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: 4LLNN

Calculation Name: 3I82-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3I82

Chain ID: A

ChEMBL ID:

UniProt ID: P76541

Base Structure: X-ray

Registration Date: 2023-09-27

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2240329.094308
FMO2-HF: Nuclear repulsion 2161303.499645
FMO2-HF: Total energy -79025.594663
FMO2-MP2: Total energy -79255.301113


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:2:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-31.036-32.60926.89-12.663-12.657-0.053
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.049 / q_NPA : -0.028
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].
3A4LEU0-0.047-0.0373.517-1.991-0.6280.015-0.609-0.7690.001
4A5ASP-1-0.858-0.9041.918-19.055-17.8999.231-5.616-4.770-0.066
5A6LEU0-0.054-0.0394.5991.2951.376-0.001-0.013-0.0680.000
6A7ILE0-0.0010.0047.7830.1690.1690.0000.0000.0000.000
7A8ARG10.7900.8889.1720.3330.3330.0000.0000.0000.000
8A9PRO0-0.0140.02111.8630.0980.0980.0000.0000.0000.000
9A10SER0-0.060-0.06915.051-0.041-0.0410.0000.0000.0000.000
10A11VAL00.008-0.00618.2450.0110.0110.0000.0000.0000.000
11A12THR0-0.024-0.01820.9460.0060.0060.0000.0000.0000.000
12A13ALA0-0.050-0.03623.3340.0060.0060.0000.0000.0000.000
13A14MET00.0530.04627.022-0.009-0.0090.0000.0000.0000.000
14A15ARG10.8240.90429.417-0.023-0.0230.0000.0000.0000.000
15A16VAL00.0440.02433.269-0.004-0.0040.0000.0000.0000.000
16A17ILE0-0.0260.00536.0770.0020.0020.0000.0000.0000.000
17A18ALA00.011-0.00639.368-0.003-0.0030.0000.0000.0000.000
18A19SER00.0270.01441.786-0.003-0.0030.0000.0000.0000.000
19A20VAL0-0.030-0.00340.9530.0030.0030.0000.0000.0000.000
20A21ASN0-0.0020.00043.642-0.002-0.0020.0000.0000.0000.000
21A22ALA00.0460.00546.3580.0000.0000.0000.0000.0000.000
22A23ASP-1-0.868-0.91648.8820.0100.0100.0000.0000.0000.000
23A24PHE00.0460.01539.0470.0000.0000.0000.0000.0000.000
24A25ALA00.019-0.00243.9280.0000.0000.0000.0000.0000.000
25A26ARG10.8410.92244.999-0.007-0.0070.0000.0000.0000.000
26A27GLU-1-0.817-0.90443.8120.0120.0120.0000.0000.0000.000
27A28LEU0-0.025-0.00638.6360.0010.0010.0000.0000.0000.000
28A29LYS10.7630.87241.435-0.011-0.0110.0000.0000.0000.000
29A30LEU00.0050.01640.125-0.002-0.0020.0000.0000.0000.000
30A31PRO00.0670.03441.9400.0010.0010.0000.0000.0000.000
31A32PRO0-0.025-0.00544.8730.0010.0010.0000.0000.0000.000
32A33HIS0-0.057-0.03741.8990.0030.0030.0000.0000.0000.000
33A34ILE0-0.0120.02339.633-0.001-0.0010.0000.0000.0000.000
34A35ARG10.8600.91143.3060.0120.0120.0000.0000.0000.000
35A36SER0-0.024-0.00840.2660.0030.0030.0000.0000.0000.000
36A37LEU00.012-0.00236.420-0.002-0.0020.0000.0000.0000.000
37A38GLY00.0080.00133.7920.0030.0030.0000.0000.0000.000
38A39LEU0-0.047-0.02632.0670.0010.0010.0000.0000.0000.000
39A40ILE00.029-0.00325.3410.0010.0010.0000.0000.0000.000
40A41SER00.0200.00925.481-0.005-0.0050.0000.0000.0000.000
41A42ALA00.0450.02120.438-0.008-0.0080.0000.0000.0000.000
42A43ASP-1-0.811-0.87216.9650.1280.1280.0000.0000.0000.000
43A44SER00.0340.02515.9250.0130.0130.0000.0000.0000.000
44A45ASP-1-0.749-0.83817.9670.0120.0120.0000.0000.0000.000
45A46ASP-1-0.775-0.88219.096-0.059-0.0590.0000.0000.0000.000
46A47VAL0-0.0200.00215.672-0.025-0.0250.0000.0000.0000.000
47A48THR00.000-0.01819.072-0.014-0.0140.0000.0000.0000.000
48A49TYR0-0.037-0.04522.158-0.004-0.0040.0000.0000.0000.000
49A50ILE0-0.0020.00119.573-0.007-0.0070.0000.0000.0000.000
50A51ALA00.0020.00722.007-0.004-0.0040.0000.0000.0000.000
51A52ALA0-0.004-0.00923.8510.0030.0030.0000.0000.0000.000
52A53ASP-1-0.752-0.88426.639-0.095-0.0950.0000.0000.0000.000
53A54GLU-1-0.838-0.91325.434-0.145-0.1450.0000.0000.0000.000
54A55ALA00.0170.00527.5190.0030.0030.0000.0000.0000.000
55A56THR0-0.085-0.05329.6680.0010.0010.0000.0000.0000.000
56A57LYS10.7610.90127.3810.1340.1340.0000.0000.0000.000
57A58GLN0-0.107-0.06128.7460.0040.0040.0000.0000.0000.000
58A59ALA0-0.0070.01232.1110.0030.0030.0000.0000.0000.000
59A60MET0-0.054-0.02934.9270.0010.0010.0000.0000.0000.000
60A61VAL0-0.053-0.03833.0170.0070.0070.0000.0000.0000.000
61A62GLU-1-0.848-0.92934.963-0.035-0.0350.0000.0000.0000.000
62A63VAL00.0050.00130.5280.0040.0040.0000.0000.0000.000
63A64VAL0-0.045-0.00833.6470.0020.0020.0000.0000.0000.000
64A65TYR00.007-0.01732.2640.0030.0030.0000.0000.0000.000
65A66GLY00.0310.00429.899-0.004-0.0040.0000.0000.0000.000
66A67ARG10.7820.89728.773-0.041-0.0410.0000.0000.0000.000
67A68SER00.0690.02523.715-0.004-0.0040.0000.0000.0000.000
68A69LEU0-0.084-0.03624.758-0.001-0.0010.0000.0000.0000.000
69A70TYR00.006-0.01424.5950.0050.0050.0000.0000.0000.000
70A71ALA0-0.025-0.01123.3740.0060.0060.0000.0000.0000.000
71A72GLY00.0680.05320.4430.0310.0310.0000.0000.0000.000
72A73ALA0-0.007-0.00517.9710.0100.0100.0000.0000.0000.000
73A74ALA0-0.052-0.02317.0390.0060.0060.0000.0000.0000.000
74A75HIS0-0.091-0.06019.0090.0290.0290.0000.0000.0000.000
75A76GLY00.0360.04322.489-0.027-0.0270.0000.0000.0000.000
76A77PRO0-0.047-0.03124.3940.0050.0050.0000.0000.0000.000
77A78SER0-0.021-0.02826.327-0.005-0.0050.0000.0000.0000.000
78A79PRO00.0370.01723.1590.0020.0020.0000.0000.0000.000
79A80THR00.0140.00523.422-0.002-0.0020.0000.0000.0000.000
80A81ALA0-0.0350.00225.854-0.015-0.0150.0000.0000.0000.000
81A82GLY00.0310.02821.601-0.011-0.0110.0000.0000.0000.000
82A83GLU-1-0.816-0.92018.7650.1790.1790.0000.0000.0000.000
83A84VAL00.0090.01622.075-0.012-0.0120.0000.0000.0000.000
84A85LEU0-0.080-0.02224.8420.0030.0030.0000.0000.0000.000
85A86ILE00.0090.01026.759-0.005-0.0050.0000.0000.0000.000
86A87MET0-0.071-0.03529.3700.0030.0030.0000.0000.0000.000
87A88LEU00.0540.03730.045-0.003-0.0030.0000.0000.0000.000
88A89GLY00.003-0.00833.7500.0040.0040.0000.0000.0000.000
89A90GLY00.0780.01637.213-0.005-0.0050.0000.0000.0000.000
90A91PRO00.0050.00539.3210.0040.0040.0000.0000.0000.000
91A92ASN0-0.0110.00141.2540.0020.0020.0000.0000.0000.000
92A93PRO00.019-0.01439.515-0.001-0.0010.0000.0000.0000.000
93A94ALA0-0.043-0.00638.0920.0000.0000.0000.0000.0000.000
94A95GLU-1-0.817-0.91336.790-0.053-0.0530.0000.0000.0000.000
95A96VAL0-0.0110.00635.097-0.003-0.0030.0000.0000.0000.000
96A97ARG10.9050.95633.4580.0190.0190.0000.0000.0000.000
97A98ALA00.0800.04832.087-0.002-0.0020.0000.0000.0000.000
98A99GLY00.0330.01631.138-0.008-0.0080.0000.0000.0000.000
99A100LEU0-0.016-0.03129.116-0.003-0.0030.0000.0000.0000.000
100A101ASP-1-0.915-0.95927.555-0.055-0.0550.0000.0000.0000.000
101A102ALA0-0.021-0.00726.526-0.011-0.0110.0000.0000.0000.000
102A103MET0-0.043-0.01624.948-0.009-0.0090.0000.0000.0000.000
103A104ILE00.005-0.00123.150-0.004-0.0040.0000.0000.0000.000
104A105ALA0-0.0080.00421.673-0.010-0.0100.0000.0000.0000.000
105A106HIS0-0.027-0.02120.624-0.038-0.0380.0000.0000.0000.000
106A107ILE00.0080.01318.774-0.021-0.0210.0000.0000.0000.000
107A108GLU-1-0.923-0.96417.118-0.098-0.0980.0000.0000.0000.000
108A109ASN0-0.094-0.05916.133-0.075-0.0750.0000.0000.0000.000
109A110GLY00.0340.03717.538-0.024-0.0240.0000.0000.0000.000
110A111ALA0-0.043-0.02315.888-0.058-0.0580.0000.0000.0000.000
111A112ALA00.024-0.00211.7170.0380.0380.0000.0000.0000.000
112A113PHE00.0380.02211.779-0.067-0.0670.0000.0000.0000.000
113A114GLN0-0.073-0.0418.2140.1050.1050.0000.0000.0000.000
114A115TRP00.0410.0303.8130.1610.5350.001-0.065-0.3100.000
115A116ALA0-0.010-0.0176.779-0.808-0.8080.0000.0000.0000.000
116A117ASN0-0.017-0.0516.0260.0360.0360.0000.0000.0000.000
117A118ASP-1-0.846-0.9292.138-3.294-1.2623.999-3.252-2.780-0.017
118A119ALA0-0.067-0.0253.0432.7972.217-0.0141.013-0.420-0.001
119A120GLN0-0.070-0.0451.928-10.838-16.83713.659-4.121-3.5400.030
120A121ASP-1-0.870-0.8896.4980.4500.4500.0000.0000.0000.000
121A122THR0-0.011-0.0149.185-0.299-0.2990.0000.0000.0000.000
122A123ALA0-0.021-0.0069.3600.0000.0000.0000.0000.0000.000
123A124PHE0-0.025-0.0219.2810.0040.0040.0000.0000.0000.000
124A125LEU00.0010.01112.573-0.068-0.0680.0000.0000.0000.000
125A126ALA00.0280.01014.7620.0390.0390.0000.0000.0000.000
126A127HIS00.0200.01616.444-0.090-0.0900.0000.0000.0000.000
127A128VAL00.004-0.01318.3720.0350.0350.0000.0000.0000.000
128A129VAL00.0010.01621.612-0.010-0.0100.0000.0000.0000.000
129A130SER0-0.009-0.01624.2850.0180.0180.0000.0000.0000.000
130A131ARG10.9100.95726.0190.1160.1160.0000.0000.0000.000
131A132THR00.0090.00528.2540.0020.0020.0000.0000.0000.000
132A133GLY00.0290.00729.6950.0020.0020.0000.0000.0000.000
133A134SER0-0.0160.01231.5470.0010.0010.0000.0000.0000.000
134A135TYR0-0.0210.01627.1780.0080.0080.0000.0000.0000.000
135A136LEU00.0430.00425.4250.0050.0050.0000.0000.0000.000
136A137SER0-0.042-0.03429.9440.0050.0050.0000.0000.0000.000
137A138SER0-0.034-0.02133.2560.0060.0060.0000.0000.0000.000
138A139THR0-0.085-0.05131.0690.0090.0090.0000.0000.0000.000
139A140ALA0-0.041-0.03433.634-0.005-0.0050.0000.0000.0000.000
140A141GLY00.0450.02534.2580.0010.0010.0000.0000.0000.000
141A142ILE0-0.020-0.00329.537-0.007-0.0070.0000.0000.0000.000
142A143THR0-0.014-0.02033.5410.0090.0090.0000.0000.0000.000
143A144LEU0-0.029-0.02034.174-0.006-0.0060.0000.0000.0000.000
144A145GLY0-0.023-0.01132.9910.0010.0010.0000.0000.0000.000
145A146ASP-1-0.827-0.89032.163-0.102-0.1020.0000.0000.0000.000
146A147PRO0-0.054-0.03127.650-0.005-0.0050.0000.0000.0000.000
147A148MET00.0000.01224.6680.0150.0150.0000.0000.0000.000
148A149ALA0-0.030-0.01522.204-0.022-0.0220.0000.0000.0000.000
149A150TYR0-0.052-0.06920.6790.0210.0210.0000.0000.0000.000
150A151LEU0-0.0120.00019.183-0.036-0.0360.0000.0000.0000.000
151A152VAL00.0170.00617.5120.0320.0320.0000.0000.0000.000
152A153ALA00.0220.01316.124-0.037-0.0370.0000.0000.0000.000
153A154PRO00.0550.03315.3300.0030.0030.0000.0000.0000.000
154A155PRO00.010-0.00418.340-0.033-0.0330.0000.0000.0000.000
155A156LEU0-0.0300.00820.007-0.021-0.0210.0000.0000.0000.000
156A157GLU-1-0.788-0.93215.3430.0920.0920.0000.0000.0000.000
157A158ALA00.0060.02418.345-0.041-0.0410.0000.0000.0000.000
158A159THR0-0.020-0.02420.172-0.022-0.0220.0000.0000.0000.000
159A160TYR0-0.094-0.06218.8640.0020.0020.0000.0000.0000.000
160A161GLY00.0520.02419.420-0.018-0.0180.0000.0000.0000.000
161A162ILE0-0.020-0.01920.227-0.021-0.0210.0000.0000.0000.000
162A163ASP-1-0.843-0.90223.507-0.082-0.0820.0000.0000.0000.000
163A164ALA00.0330.01321.343-0.003-0.0030.0000.0000.0000.000
164A165ALA0-0.018-0.00321.768-0.010-0.0100.0000.0000.0000.000
165A166LEU0-0.026-0.01523.306-0.003-0.0030.0000.0000.0000.000
166A167LYS10.7500.86926.0710.0920.0920.0000.0000.0000.000
167A168SER0-0.073-0.03923.183-0.010-0.0100.0000.0000.0000.000
168A169ALA0-0.034-0.02324.911-0.012-0.0120.0000.0000.0000.000
169A170ASP-1-0.952-0.96826.957-0.107-0.1070.0000.0000.0000.000
170A171VAL0-0.030-0.02426.027-0.006-0.0060.0000.0000.0000.000
171A172GLN0-0.012-0.00629.2860.0110.0110.0000.0000.0000.000
172A173LEU00.007-0.00527.839-0.006-0.0060.0000.0000.0000.000
173A174ALA0-0.0320.00430.2260.0090.0090.0000.0000.0000.000
174A175THR0-0.015-0.01628.3970.0080.0080.0000.0000.0000.000
175A176TYR00.008-0.00825.379-0.006-0.0060.0000.0000.0000.000
176A177VAL00.0050.01725.7860.0070.0070.0000.0000.0000.000
177A178PRO00.0210.02625.8780.0010.0010.0000.0000.0000.000
178A179PRO0-0.0280.02223.9330.0060.0060.0000.0000.0000.000
179A180PRO0-0.072-0.03324.945-0.001-0.0010.0000.0000.0000.000
180A181SER00.0690.01422.609-0.005-0.0050.0000.0000.0000.000
181A182GLU-1-0.836-0.92025.3830.0620.0620.0000.0000.0000.000
182A183THR00.020-0.00720.2720.0160.0160.0000.0000.0000.000
183A184ASN0-0.114-0.05220.6600.0170.0170.0000.0000.0000.000
184A185TYR00.0290.02515.2070.0130.0130.0000.0000.0000.000
185A186SER0-0.065-0.05720.727-0.006-0.0060.0000.0000.0000.000
186A187ALA00.0600.01621.036-0.012-0.0120.0000.0000.0000.000
187A188ALA0-0.005-0.00722.9910.0100.0100.0000.0000.0000.000
188A189PHE0-0.0260.00723.842-0.018-0.0180.0000.0000.0000.000
189A190LEU0-0.008-0.00524.4470.0090.0090.0000.0000.0000.000
190A191THR00.0520.02627.142-0.015-0.0150.0000.0000.0000.000
191A192GLY00.0680.02029.6970.0020.0020.0000.0000.0000.000
192A193SER00.0130.01429.601-0.006-0.0060.0000.0000.0000.000
193A194GLN00.0270.01425.174-0.022-0.0220.0000.0000.0000.000
194A195ALA00.0070.00024.557-0.019-0.0190.0000.0000.0000.000
195A196ALA00.0130.01524.055-0.019-0.0190.0000.0000.0000.000
196A197CYS00.0140.01124.119-0.003-0.0030.0000.0000.0000.000
197A198LYS10.9270.96015.1650.5110.5110.0000.0000.0000.000
198A199ALA0-0.020-0.01119.622-0.034-0.0340.0000.0000.0000.000
199A200ALA00.0340.02120.554-0.015-0.0150.0000.0000.0000.000
200A201CYS0-0.042-0.01517.4880.0060.0060.0000.0000.0000.000
201A202ASN0-0.0090.00715.912-0.069-0.0690.0000.0000.0000.000
202A203ALA00.0570.03016.384-0.025-0.0250.0000.0000.0000.000
203A204PHE0-0.029-0.00416.4040.0140.0140.0000.0000.0000.000
204A205THR0-0.007-0.01811.807-0.007-0.0070.0000.0000.0000.000
205A206ASP-1-0.913-0.96113.681-0.517-0.5170.0000.0000.0000.000
206A207ALA0-0.0060.00515.0250.0280.0280.0000.0000.0000.000
207A208VAL00.0270.00412.2870.0560.0560.0000.0000.0000.000
208A209LEU00.0140.0038.8840.0480.0480.0000.0000.0000.000
209A210GLU-1-0.957-0.95312.022-0.123-0.1230.0000.0000.0000.000
210A211ILE0-0.0180.00714.8400.0470.0470.0000.0000.0000.000
211A212ALA00.007-0.0039.9860.0580.0580.0000.0000.0000.000
212A213ARG10.8380.91910.2460.4590.4590.0000.0000.0000.000
213A214ASN0-0.061-0.03412.0440.0760.0760.0000.0000.0000.000
214A215PRO00.0400.03014.341-0.025-0.0250.0000.0000.0000.000
215A216ILE0-0.054-0.03216.980-0.008-0.0080.0000.0000.0000.000
216A217GLN0-0.0150.00819.722-0.005-0.0050.0000.0000.0000.000