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: 7M23K

Calculation Name: 4FRW-A-Xray372

Preferred Name: Nectin-4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4FRW

Chain ID: A

ChEMBL ID: CHEMBL3712928

UniProt ID: Q96NY8

Base Structure: X-ray

Registration Date: 2023-09-26

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2017048.130781
FMO2-HF: Nuclear repulsion 1936399.041435
FMO2-HF: Total energy -80649.089347
FMO2-MP2: Total energy -80885.421855


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:32:GLY)


Summations of interaction energy for fragment #1(A:32:GLY)
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.
-4.772-0.650.681-2.444-2.358-0.014
Interaction energy analysis for fragmet #1(A:32:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : 0.000
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].
3A34LEU0-0.022-0.0343.799-0.5070.604-0.018-0.617-0.4770.002
4A35GLU-1-0.864-0.9057.117-0.476-0.4760.0000.0000.0000.000
5A36THR0-0.011-0.0369.2970.0910.0910.0000.0000.0000.000
6A37SER0-0.042-0.02213.0240.0190.0190.0000.0000.0000.000
7A38ASP-1-0.856-0.92416.334-0.174-0.1740.0000.0000.0000.000
8A39VAL0-0.062-0.05018.2510.0190.0190.0000.0000.0000.000
9A40VAL0-0.0200.01820.3030.0000.0000.0000.0000.0000.000
10A41THR00.001-0.01122.7250.0160.0160.0000.0000.0000.000
11A42VAL0-0.0090.01126.307-0.003-0.0030.0000.0000.0000.000
12A43VAL00.0100.02128.7780.0050.0050.0000.0000.0000.000
13A44LEU00.003-0.02632.396-0.003-0.0030.0000.0000.0000.000
14A45GLY0-0.019-0.01134.0670.0020.0020.0000.0000.0000.000
15A46GLN0-0.0200.00830.177-0.002-0.0020.0000.0000.0000.000
16A47ASP-1-0.813-0.88327.725-0.103-0.1030.0000.0000.0000.000
17A48ALA0-0.035-0.00724.950-0.004-0.0040.0000.0000.0000.000
18A49LYS10.9540.98217.9720.2410.2410.0000.0000.0000.000
19A50LEU0-0.018-0.00419.586-0.004-0.0040.0000.0000.0000.000
20A51PRO0-0.029-0.01015.016-0.012-0.0120.0000.0000.0000.000
21A52CYS0-0.0070.00412.848-0.020-0.0200.0000.0000.0000.000
22A53PHE00.0140.0149.0100.0200.0200.0000.0000.0000.000
23A54TYR0-0.031-0.0373.614-0.569-0.2680.012-0.126-0.186-0.001
24A55ARG10.8260.9244.1911.0551.165-0.001-0.019-0.0900.000
25A56GLY00.0390.0222.810-2.134-1.1040.598-0.870-0.758-0.008
26A57ASP-1-0.911-0.9633.9330.1860.3120.000-0.032-0.0940.000
27A58SER0-0.055-0.0535.441-0.084-0.0840.0000.0000.0000.000
28A59GLY0-0.047-0.0167.5620.0000.0000.0000.0000.0000.000
29A60GLU-1-0.851-0.9053.122-2.461-1.0170.090-0.780-0.753-0.007
30A61GLN0-0.034-0.0207.847-0.090-0.0900.0000.0000.0000.000
31A62VAL00.0160.0139.358-0.024-0.0240.0000.0000.0000.000
32A63GLY0-0.029-0.00911.2510.0630.0630.0000.0000.0000.000
33A64GLN0-0.015-0.03814.3200.0440.0440.0000.0000.0000.000
34A65VAL00.0100.01913.548-0.027-0.0270.0000.0000.0000.000
35A66ALA00.000-0.00115.9500.0320.0320.0000.0000.0000.000
36A67TRP00.0010.00416.734-0.016-0.0160.0000.0000.0000.000
37A68ALA00.0270.01920.3600.0210.0210.0000.0000.0000.000
38A69ARG10.9010.95622.1690.0750.0750.0000.0000.0000.000
39A70VAL0-0.046-0.01521.9080.0080.0080.0000.0000.0000.000
40A71ASP-1-0.839-0.92124.807-0.069-0.0690.0000.0000.0000.000
41A72ALA0-0.054-0.02728.5800.0040.0040.0000.0000.0000.000
42A73GLY0-0.039-0.02729.9520.0030.0030.0000.0000.0000.000
43A74GLU-1-0.972-0.96632.311-0.042-0.0420.0000.0000.0000.000
44A75GLY0-0.020-0.01131.025-0.004-0.0040.0000.0000.0000.000
45A76ALA00.012-0.00525.658-0.002-0.0020.0000.0000.0000.000
46A77GLN0-0.0060.01227.5400.0010.0010.0000.0000.0000.000
47A78GLU-1-0.915-0.97724.223-0.118-0.1180.0000.0000.0000.000
48A79LEU0-0.033-0.01623.5600.0050.0050.0000.0000.0000.000
49A80ALA00.0210.00123.0940.0100.0100.0000.0000.0000.000
50A81LEU0-0.0110.02020.722-0.017-0.0170.0000.0000.0000.000
51A82LEU0-0.011-0.00216.5910.0170.0170.0000.0000.0000.000
52A83HIS00.0130.01618.118-0.025-0.0250.0000.0000.0000.000
53A84SER0-0.016-0.01016.4670.0130.0130.0000.0000.0000.000
54A85LYS10.9230.97217.9560.0930.0930.0000.0000.0000.000
55A86TYR0-0.046-0.06421.5550.0070.0070.0000.0000.0000.000
56A87GLY00.0270.03922.1570.0080.0080.0000.0000.0000.000
57A88LEU00.0010.00621.892-0.013-0.0130.0000.0000.0000.000
58A89HIS00.0040.00623.7300.0180.0180.0000.0000.0000.000
59A90VAL0-0.010-0.01825.394-0.008-0.0080.0000.0000.0000.000
60A91SER0-0.0080.00327.2840.0110.0110.0000.0000.0000.000
61A92PRO00.0470.00429.0350.0000.0000.0000.0000.0000.000
62A93ALA0-0.0150.00731.2010.0030.0030.0000.0000.0000.000
63A94TYR0-0.034-0.02828.7850.0010.0010.0000.0000.0000.000
64A95GLU-1-0.900-0.95230.342-0.072-0.0720.0000.0000.0000.000
65A96GLY0-0.0060.00231.3910.0040.0040.0000.0000.0000.000
66A97ARG10.8060.88230.0070.0900.0900.0000.0000.0000.000
67A98VAL0-0.0240.00124.277-0.006-0.0060.0000.0000.0000.000
68A99GLU-1-0.883-0.94225.514-0.104-0.1040.0000.0000.0000.000
69A100GLN00.003-0.01019.732-0.029-0.0290.0000.0000.0000.000
70A101PRO0-0.0040.01219.1070.0140.0140.0000.0000.0000.000
71A102PRO00.0430.00222.064-0.003-0.0030.0000.0000.0000.000
72A103PRO0-0.0420.00721.535-0.013-0.0130.0000.0000.0000.000
73A104PRO00.010-0.01519.7500.0110.0110.0000.0000.0000.000
74A105ARG10.9280.96317.4110.1890.1890.0000.0000.0000.000
75A106ASN00.0360.03010.6700.0170.0170.0000.0000.0000.000
76A107PRO00.0320.01713.307-0.011-0.0110.0000.0000.0000.000
77A108LEU00.013-0.0027.3370.0260.0260.0000.0000.0000.000
78A109ASP-1-0.916-0.93910.797-0.503-0.5030.0000.0000.0000.000
79A110GLY00.0370.01812.8160.0550.0550.0000.0000.0000.000
80A111SER0-0.085-0.06814.8850.0420.0420.0000.0000.0000.000
81A112VAL0-0.026-0.00416.8880.0250.0250.0000.0000.0000.000
82A113LEU0-0.036-0.03320.635-0.006-0.0060.0000.0000.0000.000
83A114LEU00.0090.00023.8260.0070.0070.0000.0000.0000.000
84A115ARG10.9210.95626.4740.0950.0950.0000.0000.0000.000
85A116ASN0-0.079-0.05929.6690.0070.0070.0000.0000.0000.000
86A117ALA0-0.0030.01129.3100.0030.0030.0000.0000.0000.000
87A118VAL00.0320.00731.1600.0070.0070.0000.0000.0000.000
88A119GLN00.0370.01132.5570.0000.0000.0000.0000.0000.000
89A120ALA0-0.043-0.03433.465-0.001-0.0010.0000.0000.0000.000
90A121ASP-1-0.777-0.86328.792-0.093-0.0930.0000.0000.0000.000
91A122GLU-1-0.862-0.92228.392-0.077-0.0770.0000.0000.0000.000
92A123GLY0-0.020-0.01127.5990.0070.0070.0000.0000.0000.000
93A124GLU-1-0.963-0.98022.478-0.110-0.1100.0000.0000.0000.000
94A125TYR0-0.030-0.02521.2730.0110.0110.0000.0000.0000.000
95A126GLU-1-0.959-0.98617.798-0.146-0.1460.0000.0000.0000.000
96A128ARG10.9460.96014.5830.1090.1090.0000.0000.0000.000
97A129VAL00.0480.0189.5440.0080.0080.0000.0000.0000.000
98A130SER0-0.048-0.03211.9370.0250.0250.0000.0000.0000.000
99A131THR00.0060.0096.4830.1340.1340.0000.0000.0000.000
100A132PHE0-0.0120.0099.5350.1280.1280.0000.0000.0000.000
101A133PRO00.018-0.0037.850-0.098-0.0980.0000.0000.0000.000
102A134ALA00.0200.0145.2630.1020.1020.0000.0000.0000.000
103A135GLY00.0200.0257.3640.1750.1750.0000.0000.0000.000
104A136SER0-0.046-0.0389.367-0.133-0.1330.0000.0000.0000.000
105A137PHE00.0000.0115.414-0.058-0.0580.0000.0000.0000.000
106A138GLN00.005-0.01310.673-0.012-0.0120.0000.0000.0000.000
107A139ALA00.0240.03211.9560.0060.0060.0000.0000.0000.000
108A140ARG10.9260.96013.8700.1310.1310.0000.0000.0000.000
109A141LEU00.0660.04916.837-0.015-0.0150.0000.0000.0000.000
110A142ARG10.9480.97319.3320.1120.1120.0000.0000.0000.000
111A143LEU00.0000.00823.006-0.005-0.0050.0000.0000.0000.000
112A144ARG10.7630.85224.9970.0890.0890.0000.0000.0000.000
113A145VAL00.0400.01127.949-0.004-0.0040.0000.0000.0000.000
114A146LEU0-0.038-0.01430.8700.0060.0060.0000.0000.0000.000
115A147VAL00.017-0.01033.445-0.001-0.0010.0000.0000.0000.000
116A148PRO00.0210.01236.9060.0030.0030.0000.0000.0000.000
117A149PRO00.0110.00739.6000.0010.0010.0000.0000.0000.000
118A150LEU0-0.007-0.01643.1660.0000.0000.0000.0000.0000.000
119A151PRO0-0.054-0.00846.3180.0020.0020.0000.0000.0000.000
120A152SER00.0160.00348.9600.0010.0010.0000.0000.0000.000
121A153LEU0-0.022-0.01552.6860.0000.0000.0000.0000.0000.000
122A154ASN0-0.019-0.01655.7180.0000.0000.0000.0000.0000.000
123A155PRO0-0.007-0.00758.8450.0000.0000.0000.0000.0000.000
124A156GLY00.0200.01762.0860.0000.0000.0000.0000.0000.000
125A157PRO0-0.037-0.03064.1610.0000.0000.0000.0000.0000.000
126A158ALA00.0180.01067.8460.0000.0000.0000.0000.0000.000
127A159LEU0-0.0400.00066.0140.0000.0000.0000.0000.0000.000
128A160GLU-1-0.896-0.96870.585-0.012-0.0120.0000.0000.0000.000
129A161GLU-1-0.925-0.99173.823-0.012-0.0120.0000.0000.0000.000
130A162GLY00.0230.02475.4430.0000.0000.0000.0000.0000.000
131A163GLN0-0.0310.00570.1600.0010.0010.0000.0000.0000.000
132A164GLY00.0630.02071.8680.0000.0000.0000.0000.0000.000
133A165LEU0-0.035-0.03164.1870.0000.0000.0000.0000.0000.000
134A166THR0-0.032-0.01466.5870.0000.0000.0000.0000.0000.000
135A167LEU00.0320.03660.4390.0000.0000.0000.0000.0000.000
136A168ALA00.0370.02361.7590.0000.0000.0000.0000.0000.000
137A169ALA0-0.017-0.01359.0620.0000.0000.0000.0000.0000.000
138A170SER00.0070.01356.0650.0000.0000.0000.0000.0000.000
139A171CYS0-0.083-0.02551.761-0.001-0.0010.0000.0000.0000.000
140A172THR0-0.013-0.01250.0130.0000.0000.0000.0000.0000.000
141A173ALA00.0310.01345.737-0.001-0.0010.0000.0000.0000.000
142A174GLU-1-0.819-0.90743.267-0.037-0.0370.0000.0000.0000.000
143A175GLY00.0420.02240.776-0.001-0.0010.0000.0000.0000.000
144A176SER0-0.0260.01135.6940.0020.0020.0000.0000.0000.000
145A177PRO00.010-0.00934.381-0.004-0.0040.0000.0000.0000.000
146A178ALA00.0240.00236.8750.0000.0000.0000.0000.0000.000
147A179PRO0-0.0210.02040.329-0.001-0.0010.0000.0000.0000.000
148A180SER0-0.0130.00142.2170.0030.0030.0000.0000.0000.000
149A181VAL0-0.022-0.01644.249-0.001-0.0010.0000.0000.0000.000
150A182THR0-0.022-0.00847.7570.0020.0020.0000.0000.0000.000
151A183TRP0-0.002-0.02050.4060.0000.0000.0000.0000.0000.000
152A184ASP-1-0.911-0.96153.174-0.025-0.0250.0000.0000.0000.000
153A185THR0-0.044-0.04054.9870.0000.0000.0000.0000.0000.000
154A186GLU-1-0.840-0.90458.741-0.020-0.0200.0000.0000.0000.000
155A187VAL0-0.072-0.02061.8630.0010.0010.0000.0000.0000.000
156A188LYS10.9540.95761.9300.0150.0150.0000.0000.0000.000
157A189GLY00.0340.00461.7120.0000.0000.0000.0000.0000.000
158A190THR0-0.048-0.01259.3590.0000.0000.0000.0000.0000.000
159A191THR00.0310.01754.3370.0000.0000.0000.0000.0000.000
160A192SER0-0.027-0.00755.0770.0010.0010.0000.0000.0000.000
161A193SER00.0280.00650.7140.0000.0000.0000.0000.0000.000
162A194ARG10.8780.94850.8040.0210.0210.0000.0000.0000.000
163A195SER00.010-0.00944.720-0.002-0.0020.0000.0000.0000.000
164A196PHE00.0370.03346.2680.0010.0010.0000.0000.0000.000
165A197LYS10.9410.97238.1380.0380.0380.0000.0000.0000.000
166A198HIS0-0.026-0.02742.5980.0040.0040.0000.0000.0000.000
167A199SER0-0.022-0.02140.030-0.001-0.0010.0000.0000.0000.000
168A200ARG10.9700.98232.7930.0580.0580.0000.0000.0000.000
169A201SER0-0.031-0.00337.233-0.004-0.0040.0000.0000.0000.000
170A202ALA0-0.042-0.03239.6300.0020.0020.0000.0000.0000.000
171A203ALA00.0630.04842.277-0.001-0.0010.0000.0000.0000.000
172A204VAL0-0.027-0.00644.8520.0020.0020.0000.0000.0000.000
173A205THR0-0.041-0.01147.3950.0000.0000.0000.0000.0000.000
174A206SER00.0630.02751.0180.0010.0010.0000.0000.0000.000
175A207GLU-1-0.848-0.94053.052-0.020-0.0200.0000.0000.0000.000
176A208PHE00.0160.02156.7780.0000.0000.0000.0000.0000.000
177A209HIS0-0.056-0.04459.0450.0010.0010.0000.0000.0000.000
178A210LEU00.016-0.00862.3010.0000.0000.0000.0000.0000.000
179A211VAL0-0.035-0.01265.3380.0000.0000.0000.0000.0000.000
180A212PRO0-0.0130.00369.0710.0000.0000.0000.0000.0000.000
181A213SER00.0930.04670.5990.0000.0000.0000.0000.0000.000
182A214ARG10.9000.93471.7250.0140.0140.0000.0000.0000.000
183A215SER0-0.084-0.04571.479-0.001-0.0010.0000.0000.0000.000
184A216MET00.0030.01066.5620.0000.0000.0000.0000.0000.000
185A217ASN0-0.007-0.01468.083-0.001-0.0010.0000.0000.0000.000
186A218GLY0-0.052-0.02168.0130.0000.0000.0000.0000.0000.000
187A219GLN0-0.019-0.00365.064-0.001-0.0010.0000.0000.0000.000
188A220PRO00.0120.00660.1710.0000.0000.0000.0000.0000.000
189A221LEU00.0060.01058.3190.0000.0000.0000.0000.0000.000
190A222THR0-0.003-0.00453.934-0.001-0.0010.0000.0000.0000.000
191A224VAL0-0.036-0.01647.946-0.001-0.0010.0000.0000.0000.000
192A225VAL00.004-0.00944.5880.0000.0000.0000.0000.0000.000
193A226SER0-0.0230.00541.852-0.002-0.0020.0000.0000.0000.000
194A227HIS00.007-0.02836.527-0.001-0.0010.0000.0000.0000.000
195A228PRO00.0410.01234.221-0.001-0.0010.0000.0000.0000.000
196A229GLY0-0.039-0.02634.907-0.004-0.0040.0000.0000.0000.000
197A230LEU0-0.046-0.02635.8790.0000.0000.0000.0000.0000.000
198A231LEU00.0180.01334.6700.0010.0010.0000.0000.0000.000
199A232GLN0-0.036-0.01638.6340.0030.0030.0000.0000.0000.000
200A233ASP-1-0.840-0.91342.467-0.042-0.0420.0000.0000.0000.000
201A234GLN00.0090.00544.3770.0000.0000.0000.0000.0000.000
202A235ARG10.9180.94546.8940.0310.0310.0000.0000.0000.000
203A236ILE0-0.0060.01150.5710.0000.0000.0000.0000.0000.000
204A237THR0-0.006-0.01253.5600.0010.0010.0000.0000.0000.000
205A238HIS00.0230.01757.1230.0000.0000.0000.0000.0000.000
206A239ILE0-0.0020.00060.2840.0000.0000.0000.0000.0000.000
207A240LEU00.0330.02763.5640.0000.0000.0000.0000.0000.000
208A241HIS0-0.033-0.03565.6970.0010.0010.0000.0000.0000.000
209A242VAL00.0210.02969.2820.0000.0000.0000.0000.0000.000
210A243SER0-0.042-0.01372.0530.0000.0000.0000.0000.0000.000
211A244HIS00.0350.01975.7690.0000.0000.0000.0000.0000.000
212A245HIS00.0290.02978.8150.0000.0000.0000.0000.0000.000
213A246HIS0-0.036-0.00680.3450.0000.0000.0000.0000.0000.000