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: QY5VY

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 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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2424993.352104
FMO2-HF: Nuclear repulsion 2337492.127915
FMO2-HF: Total energy -87501.224189
FMO2-MP2: Total energy -87754.722938


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.
0.323.7343.219-2.365-4.266-0.001
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 : -0.003 / q_NPA : -0.015
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].
3B5LEU00.0090.0053.176-0.9411.538-0.002-1.200-1.2760.001
4B6GLU-1-0.857-0.9004.402-2.638-2.431-0.001-0.024-0.1810.000
5B7GLN00.0380.0005.9930.6240.6240.0000.0000.0000.000
6B8SER00.0180.0378.822-0.070-0.0700.0000.0000.0000.000
7B9GLY0-0.022-0.00811.774-0.065-0.0650.0000.0000.0000.000
8B10ALA00.0120.00213.1360.0850.0850.0000.0000.0000.000
9B11GLU-1-0.798-0.89815.230-0.335-0.3350.0000.0000.0000.000
10B12VAL0-0.029-0.02018.9460.0130.0130.0000.0000.0000.000
11B13LYS10.8080.90620.9890.2990.2990.0000.0000.0000.000
12B14LYS10.8940.94924.7050.2070.2070.0000.0000.0000.000
13B15PRO00.0100.00128.3320.0040.0040.0000.0000.0000.000
14B16GLY0-0.049-0.01729.7020.0060.0060.0000.0000.0000.000
15B17SER0-0.042-0.02926.9040.0020.0020.0000.0000.0000.000
16B18SER00.0650.01324.7430.0110.0110.0000.0000.0000.000
17B19VAL0-0.054-0.02618.578-0.019-0.0190.0000.0000.0000.000
18B20GLN00.000-0.00618.1870.0140.0140.0000.0000.0000.000
19B21VAL0-0.040-0.00612.871-0.055-0.0550.0000.0000.0000.000
20B22SER00.0450.01613.3530.0350.0350.0000.0000.0000.000
21B23CYS0-0.045-0.0258.4850.0140.0140.0000.0000.0000.000
22B24LYS10.9020.9518.4561.0931.0930.0000.0000.0000.000
23B25ALA00.0450.0217.876-0.343-0.3430.0000.0000.0000.000
24B26SER0-0.055-0.0345.633-0.080-0.0800.0000.0000.0000.000
25B27GLY0-0.010-0.0027.7860.3560.3560.0000.0000.0000.000
26B28GLY0-0.032-0.0109.224-0.060-0.0600.0000.0000.0000.000
27B29THR00.012-0.00312.166-0.095-0.0950.0000.0000.0000.000
28B30PHE00.0010.00012.3310.1380.1380.0000.0000.0000.000
29B31SER0-0.017-0.00914.0660.0550.0550.0000.0000.0000.000
30B32MET00.0620.03115.758-0.127-0.1270.0000.0000.0000.000
31B33TYR0-0.027-0.01110.7560.1220.1220.0000.0000.0000.000
32B34GLY00.0000.00514.798-0.125-0.1250.0000.0000.0000.000
33B35PHE0-0.062-0.03110.2820.1180.1180.0000.0000.0000.000
34B35ASN00.0250.00713.120-0.136-0.1360.0000.0000.0000.000
35B36TRP0-0.014-0.00212.965-0.006-0.0060.0000.0000.0000.000
36B37VAL00.002-0.00213.8750.0310.0310.0000.0000.0000.000
37B38ARG10.7740.86414.2650.0660.0660.0000.0000.0000.000
38B39GLN00.0350.02015.358-0.006-0.0060.0000.0000.0000.000
39B40ALA00.0440.03717.810-0.048-0.0480.0000.0000.0000.000
40B41PRO00.004-0.02019.0580.0000.0000.0000.0000.0000.000
41B42GLY0-0.0010.01219.6790.0250.0250.0000.0000.0000.000
42B43HIS0-0.057-0.01820.7950.0430.0430.0000.0000.0000.000
43B44GLY00.0290.01419.955-0.015-0.0150.0000.0000.0000.000
44B45LEU0-0.003-0.00614.757-0.029-0.0290.0000.0000.0000.000
45B46GLU-1-0.763-0.85018.724-0.049-0.0490.0000.0000.0000.000
46B47TRP0-0.013-0.00717.136-0.054-0.0540.0000.0000.0000.000
47B48MET0-0.054-0.01918.427-0.025-0.0250.0000.0000.0000.000
48B49GLY00.0520.00018.823-0.002-0.0020.0000.0000.0000.000
49B50GLY00.0230.02617.587-0.005-0.0050.0000.0000.0000.000
50B51ILE0-0.049-0.00417.042-0.030-0.0300.0000.0000.0000.000
51B52ILE00.0780.03717.4120.0470.0470.0000.0000.0000.000
52B52PRO0-0.048-0.02616.611-0.025-0.0250.0000.0000.0000.000
53B53ILE0-0.0040.01219.507-0.036-0.0360.0000.0000.0000.000
54B54PHE00.0360.02721.383-0.018-0.0180.0000.0000.0000.000
55B55GLY0-0.0190.00123.400-0.029-0.0290.0000.0000.0000.000
56B56THR0-0.0240.00123.386-0.031-0.0310.0000.0000.0000.000
57B57SER0-0.039-0.04921.5460.0090.0090.0000.0000.0000.000
58B58ASN0-0.002-0.00222.365-0.004-0.0040.0000.0000.0000.000
59B59TYR00.0480.01322.217-0.005-0.0050.0000.0000.0000.000
60B60ALA00.0200.02323.4560.0050.0050.0000.0000.0000.000
61B61GLN00.031-0.00525.300-0.021-0.0210.0000.0000.0000.000
62B62LYS10.8330.90924.6500.0600.0600.0000.0000.0000.000
63B63PHE00.0170.00622.638-0.017-0.0170.0000.0000.0000.000
64B64ARG10.9530.97026.374-0.031-0.0310.0000.0000.0000.000
65B65GLY0-0.034-0.00929.159-0.006-0.0060.0000.0000.0000.000
66B66ARG10.7610.86025.8510.0920.0920.0000.0000.0000.000
67B67VAL00.0240.01521.987-0.019-0.0190.0000.0000.0000.000
68B68THR0-0.050-0.02422.7360.0200.0200.0000.0000.0000.000
69B69PHE00.0150.01717.873-0.027-0.0270.0000.0000.0000.000
70B70THR0-0.0020.00019.2890.0120.0120.0000.0000.0000.000
71B71ALA00.010-0.00617.518-0.005-0.0050.0000.0000.0000.000
72B72ASP-1-0.779-0.85017.6610.0590.0590.0000.0000.0000.000
73B73GLN00.0190.00517.430-0.024-0.0240.0000.0000.0000.000
74B74ALA0-0.034-0.01217.9590.0350.0350.0000.0000.0000.000
75B75THR0-0.045-0.06115.651-0.011-0.0110.0000.0000.0000.000
76B76SER0-0.0170.00613.356-0.015-0.0150.0000.0000.0000.000
77B77THR0-0.043-0.02712.613-0.068-0.0680.0000.0000.0000.000
78B78ALA00.0080.00513.1310.0530.0530.0000.0000.0000.000
79B79TYR0-0.009-0.02413.934-0.134-0.1340.0000.0000.0000.000
80B80MET00.0100.02416.3110.0660.0660.0000.0000.0000.000
81B81GLU-1-0.923-0.95518.101-0.179-0.1790.0000.0000.0000.000
82B82LEU0-0.008-0.00520.9730.0270.0270.0000.0000.0000.000
83B82THR00.0640.00522.683-0.020-0.0200.0000.0000.0000.000
84B82ASN0-0.038-0.00726.2560.0080.0080.0000.0000.0000.000
85B82LEU0-0.0120.00522.9790.0060.0060.0000.0000.0000.000
86B83ARG10.9280.95426.7720.1120.1120.0000.0000.0000.000
87B84SER00.0660.02826.343-0.009-0.0090.0000.0000.0000.000
88B85ASP-1-0.918-0.95625.826-0.137-0.1370.0000.0000.0000.000
89B86ASP-1-0.724-0.81822.739-0.132-0.1320.0000.0000.0000.000
90B87THR0-0.046-0.01821.281-0.032-0.0320.0000.0000.0000.000
91B88ALA00.0000.00218.3590.0140.0140.0000.0000.0000.000
92B89VAL00.004-0.00112.388-0.042-0.0420.0000.0000.0000.000
93B90TYR0-0.012-0.03114.0530.0870.0870.0000.0000.0000.000
94B91TYR00.003-0.0109.131-0.157-0.1570.0000.0000.0000.000
95B93ALA00.0130.0008.6150.0080.0080.0000.0000.0000.000
96B94ARG10.8190.8867.561-2.758-2.7580.0000.0000.0000.000
97B95ASP-1-0.754-0.86511.3990.6870.6870.0000.0000.0000.000
98B96PHE00.011-0.02513.2350.1110.1110.0000.0000.0000.000
99B97GLY00.0840.04916.038-0.048-0.0480.0000.0000.0000.000
100B98PRO0-0.070-0.02018.8170.0280.0280.0000.0000.0000.000
101B99ASP-1-0.779-0.89720.3470.4520.4520.0000.0000.0000.000
102B100TRP0-0.053-0.02923.925-0.029-0.0290.0000.0000.0000.000
103B100GLU-1-0.950-0.97522.6880.5520.5520.0000.0000.0000.000
104B100ASP-1-0.849-0.89024.9470.3260.3260.0000.0000.0000.000
105B100GLY0-0.078-0.04822.8550.0470.0470.0000.0000.0000.000
106B100ASP-1-0.899-0.96122.5230.4470.4470.0000.0000.0000.000
107B100SER0-0.111-0.07124.941-0.033-0.0330.0000.0000.0000.000
108B100TYR0-0.039-0.02626.766-0.033-0.0330.0000.0000.0000.000
109B100ASP-1-0.905-0.94125.2260.4520.4520.0000.0000.0000.000
110B100GLY0-0.008-0.01526.737-0.023-0.0230.0000.0000.0000.000
111B100SER0-0.131-0.07523.656-0.036-0.0360.0000.0000.0000.000
112B100GLY00.1090.08122.0220.0380.0380.0000.0000.0000.000
113B100ARG10.7640.85017.578-0.585-0.5850.0000.0000.0000.000
114B100GLY0-0.086-0.03418.948-0.008-0.0080.0000.0000.0000.000
115B100PHE0-0.055-0.02015.240-0.040-0.0400.0000.0000.0000.000
116B100PHE0-0.009-0.02412.1580.0110.0110.0000.0000.0000.000
117B101ASP-1-0.791-0.86210.3372.1142.1140.0000.0000.0000.000
118B102PHE0-0.045-0.0242.297-1.496-0.9393.224-1.124-2.657-0.002
119B103TRP00.015-0.0076.117-0.716-0.7160.0000.0000.0000.000
120B104GLY00.0360.0324.1130.3770.472-0.001-0.015-0.0790.000
121B105GLN0-0.117-0.0714.7050.4800.556-0.001-0.002-0.0730.000
122B106GLY00.0180.0216.0460.2510.2510.0000.0000.0000.000
123B107THR0-0.045-0.0289.483-0.126-0.1260.0000.0000.0000.000
124B108LEU0-0.035-0.01912.4550.1010.1010.0000.0000.0000.000
125B109VAL00.0240.02215.383-0.012-0.0120.0000.0000.0000.000
126B110THR00.002-0.00718.5070.0280.0280.0000.0000.0000.000
127B111VAL0-0.0120.00421.9600.0010.0010.0000.0000.0000.000
128B112SER00.020-0.00225.2680.0180.0180.0000.0000.0000.000
129B113SER00.0390.01228.189-0.005-0.0050.0000.0000.0000.000
130B114ALA00.0140.02529.0740.0040.0040.0000.0000.0000.000
131B115SER0-0.008-0.00528.7140.0010.0010.0000.0000.0000.000
132B116THR0-0.029-0.02723.981-0.013-0.0130.0000.0000.0000.000
133B117LYS10.8350.90925.7620.3160.3160.0000.0000.0000.000
134B118GLY00.0580.03224.182-0.025-0.0250.0000.0000.0000.000
135B119PRO0-0.033-0.01521.9450.0270.0270.0000.0000.0000.000
136B120SER00.005-0.00825.2470.0070.0070.0000.0000.0000.000
137B121VAL0-0.0050.00623.5330.0020.0020.0000.0000.0000.000
138B122PHE0-0.008-0.00826.8380.0190.0190.0000.0000.0000.000
139B123PRO00.0190.01828.412-0.018-0.0180.0000.0000.0000.000
140B124LEU0-0.037-0.01827.4820.0220.0220.0000.0000.0000.000
141B125ALA00.0190.00029.994-0.012-0.0120.0000.0000.0000.000
142B126PRO00.0150.03030.4220.0080.0080.0000.0000.0000.000
143B127SER00.035-0.00132.6910.0170.0170.0000.0000.0000.000
144B128SER00.0430.01736.256-0.003-0.0030.0000.0000.0000.000
145B129LYS10.8600.91737.7390.1770.1770.0000.0000.0000.000
146B130SER0-0.0090.00332.4890.0030.0030.0000.0000.0000.000
147B131THR0-0.0120.00233.010-0.012-0.0120.0000.0000.0000.000
148B132SER0-0.012-0.01633.7580.0140.0140.0000.0000.0000.000
149B133GLY00.0570.03233.998-0.008-0.0080.0000.0000.0000.000
150B134GLY00.000-0.00133.8960.0010.0010.0000.0000.0000.000
151B135THR0-0.049-0.00728.701-0.011-0.0110.0000.0000.0000.000
152B136ALA00.0250.00930.1020.0180.0180.0000.0000.0000.000
153B137ALA00.0150.02028.348-0.023-0.0230.0000.0000.0000.000
154B138LEU0-0.0160.00625.6740.0250.0250.0000.0000.0000.000
155B139GLY00.0620.00725.160-0.027-0.0270.0000.0000.0000.000
156B140CYS0-0.0520.01520.332-0.024-0.0240.0000.0000.0000.000
157B141LEU00.0430.03324.833-0.018-0.0180.0000.0000.0000.000
158B142VAL0-0.037-0.02222.127-0.001-0.0010.0000.0000.0000.000
159B143LYS10.9080.91625.3840.2520.2520.0000.0000.0000.000
160B144ASP-1-0.808-0.86528.158-0.262-0.2620.0000.0000.0000.000
161B145TYR0-0.025-0.02921.3820.0080.0080.0000.0000.0000.000
162B146PHE00.0620.03624.9460.0080.0080.0000.0000.0000.000
163B147PRO00.0310.03521.1960.0010.0010.0000.0000.0000.000
164B148GLU-1-0.749-0.86319.247-0.544-0.5440.0000.0000.0000.000
165B149PRO0-0.0020.00214.7960.0220.0220.0000.0000.0000.000
166B150VAL0-0.034-0.02717.614-0.007-0.0070.0000.0000.0000.000
167B151THR0-0.018-0.00212.3540.0060.0060.0000.0000.0000.000
168B152VAL0-0.008-0.02115.1950.0690.0690.0000.0000.0000.000
169B153SER00.0000.01613.645-0.101-0.1010.0000.0000.0000.000
170B154TRP00.0190.00215.6980.1260.1260.0000.0000.0000.000
171B155ASN00.007-0.00616.763-0.067-0.0670.0000.0000.0000.000
172B156SER0-0.025-0.02315.1560.0010.0010.0000.0000.0000.000
173B157GLY00.0140.01512.463-0.135-0.1350.0000.0000.0000.000
174B158ALA0-0.039-0.01013.347-0.046-0.0460.0000.0000.0000.000
175B159LEU0-0.033-0.01315.5980.0890.0890.0000.0000.0000.000
176B160THR00.0180.00012.501-0.004-0.0040.0000.0000.0000.000
177B161SER00.0420.01515.9650.0470.0470.0000.0000.0000.000
178B162GLY00.0470.01718.4590.0160.0160.0000.0000.0000.000
179B163VAL0-0.056-0.01917.7940.0360.0360.0000.0000.0000.000
180B164HIS00.0050.01219.663-0.018-0.0180.0000.0000.0000.000
181B165THR0-0.011-0.01217.5650.0310.0310.0000.0000.0000.000
182B166PHE0-0.0100.01319.817-0.005-0.0050.0000.0000.0000.000
183B167PRO00.0300.01320.709-0.032-0.0320.0000.0000.0000.000
184B168ALA0-0.013-0.00621.6410.0280.0280.0000.0000.0000.000
185B169VAL0-0.007-0.00423.5280.0210.0210.0000.0000.0000.000
186B170LEU0-0.034-0.01627.248-0.006-0.0060.0000.0000.0000.000
187B171GLN0-0.026-0.02328.7100.0220.0220.0000.0000.0000.000
188B172SER00.0410.00832.035-0.001-0.0010.0000.0000.0000.000
189B173SER0-0.0080.00033.0670.0060.0060.0000.0000.0000.000
190B174GLY00.0270.01731.8780.0020.0020.0000.0000.0000.000
191B175LEU0-0.059-0.02128.779-0.014-0.0140.0000.0000.0000.000
192B176TYR00.0390.01624.4900.0090.0090.0000.0000.0000.000
193B177SER0-0.017-0.00626.3370.0060.0060.0000.0000.0000.000
194B178LEU00.0190.02919.7100.0060.0060.0000.0000.0000.000
195B179SER00.001-0.01523.6240.0200.0200.0000.0000.0000.000
196B180SER00.0120.00619.669-0.025-0.0250.0000.0000.0000.000
197B181VAL00.014-0.00522.2160.0320.0320.0000.0000.0000.000
198B182VAL00.0250.01321.414-0.041-0.0410.0000.0000.0000.000
199B183THR0-0.0190.00023.7850.0360.0360.0000.0000.0000.000
200B184VAL00.0170.00624.079-0.024-0.0240.0000.0000.0000.000
201B185PRO00.0690.03025.9890.0250.0250.0000.0000.0000.000
202B186SER00.0460.01629.203-0.012-0.0120.0000.0000.0000.000
203B187SER0-0.010-0.00431.917-0.002-0.0020.0000.0000.0000.000
204B188SER0-0.020-0.00927.786-0.005-0.0050.0000.0000.0000.000
205B189LEU00.002-0.00429.647-0.009-0.0090.0000.0000.0000.000
206B190GLY00.0020.01031.3910.0010.0010.0000.0000.0000.000
207B191THR0-0.047-0.02430.4680.0040.0040.0000.0000.0000.000
208B192GLN0-0.032-0.01223.601-0.002-0.0020.0000.0000.0000.000
209B193THR00.0130.00925.1040.0050.0050.0000.0000.0000.000
210B194TYR00.0350.00523.053-0.043-0.0430.0000.0000.0000.000
211B195ILE00.013-0.01121.3680.0340.0340.0000.0000.0000.000
212B197ASN00.002-0.01916.387-0.008-0.0080.0000.0000.0000.000
213B198VAL00.0380.02416.876-0.077-0.0770.0000.0000.0000.000
214B199ASN0-0.024-0.02514.242-0.071-0.0710.0000.0000.0000.000
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