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

tag_button

FMODB ID: JLV79

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 OptH
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 -3008568.326563
FMO2-HF: Nuclear repulsion 2915940.347223
FMO2-HF: Total energy -92627.97934
FMO2-MP2: Total energy -92898.63737


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.
-26.143-20.5555.032-4.75-5.8720.027
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 : -0.006 / q_NPA : -0.021
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].
3B45ARG10.8900.9382.661-12.059-8.3461.134-2.179-2.6690.026
4B46VAL0-0.011-0.0132.022-3.162-3.2433.831-2.033-1.7180.004
5B47GLN00.0860.0623.876-1.146-0.8880.001-0.063-0.1960.000
6B48PHE0-0.032-0.0175.810-0.256-0.2560.0000.0000.0000.000
7B49ILE0-0.032-0.0157.966-0.160-0.1600.0000.0000.0000.000
8B50LEU00.0700.0547.702-0.187-0.1870.0000.0000.0000.000
9B51GLY00.006-0.00210.549-0.074-0.0740.0000.0000.0000.000
10B52THR0-0.143-0.07412.624-0.040-0.0400.0000.0000.0000.000
11B53GLU-1-0.890-0.93613.0400.5010.5010.0000.0000.0000.000
12B54GLU-1-0.998-0.99215.9340.1530.1530.0000.0000.0000.000
13B55ASP-1-0.887-0.95917.6610.0340.0340.0000.0000.0000.000
14B56GLU-1-0.998-0.98720.9010.0620.0620.0000.0000.0000.000
15B57GLU-1-0.924-0.98024.337-0.096-0.0960.0000.0000.0000.000
16B58HIS10.8380.90918.6530.0680.0680.0000.0000.0000.000
17B59VAL0-0.041-0.01619.929-0.004-0.0040.0000.0000.0000.000
18B60PRO00.0550.02118.354-0.023-0.0230.0000.0000.0000.000
19B61HIS10.8150.92120.9620.1400.1400.0000.0000.0000.000
20B62GLU-1-0.923-0.95122.304-0.145-0.1450.0000.0000.0000.000
21B63LEU00.011-0.01220.0420.0010.0010.0000.0000.0000.000
22B64PHE0-0.054-0.00323.945-0.003-0.0030.0000.0000.0000.000
23B65THR0-0.044-0.02522.185-0.024-0.0240.0000.0000.0000.000
24B66GLU-1-0.715-0.85425.036-0.196-0.1960.0000.0000.0000.000
25B67LEU0-0.051-0.02124.648-0.028-0.0280.0000.0000.0000.000
26B68ASP-1-0.752-0.86627.064-0.207-0.2070.0000.0000.0000.000
27B69GLU-1-0.821-0.91428.502-0.323-0.3230.0000.0000.0000.000
28B70ILE0-0.021-0.00730.8330.0210.0210.0000.0000.0000.000
29B71CYS0-0.077-0.04732.561-0.009-0.0090.0000.0000.0000.000
30B72MET00.0110.00935.2320.0100.0100.0000.0000.0000.000
31B73LYS10.8020.87536.6710.1770.1770.0000.0000.0000.000
32B74GLU-1-0.885-0.92338.190-0.139-0.1390.0000.0000.0000.000
33B75GLY0-0.014-0.00342.0660.0000.0000.0000.0000.0000.000
34B76GLU-1-0.910-0.95140.890-0.149-0.1490.0000.0000.0000.000
35B77ASP-1-0.889-0.94742.402-0.135-0.1350.0000.0000.0000.000
36B78ALA0-0.045-0.01438.6860.0010.0010.0000.0000.0000.000
37B79GLU-1-0.942-0.98038.132-0.144-0.1440.0000.0000.0000.000
38B80TRP0-0.065-0.02829.157-0.009-0.0090.0000.0000.0000.000
39B81LYS10.8840.93334.0970.1790.1790.0000.0000.0000.000
40B82GLU-1-0.746-0.87931.547-0.202-0.2020.0000.0000.0000.000
41B83THR0-0.113-0.06629.2190.0060.0060.0000.0000.0000.000
42B84ALA00.0290.01827.0900.0010.0010.0000.0000.0000.000
43B85ARG10.8110.91927.4680.1730.1730.0000.0000.0000.000
44B86TRP00.007-0.00522.377-0.002-0.0020.0000.0000.0000.000
45B87LEU0-0.002-0.01725.4390.0140.0140.0000.0000.0000.000
46B88LYS10.9090.97720.6510.2560.2560.0000.0000.0000.000
47B89PHE0-0.067-0.04423.080-0.013-0.0130.0000.0000.0000.000
48B90GLU-1-0.713-0.85524.010-0.353-0.3530.0000.0000.0000.000
49B91GLU-1-0.917-0.96126.453-0.149-0.1490.0000.0000.0000.000
50B92ASP-1-0.795-0.90128.186-0.285-0.2850.0000.0000.0000.000
51B93VAL0-0.0020.00930.9610.0170.0170.0000.0000.0000.000
52B94GLU-1-0.933-0.97734.107-0.177-0.1770.0000.0000.0000.000
53B95ASP-1-0.950-0.98136.557-0.134-0.1340.0000.0000.0000.000
54B96GLY0-0.036-0.02239.2140.0070.0070.0000.0000.0000.000
55B97GLY00.003-0.01538.3380.0020.0020.0000.0000.0000.000
56B98GLU-1-1.008-0.98939.363-0.113-0.1130.0000.0000.0000.000
57B99ARG10.8630.93438.8260.1300.1300.0000.0000.0000.000
58B100TRP00.0230.03031.433-0.005-0.0050.0000.0000.0000.000
59B101SER00.0300.02731.8730.0070.0070.0000.0000.0000.000
60B102LYS10.8870.92933.9370.1300.1300.0000.0000.0000.000
61B103PRO00.0370.02729.977-0.010-0.0100.0000.0000.0000.000
62B104TYR0-0.125-0.05825.2580.0090.0090.0000.0000.0000.000
63B105VAL0-0.007-0.01222.028-0.009-0.0090.0000.0000.0000.000
64B106ALA00.0350.03421.035-0.002-0.0020.0000.0000.0000.000
65B107THR0-0.027-0.01119.753-0.020-0.0200.0000.0000.0000.000
66B108LEU00.0590.02515.6180.0080.0080.0000.0000.0000.000
67B109SER00.0160.01518.670-0.012-0.0120.0000.0000.0000.000
68B110LEU00.0560.02212.199-0.015-0.0150.0000.0000.0000.000
69B111HIS0-0.087-0.05615.282-0.106-0.1060.0000.0000.0000.000
70B112SER00.0120.00817.231-0.036-0.0360.0000.0000.0000.000
71B113LEU00.0520.02412.231-0.020-0.0200.0000.0000.0000.000
72B114PHE0-0.027-0.01210.466-0.097-0.0970.0000.0000.0000.000
73B115GLU-1-0.836-0.91313.715-0.611-0.6110.0000.0000.0000.000
74B116LEU00.0270.02313.7630.0210.0210.0000.0000.0000.000
75B117ARG10.8060.8756.2183.2083.2080.0000.0000.0000.000
76B118SER0-0.056-0.03512.1650.0120.0120.0000.0000.0000.000
77B119CYS0-0.015-0.01014.4570.0970.0970.0000.0000.0000.000
78B120LEU00.0240.01211.7800.0860.0860.0000.0000.0000.000
79B121ILE0-0.058-0.00910.2660.0110.0110.0000.0000.0000.000
80B122ASN0-0.028-0.02413.4300.0620.0620.0000.0000.0000.000
81B123GLY00.0280.04216.8380.0730.0730.0000.0000.0000.000
82B124THR0-0.005-0.00218.1660.0020.0020.0000.0000.0000.000
83B125VAL00.0080.00114.911-0.032-0.0320.0000.0000.0000.000
84B126LEU0-0.041-0.01518.1700.0390.0390.0000.0000.0000.000
85B127LEU00.005-0.00615.109-0.013-0.0130.0000.0000.0000.000
86B128ASP-1-0.812-0.88019.770-0.121-0.1210.0000.0000.0000.000
87B129MET0-0.0110.01022.4150.0250.0250.0000.0000.0000.000
88B130HIS0-0.0100.02325.1130.0050.0050.0000.0000.0000.000
89B131ALA00.0260.02528.4770.0060.0060.0000.0000.0000.000
90B132ASN0-0.059-0.03430.322-0.003-0.0030.0000.0000.0000.000
91B133SER00.023-0.00132.6950.0020.0020.0000.0000.0000.000
92B134ILE00.1110.05230.551-0.007-0.0070.0000.0000.0000.000
93B135GLU-1-0.914-0.94032.224-0.143-0.1430.0000.0000.0000.000
94B136GLU-1-0.904-0.95031.781-0.126-0.1260.0000.0000.0000.000
95B137ILE00.0200.00027.006-0.006-0.0060.0000.0000.0000.000
96B138SER0-0.047-0.06028.558-0.018-0.0180.0000.0000.0000.000
97B139ASP-1-0.821-0.91530.266-0.157-0.1570.0000.0000.0000.000
98B140LEU00.0050.00827.680-0.002-0.0020.0000.0000.0000.000
99B141ILE0-0.053-0.01825.013-0.012-0.0120.0000.0000.0000.000
100B142LEU0-0.040-0.04327.046-0.004-0.0040.0000.0000.0000.000
101B143ASP-1-0.937-0.96029.763-0.153-0.1530.0000.0000.0000.000
102B144GLN0-0.061-0.02124.222-0.005-0.0050.0000.0000.0000.000
103B145GLN0-0.037-0.02727.4890.0040.0040.0000.0000.0000.000
104B146GLU-1-0.958-0.98423.733-0.288-0.2880.0000.0000.0000.000
105B147LEU00.0960.05023.801-0.002-0.0020.0000.0000.0000.000
106B148SER0-0.068-0.02926.8050.0070.0070.0000.0000.0000.000
107B149SER0-0.090-0.05629.0450.0210.0210.0000.0000.0000.000
108B150ASP-1-0.875-0.91426.287-0.289-0.2890.0000.0000.0000.000
109B151LEU0-0.096-0.07228.9990.0000.0000.0000.0000.0000.000
110B152ASN0-0.005-0.01532.3090.0120.0120.0000.0000.0000.000
111B153ASP-1-0.827-0.92535.651-0.137-0.1370.0000.0000.0000.000
112B154SER0-0.087-0.05738.288-0.001-0.0010.0000.0000.0000.000
113B155MET00.0090.02431.9030.0050.0050.0000.0000.0000.000
114B156ARG10.9921.01633.6120.1510.1510.0000.0000.0000.000
115B157VAL0-0.069-0.02934.970-0.001-0.0010.0000.0000.0000.000
116B158LYS10.9740.98036.7860.1480.1480.0000.0000.0000.000
117B159VAL00.0690.04430.520-0.001-0.0010.0000.0000.0000.000
118B160ARG10.8750.93233.4290.1370.1370.0000.0000.0000.000
119B161GLU-1-0.976-0.98834.676-0.141-0.1410.0000.0000.0000.000
120B162ALA00.0270.00333.4320.0030.0030.0000.0000.0000.000
121B163LEU0-0.0010.00328.786-0.001-0.0010.0000.0000.0000.000
122B164LEU0-0.039-0.00232.7310.0030.0030.0000.0000.0000.000
123B165LYS10.8110.92335.9000.1580.1580.0000.0000.0000.000
124B166LYS10.9030.94136.2330.1250.1250.0000.0000.0000.000
125B167HIS10.8830.92231.2620.2000.2000.0000.0000.0000.000
126B168HIS0-0.0120.02436.3160.0080.0080.0000.0000.0000.000
127B169HIS10.8440.92434.1790.1610.1610.0000.0000.0000.000
128B170GLN00.0120.01536.1110.0010.0010.0000.0000.0000.000
129B171ASN0-0.089-0.03937.9220.0080.0080.0000.0000.0000.000
130B241ILE0-0.019-0.02932.0270.0000.0000.0000.0000.0000.000
131B242PRO00.0340.02028.3540.0110.0110.0000.0000.0000.000
132B243THR0-0.014-0.00331.228-0.001-0.0010.0000.0000.0000.000
133B244GLY0-0.007-0.00730.1910.0010.0010.0000.0000.0000.000
134B245ALA00.0020.01527.443-0.003-0.0030.0000.0000.0000.000
135B246GLU-1-0.788-0.88224.700-0.145-0.1450.0000.0000.0000.000
136B247ALA00.017-0.00126.137-0.012-0.0120.0000.0000.0000.000
137B248SER00.0050.00121.912-0.015-0.0150.0000.0000.0000.000
138B249ASN00.0190.00024.0570.0040.0040.0000.0000.0000.000
139B250VAL0-0.0110.01021.763-0.020-0.0200.0000.0000.0000.000
140B251LEU00.001-0.00424.2610.0250.0250.0000.0000.0000.000
141B252VAL00.0160.00623.619-0.021-0.0210.0000.0000.0000.000
142B253GLY00.0490.01426.7050.0240.0240.0000.0000.0000.000
143B254GLU-1-0.863-0.93529.138-0.257-0.2570.0000.0000.0000.000
144B255VAL00.010-0.02131.7740.0140.0140.0000.0000.0000.000
145B256ASP-1-0.877-0.93033.798-0.180-0.1800.0000.0000.0000.000
146B257ILE0-0.076-0.03335.655-0.001-0.0010.0000.0000.0000.000
147B258LEU0-0.068-0.02329.4250.0030.0030.0000.0000.0000.000
148B259ASP-1-0.897-0.95131.848-0.231-0.2310.0000.0000.0000.000
149B260ARG10.9010.95626.6410.2420.2420.0000.0000.0000.000
150B261PRO0-0.029-0.02923.7100.0120.0120.0000.0000.0000.000
151B262ILE0-0.008-0.00324.683-0.002-0.0020.0000.0000.0000.000
152B263VAL00.0280.00218.598-0.003-0.0030.0000.0000.0000.000
153B264ALA0-0.016-0.00520.7810.0110.0110.0000.0000.0000.000
154B265PHE0-0.0120.00816.705-0.019-0.0190.0000.0000.0000.000
155B266VAL00.0090.00019.2050.0160.0160.0000.0000.0000.000
156B267ARG10.7960.87915.9880.2580.2580.0000.0000.0000.000
157B268LEU0-0.035-0.01521.2450.0200.0200.0000.0000.0000.000
158B269SER00.033-0.02924.138-0.003-0.0030.0000.0000.0000.000
159B270PRO0-0.0240.02325.5030.0080.0080.0000.0000.0000.000
160B271ALA00.0300.00826.721-0.012-0.0120.0000.0000.0000.000
161B272VAL0-0.003-0.00928.0340.0190.0190.0000.0000.0000.000
162B273LEU0-0.042-0.01030.913-0.011-0.0110.0000.0000.0000.000
163B274LEU0-0.0010.01129.2490.0100.0100.0000.0000.0000.000
164B275SER0-0.015-0.02133.505-0.003-0.0030.0000.0000.0000.000
165B276GLY0-0.017-0.01136.527-0.004-0.0040.0000.0000.0000.000
166B277LEU0-0.0060.00929.348-0.003-0.0030.0000.0000.0000.000
167B278THR00.0100.01530.435-0.014-0.0140.0000.0000.0000.000
168B279GLU-1-0.867-0.92432.582-0.156-0.1560.0000.0000.0000.000
169B280VAL0-0.010-0.01633.3680.0140.0140.0000.0000.0000.000
170B281PRO0-0.057-0.03433.659-0.007-0.0070.0000.0000.0000.000
171B282ILE00.0000.00029.5260.0100.0100.0000.0000.0000.000
172B283PRO0-0.032-0.01629.876-0.008-0.0080.0000.0000.0000.000
173B284THR00.0360.01326.0790.0000.0000.0000.0000.0000.000
174B285ARG10.7680.88821.8800.1740.1740.0000.0000.0000.000
175B286PHE0-0.001-0.00718.042-0.015-0.0150.0000.0000.0000.000
176B287LEU00.0040.00221.9760.0270.0270.0000.0000.0000.000
177B288PHE00.000-0.00417.751-0.040-0.0400.0000.0000.0000.000
178B289ILE00.0010.00221.6970.0320.0320.0000.0000.0000.000
179B290LEU0-0.010-0.00221.295-0.029-0.0290.0000.0000.0000.000
180B291LEU00.0110.01424.0380.0260.0260.0000.0000.0000.000
181B292GLY00.0490.00326.751-0.018-0.0180.0000.0000.0000.000
182B293PRO0-0.0260.01228.2210.0160.0160.0000.0000.0000.000
183B294VAL00.0260.00430.807-0.013-0.0130.0000.0000.0000.000
184B295GLY0-0.030-0.01632.3430.0010.0010.0000.0000.0000.000
185B296LYS10.8960.94925.0490.3720.3720.0000.0000.0000.000
186B297GLY00.0480.03027.332-0.025-0.0250.0000.0000.0000.000
187B298GLN00.007-0.00728.082-0.022-0.0220.0000.0000.0000.000
188B299GLN00.0090.00123.860-0.025-0.0250.0000.0000.0000.000
189B300TYR00.0270.01323.201-0.031-0.0310.0000.0000.0000.000
190B301HIS10.9030.94923.9010.3030.3030.0000.0000.0000.000
191B302GLU-1-0.826-0.91721.671-0.423-0.4230.0000.0000.0000.000
192B303ILE0-0.035-0.00318.432-0.043-0.0430.0000.0000.0000.000
193B304GLY00.0050.00119.361-0.047-0.0470.0000.0000.0000.000
194B305ARG10.7580.85321.2140.3940.3940.0000.0000.0000.000
195B306SER0-0.015-0.00816.178-0.016-0.0160.0000.0000.0000.000
196B307MET0-0.024-0.00615.003-0.067-0.0670.0000.0000.0000.000
197B308ALA00.0350.00917.594-0.009-0.0090.0000.0000.0000.000
198B309THR00.011-0.01017.4810.0330.0330.0000.0000.0000.000
199B310ILE0-0.0070.03010.7800.0190.0190.0000.0000.0000.000
200B311MET0-0.040-0.00414.726-0.035-0.0350.0000.0000.0000.000
201B312THR0-0.129-0.09717.0840.0830.0830.0000.0000.0000.000
202B313ASP-1-0.856-0.92412.493-0.586-0.5860.0000.0000.0000.000
203B314GLU-1-0.946-0.98315.465-0.189-0.1890.0000.0000.0000.000
204B315ILE00.0650.03110.2400.0640.0640.0000.0000.0000.000
205B316PHE0-0.006-0.0119.715-0.008-0.0080.0000.0000.0000.000
206B317HIS10.8070.89312.0530.2820.2820.0000.0000.0000.000
207B318ASP-1-0.883-0.95014.424-0.110-0.1100.0000.0000.0000.000
208B319VAL0-0.039-0.0159.2540.0770.0770.0000.0000.0000.000
209B320ALA00.0120.01012.3810.0390.0390.0000.0000.0000.000
210B321TYR0-0.056-0.02914.5520.0450.0450.0000.0000.0000.000
211B322LYS10.8280.91913.910-0.077-0.0770.0000.0000.0000.000
212B323ALA0-0.056-0.00112.1780.0560.0560.0000.0000.0000.000
213B324LYS10.9620.97112.689-0.066-0.0660.0000.0000.0000.000
214B325GLU-1-0.963-0.97410.730-0.142-0.1420.0000.0000.0000.000
215B326ARG10.8600.90111.7570.5980.5980.0000.0000.0000.000
216B327ASP-1-0.882-0.9477.821-1.112-1.1120.0000.0000.0000.000
217B328ASP-1-0.792-0.9037.167-0.814-0.8140.0000.0000.0000.000
218B329LEU0-0.009-0.0097.865-0.318-0.3180.0000.0000.0000.000
219B330LEU0-0.040-0.0186.797-0.240-0.2400.0000.0000.0000.000
220B331ALA00.0000.0013.347-1.580-1.2980.013-0.086-0.2090.000
221B332GLY00.0340.0254.324-0.830-0.856-0.001-0.0170.0430.000
222B333ILE0-0.016-0.0157.1400.0630.0630.0000.0000.0000.000
223B334ASP-1-0.823-0.8922.956-5.944-5.2260.053-0.225-0.546-0.002
224B335GLU-1-0.953-0.9783.608-1.565-1.0270.003-0.123-0.418-0.001
225B336PHE00.0610.0294.2680.9971.074-0.001-0.018-0.0580.000
226B337LEU0-0.110-0.0776.6120.5480.5480.0000.0000.0000.000
227B338ASP-1-0.978-0.9774.251-0.538-0.429-0.001-0.006-0.1010.000
228B339GLN0-0.019-0.0106.4020.5630.5630.0000.0000.0000.000
229B340VAL0-0.071-0.0039.2630.2520.2520.0000.0000.0000.000
230B341THR0-0.046-0.02212.0560.0260.0260.0000.0000.0000.000
231B342VAL00.009-0.00314.403-0.026-0.0260.0000.0000.0000.000
232B343LEU0-0.005-0.00817.0460.0610.0610.0000.0000.0000.000
233B344PRO0-0.040-0.01320.751-0.018-0.0180.0000.0000.0000.000