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: R9488

Calculation Name: 1RHH-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RHH

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2425845.833017
FMO2-HF: Nuclear repulsion 2338345.009464
FMO2-HF: Total energy -87500.823553
FMO2-MP2: Total energy -87754.376005


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:3:GLN)


Summations of interaction energy for fragment #1(B:3:GLN)
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.
0.6843.8244.895-2.803-5.233-0.006
Interaction energy analysis for fragmet #1(B:3:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.010
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].
3B5LEU00.0400.0082.723-0.3042.4860.040-1.226-1.6030.003
4B6GLU-1-0.912-0.9273.590-4.100-3.4690.006-0.284-0.354-0.002
5B7GLN00.0430.0035.5210.8180.8180.0000.0000.0000.000
6B8SER00.0420.0448.234-0.104-0.1040.0000.0000.0000.000
7B9GLY0-0.036-0.01811.263-0.071-0.0710.0000.0000.0000.000
8B10ALA00.002-0.00213.1120.0870.0870.0000.0000.0000.000
9B11GLU-1-0.791-0.89315.195-0.357-0.3570.0000.0000.0000.000
10B12VAL0-0.029-0.01018.8180.0210.0210.0000.0000.0000.000
11B13LYS10.8050.89920.5210.3020.3020.0000.0000.0000.000
12B14LYS10.9500.98324.1140.2080.2080.0000.0000.0000.000
13B15PRO00.0160.00527.5110.0040.0040.0000.0000.0000.000
14B16GLY0-0.065-0.03328.9430.0040.0040.0000.0000.0000.000
15B17SER0-0.063-0.03526.1220.0010.0010.0000.0000.0000.000
16B18SER00.0750.01724.4210.0120.0120.0000.0000.0000.000
17B19VAL0-0.060-0.02118.216-0.022-0.0220.0000.0000.0000.000
18B20GLN00.0070.00017.7780.0130.0130.0000.0000.0000.000
19B21VAL0-0.045-0.01012.421-0.066-0.0660.0000.0000.0000.000
20B22SER00.020-0.00312.6550.0400.0400.0000.0000.0000.000
21B23CYS0-0.044-0.0117.9240.0180.0180.0000.0000.0000.000
22B24LYS10.9260.9698.3791.2511.2510.0000.0000.0000.000
23B25ALA00.0440.0337.236-0.330-0.3300.0000.0000.0000.000
24B26SER0-0.056-0.0475.785-0.321-0.3210.0000.0000.0000.000
25B27GLY0-0.013-0.0017.7500.1740.1740.0000.0000.0000.000
26B28GLY0-0.026-0.0059.664-0.067-0.0670.0000.0000.0000.000
27B29THR00.008-0.00812.198-0.056-0.0560.0000.0000.0000.000
28B30PHE00.0040.01012.3770.1550.1550.0000.0000.0000.000
29B31SER0-0.0100.00113.9860.0850.0850.0000.0000.0000.000
30B32MET00.0520.01615.812-0.131-0.1310.0000.0000.0000.000
31B33TYR0-0.023-0.01110.7670.1400.1400.0000.0000.0000.000
32B34GLY0-0.0010.00114.686-0.154-0.1540.0000.0000.0000.000
33B35PHE0-0.068-0.0429.8370.1610.1610.0000.0000.0000.000
34B35ASN00.0290.00812.990-0.207-0.2070.0000.0000.0000.000
35B36TRP00.0110.01312.6900.0210.0210.0000.0000.0000.000
36B37VAL0-0.010-0.00213.6010.0140.0140.0000.0000.0000.000
37B38ARG10.7960.87614.1220.0070.0070.0000.0000.0000.000
38B39GLN00.0250.00315.1710.0060.0060.0000.0000.0000.000
39B40ALA00.0360.03617.577-0.056-0.0560.0000.0000.0000.000
40B41PRO00.019-0.01218.5350.0090.0090.0000.0000.0000.000
41B42GLY0-0.0010.01119.6290.0180.0180.0000.0000.0000.000
42B43HIS0-0.064-0.03120.7500.0410.0410.0000.0000.0000.000
43B44GLY00.0320.01419.812-0.010-0.0100.0000.0000.0000.000
44B45LEU00.0010.00514.665-0.030-0.0300.0000.0000.0000.000
45B46GLU-1-0.770-0.85518.3430.0130.0130.0000.0000.0000.000
46B47TRP0-0.002-0.00517.269-0.059-0.0590.0000.0000.0000.000
47B48MET0-0.050-0.01918.199-0.045-0.0450.0000.0000.0000.000
48B49GLY00.047-0.00218.453-0.016-0.0160.0000.0000.0000.000
49B50GLY00.0200.02517.2860.0150.0150.0000.0000.0000.000
50B51ILE0-0.039-0.00416.980-0.044-0.0440.0000.0000.0000.000
51B52ILE00.0630.04017.0580.0590.0590.0000.0000.0000.000
52B52PRO0-0.051-0.03616.140-0.044-0.0440.0000.0000.0000.000
53B53ILE0-0.0040.01419.298-0.041-0.0410.0000.0000.0000.000
54B54PHE00.0330.02721.142-0.026-0.0260.0000.0000.0000.000
55B55GLY0-0.0170.00722.552-0.035-0.0350.0000.0000.0000.000
56B56THR0-0.038-0.00722.875-0.031-0.0310.0000.0000.0000.000
57B57SER0-0.017-0.03121.1420.0140.0140.0000.0000.0000.000
58B58ASN00.0010.00522.111-0.004-0.0040.0000.0000.0000.000
59B59TYR00.0320.00221.9820.0020.0020.0000.0000.0000.000
60B60ALA00.0190.02423.2190.0040.0040.0000.0000.0000.000
61B61GLN00.0460.00024.981-0.029-0.0290.0000.0000.0000.000
62B62LYS10.8300.91624.427-0.009-0.0090.0000.0000.0000.000
63B63PHE00.000-0.01022.307-0.019-0.0190.0000.0000.0000.000
64B64ARG10.9720.98426.130-0.065-0.0650.0000.0000.0000.000
65B65GLY0-0.051-0.02028.700-0.009-0.0090.0000.0000.0000.000
66B66ARG10.7590.85725.5880.0570.0570.0000.0000.0000.000
67B67VAL00.0070.00721.747-0.019-0.0190.0000.0000.0000.000
68B68THR0-0.032-0.00522.3280.0200.0200.0000.0000.0000.000
69B69PHE00.0210.01017.506-0.025-0.0250.0000.0000.0000.000
70B70THR00.0060.00518.9250.0120.0120.0000.0000.0000.000
71B71ALA00.011-0.00117.025-0.003-0.0030.0000.0000.0000.000
72B72ASP-1-0.787-0.86217.1130.0080.0080.0000.0000.0000.000
73B73GLN00.002-0.01117.097-0.031-0.0310.0000.0000.0000.000
74B74ALA0-0.031-0.00617.9640.0210.0210.0000.0000.0000.000
75B75THR0-0.035-0.05215.471-0.023-0.0230.0000.0000.0000.000
76B76SER0-0.0250.00412.919-0.025-0.0250.0000.0000.0000.000
77B77THR0-0.042-0.03312.119-0.075-0.0750.0000.0000.0000.000
78B78ALA00.0010.00112.5450.0570.0570.0000.0000.0000.000
79B79TYR00.005-0.02613.548-0.139-0.1390.0000.0000.0000.000
80B80MET00.0130.01916.0100.0720.0720.0000.0000.0000.000
81B81GLU-1-0.931-0.95717.694-0.168-0.1680.0000.0000.0000.000
82B82LEU0-0.007-0.00120.6690.0300.0300.0000.0000.0000.000
83B82THR00.0590.00022.327-0.024-0.0240.0000.0000.0000.000
84B82ASN0-0.047-0.01725.8470.0120.0120.0000.0000.0000.000
85B82LEU0-0.0090.01222.3820.0070.0070.0000.0000.0000.000
86B83ARG10.9750.98026.3770.0910.0910.0000.0000.0000.000
87B84SER00.0720.02326.019-0.008-0.0080.0000.0000.0000.000
88B85ASP-1-0.937-0.96325.598-0.101-0.1010.0000.0000.0000.000
89B86ASP-1-0.722-0.81322.588-0.086-0.0860.0000.0000.0000.000
90B87THR0-0.037-0.00621.100-0.031-0.0310.0000.0000.0000.000
91B88ALA0-0.027-0.01418.0610.0230.0230.0000.0000.0000.000
92B89VAL0-0.0010.00612.215-0.053-0.0530.0000.0000.0000.000
93B90TYR0-0.025-0.04713.7740.1010.1010.0000.0000.0000.000
94B91TYR0-0.006-0.0099.009-0.182-0.1820.0000.0000.0000.000
95B93ALA00.009-0.0128.3600.1010.1010.0000.0000.0000.000
96B94ARG10.8360.8987.660-3.480-3.4800.0000.0000.0000.000
97B95ASP-1-0.758-0.87611.0190.8900.8900.0000.0000.0000.000
98B96PHE0-0.007-0.02313.2960.0520.0520.0000.0000.0000.000
99B97GLY00.0700.02215.648-0.058-0.0580.0000.0000.0000.000
100B98PRO0-0.0580.00218.307-0.009-0.0090.0000.0000.0000.000
101B99ASP-1-0.766-0.89620.4630.5340.5340.0000.0000.0000.000
102B100TRP0-0.078-0.04123.732-0.037-0.0370.0000.0000.0000.000
103B100GLU-1-0.939-0.96322.5850.5880.5880.0000.0000.0000.000
104B100ASP-1-0.888-0.92324.7650.3900.3900.0000.0000.0000.000
105B100GLY0-0.056-0.03222.6920.0510.0510.0000.0000.0000.000
106B100ASP-1-0.875-0.96222.6500.5460.5460.0000.0000.0000.000
107B100SER0-0.123-0.08225.130-0.042-0.0420.0000.0000.0000.000
108B100TYR0-0.025-0.02426.888-0.037-0.0370.0000.0000.0000.000
109B100ASP-1-0.884-0.92325.0620.5400.5400.0000.0000.0000.000
110B100GLY0-0.036-0.03027.141-0.013-0.0130.0000.0000.0000.000
111B100SER0-0.114-0.04623.382-0.035-0.0350.0000.0000.0000.000
112B100GLY00.0950.05422.6810.0290.0290.0000.0000.0000.000
113B100ARG10.7370.86817.454-0.666-0.6660.0000.0000.0000.000
114B100GLY0-0.041-0.01618.942-0.013-0.0130.0000.0000.0000.000
115B100PHE0-0.059-0.01715.126-0.029-0.0290.0000.0000.0000.000
116B100PHE00.004-0.02411.9520.0270.0270.0000.0000.0000.000
117B101ASP-1-0.799-0.86810.1882.6692.6690.0000.0000.0000.000
118B102PHE0-0.043-0.0262.137-0.498-0.9674.851-1.277-3.106-0.007
119B103TRP00.0160.0056.697-0.761-0.7610.0000.0000.0000.000
120B104GLY00.0310.0283.9460.5310.637-0.001-0.013-0.0920.000
121B105GLN0-0.094-0.0604.5930.4260.508-0.001-0.003-0.0780.000
122B106GLY00.0170.0176.0430.2630.2630.0000.0000.0000.000
123B107THR0-0.033-0.0189.290-0.175-0.1750.0000.0000.0000.000
124B108LEU0-0.045-0.01812.0110.1190.1190.0000.0000.0000.000
125B109VAL00.0330.02615.254-0.023-0.0230.0000.0000.0000.000
126B110THR0-0.004-0.00818.1700.0410.0410.0000.0000.0000.000
127B111VAL0-0.0060.01121.498-0.004-0.0040.0000.0000.0000.000
128B112SER00.0310.00024.6120.0170.0170.0000.0000.0000.000
129B113SER00.0080.00027.470-0.007-0.0070.0000.0000.0000.000
130B114ALA0-0.012-0.00229.0070.0040.0040.0000.0000.0000.000
131B115SER00.008-0.00127.906-0.007-0.0070.0000.0000.0000.000
132B116THR0-0.039-0.03623.522-0.013-0.0130.0000.0000.0000.000
133B117LYS10.8820.93125.3530.3140.3140.0000.0000.0000.000
134B118GLY00.0320.02323.992-0.022-0.0220.0000.0000.0000.000
135B119PRO0-0.022-0.01422.1090.0280.0280.0000.0000.0000.000
136B120SER0-0.0160.00625.4010.0050.0050.0000.0000.0000.000
137B121VAL00.006-0.00223.453-0.001-0.0010.0000.0000.0000.000
138B122PHE0-0.002-0.00626.7850.0150.0150.0000.0000.0000.000
139B123PRO00.0250.01728.310-0.019-0.0190.0000.0000.0000.000
140B124LEU0-0.0320.00327.3720.0220.0220.0000.0000.0000.000
141B125ALA00.007-0.01729.970-0.013-0.0130.0000.0000.0000.000
142B126PRO00.0350.04230.3600.0110.0110.0000.0000.0000.000
143B127SER0-0.001-0.02132.6520.0140.0140.0000.0000.0000.000
144B128SER00.0380.01236.294-0.001-0.0010.0000.0000.0000.000
145B129LYS10.9060.94838.2520.1680.1680.0000.0000.0000.000
146B130SER0-0.0110.01032.6300.0040.0040.0000.0000.0000.000
147B131THR0-0.019-0.00833.310-0.011-0.0110.0000.0000.0000.000
148B132SER00.0090.00233.8080.0140.0140.0000.0000.0000.000
149B133GLY00.0460.03534.166-0.008-0.0080.0000.0000.0000.000
150B134GLY00.001-0.00234.1860.0020.0020.0000.0000.0000.000
151B135THR0-0.047-0.01428.963-0.015-0.0150.0000.0000.0000.000
152B136ALA00.0260.01530.2900.0170.0170.0000.0000.0000.000
153B137ALA0-0.0010.00428.601-0.022-0.0220.0000.0000.0000.000
154B138LEU0-0.016-0.00525.6120.0200.0200.0000.0000.0000.000
155B139GLY00.0720.00725.178-0.022-0.0220.0000.0000.0000.000
156B140CYS0-0.089-0.00120.258-0.028-0.0280.0000.0000.0000.000
157B141LEU00.0320.02325.019-0.011-0.0110.0000.0000.0000.000
158B142VAL0-0.033-0.02121.8310.0020.0020.0000.0000.0000.000
159B143LYS10.8960.90425.1580.2620.2620.0000.0000.0000.000
160B144ASP-1-0.819-0.88327.752-0.269-0.2690.0000.0000.0000.000
161B145TYR00.003-0.00921.2270.0050.0050.0000.0000.0000.000
162B146PHE00.0340.04324.5350.0120.0120.0000.0000.0000.000
163B147PRO00.0170.02320.958-0.004-0.0040.0000.0000.0000.000
164B148GLU-1-0.751-0.85419.081-0.512-0.5120.0000.0000.0000.000
165B149PRO00.000-0.00814.7240.0150.0150.0000.0000.0000.000
166B150VAL0-0.003-0.01917.523-0.018-0.0180.0000.0000.0000.000
167B151THR0-0.0200.00111.9810.0310.0310.0000.0000.0000.000
168B152VAL0-0.010-0.02115.0820.0460.0460.0000.0000.0000.000
169B153SER00.0010.01013.611-0.089-0.0890.0000.0000.0000.000
170B154TRP00.0150.00615.6900.1160.1160.0000.0000.0000.000
171B155ASN00.000-0.01216.953-0.051-0.0510.0000.0000.0000.000
172B156SER0-0.016-0.02414.933-0.009-0.0090.0000.0000.0000.000
173B157GLY00.0070.01112.495-0.154-0.1540.0000.0000.0000.000
174B158ALA0-0.029-0.00313.343-0.040-0.0400.0000.0000.0000.000
175B159LEU0-0.041-0.01315.5660.0840.0840.0000.0000.0000.000
176B160THR00.017-0.00412.7220.0080.0080.0000.0000.0000.000
177B161SER00.0170.00216.1900.0480.0480.0000.0000.0000.000
178B162GLY00.0540.02118.8880.0180.0180.0000.0000.0000.000
179B163VAL0-0.068-0.03117.9800.0290.0290.0000.0000.0000.000
180B164HIS00.0160.01819.739-0.014-0.0140.0000.0000.0000.000
181B165THR0-0.010-0.00817.6120.0290.0290.0000.0000.0000.000
182B166PHE0-0.0130.00419.8410.0020.0020.0000.0000.0000.000
183B167PRO00.0200.01920.746-0.034-0.0340.0000.0000.0000.000
184B168ALA00.002-0.00821.6540.0220.0220.0000.0000.0000.000
185B169VAL0-0.016-0.00123.5400.0230.0230.0000.0000.0000.000
186B170LEU0-0.038-0.01727.121-0.013-0.0130.0000.0000.0000.000
187B171GLN0-0.034-0.03428.7660.0210.0210.0000.0000.0000.000
188B172SER00.0590.02131.920-0.001-0.0010.0000.0000.0000.000
189B173SER0-0.017-0.00832.9910.0050.0050.0000.0000.0000.000
190B174GLY00.0290.01831.3970.0010.0010.0000.0000.0000.000
191B175LEU0-0.069-0.02528.477-0.016-0.0160.0000.0000.0000.000
192B176TYR00.0320.00824.4810.0110.0110.0000.0000.0000.000
193B177SER0-0.022-0.01626.230-0.001-0.0010.0000.0000.0000.000
194B178LEU00.0260.04019.8650.0110.0110.0000.0000.0000.000
195B179SER00.010-0.00423.8470.0090.0090.0000.0000.0000.000
196B180SER0-0.008-0.00419.795-0.017-0.0170.0000.0000.0000.000
197B181VAL00.020-0.00122.4180.0190.0190.0000.0000.0000.000
198B182VAL00.0340.02221.577-0.036-0.0360.0000.0000.0000.000
199B183THR0-0.0090.00123.9070.0350.0350.0000.0000.0000.000
200B184VAL00.0050.00124.134-0.023-0.0230.0000.0000.0000.000
201B185PRO00.0770.03826.0710.0260.0260.0000.0000.0000.000
202B186SER00.0600.02329.325-0.013-0.0130.0000.0000.0000.000
203B187SER0-0.019-0.00932.089-0.005-0.0050.0000.0000.0000.000
204B188SER0-0.013-0.01027.882-0.007-0.0070.0000.0000.0000.000
205B189LEU0-0.009-0.00729.601-0.012-0.0120.0000.0000.0000.000
206B190GLY00.0010.01331.285-0.002-0.0020.0000.0000.0000.000
207B191THR0-0.036-0.02330.4100.0010.0010.0000.0000.0000.000
208B192GLN0-0.043-0.01923.400-0.002-0.0020.0000.0000.0000.000
209B193THR0-0.0120.00324.7170.0120.0120.0000.0000.0000.000
210B194TYR00.0360.00223.184-0.048-0.0480.0000.0000.0000.000
211B195ILE00.0150.00121.1110.0350.0350.0000.0000.0000.000
212B197ASN00.009-0.01416.218-0.014-0.0140.0000.0000.0000.000
213B198VAL00.0360.01617.067-0.064-0.0640.0000.0000.0000.000
214B199ASN0-0.029-0.01513.807-0.074-0.0740.0000.0000.0000.000
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