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: N9RZQ

Calculation Name: 4RZI-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RZI

Chain ID: B

ChEMBL ID:

UniProt ID: P73826

Base Structure: X-ray

Registration Date: 2023-09-20

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 239
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2751353.17157
FMO2-HF: Nuclear repulsion 2663398.581364
FMO2-HF: Total energy -87954.590206
FMO2-MP2: Total energy -88212.780007


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(B:2:LEU)


Summations of interaction energy for fragment #1(B:2:LEU)
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.
-1.5590.602-0.016-1.171-0.9740.001
Interaction energy analysis for fragmet #1(B:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.028
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].
3B4LEU00.0050.0033.8790.1672.328-0.016-1.171-0.9740.001
4B5GLY00.0490.0307.301-0.226-0.2260.0000.0000.0000.000
5B6LEU0-0.060-0.0748.9800.0480.0480.0000.0000.0000.000
6B7GLU-1-0.769-0.8716.514-0.641-0.6410.0000.0000.0000.000
7B8ASP-1-0.905-0.95811.202-0.114-0.1140.0000.0000.0000.000
8B9LYS10.8560.95112.843-0.050-0.0500.0000.0000.0000.000
9B10VAL00.0370.03215.985-0.024-0.0240.0000.0000.0000.000
10B11ILE0-0.023-0.01715.8850.0290.0290.0000.0000.0000.000
11B12VAL00.0300.02820.429-0.013-0.0130.0000.0000.0000.000
12B13VAL0-0.020-0.00922.0730.0110.0110.0000.0000.0000.000
13B14THR00.0480.02224.833-0.004-0.0040.0000.0000.0000.000
14B15GLY00.002-0.00527.7710.0000.0000.0000.0000.0000.000
15B16GLY0-0.016-0.01426.624-0.003-0.0030.0000.0000.0000.000
16B17ASN00.0260.01626.888-0.014-0.0140.0000.0000.0000.000
17B18ARG10.8570.90929.1700.0560.0560.0000.0000.0000.000
18B19GLY00.004-0.00128.3000.0020.0020.0000.0000.0000.000
19B20ILE00.011-0.01423.487-0.009-0.0090.0000.0000.0000.000
20B21GLY00.0630.02923.668-0.007-0.0070.0000.0000.0000.000
21B22ALA00.0280.03023.949-0.007-0.0070.0000.0000.0000.000
22B23ALA0-0.021-0.01321.641-0.016-0.0160.0000.0000.0000.000
23B24ILE0-0.027-0.01819.283-0.019-0.0190.0000.0000.0000.000
24B25VAL0-0.017-0.00919.064-0.016-0.0160.0000.0000.0000.000
25B26LYS10.8550.90318.5970.2330.2330.0000.0000.0000.000
26B27LEU0-0.0080.00213.785-0.023-0.0230.0000.0000.0000.000
27B28LEU0-0.010-0.02014.668-0.044-0.0440.0000.0000.0000.000
28B29GLN00.0930.06214.538-0.029-0.0290.0000.0000.0000.000
29B30GLU-1-0.854-0.88214.040-0.326-0.3260.0000.0000.0000.000
30B31MET0-0.081-0.04410.399-0.071-0.0710.0000.0000.0000.000
31B32GLY00.0040.00610.424-0.039-0.0390.0000.0000.0000.000
32B33ALA0-0.0300.00712.4730.0480.0480.0000.0000.0000.000
33B34LYS10.8460.92015.0200.1070.1070.0000.0000.0000.000
34B35VAL0-0.050-0.02618.1130.0250.0250.0000.0000.0000.000
35B36ALA00.0700.04720.489-0.001-0.0010.0000.0000.0000.000
36B37PHE0-0.052-0.01624.1710.0050.0050.0000.0000.0000.000
37B38THR00.0470.02526.6600.0020.0020.0000.0000.0000.000
38B39ASP-1-0.848-0.93730.292-0.044-0.0440.0000.0000.0000.000
39B40LEU0-0.015-0.00732.9070.0020.0020.0000.0000.0000.000
40B41ALA0-0.0170.00034.9020.0010.0010.0000.0000.0000.000
41B42THR0-0.009-0.01531.4410.0000.0000.0000.0000.0000.000
42B43ASP-1-0.828-0.87332.614-0.059-0.0590.0000.0000.0000.000
43B44GLY0-0.0120.02029.234-0.002-0.0020.0000.0000.0000.000
44B45GLY0-0.014-0.04629.6930.0060.0060.0000.0000.0000.000
45B46ASN0-0.036-0.03322.217-0.009-0.0090.0000.0000.0000.000
46B47THR00.0380.00825.8550.0080.0080.0000.0000.0000.000
47B48GLU-1-0.954-0.97319.944-0.197-0.1970.0000.0000.0000.000
48B49ALA0-0.021-0.01222.612-0.004-0.0040.0000.0000.0000.000
49B50LEU0-0.0020.00923.9090.0080.0080.0000.0000.0000.000
50B51GLY00.0230.00926.6910.0040.0040.0000.0000.0000.000
51B52VAL0-0.009-0.01329.2550.0030.0030.0000.0000.0000.000
52B53VAL0-0.031-0.01731.7090.0020.0020.0000.0000.0000.000
53B54ALA00.003-0.00433.6340.0030.0030.0000.0000.0000.000
54B55ASN00.0630.04035.486-0.001-0.0010.0000.0000.0000.000
55B56VAL00.0330.00932.3710.0020.0020.0000.0000.0000.000
56B57THR0-0.101-0.07835.4730.0040.0040.0000.0000.0000.000
57B58ASP-1-0.862-0.92738.706-0.004-0.0040.0000.0000.0000.000
58B59LEU00.017-0.00336.458-0.001-0.0010.0000.0000.0000.000
59B60GLU-1-0.910-0.94637.754-0.001-0.0010.0000.0000.0000.000
60B61SER0-0.0280.00337.721-0.002-0.0020.0000.0000.0000.000
61B62MET0-0.028-0.00430.982-0.004-0.0040.0000.0000.0000.000
62B63THR0-0.023-0.03433.3190.0010.0010.0000.0000.0000.000
63B64ALA0-0.0050.01034.4620.0000.0000.0000.0000.0000.000
64B65ALA00.0390.01831.561-0.002-0.0020.0000.0000.0000.000
65B66ALA0-0.015-0.00529.744-0.004-0.0040.0000.0000.0000.000
66B67ALA0-0.0050.00529.889-0.001-0.0010.0000.0000.0000.000
67B68GLU-1-0.822-0.89131.201-0.040-0.0400.0000.0000.0000.000
68B69ILE0-0.005-0.02125.495-0.005-0.0050.0000.0000.0000.000
69B70THR0-0.068-0.05626.500-0.002-0.0020.0000.0000.0000.000
70B71ASP-1-0.995-0.98727.006-0.029-0.0290.0000.0000.0000.000
71B72LYS10.8370.91127.5200.0410.0410.0000.0000.0000.000
72B73LEU0-0.043-0.01622.207-0.010-0.0100.0000.0000.0000.000
73B74GLY00.0070.02122.323-0.004-0.0040.0000.0000.0000.000
74B75PRO0-0.037-0.03821.9180.0020.0020.0000.0000.0000.000
75B76VAL00.0150.01721.6870.0000.0000.0000.0000.0000.000
76B77TYR0-0.058-0.03315.1250.0270.0270.0000.0000.0000.000
77B78GLY00.0240.00219.5480.0210.0210.0000.0000.0000.000
78B79VAL00.0080.00620.334-0.014-0.0140.0000.0000.0000.000
79B80VAL0-0.003-0.00820.5770.0110.0110.0000.0000.0000.000
80B81ALA0-0.022-0.00623.443-0.008-0.0080.0000.0000.0000.000
81B82ASN0-0.048-0.06125.2450.0040.0040.0000.0000.0000.000
82B83ALA0-0.0160.01827.313-0.002-0.0020.0000.0000.0000.000
83B84GLY0-0.020-0.01830.8340.0060.0060.0000.0000.0000.000
84B85ILE0-0.035-0.01533.163-0.004-0.0040.0000.0000.0000.000
85B86THR0-0.030-0.04136.1670.0030.0030.0000.0000.0000.000
86B87LYS10.8900.93638.5700.0080.0080.0000.0000.0000.000
87B88ASP-1-0.785-0.86239.758-0.009-0.0090.0000.0000.0000.000
88B89ASN00.0600.01342.693-0.001-0.0010.0000.0000.0000.000
89B90PHE0-0.027-0.01645.4560.0010.0010.0000.0000.0000.000
90B91PHE00.0670.01846.6120.0000.0000.0000.0000.0000.000
91B92PRO0-0.005-0.00548.2320.0000.0000.0000.0000.0000.000
92B93LYS10.9010.95650.1470.0040.0040.0000.0000.0000.000
93B94LEU0-0.061-0.00144.822-0.001-0.0010.0000.0000.0000.000
94B95THR00.020-0.01248.9160.0010.0010.0000.0000.0000.000
95B96PRO00.0670.00948.5180.0000.0000.0000.0000.0000.000
96B97ALA00.0580.04547.8770.0000.0000.0000.0000.0000.000
97B98ASP-1-0.817-0.88545.412-0.007-0.0070.0000.0000.0000.000
98B99TRP0-0.007-0.01042.7680.0010.0010.0000.0000.0000.000
99B100ASP-1-0.862-0.94143.2190.0040.0040.0000.0000.0000.000
100B101ALA0-0.030-0.00942.4600.0000.0000.0000.0000.0000.000
101B102VAL00.015-0.00338.6240.0000.0000.0000.0000.0000.000
102B103LEU00.0070.00338.1850.0010.0010.0000.0000.0000.000
103B104ASN0-0.021-0.00238.7060.0040.0040.0000.0000.0000.000
104B105VAL00.0420.02634.7970.0010.0010.0000.0000.0000.000
105B106ASN0-0.030-0.01633.946-0.002-0.0020.0000.0000.0000.000
106B107LEU0-0.015-0.00333.6090.0030.0030.0000.0000.0000.000
107B108LYS10.8950.94634.793-0.005-0.0050.0000.0000.0000.000
108B109GLY00.0610.03535.2780.0010.0010.0000.0000.0000.000
109B110VAL0-0.0140.00729.493-0.001-0.0010.0000.0000.0000.000
110B111ALA00.0380.01131.2450.0020.0020.0000.0000.0000.000
111B112TYR0-0.056-0.04533.0830.0020.0020.0000.0000.0000.000
112B113SER00.009-0.01229.615-0.004-0.0040.0000.0000.0000.000
113B114ILE0-0.014-0.00727.408-0.001-0.0010.0000.0000.0000.000
114B115LYS10.9390.97029.726-0.022-0.0220.0000.0000.0000.000
115B116PRO00.0050.00731.1620.0030.0030.0000.0000.0000.000
116B117PHE00.0460.02326.416-0.002-0.0020.0000.0000.0000.000
117B118ILE0-0.021-0.00726.9550.0060.0060.0000.0000.0000.000
118B119GLU-1-0.926-0.95728.2180.0420.0420.0000.0000.0000.000
119B120GLY00.0530.02227.7280.0040.0040.0000.0000.0000.000
120B121MET0-0.056-0.02622.9430.0090.0090.0000.0000.0000.000
121B122TYR00.009-0.00324.4090.0160.0160.0000.0000.0000.000
122B123GLU-1-0.919-0.95126.6780.0520.0520.0000.0000.0000.000
123B124ARG10.8750.93121.971-0.041-0.0410.0000.0000.0000.000
124B125LYS10.7910.90521.860-0.084-0.0840.0000.0000.0000.000
125B126ALA00.0170.01318.4280.0260.0260.0000.0000.0000.000
126B127GLY00.0410.00819.221-0.024-0.0240.0000.0000.0000.000
127B128SER0-0.101-0.03717.2050.0180.0180.0000.0000.0000.000
128B129ILE00.0320.00619.686-0.025-0.0250.0000.0000.0000.000
129B130VAL0-0.005-0.01418.9040.0130.0130.0000.0000.0000.000
130B131ALA00.0370.03122.349-0.014-0.0140.0000.0000.0000.000
131B132ILE0-0.008-0.00522.7820.0040.0040.0000.0000.0000.000
132B133SER0-0.010-0.01226.002-0.002-0.0020.0000.0000.0000.000
133B134SER00.012-0.00527.8510.0040.0040.0000.0000.0000.000
134B135ILE00.0450.03029.3810.0060.0060.0000.0000.0000.000
135B136SER0-0.004-0.02330.5090.0030.0030.0000.0000.0000.000
136B137GLY0-0.0190.01632.3460.0010.0010.0000.0000.0000.000
137B138GLU-1-0.841-0.89728.2670.0400.0400.0000.0000.0000.000
138B139ARG10.8300.94032.670-0.001-0.0010.0000.0000.0000.000
139B140GLY00.0420.03634.8590.0000.0000.0000.0000.0000.000
140B141ASN0-0.042-0.06036.827-0.001-0.0010.0000.0000.0000.000
141B142VAL00.0310.01538.8780.0010.0010.0000.0000.0000.000
142B143GLY0-0.027-0.00141.624-0.002-0.0020.0000.0000.0000.000
143B144GLN00.0130.00036.4900.0000.0000.0000.0000.0000.000
144B145THR0-0.0120.00339.6790.0020.0020.0000.0000.0000.000
145B146ASN00.0220.00541.2270.0020.0020.0000.0000.0000.000
146B147TYR00.0220.00631.8130.0020.0020.0000.0000.0000.000
147B148SER0-0.023-0.01835.8650.0020.0020.0000.0000.0000.000
148B149ALA00.0510.02736.0290.0030.0030.0000.0000.0000.000
149B150THR0-0.031-0.02835.7350.0020.0020.0000.0000.0000.000
150B151LYS10.8640.92429.7420.0010.0010.0000.0000.0000.000
151B152ALA00.0280.02631.4210.0040.0040.0000.0000.0000.000
152B153GLY0-0.006-0.00533.2700.0050.0050.0000.0000.0000.000
153B154VAL00.002-0.00629.2720.0040.0040.0000.0000.0000.000
154B155ILE00.0250.02427.9360.0070.0070.0000.0000.0000.000
155B156GLY0-0.0050.00629.4960.0080.0080.0000.0000.0000.000
156B157MET0-0.043-0.01431.0280.0040.0040.0000.0000.0000.000
157B158MET00.0100.00425.9180.0050.0050.0000.0000.0000.000
158B159LYS10.8850.94126.432-0.072-0.0720.0000.0000.0000.000
159B160SER0-0.048-0.02528.5780.0070.0070.0000.0000.0000.000
160B161LEU00.0430.02227.2480.0030.0030.0000.0000.0000.000
161B162ALA0-0.0120.00424.9220.0060.0060.0000.0000.0000.000
162B163ARG10.9020.93926.277-0.085-0.0850.0000.0000.0000.000
163B164GLU-1-0.960-0.96428.8000.0640.0640.0000.0000.0000.000
164B165GLY00.000-0.00526.3970.0010.0010.0000.0000.0000.000
165B166ALA00.0440.02424.4410.0100.0100.0000.0000.0000.000
166B167ARG10.8700.94824.823-0.075-0.0750.0000.0000.0000.000
167B168TYR0-0.035-0.02525.259-0.003-0.0030.0000.0000.0000.000
168B169GLY00.0200.01321.2760.0040.0040.0000.0000.0000.000
169B170VAL0-0.059-0.01620.2280.0140.0140.0000.0000.0000.000
170B171ARG10.7930.90215.403-0.261-0.2610.0000.0000.0000.000
171B172ALA00.0250.02221.355-0.017-0.0170.0000.0000.0000.000
172B173ASN0-0.012-0.01419.2200.0130.0130.0000.0000.0000.000
173B174ALA00.0270.01022.332-0.014-0.0140.0000.0000.0000.000
174B175VAL00.0540.04019.8550.0080.0080.0000.0000.0000.000
175B176ALA0-0.0020.00522.626-0.008-0.0080.0000.0000.0000.000
176B177PRO00.0110.00724.0720.0000.0000.0000.0000.0000.000
177B178GLY00.000-0.01425.5430.0050.0050.0000.0000.0000.000
178B179PHE0-0.018-0.00228.069-0.001-0.0010.0000.0000.0000.000
179B180ILE00.0120.01824.696-0.004-0.0040.0000.0000.0000.000
180B181ASP-1-0.762-0.84527.941-0.053-0.0530.0000.0000.0000.000
181B182THR0-0.031-0.01528.221-0.007-0.0070.0000.0000.0000.000
182B183GLU-1-0.866-0.95730.326-0.060-0.0600.0000.0000.0000.000
183B184MET0-0.0020.01333.4390.0030.0030.0000.0000.0000.000
184B185THR0-0.036-0.06331.4970.0010.0010.0000.0000.0000.000
185B186LEU0-0.018-0.00231.3640.0010.0010.0000.0000.0000.000
186B187ALA00.0140.02535.2490.0000.0000.0000.0000.0000.000
187B188ILE0-0.072-0.01736.3960.0030.0030.0000.0000.0000.000
188B189ARG10.8500.88639.5840.0190.0190.0000.0000.0000.000
189B190GLU-1-0.815-0.91338.857-0.035-0.0350.0000.0000.0000.000
190B191ASP-1-0.821-0.89140.600-0.020-0.0200.0000.0000.0000.000
191B192ILE0-0.040-0.02239.4920.0020.0020.0000.0000.0000.000
192B193ARG10.8790.92032.5590.0440.0440.0000.0000.0000.000
193B194GLU-1-0.770-0.84536.642-0.027-0.0270.0000.0000.0000.000
194B195LYS10.8310.91038.3330.0100.0100.0000.0000.0000.000
195B196ILE0-0.009-0.01034.1380.0020.0020.0000.0000.0000.000
196B197THR00.0340.00432.5980.0010.0010.0000.0000.0000.000
197B198LYS10.8120.88633.9070.0200.0200.0000.0000.0000.000
198B199GLU-1-0.861-0.90035.139-0.004-0.0040.0000.0000.0000.000
199B200ILE0-0.0340.00029.1060.0040.0040.0000.0000.0000.000
200B201PRO0-0.0110.00329.115-0.004-0.0040.0000.0000.0000.000
201B202PHE0-0.009-0.01522.281-0.002-0.0020.0000.0000.0000.000
202B203ARG10.8310.91928.1640.0140.0140.0000.0000.0000.000
203B204ARG10.7950.86822.1110.0710.0710.0000.0000.0000.000
204B205PHE00.0150.01628.6700.0050.0050.0000.0000.0000.000
205B206GLY00.018-0.00224.964-0.005-0.0050.0000.0000.0000.000
206B207LYS10.8800.91022.5800.0800.0800.0000.0000.0000.000
207B208PRO00.0520.00822.7060.0020.0020.0000.0000.0000.000
208B209GLU-1-0.853-0.92416.656-0.237-0.2370.0000.0000.0000.000
209B210GLU-1-0.754-0.83617.898-0.096-0.0960.0000.0000.0000.000
210B211ILE0-0.033-0.01918.5220.0140.0140.0000.0000.0000.000
211B212ALA00.0180.01518.0490.0170.0170.0000.0000.0000.000
212B213TRP00.0610.0219.5410.0090.0090.0000.0000.0000.000
213B214ALA0-0.054-0.01214.1510.0290.0290.0000.0000.0000.000
214B215VAL00.010-0.01416.1280.0370.0370.0000.0000.0000.000
215B216ALA00.0420.03112.6040.0320.0320.0000.0000.0000.000
216B217PHE0-0.0070.00010.6600.0430.0430.0000.0000.0000.000
217B218LEU0-0.0160.01112.5400.0890.0890.0000.0000.0000.000
218B219LEU00.0440.03515.0670.0350.0350.0000.0000.0000.000
219B220SER00.0440.0328.6960.0710.0710.0000.0000.0000.000
220B221PRO0-0.0360.00010.9470.0570.0570.0000.0000.0000.000
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