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: 1N17Z

Calculation Name: 4RZ9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RZ9

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NAV1

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2103451.125802
FMO2-HF: Nuclear repulsion 2028570.168897
FMO2-HF: Total energy -74880.956905
FMO2-MP2: Total energy -75096.178586


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-13.156-9.07715.085-5.782-13.377-0.02
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.020
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].
3A3ASN00.0130.0191.922-3.797-1.4125.065-2.634-4.814-0.008
4A4ARG10.9480.9681.846-10.384-10.1579.251-2.858-6.619-0.006
5A5THR00.025-0.0063.4660.2020.2590.0600.178-0.2940.000
6A6VAL00.0120.0346.9380.0220.0220.0000.0000.0000.000
7A7LYS10.9440.9529.585-0.024-0.0240.0000.0000.0000.000
8A8ASP-1-0.941-0.96411.3930.0290.0290.0000.0000.0000.000
9A9ALA00.0150.03111.388-0.001-0.0010.0000.0000.0000.000
10A10HIS0-0.022-0.00913.4650.0200.0200.0000.0000.0000.000
11A11SER0-0.083-0.04413.743-0.010-0.0100.0000.0000.0000.000
12A12ILE00.0460.01914.579-0.001-0.0010.0000.0000.0000.000
13A13HIS00.008-0.00515.766-0.007-0.0070.0000.0000.0000.000
14A14GLY0-0.0050.00517.463-0.005-0.0050.0000.0000.0000.000
15A15THR0-0.013-0.00512.071-0.001-0.0010.0000.0000.0000.000
16A16ASN00.0390.0416.2240.0300.0300.0000.0000.0000.000
17A17PRO00.1410.07010.343-0.023-0.0230.0000.0000.0000.000
18A18GLN00.029-0.0014.9350.3090.3090.0000.0000.0000.000
19A19TYR0-0.144-0.0835.3210.0640.0640.0000.0000.0000.000
20A20LEU00.0430.0389.560-0.005-0.0050.0000.0000.0000.000
21A21VAL00.0290.03310.2970.0070.0070.0000.0000.0000.000
22A22GLU-1-0.878-0.9419.946-0.164-0.1640.0000.0000.0000.000
23A23LYS10.9850.9905.5790.5340.5340.0000.0000.0000.000
24A24ILE0-0.027-0.0277.040-0.036-0.0360.0000.0000.0000.000
25A25ILE00.0720.0319.4190.0470.0470.0000.0000.0000.000
26A26ARG10.9210.9664.7070.3730.487-0.001-0.002-0.1100.000
27A27THR0-0.070-0.0315.6570.1170.1170.0000.0000.0000.000
28A28ARG10.9520.9816.5050.1560.1560.0000.0000.0000.000
29A29ILE00.0280.0159.0550.0150.0150.0000.0000.0000.000
30A30TYR0-0.054-0.0413.008-0.4330.8630.710-0.466-1.540-0.006
31A31GLU-1-0.954-0.9637.5880.0510.0510.0000.0000.0000.000
32A32SER0-0.043-0.03410.297-0.130-0.1300.0000.0000.0000.000
33A33LYS10.8640.91612.987-0.011-0.0110.0000.0000.0000.000
34A34TYR00.0910.03814.984-0.007-0.0070.0000.0000.0000.000
35A35TRP00.010-0.0087.0330.0100.0100.0000.0000.0000.000
36A36LYS10.8780.93010.867-0.185-0.1850.0000.0000.0000.000
37A37GLU-1-0.852-0.93512.705-0.012-0.0120.0000.0000.0000.000
38A38GLU-1-0.853-0.89615.9030.0120.0120.0000.0000.0000.000
39A39CYS0-0.038-0.01212.4070.0010.0010.0000.0000.0000.000
40A40PHE0-0.034-0.00711.342-0.020-0.0200.0000.0000.0000.000
41A41GLY0-0.015-0.01911.167-0.009-0.0090.0000.0000.0000.000
42A42LEU0-0.041-0.01112.7400.0030.0030.0000.0000.0000.000
43A43THR00.0550.04013.430-0.009-0.0090.0000.0000.0000.000
44A44ALA00.0350.00416.0390.0100.0100.0000.0000.0000.000
45A45GLU-1-0.876-0.95217.899-0.002-0.0020.0000.0000.0000.000
46A46LEU0-0.0140.00318.3560.0000.0000.0000.0000.0000.000
47A47VAL0-0.055-0.02316.5460.0060.0060.0000.0000.0000.000
48A48VAL00.0380.01119.1270.0050.0050.0000.0000.0000.000
49A49ASP-1-0.862-0.92922.0500.0020.0020.0000.0000.0000.000
50A50LYS10.8340.89718.206-0.017-0.0170.0000.0000.0000.000
51A51ALA0-0.024-0.02621.2640.0030.0030.0000.0000.0000.000
52A52MET0-0.043-0.01622.450-0.001-0.0010.0000.0000.0000.000
53A53GLU-1-0.961-0.95723.6250.0150.0150.0000.0000.0000.000
54A54LEU0-0.085-0.03120.2080.0020.0020.0000.0000.0000.000
55A55ARG10.9070.93924.237-0.020-0.0200.0000.0000.0000.000
56A56PHE0-0.084-0.05522.646-0.003-0.0030.0000.0000.0000.000
57A57VAL00.0400.03823.4710.0050.0050.0000.0000.0000.000
58A58GLY00.0580.01021.907-0.003-0.0030.0000.0000.0000.000
59A59GLY00.0540.03918.1930.0050.0050.0000.0000.0000.000
60A60VAL0-0.071-0.04514.7420.0130.0130.0000.0000.0000.000
61A61TYR00.0230.00817.872-0.010-0.0100.0000.0000.0000.000
62A62GLY00.0300.01919.8020.0030.0030.0000.0000.0000.000
63A63GLY00.0100.00220.562-0.002-0.0020.0000.0000.0000.000
64A64ASN0-0.013-0.00417.530-0.002-0.0020.0000.0000.0000.000
65A65ILE0-0.065-0.03313.7200.0030.0030.0000.0000.0000.000
66A66LYS10.9600.97815.046-0.011-0.0110.0000.0000.0000.000
67A67PRO00.0310.02012.866-0.011-0.0110.0000.0000.0000.000
68A68THR0-0.008-0.00715.7080.0030.0030.0000.0000.0000.000
69A69PRO00.0350.00516.9250.0150.0150.0000.0000.0000.000
70A70PHE00.0530.04017.3690.0110.0110.0000.0000.0000.000
71A71LEU00.0120.02714.0270.0040.0040.0000.0000.0000.000
72A72CYS0-0.070-0.03212.8770.0330.0330.0000.0000.0000.000
73A73LEU00.0370.01512.9800.0330.0330.0000.0000.0000.000
74A74THR00.0380.02215.149-0.009-0.0090.0000.0000.0000.000
75A75LEU0-0.052-0.0277.613-0.007-0.0070.0000.0000.0000.000
76A76LYS10.8640.9338.933-0.066-0.0660.0000.0000.0000.000
77A77MET00.0230.01611.644-0.033-0.0330.0000.0000.0000.000
78A78LEU0-0.016-0.00111.400-0.013-0.0130.0000.0000.0000.000
79A79GLN0-0.095-0.0455.6730.1390.1390.0000.0000.0000.000
80A80ILE0-0.015-0.0349.542-0.047-0.0470.0000.0000.0000.000
81A81GLN0-0.0290.01212.098-0.001-0.0010.0000.0000.0000.000
82A82PRO00.0070.00714.864-0.002-0.0020.0000.0000.0000.000
83A83GLU-1-0.835-0.91018.0010.0070.0070.0000.0000.0000.000
84A84LYS10.8450.90221.240-0.014-0.0140.0000.0000.0000.000
85A85ASP-1-0.908-0.96623.4770.0090.0090.0000.0000.0000.000
86A86ILE00.1390.08920.7850.0000.0000.0000.0000.0000.000
87A87ILE0-0.053-0.02219.5390.0020.0020.0000.0000.0000.000
88A88VAL0-0.051-0.03423.5790.0000.0000.0000.0000.0000.000
89A89GLU-1-0.893-0.94826.4660.0070.0070.0000.0000.0000.000
90A90PHE0-0.034-0.03920.7220.0010.0010.0000.0000.0000.000
91A91ILE0-0.051-0.02025.5750.0000.0000.0000.0000.0000.000
92A92LYS10.9100.94528.385-0.010-0.0100.0000.0000.0000.000
93A93ASN00.0450.04728.710-0.001-0.0010.0000.0000.0000.000
94A94GLU-1-0.926-0.96931.2290.0070.0070.0000.0000.0000.000
95A95ASP-1-0.929-0.94332.0080.0060.0060.0000.0000.0000.000
96A96PHE0-0.063-0.04628.6590.0010.0010.0000.0000.0000.000
97A97LYS10.9320.96729.439-0.010-0.0100.0000.0000.0000.000
98A98TYR00.0310.01625.2710.0000.0000.0000.0000.0000.000
99A99VAL00.0570.04824.7010.0030.0030.0000.0000.0000.000
100A100ARG10.9000.94925.182-0.009-0.0090.0000.0000.0000.000
101A101MET0-0.059-0.02525.7060.0000.0000.0000.0000.0000.000
102A102LEU0-0.0030.00218.5740.0010.0010.0000.0000.0000.000
103A103GLY00.0340.01021.5690.0020.0020.0000.0000.0000.000
104A104ALA00.0100.00323.282-0.001-0.0010.0000.0000.0000.000
105A105LEU00.0440.01118.900-0.001-0.0010.0000.0000.0000.000
106A106TYR00.0440.00715.2010.0000.0000.0000.0000.0000.000
107A107MET00.0260.01619.855-0.002-0.0020.0000.0000.0000.000
108A108ARG10.8410.91522.569-0.008-0.0080.0000.0000.0000.000
109A109LEU0-0.069-0.03416.292-0.002-0.0020.0000.0000.0000.000
110A110THR0-0.055-0.04816.605-0.003-0.0030.0000.0000.0000.000
111A111GLY00.0270.03019.3070.0010.0010.0000.0000.0000.000
112A112THR0-0.002-0.00522.920-0.001-0.0010.0000.0000.0000.000
113A113ALA00.0470.00825.4810.0000.0000.0000.0000.0000.000
114A114ILE00.0420.02428.0420.0000.0000.0000.0000.0000.000
115A115ASP-1-0.849-0.93226.5810.0130.0130.0000.0000.0000.000
116A116CYS0-0.052-0.01225.5510.0000.0000.0000.0000.0000.000
117A117TYR00.033-0.00527.8920.0000.0000.0000.0000.0000.000
118A118LYS10.9660.99431.324-0.011-0.0110.0000.0000.0000.000
119A119TYR0-0.074-0.05928.1330.0000.0000.0000.0000.0000.000
120A120LEU0-0.0070.00526.3460.0000.0000.0000.0000.0000.000
121A121GLU-1-0.741-0.83930.5030.0070.0070.0000.0000.0000.000
122A122PRO0-0.051-0.01633.1980.0000.0000.0000.0000.0000.000
123A123LEU0-0.014-0.01830.0150.0000.0000.0000.0000.0000.000
124A124TYR00.000-0.01334.0220.0000.0000.0000.0000.0000.000
125A125ASN0-0.061-0.02436.398-0.001-0.0010.0000.0000.0000.000
126A126ASP-1-0.791-0.86134.1690.0090.0090.0000.0000.0000.000
127A127TYR00.0440.01536.1560.0000.0000.0000.0000.0000.000
128A128ARG10.7660.86533.513-0.009-0.0090.0000.0000.0000.000
129A129LYS10.9910.99935.064-0.005-0.0050.0000.0000.0000.000
130A130ILE0-0.046-0.02728.7900.0010.0010.0000.0000.0000.000
131A131LYS10.9150.96428.916-0.015-0.0150.0000.0000.0000.000
132A132SER00.0430.01626.6180.0030.0030.0000.0000.0000.000
133A133GLN0-0.063-0.03423.1140.0030.0030.0000.0000.0000.000
134A134ASN00.0450.02824.1560.0010.0010.0000.0000.0000.000
135A135ARG10.9330.97219.3650.0030.0030.0000.0000.0000.000
136A136ASN0-0.008-0.02923.0180.0010.0010.0000.0000.0000.000
137A137GLY0-0.049-0.02824.5120.0000.0000.0000.0000.0000.000
138A138GLU-1-0.897-0.93425.3750.0070.0070.0000.0000.0000.000
139A139PHE0-0.068-0.04625.9490.0010.0010.0000.0000.0000.000
140A140GLU-1-0.867-0.92329.6810.0040.0040.0000.0000.0000.000
141A141LEU0-0.084-0.06431.0550.0020.0020.0000.0000.0000.000
142A142MET00.0250.04029.3530.0000.0000.0000.0000.0000.000
143A143HIS00.0320.00733.3440.0010.0010.0000.0000.0000.000
144A144VAL0-0.069-0.04131.3030.0010.0010.0000.0000.0000.000
145A145ASP-1-0.834-0.92931.8580.0070.0070.0000.0000.0000.000
146A146GLU-1-0.815-0.90932.9640.0060.0060.0000.0000.0000.000
147A147PHE0-0.020-0.01323.5600.0010.0010.0000.0000.0000.000
148A148ILE0-0.030-0.02628.4310.0000.0000.0000.0000.0000.000
149A149ASP-1-0.828-0.90930.0300.0050.0050.0000.0000.0000.000
150A150GLU-1-0.944-0.96827.3310.0070.0070.0000.0000.0000.000
151A151LEU0-0.086-0.04423.8700.0000.0000.0000.0000.0000.000
152A152LEU0-0.037-0.01726.603-0.001-0.0010.0000.0000.0000.000
153A153HIS0-0.070-0.02329.251-0.001-0.0010.0000.0000.0000.000
154A154SER0-0.022-0.00226.787-0.001-0.0010.0000.0000.0000.000
155A155GLU-1-0.957-0.98124.294-0.008-0.0080.0000.0000.0000.000
156A156ARG10.8910.93919.8080.0150.0150.0000.0000.0000.000
157A157VAL00.1120.06621.2250.0010.0010.0000.0000.0000.000
158A158CYS0-0.042-0.01119.2950.0020.0020.0000.0000.0000.000
159A159ASP-1-0.897-0.95817.3820.0170.0170.0000.0000.0000.000
160A160ILE0-0.030-0.01115.192-0.006-0.0060.0000.0000.0000.000
161A161ILE0-0.030-0.02017.1410.0010.0010.0000.0000.0000.000
162A162LEU00.0030.01118.2550.0000.0000.0000.0000.0000.000
163A163PRO0-0.0040.00918.290-0.003-0.0030.0000.0000.0000.000
164A164ARG10.9430.96220.7240.0000.0000.0000.0000.0000.000
165A165LEU00.0260.03624.0740.0020.0020.0000.0000.0000.000
166A166GLN0-0.0100.00626.773-0.002-0.0020.0000.0000.0000.000
167A167LYS10.9830.98729.991-0.003-0.0030.0000.0000.0000.000
168A168ARG10.8160.85833.166-0.006-0.0060.0000.0000.0000.000
169A169TYR00.0530.02135.2240.0000.0000.0000.0000.0000.000
170A170VAL0-0.0030.00634.4810.0000.0000.0000.0000.0000.000
171A171LEU0-0.023-0.01831.4410.0010.0010.0000.0000.0000.000
172A172GLU-1-0.885-0.93235.7120.0070.0070.0000.0000.0000.000
173A173GLU-1-0.944-0.97739.2090.0070.0070.0000.0000.0000.000
174A174ALA0-0.074-0.02036.6010.0000.0000.0000.0000.0000.000
175A175GLU-1-0.939-0.97038.2650.0100.0100.0000.0000.0000.000
176A176GLN0-0.091-0.05133.1430.0000.0000.0000.0000.0000.000
177A177LEU0-0.072-0.04533.7230.0000.0000.0000.0000.0000.000
178A178GLU-1-0.913-0.94637.5150.0070.0070.0000.0000.0000.000
179A179PRO0-0.0140.00940.4280.0000.0000.0000.0000.0000.000