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: LZV99

Calculation Name: 5JHO-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5JHO

Chain ID: B

ChEMBL ID:

UniProt ID: Q2Y0W8

Base Structure: X-ray

Registration Date: 2023-06-22

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3014165.481554
FMO2-HF: Nuclear repulsion 2921535.451712
FMO2-HF: Total energy -92630.029842
FMO2-MP2: Total energy -92900.689119


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:43:SER)


Summations of interaction energy for fragment #1(B:43:SER)
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.
-24.726-18.2050.538-2.942-4.116-0.001
Interaction energy analysis for fragmet #1(B:43:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.012
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].
3B45ARG10.8790.9383.201-8.870-6.3880.081-1.195-1.3670.007
4B46VAL00.0100.0053.417-2.030-1.1980.029-0.225-0.6360.001
5B47GLN00.0570.0134.217-0.595-0.224-0.001-0.132-0.2390.000
6B48PHE0-0.029-0.0156.0900.0640.0640.0000.0000.0000.000
7B49ILE0-0.005-0.0058.590-0.124-0.1240.0000.0000.0000.000
8B50LEU00.0500.0327.415-0.129-0.1290.0000.0000.0000.000
9B51GLY00.0420.02510.495-0.073-0.0730.0000.0000.0000.000
10B52THR0-0.108-0.05612.4680.0130.0130.0000.0000.0000.000
11B53GLU-1-0.903-0.91313.4630.3150.3150.0000.0000.0000.000
12B54GLU-1-0.961-0.96515.7470.1200.1200.0000.0000.0000.000
13B55ASP-1-0.833-0.93517.2470.0110.0110.0000.0000.0000.000
14B56GLU-1-0.951-0.96920.6360.0310.0310.0000.0000.0000.000
15B57GLU-1-0.864-0.89523.599-0.112-0.1120.0000.0000.0000.000
16B58HIS10.8170.87118.9850.0710.0710.0000.0000.0000.000
17B59VAL0-0.028-0.00419.715-0.011-0.0110.0000.0000.0000.000
18B60PRO00.0220.00717.776-0.010-0.0100.0000.0000.0000.000
19B61HIS10.8260.93520.3860.1870.1870.0000.0000.0000.000
20B62GLU-1-0.890-0.95321.402-0.222-0.2220.0000.0000.0000.000
21B63LEU0-0.013-0.02019.3230.0080.0080.0000.0000.0000.000
22B64PHE0-0.0280.00923.341-0.009-0.0090.0000.0000.0000.000
23B65THR0-0.025-0.01921.3290.0000.0000.0000.0000.0000.000
24B66GLU-1-0.743-0.86924.355-0.204-0.2040.0000.0000.0000.000
25B67LEU0-0.0150.00124.168-0.024-0.0240.0000.0000.0000.000
26B68ASP-1-0.791-0.86826.704-0.197-0.1970.0000.0000.0000.000
27B69GLU-1-0.807-0.88428.425-0.313-0.3130.0000.0000.0000.000
28B70ILE0-0.004-0.00330.5780.0190.0190.0000.0000.0000.000
29B71CYS0-0.088-0.04832.387-0.007-0.0070.0000.0000.0000.000
30B72MET0-0.011-0.00835.0310.0070.0070.0000.0000.0000.000
31B73LYS10.8190.86937.2610.1620.1620.0000.0000.0000.000
32B74GLU-1-0.895-0.91438.562-0.121-0.1210.0000.0000.0000.000
33B75GLY0-0.026-0.00942.4090.0010.0010.0000.0000.0000.000
34B76GLU-1-0.899-0.93440.475-0.141-0.1410.0000.0000.0000.000
35B77ASP-1-0.859-0.92442.679-0.119-0.1190.0000.0000.0000.000
36B78ALA0-0.037-0.00538.399-0.002-0.0020.0000.0000.0000.000
37B79GLU-1-0.885-0.93438.012-0.137-0.1370.0000.0000.0000.000
38B80TRP0-0.037-0.03028.940-0.010-0.0100.0000.0000.0000.000
39B81LYS10.8230.88633.7350.1700.1700.0000.0000.0000.000
40B82GLU-1-0.745-0.87131.136-0.212-0.2120.0000.0000.0000.000
41B83THR0-0.100-0.07728.9960.0080.0080.0000.0000.0000.000
42B84ALA00.0150.01326.7090.0000.0000.0000.0000.0000.000
43B85ARG10.7560.85426.9760.1990.1990.0000.0000.0000.000
44B86TRP00.010-0.00822.1280.0000.0000.0000.0000.0000.000
45B87LEU0-0.020-0.01724.9180.0150.0150.0000.0000.0000.000
46B88LYS10.8170.89818.9620.4030.4030.0000.0000.0000.000
47B89PHE0-0.071-0.02922.558-0.019-0.0190.0000.0000.0000.000
48B90GLU-1-0.746-0.85923.557-0.421-0.4210.0000.0000.0000.000
49B91GLU-1-0.835-0.90325.988-0.188-0.1880.0000.0000.0000.000
50B92ASP-1-0.796-0.88928.060-0.324-0.3240.0000.0000.0000.000
51B93VAL0-0.019-0.00330.4660.0160.0160.0000.0000.0000.000
52B94GLU-1-0.899-0.96933.869-0.198-0.1980.0000.0000.0000.000
53B95ASP-1-0.858-0.92836.272-0.148-0.1480.0000.0000.0000.000
54B96GLY0-0.047-0.02839.0320.0080.0080.0000.0000.0000.000
55B97GLY00.0190.01338.4490.0030.0030.0000.0000.0000.000
56B98GLU-1-0.939-0.94739.468-0.121-0.1210.0000.0000.0000.000
57B99ARG10.6990.81938.0450.1490.1490.0000.0000.0000.000
58B100TRP00.0300.04231.032-0.007-0.0070.0000.0000.0000.000
59B101SER00.0040.01231.5530.0050.0050.0000.0000.0000.000
60B102LYS10.8920.93133.7660.1670.1670.0000.0000.0000.000
61B103PRO00.0270.02729.757-0.011-0.0110.0000.0000.0000.000
62B104TYR0-0.136-0.08225.1870.0030.0030.0000.0000.0000.000
63B105VAL0-0.007-0.01622.211-0.009-0.0090.0000.0000.0000.000
64B106ALA00.0630.05020.632-0.001-0.0010.0000.0000.0000.000
65B107THR0-0.050-0.02319.887-0.031-0.0310.0000.0000.0000.000
66B108LEU00.0520.03216.0830.0180.0180.0000.0000.0000.000
67B109SER0-0.010-0.00119.194-0.005-0.0050.0000.0000.0000.000
68B110LEU00.0550.01212.483-0.024-0.0240.0000.0000.0000.000
69B111HIS0-0.068-0.02815.516-0.099-0.0990.0000.0000.0000.000
70B112SER00.0350.01317.320-0.019-0.0190.0000.0000.0000.000
71B113LEU00.0430.03012.578-0.005-0.0050.0000.0000.0000.000
72B114PHE0-0.018-0.01211.093-0.095-0.0950.0000.0000.0000.000
73B115GLU-1-0.799-0.90513.969-0.498-0.4980.0000.0000.0000.000
74B116LEU00.0240.02313.8060.0430.0430.0000.0000.0000.000
75B117ARG10.8320.8835.8732.5132.5130.0000.0000.0000.000
76B118SER0-0.022-0.01512.2010.0560.0560.0000.0000.0000.000
77B119CYS0-0.039-0.02314.8030.0950.0950.0000.0000.0000.000
78B120LEU00.0400.01412.0810.0750.0750.0000.0000.0000.000
79B121ILE0-0.051-0.01010.3130.0370.0370.0000.0000.0000.000
80B122ASN0-0.069-0.04613.6230.1310.1310.0000.0000.0000.000
81B123GLY00.0390.03817.4200.0570.0570.0000.0000.0000.000
82B124THR00.001-0.00118.3040.0130.0130.0000.0000.0000.000
83B125VAL0-0.002-0.01114.886-0.040-0.0400.0000.0000.0000.000
84B126LEU0-0.045-0.01618.1970.0400.0400.0000.0000.0000.000
85B127LEU00.0250.00714.389-0.013-0.0130.0000.0000.0000.000
86B128ASP-1-0.813-0.87419.126-0.094-0.0940.0000.0000.0000.000
87B129MET00.0060.01522.0630.0260.0260.0000.0000.0000.000
88B130HIS00.0000.01024.707-0.004-0.0040.0000.0000.0000.000
89B131ALA0-0.020-0.00428.0610.0070.0070.0000.0000.0000.000
90B132ASN0-0.107-0.07529.840-0.003-0.0030.0000.0000.0000.000
91B133SER00.015-0.00432.5760.0000.0000.0000.0000.0000.000
92B134ILE00.0800.03330.280-0.005-0.0050.0000.0000.0000.000
93B135GLU-1-0.900-0.95732.417-0.126-0.1260.0000.0000.0000.000
94B136GLU-1-0.796-0.86432.114-0.097-0.0970.0000.0000.0000.000
95B137ILE00.0390.00627.060-0.001-0.0010.0000.0000.0000.000
96B138SER0-0.039-0.03228.728-0.013-0.0130.0000.0000.0000.000
97B139ASP-1-0.828-0.89930.481-0.116-0.1160.0000.0000.0000.000
98B140LEU0-0.025-0.01227.5740.0000.0000.0000.0000.0000.000
99B141ILE0-0.0070.01324.855-0.007-0.0070.0000.0000.0000.000
100B142LEU0-0.011-0.02027.0620.0000.0000.0000.0000.0000.000
101B143ASP-1-0.865-0.93129.983-0.102-0.1020.0000.0000.0000.000
102B144GLN0-0.050-0.02124.6970.0180.0180.0000.0000.0000.000
103B145GLN0-0.035-0.00627.6180.0000.0000.0000.0000.0000.000
104B146GLU-1-0.971-0.97723.506-0.184-0.1840.0000.0000.0000.000
105B147LEU00.0800.03224.213-0.001-0.0010.0000.0000.0000.000
106B148SER0-0.055-0.04726.8340.0030.0030.0000.0000.0000.000
107B149SER0-0.075-0.03729.4530.0110.0110.0000.0000.0000.000
108B150ASP-1-0.838-0.89627.319-0.185-0.1850.0000.0000.0000.000
109B151LEU0-0.032-0.02129.906-0.009-0.0090.0000.0000.0000.000
110B152ASN0-0.027-0.03832.8230.0160.0160.0000.0000.0000.000
111B153ASP-1-0.865-0.94136.246-0.096-0.0960.0000.0000.0000.000
112B154SER0-0.040-0.03238.393-0.003-0.0030.0000.0000.0000.000
113B155MET00.0250.05532.6610.0030.0030.0000.0000.0000.000
114B156ARG10.8720.93133.3550.1060.1060.0000.0000.0000.000
115B157VAL0-0.049-0.02735.104-0.002-0.0020.0000.0000.0000.000
116B158LYS10.8820.92236.9270.1250.1250.0000.0000.0000.000
117B159VAL00.0320.02230.678-0.006-0.0060.0000.0000.0000.000
118B160ARG10.8760.93133.5420.1070.1070.0000.0000.0000.000
119B161GLU-1-0.884-0.93335.093-0.124-0.1240.0000.0000.0000.000
120B162ALA00.0320.00533.5540.0000.0000.0000.0000.0000.000
121B163LEU0-0.0110.00429.009-0.004-0.0040.0000.0000.0000.000
122B164LEU0-0.0320.00532.8850.0010.0010.0000.0000.0000.000
123B165LYS10.8080.91336.0940.1390.1390.0000.0000.0000.000
124B166LYS10.8420.90836.1610.1180.1180.0000.0000.0000.000
125B167HIS10.8590.91131.0480.1890.1890.0000.0000.0000.000
126B168HIS00.0150.03135.9250.0050.0050.0000.0000.0000.000
127B169HIS10.8590.91932.5680.1720.1720.0000.0000.0000.000
128B170GLN0-0.009-0.00635.6730.0040.0040.0000.0000.0000.000
129B171ASN0-0.145-0.06836.4970.0190.0190.0000.0000.0000.000
130B241ILE00.0260.00531.111-0.001-0.0010.0000.0000.0000.000
131B242PRO0-0.033-0.01927.3430.0140.0140.0000.0000.0000.000
132B243THR0-0.013-0.01330.128-0.001-0.0010.0000.0000.0000.000
133B244GLY00.0010.00429.4990.0070.0070.0000.0000.0000.000
134B245ALA0-0.0250.00626.315-0.003-0.0030.0000.0000.0000.000
135B246GLU-1-0.770-0.83324.362-0.161-0.1610.0000.0000.0000.000
136B247ALA00.010-0.00125.574-0.016-0.0160.0000.0000.0000.000
137B248SER00.0080.00420.713-0.001-0.0010.0000.0000.0000.000
138B249ASN00.0450.01223.615-0.003-0.0030.0000.0000.0000.000
139B250VAL0-0.012-0.00321.527-0.009-0.0090.0000.0000.0000.000
140B251LEU0-0.010-0.00124.0340.0240.0240.0000.0000.0000.000
141B252VAL0-0.007-0.00823.326-0.009-0.0090.0000.0000.0000.000
142B253GLY00.0410.00226.4650.0180.0180.0000.0000.0000.000
143B254GLU-1-0.817-0.89829.145-0.236-0.2360.0000.0000.0000.000
144B255VAL00.013-0.01531.8930.0120.0120.0000.0000.0000.000
145B256ASP-1-0.865-0.93434.208-0.149-0.1490.0000.0000.0000.000
146B257ILE0-0.075-0.03236.0240.0010.0010.0000.0000.0000.000
147B258LEU0-0.026-0.00330.1520.0040.0040.0000.0000.0000.000
148B259ASP-1-0.856-0.92731.897-0.174-0.1740.0000.0000.0000.000
149B260ARG10.7760.86727.1160.1650.1650.0000.0000.0000.000
150B261PRO0-0.063-0.03223.5140.0060.0060.0000.0000.0000.000
151B262ILE00.0270.01324.754-0.003-0.0030.0000.0000.0000.000
152B263VAL0-0.005-0.01019.193-0.014-0.0140.0000.0000.0000.000
153B264ALA0-0.017-0.00720.9660.0200.0200.0000.0000.0000.000
154B265PHE0-0.0040.00716.660-0.030-0.0300.0000.0000.0000.000
155B266VAL0-0.001-0.00419.5670.0280.0280.0000.0000.0000.000
156B267ARG10.7760.86215.8280.2070.2070.0000.0000.0000.000
157B268LEU0-0.036-0.00921.1260.0220.0220.0000.0000.0000.000
158B269SER0-0.004-0.02323.932-0.005-0.0050.0000.0000.0000.000
159B270PRO0-0.0160.01125.1250.0060.0060.0000.0000.0000.000
160B271ALA00.0220.01126.432-0.012-0.0120.0000.0000.0000.000
161B272VAL0-0.023-0.02327.7350.0180.0180.0000.0000.0000.000
162B273LEU0-0.030-0.00730.752-0.012-0.0120.0000.0000.0000.000
163B274LEU00.0000.00529.2960.0100.0100.0000.0000.0000.000
164B275SER0-0.015-0.01633.273-0.006-0.0060.0000.0000.0000.000
165B276GLY0-0.009-0.00736.368-0.001-0.0010.0000.0000.0000.000
166B277LEU0-0.0140.00429.058-0.004-0.0040.0000.0000.0000.000
167B278THR00.0060.01229.776-0.015-0.0150.0000.0000.0000.000
168B279GLU-1-0.863-0.90131.936-0.168-0.1680.0000.0000.0000.000
169B280VAL0-0.002-0.00532.9270.0140.0140.0000.0000.0000.000
170B281PRO0-0.055-0.03933.224-0.006-0.0060.0000.0000.0000.000
171B282ILE00.0160.01228.8350.0080.0080.0000.0000.0000.000
172B283PRO0-0.037-0.01829.441-0.004-0.0040.0000.0000.0000.000
173B284THR00.0340.00726.169-0.003-0.0030.0000.0000.0000.000
174B285ARG10.7360.83421.8720.1780.1780.0000.0000.0000.000
175B286PHE00.000-0.00917.908-0.004-0.0040.0000.0000.0000.000
176B287LEU0-0.0020.00522.2130.0170.0170.0000.0000.0000.000
177B288PHE00.0070.00117.904-0.030-0.0300.0000.0000.0000.000
178B289ILE00.0010.00521.7790.0220.0220.0000.0000.0000.000
179B290LEU0-0.009-0.00421.336-0.025-0.0250.0000.0000.0000.000
180B291LEU00.0140.02124.3150.0120.0120.0000.0000.0000.000
181B292GLY00.0490.01527.561-0.005-0.0050.0000.0000.0000.000
182B293PRO0-0.0250.00628.4830.0110.0110.0000.0000.0000.000
183B294VAL00.0070.00630.918-0.013-0.0130.0000.0000.0000.000
184B295GLY0-0.031-0.01432.4790.0040.0040.0000.0000.0000.000
185B296LYS10.8450.91225.9060.3080.3080.0000.0000.0000.000
186B297GLY00.0270.01627.429-0.025-0.0250.0000.0000.0000.000
187B298GLN0-0.001-0.00627.883-0.024-0.0240.0000.0000.0000.000
188B299GLN0-0.016-0.00422.7770.0190.0190.0000.0000.0000.000
189B300TYR00.016-0.00423.204-0.032-0.0320.0000.0000.0000.000
190B301HIS10.9020.95023.6690.3090.3090.0000.0000.0000.000
191B302GLU-1-0.806-0.89621.839-0.451-0.4510.0000.0000.0000.000
192B303ILE0-0.038-0.00518.235-0.055-0.0550.0000.0000.0000.000
193B304GLY00.0210.01319.207-0.045-0.0450.0000.0000.0000.000
194B305ARG10.7600.82520.8940.4210.4210.0000.0000.0000.000
195B306SER0-0.047-0.03916.186-0.038-0.0380.0000.0000.0000.000
196B307MET0-0.016-0.00614.865-0.073-0.0730.0000.0000.0000.000
197B308ALA00.009-0.00217.294-0.014-0.0140.0000.0000.0000.000
198B309THR00.0300.00417.1050.0210.0210.0000.0000.0000.000
199B310ILE0-0.0240.01110.1500.0030.0030.0000.0000.0000.000
200B311MET0-0.039-0.01214.421-0.045-0.0450.0000.0000.0000.000
201B312THR0-0.086-0.05616.6040.0810.0810.0000.0000.0000.000
202B313ASP-1-0.829-0.92111.979-0.854-0.8540.0000.0000.0000.000
203B314GLU-1-0.873-0.91515.145-0.343-0.3430.0000.0000.0000.000
204B315ILE00.0460.0399.1720.0740.0740.0000.0000.0000.000
205B316PHE00.009-0.0069.0240.0180.0180.0000.0000.0000.000
206B317HIS10.8220.90111.2940.4720.4720.0000.0000.0000.000
207B318ASP-1-0.896-0.95413.900-0.248-0.2480.0000.0000.0000.000
208B319VAL0-0.022-0.0148.8480.0890.0890.0000.0000.0000.000
209B320ALA0-0.0030.00212.0960.0680.0680.0000.0000.0000.000
210B321TYR0-0.063-0.06414.4100.0620.0620.0000.0000.0000.000
211B322LYS10.7920.88213.9210.0240.0240.0000.0000.0000.000
212B323ALA0-0.0410.00211.7550.0770.0770.0000.0000.0000.000
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