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: 39M8L

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 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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3009098.567014
FMO2-HF: Nuclear repulsion 2916469.146219
FMO2-HF: Total energy -92629.420795
FMO2-MP2: Total energy -92900.057914


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.
-27.14-211.684-3.096-4.730.024
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 : 0.001 / q_NPA : -0.014
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].
3B45ARG10.8870.9382.678-11.896-8.3421.013-2.058-2.5100.024
4B46VAL0-0.010-0.0182.618-4.087-2.8390.626-0.668-1.2070.001
5B47GLN00.0490.0233.889-0.615-0.3710.001-0.054-0.1910.000
6B48PHE0-0.026-0.0125.812-0.081-0.0810.0000.0000.0000.000
7B49ILE0-0.033-0.0177.951-0.106-0.1060.0000.0000.0000.000
8B50LEU00.0450.0387.434-0.158-0.1580.0000.0000.0000.000
9B51GLY00.0350.01410.549-0.046-0.0460.0000.0000.0000.000
10B52THR0-0.082-0.04112.6250.0060.0060.0000.0000.0000.000
11B53GLU-1-0.888-0.90613.4760.3510.3510.0000.0000.0000.000
12B54GLU-1-0.972-0.98015.9260.1230.1230.0000.0000.0000.000
13B55ASP-1-0.843-0.94017.436-0.016-0.0160.0000.0000.0000.000
14B56GLU-1-0.965-0.96920.8990.0300.0300.0000.0000.0000.000
15B57GLU-1-0.851-0.91824.337-0.137-0.1370.0000.0000.0000.000
16B58HIS10.8040.88018.9030.1130.1130.0000.0000.0000.000
17B59VAL0-0.027-0.00819.936-0.012-0.0120.0000.0000.0000.000
18B60PRO00.0430.01918.321-0.017-0.0170.0000.0000.0000.000
19B61HIS10.8140.92120.8790.2000.2000.0000.0000.0000.000
20B62GLU-1-0.897-0.95622.027-0.207-0.2070.0000.0000.0000.000
21B63LEU0-0.003-0.01519.6580.0040.0040.0000.0000.0000.000
22B64PHE0-0.0310.00923.745-0.005-0.0050.0000.0000.0000.000
23B65THR0-0.033-0.02621.910-0.006-0.0060.0000.0000.0000.000
24B66GLU-1-0.728-0.85124.953-0.220-0.2200.0000.0000.0000.000
25B67LEU0-0.023-0.00624.705-0.027-0.0270.0000.0000.0000.000
26B68ASP-1-0.796-0.87027.060-0.225-0.2250.0000.0000.0000.000
27B69GLU-1-0.797-0.89028.449-0.349-0.3490.0000.0000.0000.000
28B70ILE0-0.010-0.00230.7890.0220.0220.0000.0000.0000.000
29B71CYS0-0.076-0.04532.579-0.009-0.0090.0000.0000.0000.000
30B72MET00.0270.01635.2620.0090.0090.0000.0000.0000.000
31B73LYS10.7940.86736.7530.1900.1900.0000.0000.0000.000
32B74GLU-1-0.887-0.91838.257-0.145-0.1450.0000.0000.0000.000
33B75GLY0-0.015-0.00742.1680.0000.0000.0000.0000.0000.000
34B76GLU-1-0.904-0.94240.729-0.161-0.1610.0000.0000.0000.000
35B77ASP-1-0.870-0.93742.713-0.143-0.1430.0000.0000.0000.000
36B78ALA0-0.041-0.00138.7070.0000.0000.0000.0000.0000.000
37B79GLU-1-0.881-0.93338.148-0.161-0.1610.0000.0000.0000.000
38B80TRP0-0.040-0.03129.238-0.010-0.0100.0000.0000.0000.000
39B81LYS10.8400.89334.0230.1910.1910.0000.0000.0000.000
40B82GLU-1-0.728-0.86331.766-0.226-0.2260.0000.0000.0000.000
41B83THR0-0.107-0.08429.4610.0070.0070.0000.0000.0000.000
42B84ALA00.0280.01827.3840.0010.0010.0000.0000.0000.000
43B85ARG10.7650.86227.5770.2050.2050.0000.0000.0000.000
44B86TRP0-0.010-0.01722.986-0.004-0.0040.0000.0000.0000.000
45B87LEU00.018-0.00625.6000.0150.0150.0000.0000.0000.000
46B88LYS10.8270.92520.0360.3790.3790.0000.0000.0000.000
47B89PHE0-0.073-0.04323.596-0.017-0.0170.0000.0000.0000.000
48B90GLU-1-0.706-0.83024.365-0.418-0.4180.0000.0000.0000.000
49B91GLU-1-0.869-0.92526.949-0.183-0.1830.0000.0000.0000.000
50B92ASP-1-0.804-0.89729.043-0.327-0.3270.0000.0000.0000.000
51B93VAL0-0.0050.00731.4140.0180.0180.0000.0000.0000.000
52B94GLU-1-0.906-0.96534.559-0.203-0.2030.0000.0000.0000.000
53B95ASP-1-0.892-0.94737.055-0.153-0.1530.0000.0000.0000.000
54B96GLY0-0.040-0.02739.6820.0080.0080.0000.0000.0000.000
55B97GLY00.006-0.00938.6420.0030.0030.0000.0000.0000.000
56B98GLU-1-0.982-0.97039.676-0.129-0.1290.0000.0000.0000.000
57B99ARG10.7560.87939.3050.1540.1540.0000.0000.0000.000
58B100TRP00.0260.02731.892-0.007-0.0070.0000.0000.0000.000
59B101SER00.0240.02832.4880.0060.0060.0000.0000.0000.000
60B102LYS10.8920.92834.5980.1600.1600.0000.0000.0000.000
61B103PRO00.0380.02930.512-0.011-0.0110.0000.0000.0000.000
62B104TYR0-0.132-0.07226.0920.0070.0070.0000.0000.0000.000
63B105VAL0-0.006-0.01522.650-0.011-0.0110.0000.0000.0000.000
64B106ALA00.0390.04121.6180.0000.0000.0000.0000.0000.000
65B107THR0-0.016-0.01120.392-0.025-0.0250.0000.0000.0000.000
66B108LEU00.0370.02416.4500.0110.0110.0000.0000.0000.000
67B109SER0-0.0010.00019.1970.0060.0060.0000.0000.0000.000
68B110LEU00.0540.01512.484-0.023-0.0230.0000.0000.0000.000
69B111HIS0-0.068-0.03515.730-0.100-0.1000.0000.0000.0000.000
70B112SER00.0390.02117.692-0.014-0.0140.0000.0000.0000.000
71B113LEU00.0150.01312.977-0.014-0.0140.0000.0000.0000.000
72B114PHE0-0.017-0.01210.904-0.094-0.0940.0000.0000.0000.000
73B115GLU-1-0.786-0.89014.174-0.610-0.6100.0000.0000.0000.000
74B116LEU00.0240.02714.1650.0300.0300.0000.0000.0000.000
75B117ARG10.8010.8546.3433.1203.1200.0000.0000.0000.000
76B118SER0-0.033-0.02612.2570.0210.0210.0000.0000.0000.000
77B119CYS0-0.040-0.02814.6760.1030.1030.0000.0000.0000.000
78B120LEU00.0330.01411.9970.0840.0840.0000.0000.0000.000
79B121ILE0-0.062-0.01010.5620.0230.0230.0000.0000.0000.000
80B122ASN0-0.051-0.03413.8110.1200.1200.0000.0000.0000.000
81B123GLY00.0430.05017.1540.0700.0700.0000.0000.0000.000
82B124THR0-0.008-0.00118.5350.0060.0060.0000.0000.0000.000
83B125VAL00.008-0.00115.195-0.037-0.0370.0000.0000.0000.000
84B126LEU0-0.041-0.01518.4740.0410.0410.0000.0000.0000.000
85B127LEU00.002-0.00415.070-0.018-0.0180.0000.0000.0000.000
86B128ASP-1-0.812-0.86219.781-0.164-0.1640.0000.0000.0000.000
87B129MET0-0.0100.01022.4240.0290.0290.0000.0000.0000.000
88B130HIS0-0.0110.00625.1240.0040.0040.0000.0000.0000.000
89B131ALA0-0.0050.00428.4860.0080.0080.0000.0000.0000.000
90B132ASN0-0.104-0.07630.4450.0000.0000.0000.0000.0000.000
91B133SER00.006-0.00432.8070.0030.0030.0000.0000.0000.000
92B134ILE00.0930.03930.516-0.007-0.0070.0000.0000.0000.000
93B135GLU-1-0.911-0.96132.379-0.158-0.1580.0000.0000.0000.000
94B136GLU-1-0.817-0.89532.448-0.134-0.1340.0000.0000.0000.000
95B137ILE00.0360.01227.157-0.005-0.0050.0000.0000.0000.000
96B138SER0-0.038-0.02528.783-0.018-0.0180.0000.0000.0000.000
97B139ASP-1-0.812-0.89430.524-0.160-0.1600.0000.0000.0000.000
98B140LEU00.0060.00828.0120.0000.0000.0000.0000.0000.000
99B141ILE0-0.033-0.00225.066-0.010-0.0100.0000.0000.0000.000
100B142LEU0-0.013-0.02627.339-0.003-0.0030.0000.0000.0000.000
101B143ASP-1-0.876-0.93030.084-0.154-0.1540.0000.0000.0000.000
102B144GLN0-0.058-0.02724.7730.0080.0080.0000.0000.0000.000
103B145GLN0-0.035-0.01527.8980.0030.0030.0000.0000.0000.000
104B146GLU-1-0.964-0.98324.025-0.285-0.2850.0000.0000.0000.000
105B147LEU00.0780.03824.164-0.003-0.0030.0000.0000.0000.000
106B148SER0-0.050-0.02927.2080.0050.0050.0000.0000.0000.000
107B149SER0-0.089-0.04829.3880.0200.0200.0000.0000.0000.000
108B150ASP-1-0.807-0.90026.828-0.276-0.2760.0000.0000.0000.000
109B151LEU0-0.075-0.03629.700-0.001-0.0010.0000.0000.0000.000
110B152ASN0-0.033-0.04032.6770.0150.0150.0000.0000.0000.000
111B153ASP-1-0.846-0.92736.008-0.134-0.1340.0000.0000.0000.000
112B154SER0-0.075-0.05838.649-0.002-0.0020.0000.0000.0000.000
113B155MET00.0290.04232.3470.0060.0060.0000.0000.0000.000
114B156ARG10.8790.94433.9190.1530.1530.0000.0000.0000.000
115B157VAL0-0.059-0.02535.269-0.002-0.0020.0000.0000.0000.000
116B158LYS10.8840.92536.9060.1540.1540.0000.0000.0000.000
117B159VAL00.0560.03430.688-0.003-0.0030.0000.0000.0000.000
118B160ARG10.8820.93333.6120.1440.1440.0000.0000.0000.000
119B161GLU-1-0.884-0.93234.887-0.151-0.1510.0000.0000.0000.000
120B162ALA00.0300.00433.6010.0030.0030.0000.0000.0000.000
121B163LEU00.0010.01129.073-0.002-0.0020.0000.0000.0000.000
122B164LEU0-0.0250.00632.8540.0030.0030.0000.0000.0000.000
123B165LYS10.7920.90136.0050.1700.1700.0000.0000.0000.000
124B166LYS10.8500.91436.2700.1420.1420.0000.0000.0000.000
125B167HIS10.8660.90631.1890.2200.2200.0000.0000.0000.000
126B168HIS0-0.0070.02936.2670.0070.0070.0000.0000.0000.000
127B169HIS10.8690.93733.2270.1900.1900.0000.0000.0000.000
128B170GLN00.0100.00236.2460.0010.0010.0000.0000.0000.000
129B171ASN0-0.120-0.05737.6740.0180.0180.0000.0000.0000.000
130B241ILE00.0200.00532.077-0.001-0.0010.0000.0000.0000.000
131B242PRO0-0.028-0.02228.1940.0140.0140.0000.0000.0000.000
132B243THR0-0.016-0.00731.1220.0000.0000.0000.0000.0000.000
133B244GLY0-0.004-0.00129.9420.0030.0030.0000.0000.0000.000
134B245ALA0-0.0010.01227.191-0.006-0.0060.0000.0000.0000.000
135B246GLU-1-0.766-0.84224.491-0.193-0.1930.0000.0000.0000.000
136B247ALA00.016-0.00125.932-0.014-0.0140.0000.0000.0000.000
137B248SER00.0150.00421.702-0.018-0.0180.0000.0000.0000.000
138B249ASN00.005-0.00823.9350.0030.0030.0000.0000.0000.000
139B250VAL0-0.0240.00221.739-0.019-0.0190.0000.0000.0000.000
140B251LEU00.0030.00124.1940.0250.0250.0000.0000.0000.000
141B252VAL00.010-0.00323.563-0.019-0.0190.0000.0000.0000.000
142B253GLY00.0510.01926.7160.0240.0240.0000.0000.0000.000
143B254GLU-1-0.852-0.93029.220-0.273-0.2730.0000.0000.0000.000
144B255VAL00.006-0.02031.8570.0140.0140.0000.0000.0000.000
145B256ASP-1-0.892-0.94433.970-0.186-0.1860.0000.0000.0000.000
146B257ILE0-0.059-0.02435.9300.0000.0000.0000.0000.0000.000
147B258LEU0-0.050-0.01429.7750.0040.0040.0000.0000.0000.000
148B259ASP-1-0.867-0.93032.118-0.232-0.2320.0000.0000.0000.000
149B260ARG10.7920.89227.0390.2320.2320.0000.0000.0000.000
150B261PRO0-0.034-0.03223.8300.0100.0100.0000.0000.0000.000
151B262ILE0-0.017-0.01024.9560.0000.0000.0000.0000.0000.000
152B263VAL00.0180.00518.669-0.006-0.0060.0000.0000.0000.000
153B264ALA0-0.014-0.00721.0150.0150.0150.0000.0000.0000.000
154B265PHE0-0.0150.00516.602-0.024-0.0240.0000.0000.0000.000
155B266VAL00.007-0.00519.3620.0190.0190.0000.0000.0000.000
156B267ARG10.7830.85716.0180.3070.3070.0000.0000.0000.000
157B268LEU0-0.032-0.01621.3410.0230.0230.0000.0000.0000.000
158B269SER00.019-0.02324.179-0.007-0.0070.0000.0000.0000.000
159B270PRO0-0.0350.01425.5130.0080.0080.0000.0000.0000.000
160B271ALA00.0340.00526.625-0.010-0.0100.0000.0000.0000.000
161B272VAL0-0.006-0.01028.0200.0210.0210.0000.0000.0000.000
162B273LEU0-0.038-0.01030.893-0.012-0.0120.0000.0000.0000.000
163B274LEU00.0000.01329.3780.0120.0120.0000.0000.0000.000
164B275SER0-0.013-0.02133.505-0.004-0.0040.0000.0000.0000.000
165B276GLY0-0.013-0.01036.518-0.004-0.0040.0000.0000.0000.000
166B277LEU0-0.0080.01029.517-0.003-0.0030.0000.0000.0000.000
167B278THR00.0040.00230.187-0.014-0.0140.0000.0000.0000.000
168B279GLU-1-0.877-0.91432.460-0.179-0.1790.0000.0000.0000.000
169B280VAL0-0.017-0.01333.1830.0160.0160.0000.0000.0000.000
170B281PRO0-0.051-0.03333.490-0.007-0.0070.0000.0000.0000.000
171B282ILE0-0.0030.00329.3130.0100.0100.0000.0000.0000.000
172B283PRO0-0.035-0.01529.664-0.006-0.0060.0000.0000.0000.000
173B284THR00.0210.00526.238-0.003-0.0030.0000.0000.0000.000
174B285ARG10.7560.86221.8770.2130.2130.0000.0000.0000.000
175B286PHE00.005-0.00517.873-0.015-0.0150.0000.0000.0000.000
176B287LEU00.0060.00522.0350.0290.0290.0000.0000.0000.000
177B288PHE0-0.006-0.01017.731-0.040-0.0400.0000.0000.0000.000
178B289ILE0-0.012-0.00321.7380.0320.0320.0000.0000.0000.000
179B290LEU0-0.004-0.00121.459-0.028-0.0280.0000.0000.0000.000
180B291LEU00.0100.01724.1440.0240.0240.0000.0000.0000.000
181B292GLY00.0510.00826.932-0.016-0.0160.0000.0000.0000.000
182B293PRO0-0.0210.01428.3820.0150.0150.0000.0000.0000.000
183B294VAL00.0200.00130.922-0.013-0.0130.0000.0000.0000.000
184B295GLY0-0.032-0.01432.5260.0020.0020.0000.0000.0000.000
185B296LYS10.8570.92925.6990.3740.3740.0000.0000.0000.000
186B297GLY00.0490.02527.505-0.027-0.0270.0000.0000.0000.000
187B298GLN0-0.009-0.01128.493-0.021-0.0210.0000.0000.0000.000
188B299GLN0-0.023-0.01823.2530.0110.0110.0000.0000.0000.000
189B300TYR00.0360.01323.505-0.034-0.0340.0000.0000.0000.000
190B301HIS10.9030.96024.0410.3330.3330.0000.0000.0000.000
191B302GLU-1-0.802-0.90222.201-0.473-0.4730.0000.0000.0000.000
192B303ILE0-0.0420.00418.455-0.054-0.0540.0000.0000.0000.000
193B304GLY00.0140.00719.503-0.051-0.0510.0000.0000.0000.000
194B305ARG10.7520.82521.3380.4400.4400.0000.0000.0000.000
195B306SER0-0.041-0.04516.601-0.032-0.0320.0000.0000.0000.000
196B307MET0-0.025-0.00614.958-0.075-0.0750.0000.0000.0000.000
197B308ALA00.0340.00917.601-0.017-0.0170.0000.0000.0000.000
198B309THR00.009-0.00517.9690.0260.0260.0000.0000.0000.000
199B310ILE0-0.0220.00710.8330.0040.0040.0000.0000.0000.000
200B311MET0-0.031-0.00414.870-0.059-0.0590.0000.0000.0000.000
201B312THR0-0.108-0.06217.0620.0850.0850.0000.0000.0000.000
202B313ASP-1-0.844-0.92512.848-0.790-0.7900.0000.0000.0000.000
203B314GLU-1-0.882-0.93115.555-0.317-0.3170.0000.0000.0000.000
204B315ILE00.0600.03610.3920.0750.0750.0000.0000.0000.000
205B316PHE0-0.001-0.0109.517-0.024-0.0240.0000.0000.0000.000
206B317HIS10.8190.90011.9080.4100.4100.0000.0000.0000.000
207B318ASP-1-0.895-0.95714.274-0.220-0.2200.0000.0000.0000.000
208B319VAL0-0.042-0.0159.0580.0650.0650.0000.0000.0000.000
209B320ALA00.0160.01012.2330.0650.0650.0000.0000.0000.000
210B321TYR0-0.056-0.05014.4850.0600.0600.0000.0000.0000.000
211B322LYS10.7960.90014.0840.0340.0340.0000.0000.0000.000
212B323ALA0-0.060-0.00612.2120.0670.0670.0000.0000.0000.000
213B324LYS10.8170.88112.6900.0090.0090.0000.0000.0000.000
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