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: G5JL1

Calculation Name: 4J2P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J2P

Chain ID: A

ChEMBL ID:

UniProt ID: P09142

Base Structure: X-ray

Registration Date: 2023-09-23

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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2964222.601465
FMO2-HF: Nuclear repulsion 2871699.059077
FMO2-HF: Total energy -92523.542389
FMO2-MP2: Total energy -92792.336571


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-8.473-2.4767.304-4.586-8.714-0.008
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.022
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].
3A3LYS10.9150.9753.793-1.3362.262-0.030-1.917-1.6500.005
4A4TRP0-0.0070.0125.7920.2740.2740.0000.0000.0000.000
5A5ASN0-0.086-0.0597.9890.1810.1810.0000.0000.0000.000
6A6TYR00.0470.0108.7160.0420.0420.0000.0000.0000.000
7A7GLY00.0800.06614.1950.0110.0110.0000.0000.0000.000
8A8VAL0-0.0250.00117.9240.0070.0070.0000.0000.0000.000
9A9PHE0-0.063-0.03821.166-0.006-0.0060.0000.0000.0000.000
10A10PHE00.0640.03524.1410.0130.0130.0000.0000.0000.000
11A11LEU0-0.013-0.01127.699-0.007-0.0070.0000.0000.0000.000
12A12ASN0-0.069-0.02630.0830.0180.0180.0000.0000.0000.000
13A13PHE00.019-0.00933.0090.0060.0060.0000.0000.0000.000
14A14TYR00.0050.00035.7080.0020.0020.0000.0000.0000.000
15A15HIS10.8530.93538.3650.1000.1000.0000.0000.0000.000
16A16VAL00.0870.04533.559-0.002-0.0020.0000.0000.0000.000
17A17GLY00.0220.01635.9290.0030.0030.0000.0000.0000.000
18A18GLN0-0.011-0.00936.6600.0060.0060.0000.0000.0000.000
19A19GLN0-0.079-0.03234.4240.0070.0070.0000.0000.0000.000
20A20GLU-1-0.876-0.94039.544-0.080-0.0800.0000.0000.0000.000
21A21PRO00.011-0.00739.087-0.005-0.0050.0000.0000.0000.000
22A22SER00.0030.00138.567-0.007-0.0070.0000.0000.0000.000
23A23LEU00.0430.03637.033-0.003-0.0030.0000.0000.0000.000
24A24THR00.0470.01533.929-0.004-0.0040.0000.0000.0000.000
25A25MET0-0.029-0.00133.927-0.011-0.0110.0000.0000.0000.000
26A26SER0-0.055-0.03334.321-0.005-0.0050.0000.0000.0000.000
27A27ASN00.0260.00531.8630.0000.0000.0000.0000.0000.000
28A28ALA00.0300.01729.880-0.009-0.0090.0000.0000.0000.000
29A29LEU0-0.011-0.02529.518-0.014-0.0140.0000.0000.0000.000
30A30GLU-1-0.790-0.86529.228-0.135-0.1350.0000.0000.0000.000
31A31THR0-0.072-0.07224.680-0.002-0.0020.0000.0000.0000.000
32A32LEU0-0.035-0.02825.595-0.018-0.0180.0000.0000.0000.000
33A33ARG10.7270.84926.6000.1280.1280.0000.0000.0000.000
34A34ILE0-0.0020.00022.993-0.003-0.0030.0000.0000.0000.000
35A35ILE0-0.096-0.05321.486-0.013-0.0130.0000.0000.0000.000
36A36ASP-1-0.975-0.98122.594-0.225-0.2250.0000.0000.0000.000
37A37GLU-1-0.910-0.93725.124-0.138-0.1380.0000.0000.0000.000
38A38ASP-1-0.868-0.93023.996-0.130-0.1300.0000.0000.0000.000
39A39THR0-0.131-0.06918.934-0.007-0.0070.0000.0000.0000.000
40A40SER0-0.013-0.02016.852-0.011-0.0110.0000.0000.0000.000
41A41ILE0-0.130-0.06713.116-0.070-0.0700.0000.0000.0000.000
42A42TYR0-0.061-0.03815.201-0.089-0.0890.0000.0000.0000.000
43A43ASP-1-0.749-0.86215.629-0.710-0.7100.0000.0000.0000.000
44A44VAL0-0.063-0.02417.8930.0320.0320.0000.0000.0000.000
45A45VAL00.0390.01220.5840.0010.0010.0000.0000.0000.000
46A46ALA0-0.031-0.01423.391-0.001-0.0010.0000.0000.0000.000
47A47PHE00.0430.01525.1490.0110.0110.0000.0000.0000.000
48A48SER00.0110.01427.269-0.009-0.0090.0000.0000.0000.000
49A49GLU-1-0.861-0.95028.739-0.190-0.1900.0000.0000.0000.000
50A50HIS0-0.041-0.02727.9500.0030.0030.0000.0000.0000.000
51A51HIS0-0.042-0.03332.5180.0020.0020.0000.0000.0000.000
52A52ILE00.0160.00435.1960.0110.0110.0000.0000.0000.000
53A53ASP-1-0.849-0.92835.288-0.166-0.1660.0000.0000.0000.000
54A54LYS10.9600.99733.3570.1570.1570.0000.0000.0000.000
55A55SER0-0.089-0.02837.1450.0080.0080.0000.0000.0000.000
56A56TYR0-0.119-0.07239.9870.0090.0090.0000.0000.0000.000
57A57ASN0-0.010-0.00439.4660.0040.0040.0000.0000.0000.000
58A58ASP-1-0.890-0.94533.835-0.173-0.1730.0000.0000.0000.000
59A59GLU-1-0.932-0.97635.937-0.129-0.1290.0000.0000.0000.000
60A60THR0-0.0020.00839.1960.0000.0000.0000.0000.0000.000
61A61LYS10.8780.95632.6210.1970.1970.0000.0000.0000.000
62A62LEU0-0.0130.00133.6970.0020.0020.0000.0000.0000.000
63A63ALA00.021-0.01030.212-0.002-0.0020.0000.0000.0000.000
64A64PRO00.0220.03328.9880.0000.0000.0000.0000.0000.000
65A65PHE0-0.025-0.02427.626-0.018-0.0180.0000.0000.0000.000
66A66VAL00.0450.01424.9810.0150.0150.0000.0000.0000.000
67A67SER0-0.055-0.01424.873-0.039-0.0390.0000.0000.0000.000
68A68LEU00.0420.02519.7820.0120.0120.0000.0000.0000.000
69A69GLY00.0530.02121.689-0.047-0.0470.0000.0000.0000.000
70A70LYS10.9360.95622.3560.4900.4900.0000.0000.0000.000
71A71GLN0-0.028-0.00517.8910.0520.0520.0000.0000.0000.000
72A72ILE00.0020.00821.8980.0130.0130.0000.0000.0000.000
73A73HIS0-0.010-0.01017.667-0.048-0.0480.0000.0000.0000.000
74A74ILE0-0.014-0.01122.8690.0380.0380.0000.0000.0000.000
75A75LEU0-0.0060.00323.841-0.020-0.0200.0000.0000.0000.000
76A76ALA0-0.014-0.01823.2620.0190.0190.0000.0000.0000.000
77A77THR0-0.007-0.01325.3900.0070.0070.0000.0000.0000.000
78A78SER00.0560.02928.4900.0120.0120.0000.0000.0000.000
79A79PRO00.0580.02527.651-0.018-0.0180.0000.0000.0000.000
80A80GLU-1-0.897-0.95928.438-0.160-0.1600.0000.0000.0000.000
81A81THR0-0.034-0.01827.482-0.003-0.0030.0000.0000.0000.000
82A82VAL0-0.009-0.00423.840-0.018-0.0180.0000.0000.0000.000
83A83VAL00.0060.01324.976-0.017-0.0170.0000.0000.0000.000
84A84LYS10.9150.94526.9830.1730.1730.0000.0000.0000.000
85A85ALA00.0320.02523.645-0.004-0.0040.0000.0000.0000.000
86A86ALA00.0170.01522.571-0.024-0.0240.0000.0000.0000.000
87A87LYS10.8640.94523.5750.1910.1910.0000.0000.0000.000
88A88TYR0-0.038-0.02925.7150.0170.0170.0000.0000.0000.000
89A89GLY00.0180.01521.442-0.014-0.0140.0000.0000.0000.000
90A90MET0-0.053-0.01620.340-0.033-0.0330.0000.0000.0000.000
91A91PRO00.0160.03117.4300.0120.0120.0000.0000.0000.000
92A92LEU00.019-0.01018.8200.0540.0540.0000.0000.0000.000
93A93LEU0-0.013-0.00119.383-0.058-0.0580.0000.0000.0000.000
94A94PHE00.019-0.01117.4150.0420.0420.0000.0000.0000.000
95A95LYS10.8790.94221.8500.1870.1870.0000.0000.0000.000
96A96TRP00.0560.01423.4750.0020.0020.0000.0000.0000.000
97A97ASP-1-0.837-0.91024.448-0.188-0.1880.0000.0000.0000.000
98A98ASP-1-0.872-0.92825.391-0.189-0.1890.0000.0000.0000.000
99A99SER00.0490.01825.163-0.012-0.0120.0000.0000.0000.000
100A100GLN00.0990.02117.373-0.025-0.0250.0000.0000.0000.000
101A101GLN0-0.033-0.01322.138-0.022-0.0220.0000.0000.0000.000
102A102LYS10.9991.01224.2680.1570.1570.0000.0000.0000.000
103A103ARG10.8220.91720.4230.2490.2490.0000.0000.0000.000
104A104ILE00.0190.01118.962-0.024-0.0240.0000.0000.0000.000
105A105GLU-1-0.951-0.96820.901-0.142-0.1420.0000.0000.0000.000
106A106LEU0-0.059-0.02723.108-0.004-0.0040.0000.0000.0000.000
107A107LEU00.0080.01015.309-0.013-0.0130.0000.0000.0000.000
108A108ASN0-0.013-0.02219.412-0.029-0.0290.0000.0000.0000.000
109A109HIS0-0.0040.00121.1620.0050.0050.0000.0000.0000.000
110A110TYR0-0.038-0.02818.012-0.010-0.0100.0000.0000.0000.000
111A111GLN0-0.002-0.02415.457-0.074-0.0740.0000.0000.0000.000
112A112ALA0-0.0010.01519.9430.0090.0090.0000.0000.0000.000
113A113ALA0-0.032-0.02323.2150.0130.0130.0000.0000.0000.000
114A114ALA00.0330.01120.5940.0100.0100.0000.0000.0000.000
115A115ALA00.0200.02521.6290.0030.0030.0000.0000.0000.000
116A116LYS10.9130.96722.8860.1670.1670.0000.0000.0000.000
117A117PHE0-0.081-0.03825.8000.0180.0180.0000.0000.0000.000
118A118ASN0-0.023-0.00524.091-0.004-0.0040.0000.0000.0000.000
119A119VAL0-0.031-0.00521.236-0.011-0.0110.0000.0000.0000.000
120A120ASP-1-0.873-0.94416.751-0.558-0.5580.0000.0000.0000.000
121A121ILE00.001-0.01516.225-0.021-0.0210.0000.0000.0000.000
122A122ALA0-0.036-0.00812.553-0.071-0.0710.0000.0000.0000.000
123A123GLY0-0.029-0.02111.302-0.136-0.1360.0000.0000.0000.000
124A124VAL0-0.042-0.00412.057-0.134-0.1340.0000.0000.0000.000
125A125ARG10.8190.9138.1571.6541.6540.0000.0000.0000.000
126A126HIS00.0460.03413.0460.0810.0810.0000.0000.0000.000
127A127ARG10.7950.88214.8410.6480.6480.0000.0000.0000.000
128A128LEU00.0040.00416.0100.0630.0630.0000.0000.0000.000
129A129MET0-0.046-0.01318.071-0.016-0.0160.0000.0000.0000.000
130A130LEU0-0.007-0.00817.0830.0180.0180.0000.0000.0000.000
131A131PHE00.014-0.00321.066-0.009-0.0090.0000.0000.0000.000
132A132VAL0-0.014-0.00818.9930.0000.0000.0000.0000.0000.000
133A133ASN0-0.060-0.04922.1170.0140.0140.0000.0000.0000.000
134A134VAL00.036-0.00620.3860.0090.0090.0000.0000.0000.000
135A135ASN00.0210.00123.6920.0140.0140.0000.0000.0000.000
136A136ASP-1-0.859-0.93225.854-0.021-0.0210.0000.0000.0000.000
137A137ASN0-0.059-0.02327.1590.0150.0150.0000.0000.0000.000
138A138PRO00.012-0.01125.913-0.010-0.0100.0000.0000.0000.000
139A139THR00.017-0.00427.685-0.009-0.0090.0000.0000.0000.000
140A140GLN00.0150.00831.069-0.008-0.0080.0000.0000.0000.000
141A141ALA00.0340.03626.496-0.004-0.0040.0000.0000.0000.000
142A142LYS10.9010.94525.5770.0690.0690.0000.0000.0000.000
143A143ALA00.0020.01129.528-0.004-0.0040.0000.0000.0000.000
144A144GLU-1-0.820-0.91630.374-0.096-0.0960.0000.0000.0000.000
145A145LEU0-0.029-0.01326.441-0.005-0.0050.0000.0000.0000.000
146A146SER00.003-0.01930.389-0.004-0.0040.0000.0000.0000.000
147A147ILE00.0060.00233.256-0.001-0.0010.0000.0000.0000.000
148A148TYR0-0.052-0.02330.695-0.001-0.0010.0000.0000.0000.000
149A149LEU00.003-0.01629.419-0.004-0.0040.0000.0000.0000.000
150A150GLU-1-0.912-0.93133.925-0.076-0.0760.0000.0000.0000.000
151A151ASP-1-0.828-0.92637.441-0.087-0.0870.0000.0000.0000.000
152A152TYR0-0.024-0.02132.378-0.003-0.0030.0000.0000.0000.000
153A153LEU0-0.007-0.02032.769-0.003-0.0030.0000.0000.0000.000
154A154SER00.0270.02536.6280.0040.0040.0000.0000.0000.000
155A155TYR0-0.079-0.02938.4290.0030.0030.0000.0000.0000.000
156A156THR0-0.098-0.06635.135-0.002-0.0020.0000.0000.0000.000
157A157GLN0-0.050-0.00838.2050.0030.0030.0000.0000.0000.000
158A158ALA00.0150.00835.1330.0000.0000.0000.0000.0000.000
159A159GLU-1-0.821-0.90635.852-0.087-0.0870.0000.0000.0000.000
160A160THR0-0.059-0.03536.922-0.001-0.0010.0000.0000.0000.000
161A161SER0-0.052-0.03132.467-0.001-0.0010.0000.0000.0000.000
162A162ILE00.0460.02131.594-0.009-0.0090.0000.0000.0000.000
163A163ASP-1-0.867-0.93830.914-0.075-0.0750.0000.0000.0000.000
164A164GLU-1-0.970-0.98528.093-0.106-0.1060.0000.0000.0000.000
165A165ILE00.006-0.00427.202-0.014-0.0140.0000.0000.0000.000
166A166ILE0-0.045-0.01626.168-0.017-0.0170.0000.0000.0000.000
167A167ASN0-0.015-0.01325.277-0.005-0.0050.0000.0000.0000.000
168A168SER0-0.0200.00822.610-0.006-0.0060.0000.0000.0000.000
169A169ASN0-0.036-0.03421.751-0.057-0.0570.0000.0000.0000.000
170A170ALA00.0250.02219.2330.0160.0160.0000.0000.0000.000
171A171ALA00.0630.03121.290-0.001-0.0010.0000.0000.0000.000
172A172GLY0-0.019-0.02123.6260.0160.0160.0000.0000.0000.000
173A173ASN00.0810.06321.787-0.014-0.0140.0000.0000.0000.000
174A174PHE00.0520.00315.743-0.018-0.0180.0000.0000.0000.000
175A175ASP-1-0.867-0.94116.730-0.017-0.0170.0000.0000.0000.000
176A176THR0-0.036-0.02116.727-0.004-0.0040.0000.0000.0000.000
177A177CYS0-0.060-0.00418.169-0.019-0.0190.0000.0000.0000.000
178A178LEU0-0.010-0.01012.806-0.047-0.0470.0000.0000.0000.000
179A179HIS0-0.0190.00113.437-0.055-0.0550.0000.0000.0000.000
180A180HIS00.0330.01914.552-0.022-0.0220.0000.0000.0000.000
181A181VAL0-0.029-0.01212.679-0.025-0.0250.0000.0000.0000.000
182A182ALA0-0.027-0.01710.331-0.077-0.0770.0000.0000.0000.000
183A183GLU-1-0.902-0.95711.814-0.076-0.0760.0000.0000.0000.000
184A184MET0-0.042-0.01614.449-0.002-0.0020.0000.0000.0000.000
185A185ALA00.0130.00510.824-0.018-0.0180.0000.0000.0000.000
186A186GLN0-0.0030.00810.492-0.030-0.0300.0000.0000.0000.000
187A187GLY0-0.029-0.01712.2930.0390.0390.0000.0000.0000.000
188A188LEU0-0.042-0.01914.7810.0230.0230.0000.0000.0000.000
189A189ASN0-0.017-0.01911.854-0.047-0.0470.0000.0000.0000.000
190A190ASN0-0.007-0.0047.703-0.157-0.1570.0000.0000.0000.000
191A191LYS10.9010.9568.5630.4820.4820.0000.0000.0000.000
192A192VAL0-0.0070.00711.1080.0480.0480.0000.0000.0000.000
193A193ASP-1-0.789-0.87310.846-1.608-1.6080.0000.0000.0000.000
194A194PHE00.004-0.01410.5790.1200.1200.0000.0000.0000.000
195A195LEU0-0.039-0.01115.355-0.021-0.0210.0000.0000.0000.000
196A196PHE00.0210.00214.5300.0150.0150.0000.0000.0000.000
197A197CYS0-0.0170.01619.9930.0130.0130.0000.0000.0000.000
198A198PHE00.0840.01118.8750.0090.0090.0000.0000.0000.000
199A199GLU-1-0.766-0.88224.702-0.166-0.1660.0000.0000.0000.000
200A200SER0-0.057-0.00727.1760.0150.0150.0000.0000.0000.000
201A201MET0-0.0350.00724.9570.0040.0040.0000.0000.0000.000
202A202LYS10.9160.96829.0020.0860.0860.0000.0000.0000.000
203A203ASP-1-0.881-0.91330.637-0.074-0.0740.0000.0000.0000.000
204A204GLN00.046-0.00929.661-0.015-0.0150.0000.0000.0000.000
205A205GLU-1-0.885-0.93628.881-0.091-0.0910.0000.0000.0000.000
206A206ASN0-0.020-0.02127.1470.0000.0000.0000.0000.0000.000
207A207LYS10.8340.93325.1530.1500.1500.0000.0000.0000.000
208A208LYS11.0191.01023.9510.0870.0870.0000.0000.0000.000
209A209SER0-0.029-0.01723.357-0.007-0.0070.0000.0000.0000.000
210A210LEU0-0.044-0.01119.328-0.002-0.0020.0000.0000.0000.000
211A211MET0-0.019-0.00119.351-0.015-0.0150.0000.0000.0000.000
212A212ILE00.0750.03718.803-0.030-0.0300.0000.0000.0000.000
213A213ASN0-0.037-0.01818.1580.0050.0050.0000.0000.0000.000
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215A215ASP-1-0.758-0.87513.807-0.365-0.3650.0000.0000.0000.000
216A216LYS10.9820.97714.0220.0560.0560.0000.0000.0000.000
217A217ARG10.9240.97110.4330.1730.1730.0000.0000.0000.000
218A218VAL00.0130.0099.300-0.019-0.0190.0000.0000.0000.000
219A219ILE00.0010.0059.218-0.077-0.0770.0000.0000.0000.000
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221A221TYR00.0310.0292.467-1.679-1.2891.982-0.626-1.745-0.009
222A222ARG10.9210.9475.7191.3951.3950.0000.0000.0000.000
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225A225HIS10.8550.9202.957-5.266-3.9752.931-1.312-2.910-0.001
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228A228ASN0-0.025-0.0146.0150.0300.0300.0000.0000.0000.000