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: 6GNLZ

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 OptAll
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 -2019355.67182
FMO2-HF: Nuclear repulsion 1938703.920926
FMO2-HF: Total energy -80651.750894
FMO2-MP2: Total energy -80888.067561


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.
-6.647-2.4815.255-5.114-4.309-0.04
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 : 0.002
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].
3A34LEU0-0.035-0.0333.8830.0941.218-0.012-0.656-0.4570.002
4A35GLU-1-0.788-0.8467.2730.6700.6700.0000.0000.0000.000
5A36THR00.012-0.0289.530-0.038-0.0380.0000.0000.0000.000
6A37SER0-0.064-0.04213.2960.0760.0760.0000.0000.0000.000
7A38ASP-1-0.829-0.90016.514-0.060-0.0600.0000.0000.0000.000
8A39VAL0-0.023-0.02118.854-0.016-0.0160.0000.0000.0000.000
9A40VAL00.0330.02920.1430.0150.0150.0000.0000.0000.000
10A41THR0-0.007-0.01222.531-0.003-0.0030.0000.0000.0000.000
11A42VAL0-0.0110.00426.1080.0040.0040.0000.0000.0000.000
12A43VAL00.0160.02128.7060.0000.0000.0000.0000.0000.000
13A44LEU0-0.012-0.01832.091-0.004-0.0040.0000.0000.0000.000
14A45GLY00.0170.01133.9010.0040.0040.0000.0000.0000.000
15A46GLN0-0.047-0.01530.3190.0020.0020.0000.0000.0000.000
16A47ASP-1-0.789-0.86927.696-0.050-0.0500.0000.0000.0000.000
17A48ALA0-0.002-0.00125.0270.0070.0070.0000.0000.0000.000
18A49LYS10.8540.94516.6530.0720.0720.0000.0000.0000.000
19A50LEU00.0110.01519.3120.0110.0110.0000.0000.0000.000
20A51PRO0-0.030-0.02714.736-0.016-0.0160.0000.0000.0000.000
21A52CYS0-0.0410.00512.725-0.054-0.0540.0000.0000.0000.000
22A53PHE0-0.0190.0068.261-0.013-0.0130.0000.0000.0000.000
23A54TYR0-0.031-0.0493.092-0.958-0.3200.124-0.328-0.435-0.002
24A55ARG10.8050.8804.525-0.628-0.492-0.001-0.037-0.0980.000
25A56GLY00.0460.0152.376-1.795-1.0733.873-2.959-1.635-0.022
26A57ASP-1-0.895-0.9533.3480.319-0.061-0.0030.497-0.1150.000
27A58SER0-0.110-0.0745.343-0.261-0.282-0.001-0.0040.0260.000
28A59GLY0-0.019-0.0037.334-0.013-0.0130.0000.0000.0000.000
29A60GLU-1-0.821-0.8832.555-4.752-2.8051.275-1.627-1.595-0.018
30A61GLN0-0.0030.0057.3970.1190.1190.0000.0000.0000.000
31A62VAL00.0350.0158.930-0.129-0.1290.0000.0000.0000.000
32A63GLY0-0.024-0.00610.7130.1000.1000.0000.0000.0000.000
33A64GLN0-0.024-0.02013.9960.0910.0910.0000.0000.0000.000
34A65VAL00.0180.01812.756-0.088-0.0880.0000.0000.0000.000
35A66ALA0-0.003-0.00515.3900.0560.0560.0000.0000.0000.000
36A67TRP00.006-0.00416.598-0.034-0.0340.0000.0000.0000.000
37A68ALA00.0320.01519.9950.0220.0220.0000.0000.0000.000
38A69ARG10.7980.86922.0800.0880.0880.0000.0000.0000.000
39A70VAL0-0.027-0.01421.848-0.001-0.0010.0000.0000.0000.000
40A71ASP-1-0.814-0.87924.945-0.095-0.0950.0000.0000.0000.000
41A72ALA00.0020.00728.736-0.003-0.0030.0000.0000.0000.000
42A73GLY0-0.028-0.03230.0470.0090.0090.0000.0000.0000.000
43A74GLU-1-0.964-0.96132.394-0.078-0.0780.0000.0000.0000.000
44A75GLY0-0.037-0.02830.925-0.004-0.0040.0000.0000.0000.000
45A76ALA0-0.014-0.01025.654-0.007-0.0070.0000.0000.0000.000
46A77GLN0-0.0010.01127.0590.0010.0010.0000.0000.0000.000
47A78GLU-1-0.907-0.95223.442-0.197-0.1970.0000.0000.0000.000
48A79LEU0-0.025-0.01123.6120.0150.0150.0000.0000.0000.000
49A80ALA00.005-0.00822.5060.0150.0150.0000.0000.0000.000
50A81LEU0-0.0100.02120.202-0.027-0.0270.0000.0000.0000.000
51A82LEU0-0.003-0.00416.1340.0290.0290.0000.0000.0000.000
52A83HIS00.0220.01417.735-0.028-0.0280.0000.0000.0000.000
53A84SER0-0.019-0.01515.3810.0370.0370.0000.0000.0000.000
54A85LYS10.8770.94617.3290.1660.1660.0000.0000.0000.000
55A86TYR0-0.013-0.03421.0310.0250.0250.0000.0000.0000.000
56A87GLY00.0220.03121.5350.0120.0120.0000.0000.0000.000
57A88LEU0-0.038-0.03021.190-0.022-0.0220.0000.0000.0000.000
58A89HIS0-0.0120.00823.4620.0230.0230.0000.0000.0000.000
59A90VAL00.0140.00524.834-0.013-0.0130.0000.0000.0000.000
60A91SER00.0050.00426.7910.0070.0070.0000.0000.0000.000
61A92PRO00.0590.01128.3940.0070.0070.0000.0000.0000.000
62A93ALA0-0.032-0.00630.5440.0070.0070.0000.0000.0000.000
63A94TYR0-0.058-0.05228.4690.0030.0030.0000.0000.0000.000
64A95GLU-1-0.922-0.95130.077-0.081-0.0810.0000.0000.0000.000
65A96GLY0-0.032-0.01431.6220.0060.0060.0000.0000.0000.000
66A97ARG10.7550.85230.1920.0740.0740.0000.0000.0000.000
67A98VAL0-0.0120.00224.0650.0000.0000.0000.0000.0000.000
68A99GLU-1-0.856-0.91125.203-0.069-0.0690.0000.0000.0000.000
69A100GLN00.0310.01019.760-0.002-0.0020.0000.0000.0000.000
70A101PRO00.0130.00518.5730.0140.0140.0000.0000.0000.000
71A102PRO00.0320.02421.789-0.007-0.0070.0000.0000.0000.000
72A103PRO0-0.0350.00321.610-0.001-0.0010.0000.0000.0000.000
73A104PRO00.004-0.01219.6690.0070.0070.0000.0000.0000.000
74A105ARG10.9020.93616.6710.1180.1180.0000.0000.0000.000
75A106ASN00.0310.01610.387-0.052-0.0520.0000.0000.0000.000
76A107PRO00.0180.00212.874-0.023-0.0230.0000.0000.0000.000
77A108LEU00.0260.0216.938-0.031-0.0310.0000.0000.0000.000
78A109ASP-1-0.865-0.89410.428-0.254-0.2540.0000.0000.0000.000
79A110GLY00.0260.01612.8260.0230.0230.0000.0000.0000.000
80A111SER0-0.052-0.07414.8410.0220.0220.0000.0000.0000.000
81A112VAL0-0.031-0.00816.7940.0090.0090.0000.0000.0000.000
82A113LEU0-0.033-0.02520.5830.0110.0110.0000.0000.0000.000
83A114LEU00.0150.01723.794-0.002-0.0020.0000.0000.0000.000
84A115ARG10.8140.88126.0970.0620.0620.0000.0000.0000.000
85A116ASN0-0.046-0.04929.3010.0000.0000.0000.0000.0000.000
86A117ALA0-0.0010.02428.847-0.003-0.0030.0000.0000.0000.000
87A118VAL00.028-0.00530.8360.0080.0080.0000.0000.0000.000
88A119GLN0-0.017-0.03032.385-0.001-0.0010.0000.0000.0000.000
89A120ALA00.009-0.00333.731-0.002-0.0020.0000.0000.0000.000
90A121ASP-1-0.706-0.81528.661-0.078-0.0780.0000.0000.0000.000
91A122GLU-1-0.802-0.84028.350-0.047-0.0470.0000.0000.0000.000
92A123GLY00.0470.02127.4470.0000.0000.0000.0000.0000.000
93A124GLU-1-0.882-0.93522.388-0.132-0.1320.0000.0000.0000.000
94A125TYR0-0.055-0.06221.195-0.001-0.0010.0000.0000.0000.000
95A126GLU-1-0.806-0.88817.290-0.318-0.3180.0000.0000.0000.000
96A128ARG10.8670.90514.2810.3710.3710.0000.0000.0000.000
97A129VAL00.0370.0069.0480.0500.0500.0000.0000.0000.000
98A130SER0-0.032-0.02311.542-0.036-0.0360.0000.0000.0000.000
99A131THR0-0.011-0.0045.9410.2350.2350.0000.0000.0000.000
100A132PHE0-0.0010.0228.9930.0070.0070.0000.0000.0000.000
101A133PRO00.037-0.0057.7360.0350.0350.0000.0000.0000.000
102A134ALA00.0010.0075.0140.1250.1250.0000.0000.0000.000
103A135GLY00.0330.0267.0470.0660.0660.0000.0000.0000.000
104A136SER0-0.056-0.0349.406-0.021-0.0210.0000.0000.0000.000
105A137PHE00.0040.0075.4610.0260.0260.0000.0000.0000.000
106A138GLN00.0100.00410.4940.1530.1530.0000.0000.0000.000
107A139ALA00.0190.01911.690-0.033-0.0330.0000.0000.0000.000
108A140ARG10.8050.88213.7290.2320.2320.0000.0000.0000.000
109A141LEU00.0030.02616.8260.0170.0170.0000.0000.0000.000
110A142ARG10.8790.92519.3380.0370.0370.0000.0000.0000.000
111A143LEU0-0.0180.00623.1100.0130.0130.0000.0000.0000.000
112A144ARG10.7930.87525.2490.0320.0320.0000.0000.0000.000
113A145VAL00.0460.01128.0810.0050.0050.0000.0000.0000.000
114A146LEU0-0.040-0.02330.8650.0010.0010.0000.0000.0000.000
115A147VAL00.0310.01633.3440.0010.0010.0000.0000.0000.000
116A148PRO00.0100.00536.7860.0010.0010.0000.0000.0000.000
117A149PRO0-0.008-0.00639.387-0.002-0.0020.0000.0000.0000.000
118A150LEU0-0.005-0.00343.0920.0010.0010.0000.0000.0000.000
119A151PRO0-0.031-0.00146.101-0.001-0.0010.0000.0000.0000.000
120A152SER0-0.018-0.01648.686-0.001-0.0010.0000.0000.0000.000
121A153LEU0-0.008-0.01052.4710.0000.0000.0000.0000.0000.000
122A154ASN0-0.0110.00155.555-0.001-0.0010.0000.0000.0000.000
123A155PRO00.000-0.01158.7510.0000.0000.0000.0000.0000.000
124A156GLY00.0060.01362.018-0.001-0.0010.0000.0000.0000.000
125A157PRO0-0.046-0.03064.0380.0000.0000.0000.0000.0000.000
126A158ALA00.0090.01167.7720.0000.0000.0000.0000.0000.000
127A159LEU0-0.017-0.00566.5940.0000.0000.0000.0000.0000.000
128A160GLU-1-0.808-0.87971.1140.0000.0000.0000.0000.0000.000
129A161GLU-1-0.849-0.94074.2150.0030.0030.0000.0000.0000.000
130A162GLY0-0.0080.01975.7070.0000.0000.0000.0000.0000.000
131A163GLN0-0.064-0.02269.9170.0000.0000.0000.0000.0000.000
132A164GLY00.0460.01172.0960.0000.0000.0000.0000.0000.000
133A165LEU0-0.039-0.02264.6210.0000.0000.0000.0000.0000.000
134A166THR0-0.018-0.00666.729-0.001-0.0010.0000.0000.0000.000
135A167LEU00.0040.01460.0840.0000.0000.0000.0000.0000.000
136A168ALA00.0350.01762.1340.0000.0000.0000.0000.0000.000
137A169ALA0-0.018-0.01559.1520.0000.0000.0000.0000.0000.000
138A170SER00.0110.00856.2700.0000.0000.0000.0000.0000.000
139A171CYS0-0.057-0.00251.6910.0000.0000.0000.0000.0000.000
140A172THR0-0.013-0.00749.6660.0000.0000.0000.0000.0000.000
141A173ALA00.0200.00645.5980.0000.0000.0000.0000.0000.000
142A174GLU-1-0.798-0.86542.969-0.020-0.0200.0000.0000.0000.000
143A175GLY00.0320.02440.4030.0000.0000.0000.0000.0000.000
144A176SER0-0.031-0.01135.8060.0000.0000.0000.0000.0000.000
145A177PRO0-0.009-0.01834.116-0.001-0.0010.0000.0000.0000.000
146A178ALA00.0410.00836.7580.0000.0000.0000.0000.0000.000
147A179PRO0-0.0240.01440.1970.0020.0020.0000.0000.0000.000
148A180SER0-0.007-0.00242.1270.0000.0000.0000.0000.0000.000
149A181VAL0-0.019-0.02244.2920.0010.0010.0000.0000.0000.000
150A182THR0-0.042-0.01547.8500.0010.0010.0000.0000.0000.000
151A183TRP00.004-0.02450.391-0.001-0.0010.0000.0000.0000.000
152A184ASP-1-0.823-0.88653.4600.0110.0110.0000.0000.0000.000
153A185THR0-0.034-0.04655.394-0.001-0.0010.0000.0000.0000.000
154A186GLU-1-0.879-0.92259.2150.0110.0110.0000.0000.0000.000
155A187VAL0-0.069-0.02562.2530.0000.0000.0000.0000.0000.000
156A188LYS10.9470.95862.369-0.009-0.0090.0000.0000.0000.000
157A189GLY00.0370.00962.466-0.001-0.0010.0000.0000.0000.000
158A190THR0-0.061-0.02259.9340.0010.0010.0000.0000.0000.000
159A191THR00.0220.01355.3980.0000.0000.0000.0000.0000.000
160A192SER0-0.082-0.04756.0100.0000.0000.0000.0000.0000.000
161A193SER00.016-0.00850.9360.0000.0000.0000.0000.0000.000
162A194ARG10.8610.93650.9140.0040.0040.0000.0000.0000.000
163A195SER00.0140.00944.5940.0000.0000.0000.0000.0000.000
164A196PHE00.0140.01546.7250.0000.0000.0000.0000.0000.000
165A197LYS10.9490.97637.8160.0170.0170.0000.0000.0000.000
166A198HIS0-0.024-0.02842.1700.0000.0000.0000.0000.0000.000
167A199SER00.004-0.02040.0630.0000.0000.0000.0000.0000.000
168A200ARG10.8800.93731.7500.0540.0540.0000.0000.0000.000
169A201SER0-0.027-0.01836.8790.0000.0000.0000.0000.0000.000
170A202ALA0-0.032-0.02739.4490.0000.0000.0000.0000.0000.000
171A203ALA00.0560.04442.3380.0010.0010.0000.0000.0000.000
172A204VAL0-0.016-0.00245.1000.0000.0000.0000.0000.0000.000
173A205THR00.003-0.01447.2630.0000.0000.0000.0000.0000.000
174A206SER00.0290.00451.0060.0010.0010.0000.0000.0000.000
175A207GLU-1-0.800-0.88053.114-0.003-0.0030.0000.0000.0000.000
176A208PHE00.0370.02956.8700.0010.0010.0000.0000.0000.000
177A209HIS0-0.037-0.02659.2870.0000.0000.0000.0000.0000.000
178A210LEU00.031-0.00162.7210.0010.0010.0000.0000.0000.000
179A211VAL00.0100.01365.636-0.001-0.0010.0000.0000.0000.000
180A212PRO0-0.022-0.00969.0030.0010.0010.0000.0000.0000.000
181A213SER00.0740.02770.5140.0000.0000.0000.0000.0000.000
182A214ARG10.8750.92271.728-0.002-0.0020.0000.0000.0000.000
183A215SER0-0.056-0.03571.8620.0000.0000.0000.0000.0000.000
184A216MET00.0030.00667.5950.0000.0000.0000.0000.0000.000
185A217ASN0-0.018-0.00968.056-0.001-0.0010.0000.0000.0000.000
186A218GLY0-0.036-0.02267.9520.0000.0000.0000.0000.0000.000
187A219GLN0-0.0160.00665.0860.0010.0010.0000.0000.0000.000
188A220PRO00.0120.01260.010-0.001-0.0010.0000.0000.0000.000
189A221LEU00.0050.02158.2540.0010.0010.0000.0000.0000.000
190A222THR0-0.011-0.00653.864-0.001-0.0010.0000.0000.0000.000
191A224VAL0-0.025-0.02048.1590.0000.0000.0000.0000.0000.000
192A225VAL0-0.013-0.01144.6340.0000.0000.0000.0000.0000.000
193A226SER0-0.002-0.00241.6040.0000.0000.0000.0000.0000.000
194A227HIS00.003-0.02936.4650.0000.0000.0000.0000.0000.000
195A228PRO00.008-0.00234.0280.0010.0010.0000.0000.0000.000
196A229GLY0-0.007-0.00234.5810.0010.0010.0000.0000.0000.000
197A230LEU0-0.043-0.02235.723-0.002-0.0020.0000.0000.0000.000
198A231LEU00.0000.00434.4920.0020.0020.0000.0000.0000.000
199A232GLN0-0.049-0.03738.6000.0020.0020.0000.0000.0000.000
200A233ASP-1-0.811-0.87442.4780.0100.0100.0000.0000.0000.000
201A234GLN00.0230.02244.5270.0000.0000.0000.0000.0000.000
202A235ARG10.8420.88446.853-0.009-0.0090.0000.0000.0000.000
203A236ILE0-0.040-0.00750.575-0.001-0.0010.0000.0000.0000.000
204A237THR0-0.003-0.02353.4510.0000.0000.0000.0000.0000.000
205A238HIS00.0280.02057.022-0.001-0.0010.0000.0000.0000.000
206A239ILE00.0130.00060.4000.0010.0010.0000.0000.0000.000
207A240LEU00.0220.03062.927-0.001-0.0010.0000.0000.0000.000
208A241HIS0-0.036-0.03365.8240.0000.0000.0000.0000.0000.000
209A242VAL0-0.0040.00969.4220.0000.0000.0000.0000.0000.000
210A243SER0-0.0100.01072.2100.0000.0000.0000.0000.0000.000
211A244HIS00.0570.01175.9080.0000.0000.0000.0000.0000.000
212A245HIS0-0.019-0.00478.6790.0000.0000.0000.0000.0000.000
213A246HIS0-0.105-0.07480.3030.0000.0000.0000.0000.0000.000