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: LZ7Y9

Calculation Name: 4FGP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FGP

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZXA4

Base Structure: X-ray

Registration Date: 2023-06-22

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 OptH
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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2110757.579318
FMO2-HF: Nuclear repulsion 2036935.784844
FMO2-HF: Total energy -73821.794474
FMO2-MP2: Total energy -74038.823374


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:56:ALA)


Summations of interaction energy for fragment #1(A:56:ALA)
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.
0.9372.7250.003-0.743-1.0510.005
Interaction energy analysis for fragmet #1(A:56:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : 0.029
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].
3A58LEU00.011-0.0123.830-0.2781.064-0.018-0.646-0.6790.005
4A59ILE00.0050.0156.5800.4490.4490.0000.0000.0000.000
5A60SER0-0.027-0.02410.127-0.020-0.0200.0000.0000.0000.000
6A61VAL00.0650.02912.4920.0380.0380.0000.0000.0000.000
7A62GLU-1-0.865-0.93415.420-0.529-0.5290.0000.0000.0000.000
8A63LYS10.8650.9298.2201.7861.7860.0000.0000.0000.000
9A64ILE00.0170.02014.7130.0540.0540.0000.0000.0000.000
10A65GLN00.0100.00017.0900.0450.0450.0000.0000.0000.000
11A66LYS10.9220.95717.3230.4870.4870.0000.0000.0000.000
12A67LEU00.0380.03015.2780.0360.0360.0000.0000.0000.000
13A68ALA00.0170.03519.4270.0410.0410.0000.0000.0000.000
14A69GLN0-0.022-0.00622.5620.0230.0230.0000.0000.0000.000
15A70SER0-0.069-0.05021.6620.0170.0170.0000.0000.0000.000
16A71TYR00.0550.03819.8100.0290.0290.0000.0000.0000.000
17A72GLN00.000-0.02725.6260.0080.0080.0000.0000.0000.000
18A73GLY00.0160.00428.646-0.003-0.0030.0000.0000.0000.000
19A74ASP-1-0.836-0.93529.283-0.147-0.1470.0000.0000.0000.000
20A75THR00.0180.01323.836-0.008-0.0080.0000.0000.0000.000
21A76ARG10.8700.95124.3200.1760.1760.0000.0000.0000.000
22A77LYS10.9300.95224.8780.1360.1360.0000.0000.0000.000
23A78ARG10.8940.96723.1060.1850.1850.0000.0000.0000.000
24A79PHE00.0290.02017.594-0.020-0.0200.0000.0000.0000.000
25A80THR0-0.039-0.02320.799-0.024-0.0240.0000.0000.0000.000
26A81ALA0-0.017-0.00622.770-0.008-0.0080.0000.0000.0000.000
27A82TRP00.0330.01413.498-0.003-0.0030.0000.0000.0000.000
28A83GLY00.0290.00818.065-0.027-0.0270.0000.0000.0000.000
29A84ASN00.022-0.00419.129-0.014-0.0140.0000.0000.0000.000
30A85LEU0-0.0280.00718.4080.0100.0100.0000.0000.0000.000
31A86ILE00.007-0.00713.9600.0090.0090.0000.0000.0000.000
32A87ASP-1-0.834-0.93417.516-0.385-0.3850.0000.0000.0000.000
33A88SER0-0.141-0.06319.7580.0290.0290.0000.0000.0000.000
34A89LEU00.006-0.01018.5870.0320.0320.0000.0000.0000.000
35A90LYS10.9731.00514.9370.5180.5180.0000.0000.0000.000
36A91LYS10.9130.94618.5560.2790.2790.0000.0000.0000.000
37A92LYS10.8880.98020.3530.2380.2380.0000.0000.0000.000
38A93PRO00.0330.00720.866-0.006-0.0060.0000.0000.0000.000
39A94VAL00.1160.05818.251-0.006-0.0060.0000.0000.0000.000
40A95LYS10.9530.98520.2530.0750.0750.0000.0000.0000.000
41A96ILE00.0150.00422.8190.0000.0000.0000.0000.0000.000
42A97GLN0-0.025-0.02017.0980.0070.0070.0000.0000.0000.000
43A98LEU00.0300.00917.247-0.014-0.0140.0000.0000.0000.000
44A99GLU-1-0.901-0.96219.635-0.116-0.1160.0000.0000.0000.000
45A100LYS10.9190.95922.0230.1700.1700.0000.0000.0000.000
46A101VAL00.0270.02615.993-0.004-0.0040.0000.0000.0000.000
47A102ASN00.0310.01719.343-0.005-0.0050.0000.0000.0000.000
48A103SER0-0.027-0.03221.1360.0040.0040.0000.0000.0000.000
49A104PHE0-0.0190.00120.5010.0060.0060.0000.0000.0000.000
50A105PHE00.036-0.01817.0590.0010.0010.0000.0000.0000.000
51A106ASN00.0480.03221.5990.0020.0020.0000.0000.0000.000
52A107GLN0-0.088-0.02024.4160.0210.0210.0000.0000.0000.000
53A108PHE0-0.077-0.03022.153-0.001-0.0010.0000.0000.0000.000
54A109ASN00.0220.01725.5620.0160.0160.0000.0000.0000.000
55A110TYR00.0230.00024.616-0.010-0.0100.0000.0000.0000.000
56A111GLU-1-0.901-0.95824.303-0.103-0.1030.0000.0000.0000.000
57A112THR0-0.017-0.02126.1360.0010.0010.0000.0000.0000.000
58A113ASP-1-0.756-0.87127.669-0.017-0.0170.0000.0000.0000.000
59A114PRO0-0.086-0.04029.1440.0020.0020.0000.0000.0000.000
60A115ILE0-0.078-0.04232.1680.0030.0030.0000.0000.0000.000
61A116THR0-0.039-0.02829.2470.0020.0020.0000.0000.0000.000
62A117GLY0-0.0040.01431.5990.0020.0020.0000.0000.0000.000
63A118ALA0-0.034-0.02527.363-0.003-0.0030.0000.0000.0000.000
64A119SER0-0.075-0.03522.295-0.005-0.0050.0000.0000.0000.000
65A120ASP-1-0.863-0.93923.173-0.040-0.0400.0000.0000.0000.000
66A121ASP-1-0.962-0.98321.9650.0350.0350.0000.0000.0000.000
67A122TYR0-0.134-0.09617.2070.0260.0260.0000.0000.0000.000
68A123TRP00.0140.01313.0300.0090.0090.0000.0000.0000.000
69A124LYS10.7930.87115.4320.1280.1280.0000.0000.0000.000
70A125SER0-0.029-0.02411.763-0.048-0.0480.0000.0000.0000.000
71A126PRO00.018-0.01511.1210.0310.0310.0000.0000.0000.000
72A127VAL00.0290.00013.6330.0410.0410.0000.0000.0000.000
73A128GLU-1-0.722-0.83115.638-0.185-0.1850.0000.0000.0000.000
74A129PHE00.0570.05416.9950.0210.0210.0000.0000.0000.000
75A130ILE0-0.038-0.02117.8780.0260.0260.0000.0000.0000.000
76A131VAL0-0.040-0.03719.8630.0250.0250.0000.0000.0000.000
77A132ASP-1-0.820-0.88821.531-0.148-0.1480.0000.0000.0000.000
78A133GLY0-0.090-0.03422.8090.0160.0160.0000.0000.0000.000
79A134GLY00.002-0.01622.6070.0120.0120.0000.0000.0000.000
80A135GLY00.0110.01521.179-0.013-0.0130.0000.0000.0000.000
81A136ASP-1-0.648-0.79320.683-0.067-0.0670.0000.0000.0000.000
82A137CYS0-0.037-0.02121.114-0.014-0.0140.0000.0000.0000.000
83A138GLU-1-0.865-0.95917.701-0.015-0.0150.0000.0000.0000.000
84A139ASP-1-0.756-0.88016.737-0.154-0.1540.0000.0000.0000.000
85A140PHE0-0.098-0.04616.868-0.049-0.0490.0000.0000.0000.000
86A141ALA0-0.050-0.01816.293-0.033-0.0330.0000.0000.0000.000
87A142ILE00.0360.01611.501-0.049-0.0490.0000.0000.0000.000
88A143ILE0-0.0260.00112.153-0.108-0.1080.0000.0000.0000.000
89A144LYS10.8040.90113.7090.0960.0960.0000.0000.0000.000
90A145TYR00.0160.0006.409-0.042-0.0420.0000.0000.0000.000
91A146PHE00.0520.0055.439-0.046-0.0460.0000.0000.0000.000
92A147THR0-0.050-0.0249.781-0.112-0.1120.0000.0000.0000.000
93A148LEU0-0.010-0.01512.779-0.002-0.0020.0000.0000.0000.000
94A149VAL00.0360.0296.1660.0220.0220.0000.0000.0000.000
95A150ALA0-0.048-0.0149.633-0.030-0.0300.0000.0000.0000.000
96A151VAL0-0.101-0.04610.9670.0540.0540.0000.0000.0000.000
97A152GLY0-0.045-0.02712.3080.0630.0630.0000.0000.0000.000
98A153VAL0-0.044-0.00812.9260.0630.0630.0000.0000.0000.000
99A154PRO00.0230.01310.647-0.090-0.0900.0000.0000.0000.000
100A155SER00.009-0.0156.468-0.014-0.0140.0000.0000.0000.000
101A156ASP-1-0.900-0.9468.6420.0640.0640.0000.0000.0000.000
102A157GLN0-0.058-0.02810.8000.0130.0130.0000.0000.0000.000
103A158LEU0-0.050-0.01510.750-0.004-0.0040.0000.0000.0000.000
104A159ARG10.9280.97311.182-0.114-0.1140.0000.0000.0000.000
105A160ILE00.0520.02811.026-0.028-0.0280.0000.0000.0000.000
106A161THR0-0.034-0.02414.2480.0560.0560.0000.0000.0000.000
107A162TYR00.0640.04417.678-0.015-0.0150.0000.0000.0000.000
108A163ALA00.013-0.01620.0230.0150.0150.0000.0000.0000.000
109A164ALA00.0270.02223.508-0.003-0.0030.0000.0000.0000.000
110A165SER00.0380.02627.082-0.002-0.0020.0000.0000.0000.000
111A166LEU0-0.065-0.05429.1160.0030.0030.0000.0000.0000.000
112A167THR0-0.014-0.01132.2090.0010.0010.0000.0000.0000.000
113A168LEU00.0100.00429.221-0.001-0.0010.0000.0000.0000.000
114A169ASN0-0.072-0.01832.6530.0030.0030.0000.0000.0000.000
115A170GLN00.0380.02328.5180.0050.0050.0000.0000.0000.000
116A171ALA0-0.039-0.01924.1990.0000.0000.0000.0000.0000.000
117A172HIS00.007-0.02224.292-0.002-0.0020.0000.0000.0000.000
118A173MET0-0.0300.00717.3280.0070.0070.0000.0000.0000.000
119A174VAL0-0.0080.00519.449-0.015-0.0150.0000.0000.0000.000
120A175LEU0-0.021-0.00913.3390.0060.0060.0000.0000.0000.000
121A176SER0-0.044-0.02316.325-0.003-0.0030.0000.0000.0000.000
122A177PHE00.019-0.00615.803-0.005-0.0050.0000.0000.0000.000
123A178TYR00.002-0.01416.1650.0190.0190.0000.0000.0000.000
124A179PRO0-0.045-0.01817.600-0.008-0.0080.0000.0000.0000.000
125A180THR00.0460.04119.328-0.005-0.0050.0000.0000.0000.000
126A181PRO00.0310.00717.028-0.005-0.0050.0000.0000.0000.000
127A182GLU-1-0.902-0.95719.2150.0720.0720.0000.0000.0000.000
128A183SER0-0.090-0.04222.000-0.008-0.0080.0000.0000.0000.000
129A184GLU-1-0.812-0.88922.5190.0000.0000.0000.0000.0000.000
130A185PRO0-0.0160.00219.879-0.009-0.0090.0000.0000.0000.000
131A186LEU0-0.058-0.04420.8140.0010.0010.0000.0000.0000.000
132A187ILE00.0050.00320.399-0.007-0.0070.0000.0000.0000.000
133A188LEU0-0.022-0.02217.720-0.006-0.0060.0000.0000.0000.000
134A189ASP-1-0.725-0.84920.325-0.062-0.0620.0000.0000.0000.000
135A190SER0-0.022-0.03322.495-0.010-0.0100.0000.0000.0000.000
136A191LEU0-0.0070.01324.137-0.001-0.0010.0000.0000.0000.000
137A192GLU-1-0.866-0.93426.795-0.050-0.0500.0000.0000.0000.000
138A193SER0-0.036-0.01926.440-0.010-0.0100.0000.0000.0000.000
139A194LYS10.8640.93926.9270.0450.0450.0000.0000.0000.000
140A195ILE00.0060.02021.8420.0000.0000.0000.0000.0000.000
141A196LEU0-0.038-0.02125.2370.0040.0040.0000.0000.0000.000
142A197LYS10.9730.98425.1760.0240.0240.0000.0000.0000.000
143A198ALA00.0720.03524.3370.0010.0010.0000.0000.0000.000
144A199SER0-0.068-0.06026.1120.0000.0000.0000.0000.0000.000
145A200ALA0-0.103-0.04929.1360.0010.0010.0000.0000.0000.000
146A201ARG10.7660.86026.1950.0330.0330.0000.0000.0000.000
147A202PRO00.0330.02528.7700.0050.0050.0000.0000.0000.000
148A203ASP-1-0.822-0.89929.975-0.016-0.0160.0000.0000.0000.000
149A204LEU0-0.0060.01024.2450.0020.0020.0000.0000.0000.000
150A205LYS10.9750.98627.136-0.043-0.0430.0000.0000.0000.000
151A206PRO0-0.017-0.01121.7890.0050.0050.0000.0000.0000.000
152A207VAL0-0.026-0.00122.2580.0070.0070.0000.0000.0000.000
153A208TYR0-0.039-0.02416.0290.0210.0210.0000.0000.0000.000
154A209SER0-0.016-0.00115.633-0.026-0.0260.0000.0000.0000.000
155A210PHE00.0520.00510.7790.0610.0610.0000.0000.0000.000
156A211ASN00.0240.0198.0890.0330.0330.0000.0000.0000.000
157A212ALA00.0310.0093.265-0.0990.1050.022-0.065-0.1620.000
158A213GLU-1-0.874-0.9174.2200.6090.851-0.001-0.032-0.2100.000
159A214GLY00.0110.0026.4870.1220.1220.0000.0000.0000.000
160A215LEU00.0030.00910.165-0.097-0.0970.0000.0000.0000.000
161A216TRP0-0.033-0.02010.7510.0020.0020.0000.0000.0000.000
162A217LEU00.0210.00916.730-0.027-0.0270.0000.0000.0000.000
163A218ALA00.0320.02020.252-0.001-0.0010.0000.0000.0000.000
164A219LYS10.7670.91422.069-0.120-0.1200.0000.0000.0000.000
165A220THR00.0280.01625.254-0.011-0.0110.0000.0000.0000.000
166A221ARG10.8990.95921.324-0.166-0.1660.0000.0000.0000.000
167A222GLY00.035-0.01026.7740.0010.0010.0000.0000.0000.000
168A223GLU-1-0.782-0.93024.8290.1140.1140.0000.0000.0000.000
169A224SER0-0.038-0.02620.312-0.008-0.0080.0000.0000.0000.000
170A225SER0-0.037-0.01319.043-0.019-0.0190.0000.0000.0000.000
171A226LEU0-0.010-0.00117.8990.0100.0100.0000.0000.0000.000
172A227MET0-0.0430.0029.915-0.065-0.0650.0000.0000.0000.000
173A228GLY00.0050.00914.6700.0350.0350.0000.0000.0000.000
174A229ASP-1-0.815-0.9319.9751.2671.2670.0000.0000.0000.000
175A230SER00.0030.0127.083-0.098-0.0980.0000.0000.0000.000
176A231LYS10.8960.9345.989-2.064-2.0640.0000.0000.0000.000
177A232SER0-0.075-0.03010.118-0.134-0.1340.0000.0000.0000.000
178A233LEU00.0000.01312.261-0.090-0.0900.0000.0000.0000.000
179A234GLY00.0410.01112.3690.0210.0210.0000.0000.0000.000
180A235LYS10.9250.96213.358-0.046-0.0460.0000.0000.0000.000
181A236TRP00.0110.0037.610-0.147-0.1470.0000.0000.0000.000
182A237ASP-1-0.793-0.9008.4330.8420.8420.0000.0000.0000.000
183A238ALA0-0.023-0.0138.887-0.024-0.0240.0000.0000.0000.000
184A239LEU0-0.0270.0049.108-0.106-0.1060.0000.0000.0000.000
185A240MET0-0.011-0.0244.900-0.160-0.1600.0000.0000.0000.000
186A241LYS10.8640.9326.681-0.923-0.9230.0000.0000.0000.000
187A242ARG10.8240.9198.2570.0200.0200.0000.0000.0000.000
188A243MET0-0.099-0.0277.339-0.012-0.0120.0000.0000.0000.000
189A244GLU-1-1.046-1.0055.038-0.328-0.3280.0000.0000.0000.000