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: 98Z82

Calculation Name: 4XVW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XVW

Chain ID: A

ChEMBL ID:

UniProt ID:

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2495828.13867
FMO2-HF: Nuclear repulsion 2409980.380668
FMO2-HF: Total energy -85847.758002
FMO2-MP2: Total energy -86099.1931


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:3:ALA)


Summations of interaction energy for fragment #1(A:3:ALA)
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.
4.354-5.27618.329-4.659-4.039-0.006
Interaction energy analysis for fragmet #1(A:3:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.030
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].
3A5LEU00.0320.0191.4626.222-4.38616.980-3.849-2.5230.005
4A6ASN00.0350.0212.506-2.634-1.7031.350-0.809-1.472-0.011
5A7ALA00.1020.0324.9990.3060.353-0.001-0.001-0.0440.000
6A8ALA0-0.022-0.0167.0350.1380.1380.0000.0000.0000.000
7A9GLN00.0650.0307.0400.0240.0240.0000.0000.0000.000
8A10GLU-1-0.838-0.9135.236-0.318-0.3180.0000.0000.0000.000
9A11LYS10.8960.9467.6890.1200.1200.0000.0000.0000.000
10A12GLU-1-0.927-0.96111.0780.1330.1330.0000.0000.0000.000
11A13VAL00.0230.0158.8800.0090.0090.0000.0000.0000.000
12A14ARG10.8170.8878.1280.0790.0790.0000.0000.0000.000
13A15ALA0-0.0120.00213.092-0.017-0.0170.0000.0000.0000.000
14A16LEU00.0450.01913.872-0.005-0.0050.0000.0000.0000.000
15A17VAL00.0000.02615.122-0.006-0.0060.0000.0000.0000.000
16A18ARG10.8820.93317.208-0.075-0.0750.0000.0000.0000.000
17A19ASP-1-0.828-0.91919.7040.0790.0790.0000.0000.0000.000
18A20THR0-0.027-0.00118.8620.0000.0000.0000.0000.0000.000
19A21LEU0-0.018-0.00720.377-0.005-0.0050.0000.0000.0000.000
20A22VAL0-0.055-0.02423.109-0.011-0.0110.0000.0000.0000.000
21A23SER0-0.068-0.05323.710-0.005-0.0050.0000.0000.0000.000
22A24ASN0-0.032-0.03125.1840.0000.0000.0000.0000.0000.000
23A25PRO00.0320.00925.9020.0090.0090.0000.0000.0000.000
24A26GLU-1-0.890-0.93527.9500.1010.1010.0000.0000.0000.000
25A27ILE00.0220.01622.4150.0060.0060.0000.0000.0000.000
26A28LEU0-0.050-0.01924.9300.0070.0070.0000.0000.0000.000
27A29GLU-1-0.932-0.98026.6060.0910.0910.0000.0000.0000.000
28A30GLU-1-0.915-0.94726.8270.1620.1620.0000.0000.0000.000
29A31ALA00.003-0.01324.3390.0040.0040.0000.0000.0000.000
30A32ILE0-0.061-0.02726.237-0.003-0.0030.0000.0000.0000.000
31A33MET00.0070.00229.044-0.004-0.0040.0000.0000.0000.000
32A34ALA00.0380.04326.854-0.003-0.0030.0000.0000.0000.000
33A35LEU0-0.0040.00325.0120.0010.0010.0000.0000.0000.000
34A36GLN0-0.013-0.00928.184-0.005-0.0050.0000.0000.0000.000
35A37THR0-0.007-0.00730.724-0.008-0.0080.0000.0000.0000.000
36A38LYS10.9380.96223.896-0.163-0.1630.0000.0000.0000.000
37A39LYS10.7960.88829.474-0.088-0.0880.0000.0000.0000.000
38A40ALA00.0400.01831.308-0.005-0.0050.0000.0000.0000.000
39A41ASP-1-0.857-0.92731.0240.1160.1160.0000.0000.0000.000
40A42GLU-1-0.839-0.89827.4540.1230.1230.0000.0000.0000.000
41A43GLN0-0.060-0.03432.163-0.003-0.0030.0000.0000.0000.000
42A44GLN0-0.107-0.04235.410-0.005-0.0050.0000.0000.0000.000
43A45ALA00.0520.04633.6070.0030.0030.0000.0000.0000.000
44A46GLN0-0.025-0.02235.711-0.008-0.0080.0000.0000.0000.000
45A47PHE00.0930.03636.4230.0030.0030.0000.0000.0000.000
46A48ARG10.9030.92737.088-0.053-0.0530.0000.0000.0000.000
47A49GLN00.0120.00133.6450.0020.0020.0000.0000.0000.000
48A50ALA00.0170.04032.7640.0070.0070.0000.0000.0000.000
49A51LEU0-0.045-0.02432.5500.0020.0020.0000.0000.0000.000
50A52ALA0-0.071-0.03833.929-0.001-0.0010.0000.0000.0000.000
51A53SER0-0.047-0.03729.3840.0030.0030.0000.0000.0000.000
52A54GLU-1-0.827-0.91327.1390.1290.1290.0000.0000.0000.000
53A55HIS0-0.027-0.02629.512-0.012-0.0120.0000.0000.0000.000
54A56ASP-1-0.838-0.92125.7060.0890.0890.0000.0000.0000.000
55A57ALA0-0.0120.00825.496-0.004-0.0040.0000.0000.0000.000
56A58LEU0-0.061-0.03126.462-0.008-0.0080.0000.0000.0000.000
57A59TYR0-0.036-0.02729.819-0.007-0.0070.0000.0000.0000.000
58A60ASN0-0.078-0.03426.252-0.006-0.0060.0000.0000.0000.000
59A61ASP-1-0.722-0.83123.0910.0650.0650.0000.0000.0000.000
60A62ALA0-0.010-0.00822.084-0.009-0.0090.0000.0000.0000.000
61A63ALA0-0.080-0.04721.582-0.014-0.0140.0000.0000.0000.000
62A64SER0-0.016-0.03323.658-0.002-0.0020.0000.0000.0000.000
63A65PRO0-0.014-0.00227.223-0.002-0.0020.0000.0000.0000.000
64A66ARG10.8920.94329.939-0.016-0.0160.0000.0000.0000.000
65A67ILE00.0020.00732.840-0.005-0.0050.0000.0000.0000.000
66A68GLY00.1040.04636.4420.0030.0030.0000.0000.0000.000
67A69ALA00.0050.01636.764-0.002-0.0020.0000.0000.0000.000
68A70LYS10.9610.96232.0220.0140.0140.0000.0000.0000.000
69A71ASP-1-0.850-0.91633.8970.0190.0190.0000.0000.0000.000
70A72ALA00.0010.00436.132-0.002-0.0020.0000.0000.0000.000
71A73LYS10.8350.90537.232-0.013-0.0130.0000.0000.0000.000
72A74LEU00.0110.02739.1020.0030.0030.0000.0000.0000.000
73A75VAL00.000-0.00534.072-0.003-0.0030.0000.0000.0000.000
74A76LEU00.0120.01037.4590.0040.0040.0000.0000.0000.000
75A77VAL00.0180.01632.386-0.001-0.0010.0000.0000.0000.000
76A78SER00.0250.02235.3260.0020.0020.0000.0000.0000.000
77A79PHE00.0180.00330.922-0.001-0.0010.0000.0000.0000.000
78A80THR0-0.022-0.02934.356-0.003-0.0030.0000.0000.0000.000
79A81ASP-1-0.691-0.84934.5280.0290.0290.0000.0000.0000.000
80A82TYR00.009-0.02032.453-0.001-0.0010.0000.0000.0000.000
81A83ASN0-0.025-0.03636.788-0.005-0.0050.0000.0000.0000.000
82A84CYS0-0.096-0.02439.6770.0000.0000.0000.0000.0000.000
83A85PRO00.027-0.00441.544-0.001-0.0010.0000.0000.0000.000
84A86TYR00.007-0.00444.480-0.002-0.0020.0000.0000.0000.000
85A87CYS00.0260.02740.1320.0010.0010.0000.0000.0000.000
86A88LYS10.8820.94340.828-0.010-0.0100.0000.0000.0000.000
87A89ARG10.8560.92343.553-0.015-0.0150.0000.0000.0000.000
88A90PHE00.0420.02442.330-0.001-0.0010.0000.0000.0000.000
89A91ASP-1-0.828-0.90939.1230.0110.0110.0000.0000.0000.000
90A92PRO00.0670.02942.1750.0000.0000.0000.0000.0000.000
91A93LEU0-0.047-0.01744.743-0.001-0.0010.0000.0000.0000.000
92A94LEU0-0.003-0.00639.9540.0010.0010.0000.0000.0000.000
93A95GLU-1-0.839-0.90740.4690.0020.0020.0000.0000.0000.000
94A96LYS10.8370.94542.954-0.009-0.0090.0000.0000.0000.000
95A97ILE00.0180.00343.984-0.001-0.0010.0000.0000.0000.000
96A98THR0-0.049-0.02040.0540.0000.0000.0000.0000.0000.000
97A99GLU-1-0.949-0.97243.133-0.001-0.0010.0000.0000.0000.000
98A100GLN0-0.0500.00345.804-0.001-0.0010.0000.0000.0000.000
99A101TYR0-0.092-0.08946.1440.0000.0000.0000.0000.0000.000
100A102PRO00.0560.03243.9490.0010.0010.0000.0000.0000.000
101A103ASP-1-0.990-0.98042.4520.0120.0120.0000.0000.0000.000
102A104VAL0-0.040-0.03241.2090.0030.0030.0000.0000.0000.000
103A105ALA0-0.023-0.00636.558-0.003-0.0030.0000.0000.0000.000
104A106VAL00.000-0.01336.6980.0030.0030.0000.0000.0000.000
105A107ILE0-0.0250.00630.605-0.004-0.0040.0000.0000.0000.000
106A108ILE0-0.036-0.01832.3800.0030.0030.0000.0000.0000.000
107A109LYS10.8570.92427.207-0.059-0.0590.0000.0000.0000.000
108A110PRO0-0.021-0.00229.3100.0020.0020.0000.0000.0000.000
109A111LEU00.0270.00630.2870.0060.0060.0000.0000.0000.000
110A112PRO0-0.035-0.02129.106-0.005-0.0050.0000.0000.0000.000
111A113PHE0-0.011-0.00232.1520.0010.0010.0000.0000.0000.000
112A114LYS10.9010.94235.284-0.028-0.0280.0000.0000.0000.000
113A115GLY00.0220.01535.527-0.003-0.0030.0000.0000.0000.000
114A116GLU-1-0.898-0.95131.1490.0140.0140.0000.0000.0000.000
115A117SER00.1020.04831.9540.0000.0000.0000.0000.0000.000
116A118SER0-0.023-0.01433.341-0.003-0.0030.0000.0000.0000.000
117A119ALA00.0090.01828.4890.0000.0000.0000.0000.0000.000
118A120LYS10.9030.97126.6300.0060.0060.0000.0000.0000.000
119A121ALA00.022-0.00429.614-0.005-0.0050.0000.0000.0000.000
120A122SER0-0.013-0.03329.009-0.002-0.0020.0000.0000.0000.000
121A123GLN00.0230.00822.810-0.002-0.0020.0000.0000.0000.000
122A124ALA0-0.0010.00825.910-0.007-0.0070.0000.0000.0000.000
123A125VAL00.0100.00527.937-0.006-0.0060.0000.0000.0000.000
124A126LEU00.0100.00224.742-0.002-0.0020.0000.0000.0000.000
125A127SER0-0.045-0.03423.521-0.004-0.0040.0000.0000.0000.000
126A128VAL0-0.0020.00124.533-0.009-0.0090.0000.0000.0000.000
127A129TRP0-0.0190.01025.465-0.007-0.0070.0000.0000.0000.000
128A130LYS10.8960.95519.188-0.017-0.0170.0000.0000.0000.000
129A131GLU-1-0.908-0.93223.210-0.097-0.0970.0000.0000.0000.000
130A132ASP-1-0.869-0.95824.372-0.047-0.0470.0000.0000.0000.000
131A133PRO00.0150.00427.0260.0050.0050.0000.0000.0000.000
132A134LYS10.8790.94129.6110.0350.0350.0000.0000.0000.000
133A135ALA00.0350.02531.4960.0030.0030.0000.0000.0000.000
134A136PHE00.0010.00130.6800.0020.0020.0000.0000.0000.000
135A137LEU00.0350.02832.5640.0020.0020.0000.0000.0000.000
136A138ALA00.0390.01936.0880.0020.0020.0000.0000.0000.000
137A139LEU0-0.009-0.00531.6100.0020.0020.0000.0000.0000.000
138A140HIS00.0150.00834.4310.0020.0020.0000.0000.0000.000
139A141GLN00.004-0.03035.8780.0000.0000.0000.0000.0000.000
140A142ARG10.9000.96438.6350.0170.0170.0000.0000.0000.000
141A143LEU0-0.022-0.00233.6450.0010.0010.0000.0000.0000.000
142A144MET0-0.0330.01837.6870.0030.0030.0000.0000.0000.000
143A145GLN0-0.064-0.05639.8040.0010.0010.0000.0000.0000.000
144A146LYS10.8960.97840.6520.0000.0000.0000.0000.0000.000
145A147LYS10.9700.99043.148-0.003-0.0030.0000.0000.0000.000
146A148THR0-0.046-0.03645.206-0.001-0.0010.0000.0000.0000.000
147A149MET00.0290.02338.4030.0000.0000.0000.0000.0000.000
148A150LEU00.003-0.00336.278-0.002-0.0020.0000.0000.0000.000
149A151ASP-1-0.786-0.88536.576-0.004-0.0040.0000.0000.0000.000
150A152ASN00.046-0.00331.580-0.001-0.0010.0000.0000.0000.000
151A153ALA00.0640.05134.385-0.003-0.0030.0000.0000.0000.000
152A154SER0-0.013-0.02937.292-0.001-0.0010.0000.0000.0000.000
153A155ILE0-0.071-0.03832.1970.0000.0000.0000.0000.0000.000
154A156GLU-1-0.952-0.99232.155-0.029-0.0290.0000.0000.0000.000
155A157ASP-1-0.942-0.95334.845-0.020-0.0200.0000.0000.0000.000
156A158ALA0-0.066-0.03936.664-0.001-0.0010.0000.0000.0000.000
157A159MET00.0540.04229.0580.0000.0000.0000.0000.0000.000
158A160LYS10.9691.00333.0390.0470.0470.0000.0000.0000.000
159A161SER0-0.0230.01435.9600.0000.0000.0000.0000.0000.000
160A162THR0-0.067-0.06335.6650.0020.0020.0000.0000.0000.000
161A163ASN0-0.075-0.04235.240-0.003-0.0030.0000.0000.0000.000
162A164THR00.047-0.00330.823-0.003-0.0030.0000.0000.0000.000
163A165SER00.0490.01330.0810.0000.0000.0000.0000.0000.000
164A166LYS10.7990.91725.1500.0920.0920.0000.0000.0000.000
165A167ILE0-0.011-0.00225.277-0.009-0.0090.0000.0000.0000.000
166A168LYS10.9450.99018.1040.0810.0810.0000.0000.0000.000
167A169LEU00.0160.00123.4180.0030.0030.0000.0000.0000.000
168A170THR0-0.049-0.02118.7630.0000.0000.0000.0000.0000.000
169A171ASP-1-0.811-0.92117.008-0.020-0.0200.0000.0000.0000.000
170A172ASP-1-0.829-0.91214.9560.0360.0360.0000.0000.0000.000
171A173SER0-0.128-0.06617.8280.0170.0170.0000.0000.0000.000
172A174LEU00.0420.01220.6760.0060.0060.0000.0000.0000.000
173A175LYS10.9020.94913.654-0.121-0.1210.0000.0000.0000.000
174A176THR00.0520.02720.0210.0060.0060.0000.0000.0000.000
175A177LEU0-0.0060.00822.6770.0020.0020.0000.0000.0000.000
176A178GLN0-0.007-0.00722.2160.0020.0020.0000.0000.0000.000
177A179ASN0-0.013-0.01121.024-0.001-0.0010.0000.0000.0000.000
178A180ASN00.008-0.00624.4790.0030.0030.0000.0000.0000.000
179A181LEU0-0.023-0.01227.206-0.003-0.0030.0000.0000.0000.000
180A182GLU-1-0.856-0.92323.6620.1450.1450.0000.0000.0000.000
181A183LEU00.0070.00226.680-0.002-0.0020.0000.0000.0000.000
182A184SER0-0.088-0.04829.740-0.005-0.0050.0000.0000.0000.000
183A185ARG10.8350.89627.262-0.104-0.1040.0000.0000.0000.000
184A186LYS10.8670.94225.981-0.130-0.1300.0000.0000.0000.000
185A187LEU0-0.041-0.02033.002-0.003-0.0030.0000.0000.0000.000
186A188GLY0-0.0030.01935.622-0.004-0.0040.0000.0000.0000.000
187A189ILE0-0.051-0.02035.213-0.005-0.0050.0000.0000.0000.000
188A190GLN0-0.013-0.01837.4240.0040.0040.0000.0000.0000.000
189A191GLY0-0.010-0.01139.880-0.003-0.0030.0000.0000.0000.000
190A192THR0-0.0380.02637.4190.0000.0000.0000.0000.0000.000
191A193PRO00.017-0.04139.747-0.002-0.0020.0000.0000.0000.000
192A194ALA00.0330.01738.0240.0010.0010.0000.0000.0000.000
193A195THR0-0.016-0.00238.0750.0000.0000.0000.0000.0000.000
194A196VAL00.0190.01535.1720.0000.0000.0000.0000.0000.000
195A197ILE0-0.008-0.01838.587-0.003-0.0030.0000.0000.0000.000
196A198GLY00.0280.01639.897-0.001-0.0010.0000.0000.0000.000
197A199ASP-1-0.833-0.89639.5840.0520.0520.0000.0000.0000.000
198A200THR0-0.047-0.02741.4440.0010.0010.0000.0000.0000.000
199A201ILE00.0090.01037.514-0.001-0.0010.0000.0000.0000.000
200A202LEU00.010-0.00241.386-0.001-0.0010.0000.0000.0000.000
201A203PRO0-0.017-0.01142.687-0.001-0.0010.0000.0000.0000.000
202A204GLY00.0420.01843.507-0.001-0.0010.0000.0000.0000.000
203A205ALA0-0.073-0.03845.286-0.001-0.0010.0000.0000.0000.000
204A206VAL0-0.034-0.01746.7820.0000.0000.0000.0000.0000.000
205A207ASP-1-0.849-0.92049.3070.0120.0120.0000.0000.0000.000
206A208TYR00.028-0.01048.0880.0010.0010.0000.0000.0000.000
207A209ASP-1-0.831-0.92651.1550.0120.0120.0000.0000.0000.000
208A210GLN0-0.065-0.04152.0000.0010.0010.0000.0000.0000.000
209A211LEU0-0.018-0.01144.9630.0010.0010.0000.0000.0000.000
210A212GLU-1-0.818-0.88348.4500.0120.0120.0000.0000.0000.000
211A213ILE0-0.015-0.01750.2940.0000.0000.0000.0000.0000.000
212A214ILE00.0150.01546.4490.0010.0010.0000.0000.0000.000
213A215VAL00.0290.00544.5940.0020.0020.0000.0000.0000.000
214A216LYS10.9360.96546.797-0.012-0.0120.0000.0000.0000.000
215A217GLU-1-0.883-0.91449.4470.0260.0260.0000.0000.0000.000
216A218GLN00.004-0.01544.2170.0020.0020.0000.0000.0000.000
217A219LEU00.0150.01944.5340.0010.0010.0000.0000.0000.000
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