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: 2LJ7R

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2017387.94948
FMO2-HF: Nuclear repulsion 1936737.061157
FMO2-HF: Total energy -80650.888324
FMO2-MP2: Total energy -80887.075738


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.
-6.936-2.8240.797-2.446-2.466-0.015
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 : -0.006 / q_NPA : -0.001
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].
3A34LEU0-0.037-0.0363.799-0.7460.297-0.018-0.591-0.4350.002
4A35GLU-1-0.793-0.8457.1290.8830.8830.0000.0000.0000.000
5A36THR0-0.017-0.0499.291-0.097-0.0970.0000.0000.0000.000
6A37SER0-0.045-0.02313.0180.0730.0730.0000.0000.0000.000
7A38ASP-1-0.884-0.93116.3270.0480.0480.0000.0000.0000.000
8A39VAL0-0.037-0.04218.300-0.023-0.0230.0000.0000.0000.000
9A40VAL0-0.0220.01520.2590.0130.0130.0000.0000.0000.000
10A41THR00.003-0.01322.719-0.005-0.0050.0000.0000.0000.000
11A42VAL00.0050.01726.3010.0030.0030.0000.0000.0000.000
12A43VAL00.0090.01728.7730.0010.0010.0000.0000.0000.000
13A44LEU00.006-0.01332.392-0.004-0.0040.0000.0000.0000.000
14A45GLY0-0.002-0.00634.0660.0030.0030.0000.0000.0000.000
15A46GLN0-0.054-0.01330.4280.0000.0000.0000.0000.0000.000
16A47ASP-1-0.785-0.88027.688-0.040-0.0400.0000.0000.0000.000
17A48ALA0-0.026-0.00225.0410.0080.0080.0000.0000.0000.000
18A49LYS10.9430.98017.3310.0560.0560.0000.0000.0000.000
19A50LEU00.0010.00519.5680.0160.0160.0000.0000.0000.000
20A51PRO0-0.054-0.02914.848-0.024-0.0240.0000.0000.0000.000
21A52CYS0-0.0010.01812.828-0.042-0.0420.0000.0000.0000.000
22A53PHE00.0130.0208.641-0.035-0.0350.0000.0000.0000.000
23A54TYR0-0.032-0.0533.818-0.0040.1570.001-0.056-0.1060.000
24A55ARG10.7880.8714.644-0.554-0.454-0.001-0.012-0.0870.000
25A56GLY00.0310.0252.810-1.763-0.6920.538-0.854-0.756-0.008
26A57ASP-1-0.910-0.9843.847-0.1310.0400.000-0.038-0.1340.000
27A58SER0-0.101-0.0575.450-0.246-0.2460.0000.0000.0000.000
28A59GLY0-0.011-0.0017.6410.0440.0440.0000.0000.0000.000
29A60GLU-1-0.828-0.8792.911-5.118-3.5520.277-0.895-0.948-0.009
30A61GLN0-0.0100.0017.8400.0680.0680.0000.0000.0000.000
31A62VAL00.0270.0099.356-0.145-0.1450.0000.0000.0000.000
32A63GLY0-0.015-0.00411.2430.1100.1100.0000.0000.0000.000
33A64GLN00.005-0.02314.3260.1030.1030.0000.0000.0000.000
34A65VAL00.0060.01713.350-0.073-0.0730.0000.0000.0000.000
35A66ALA0-0.002-0.00115.9430.0540.0540.0000.0000.0000.000
36A67TRP0-0.007-0.00416.840-0.019-0.0190.0000.0000.0000.000
37A68ALA00.0230.01520.3600.0180.0180.0000.0000.0000.000
38A69ARG10.8030.87722.1690.0710.0710.0000.0000.0000.000
39A70VAL0-0.056-0.03122.005-0.003-0.0030.0000.0000.0000.000
40A71ASP-1-0.771-0.85124.807-0.067-0.0670.0000.0000.0000.000
41A72ALA0-0.030-0.01728.580-0.004-0.0040.0000.0000.0000.000
42A73GLY0-0.030-0.02129.9520.0070.0070.0000.0000.0000.000
43A74GLU-1-0.953-0.96632.319-0.059-0.0590.0000.0000.0000.000
44A75GLY0-0.031-0.01731.025-0.004-0.0040.0000.0000.0000.000
45A76ALA0-0.001-0.00825.662-0.002-0.0020.0000.0000.0000.000
46A77GLN00.0130.02027.554-0.006-0.0060.0000.0000.0000.000
47A78GLU-1-0.920-0.97524.034-0.183-0.1830.0000.0000.0000.000
48A79LEU0-0.043-0.02023.6630.0110.0110.0000.0000.0000.000
49A80ALA00.0290.00623.1250.0120.0120.0000.0000.0000.000
50A81LEU0-0.0100.01620.720-0.024-0.0240.0000.0000.0000.000
51A82LEU0-0.0050.00016.6880.0250.0250.0000.0000.0000.000
52A83HIS00.0060.00918.110-0.034-0.0340.0000.0000.0000.000
53A84SER0-0.024-0.00916.1040.0350.0350.0000.0000.0000.000
54A85LYS10.8980.95117.9470.1960.1960.0000.0000.0000.000
55A86TYR0-0.033-0.04921.5450.0220.0220.0000.0000.0000.000
56A87GLY00.0330.04422.1420.0180.0180.0000.0000.0000.000
57A88LEU0-0.018-0.00522.119-0.022-0.0220.0000.0000.0000.000
58A89HIS00.0030.00623.7200.0230.0230.0000.0000.0000.000
59A90VAL0-0.002-0.01425.386-0.011-0.0110.0000.0000.0000.000
60A91SER0-0.0090.00127.2830.0070.0070.0000.0000.0000.000
61A92PRO00.047-0.00929.0290.0060.0060.0000.0000.0000.000
62A93ALA0-0.0150.01831.2040.0070.0070.0000.0000.0000.000
63A94TYR0-0.040-0.02928.8120.0050.0050.0000.0000.0000.000
64A95GLU-1-0.910-0.95430.343-0.079-0.0790.0000.0000.0000.000
65A96GLY0-0.0050.00231.3950.0060.0060.0000.0000.0000.000
66A97ARG10.7570.85330.1650.0610.0610.0000.0000.0000.000
67A98VAL0-0.021-0.00224.3110.0020.0020.0000.0000.0000.000
68A99GLU-1-0.857-0.92325.464-0.070-0.0700.0000.0000.0000.000
69A100GLN00.0300.01420.019-0.014-0.0140.0000.0000.0000.000
70A101PRO00.0000.01119.0500.0130.0130.0000.0000.0000.000
71A102PRO00.0380.02222.067-0.011-0.0110.0000.0000.0000.000
72A103PRO0-0.0470.01121.533-0.001-0.0010.0000.0000.0000.000
73A104PRO00.015-0.01619.7730.0090.0090.0000.0000.0000.000
74A105ARG10.9200.94417.1440.1550.1550.0000.0000.0000.000
75A106ASN00.0210.00710.571-0.052-0.0520.0000.0000.0000.000
76A107PRO00.0380.01813.627-0.016-0.0160.0000.0000.0000.000
77A108LEU00.0040.0057.389-0.005-0.0050.0000.0000.0000.000
78A109ASP-1-0.925-0.93210.802-0.296-0.2960.0000.0000.0000.000
79A110GLY00.0420.01812.8190.0210.0210.0000.0000.0000.000
80A111SER0-0.099-0.08314.9520.0440.0440.0000.0000.0000.000
81A112VAL0-0.030-0.00716.8880.0070.0070.0000.0000.0000.000
82A113LEU0-0.038-0.03220.6350.0150.0150.0000.0000.0000.000
83A114LEU00.0080.00323.825-0.005-0.0050.0000.0000.0000.000
84A115ARG10.8670.92926.4720.0590.0590.0000.0000.0000.000
85A116ASN0-0.079-0.06429.6680.0000.0000.0000.0000.0000.000
86A117ALA00.0050.01929.283-0.003-0.0030.0000.0000.0000.000
87A118VAL00.035-0.00131.1570.0070.0070.0000.0000.0000.000
88A119GLN00.007-0.01732.554-0.001-0.0010.0000.0000.0000.000
89A120ALA0-0.034-0.01933.4610.0000.0000.0000.0000.0000.000
90A121ASP-1-0.737-0.83928.785-0.058-0.0580.0000.0000.0000.000
91A122GLU-1-0.820-0.84428.388-0.017-0.0170.0000.0000.0000.000
92A123GLY00.0220.00527.599-0.003-0.0030.0000.0000.0000.000
93A124GLU-1-0.945-0.97922.018-0.057-0.0570.0000.0000.0000.000
94A125TYR0-0.040-0.04621.323-0.006-0.0060.0000.0000.0000.000
95A126GLU-1-0.829-0.90017.601-0.245-0.2450.0000.0000.0000.000
96A128ARG10.8540.90414.5830.3150.3150.0000.0000.0000.000
97A129VAL00.0420.0089.6080.0320.0320.0000.0000.0000.000
98A130SER0-0.030-0.02511.936-0.065-0.0650.0000.0000.0000.000
99A131THR0-0.0090.0006.4780.2150.2150.0000.0000.0000.000
100A132PHE0-0.0090.0219.5670.0980.0980.0000.0000.0000.000
101A133PRO00.023-0.0037.617-0.018-0.0180.0000.0000.0000.000
102A134ALA00.0130.0085.5090.1300.1300.0000.0000.0000.000
103A135GLY00.0330.0267.3690.1810.1810.0000.0000.0000.000
104A136SER0-0.079-0.0479.369-0.099-0.0990.0000.0000.0000.000
105A137PHE00.0110.0145.7880.0290.0290.0000.0000.0000.000
106A138GLN00.0310.00910.6760.0940.0940.0000.0000.0000.000
107A139ALA00.0240.02611.8400.0160.0160.0000.0000.0000.000
108A140ARG10.8520.92013.8700.1460.1460.0000.0000.0000.000
109A141LEU00.0500.03816.8370.0240.0240.0000.0000.0000.000
110A142ARG10.9560.97619.332-0.019-0.0190.0000.0000.0000.000
111A143LEU0-0.0050.00723.0000.0120.0120.0000.0000.0000.000
112A144ARG10.7790.85724.991-0.001-0.0010.0000.0000.0000.000
113A145VAL00.0460.00527.9430.0030.0030.0000.0000.0000.000
114A146LEU0-0.059-0.02330.8650.0020.0020.0000.0000.0000.000
115A147VAL00.036-0.00233.439-0.002-0.0020.0000.0000.0000.000
116A148PRO00.0220.00936.9340.0010.0010.0000.0000.0000.000
117A149PRO00.0020.00639.594-0.002-0.0020.0000.0000.0000.000
118A150LEU0-0.009-0.01943.1600.0000.0000.0000.0000.0000.000
119A151PRO0-0.052-0.00746.347-0.001-0.0010.0000.0000.0000.000
120A152SER0-0.001-0.00248.954-0.001-0.0010.0000.0000.0000.000
121A153LEU0-0.010-0.01352.6800.0010.0010.0000.0000.0000.000
122A154ASN0-0.012-0.01455.711-0.001-0.0010.0000.0000.0000.000
123A155PRO0-0.007-0.00758.8380.0010.0010.0000.0000.0000.000
124A156GLY00.0140.01962.079-0.001-0.0010.0000.0000.0000.000
125A157PRO0-0.040-0.02764.1530.0000.0000.0000.0000.0000.000
126A158ALA00.0160.00867.8390.0000.0000.0000.0000.0000.000
127A159LEU0-0.0160.00666.0870.0000.0000.0000.0000.0000.000
128A160GLU-1-0.850-0.93470.5770.0050.0050.0000.0000.0000.000
129A161GLU-1-0.893-0.97173.8150.0080.0080.0000.0000.0000.000
130A162GLY0-0.0140.00975.4350.0000.0000.0000.0000.0000.000
131A163GLN0-0.064-0.01470.0450.0000.0000.0000.0000.0000.000
132A164GLY00.0780.02072.0740.0000.0000.0000.0000.0000.000
133A165LEU0-0.036-0.02964.4550.0000.0000.0000.0000.0000.000
134A166THR0-0.023-0.00366.725-0.001-0.0010.0000.0000.0000.000
135A167LEU00.0400.02860.1840.0010.0010.0000.0000.0000.000
136A168ALA00.0380.02461.7360.0000.0000.0000.0000.0000.000
137A169ALA0-0.025-0.01659.009-0.001-0.0010.0000.0000.0000.000
138A170SER00.0080.00856.1790.0010.0010.0000.0000.0000.000
139A171CYS0-0.083-0.01651.8660.0000.0000.0000.0000.0000.000
140A172THR00.0020.00249.9640.0010.0010.0000.0000.0000.000
141A173ALA00.0170.00345.841-0.001-0.0010.0000.0000.0000.000
142A174GLU-1-0.777-0.86043.240-0.003-0.0030.0000.0000.0000.000
143A175GLY00.0370.02240.769-0.001-0.0010.0000.0000.0000.000
144A176SER0-0.0310.01436.0400.0020.0020.0000.0000.0000.000
145A177PRO0-0.008-0.02234.319-0.001-0.0010.0000.0000.0000.000
146A178ALA00.0260.00436.867-0.001-0.0010.0000.0000.0000.000
147A179PRO0-0.0180.01540.3430.0030.0030.0000.0000.0000.000
148A180SER0-0.0050.00242.2090.0000.0000.0000.0000.0000.000
149A181VAL0-0.015-0.01644.2770.0000.0000.0000.0000.0000.000
150A182THR0-0.024-0.00647.9320.0010.0010.0000.0000.0000.000
151A183TRP00.005-0.01650.439-0.001-0.0010.0000.0000.0000.000
152A184ASP-1-0.836-0.89953.0910.0200.0200.0000.0000.0000.000
153A185THR0-0.042-0.05254.978-0.001-0.0010.0000.0000.0000.000
154A186GLU-1-0.863-0.91558.7320.0180.0180.0000.0000.0000.000
155A187VAL0-0.068-0.02061.8640.0000.0000.0000.0000.0000.000
156A188LYS10.9650.96562.041-0.017-0.0170.0000.0000.0000.000
157A189GLY00.028-0.00361.945-0.001-0.0010.0000.0000.0000.000
158A190THR0-0.043-0.00559.6840.0010.0010.0000.0000.0000.000
159A191THR00.0350.01355.2550.0000.0000.0000.0000.0000.000
160A192SER0-0.087-0.02855.3710.0000.0000.0000.0000.0000.000
161A193SER00.0840.03150.804-0.001-0.0010.0000.0000.0000.000
162A194ARG10.8720.94451.065-0.008-0.0080.0000.0000.0000.000
163A195SER00.009-0.00644.8840.0000.0000.0000.0000.0000.000
164A196PHE00.0310.02946.5020.0010.0010.0000.0000.0000.000
165A197LYS10.9510.97637.864-0.008-0.0080.0000.0000.0000.000
166A198HIS0-0.035-0.03542.618-0.001-0.0010.0000.0000.0000.000
167A199SER0-0.016-0.01840.1370.0010.0010.0000.0000.0000.000
168A200ARG10.9250.95331.8950.0310.0310.0000.0000.0000.000
169A201SER0-0.039-0.02937.2270.0000.0000.0000.0000.0000.000
170A202ALA0-0.038-0.03539.6240.0000.0000.0000.0000.0000.000
171A203ALA00.0580.04742.2700.0010.0010.0000.0000.0000.000
172A204VAL0-0.033-0.00844.9940.0000.0000.0000.0000.0000.000
173A205THR0-0.012-0.00347.3880.0000.0000.0000.0000.0000.000
174A206SER00.0260.00451.0110.0010.0010.0000.0000.0000.000
175A207GLU-1-0.846-0.93153.0970.0060.0060.0000.0000.0000.000
176A208PHE00.0180.02656.8190.0010.0010.0000.0000.0000.000
177A209HIS0-0.073-0.05859.110-0.001-0.0010.0000.0000.0000.000
178A210LEU00.023-0.00562.4370.0010.0010.0000.0000.0000.000
179A211VAL0-0.026-0.00665.474-0.001-0.0010.0000.0000.0000.000
180A212PRO0-0.029-0.00569.2270.0000.0000.0000.0000.0000.000
181A213SER00.1040.06170.6340.0000.0000.0000.0000.0000.000
182A214ARG10.9160.93871.717-0.007-0.0070.0000.0000.0000.000
183A215SER0-0.102-0.05971.8440.0000.0000.0000.0000.0000.000
184A216MET0-0.0050.00467.2430.0000.0000.0000.0000.0000.000
185A217ASN0-0.021-0.01668.0750.0000.0000.0000.0000.0000.000
186A218GLY0-0.031-0.01668.0050.0000.0000.0000.0000.0000.000
187A219GLN0-0.0180.00265.0580.0010.0010.0000.0000.0000.000
188A220PRO00.0040.00560.127-0.001-0.0010.0000.0000.0000.000
189A221LEU00.0110.02058.3420.0010.0010.0000.0000.0000.000
190A222THR00.0080.00253.943-0.001-0.0010.0000.0000.0000.000
191A224VAL0-0.031-0.02147.916-0.001-0.0010.0000.0000.0000.000
192A225VAL0-0.015-0.01244.6210.0010.0010.0000.0000.0000.000
193A226SER0-0.020-0.01741.9580.0010.0010.0000.0000.0000.000
194A227HIS00.006-0.02036.7120.0000.0000.0000.0000.0000.000
195A228PRO00.0360.01034.1740.0010.0010.0000.0000.0000.000
196A229GLY0-0.043-0.01634.8980.0020.0020.0000.0000.0000.000
197A230LEU0-0.048-0.02735.872-0.003-0.0030.0000.0000.0000.000
198A231LEU00.0130.01034.5760.0020.0020.0000.0000.0000.000
199A232GLN0-0.039-0.01738.6270.0010.0010.0000.0000.0000.000
200A233ASP-1-0.806-0.87542.4600.0240.0240.0000.0000.0000.000
201A234GLN00.0080.00544.370-0.001-0.0010.0000.0000.0000.000
202A235ARG10.8540.88646.887-0.018-0.0180.0000.0000.0000.000
203A236ILE0-0.0320.00650.564-0.001-0.0010.0000.0000.0000.000
204A237THR0-0.006-0.02353.5530.0010.0010.0000.0000.0000.000
205A238HIS00.0270.01757.116-0.001-0.0010.0000.0000.0000.000
206A239ILE00.0050.00560.2770.0010.0010.0000.0000.0000.000
207A240LEU00.0220.02163.142-0.001-0.0010.0000.0000.0000.000
208A241HIS0-0.039-0.03465.6900.0000.0000.0000.0000.0000.000
209A242VAL00.0060.01069.2740.0000.0000.0000.0000.0000.000
210A243SER0-0.0140.00472.0460.0000.0000.0000.0000.0000.000
211A244HIS00.0530.01975.7620.0000.0000.0000.0000.0000.000
212A245HIS00.0060.01978.8070.0000.0000.0000.0000.0000.000
213A246HIS0-0.077-0.03080.3370.0000.0000.0000.0000.0000.000