Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: G6641

Calculation Name: 4XD9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XD9

Chain ID: A

ChEMBL ID:

UniProt ID: C8VMF9

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptHSide
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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2901257.466937
FMO2-HF: Nuclear repulsion 2807719.15528
FMO2-HF: Total energy -93538.311657
FMO2-MP2: Total energy -93806.206239


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:19:LYS)


Summations of interaction energy for fragment #1(A:19:LYS)
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.
-100.281-100.81121.311-12.137-8.643-0.122
Interaction energy analysis for fragmet #1(A:19:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.889
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].
3A21PRO0-0.008-0.0113.309-3.683-1.4960.040-1.126-1.1010.000
4A22GLN0-0.027-0.0044.403-1.983-1.793-0.001-0.016-0.1730.000
5A23LEU0-0.016-0.0086.9351.0261.0260.0000.0000.0000.000
6A24ILE0-0.025-0.02310.1031.2691.2690.0000.0000.0000.000
7A25GLU-1-0.954-0.9647.161-31.092-31.0920.0000.0000.0000.000
8A26GLY00.0240.0157.7802.2692.2690.0000.0000.0000.000
9A27ALA0-0.050-0.0239.7201.0021.0020.0000.0000.0000.000
10A28LYS10.8690.9238.63119.60719.6070.0000.0000.0000.000
11A29ARG10.8860.9423.94258.32058.6350.002-0.050-0.2670.000
12A30VAL00.0050.0008.0491.4031.4030.0000.0000.0000.000
13A31LEU0-0.006-0.00710.204-0.522-0.5220.0000.0000.0000.000
14A32LEU0-0.013-0.00111.7232.0272.0270.0000.0000.0000.000
15A33LEU0-0.015-0.00115.150-0.051-0.0510.0000.0000.0000.000
16A34HIS00.0210.00917.0861.1471.1470.0000.0000.0000.000
17A35GLY00.0140.00320.716-0.224-0.2240.0000.0000.0000.000
18A36SER0-0.022-0.05123.464-0.058-0.0580.0000.0000.0000.000
19A37LYS10.8820.94026.6699.9859.9850.0000.0000.0000.000
20A38CYS00.0100.01925.1490.2150.2150.0000.0000.0000.000
21A39PRO00.0330.01727.1020.0080.0080.0000.0000.0000.000
22A40THR00.0600.01327.823-0.397-0.3970.0000.0000.0000.000
23A41PRO00.0470.02727.813-0.375-0.3750.0000.0000.0000.000
24A42LEU00.0440.02325.053-0.306-0.3060.0000.0000.0000.000
25A43HIS0-0.0030.00423.434-0.985-0.9850.0000.0000.0000.000
26A44THR0-0.021-0.01523.078-0.604-0.6040.0000.0000.0000.000
27A45VAL0-0.0140.00022.727-0.342-0.3420.0000.0000.0000.000
28A46LEU0-0.004-0.00118.802-0.532-0.5320.0000.0000.0000.000
29A47LYS10.8460.94018.79211.43411.4340.0000.0000.0000.000
30A48VAL0-0.010-0.00319.530-0.546-0.5460.0000.0000.0000.000
31A49PHE00.031-0.00618.099-0.198-0.1980.0000.0000.0000.000
32A50HIS00.0260.03012.268-0.889-0.8890.0000.0000.0000.000
33A51SER0-0.043-0.01615.340-0.485-0.4850.0000.0000.0000.000
34A52LEU0-0.045-0.03417.436-0.155-0.1550.0000.0000.0000.000
35A53THR00.0240.01713.2780.2730.2730.0000.0000.0000.000
36A54THR0-0.0560.00312.451-1.988-1.9880.0000.0000.0000.000
37A55PRO0-0.022-0.02710.4601.1391.1390.0000.0000.0000.000
38A56HIS0-0.011-0.0077.943-1.998-1.9980.0000.0000.0000.000
39A57SER00.0660.0308.905-1.032-1.0320.0000.0000.0000.000
40A58VAL0-0.027-0.0157.500-0.320-0.3200.0000.0000.0000.000
41A59LEU00.0040.01610.5841.2451.2450.0000.0000.0000.000
42A60PHE00.009-0.00813.5540.2260.2260.0000.0000.0000.000
43A61HIS00.025-0.00715.1591.4881.4880.0000.0000.0000.000
44A62LYS10.9080.96917.90515.69415.6940.0000.0000.0000.000
45A63LYS10.8990.95219.64113.39013.3900.0000.0000.0000.000
46A64ASN0-0.042-0.01717.8720.0180.0180.0000.0000.0000.000
47A65GLU-1-0.834-0.89221.452-11.023-11.0230.0000.0000.0000.000
48A66ASN0-0.036-0.03022.932-0.165-0.1650.0000.0000.0000.000
49A67ILE0-0.0040.01718.229-0.229-0.2290.0000.0000.0000.000
50A68HIS0-0.001-0.01522.3810.2120.2120.0000.0000.0000.000
51A69PRO00.0740.03920.5520.2380.2380.0000.0000.0000.000
52A70PHE0-0.021-0.02222.461-0.079-0.0790.0000.0000.0000.000
53A71GLU-1-0.922-0.94425.527-10.571-10.5710.0000.0000.0000.000
54A72SER00.0280.00322.701-0.096-0.0960.0000.0000.0000.000
55A73THR0-0.037-0.03118.5750.1940.1940.0000.0000.0000.000
56A74GLU-1-0.885-0.92417.766-16.063-16.0630.0000.0000.0000.000
57A75SER00.022-0.00616.683-1.195-1.1950.0000.0000.0000.000
58A76LEU0-0.025-0.02014.944-1.171-1.1710.0000.0000.0000.000
59A77GLU-1-0.735-0.86013.638-19.995-19.9950.0000.0000.0000.000
60A78PHE0-0.038-0.00612.050-2.375-2.3750.0000.0000.0000.000
61A79LEU0-0.037-0.03111.027-2.142-2.1420.0000.0000.0000.000
62A80ALA00.0330.0189.497-2.811-2.8110.0000.0000.0000.000
63A81ASN00.0400.0097.761-5.630-5.6300.0000.0000.0000.000
64A82LYS10.9050.9766.53620.03920.0390.0000.0000.0000.000
65A83ASN0-0.094-0.0615.426-3.034-3.0340.0000.0000.0000.000
66A84ASP-1-0.813-0.8731.645-128.203-131.53921.271-10.932-7.003-0.122
67A85CYS0-0.090-0.0404.594-0.977-0.863-0.001-0.013-0.0990.000
68A86GLY00.1030.0547.3141.8581.8580.0000.0000.0000.000
69A87MET0-0.041-0.0099.8233.3153.3150.0000.0000.0000.000
70A88VAL0-0.0010.00411.822-1.488-1.4880.0000.0000.0000.000
71A89ILE0-0.026-0.00714.3301.4791.4790.0000.0000.0000.000
72A90PHE00.040-0.00117.335-0.139-0.1390.0000.0000.0000.000
73A91GLY00.0170.02619.4880.7430.7430.0000.0000.0000.000
74A92SER0-0.004-0.00922.6220.0460.0460.0000.0000.0000.000
75A93SER00.0570.01525.5010.2940.2940.0000.0000.0000.000
76A94ASN00.0040.00729.2970.3840.3840.0000.0000.0000.000
77A95LYS11.0130.98732.3288.4468.4460.0000.0000.0000.000
78A96LYS10.9590.99434.2968.8848.8840.0000.0000.0000.000
79A97ARG10.9330.97129.68510.51110.5110.0000.0000.0000.000
80A98PRO00.0120.02330.709-0.364-0.3640.0000.0000.0000.000
81A99ASN0-0.010-0.02229.060-0.139-0.1390.0000.0000.0000.000
82A100CYS0-0.0240.00727.009-0.079-0.0790.0000.0000.0000.000
83A101LEU00.0400.01521.552-0.364-0.3640.0000.0000.0000.000
84A102THR0-0.033-0.02220.9480.3740.3740.0000.0000.0000.000
85A103ILE00.0210.01218.081-0.799-0.7990.0000.0000.0000.000
86A104ALA00.0150.00316.8900.7380.7380.0000.0000.0000.000
87A105ARG10.7730.85314.65615.66815.6680.0000.0000.0000.000
88A106ILE0-0.037-0.01410.7611.0651.0650.0000.0000.0000.000
89A107PHE00.013-0.00411.733-1.254-1.2540.0000.0000.0000.000
90A108ASP-1-0.887-0.93910.088-21.604-21.6040.0000.0000.0000.000
91A109SER0-0.030-0.0129.3120.1360.1360.0000.0000.0000.000
92A110LYS10.9720.99810.60418.29818.2980.0000.0000.0000.000
93A111VAL0-0.022-0.01814.108-0.770-0.7700.0000.0000.0000.000
94A112LEU0-0.059-0.02115.7350.7840.7840.0000.0000.0000.000
95A113ASP-1-0.772-0.87717.615-15.029-15.0290.0000.0000.0000.000
96A114MET0-0.032-0.03019.364-1.040-1.0400.0000.0000.0000.000
97A115ALA00.0380.01221.6350.8000.8000.0000.0000.0000.000
98A116GLU-1-0.820-0.88723.330-11.640-11.6400.0000.0000.0000.000
99A117LEU00.0040.00424.0860.4240.4240.0000.0000.0000.000
100A118LEU0-0.031-0.02627.058-0.187-0.1870.0000.0000.0000.000
101A119LEU0-0.019-0.01428.2900.1950.1950.0000.0000.0000.000
102A120LEU0-0.035-0.02630.4210.2510.2510.0000.0000.0000.000
103A121PRO0-0.057-0.03333.853-0.156-0.1560.0000.0000.0000.000
104A122ASP-1-0.770-0.87836.063-8.481-8.4810.0000.0000.0000.000
105A123ALA0-0.0010.01137.0250.1410.1410.0000.0000.0000.000
106A124ASN0-0.083-0.06839.6790.2920.2920.0000.0000.0000.000
107A125GLY0-0.0140.00640.7770.1630.1630.0000.0000.0000.000
108A126GLU-1-0.944-0.94838.402-7.997-7.9970.0000.0000.0000.000
109A127GLY0-0.090-0.05236.216-0.112-0.1120.0000.0000.0000.000
110A128ILE0-0.022-0.02429.389-0.128-0.1280.0000.0000.0000.000
111A129PRO00.0270.01031.791-0.146-0.1460.0000.0000.0000.000
112A130GLU-1-0.875-0.93528.193-11.390-11.3900.0000.0000.0000.000
113A131MET0-0.034-0.00926.4200.1220.1220.0000.0000.0000.000
114A132ASN0-0.024-0.03322.386-0.038-0.0380.0000.0000.0000.000
115A133ARG10.9400.97121.48711.81911.8190.0000.0000.0000.000
116A134LEU00.0370.03023.0830.4860.4860.0000.0000.0000.000
117A135SER00.0690.00824.9280.5630.5630.0000.0000.0000.000
118A136MET0-0.007-0.00426.238-0.595-0.5950.0000.0000.0000.000
119A137HIS0-0.0030.01428.270-0.251-0.2510.0000.0000.0000.000
120A138VAL00.0360.01823.8970.1490.1490.0000.0000.0000.000
121A139ALA00.0130.01422.530-0.232-0.2320.0000.0000.0000.000
122A140ILE0-0.015-0.02617.411-0.086-0.0860.0000.0000.0000.000
123A141GLY00.0630.03716.911-0.291-0.2910.0000.0000.0000.000
124A142LEU0-0.0390.00417.594-0.332-0.3320.0000.0000.0000.000
125A143ARG10.8960.94918.79715.24415.2440.0000.0000.0000.000
126A144PRO0-0.0070.02320.4800.6710.6710.0000.0000.0000.000
127A145LEU00.0080.00523.476-0.077-0.0770.0000.0000.0000.000
128A146MET0-0.025-0.01521.051-0.071-0.0710.0000.0000.0000.000
129A147LEU0-0.0080.00026.5310.2800.2800.0000.0000.0000.000
130A148PHE00.0190.00324.264-0.091-0.0910.0000.0000.0000.000
131A149SER00.000-0.00130.3030.1820.1820.0000.0000.0000.000
132A150GLY00.0680.02633.845-0.132-0.1320.0000.0000.0000.000
133A151SER0-0.069-0.08035.322-0.220-0.2200.0000.0000.0000.000
134A152ALA00.0570.02634.074-0.087-0.0870.0000.0000.0000.000
135A153TRP0-0.080-0.04727.971-0.422-0.4220.0000.0000.0000.000
136A154ASP-1-0.934-0.96831.455-9.401-9.4010.0000.0000.0000.000
137A155ASP-1-0.816-0.87034.088-8.685-8.6850.0000.0000.0000.000
138A156THR0-0.055-0.03931.942-0.219-0.2190.0000.0000.0000.000
139A157THR0-0.092-0.06332.410-0.122-0.1220.0000.0000.0000.000
140A158SER00.0260.02633.107-0.088-0.0880.0000.0000.0000.000
141A159THR0-0.003-0.02728.864-0.273-0.2730.0000.0000.0000.000
142A160THR00.0050.00428.122-0.462-0.4620.0000.0000.0000.000
143A161HIS00.0650.02827.764-0.452-0.4520.0000.0000.0000.000
144A162THR00.0150.01425.908-0.328-0.3280.0000.0000.0000.000
145A163MET0-0.039-0.00423.157-0.540-0.5400.0000.0000.0000.000
146A164LEU00.010-0.00523.109-0.649-0.6490.0000.0000.0000.000
147A165LYS10.9010.96123.53610.48310.4830.0000.0000.0000.000
148A166SER0-0.0100.00420.718-0.755-0.7550.0000.0000.0000.000
149A167MET0-0.022-0.00419.006-0.678-0.6780.0000.0000.0000.000
150A168LEU00.0120.00518.715-0.807-0.8070.0000.0000.0000.000
151A169VAL00.0160.00219.959-0.404-0.4040.0000.0000.0000.000
152A170ASP-1-0.815-0.88214.938-21.403-21.4030.0000.0000.0000.000
153A171LEU0-0.018-0.00215.219-1.402-1.4020.0000.0000.0000.000
154A172PHE00.003-0.02015.903-0.635-0.6350.0000.0000.0000.000
155A173LYS10.8010.90813.45021.81521.8150.0000.0000.0000.000
156A174GLY0-0.0070.00314.5660.3320.3320.0000.0000.0000.000
157A175GLU-1-0.874-0.95311.461-26.947-26.9470.0000.0000.0000.000
158A176THR0-0.035-0.01014.6541.2461.2460.0000.0000.0000.000
159A177SER00.021-0.00716.493-0.384-0.3840.0000.0000.0000.000
160A178ASP-1-0.822-0.89519.118-13.154-13.1540.0000.0000.0000.000
161A179LYS10.8450.91022.12213.15213.1520.0000.0000.0000.000
162A180ILE0-0.018-0.01723.053-0.709-0.7090.0000.0000.0000.000
163A181ASP-1-0.839-0.90125.180-10.638-10.6380.0000.0000.0000.000
164A182VAL00.018-0.00127.328-0.125-0.1250.0000.0000.0000.000
165A183GLU-1-0.908-0.95128.622-9.692-9.6920.0000.0000.0000.000
166A184GLY0-0.052-0.02925.513-0.156-0.1560.0000.0000.0000.000
167A185LEU0-0.050-0.01825.791-0.340-0.3400.0000.0000.0000.000
168A186GLN0-0.025-0.01726.9300.3380.3380.0000.0000.0000.000
169A187TYR0-0.029-0.03621.1360.5150.5150.0000.0000.0000.000
170A188ALA00.0050.00826.984-0.291-0.2910.0000.0000.0000.000
171A189LEU0-0.016-0.00123.4690.1070.1070.0000.0000.0000.000
172A190MET0-0.028-0.00527.1290.1280.1280.0000.0000.0000.000
173A191VAL00.016-0.00725.792-0.093-0.0930.0000.0000.0000.000
174A192GLY00.0080.01329.2030.1050.1050.0000.0000.0000.000
175A193ALA0-0.041-0.03232.310-0.090-0.0900.0000.0000.0000.000
176A194GLU-1-0.829-0.89933.756-8.236-8.2360.0000.0000.0000.000
177A195GLU-1-0.826-0.88237.139-8.396-8.3960.0000.0000.0000.000
178A196PRO0-0.0170.00937.7990.0770.0770.0000.0000.0000.000
179A197THR00.0300.00439.6690.2260.2260.0000.0000.0000.000
180A198ALA00.008-0.00641.526-0.154-0.1540.0000.0000.0000.000
181A199GLY0-0.008-0.00342.3740.1160.1160.0000.0000.0000.000
182A200LEU0-0.034-0.00439.124-0.031-0.0310.0000.0000.0000.000
183A201ALA0-0.050-0.02234.748-0.104-0.1040.0000.0000.0000.000
184A202PRO00.0660.02332.7100.0940.0940.0000.0000.0000.000
185A203ILE00.0210.01433.497-0.277-0.2770.0000.0000.0000.000
186A204ILE0-0.037-0.01027.2350.0170.0170.0000.0000.0000.000
187A205HIS10.7420.83931.5789.0719.0710.0000.0000.0000.000
188A206LEU00.0040.00924.634-0.125-0.1250.0000.0000.0000.000
189A207ARG10.8370.89029.0009.8119.8110.0000.0000.0000.000
190A208TRP00.0510.02323.267-0.155-0.1550.0000.0000.0000.000
191A209TYR00.0190.00428.9560.3230.3230.0000.0000.0000.000
192A210LYS10.9060.95529.8459.8009.8000.0000.0000.0000.000
193A211ILE0-0.021-0.02129.9790.3680.3680.0000.0000.0000.000
194A212VAL00.0160.01333.042-0.012-0.0120.0000.0000.0000.000
195A213THR00.0010.00435.6140.0960.0960.0000.0000.0000.000
196A214LYS10.8810.93838.2027.4347.4340.0000.0000.0000.000
197A215ARG10.9750.97441.9506.8596.8590.0000.0000.0000.000
198A216SER00.013-0.00944.3060.1460.1460.0000.0000.0000.000
199A217GLY0-0.0210.00046.2590.1350.1350.0000.0000.0000.000
200A218HIS0-0.0020.00045.6550.0280.0280.0000.0000.0000.000
201A219LYS10.9380.95643.8706.7126.7120.0000.0000.0000.000
202A220LEU00.0340.03039.164-0.158-0.1580.0000.0000.0000.000
203A221PRO00.0300.02138.0850.2140.2140.0000.0000.0000.000
204A222ARG10.8500.89940.4687.4597.4590.0000.0000.0000.000
205A223VAL00.0270.00435.833-0.068-0.0680.0000.0000.0000.000
206A224GLU-1-0.806-0.86538.125-7.325-7.3250.0000.0000.0000.000
207A225LEU0-0.013-0.00533.461-0.248-0.2480.0000.0000.0000.000
208A226GLU-1-0.895-0.95034.432-8.683-8.6830.0000.0000.0000.000
209A227GLU-1-0.877-0.92933.404-9.039-9.0390.0000.0000.0000.000
210A228ILE0-0.064-0.02627.993-0.008-0.0080.0000.0000.0000.000
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