VAL0-0.023-0.00734.361-0.005-0.0050.0000.0000.0000.000
32A41TYR0-0.051-0.03526.2270.0040.0040.0000.0000.0000.000
33A42TRP00.010-0.01528.809-0.004-0.0040.0000.0000.0000.000
34A43ALA00.0070.01427.4550.0070.0070.0000.0000.0000.000
35A44GLY00.0740.04127.7970.0090.0090.0000.0000.0000.000
36A45ILE0-0.075-0.02828.6020.0080.0080.0000.0000.0000.000
37A46GLU-1-0.847-0.91332.424-0.079-0.0790.0000.0000.0000.000
38A47PHE00.030-0.00633.8500.0060.0060.0000.0000.0000.000
39A48ASP-1-0.852-0.91137.847-0.063-0.0630.0000.0000.0000.000
40A49VAL0-0.011-0.01140.0290.0040.0040.0000.0000.0000.000
41A50SER00.0100.00342.604-0.001-0.0010.0000.0000.0000.000
42A51GLN00.0540.02144.411-0.001-0.0010.0000.0000.0000.000
43A52LYS10.8980.96347.1060.0420.0420.0000.0000.0000.000
44A53GLY00.0150.00950.4300.0000.0000.0000.0000.0000.000
45A54MET00.0670.04449.3170.0010.0010.0000.0000.0000.000
46A55ALA00.0260.02952.4530.0010.0010.0000.0000.0000.000
47A56LEU0-0.022-0.00755.6990.0010.0010.0000.0000.0000.000
48A57LEU00.0210.01251.3010.0010.0010.0000.0000.0000.000
49A58THR00.016-0.02054.2650.0010.0010.0000.0000.0000.000
50A59ARG10.9530.98456.8160.0290.0290.0000.0000.0000.000
51A60LEU0-0.041-0.00557.9450.0010.0010.0000.0000.0000.000
52A61LYS10.8120.92355.6600.0360.0360.0000.0000.0000.000
53A62THR0-0.052-0.02259.5660.0010.0010.0000.0000.0000.000
54A70ALA00.0370.00364.4040.0000.0000.0000.0000.0000.000
55A71MET00.0560.03063.7990.0000.0000.0000.0000.0000.000
56A72THR00.0350.00859.7890.0000.0000.0000.0000.0000.000
57A73ARG10.8760.92860.5840.0250.0250.0000.0000.0000.000
58A74ASN0-0.008-0.01962.2200.0000.0000.0000.0000.0000.000
59A75LEU00.0250.02960.1160.0000.0000.0000.0000.0000.000
60A76PHE00.0030.00555.4810.0000.0000.0000.0000.0000.000
61A77PRO00.0440.03058.700-0.001-0.0010.0000.0000.0000.000
62A78HIS0-0.001-0.02154.2160.0010.0010.0000.0000.0000.000
63A79LEU00.0240.01353.014-0.001-0.0010.0000.0000.0000.000
64A80PHE0-0.057-0.02955.924-0.001-0.0010.0000.0000.0000.000
65A81GLN0-0.0150.00059.4350.0000.0000.0000.0000.0000.000
66A82ASN00.0360.01956.4010.0010.0010.0000.0000.0000.000
67A83PRO00.0100.00658.515-0.001-0.0010.0000.0000.0000.000
68A84ASN0-0.008-0.01755.620-0.002-0.0020.0000.0000.0000.000
69A85SER0-0.054-0.00353.585-0.002-0.0020.0000.0000.0000.000
70A86VAL0-0.011-0.01548.8830.0000.0000.0000.0000.0000.000
71A87ILE00.0040.01249.884-0.001-0.0010.0000.0000.0000.000
72A88GLN0-0.041-0.01244.946-0.003-0.0030.0000.0000.0000.000
73A89SER00.0460.03042.6410.0020.0020.0000.0000.0000.000
74A90PRO00.032-0.00344.252-0.001-0.0010.0000.0000.0000.000
75A91ILE00.0090.01438.2930.0000.0000.0000.0000.0000.000
76A92TRP00.0250.01339.740-0.001-0.0010.0000.0000.0000.000
77A93ALA00.0270.00841.2990.0010.0010.0000.0000.0000.000
78A94LEU00.0090.01237.2070.0010.0010.0000.0000.0000.000
79A95ARG10.7880.90533.3040.0860.0860.0000.0000.0000.000
80A96VAL00.0540.02737.7500.0000.0000.0000.0000.0000.000
81A97ILE0-0.018-0.00340.3600.0020.0020.0000.0000.0000.000
82A98LEU0-0.034-0.01534.5040.0010.0010.0000.0000.0000.000
83A99ALA00.0100.00635.9590.0010.0010.0000.0000.0000.000
84A100ALA00.0320.01936.9890.0020.0020.0000.0000.0000.000
85A101GLY00.0400.01937.8980.0030.0030.0000.0000.0000.000
86A102LEU0-0.059-0.03431.6810.0010.0010.0000.0000.0000.000
87A103GLN00.013-0.00435.2970.0040.0040.0000.0000.0000.000
88A104ASP-1-0.825-0.90738.023-0.027-0.0270.0000.0000.0000.000
89A105GLN0-0.005-0.00131.610-0.001-0.0010.0000.0000.0000.000
90A106LEU0-0.057-0.03634.5640.0020.0020.0000.0000.0000.000
91A107LEU0-0.032-0.01935.8540.0020.0020.0000.0000.0000.000
92A108ASP-1-0.942-0.94838.240-0.016-0.0160.0000.0000.0000.000
93A109HIS0-0.053-0.03432.3050.0010.0010.0000.0000.0000.000
94A110SER00.0220.00634.3040.0000.0000.0000.0000.0000.000
95A111LEU0-0.012-0.00732.752-0.002-0.0020.0000.0000.0000.000
96A112VAL0-0.019-0.00731.278-0.003-0.0030.0000.0000.0000.000
97A113GLU-1-0.842-0.89428.731-0.017-0.0170.0000.0000.0000.000
98A114PRO0-0.025-0.03224.229-0.005-0.0050.0000.0000.0000.000
99A115LEU0-0.039-0.01226.460-0.008-0.0080.0000.0000.0000.000
100A116THR00.0770.02228.038-0.005-0.0050.0000.0000.0000.000
101A117GLY00.0120.01628.635-0.002-0.0020.0000.0000.0000.000
102A118ALA0-0.050-0.04225.816-0.006-0.0060.0000.0000.0000.000
103A119LEU0-0.027-0.00727.715-0.005-0.0050.0000.0000.0000.000
104A120GLY00.0690.04131.120-0.001-0.0010.0000.0000.0000.000
105A121LEU0-0.003-0.00627.360-0.004-0.0040.0000.0000.0000.000
106A122ILE0-0.028-0.02226.354-0.005-0.0050.0000.0000.0000.000
107A123SER0-0.009-0.00130.388-0.001-0.0010.0000.0000.0000.000
108A124ASP-1-0.841-0.92733.642-0.062-0.0620.0000.0000.0000.000
109A125TRP0-0.080-0.01929.371-0.001-0.0010.0000.0000.0000.000
110A126LEU0-0.031-0.00632.565-0.001-0.0010.0000.0000.0000.000
111A127LEU00.0240.01434.9420.0010.0010.0000.0000.0000.000
112A128THR0-0.061-0.04836.3350.0010.0010.0000.0000.0000.000
113A129THR0-0.069-0.03034.132-0.004-0.0040.0000.0000.0000.000
114A130THR00.030-0.00136.6530.0000.0000.0000.0000.0000.000
115A131SER0-0.026-0.00331.758-0.004-0.0040.0000.0000.0000.000
116A132THR00.0620.02131.2040.0010.0010.0000.0000.0000.000
117A133HIS0-0.0040.00023.076-0.012-0.0120.0000.0000.0000.000
118A134PHE00.0630.04726.4460.0040.0040.0000.0000.0000.000
119A135ASN00.0310.00423.671-0.013-0.0130.0000.0000.0000.000
120A136LEU0-0.020-0.00623.142-0.001-0.0010.0000.0000.0000.000
121A137ARG10.8860.91121.4060.1670.1670.0000.0000.0000.000
122A138THR00.0040.00521.541-0.011-0.0110.0000.0000.0000.000
123A139ARG10.9490.97816.6440.2460.2460.0000.0000.0000.000
124A140SER00.0800.04819.3100.0050.0050.0000.0000.0000.000
125A141VAL00.0340.02020.6320.0060.0060.0000.0000.0000.000
126A142LYS10.8590.93717.8770.2360.2360.0000.0000.0000.000
127A143ASP-1-0.858-0.94115.960-0.170-0.1700.0000.0000.0000.000
128A144GLN00.0030.00617.2340.0220.0220.0000.0000.0000.000
129A145LEU0-0.0150.01818.9440.0130.0130.0000.0000.0000.000
130A146SER0-0.027-0.03618.6050.0130.0130.0000.0000.0000.000
131A147LEU00.0300.00820.382-0.004-0.0040.0000.0000.0000.000
132A148ARG10.9460.97222.2980.0050.0050.0000.0000.0000.000
133A149MET00.0070.02124.1420.0000.0000.0000.0000.0000.000
134A150LEU00.0460.03124.0610.0000.0000.0000.0000.0000.000
135A151SER00.0060.00026.2480.0000.0000.0000.0000.0000.000
136A152LEU0-0.0270.00428.3570.0020.0020.0000.0000.0000.000
137A153ILE00.0670.03927.5590.0000.0000.0000.0000.0000.000
138A154ARG10.8140.89428.1320.0610.0610.0000.0000.0000.000
139A155SER0-0.028-0.02331.8780.0020.0020.0000.0000.0000.000
140A156ASN00.008-0.00733.7930.0040.0040.0000.0000.0000.000
141A157ILE00.0040.01733.4300.0000.0000.0000.0000.0000.000
142A158LEU00.0030.00234.7880.0010.0010.0000.0000.0000.000
143A159GLN00.0040.01437.8880.0020.0020.0000.0000.0000.000
144A160PHE00.0260.01239.3360.0010.0010.0000.0000.0000.000
145A161ILE00.001-0.00638.3160.0010.0010.0000.0000.0000.000
146A162ASN0-0.049-0.04141.4310.0020.0020.0000.0000.0000.000
147A163LYS10.7860.88841.7470.0280.0280.0000.0000.0000.000
148A164LEU00.0050.00743.3150.0010.0010.0000.0000.0000.000
149A165ASP-1-0.836-0.91946.147-0.028-0.0280.0000.0000.0000.000
150A166ALA0-0.0060.01048.0570.0010.0010.0000.0000.0000.000
151A167LEU0-0.0790.00049.2670.0010.0010.0000.0000.0000.000
152A168HIS00.0560.02551.9740.0000.0000.0000.0000.0000.000
153A169VAL0-0.028-0.02555.096-0.001-0.0010.0000.0000.0000.000
154A170VAL00.0080.00156.3410.0010.0010.0000.0000.0000.000
155A171ASN0-0.027-0.03258.6250.0000.0000.0000.0000.0000.000
156A172TYR00.009-0.00362.0720.0000.0000.0000.0000.0000.000
157A173ASN0-0.0090.00163.2290.0000.0000.0000.0000.0000.000
158A174GLY00.0110.02260.9030.0000.0000.0000.0000.0000.000
159A175LEU0-0.0230.00358.6280.0000.0000.0000.0000.0000.000
160A176LEU00.0210.01651.592-0.001-0.0010.0000.0000.0000.000
161A177SER00.0400.00254.1960.0000.0000.0000.0000.0000.000
162A178SER0-0.037-0.02951.325-0.001-0.0010.0000.0000.0000.000
163A179ILE00.0130.01245.6860.0010.0010.0000.0000.0000.000
164A180GLU-1-0.941-0.96648.244-0.030-0.0300.0000.0000.0000.000
165A181ILE0-0.022-0.01341.9080.0010.0010.0000.0000.0000.000
166A182GLY00.0140.01745.296-0.002-0.0020.0000.0000.0000.000
167A183THR00.005-0.01139.7240.0010.0010.0000.0000.0000.000
168A184SER0-0.030-0.02841.7140.0010.0010.0000.0000.0000.000
169A185THR0-0.037-0.02440.8090.0010.0010.0000.0000.0000.000
170A186HIS0-0.023-0.01141.175-0.001-0.0010.0000.0000.0000.000
171A187THR0-0.012-0.00144.6680.0020.0020.0000.0000.0000.000
172A188ILE0-0.0060.00841.334-0.001-0.0010.0000.0000.0000.000
173A189ILE00.0180.01345.9420.0020.0020.0000.0000.0000.000
174A190ILE0-0.020-0.00543.601-0.002-0.0020.0000.0000.0000.000
175A191THR00.021-0.00648.2370.0020.0020.0000.0000.0000.000
176A192ARG10.7630.87550.3250.0270.0270.0000.0000.0000.000
177A193THR0-0.015-0.03252.9090.0010.0010.0000.0000.0000.000
178A194ASN00.041-0.00154.5300.0000.0000.0000.0000.0000.000
179A195MET0-0.062-0.02454.2860.0000.0000.0000.0000.0000.000
180A196GLY0-0.012-0.00450.553-0.002-0.0020.0000.0000.0000.000
181A197PHE00.0370.02547.0010.0010.0010.0000.0000.0000.000
182A198LEU0-0.0170.00248.769-0.002-0.0020.0000.0000.0000.000
183A199VAL0-0.035-0.01144.4740.0010.0010.0000.0000.0000.000
184A200GLU-1-0.794-0.89547.938-0.033-0.0330.0000.0000.0000.000
185A201VAL00.0220.01443.7180.0000.0000.0000.0000.0000.000
186A202GLN0-0.005-0.02347.009-0.002-0.0020.0000.0000.0000.000
187A203GLU-1-0.769-0.85844.433-0.049-0.0490.0000.0000.0000.000
188A217VAL00.0100.02050.4500.0010.0010.0000.0000.0000.000
189A218LYS10.8110.89944.5000.0500.0500.0000.0000.0000.000
190A219PHE00.041-0.00348.5990.0010.0010.0000.0000.0000.000
191A220SER0-0.014-0.04246.634-0.001-0.0010.0000.0000.0000.000
192A221LEU0-0.017-0.00848.3910.0020.0020.0000.0000.0000.000
193A222LEU00.0050.02242.705-0.001-0.0010.0000.0000.0000.000
194A223HIS0-0.0050.01046.7450.0010.0010.0000.0000.0000.000
195A224GLU-1-0.752-0.87946.558-0.031-0.0310.0000.0000.0000.000
196A225SER0-0.031-0.03746.534-0.001-0.0010.0000.0000.0000.000
197A226ALA0-0.0110.00142.117-0.001-0.0010.0000.0000.0000.000
198A227PHE0-0.012-0.02940.368-0.002-0.0020.0000.0000.0000.000
199A228LYS10.8480.91943.2350.0310.0310.0000.0000.0000.000
200A229PRO0-0.036-0.00940.0190.0020.0020.0000.0000.0000.000
201A230PHE0-0.0020.00636.8940.0000.0000.0000.0000.0000.000
202A231THR0-0.056-0.00241.3480.0030.0030.0000.0000.0000.000