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: LNYN9

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2494193.176941
FMO2-HF: Nuclear repulsion 2408347.096292
FMO2-HF: Total energy -85846.080649
FMO2-MP2: Total energy -86097.536342


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.
4.383-5.67419.287-5.018-4.213-0.007
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 : -0.029 / q_NPA : -0.026
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].
3A5LEU00.0440.0201.4446.482-4.62917.818-4.165-2.5430.005
4A6ASN00.0400.0352.496-2.764-1.8811.471-0.847-1.508-0.012
5A7ALA00.1220.0374.9680.3390.385-0.001-0.001-0.0430.000
6A8ALA0-0.038-0.0247.0690.1520.1520.0000.0000.0000.000
7A9GLN00.0420.0157.0900.1380.1380.0000.0000.0000.000
8A10GLU-1-0.919-0.9624.881-0.565-0.440-0.001-0.005-0.1190.000
9A11LYS10.8760.9347.6560.1340.1340.0000.0000.0000.000
10A12GLU-1-0.924-0.95811.0360.1550.1550.0000.0000.0000.000
11A13VAL00.0210.0158.6890.0080.0080.0000.0000.0000.000
12A14ARG10.9200.9488.8320.0100.0100.0000.0000.0000.000
13A15ALA0-0.022-0.00513.109-0.021-0.0210.0000.0000.0000.000
14A16LEU00.0600.02613.793-0.005-0.0050.0000.0000.0000.000
15A17VAL0-0.0050.06115.121-0.008-0.0080.0000.0000.0000.000
16A18ARG10.9480.97117.206-0.085-0.0850.0000.0000.0000.000
17A19ASP-1-0.894-0.96119.7160.1120.1120.0000.0000.0000.000
18A20THR0-0.007-0.03418.7930.0010.0010.0000.0000.0000.000
19A21LEU0-0.021-0.00920.643-0.006-0.0060.0000.0000.0000.000
20A22VAL0-0.073-0.03323.110-0.013-0.0130.0000.0000.0000.000
21A23SER0-0.055-0.03623.657-0.007-0.0070.0000.0000.0000.000
22A24ASN0-0.008-0.00725.032-0.005-0.0050.0000.0000.0000.000
23A25PRO00.0350.00625.9080.0100.0100.0000.0000.0000.000
24A26GLU-1-0.923-0.95827.9550.1080.1080.0000.0000.0000.000
25A27ILE00.0110.01122.4380.0070.0070.0000.0000.0000.000
26A28LEU0-0.048-0.02025.0740.0080.0080.0000.0000.0000.000
27A29GLU-1-0.914-0.97226.6610.1030.1030.0000.0000.0000.000
28A30GLU-1-0.920-0.94827.0380.1790.1790.0000.0000.0000.000
29A31ALA0-0.002-0.01724.4310.0040.0040.0000.0000.0000.000
30A32ILE0-0.067-0.02426.297-0.003-0.0030.0000.0000.0000.000
31A33MET00.0100.00229.099-0.005-0.0050.0000.0000.0000.000
32A34ALA00.0390.03926.920-0.003-0.0030.0000.0000.0000.000
33A35LEU00.0060.00825.3380.0010.0010.0000.0000.0000.000
34A36GLN0-0.042-0.03528.238-0.007-0.0070.0000.0000.0000.000
35A37THR00.0040.00430.739-0.008-0.0080.0000.0000.0000.000
36A38LYS10.9991.00023.115-0.207-0.2070.0000.0000.0000.000
37A39LYS10.8140.90829.528-0.098-0.0980.0000.0000.0000.000
38A40ALA00.0440.01831.355-0.005-0.0050.0000.0000.0000.000
39A41ASP-1-0.866-0.92931.1330.1230.1230.0000.0000.0000.000
40A42GLU-1-0.958-0.99827.3960.1350.1350.0000.0000.0000.000
41A43GLN0-0.053-0.02532.208-0.003-0.0030.0000.0000.0000.000
42A44GLN0-0.111-0.04635.453-0.004-0.0040.0000.0000.0000.000
43A45ALA00.0530.04733.6530.0030.0030.0000.0000.0000.000
44A46GLN0-0.027-0.02435.755-0.009-0.0090.0000.0000.0000.000
45A47PHE00.1020.04136.4610.0030.0030.0000.0000.0000.000
46A48ARG10.9560.98137.118-0.057-0.0570.0000.0000.0000.000
47A49GLN00.0230.00233.1650.0060.0060.0000.0000.0000.000
48A50ALA00.0180.07132.7980.0070.0070.0000.0000.0000.000
49A51LEU0-0.039-0.02232.5780.0020.0020.0000.0000.0000.000
50A52ALA0-0.080-0.04633.951-0.001-0.0010.0000.0000.0000.000
51A53SER0-0.049-0.06229.4250.0020.0020.0000.0000.0000.000
52A54GLU-1-0.866-0.93127.3110.1390.1390.0000.0000.0000.000
53A55HIS0-0.014-0.00729.536-0.012-0.0120.0000.0000.0000.000
54A56ASP-1-0.841-0.93325.7060.0940.0940.0000.0000.0000.000
55A57ALA0-0.0180.00125.509-0.004-0.0040.0000.0000.0000.000
56A58LEU0-0.074-0.04126.475-0.008-0.0080.0000.0000.0000.000
57A59TYR0-0.047-0.03329.829-0.007-0.0070.0000.0000.0000.000
58A60ASN0-0.086-0.03626.173-0.005-0.0050.0000.0000.0000.000
59A61ASP-1-0.738-0.85422.9200.0770.0770.0000.0000.0000.000
60A62ALA0-0.015-0.01122.086-0.010-0.0100.0000.0000.0000.000
61A63ALA0-0.074-0.03821.586-0.014-0.0140.0000.0000.0000.000
62A64SER0-0.032-0.01923.6460.0000.0000.0000.0000.0000.000
63A65PRO00.0040.01127.215-0.003-0.0030.0000.0000.0000.000
64A66ARG10.8990.95529.924-0.018-0.0180.0000.0000.0000.000
65A67ILE0-0.0090.00332.824-0.005-0.0050.0000.0000.0000.000
66A68GLY00.1030.04436.4240.0030.0030.0000.0000.0000.000
67A69ALA00.0010.01336.740-0.003-0.0030.0000.0000.0000.000
68A70LYS10.9350.94232.2340.0140.0140.0000.0000.0000.000
69A71ASP-1-0.954-0.96933.8770.0200.0200.0000.0000.0000.000
70A72ALA00.0360.01936.112-0.002-0.0020.0000.0000.0000.000
71A73LYS10.9360.95937.221-0.016-0.0160.0000.0000.0000.000
72A74LEU00.0090.02639.0980.0040.0040.0000.0000.0000.000
73A75VAL00.0010.00034.030-0.003-0.0030.0000.0000.0000.000
74A76LEU00.0060.00737.4560.0040.0040.0000.0000.0000.000
75A77VAL00.0180.01832.588-0.001-0.0010.0000.0000.0000.000
76A78SER00.0230.02535.3330.0020.0020.0000.0000.0000.000
77A79PHE00.009-0.00631.326-0.001-0.0010.0000.0000.0000.000
78A80THR0-0.023-0.03234.360-0.003-0.0030.0000.0000.0000.000
79A81ASP-1-0.695-0.87534.5340.0350.0350.0000.0000.0000.000
80A82TYR0-0.031-0.10132.600-0.001-0.0010.0000.0000.0000.000
81A83ASN0-0.009-0.01236.825-0.005-0.0050.0000.0000.0000.000
82A84CYS0-0.101-0.03339.6810.0000.0000.0000.0000.0000.000
83A85PRO0-0.025-0.03041.550-0.002-0.0020.0000.0000.0000.000
84A86TYR00.025-0.01044.498-0.003-0.0030.0000.0000.0000.000
85A87CYS00.0350.03639.9980.0010.0010.0000.0000.0000.000
86A88LYS10.8950.95241.660-0.014-0.0140.0000.0000.0000.000
87A89ARG10.8760.94243.549-0.018-0.0180.0000.0000.0000.000
88A90PHE00.0350.02242.036-0.001-0.0010.0000.0000.0000.000
89A91ASP-1-0.832-0.91239.3780.0140.0140.0000.0000.0000.000
90A92PRO00.0680.02842.1690.0000.0000.0000.0000.0000.000
91A93LEU0-0.052-0.02144.732-0.001-0.0010.0000.0000.0000.000
92A94LEU0-0.006-0.00539.9190.0010.0010.0000.0000.0000.000
93A95GLU-1-0.851-0.92740.5160.0060.0060.0000.0000.0000.000
94A96LYS10.8760.96642.940-0.010-0.0100.0000.0000.0000.000
95A97ILE00.0390.01744.505-0.001-0.0010.0000.0000.0000.000
96A98THR0-0.090-0.05340.316-0.001-0.0010.0000.0000.0000.000
97A99GLU-1-0.940-0.97143.1170.0000.0000.0000.0000.0000.000
98A100GLN0-0.0030.06745.7830.0010.0010.0000.0000.0000.000
99A101TYR0-0.118-0.09445.9870.0000.0000.0000.0000.0000.000
100A102PRO00.0570.03143.9410.0010.0010.0000.0000.0000.000
101A103ASP-1-0.999-0.98342.4330.0120.0120.0000.0000.0000.000
102A104VAL0-0.034-0.02941.1940.0030.0030.0000.0000.0000.000
103A105ALA0-0.027-0.00736.521-0.003-0.0030.0000.0000.0000.000
104A106VAL00.003-0.01036.5670.0040.0040.0000.0000.0000.000
105A107ILE0-0.0290.00430.548-0.004-0.0040.0000.0000.0000.000
106A108ILE0-0.023-0.01332.1910.0030.0030.0000.0000.0000.000
107A109LYS10.8900.93427.422-0.063-0.0630.0000.0000.0000.000
108A110PRO0-0.021-0.00329.2610.0020.0020.0000.0000.0000.000
109A111LEU00.0230.00230.2950.0070.0070.0000.0000.0000.000
110A112PRO0-0.012-0.00729.152-0.006-0.0060.0000.0000.0000.000
111A113PHE0-0.032-0.00832.1660.0010.0010.0000.0000.0000.000
112A114LYS10.9140.94735.303-0.032-0.0320.0000.0000.0000.000
113A115GLY00.0120.01235.543-0.003-0.0030.0000.0000.0000.000
114A116GLU-1-0.902-0.94931.1510.0210.0210.0000.0000.0000.000
115A117SER00.1030.04831.9600.0000.0000.0000.0000.0000.000
116A118SER0-0.022-0.01333.341-0.004-0.0040.0000.0000.0000.000
117A119ALA00.0180.02428.4770.0000.0000.0000.0000.0000.000
118A120LYS10.9550.99826.8330.0010.0010.0000.0000.0000.000
119A121ALA00.017-0.00829.606-0.005-0.0050.0000.0000.0000.000
120A122SER0-0.019-0.04229.132-0.003-0.0030.0000.0000.0000.000
121A123GLN00.0210.01023.0890.0010.0010.0000.0000.0000.000
122A124ALA0-0.0120.03425.896-0.007-0.0070.0000.0000.0000.000
123A125VAL0-0.0020.00227.916-0.006-0.0060.0000.0000.0000.000
124A126LEU00.000-0.00324.728-0.003-0.0030.0000.0000.0000.000
125A127SER0-0.071-0.07823.487-0.003-0.0030.0000.0000.0000.000
126A128VAL0-0.006-0.00124.510-0.009-0.0090.0000.0000.0000.000
127A129TRP0-0.0300.00125.343-0.008-0.0080.0000.0000.0000.000
128A130LYS10.9350.96418.341-0.022-0.0220.0000.0000.0000.000
129A131GLU-1-0.991-0.97622.896-0.096-0.0960.0000.0000.0000.000
130A132ASP-1-0.922-0.97324.331-0.051-0.0510.0000.0000.0000.000
131A133PRO00.0250.00727.0640.0060.0060.0000.0000.0000.000
132A134LYS10.8940.93929.5770.0330.0330.0000.0000.0000.000
133A135ALA00.0460.03531.4440.0020.0020.0000.0000.0000.000
134A136PHE00.0080.00330.6620.0020.0020.0000.0000.0000.000
135A137LEU00.0460.03332.5370.0020.0020.0000.0000.0000.000
136A138ALA00.0350.01636.0630.0020.0020.0000.0000.0000.000
137A139LEU00.001-0.00231.5720.0020.0020.0000.0000.0000.000
138A140HIS00.0360.08834.5330.0020.0020.0000.0000.0000.000
139A141GLN00.014-0.01335.8600.0000.0000.0000.0000.0000.000
140A142ARG10.8850.95638.5960.0140.0140.0000.0000.0000.000
141A143LEU0-0.0150.00333.4860.0010.0010.0000.0000.0000.000
142A144MET0-0.0190.02437.7260.0030.0030.0000.0000.0000.000
143A145GLN0-0.057-0.05139.8140.0010.0010.0000.0000.0000.000
144A146LYS10.9671.01941.004-0.002-0.0020.0000.0000.0000.000
145A147LYS10.9920.99743.137-0.006-0.0060.0000.0000.0000.000
146A148THR0-0.094-0.06845.202-0.002-0.0020.0000.0000.0000.000
147A149MET00.0010.00938.3950.0000.0000.0000.0000.0000.000
148A150LEU00.0270.01336.389-0.002-0.0020.0000.0000.0000.000
149A151ASP-1-0.793-0.87336.6590.0010.0010.0000.0000.0000.000
150A152ASN00.059-0.00831.2050.0020.0020.0000.0000.0000.000
151A153ALA00.0630.04734.462-0.003-0.0030.0000.0000.0000.000
152A154SER0-0.030-0.02937.363-0.001-0.0010.0000.0000.0000.000
153A155ILE0-0.083-0.04532.300-0.001-0.0010.0000.0000.0000.000
154A156GLU-1-0.978-1.00332.155-0.027-0.0270.0000.0000.0000.000
155A157ASP-1-0.936-0.95334.918-0.018-0.0180.0000.0000.0000.000
156A158ALA0-0.059-0.03736.759-0.001-0.0010.0000.0000.0000.000
157A159MET00.0530.05029.1400.0000.0000.0000.0000.0000.000
158A160LYS10.9730.99932.3480.0470.0470.0000.0000.0000.000
159A161SER0-0.0330.01036.0300.0000.0000.0000.0000.0000.000
160A162THR0-0.045-0.05035.5930.0010.0010.0000.0000.0000.000
161A163ASN0-0.081-0.04735.302-0.003-0.0030.0000.0000.0000.000
162A164THR00.049-0.00730.969-0.003-0.0030.0000.0000.0000.000
163A165SER00.0410.01330.1570.0000.0000.0000.0000.0000.000
164A166LYS10.8700.95026.6430.0920.0920.0000.0000.0000.000
165A167ILE00.0130.01425.494-0.009-0.0090.0000.0000.0000.000
166A168LYS10.9820.99817.5030.1160.1160.0000.0000.0000.000
167A169LEU00.012-0.00123.5010.0030.0030.0000.0000.0000.000
168A170THR0-0.027-0.01118.6900.0000.0000.0000.0000.0000.000
169A171ASP-1-0.822-0.90117.0940.0100.0100.0000.0000.0000.000
170A172ASP-1-0.936-0.97515.0850.0300.0300.0000.0000.0000.000
171A173SER0-0.102-0.07017.8240.0160.0160.0000.0000.0000.000
172A174LEU00.0350.00820.6080.0060.0060.0000.0000.0000.000
173A175LYS10.9510.98113.749-0.169-0.1690.0000.0000.0000.000
174A176THR00.0410.02820.0340.0070.0070.0000.0000.0000.000
175A177LEU0-0.0080.00222.6840.0010.0010.0000.0000.0000.000
176A178GLN0-0.027-0.01522.1300.0020.0020.0000.0000.0000.000
177A179ASN0-0.016-0.03021.129-0.002-0.0020.0000.0000.0000.000
178A180ASN0-0.004-0.00924.5000.0030.0030.0000.0000.0000.000
179A181LEU0-0.024-0.01127.223-0.004-0.0040.0000.0000.0000.000
180A182GLU-1-0.865-0.89923.5440.1570.1570.0000.0000.0000.000
181A183LEU00.0140.00026.577-0.003-0.0030.0000.0000.0000.000
182A184SER0-0.092-0.06629.766-0.006-0.0060.0000.0000.0000.000
183A185ARG10.9000.94827.748-0.112-0.1120.0000.0000.0000.000
184A186LYS10.9470.98926.534-0.143-0.1430.0000.0000.0000.000
185A187LEU0-0.048-0.02433.037-0.003-0.0030.0000.0000.0000.000
186A188GLY0-0.0040.01835.651-0.005-0.0050.0000.0000.0000.000
187A189ILE0-0.049-0.01435.122-0.006-0.0060.0000.0000.0000.000
188A190GLN0-0.026-0.02137.4520.0050.0050.0000.0000.0000.000
189A191GLY0-0.009-0.01439.887-0.003-0.0030.0000.0000.0000.000
190A192THR0-0.0390.03037.2340.0000.0000.0000.0000.0000.000
191A193PRO00.001-0.05539.755-0.002-0.0020.0000.0000.0000.000
192A194ALA00.0290.01638.0110.0000.0000.0000.0000.0000.000
193A195THR00.0050.01238.0850.0000.0000.0000.0000.0000.000
194A196VAL00.0130.01135.2730.0000.0000.0000.0000.0000.000
195A197ILE00.003-0.01638.599-0.003-0.0030.0000.0000.0000.000
196A198GLY00.0170.01039.906-0.001-0.0010.0000.0000.0000.000
197A199ASP-1-0.916-0.96139.5970.0540.0540.0000.0000.0000.000
198A200THR0-0.035-0.02141.4610.0010.0010.0000.0000.0000.000
199A201ILE00.0120.00837.692-0.001-0.0010.0000.0000.0000.000
200A202LEU00.0120.00241.404-0.001-0.0010.0000.0000.0000.000
201A203PRO0-0.024-0.01342.6900.0000.0000.0000.0000.0000.000
202A204GLY00.0360.01143.507-0.001-0.0010.0000.0000.0000.000
203A205ALA0-0.069-0.03845.296-0.001-0.0010.0000.0000.0000.000
204A206VAL0-0.031-0.01046.8330.0000.0000.0000.0000.0000.000
205A207ASP-1-0.856-0.92149.3130.0140.0140.0000.0000.0000.000
206A208TYR00.003-0.06947.9830.0010.0010.0000.0000.0000.000
207A209ASP-1-0.830-0.91651.1530.0130.0130.0000.0000.0000.000
208A210GLN0-0.079-0.04951.9290.0010.0010.0000.0000.0000.000
209A211LEU0-0.028-0.02144.9440.0010.0010.0000.0000.0000.000
210A212GLU-1-0.857-0.90848.4510.0140.0140.0000.0000.0000.000
211A213ILE0-0.018-0.01850.2920.0000.0000.0000.0000.0000.000
212A214ILE00.0120.02146.4420.0010.0010.0000.0000.0000.000
213A215VAL00.0260.00344.6850.0020.0020.0000.0000.0000.000
214A216LYS10.9880.99246.796-0.014-0.0140.0000.0000.0000.000
215A217GLU-1-0.973-0.97449.3880.0270.0270.0000.0000.0000.000
216A218GLN0-0.014-0.02944.1720.0020.0020.0000.0000.0000.000
217A219LEU00.0230.02444.7590.0010.0010.0000.0000.0000.000
218A220ALA0-0.058-0.01946.916-0.001-0.0010.0000.0000.0000.000
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