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: 8556Y

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2906161.3321
FMO2-HF: Nuclear repulsion 2812622.40906
FMO2-HF: Total energy -93538.92304
FMO2-MP2: Total energy -93806.86711


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.
-91.694-92.71320.875-11.465-8.393-0.115
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 : 0.850 / q_NPA : 0.895
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].
3A21PRO0-0.021-0.0233.461-3.357-1.5680.005-0.952-0.8420.001
4A22GLN0-0.039-0.0124.071-1.778-1.495-0.001-0.042-0.2400.000
5A23LEU0-0.016-0.0076.6571.2421.2420.0000.0000.0000.000
6A24ILE0-0.017-0.0149.3571.5551.5550.0000.0000.0000.000
7A25GLU-1-0.920-0.9497.363-30.470-30.4700.0000.0000.0000.000
8A26GLY00.0350.0227.9112.2022.2020.0000.0000.0000.000
9A27ALA0-0.035-0.0369.8350.7700.7700.0000.0000.0000.000
10A28LYS10.8220.9019.10419.74919.7490.0000.0000.0000.000
11A29ARG10.8880.9483.97555.71955.945-0.001-0.030-0.1960.000
12A30VAL0-0.013-0.0068.0591.3541.3540.0000.0000.0000.000
13A31LEU0-0.0020.00410.269-0.440-0.4400.0000.0000.0000.000
14A32LEU0-0.013-0.00611.6572.0182.0180.0000.0000.0000.000
15A33LEU0-0.011-0.00315.195-0.036-0.0360.0000.0000.0000.000
16A34HIS00.0990.05717.1821.1971.1970.0000.0000.0000.000
17A35GLY00.0500.02520.868-0.275-0.2750.0000.0000.0000.000
18A36SER0-0.034-0.06523.4100.0950.0950.0000.0000.0000.000
19A37LYS10.8780.93826.7019.9319.9310.0000.0000.0000.000
20A38CYS00.0130.03725.1600.2400.2400.0000.0000.0000.000
21A39PRO00.0230.02327.0980.0090.0090.0000.0000.0000.000
22A40THR00.035-0.00527.954-0.364-0.3640.0000.0000.0000.000
23A41PRO00.0510.02927.698-0.385-0.3850.0000.0000.0000.000
24A42LEU00.0350.02424.839-0.322-0.3220.0000.0000.0000.000
25A43HIS0-0.024-0.01023.244-1.051-1.0510.0000.0000.0000.000
26A44THR00.008-0.00923.015-0.610-0.6100.0000.0000.0000.000
27A45VAL0-0.019-0.00222.392-0.316-0.3160.0000.0000.0000.000
28A46LEU0-0.006-0.00418.594-0.519-0.5190.0000.0000.0000.000
29A47LYS10.7570.87618.83611.52011.5200.0000.0000.0000.000
30A48VAL0-0.004-0.00119.644-0.525-0.5250.0000.0000.0000.000
31A49PHE00.029-0.00418.083-0.140-0.1400.0000.0000.0000.000
32A50HIS00.0580.04912.139-0.819-0.8190.0000.0000.0000.000
33A51SER0-0.058-0.01715.643-0.404-0.4040.0000.0000.0000.000
34A52LEU0-0.061-0.02718.2160.1220.1220.0000.0000.0000.000
35A53THR00.0310.00513.1060.2930.2930.0000.0000.0000.000
36A54THR0-0.044-0.00412.605-2.001-2.0010.0000.0000.0000.000
37A55PRO0-0.041-0.03310.4201.1701.1700.0000.0000.0000.000
38A56HIS0-0.015-0.0038.323-2.031-2.0310.0000.0000.0000.000
39A57SER00.0590.0158.965-1.187-1.1870.0000.0000.0000.000
40A58VAL0-0.036-0.0187.753-0.656-0.6560.0000.0000.0000.000
41A59LEU00.0190.01910.7461.1661.1660.0000.0000.0000.000
42A60PHE00.007-0.00613.1910.4680.4680.0000.0000.0000.000
43A61HIS00.030-0.00214.9711.3991.3990.0000.0000.0000.000
44A62LYS10.8650.93917.74515.78515.7850.0000.0000.0000.000
45A63LYS10.8800.93619.56013.43513.4350.0000.0000.0000.000
46A64ASN0-0.048-0.02417.968-0.221-0.2210.0000.0000.0000.000
47A65GLU-1-0.846-0.90121.409-11.074-11.0740.0000.0000.0000.000
48A66ASN0-0.014-0.01622.972-0.070-0.0700.0000.0000.0000.000
49A67ILE00.0050.01717.990-0.356-0.3560.0000.0000.0000.000
50A68HIS0-0.002-0.01122.0390.1650.1650.0000.0000.0000.000
51A69PRO00.0530.02220.2140.2760.2760.0000.0000.0000.000
52A70PHE00.015-0.00222.164-0.135-0.1350.0000.0000.0000.000
53A71GLU-1-0.875-0.90625.366-10.746-10.7460.0000.0000.0000.000
54A72SER00.003-0.00422.7590.0090.0090.0000.0000.0000.000
55A73THR0-0.018-0.02018.7480.1100.1100.0000.0000.0000.000
56A74GLU-1-0.895-0.92717.969-15.749-15.7490.0000.0000.0000.000
57A75SER00.015-0.00616.825-1.213-1.2130.0000.0000.0000.000
58A76LEU0-0.021-0.01315.097-0.980-0.9800.0000.0000.0000.000
59A77GLU-1-0.740-0.86013.715-19.872-19.8720.0000.0000.0000.000
60A78PHE0-0.041-0.00912.103-2.443-2.4430.0000.0000.0000.000
61A79LEU0-0.039-0.02711.215-2.064-2.0640.0000.0000.0000.000
62A80ALA00.0290.0179.819-2.543-2.5430.0000.0000.0000.000
63A81ASN00.024-0.0077.930-5.472-5.4720.0000.0000.0000.000
64A82LYS10.9180.9736.44419.34719.3470.0000.0000.0000.000
65A83ASN0-0.070-0.0465.863-2.757-2.7570.0000.0000.0000.000
66A84ASP-1-0.832-0.8781.659-124.716-128.14620.873-10.425-7.019-0.116
67A85CYS0-0.078-0.0334.508-0.212-0.099-0.001-0.016-0.0960.000
68A86GLY00.1060.0577.5032.4112.4110.0000.0000.0000.000
69A87MET0-0.047-0.0159.9503.2753.2750.0000.0000.0000.000
70A88VAL00.008-0.00311.743-1.679-1.6790.0000.0000.0000.000
71A89ILE0-0.0180.00414.3541.5031.5030.0000.0000.0000.000
72A90PHE00.023-0.00617.369-0.343-0.3430.0000.0000.0000.000
73A91GLY00.0250.03319.6620.7450.7450.0000.0000.0000.000
74A92SER0-0.025-0.02922.8000.0420.0420.0000.0000.0000.000
75A93SER00.0540.00725.6650.3280.3280.0000.0000.0000.000
76A94ASN00.0130.00629.5120.3440.3440.0000.0000.0000.000
77A95LYS11.0010.97732.4128.4508.4500.0000.0000.0000.000
78A96LYS10.9550.99834.7988.8108.8100.0000.0000.0000.000
79A97ARG10.8470.91128.73610.72910.7290.0000.0000.0000.000
80A98PRO00.0100.01831.045-0.343-0.3430.0000.0000.0000.000
81A99ASN0-0.021-0.03529.169-0.109-0.1090.0000.0000.0000.000
82A100CYS00.0050.02126.041-0.066-0.0660.0000.0000.0000.000
83A101LEU00.0300.02621.502-0.378-0.3780.0000.0000.0000.000
84A102THR0-0.031-0.01720.9850.3820.3820.0000.0000.0000.000
85A103ILE00.0040.00018.367-0.709-0.7090.0000.0000.0000.000
86A104ALA00.0160.00217.0810.7840.7840.0000.0000.0000.000
87A105ARG10.7660.84114.63015.82615.8260.0000.0000.0000.000
88A106ILE0-0.028-0.00610.6031.0231.0230.0000.0000.0000.000
89A107PHE00.0400.00811.303-1.133-1.1330.0000.0000.0000.000
90A108ASP-1-0.852-0.92510.503-20.068-20.0680.0000.0000.0000.000
91A109SER0-0.0110.0039.6810.0330.0330.0000.0000.0000.000
92A110LYS10.8720.95010.88920.10820.1080.0000.0000.0000.000
93A111VAL0-0.021-0.02814.208-0.806-0.8060.0000.0000.0000.000
94A112LEU0-0.066-0.01015.6170.7360.7360.0000.0000.0000.000
95A113ASP-1-0.767-0.87817.394-15.044-15.0440.0000.0000.0000.000
96A114MET0-0.027-0.02419.363-1.082-1.0820.0000.0000.0000.000
97A115ALA00.0310.01221.6840.8010.8010.0000.0000.0000.000
98A116GLU-1-0.777-0.86323.514-11.595-11.5950.0000.0000.0000.000
99A117LEU00.0130.00424.1260.4270.4270.0000.0000.0000.000
100A118LEU0-0.021-0.01627.189-0.192-0.1920.0000.0000.0000.000
101A119LEU0-0.021-0.00828.0400.2090.2090.0000.0000.0000.000
102A120LEU0-0.019-0.01930.2350.2270.2270.0000.0000.0000.000
103A121PRO0-0.053-0.02933.766-0.153-0.1530.0000.0000.0000.000
104A122ASP-1-0.745-0.87936.300-8.381-8.3810.0000.0000.0000.000
105A123ALA0-0.0070.00537.1760.1600.1600.0000.0000.0000.000
106A124ASN0-0.108-0.05839.9550.2760.2760.0000.0000.0000.000
107A125GLY0-0.012-0.01040.8570.2150.2150.0000.0000.0000.000
108A126GLU-1-0.959-0.95538.250-8.122-8.1220.0000.0000.0000.000
109A127GLY0-0.078-0.03936.588-0.142-0.1420.0000.0000.0000.000
110A128ILE0-0.017-0.02629.737-0.153-0.1530.0000.0000.0000.000
111A129PRO00.0140.00632.134-0.154-0.1540.0000.0000.0000.000
112A130GLU-1-0.804-0.88127.968-11.856-11.8560.0000.0000.0000.000
113A131MET0-0.027-0.00226.6670.1220.1220.0000.0000.0000.000
114A132ASN0-0.016-0.03022.734-0.070-0.0700.0000.0000.0000.000
115A133ARG10.9440.97921.70511.71811.7180.0000.0000.0000.000
116A134LEU00.0300.02923.2210.5090.5090.0000.0000.0000.000
117A135SER00.0660.01225.1340.5730.5730.0000.0000.0000.000
118A136MET00.0000.00026.355-0.630-0.6300.0000.0000.0000.000
119A137HIS0-0.0260.00128.360-0.368-0.3680.0000.0000.0000.000
120A138VAL00.0500.02624.3050.2120.2120.0000.0000.0000.000
121A139ALA00.0020.01122.881-0.176-0.1760.0000.0000.0000.000
122A140ILE0-0.009-0.02017.699-0.111-0.1110.0000.0000.0000.000
123A141GLY00.0520.03217.118-0.189-0.1890.0000.0000.0000.000
124A142LEU0-0.052-0.00417.849-0.342-0.3420.0000.0000.0000.000
125A143ARG10.8940.95018.77415.36215.3620.0000.0000.0000.000
126A144PRO0-0.0130.01920.7990.6330.6330.0000.0000.0000.000
127A145LEU00.0160.00323.781-0.079-0.0790.0000.0000.0000.000
128A146MET0-0.035-0.02521.211-0.074-0.0740.0000.0000.0000.000
129A147LEU0-0.008-0.00126.7610.2330.2330.0000.0000.0000.000
130A148PHE00.0280.01524.2070.0610.0610.0000.0000.0000.000
131A149SER0-0.015-0.01430.2230.2020.2020.0000.0000.0000.000
132A150GLY00.0770.04033.947-0.110-0.1100.0000.0000.0000.000
133A151SER0-0.069-0.08735.327-0.218-0.2180.0000.0000.0000.000
134A152ALA00.0360.01034.823-0.103-0.1030.0000.0000.0000.000
135A153TRP0-0.066-0.03728.180-0.436-0.4360.0000.0000.0000.000
136A154ASP-1-0.872-0.93031.436-9.915-9.9150.0000.0000.0000.000
137A155ASP-1-0.843-0.88833.945-8.657-8.6570.0000.0000.0000.000
138A156THR0-0.060-0.04131.995-0.187-0.1870.0000.0000.0000.000
139A157THR0-0.078-0.05032.830-0.087-0.0870.0000.0000.0000.000
140A158SER00.0400.02433.038-0.182-0.1820.0000.0000.0000.000
141A159THR0-0.014-0.03228.808-0.273-0.2730.0000.0000.0000.000
142A160THR00.0000.00628.124-0.467-0.4670.0000.0000.0000.000
143A161HIS00.0410.02328.053-0.429-0.4290.0000.0000.0000.000
144A162THR00.0260.00726.404-0.347-0.3470.0000.0000.0000.000
145A163MET0-0.046-0.00723.235-0.529-0.5290.0000.0000.0000.000
146A164LEU00.002-0.00623.462-0.637-0.6370.0000.0000.0000.000
147A165LYS10.8520.92423.97210.21810.2180.0000.0000.0000.000
148A166SER0-0.0030.00921.023-0.699-0.6990.0000.0000.0000.000
149A167MET0-0.034-0.00919.343-0.633-0.6330.0000.0000.0000.000
150A168LEU00.010-0.00219.048-0.809-0.8090.0000.0000.0000.000
151A169VAL00.0250.01520.077-0.283-0.2830.0000.0000.0000.000
152A170ASP-1-0.811-0.87615.090-21.105-21.1050.0000.0000.0000.000
153A171LEU0-0.020-0.00515.394-1.386-1.3860.0000.0000.0000.000
154A172PHE00.005-0.01516.167-0.552-0.5520.0000.0000.0000.000
155A173LYS10.8010.89713.34421.90221.9020.0000.0000.0000.000
156A174GLY00.0080.00914.9490.3890.3890.0000.0000.0000.000
157A175GLU-1-0.847-0.93211.761-26.569-26.5690.0000.0000.0000.000
158A176THR0-0.059-0.01914.7141.2891.2890.0000.0000.0000.000
159A177SER00.0310.00515.987-0.314-0.3140.0000.0000.0000.000
160A178ASP-1-0.831-0.90818.572-13.143-13.1430.0000.0000.0000.000
161A179LYS10.8410.91121.67013.18913.1890.0000.0000.0000.000
162A180ILE0-0.009-0.00422.366-0.741-0.7410.0000.0000.0000.000
163A181ASP-1-0.846-0.90524.850-10.541-10.5410.0000.0000.0000.000
164A182VAL00.020-0.00527.639-0.098-0.0980.0000.0000.0000.000
165A183GLU-1-0.907-0.95029.238-9.709-9.7090.0000.0000.0000.000
166A184GLY0-0.024-0.01425.887-0.220-0.2200.0000.0000.0000.000
167A185LEU0-0.047-0.01326.054-0.339-0.3390.0000.0000.0000.000
168A186GLN0-0.029-0.03227.1500.2740.2740.0000.0000.0000.000
169A187TYR0-0.035-0.04521.4570.4960.4960.0000.0000.0000.000
170A188ALA00.0080.01127.299-0.242-0.2420.0000.0000.0000.000
171A189LEU0-0.012-0.00323.7500.0060.0060.0000.0000.0000.000
172A190MET0-0.0280.00027.3610.0690.0690.0000.0000.0000.000
173A191VAL00.002-0.01326.102-0.132-0.1320.0000.0000.0000.000
174A192GLY00.0560.03429.4870.1160.1160.0000.0000.0000.000
175A193ALA0-0.040-0.02732.509-0.060-0.0600.0000.0000.0000.000
176A194GLU-1-0.846-0.90633.850-8.192-8.1920.0000.0000.0000.000
177A195GLU-1-0.799-0.86637.175-8.421-8.4210.0000.0000.0000.000
178A196PRO0-0.0100.00437.8980.1000.1000.0000.0000.0000.000
179A197THR00.019-0.00139.7150.2270.2270.0000.0000.0000.000
180A198ALA00.005-0.00441.858-0.138-0.1380.0000.0000.0000.000
181A199GLY00.0040.00542.5880.1270.1270.0000.0000.0000.000
182A200LEU0-0.057-0.01339.021-0.073-0.0730.0000.0000.0000.000
183A201ALA0-0.018-0.01234.935-0.111-0.1110.0000.0000.0000.000
184A202PRO00.0400.01832.8740.0710.0710.0000.0000.0000.000
185A203ILE00.0130.00533.600-0.294-0.2940.0000.0000.0000.000
186A204ILE0-0.032-0.01127.4620.0270.0270.0000.0000.0000.000
187A205HIS10.7630.85031.7258.9998.9990.0000.0000.0000.000
188A206LEU0-0.0060.00524.829-0.100-0.1000.0000.0000.0000.000
189A207ARG10.8470.89429.1749.8159.8150.0000.0000.0000.000
190A208TRP00.0480.02523.166-0.015-0.0150.0000.0000.0000.000
191A209TYR00.013-0.00528.8830.3370.3370.0000.0000.0000.000
192A210LYS10.8740.95130.1139.7139.7130.0000.0000.0000.000
193A211ILE0-0.019-0.01330.0760.3750.3750.0000.0000.0000.000
194A212VAL00.0120.00033.184-0.034-0.0340.0000.0000.0000.000
195A213THR0-0.0090.00435.9720.1440.1440.0000.0000.0000.000
196A214LYS10.8930.94138.3787.3967.3960.0000.0000.0000.000
197A215ARG10.8840.92842.1556.8396.8390.0000.0000.0000.000
198A216SER00.020-0.01944.3650.1050.1050.0000.0000.0000.000
199A217GLY00.0060.01946.5300.1130.1130.0000.0000.0000.000
200A218HIS00.015-0.00246.018-0.017-0.0170.0000.0000.0000.000
201A219LYS10.9590.96743.7956.7296.7290.0000.0000.0000.000
202A220LEU00.0600.04739.067-0.155-0.1550.0000.0000.0000.000
203A221PRO00.0210.03138.3350.2140.2140.0000.0000.0000.000
204A222ARG10.8510.89840.6967.4917.4910.0000.0000.0000.000
205A223VAL00.0250.00635.890-0.025-0.0250.0000.0000.0000.000
206A224GLU-1-0.793-0.84938.338-7.299-7.2990.0000.0000.0000.000
207A225LEU0-0.014-0.01433.512-0.256-0.2560.0000.0000.0000.000
208A226GLU-1-0.867-0.93834.510-8.753-8.7530.0000.0000.0000.000
209A227GLU-1-0.877-0.93433.584-9.055-9.0550.0000.0000.0000.000
210A228ILE0-0.070-0.02828.038-0.006-0.0060.0000.0000.0000.000
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