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: 1773Z

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2898694.859515
FMO2-HF: Nuclear repulsion 2805157.767536
FMO2-HF: Total energy -93537.091979
FMO2-MP2: Total energy -93804.969252


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.
-106.004-104.6721.001-12.013-10.322-0.131
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 : 0.825 / q_NPA : 0.871
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].
3A21PRO0-0.003-0.0052.959-4.139-1.6600.090-1.269-1.300-0.006
4A22GLN0-0.013-0.0033.855-3.236-2.8980.002-0.080-0.2600.000
5A23LEU0-0.0150.0006.7120.7990.7990.0000.0000.0000.000
6A24ILE0-0.017-0.0189.9381.1711.1710.0000.0000.0000.000
7A25GLU-1-0.963-0.9707.121-32.361-32.3610.0000.0000.0000.000
8A26GLY00.0350.0187.9452.4082.4080.0000.0000.0000.000
9A27ALA0-0.025-0.0149.7860.9940.9940.0000.0000.0000.000
10A28LYS10.8600.9178.20220.21520.2150.0000.0000.0000.000
11A29ARG10.9020.9603.64961.53662.0110.013-0.096-0.3920.000
12A30VAL00.0080.0037.7171.4791.4790.0000.0000.0000.000
13A31LEU00.003-0.0079.774-0.447-0.4470.0000.0000.0000.000
14A32LEU0-0.023-0.00511.2502.1192.1190.0000.0000.0000.000
15A33LEU0-0.0040.00214.661-0.016-0.0160.0000.0000.0000.000
16A34HIS00.0030.00116.7591.1071.1070.0000.0000.0000.000
17A35GLY00.0130.00420.392-0.203-0.2030.0000.0000.0000.000
18A36SER00.031-0.00723.1590.0750.0750.0000.0000.0000.000
19A37LYS10.8950.95026.41710.12710.1270.0000.0000.0000.000
20A38CYS00.0010.01724.8550.2260.2260.0000.0000.0000.000
21A39PRO00.0340.01626.7920.0220.0220.0000.0000.0000.000
22A40THR00.0640.01527.490-0.418-0.4180.0000.0000.0000.000
23A41PRO00.0450.02827.632-0.376-0.3760.0000.0000.0000.000
24A42LEU00.0540.02524.389-0.342-0.3420.0000.0000.0000.000
25A43HIS0-0.0050.00223.041-0.989-0.9890.0000.0000.0000.000
26A44THR0-0.039-0.02122.902-0.671-0.6710.0000.0000.0000.000
27A45VAL00.0070.01322.386-0.359-0.3590.0000.0000.0000.000
28A46LEU0-0.007-0.00318.605-0.576-0.5760.0000.0000.0000.000
29A47LYS10.9220.97118.58311.80411.8040.0000.0000.0000.000
30A48VAL00.0000.00619.350-0.565-0.5650.0000.0000.0000.000
31A49PHE00.0420.00317.809-0.264-0.2640.0000.0000.0000.000
32A50HIS00.0040.04312.319-0.987-0.9870.0000.0000.0000.000
33A51SER0-0.038-0.01315.142-0.445-0.4450.0000.0000.0000.000
34A52LEU0-0.043-0.03917.243-0.169-0.1690.0000.0000.0000.000
35A53THR0-0.002-0.00112.897-0.377-0.3770.0000.0000.0000.000
36A54THR0-0.0300.01912.201-2.085-2.0850.0000.0000.0000.000
37A55PRO0-0.017-0.02810.3481.1401.1400.0000.0000.0000.000
38A56HIS0-0.035-0.0187.726-2.054-2.0540.0000.0000.0000.000
39A57SER00.0650.0158.665-1.614-1.6140.0000.0000.0000.000
40A58VAL0-0.012-0.0137.350-0.139-0.1390.0000.0000.0000.000
41A59LEU0-0.0030.01310.4421.2141.2140.0000.0000.0000.000
42A60PHE00.004-0.01413.4640.3760.3760.0000.0000.0000.000
43A61HIS00.007-0.01615.0131.4251.4250.0000.0000.0000.000
44A62LYS10.9030.97017.81716.03316.0330.0000.0000.0000.000
45A63LYS10.9630.97719.56912.58212.5820.0000.0000.0000.000
46A64ASN0-0.037-0.00917.3590.1300.1300.0000.0000.0000.000
47A65GLU-1-0.932-0.96821.272-11.274-11.2740.0000.0000.0000.000
48A66ASN0-0.017-0.01922.738-0.147-0.1470.0000.0000.0000.000
49A67ILE0-0.0090.01617.975-0.233-0.2330.0000.0000.0000.000
50A68HIS0-0.005-0.01522.0650.1510.1510.0000.0000.0000.000
51A69PRO00.0780.03920.2810.2320.2320.0000.0000.0000.000
52A70PHE0-0.023-0.03121.987-0.027-0.0270.0000.0000.0000.000
53A71GLU-1-1.006-0.98025.034-10.501-10.5010.0000.0000.0000.000
54A72SER00.023-0.00522.473-0.123-0.1230.0000.0000.0000.000
55A73THR0-0.053-0.03418.1900.1590.1590.0000.0000.0000.000
56A74GLU-1-0.880-0.91417.345-16.574-16.5740.0000.0000.0000.000
57A75SER00.017-0.00916.377-1.263-1.2630.0000.0000.0000.000
58A76LEU0-0.005-0.01414.605-1.183-1.1830.0000.0000.0000.000
59A77GLU-1-0.761-0.87813.199-20.588-20.5880.0000.0000.0000.000
60A78PHE0-0.036-0.00311.691-2.600-2.6000.0000.0000.0000.000
61A79LEU0-0.041-0.03310.832-2.245-2.2450.0000.0000.0000.000
62A80ALA00.0210.0169.235-2.862-2.8620.0000.0000.0000.000
63A81ASN00.0460.0137.311-6.640-6.6400.0000.0000.0000.000
64A82LYS10.9140.9796.25819.89619.8960.0000.0000.0000.000
65A83ASN0-0.109-0.0705.317-2.303-2.3030.0000.0000.0000.000
66A84ASP-1-0.820-0.8941.731-133.223-135.36420.897-10.524-8.232-0.125
67A85CYS0-0.093-0.0434.058-1.774-1.591-0.001-0.044-0.1380.000
68A86GLY00.0980.0537.0732.1392.1390.0000.0000.0000.000
69A87MET0-0.028-0.0119.4593.7333.7330.0000.0000.0000.000
70A88VAL00.0070.01511.582-1.585-1.5850.0000.0000.0000.000
71A89ILE0-0.033-0.01213.9781.5411.5410.0000.0000.0000.000
72A90PHE00.0400.00116.962-0.108-0.1080.0000.0000.0000.000
73A91GLY00.0180.02419.0160.7660.7660.0000.0000.0000.000
74A92SER0-0.008-0.01022.1910.0760.0760.0000.0000.0000.000
75A93SER00.0630.01625.0950.3020.3020.0000.0000.0000.000
76A94ASN00.0120.01728.8930.2850.2850.0000.0000.0000.000
77A95LYS11.0130.98531.9298.5468.5460.0000.0000.0000.000
78A96LYS10.9490.99033.7569.2519.2510.0000.0000.0000.000
79A97ARG10.9320.96529.39910.55910.5590.0000.0000.0000.000
80A98PRO00.0280.03330.241-0.368-0.3680.0000.0000.0000.000
81A99ASN0-0.003-0.01528.623-0.192-0.1920.0000.0000.0000.000
82A100CYS0-0.0310.00426.554-0.097-0.0970.0000.0000.0000.000
83A101LEU00.0450.01221.392-0.367-0.3670.0000.0000.0000.000
84A102THR0-0.032-0.01920.3670.3950.3950.0000.0000.0000.000
85A103ILE00.0230.01217.806-0.861-0.8610.0000.0000.0000.000
86A104ALA00.0090.00116.5180.7830.7830.0000.0000.0000.000
87A105ARG10.7780.86014.31716.03216.0320.0000.0000.0000.000
88A106ILE0-0.035-0.01010.7641.1571.1570.0000.0000.0000.000
89A107PHE00.008-0.01011.747-1.417-1.4170.0000.0000.0000.000
90A108ASP-1-0.881-0.93310.111-22.046-22.0460.0000.0000.0000.000
91A109SER0-0.023-0.0119.1090.2420.2420.0000.0000.0000.000
92A110LYS10.9720.99210.58418.42318.4230.0000.0000.0000.000
93A111VAL0-0.010-0.01014.105-0.857-0.8570.0000.0000.0000.000
94A112LEU0-0.063-0.02115.9660.8360.8360.0000.0000.0000.000
95A113ASP-1-0.760-0.88217.623-15.518-15.5180.0000.0000.0000.000
96A114MET0-0.037-0.03119.041-1.144-1.1440.0000.0000.0000.000
97A115ALA00.0420.01021.3340.8440.8440.0000.0000.0000.000
98A116GLU-1-0.836-0.90623.060-12.038-12.0380.0000.0000.0000.000
99A117LEU0-0.0030.00323.8980.4430.4430.0000.0000.0000.000
100A118LEU0-0.045-0.02826.754-0.176-0.1760.0000.0000.0000.000
101A119LEU0-0.013-0.01228.0850.1900.1900.0000.0000.0000.000
102A120LEU0-0.039-0.02730.1160.2650.2650.0000.0000.0000.000
103A121PRO0-0.063-0.03733.579-0.157-0.1570.0000.0000.0000.000
104A122ASP-1-0.743-0.84735.878-8.771-8.7710.0000.0000.0000.000
105A123ALA0-0.001-0.00536.7580.1660.1660.0000.0000.0000.000
106A124ASN0-0.078-0.06839.3990.2370.2370.0000.0000.0000.000
107A125GLY00.0070.01340.6050.1510.1510.0000.0000.0000.000
108A126GLU-1-0.960-0.95138.235-8.027-8.0270.0000.0000.0000.000
109A127GLY0-0.116-0.06235.989-0.109-0.1090.0000.0000.0000.000
110A128ILE0-0.016-0.02229.114-0.153-0.1530.0000.0000.0000.000
111A129PRO00.0250.00831.563-0.141-0.1410.0000.0000.0000.000
112A130GLU-1-0.951-0.97328.851-10.944-10.9440.0000.0000.0000.000
113A131MET0-0.021-0.00626.0750.1120.1120.0000.0000.0000.000
114A132ASN0-0.035-0.03522.2370.0310.0310.0000.0000.0000.000
115A133ARG10.9470.97521.34712.06612.0660.0000.0000.0000.000
116A134LEU00.0420.03722.8850.4940.4940.0000.0000.0000.000
117A135SER00.0600.00524.7220.5580.5580.0000.0000.0000.000
118A136MET0-0.004-0.00126.080-0.556-0.5560.0000.0000.0000.000
119A137HIS0-0.0110.00728.139-0.185-0.1850.0000.0000.0000.000
120A138VAL00.0270.01423.5600.1350.1350.0000.0000.0000.000
121A139ALA00.0010.00722.269-0.238-0.2380.0000.0000.0000.000
122A140ILE0-0.018-0.02817.256-0.084-0.0840.0000.0000.0000.000
123A141GLY00.0540.03216.735-0.280-0.2800.0000.0000.0000.000
124A142LEU0-0.0330.00617.400-0.341-0.3410.0000.0000.0000.000
125A143ARG10.8940.96018.51515.41815.4180.0000.0000.0000.000
126A144PRO0-0.0080.02220.1470.7150.7150.0000.0000.0000.000
127A145LEU00.0200.00523.177-0.086-0.0860.0000.0000.0000.000
128A146MET0-0.029-0.01120.477-0.033-0.0330.0000.0000.0000.000
129A147LEU0-0.0040.00126.1400.2900.2900.0000.0000.0000.000
130A148PHE00.007-0.00223.931-0.121-0.1210.0000.0000.0000.000
131A149SER00.0030.00029.8930.1960.1960.0000.0000.0000.000
132A150GLY00.0780.02933.449-0.138-0.1380.0000.0000.0000.000
133A151SER0-0.061-0.07734.900-0.231-0.2310.0000.0000.0000.000
134A152ALA00.0460.02333.604-0.083-0.0830.0000.0000.0000.000
135A153TRP0-0.101-0.06227.424-0.435-0.4350.0000.0000.0000.000
136A154ASP-1-0.972-0.98431.315-9.435-9.4350.0000.0000.0000.000
137A155ASP-1-0.836-0.88733.957-8.742-8.7420.0000.0000.0000.000
138A156THR0-0.055-0.03732.284-0.229-0.2290.0000.0000.0000.000
139A157THR0-0.078-0.04732.632-0.149-0.1490.0000.0000.0000.000
140A158SER00.0190.02232.783-0.077-0.0770.0000.0000.0000.000
141A159THR00.026-0.00629.054-0.270-0.2700.0000.0000.0000.000
142A160THR00.0150.00827.879-0.508-0.5080.0000.0000.0000.000
143A161HIS00.0620.02427.377-0.498-0.4980.0000.0000.0000.000
144A162THR00.0250.02326.056-0.337-0.3370.0000.0000.0000.000
145A163MET0-0.047-0.01122.701-0.558-0.5580.0000.0000.0000.000
146A164LEU00.011-0.00222.703-0.702-0.7020.0000.0000.0000.000
147A165LYS10.9761.00023.14011.11411.1140.0000.0000.0000.000
148A166SER0-0.0140.01520.658-0.805-0.8050.0000.0000.0000.000
149A167MET0-0.019-0.00518.598-0.661-0.6610.0000.0000.0000.000
150A168LEU00.0060.00618.320-0.847-0.8470.0000.0000.0000.000
151A169VAL00.006-0.00419.568-0.387-0.3870.0000.0000.0000.000
152A170ASP-1-0.828-0.89514.757-22.081-22.0810.0000.0000.0000.000
153A171LEU0-0.042-0.01214.841-1.453-1.4530.0000.0000.0000.000
154A172PHE0-0.001-0.02115.552-0.670-0.6700.0000.0000.0000.000
155A173LYS10.8500.93513.15122.61422.6140.0000.0000.0000.000
156A174GLY0-0.0060.00414.2120.3740.3740.0000.0000.0000.000
157A175GLU-1-0.936-0.98012.063-24.926-24.9260.0000.0000.0000.000
158A176THR0-0.048-0.01814.2751.3371.3370.0000.0000.0000.000
159A177SER00.025-0.00116.594-0.447-0.4470.0000.0000.0000.000
160A178ASP-1-0.885-0.94119.230-13.310-13.3100.0000.0000.0000.000
161A179LYS10.9170.96222.19412.89512.8950.0000.0000.0000.000
162A180ILE0-0.014-0.02122.820-0.736-0.7360.0000.0000.0000.000
163A181ASP-1-0.838-0.89624.955-10.667-10.6670.0000.0000.0000.000
164A182VAL00.0190.00227.135-0.149-0.1490.0000.0000.0000.000
165A183GLU-1-0.903-0.95628.462-9.745-9.7450.0000.0000.0000.000
166A184GLY0-0.063-0.03025.303-0.165-0.1650.0000.0000.0000.000
167A185LEU0-0.045-0.01425.558-0.360-0.3600.0000.0000.0000.000
168A186GLN0-0.022-0.01926.7190.3400.3400.0000.0000.0000.000
169A187TYR0-0.032-0.04320.9210.4950.4950.0000.0000.0000.000
170A188ALA00.0030.00826.701-0.303-0.3030.0000.0000.0000.000
171A189LEU0-0.015-0.00323.1910.1000.1000.0000.0000.0000.000
172A190MET0-0.028-0.00426.7940.1330.1330.0000.0000.0000.000
173A191VAL00.014-0.00825.454-0.107-0.1070.0000.0000.0000.000
174A192GLY00.0060.01228.8400.1050.1050.0000.0000.0000.000
175A193ALA0-0.049-0.03631.925-0.101-0.1010.0000.0000.0000.000
176A194GLU-1-0.855-0.91633.383-8.326-8.3260.0000.0000.0000.000
177A195GLU-1-0.822-0.88036.771-8.489-8.4890.0000.0000.0000.000
178A196PRO0-0.0140.01137.4390.0700.0700.0000.0000.0000.000
179A197THR00.0230.00039.3000.2410.2410.0000.0000.0000.000
180A198ALA00.014-0.00541.177-0.159-0.1590.0000.0000.0000.000
181A199GLY0-0.012-0.00542.0390.1180.1180.0000.0000.0000.000
182A200LEU0-0.025-0.00338.703-0.031-0.0310.0000.0000.0000.000
183A201ALA0-0.056-0.02434.421-0.110-0.1100.0000.0000.0000.000
184A202PRO00.0730.02732.3870.1040.1040.0000.0000.0000.000
185A203ILE00.0300.01433.179-0.278-0.2780.0000.0000.0000.000
186A204ILE0-0.041-0.01027.0200.0190.0190.0000.0000.0000.000
187A205HIS10.7580.83831.2739.2379.2370.0000.0000.0000.000
188A206LEU00.0000.00724.327-0.134-0.1340.0000.0000.0000.000
189A207ARG10.8450.92028.6959.9539.9530.0000.0000.0000.000
190A208TRP00.0540.02823.032-0.166-0.1660.0000.0000.0000.000
191A209TYR00.0200.00128.6660.3190.3190.0000.0000.0000.000
192A210LYS10.9470.97429.7489.7219.7210.0000.0000.0000.000
193A211ILE0-0.021-0.02029.9160.3610.3610.0000.0000.0000.000
194A212VAL00.0120.01832.788-0.020-0.0200.0000.0000.0000.000
195A213THR00.004-0.00135.4240.0950.0950.0000.0000.0000.000
196A214LYS10.9260.96837.9607.5317.5310.0000.0000.0000.000
197A215ARG10.9920.98441.7146.9226.9220.0000.0000.0000.000
198A216SER00.008-0.01043.9160.1470.1470.0000.0000.0000.000
199A217GLY0-0.0250.00246.0000.1350.1350.0000.0000.0000.000
200A218HIS00.0030.00145.2590.0470.0470.0000.0000.0000.000
201A219LYS10.9340.95643.5406.7836.7830.0000.0000.0000.000
202A220LEU00.0340.02838.641-0.158-0.1580.0000.0000.0000.000
203A221PRO00.0280.01637.8380.2120.2120.0000.0000.0000.000
204A222ARG10.8810.93240.1787.4627.4620.0000.0000.0000.000
205A223VAL00.0100.00035.647-0.060-0.0600.0000.0000.0000.000
206A224GLU-1-0.872-0.92837.843-7.477-7.4770.0000.0000.0000.000
207A225LEU0-0.014-0.00933.329-0.272-0.2720.0000.0000.0000.000
208A226GLU-1-0.918-0.94934.306-8.660-8.6600.0000.0000.0000.000
209A227GLU-1-0.941-0.97733.151-9.021-9.0210.0000.0000.0000.000
210A228ILE0-0.069-0.02627.807-0.009-0.0090.0000.0000.0000.000
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