Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: LJMV9

Calculation Name: 4FBD-A-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FBD

Chain ID: A

ChEMBL ID:

UniProt ID:

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 -2152913.84235
FMO2-HF: Nuclear repulsion 2073194.068502
FMO2-HF: Total energy -79719.773848
FMO2-MP2: Total energy -79952.285778


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:13:ACE )


Summations of interaction energy for fragment #1(A:13: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.
0.8741.897-0.005-0.449-0.568-0.001
Interaction energy analysis for fragmet #1(A:13:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / 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].
3A15PRO 00.0660.0353.8600.2121.235-0.005-0.449-0.568-0.001
4A16ALA 00.0260.0165.5420.3820.3820.0000.0000.0000.000
5A17PRO 00.0330.0116.5350.0330.0330.0000.0000.0000.000
6A18ALA 00.0110.0149.4220.0190.0190.0000.0000.0000.000
7A19ASP -1-0.999-0.9969.089-0.570-0.5700.0000.0000.0000.000
8A20LEU 0-0.073-0.0319.127-0.074-0.0740.0000.0000.0000.000
9A21PRO 00.0230.01612.4570.0420.0420.0000.0000.0000.000
10A22LEU 0-0.012-0.02112.526-0.029-0.0290.0000.0000.0000.000
11A23GLY 00.0680.01715.7150.0410.0410.0000.0000.0000.000
12A24LEU 0-0.063-0.04419.215-0.016-0.0160.0000.0000.0000.000
13A25ASP -1-0.822-0.91021.999-0.128-0.1280.0000.0000.0000.000
14A26PRO 00.014-0.05424.3300.0030.0030.0000.0000.0000.000
15A27PHE 0-0.097-0.01827.6400.0090.0090.0000.0000.0000.000
16A28CYS 00.0200.01625.8100.0010.0010.0000.0000.0000.000
17A29TYR 0-0.0060.00325.3960.0080.0080.0000.0000.0000.000
18A30NME 0-0.0400.01625.1480.0100.0100.0000.0000.0000.000
19A39ACE 00.0520.02127.131-0.001-0.0010.0000.0000.0000.000
20A40SER 0-0.062-0.05127.1430.0040.0040.0000.0000.0000.000
21A41ARG 10.9961.00928.8090.0740.0740.0000.0000.0000.000
22A42ILE 00.0110.02126.4390.0030.0030.0000.0000.0000.000
23A43SER 0-0.024-0.03029.8040.0030.0030.0000.0000.0000.000
24A44GLY 00.001-0.00431.829-0.001-0.0010.0000.0000.0000.000
25A45VAL 00.0350.03227.9810.0020.0020.0000.0000.0000.000
26A46THR 00.0180.01729.756-0.005-0.0050.0000.0000.0000.000
27A47LYS 10.9390.96226.9370.0900.0900.0000.0000.0000.000
28A48GLU -1-0.855-0.93125.343-0.092-0.0920.0000.0000.0000.000
29A49GLU -1-0.918-0.96124.844-0.068-0.0680.0000.0000.0000.000
30A50PHE 0-0.044-0.02222.214-0.005-0.0050.0000.0000.0000.000
31A51LEU 00.0070.00119.372-0.010-0.0100.0000.0000.0000.000
32A52GLU -1-0.940-0.95720.016-0.094-0.0940.0000.0000.0000.000
33A53LYS 11.0531.01020.4490.0620.0620.0000.0000.0000.000
34A54VAL 0-0.062-0.01516.880-0.005-0.0050.0000.0000.0000.000
35A55ASN 00.004-0.01115.798-0.051-0.0510.0000.0000.0000.000
36A56GLU -1-0.927-0.93615.749-0.059-0.0590.0000.0000.0000.000
37A57LEU 0-0.077-0.06717.0460.0150.0150.0000.0000.0000.000
38A58VAL 0-0.062-0.02611.277-0.002-0.0020.0000.0000.0000.000
39A59THR 0-0.041-0.03111.9650.0140.0140.0000.0000.0000.000
40A60ARG 10.9060.97413.2250.0870.0870.0000.0000.0000.000
41A61ASP -1-0.898-0.94013.7800.0070.0070.0000.0000.0000.000
42A62ALA 00.006-0.0099.491-0.044-0.0440.0000.0000.0000.000
43A63GLY 0-0.025-0.0088.8600.0190.0190.0000.0000.0000.000
44A64ILE 0-0.064-0.02211.045-0.040-0.0400.0000.0000.0000.000
45A65GLU -1-0.943-0.9608.067-0.312-0.3120.0000.0000.0000.000
46A66PHE 00.025-0.0037.497-0.035-0.0350.0000.0000.0000.000
47A67PHE 0-0.015-0.0298.620-0.136-0.1360.0000.0000.0000.000
48A68GLN 0-0.084-0.06910.8020.0300.0300.0000.0000.0000.000
49A69GLY 00.0340.02312.0490.0630.0630.0000.0000.0000.000
50A70TYR 00.006-0.00615.7070.0420.0420.0000.0000.0000.000
51A71ALA 00.0280.04317.5220.0150.0150.0000.0000.0000.000
52A72PRO 0-0.007-0.01913.983-0.040-0.0400.0000.0000.0000.000
53A73PHE 00.0100.01114.164-0.053-0.0530.0000.0000.0000.000
54A74CYS 00.0010.02816.0490.0090.0090.0000.0000.0000.000
55A75ARG 10.9060.9467.3321.1721.1720.0000.0000.0000.000
56A76HIS 10.8310.92013.1350.3700.3700.0000.0000.0000.000
57A77LEU 00.0580.05212.036-0.075-0.0750.0000.0000.0000.000
58A78TYR 0-0.0060.01313.8210.0420.0420.0000.0000.0000.000
59A79ILE 00.0350.02415.303-0.006-0.0060.0000.0000.0000.000
60A80PRO 00.036-0.00417.6020.0090.0090.0000.0000.0000.000
61A81ASN 0-0.031-0.02420.904-0.011-0.0110.0000.0000.0000.000
62A82PHE 0-0.005-0.00521.6520.0120.0120.0000.0000.0000.000
63A83VAL 0-0.015-0.00225.3580.0050.0050.0000.0000.0000.000
64A84GLY 00.0000.00927.7420.0050.0050.0000.0000.0000.000
65A85ALA 00.0010.01127.2640.0030.0030.0000.0000.0000.000
66A86LEU 00.0410.01629.1630.0010.0010.0000.0000.0000.000
67A87PRO 0-0.0160.00729.009-0.007-0.0070.0000.0000.0000.000
68A88GLY 0-0.003-0.00429.7850.0040.0040.0000.0000.0000.000
69A89SER 0-0.085-0.05530.7990.0020.0020.0000.0000.0000.000
70A90LEU 00.0520.03332.677-0.001-0.0010.0000.0000.0000.000
71A91PRO 00.0130.00033.331-0.001-0.0010.0000.0000.0000.000
72A92ILE 0-0.046-0.00635.1750.0020.0020.0000.0000.0000.000
73A93THR 0-0.039-0.03538.3330.0010.0010.0000.0000.0000.000
74A94ALA 00.0400.00440.4310.0000.0000.0000.0000.0000.000
75A95ASP -1-0.866-0.92343.558-0.022-0.0220.0000.0000.0000.000
76A96ASN 0-0.060-0.04039.2890.0010.0010.0000.0000.0000.000
77A97GLU -1-0.908-0.94943.091-0.030-0.0300.0000.0000.0000.000
78A98HIS 0-0.018-0.01944.027-0.001-0.0010.0000.0000.0000.000
79A99LEU 0-0.024-0.01044.4430.0000.0000.0000.0000.0000.000
80A100LEU 0-0.078-0.01640.169-0.002-0.0020.0000.0000.0000.000
81A101ARG 10.8790.95443.9030.0330.0330.0000.0000.0000.000
82A102SER 0-0.018-0.02543.863-0.002-0.0020.0000.0000.0000.000
83A103GLY 00.0610.01644.6660.0020.0020.0000.0000.0000.000
84A104TYR 00.0020.00344.491-0.002-0.0020.0000.0000.0000.000
85A105ILE 00.0290.01741.6950.0010.0010.0000.0000.0000.000
86A106ALA 00.0580.03641.954-0.001-0.0010.0000.0000.0000.000
87A107ARG 10.7580.83233.1950.0750.0750.0000.0000.0000.000
88A108ARG 10.9620.97934.9320.0720.0720.0000.0000.0000.000
89A109PRO 00.0060.00240.9290.0010.0010.0000.0000.0000.000
90A110ASN 0-0.016-0.01540.6400.0010.0010.0000.0000.0000.000
91A111GLU -1-0.770-0.83437.661-0.068-0.0680.0000.0000.0000.000
92A112LEU 0-0.009-0.02442.4430.0020.0020.0000.0000.0000.000
93A113PRO 0-0.028-0.00642.669-0.002-0.0020.0000.0000.0000.000
94A114VAL 0-0.024-0.02339.3180.0010.0010.0000.0000.0000.000
95A115LEU 0-0.0280.00542.6500.0000.0000.0000.0000.0000.000
96A116THR 0-0.065-0.02838.662-0.004-0.0040.0000.0000.0000.000
97A117ARG 10.9100.93737.7950.0460.0460.0000.0000.0000.000
98A118TRP 0-0.054-0.03639.140-0.004-0.0040.0000.0000.0000.000
99A119PHE 00.0430.02037.9260.0030.0030.0000.0000.0000.000
100A120PRO 00.0300.01540.768-0.003-0.0030.0000.0000.0000.000
101A121MET 00.0600.01639.650-0.001-0.0010.0000.0000.0000.000
102A122SER 0-0.082-0.04243.0100.0010.0010.0000.0000.0000.000
103A123TYR 00.0390.02339.9960.0010.0010.0000.0000.0000.000
104A124ALA 00.020-0.00538.7360.0000.0000.0000.0000.0000.000
105A125LYS 10.8210.91739.5170.0300.0300.0000.0000.0000.000
106A126ASP -1-0.874-0.92441.067-0.031-0.0310.0000.0000.0000.000
107A127ALA 0-0.051-0.02738.7320.0010.0010.0000.0000.0000.000
108A128LEU 0-0.070-0.03833.911-0.002-0.0020.0000.0000.0000.000
109A129MET 00.0330.01733.2940.0020.0020.0000.0000.0000.000
110A130PRO 0-0.037-0.02829.732-0.005-0.0050.0000.0000.0000.000
111A131ALA 0-0.0340.00226.3380.0020.0020.0000.0000.0000.000
112A132ALA 00.0380.01324.230-0.001-0.0010.0000.0000.0000.000
113A133PHE 0-0.053-0.03619.918-0.003-0.0030.0000.0000.0000.000
114A134LEU 00.0260.01220.6360.0070.0070.0000.0000.0000.000
115A135ASP -1-0.839-0.91117.929-0.256-0.2560.0000.0000.0000.000
116A136LEU 0-0.002-0.01116.6750.0190.0190.0000.0000.0000.000
117A137ILE 0-0.005-0.01716.723-0.048-0.0480.0000.0000.0000.000
118A138LEU 0-0.013-0.01212.8800.0110.0110.0000.0000.0000.000
119A139TYR 00.0480.00516.735-0.009-0.0090.0000.0000.0000.000
120A140SER 00.0080.01315.9900.0000.0000.0000.0000.0000.000
121A141ARG 10.9430.97516.2500.2600.2600.0000.0000.0000.000
122A142GLU -1-0.901-0.96417.700-0.233-0.2330.0000.0000.0000.000
123A143GLN 0-0.048-0.04120.0130.0330.0330.0000.0000.0000.000
124A144ILE 00.0870.05520.5480.0150.0150.0000.0000.0000.000
125A145ALA 0-0.0030.03423.2220.0180.0180.0000.0000.0000.000
126A146LYS 10.9230.94922.9010.1740.1740.0000.0000.0000.000
127A147GLU -1-0.905-0.95125.042-0.145-0.1450.0000.0000.0000.000
128A148THR 00.013-0.00626.6980.0100.0100.0000.0000.0000.000
129A149ALA 0-0.035-0.01929.0980.0090.0090.0000.0000.0000.000
130A150ALA 0-0.011-0.00830.2450.0080.0080.0000.0000.0000.000
131A151GLU -1-0.970-0.97831.430-0.081-0.0810.0000.0000.0000.000
132A152SER 0-0.052-0.02433.2350.0070.0070.0000.0000.0000.000
133A153ASN 0-0.108-0.06734.4450.0050.0050.0000.0000.0000.000
134A154THR 0-0.0290.00333.9080.0060.0060.0000.0000.0000.000
135A155ALA 0-0.002-0.00333.309-0.004-0.0040.0000.0000.0000.000
136A156VAL 0-0.010-0.01327.163-0.001-0.0010.0000.0000.0000.000
137A157VAL 0-0.0130.00028.6980.0020.0020.0000.0000.0000.000
138A158ILE 0-0.021-0.01622.193-0.007-0.0070.0000.0000.0000.000
139A159ASP -1-0.821-0.90424.179-0.104-0.1040.0000.0000.0000.000
140A160PRO 0-0.047-0.03021.130-0.016-0.0160.0000.0000.0000.000
141A161ASN 0-0.025-0.02219.819-0.015-0.0150.0000.0000.0000.000
142A162ALA 0-0.0120.01520.690-0.003-0.0030.0000.0000.0000.000
143A163PRO 00.0420.01516.969-0.017-0.0170.0000.0000.0000.000
144A164ALA 00.0050.01013.0720.0010.0010.0000.0000.0000.000
145A165TRP 0-0.043-0.02110.616-0.012-0.0120.0000.0000.0000.000
146A166SER 00.0070.00115.2310.0330.0330.0000.0000.0000.000
147A167ILE 00.001-0.01618.115-0.011-0.0110.0000.0000.0000.000
148A168ILE 00.0390.02419.6570.0210.0210.0000.0000.0000.000
149A169ALA 0-0.015-0.01021.5020.0210.0210.0000.0000.0000.000
150A170VAL 00.0150.00821.409-0.020-0.0200.0000.0000.0000.000
151A171LYS 10.9040.95922.4590.1340.1340.0000.0000.0000.000
152A172ALA 00.0400.03323.217-0.008-0.0080.0000.0000.0000.000
153A173GLN 0-0.106-0.08021.7270.0040.0040.0000.0000.0000.000
154A174ASN 00.0570.02624.323-0.002-0.0020.0000.0000.0000.000
155A175GLU -1-0.828-0.88223.152-0.081-0.0810.0000.0000.0000.000
156A176LYS 10.9230.97614.9860.1330.1330.0000.0000.0000.000
157A177TYR 00.0240.00817.900-0.008-0.0080.0000.0000.0000.000
158A178SER 00.0300.01119.121-0.001-0.0010.0000.0000.0000.000
159A179LEU 00.0130.01920.7120.0120.0120.0000.0000.0000.000
160A180PRO 0-0.0180.01224.398-0.005-0.0050.0000.0000.0000.000
161A181MET 00.0390.02726.3420.0070.0070.0000.0000.0000.000
162A182ALA 00.0320.02928.7060.0050.0050.0000.0000.0000.000
163A183PRO 00.0570.01532.359-0.002-0.0020.0000.0000.0000.000
164A184ILE 00.0800.03334.027-0.001-0.0010.0000.0000.0000.000
165A185THR 0-0.036-0.01531.3770.0020.0020.0000.0000.0000.000
166A186MET 0-0.016-0.00429.817-0.002-0.0020.0000.0000.0000.000
167A187LEU 0-0.0130.00332.6360.0010.0010.0000.0000.0000.000
168A188ARG 11.0111.02035.0160.0670.0670.0000.0000.0000.000
169A189ASN 0-0.006-0.00630.2640.0020.0020.0000.0000.0000.000
170A190THR 0-0.085-0.04733.810-0.001-0.0010.0000.0000.0000.000
171A191LEU 00.0070.01035.6190.0030.0030.0000.0000.0000.000
172A192ILE 00.0530.02436.297-0.002-0.0020.0000.0000.0000.000
173A193GLU -1-0.995-0.99638.217-0.046-0.0460.0000.0000.0000.000
174A194GLU -1-0.830-0.88439.939-0.052-0.0520.0000.0000.0000.000
175A195GLY 0-0.0580.00436.218-0.003-0.0030.0000.0000.0000.000
176A196GLY 0-0.022-0.03732.9410.0000.0000.0000.0000.0000.000
177A197SER 0-0.049-0.05129.2830.0020.0020.0000.0000.0000.000
178A198GLY 00.0650.04432.1190.0030.0030.0000.0000.0000.000
179A199VAL 0-0.086-0.03729.3220.0030.0030.0000.0000.0000.000
180A200ALA 00.008-0.00432.5320.0010.0010.0000.0000.0000.000
181A201LEU 00.011-0.00231.779-0.004-0.0040.0000.0000.0000.000
182A202ASP -1-0.808-0.88726.663-0.078-0.0780.0000.0000.0000.000
183A203ARG 10.9560.94030.2080.0450.0450.0000.0000.0000.000
184A204GLU -1-0.918-0.95328.203-0.049-0.0490.0000.0000.0000.000
185A205ALA 00.0320.03126.5430.0000.0000.0000.0000.0000.000
186A206TYR 0-0.015-0.02228.0280.0000.0000.0000.0000.0000.000
187A207LYS 10.9250.95631.4910.0430.0430.0000.0000.0000.000
188A208ALA 00.0350.02926.9780.0020.0020.0000.0000.0000.000
189A209SER 0-0.020-0.04229.1190.0020.0020.0000.0000.0000.000
190A210VAL 0-0.013-0.02130.0370.0030.0030.0000.0000.0000.000
191A211ALA 0-0.047-0.03330.5730.0030.0030.0000.0000.0000.000
192A212TYR 0-0.023-0.02927.6670.0030.0030.0000.0000.0000.000
193A213TRP 0-0.023-0.01329.6410.0060.0060.0000.0000.0000.000
194A214LYS 10.9270.97533.6590.0410.0410.0000.0000.0000.000
195A215THR 00.009-0.00433.3470.0020.0020.0000.0000.0000.000
196A216HIS 10.8990.95330.5110.0600.0600.0000.0000.0000.000
197A217ALA 00.0000.00934.437-0.001-0.0010.0000.0000.0000.000
198A218ILE 00.0210.01133.357-0.001-0.0010.0000.0000.0000.000
199A219VAL 00.0250.02235.4800.0040.0040.0000.0000.0000.000
200A220MET 0-0.040-0.03037.375-0.003-0.0030.0000.0000.0000.000
201A221ASP -1-0.935-0.95940.042-0.039-0.0390.0000.0000.0000.000
202A222LYS 10.9490.97042.9360.0420.0420.0000.0000.0000.000
203A223GLU -1-0.773-0.87145.678-0.034-0.0340.0000.0000.0000.000
204A224SER 0-0.030-0.01948.2380.0010.0010.0000.0000.0000.000
205A225SER 0-0.044-0.02948.289-0.001-0.0010.0000.0000.0000.000
206A226LEU 0-0.066-0.02749.3080.0000.0000.0000.0000.0000.000
207A227GLU -2-1.889-1.92551.221-0.063-0.0630.0000.0000.0000.000