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: 9G3L2

Calculation Name: 4OR8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OR8

Chain ID: A

ChEMBL ID:

UniProt ID: P35256

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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2718109.222038
FMO2-HF: Nuclear repulsion 2628661.231222
FMO2-HF: Total energy -89447.990816
FMO2-MP2: Total energy -89709.933235


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:ASP)


Summations of interaction energy for fragment #1(A:-2:ASP)
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.
-48.283-45.836-0.025-1.293-1.130.007
Interaction energy analysis for fragmet #1(A:-2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.969 / q_NPA : -0.973
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].
3A0LYS10.8060.8813.826-26.102-23.655-0.025-1.293-1.1300.007
4A1MET00.0070.0117.083-2.221-2.2210.0000.0000.0000.000
5A2ALA0-0.004-0.0059.9820.0370.0370.0000.0000.0000.000
6A3GLU-1-0.833-0.89813.03921.81521.8150.0000.0000.0000.000
7A4LEU0-0.004-0.00415.970-0.531-0.5310.0000.0000.0000.000
8A5SER00.019-0.00118.343-0.028-0.0280.0000.0000.0000.000
9A6THR00.0360.01220.452-0.198-0.1980.0000.0000.0000.000
10A7ARG10.9100.94816.392-17.724-17.7240.0000.0000.0000.000
11A8TYR00.0290.01821.0310.3430.3430.0000.0000.0000.000
12A9ASN0-0.024-0.00425.531-0.368-0.3680.0000.0000.0000.000
13A10LEU0-0.014-0.00328.2640.0200.0200.0000.0000.0000.000
14A11PRO00.0220.02131.358-0.139-0.1390.0000.0000.0000.000
15A20ASN00.0620.04052.2400.0220.0220.0000.0000.0000.000
16A21LEU0-0.076-0.03651.9230.0450.0450.0000.0000.0000.000
17A22ASP-1-0.782-0.89355.8365.3605.3600.0000.0000.0000.000
18A23LEU00.0700.05658.2820.0700.0700.0000.0000.0000.000
19A24ASN00.0230.01659.6850.1020.1020.0000.0000.0000.000
20A25SER0-0.042-0.04354.7570.0760.0760.0000.0000.0000.000
21A26THR0-0.029-0.02454.8550.0950.0950.0000.0000.0000.000
22A27ALA0-0.0110.01156.6420.0030.0030.0000.0000.0000.000
23A28ARG10.8980.93356.306-5.575-5.5750.0000.0000.0000.000
24A29TRP00.013-0.00549.4910.0850.0850.0000.0000.0000.000
25A30ILE00.011-0.00553.448-0.077-0.0770.0000.0000.0000.000
26A31LYS10.8300.91349.265-6.102-6.1020.0000.0000.0000.000
27A32GLU-1-0.786-0.86948.4896.4886.4880.0000.0000.0000.000
28A33PRO0-0.002-0.00347.4500.1210.1210.0000.0000.0000.000
29A34SER0-0.011-0.01442.8970.0280.0280.0000.0000.0000.000
30A35VAL00.0360.01038.989-0.027-0.0270.0000.0000.0000.000
31A36GLY00.0390.01838.8340.2410.2410.0000.0000.0000.000
32A37GLY0-0.046-0.02439.6740.0170.0170.0000.0000.0000.000
33A38TRP0-0.006-0.00243.134-0.133-0.1330.0000.0000.0000.000
34A39THR0-0.025-0.00444.0040.2540.2540.0000.0000.0000.000
35A40VAL00.0090.01046.043-0.167-0.1670.0000.0000.0000.000
36A41LYS10.7910.88647.664-6.550-6.5500.0000.0000.0000.000
37A42TRP00.010-0.00649.733-0.102-0.1020.0000.0000.0000.000
38A43GLY00.039-0.00250.3680.1050.1050.0000.0000.0000.000
39A44ASN0-0.038-0.03747.746-0.007-0.0070.0000.0000.0000.000
40A45PHE0-0.0060.01545.0420.1740.1740.0000.0000.0000.000
41A46VAL0-0.009-0.02043.709-0.140-0.1400.0000.0000.0000.000
42A47PHE00.0080.01143.1510.1920.1920.0000.0000.0000.000
43A48HIS00.003-0.01040.045-0.186-0.1860.0000.0000.0000.000
44A49ILE0-0.027-0.01841.2380.0820.0820.0000.0000.0000.000
45A50PRO00.0040.01438.448-0.052-0.0520.0000.0000.0000.000
46A51ASN00.014-0.01240.570-0.038-0.0380.0000.0000.0000.000
47A52THR00.0090.01336.752-0.127-0.1270.0000.0000.0000.000
48A53GLY00.0320.01839.063-0.057-0.0570.0000.0000.0000.000
49A54MET0-0.011-0.00339.902-0.082-0.0820.0000.0000.0000.000
50A55THR00.0220.00241.331-0.199-0.1990.0000.0000.0000.000
51A56LEU00.0320.03239.216-0.125-0.1250.0000.0000.0000.000
52A57LEU00.0230.00942.946-0.102-0.1020.0000.0000.0000.000
53A58HIS00.0600.02445.981-0.167-0.1670.0000.0000.0000.000
54A59HIS0-0.033-0.00444.479-0.128-0.1280.0000.0000.0000.000
55A60LEU0-0.0040.00242.910-0.087-0.0870.0000.0000.0000.000
56A61LYS10.8120.91746.839-5.715-5.7150.0000.0000.0000.000
57A62SER0-0.033-0.02549.960-0.158-0.1580.0000.0000.0000.000
58A63ASN0-0.034-0.01348.8390.0110.0110.0000.0000.0000.000
59A64PHE00.0120.02646.8610.0280.0280.0000.0000.0000.000
60A65VAL0-0.031-0.02743.0740.1590.1590.0000.0000.0000.000
61A66VAL00.0710.04138.781-0.143-0.1430.0000.0000.0000.000
62A67PRO00.033-0.01341.930-0.006-0.0060.0000.0000.0000.000
63A68GLU-1-0.859-0.91336.8217.9087.9080.0000.0000.0000.000
64A69TRP00.006-0.01237.212-0.074-0.0740.0000.0000.0000.000
65A70GLN0-0.003-0.00742.231-0.193-0.1930.0000.0000.0000.000
66A71GLN0-0.0100.00539.211-0.184-0.1840.0000.0000.0000.000
67A72THR00.0360.01641.141-0.094-0.0940.0000.0000.0000.000
68A73ARG10.8250.89144.045-6.285-6.2850.0000.0000.0000.000
69A74ASN00.0160.01147.236-0.260-0.2600.0000.0000.0000.000
70A75LEU00.0120.01843.701-0.121-0.1210.0000.0000.0000.000
71A76PHE00.0330.01443.476-0.055-0.0550.0000.0000.0000.000
72A77SER00.0210.01048.686-0.077-0.0770.0000.0000.0000.000
73A78HIS0-0.039-0.02551.718-0.031-0.0310.0000.0000.0000.000
74A79LEU00.0130.02048.561-0.078-0.0780.0000.0000.0000.000
75A80PHE0-0.007-0.01545.829-0.051-0.0510.0000.0000.0000.000
76A81LYS10.8780.93950.789-5.869-5.8690.0000.0000.0000.000
77A82ASN00.0360.03053.638-0.201-0.2010.0000.0000.0000.000
78A83PRO00.014-0.00656.5250.0390.0390.0000.0000.0000.000
79A84LYS10.8360.92058.554-5.082-5.0820.0000.0000.0000.000
80A85SER0-0.024-0.00153.931-0.041-0.0410.0000.0000.0000.000
81A86THR0-0.031-0.03155.711-0.035-0.0350.0000.0000.0000.000
82A87ILE0-0.0040.01049.5080.0450.0450.0000.0000.0000.000
83A88ILE0-0.011-0.01151.251-0.088-0.0880.0000.0000.0000.000
84A89GLU-1-0.788-0.89048.7236.3466.3460.0000.0000.0000.000
85A90PRO00.0600.01444.525-0.085-0.0850.0000.0000.0000.000
86A91PHE00.0120.00846.931-0.002-0.0020.0000.0000.0000.000
87A92LEU00.0020.00149.254-0.077-0.0770.0000.0000.0000.000
88A93ALA00.0060.00547.876-0.064-0.0640.0000.0000.0000.000
89A94LEU00.0150.00145.664-0.008-0.0080.0000.0000.0000.000
90A95ARG10.7740.91248.711-5.537-5.5370.0000.0000.0000.000
91A96ILE00.0370.01752.229-0.053-0.0530.0000.0000.0000.000
92A97LEU0-0.006-0.00445.718-0.041-0.0410.0000.0000.0000.000
93A98LEU00.0100.00849.9480.0180.0180.0000.0000.0000.000
94A99GLY00.0620.01151.334-0.065-0.0650.0000.0000.0000.000
95A100VAL0-0.040-0.01152.081-0.110-0.1100.0000.0000.0000.000
96A101ALA00.0180.02150.146-0.041-0.0410.0000.0000.0000.000
97A102LEU0-0.046-0.02051.966-0.033-0.0330.0000.0000.0000.000
98A103LYS10.7950.88155.254-5.337-5.3370.0000.0000.0000.000
99A104ASP-1-0.796-0.86750.8926.0996.0990.0000.0000.0000.000
100A105GLN00.009-0.00454.254-0.069-0.0690.0000.0000.0000.000
101A106GLU-1-0.784-0.88550.1176.2366.2360.0000.0000.0000.000
102A107LEU0-0.0210.01352.979-0.005-0.0050.0000.0000.0000.000
103A108GLN0-0.003-0.01254.519-0.139-0.1390.0000.0000.0000.000
104A109GLN0-0.046-0.02356.533-0.067-0.0670.0000.0000.0000.000
105A110SER0-0.067-0.04055.510-0.035-0.0350.0000.0000.0000.000
106A111LEU0-0.0100.01157.039-0.025-0.0250.0000.0000.0000.000
107A112ILE00.0570.03060.125-0.067-0.0670.0000.0000.0000.000
108A113PRO00.053-0.00163.8370.0200.0200.0000.0000.0000.000
109A114GLY00.0030.00266.315-0.012-0.0120.0000.0000.0000.000
110A115PHE00.0260.00758.252-0.009-0.0090.0000.0000.0000.000
111A116ARG10.8870.94661.730-5.092-5.0920.0000.0000.0000.000
112A117SER00.0300.02063.0830.0560.0560.0000.0000.0000.000
113A118ILE00.0180.00762.1680.0050.0050.0000.0000.0000.000
114A119VAL00.0260.00857.6590.0410.0410.0000.0000.0000.000
115A120HIS0-0.020-0.00559.8010.1210.1210.0000.0000.0000.000
116A121MET0-0.016-0.01262.080-0.018-0.0180.0000.0000.0000.000
117A122LEU0-0.024-0.00558.4410.0130.0130.0000.0000.0000.000
118A123SER0-0.029-0.02257.6280.0270.0270.0000.0000.0000.000
119A124GLU-1-0.782-0.90358.7785.0035.0030.0000.0000.0000.000
120A125TRP0-0.028-0.00657.5980.0260.0260.0000.0000.0000.000
121A126LEU0-0.030-0.00754.3260.0310.0310.0000.0000.0000.000
122A127LEU0-0.032-0.01455.6080.0740.0740.0000.0000.0000.000
123A128LEU0-0.074-0.03558.327-0.007-0.0070.0000.0000.0000.000
124A129GLU-1-0.803-0.87960.3504.9364.9360.0000.0000.0000.000
125A130VAL0-0.051-0.03057.8890.1160.1160.0000.0000.0000.000
126A131THR0-0.027-0.01459.1270.0760.0760.0000.0000.0000.000
127A132SER00.0160.00558.0240.0310.0310.0000.0000.0000.000
128A133ALA0-0.026-0.01858.3950.0940.0940.0000.0000.0000.000
129A134ILE00.0060.02060.870-0.066-0.0660.0000.0000.0000.000
130A135HIS00.0060.00263.4590.0850.0850.0000.0000.0000.000
131A136ILE00.0130.00063.809-0.034-0.0340.0000.0000.0000.000
132A137SER00.0100.00167.8340.0180.0180.0000.0000.0000.000
133A138PRO00.0560.01570.7100.0020.0020.0000.0000.0000.000
134A139ASN00.0040.00571.7320.0420.0420.0000.0000.0000.000
135A140LEU00.0130.00569.691-0.027-0.0270.0000.0000.0000.000
136A141LEU0-0.063-0.01966.3800.0550.0550.0000.0000.0000.000
137A142GLY0-0.0030.00469.611-0.035-0.0350.0000.0000.0000.000
138A143ILE0-0.042-0.01865.728-0.032-0.0320.0000.0000.0000.000
139A144TYR00.0270.01266.9800.0450.0450.0000.0000.0000.000
140A145LEU00.007-0.00462.3570.0350.0350.0000.0000.0000.000
141A146THR00.023-0.01059.9130.0340.0340.0000.0000.0000.000
142A147SER00.0690.00456.3130.0950.0950.0000.0000.0000.000
143A148ASP-1-0.854-0.90955.6475.8185.8180.0000.0000.0000.000
144A149MET00.0030.02955.9490.0590.0590.0000.0000.0000.000
145A150PHE00.0530.02655.4810.0470.0470.0000.0000.0000.000
146A151LYS10.8320.90051.847-5.869-5.8690.0000.0000.0000.000
147A152ILE00.0020.00051.4680.1290.1290.0000.0000.0000.000
148A153LEU00.0070.01952.5890.0460.0460.0000.0000.0000.000
149A154MET0-0.047-0.00248.9990.0790.0790.0000.0000.0000.000
150A155ALA00.0100.00647.8690.1350.1350.0000.0000.0000.000
151A156GLY00.0230.01148.1450.0950.0950.0000.0000.0000.000
152A157VAL00.0030.00047.8910.0370.0370.0000.0000.0000.000
153A158LYS10.8330.91242.036-7.408-7.4080.0000.0000.0000.000
154A159ASN0-0.005-0.00244.5270.2610.2610.0000.0000.0000.000
155A160PHE00.0060.00345.8040.0740.0740.0000.0000.0000.000
156A161PHE0-0.020-0.02842.8550.0550.0550.0000.0000.0000.000
157A162ASN0-0.036-0.02439.4400.0790.0790.0000.0000.0000.000
158A163LYS10.8120.88641.531-6.268-6.2680.0000.0000.0000.000
159A164MET0-0.0170.02143.3690.0020.0020.0000.0000.0000.000
160A165PHE0-0.068-0.03236.5840.1320.1320.0000.0000.0000.000
161A166THR0-0.048-0.02638.2510.1890.1890.0000.0000.0000.000
162A167LEU0-0.054-0.00140.3360.0010.0010.0000.0000.0000.000
163A168HIS0-0.014-0.00537.7210.3480.3480.0000.0000.0000.000
164A169VAL0-0.0060.00136.020-0.163-0.1630.0000.0000.0000.000
165A170VAL00.001-0.00738.888-0.051-0.0510.0000.0000.0000.000
166A171ASN0-0.068-0.04839.1220.1190.1190.0000.0000.0000.000
167A172ASP-1-0.841-0.92138.9437.4227.4220.0000.0000.0000.000
168A173HIS0-0.005-0.00336.472-0.012-0.0120.0000.0000.0000.000
169A174GLY00.0160.01441.996-0.052-0.0520.0000.0000.0000.000
170A175LYS10.8490.93637.081-7.937-7.9370.0000.0000.0000.000
171A176PRO00.0480.01542.9590.0240.0240.0000.0000.0000.000
172A177SER00.0610.03442.4480.1360.1360.0000.0000.0000.000
173A178SER0-0.012-0.01143.6130.0910.0910.0000.0000.0000.000
174A179ILE00.0090.02346.776-0.032-0.0320.0000.0000.0000.000
175A180GLU-1-0.864-0.93249.2725.7195.7190.0000.0000.0000.000
176A181ILE0-0.0020.00152.909-0.028-0.0280.0000.0000.0000.000
177A182LYS10.8560.92856.018-5.045-5.0450.0000.0000.0000.000
178A183LEU00.0360.01358.588-0.026-0.0260.0000.0000.0000.000
179A184THR00.042-0.00262.122-0.026-0.0260.0000.0000.0000.000
180A185GLY0-0.0050.00964.8190.0210.0210.0000.0000.0000.000
181A186GLN0-0.007-0.00558.585-0.045-0.0450.0000.0000.0000.000
182A187GLN0-0.051-0.02956.231-0.110-0.1100.0000.0000.0000.000
183A188ILE0-0.015-0.00252.6800.0030.0030.0000.0000.0000.000
184A189ILE00.0050.01349.740-0.008-0.0080.0000.0000.0000.000
185A190ILE0-0.014-0.00545.9210.0440.0440.0000.0000.0000.000
186A191THR00.002-0.01144.126-0.014-0.0140.0000.0000.0000.000
187A192ARG10.8080.89735.953-8.088-8.0880.0000.0000.0000.000
188A193VAL00.013-0.01139.413-0.016-0.0160.0000.0000.0000.000
189A194ASN00.0410.00134.1980.0750.0750.0000.0000.0000.000
190A195MET0-0.019-0.00534.5780.1340.1340.0000.0000.0000.000
191A196GLY0-0.009-0.00436.9060.0180.0180.0000.0000.0000.000
192A197PHE00.0170.01339.198-0.020-0.0200.0000.0000.0000.000
193A198LEU0-0.0040.00342.761-0.062-0.0620.0000.0000.0000.000
194A199VAL0-0.013-0.00145.247-0.052-0.0520.0000.0000.0000.000
195A200GLU-1-0.777-0.87448.7115.8545.8540.0000.0000.0000.000
196A201VAL00.0210.00852.037-0.025-0.0250.0000.0000.0000.000
197A202ARG10.8230.88652.930-5.724-5.7240.0000.0000.0000.000
198A203ARG10.9670.97658.319-5.146-5.1460.0000.0000.0000.000
199A204ILE0-0.020-0.02062.074-0.013-0.0130.0000.0000.0000.000
200A216SER00.0260.00466.9460.0000.0000.0000.0000.0000.000
201A217GLU-1-0.796-0.87959.8555.1795.1790.0000.0000.0000.000
202A218SER0-0.053-0.01460.5970.0230.0230.0000.0000.0000.000
203A219VAL00.0110.01154.6680.0070.0070.0000.0000.0000.000
204A220VAL00.0090.00954.6960.0010.0010.0000.0000.0000.000
205A221PHE00.014-0.00348.4320.0400.0400.0000.0000.0000.000
206A222GLY00.0500.02248.303-0.030-0.0300.0000.0000.0000.000
207A223LEU0-0.032-0.01040.4850.0130.0130.0000.0000.0000.000
208A224VAL00.0140.01642.7460.0320.0320.0000.0000.0000.000
209A225ALA00.0260.00938.5340.1060.1060.0000.0000.0000.000
210A226GLU-1-0.733-0.85834.8168.7408.7400.0000.0000.0000.000
211A227ALA00.003-0.00135.331-0.021-0.0210.0000.0000.0000.000
212A228VAL0-0.016-0.00136.820-0.004-0.0040.0000.0000.0000.000
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