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: R81G8

Calculation Name: 4ECC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ECC

Chain ID: A

ChEMBL ID:

UniProt ID: P08515

Base Structure: X-ray

Registration Date: 2023-09-20

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2557653.628259
FMO2-HF: Nuclear repulsion 2472716.447026
FMO2-HF: Total energy -84937.181233
FMO2-MP2: Total energy -85181.040504


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:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-32.315-35.86825.374-12.092-9.73-0.048
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.052 / q_NPA : -0.064
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].
3A4ILE0-0.0020.0133.632-2.682-1.2130.009-0.674-0.8040.001
4A5LEU0-0.026-0.0125.9061.1531.1530.0000.0000.0000.000
5A6GLY00.0230.0209.213-0.217-0.2170.0000.0000.0000.000
6A7TYR0-0.012-0.02912.1180.2560.2560.0000.0000.0000.000
7A8TRP00.0520.03915.248-0.082-0.0820.0000.0000.0000.000
8A9LYS10.8400.92716.3560.6200.6200.0000.0000.0000.000
9A10ILE0-0.036-0.01417.5560.0590.0590.0000.0000.0000.000
10A11LYS10.8120.91318.0270.1430.1430.0000.0000.0000.000
11A12GLY0-0.001-0.00519.069-0.014-0.0140.0000.0000.0000.000
12A13LEU0-0.035-0.03520.0880.0370.0370.0000.0000.0000.000
13A14VAL00.002-0.00114.1800.0320.0320.0000.0000.0000.000
14A15GLN00.0660.05815.596-0.043-0.0430.0000.0000.0000.000
15A16PRO00.009-0.00716.8110.0360.0360.0000.0000.0000.000
16A17THR00.009-0.00212.7070.0840.0840.0000.0000.0000.000
17A18ARG10.8170.89111.6060.6400.6400.0000.0000.0000.000
18A19LEU0-0.029-0.00613.1190.1030.1030.0000.0000.0000.000
19A20LEU00.005-0.00214.9690.0580.0580.0000.0000.0000.000
20A21LEU00.0150.0048.6930.1200.1200.0000.0000.0000.000
21A22GLU-1-0.760-0.84410.9500.2200.2200.0000.0000.0000.000
22A23TYR0-0.018-0.01012.9960.0760.0760.0000.0000.0000.000
23A24LEU0-0.032-0.01912.4770.0060.0060.0000.0000.0000.000
24A25GLU-1-0.865-0.91912.1110.6610.6610.0000.0000.0000.000
25A26GLU-1-0.863-0.9127.4262.8302.8300.0000.0000.0000.000
26A27LYS10.7420.8682.130-1.5960.3883.608-2.562-3.0300.029
27A28TYR0-0.044-0.0483.2111.6772.4690.055-0.341-0.5070.002
28A29GLU-1-0.817-0.8711.619-31.965-39.76421.703-8.512-5.392-0.080
29A30GLU-1-0.817-0.9144.709-0.384-0.383-0.001-0.0030.0030.000
30A31HIS0-0.047-0.0207.8210.1790.1790.0000.0000.0000.000
31A32LEU0-0.025-0.02010.9900.2170.2170.0000.0000.0000.000
32A33TYR00.0320.02513.2100.0610.0610.0000.0000.0000.000
33A34GLU-1-0.763-0.90916.920-0.498-0.4980.0000.0000.0000.000
34A35ARG10.7870.88419.8780.3060.3060.0000.0000.0000.000
35A36ASP-1-0.927-0.96423.474-0.412-0.4120.0000.0000.0000.000
36A37GLU-1-0.885-0.92418.127-0.799-0.7990.0000.0000.0000.000
37A38GLY0-0.067-0.03721.274-0.021-0.0210.0000.0000.0000.000
38A39ASP-1-0.994-0.99221.250-0.402-0.4020.0000.0000.0000.000
39A62GLY00.0030.00815.7710.0110.0110.0000.0000.0000.000
40A63LEU0-0.026-0.05513.550-0.066-0.0660.0000.0000.0000.000
41A64GLU-1-0.896-0.94916.555-0.151-0.1510.0000.0000.0000.000
42A65PHE0-0.0120.00919.4470.0240.0240.0000.0000.0000.000
43A66PRO00.0060.01719.248-0.023-0.0230.0000.0000.0000.000
44A67ASN0-0.008-0.00218.9020.0180.0180.0000.0000.0000.000
45A68LEU00.0230.03716.110-0.077-0.0770.0000.0000.0000.000
46A69PRO0-0.060-0.03515.0110.0670.0670.0000.0000.0000.000
47A70TYR00.015-0.00710.7910.0500.0500.0000.0000.0000.000
48A71TYR0-0.060-0.0637.740-0.240-0.2400.0000.0000.0000.000
49A72ILE00.0060.0116.8160.3020.3020.0000.0000.0000.000
50A73ASP-1-0.734-0.8415.6760.5500.5500.0000.0000.0000.000
51A74GLY00.0300.0165.644-0.112-0.1120.0000.0000.0000.000
52A75ASP-1-0.853-0.9227.369-0.185-0.1850.0000.0000.0000.000
53A76VAL0-0.0310.0059.430-0.226-0.2260.0000.0000.0000.000
54A77LYS10.7980.8869.8340.0580.0580.0000.0000.0000.000
55A78LEU0-0.0150.00112.7810.0810.0810.0000.0000.0000.000
56A79THR0-0.004-0.02814.463-0.123-0.1230.0000.0000.0000.000
57A80GLN00.0620.03517.1510.0590.0590.0000.0000.0000.000
58A81SER00.0420.01817.6700.0270.0270.0000.0000.0000.000
59A82MET00.0120.00718.1590.0280.0280.0000.0000.0000.000
60A83ALA00.0020.00718.4830.0480.0480.0000.0000.0000.000
61A84ILE00.0050.01412.8770.0710.0710.0000.0000.0000.000
62A85ILE0-0.007-0.00214.7130.1020.1020.0000.0000.0000.000
63A86ARG10.8750.92016.573-0.055-0.0550.0000.0000.0000.000
64A87TYR00.0220.00110.2840.0680.0680.0000.0000.0000.000
65A88ILE0-0.0020.00010.3360.1340.1340.0000.0000.0000.000
66A89ALA00.0330.01413.3790.1170.1170.0000.0000.0000.000
67A90ASP-1-0.938-0.96816.5640.4780.4780.0000.0000.0000.000
68A91LYS10.8490.9339.018-1.338-1.3380.0000.0000.0000.000
69A92HIS10.7730.86510.459-1.054-1.0540.0000.0000.0000.000
70A93ASN0-0.041-0.01915.398-0.070-0.0700.0000.0000.0000.000
71A94MET0-0.0130.00217.545-0.037-0.0370.0000.0000.0000.000
72A95LEU0-0.043-0.00919.656-0.051-0.0510.0000.0000.0000.000
73A96GLY00.0390.02622.028-0.038-0.0380.0000.0000.0000.000
74A97GLY00.0280.02224.8090.0160.0160.0000.0000.0000.000
75A98CYS0-0.056-0.01026.668-0.008-0.0080.0000.0000.0000.000
76A99PRO00.042-0.00429.043-0.001-0.0010.0000.0000.0000.000
77A100LYS10.9110.94630.495-0.120-0.1200.0000.0000.0000.000
78A101GLU-1-0.820-0.92527.7790.2110.2110.0000.0000.0000.000
79A102ARG10.9010.94224.452-0.243-0.2430.0000.0000.0000.000
80A103ALA0-0.0110.00227.326-0.009-0.0090.0000.0000.0000.000
81A104GLU-1-0.812-0.87630.1320.0980.0980.0000.0000.0000.000
82A105ILE00.0230.00923.978-0.013-0.0130.0000.0000.0000.000
83A106SER0-0.006-0.03526.236-0.005-0.0050.0000.0000.0000.000
84A107MET0-0.058-0.01127.789-0.017-0.0170.0000.0000.0000.000
85A108LEU0-0.017-0.00728.319-0.013-0.0130.0000.0000.0000.000
86A109GLU-1-0.745-0.84023.4680.0790.0790.0000.0000.0000.000
87A110GLY00.0050.00426.908-0.018-0.0180.0000.0000.0000.000
88A111ALA0-0.002-0.00429.672-0.013-0.0130.0000.0000.0000.000
89A112VAL0-0.012-0.00226.020-0.010-0.0100.0000.0000.0000.000
90A113LEU0-0.023-0.02424.177-0.017-0.0170.0000.0000.0000.000
91A114ASP-1-0.839-0.90727.983-0.051-0.0510.0000.0000.0000.000
92A115ILE00.0230.01930.343-0.008-0.0080.0000.0000.0000.000
93A116ARG10.8170.89723.1830.1400.1400.0000.0000.0000.000
94A117TYR0-0.014-0.02424.760-0.013-0.0130.0000.0000.0000.000
95A118GLY0-0.0010.00829.389-0.008-0.0080.0000.0000.0000.000
96A119VAL00.0430.02129.811-0.004-0.0040.0000.0000.0000.000
97A120SER0-0.034-0.03027.552-0.015-0.0150.0000.0000.0000.000
98A121ARG10.7970.89529.8200.0530.0530.0000.0000.0000.000
99A122ILE0-0.005-0.00132.9410.0020.0020.0000.0000.0000.000
100A123ALA0-0.0120.00430.690-0.002-0.0020.0000.0000.0000.000
101A124TYR00.0160.00626.258-0.015-0.0150.0000.0000.0000.000
102A125SER00.0000.01833.073-0.001-0.0010.0000.0000.0000.000
103A126LYS10.9290.97036.8760.0880.0880.0000.0000.0000.000
104A127ASP-1-0.874-0.94739.818-0.085-0.0850.0000.0000.0000.000
105A128PHE00.0140.00934.9900.0050.0050.0000.0000.0000.000
106A129GLU-1-0.758-0.89038.638-0.081-0.0810.0000.0000.0000.000
107A130THR0-0.0160.00140.9610.0050.0050.0000.0000.0000.000
108A131LEU00.0190.00539.0440.0040.0040.0000.0000.0000.000
109A132LYS10.8060.89837.9510.0840.0840.0000.0000.0000.000
110A133VAL0-0.0040.00339.3390.0050.0050.0000.0000.0000.000
111A134ASP-1-0.891-0.95041.569-0.047-0.0470.0000.0000.0000.000
112A135PHE0-0.033-0.02433.2800.0050.0050.0000.0000.0000.000
113A136LEU00.019-0.00436.9360.0060.0060.0000.0000.0000.000
114A137SER0-0.047-0.01739.7500.0060.0060.0000.0000.0000.000
115A138LYS10.8040.87540.1650.0240.0240.0000.0000.0000.000
116A139LEU00.0120.01934.0840.0050.0050.0000.0000.0000.000
117A140PRO00.0320.00437.5360.0060.0060.0000.0000.0000.000
118A141GLU-1-0.826-0.88639.862-0.006-0.0060.0000.0000.0000.000
119A142MET0-0.038-0.01734.3930.0040.0040.0000.0000.0000.000
120A143LEU0-0.0020.00633.5370.0070.0070.0000.0000.0000.000
121A144LYS10.8920.92436.062-0.017-0.0170.0000.0000.0000.000
122A145MET0-0.0030.00536.2430.0060.0060.0000.0000.0000.000
123A146PHE00.009-0.00930.8660.0110.0110.0000.0000.0000.000
124A147GLU-1-0.743-0.86634.4840.0380.0380.0000.0000.0000.000
125A148ASP-1-0.840-0.89736.8800.0390.0390.0000.0000.0000.000
126A149ARG10.7540.85031.410-0.092-0.0920.0000.0000.0000.000
127A150LEU0-0.001-0.00530.7020.0090.0090.0000.0000.0000.000
128A151CYS0-0.085-0.03334.866-0.001-0.0010.0000.0000.0000.000
129A152HIS0-0.035-0.00837.3210.0030.0030.0000.0000.0000.000
130A153LYS10.8610.92632.433-0.114-0.1140.0000.0000.0000.000
131A154THR0-0.019-0.00129.893-0.012-0.0120.0000.0000.0000.000
132A155TYR00.0030.00726.447-0.011-0.0110.0000.0000.0000.000
133A156LEU00.0070.00126.979-0.002-0.0020.0000.0000.0000.000
134A157ASN00.0240.01727.165-0.022-0.0220.0000.0000.0000.000
135A158GLY0-0.003-0.00429.328-0.002-0.0020.0000.0000.0000.000
136A159ASP-1-0.862-0.92329.6470.1480.1480.0000.0000.0000.000
137A160HIS0-0.013-0.00224.2260.0220.0220.0000.0000.0000.000
138A161VAL0-0.0230.00621.721-0.020-0.0200.0000.0000.0000.000
139A162THR0-0.041-0.03921.8200.0280.0280.0000.0000.0000.000
140A163HIS00.045-0.00819.1520.0120.0120.0000.0000.0000.000
141A164PRO00.014-0.01220.825-0.033-0.0330.0000.0000.0000.000
142A165ASP-1-0.749-0.85023.3010.1160.1160.0000.0000.0000.000
143A166PHE00.0580.01719.144-0.020-0.0200.0000.0000.0000.000
144A167MET0-0.0240.00221.362-0.026-0.0260.0000.0000.0000.000
145A168LEU0-0.0060.00422.957-0.021-0.0210.0000.0000.0000.000
146A169TYR0-0.064-0.06122.113-0.015-0.0150.0000.0000.0000.000
147A170ASP-1-0.799-0.90421.632-0.157-0.1570.0000.0000.0000.000
148A171ALA0-0.023-0.01223.713-0.014-0.0140.0000.0000.0000.000
149A172LEU0-0.007-0.01327.044-0.004-0.0040.0000.0000.0000.000
150A173ASP-1-0.807-0.89925.252-0.105-0.1050.0000.0000.0000.000
151A174VAL0-0.016-0.01625.472-0.007-0.0070.0000.0000.0000.000
152A175VAL0-0.002-0.01028.125-0.004-0.0040.0000.0000.0000.000
153A176LEU0-0.0040.00730.1670.0010.0010.0000.0000.0000.000
154A177TYR0-0.065-0.03826.275-0.005-0.0050.0000.0000.0000.000
155A178MET0-0.091-0.02732.313-0.002-0.0020.0000.0000.0000.000
156A179ASP-1-0.829-0.93734.733-0.042-0.0420.0000.0000.0000.000
157A180PRO0-0.016-0.00435.4390.0050.0050.0000.0000.0000.000
158A181MET00.0150.01336.5080.0050.0050.0000.0000.0000.000
159A182CYS0-0.072-0.01435.3990.0070.0070.0000.0000.0000.000
160A183LEU0-0.005-0.02532.1180.0070.0070.0000.0000.0000.000
161A184ASP-1-0.888-0.94036.833-0.013-0.0130.0000.0000.0000.000
162A185ALA0-0.077-0.03340.0120.0040.0040.0000.0000.0000.000
163A186PHE0-0.054-0.02237.0130.0050.0050.0000.0000.0000.000
164A187PRO00.0580.02736.7530.0010.0010.0000.0000.0000.000
165A188LYS10.8250.88235.481-0.049-0.0490.0000.0000.0000.000
166A189LEU00.0230.01331.9070.0070.0070.0000.0000.0000.000
167A190VAL00.0100.01331.9770.0000.0000.0000.0000.0000.000
168A191CYS0-0.078-0.02532.7780.0030.0030.0000.0000.0000.000
169A192PHE00.012-0.00326.4040.0080.0080.0000.0000.0000.000
170A193LYS10.8460.92026.3390.0500.0500.0000.0000.0000.000
171A194LYS10.9430.97226.836-0.005-0.0050.0000.0000.0000.000
172A195ARG10.8510.92127.765-0.081-0.0810.0000.0000.0000.000
173A196ILE00.0050.00222.2800.0200.0200.0000.0000.0000.000
174A197GLU-1-0.811-0.89022.9530.0020.0020.0000.0000.0000.000
175A198ALA0-0.035-0.01623.5920.0040.0040.0000.0000.0000.000
176A199ILE0-0.0330.00220.1350.0230.0230.0000.0000.0000.000
177A200PRO00.0120.00320.656-0.013-0.0130.0000.0000.0000.000
178A201GLN00.013-0.01015.950-0.083-0.0830.0000.0000.0000.000
179A202ILE0-0.026-0.00316.802-0.033-0.0330.0000.0000.0000.000
180A203ASP-1-0.795-0.87418.9960.0020.0020.0000.0000.0000.000
181A204LYS10.8110.88613.837-0.450-0.4500.0000.0000.0000.000
182A205TYR0-0.0100.00413.315-0.023-0.0230.0000.0000.0000.000
183A206LEU0-0.0060.00416.378-0.068-0.0680.0000.0000.0000.000
184A207LYS10.7880.88719.596-0.041-0.0410.0000.0000.0000.000
185A208SER0-0.063-0.03415.065-0.036-0.0360.0000.0000.0000.000
186A209SER0-0.008-0.02514.774-0.003-0.0030.0000.0000.0000.000
187A210LYS10.8550.9139.8680.0490.0490.0000.0000.0000.000
188A211TYR00.0070.01713.813-0.015-0.0150.0000.0000.0000.000
189A212ILE00.0120.01815.1560.0010.0010.0000.0000.0000.000
190A213ALA00.011-0.00118.2000.0350.0350.0000.0000.0000.000
191A214TRP0-0.036-0.00321.7730.0400.0400.0000.0000.0000.000
192A215PRO00.0150.01521.984-0.031-0.0310.0000.0000.0000.000
193A216LEU0-0.006-0.00522.653-0.017-0.0170.0000.0000.0000.000
194A217GLN0-0.0230.00524.0480.0060.0060.0000.0000.0000.000
195A218GLY00.0710.03424.271-0.025-0.0250.0000.0000.0000.000
196A219TRP00.0570.01320.5190.0450.0450.0000.0000.0000.000
197A220GLN0-0.015-0.00526.7460.0100.0100.0000.0000.0000.000
198A221ALA0-0.049-0.01929.0630.0150.0150.0000.0000.0000.000
199A222THR0-0.040-0.03230.865-0.004-0.0040.0000.0000.0000.000
200A223PHE00.0060.00830.7160.0060.0060.0000.0000.0000.000
201A224GLY00.0340.00128.852-0.006-0.0060.0000.0000.0000.000
202A225GLY00.0220.02727.176-0.020-0.0200.0000.0000.0000.000
203A226GLY00.010-0.00428.6390.0090.0090.0000.0000.0000.000
204A227ASP-1-0.817-0.91526.237-0.295-0.2950.0000.0000.0000.000
205A228HIS0-0.091-0.05226.273-0.003-0.0030.0000.0000.0000.000
206A229PRO00.0150.02927.5750.0090.0090.0000.0000.0000.000