FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

tag_button

FMODB ID: 3JMVL

Calculation Name: 3DHN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DHN

Chain ID: A

ChEMBL ID:

UniProt ID: Q89Z24

Base Structure: X-ray

Registration Date: 2023-09-23

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2661462.891853
FMO2-HF: Nuclear repulsion 2575217.069616
FMO2-HF: Total energy -86245.822236
FMO2-MP2: Total energy -86497.371327


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(A:3:LYS)


Summations of interaction energy for fragment #1(A:3:LYS)
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.
-148.094-144.15513.335-8.499-8.775-0.084
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.923 / q_NPA : 0.957
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].
3A5LYS10.9130.9521.7531.6832.13812.828-6.959-6.324-0.067
4A6LYS10.9740.9874.09830.76831.0610.001-0.085-0.2090.000
5A7ILE00.0350.0286.6470.3980.3980.0000.0000.0000.000
6A8VAL0-0.005-0.0049.3711.7111.7110.0000.0000.0000.000
7A9LEU0-0.0040.00113.036-0.284-0.2840.0000.0000.0000.000
8A10ILE00.0420.00814.6931.1551.1550.0000.0000.0000.000
9A11GLY00.0240.01818.2870.1470.1470.0000.0000.0000.000
10A12ALA00.0040.01817.401-0.026-0.0260.0000.0000.0000.000
11A13SER0-0.038-0.03518.9200.5680.5680.0000.0000.0000.000
12A14GLY00.0460.01922.018-0.060-0.0600.0000.0000.0000.000
13A15PHE00.0410.01422.194-0.557-0.5570.0000.0000.0000.000
14A16VAL00.0750.02918.681-0.537-0.5370.0000.0000.0000.000
15A17GLY00.0580.03618.056-0.985-0.9850.0000.0000.0000.000
16A18SER0-0.054-0.04817.271-0.965-0.9650.0000.0000.0000.000
17A19ALA0-0.0070.00017.231-0.763-0.7630.0000.0000.0000.000
18A20LEU0-0.006-0.00413.305-1.098-1.0980.0000.0000.0000.000
19A21LEU0-0.0120.00012.506-1.986-1.9860.0000.0000.0000.000
20A22ASN00.005-0.01613.024-1.508-1.5080.0000.0000.0000.000
21A23GLU-1-0.803-0.89210.393-26.364-26.3640.0000.0000.0000.000
22A24ALA00.0200.0088.388-2.486-2.4860.0000.0000.0000.000
23A25LEU0-0.029-0.0168.132-3.655-3.6550.0000.0000.0000.000
24A26ASN0-0.024-0.0189.806-1.100-1.1000.0000.0000.0000.000
25A27ARG10.7370.8516.24236.43136.4310.0000.0000.0000.000
26A28GLY0-0.0100.0105.309-7.803-7.8030.0000.0000.0000.000
27A29PHE0-0.050-0.0142.787-10.567-8.7830.326-1.003-1.107-0.013
28A30GLU-1-0.976-0.9946.197-24.642-24.6420.0000.0000.0000.000
29A31VAL00.0080.0028.984-0.583-0.5830.0000.0000.0000.000
30A32THR0-0.048-0.02611.2842.5492.5490.0000.0000.0000.000
31A33ALA00.0310.01714.486-0.156-0.1560.0000.0000.0000.000
32A34VAL00.0180.01016.7410.9460.9460.0000.0000.0000.000
33A35VAL0-0.017-0.00519.7810.1160.1160.0000.0000.0000.000
34A36ARG11.0050.98522.86711.24911.2490.0000.0000.0000.000
35A37HIS0-0.048-0.02326.1350.4220.4220.0000.0000.0000.000
36A38PRO00.0480.01624.245-0.247-0.2470.0000.0000.0000.000
37A39GLU-1-0.863-0.92925.142-11.324-11.3240.0000.0000.0000.000
38A40LYS10.9070.93525.92511.27111.2710.0000.0000.0000.000
39A41ILE0-0.0080.01320.070-0.114-0.1140.0000.0000.0000.000
40A42LYS10.8960.94623.40411.93111.9310.0000.0000.0000.000
41A43ILE00.0010.01516.8680.1980.1980.0000.0000.0000.000
42A44GLU-1-0.928-0.95519.891-13.685-13.6850.0000.0000.0000.000
43A45ASN00.0320.00512.524-0.888-0.8880.0000.0000.0000.000
44A46GLU-1-0.843-0.92713.974-21.007-21.0070.0000.0000.0000.000
45A47HIS10.7930.9068.69427.95127.9510.0000.0000.0000.000
46A48LEU00.0300.02412.151-1.587-1.5870.0000.0000.0000.000
47A49LYS10.9100.95814.85322.00922.0090.0000.0000.0000.000
48A50VAL00.0390.02217.065-0.535-0.5350.0000.0000.0000.000
49A51LYS10.9180.95317.72817.75817.7580.0000.0000.0000.000
50A52LYS10.9550.98121.60010.95610.9560.0000.0000.0000.000
51A53ALA00.0120.00022.727-0.130-0.1300.0000.0000.0000.000
52A54ASP-1-0.845-0.88524.754-10.832-10.8320.0000.0000.0000.000
53A55VAL0-0.045-0.03023.010-0.034-0.0340.0000.0000.0000.000
54A56SER0-0.067-0.05225.518-0.008-0.0080.0000.0000.0000.000
55A57SER0-0.0040.00127.8330.2720.2720.0000.0000.0000.000
56A58LEU00.0460.00524.963-0.478-0.4780.0000.0000.0000.000
57A59ASP-1-0.904-0.95925.072-11.567-11.5670.0000.0000.0000.000
58A60GLU-1-0.871-0.93525.207-11.971-11.9710.0000.0000.0000.000
59A61VAL0-0.051-0.01220.766-0.776-0.7760.0000.0000.0000.000
60A62CYS0-0.042-0.00520.542-0.815-0.8150.0000.0000.0000.000
61A63GLU-1-0.871-0.93720.027-14.374-14.3740.0000.0000.0000.000
62A64VAL0-0.064-0.03317.929-0.629-0.6290.0000.0000.0000.000
63A65CYS0-0.052-0.02616.024-1.369-1.3690.0000.0000.0000.000
64A66LYS10.9090.96315.17912.68412.6840.0000.0000.0000.000
65A67GLY0-0.061-0.03012.863-0.136-0.1360.0000.0000.0000.000
66A68ALA0-0.097-0.03310.873-1.942-1.9420.0000.0000.0000.000
67A69ASP-1-0.773-0.8835.627-42.721-42.7210.0000.0000.0000.000
68A70ALA0-0.044-0.0288.2690.6190.6190.0000.0000.0000.000
69A71VAL0-0.005-0.00110.1450.0290.0290.0000.0000.0000.000
70A72ILE00.0380.0279.8620.3910.3910.0000.0000.0000.000
71A73SER0-0.015-0.01413.9320.7770.7770.0000.0000.0000.000
72A74ALA00.009-0.01217.6530.0900.0900.0000.0000.0000.000
73A75PHE0-0.043-0.01919.4450.6470.6470.0000.0000.0000.000
74A76ASN00.0240.03322.7890.3460.3460.0000.0000.0000.000
75A77PRO00.0160.01525.970-0.037-0.0370.0000.0000.0000.000
76A78GLY00.012-0.05328.7440.2330.2330.0000.0000.0000.000
77A79TRP0-0.046-0.04230.5880.1300.1300.0000.0000.0000.000
78A80ASN00.0590.04733.3900.0090.0090.0000.0000.0000.000
79A81ASN0-0.056-0.05635.351-0.033-0.0330.0000.0000.0000.000
80A82PRO0-0.048-0.01535.8050.1610.1610.0000.0000.0000.000
81A83ASP-1-0.905-0.94038.409-8.067-8.0670.0000.0000.0000.000
82A84ILE0-0.0030.01338.1530.1720.1720.0000.0000.0000.000
83A85TYR0-0.054-0.04634.487-0.240-0.2400.0000.0000.0000.000
84A86ASP-1-0.848-0.90135.589-8.536-8.5360.0000.0000.0000.000
85A87GLU-1-0.795-0.89533.144-9.918-9.9180.0000.0000.0000.000
86A88THR0-0.0130.00329.659-0.178-0.1780.0000.0000.0000.000
87A89ILE0-0.0120.00329.776-0.419-0.4190.0000.0000.0000.000
88A90LYS10.8820.92729.6439.6189.6180.0000.0000.0000.000
89A91VAL0-0.030-0.01626.569-0.261-0.2610.0000.0000.0000.000
90A92TYR0-0.031-0.02224.941-0.532-0.5320.0000.0000.0000.000
91A93LEU00.0200.00524.648-0.556-0.5560.0000.0000.0000.000
92A94THR0-0.0140.01325.152-0.207-0.2070.0000.0000.0000.000
93A95ILE0-0.026-0.00420.577-0.463-0.4630.0000.0000.0000.000
94A96ILE0-0.0010.00419.461-0.716-0.7160.0000.0000.0000.000
95A97ASP-1-0.838-0.93620.534-12.821-12.8210.0000.0000.0000.000
96A98GLY0-0.013-0.01822.2180.0350.0350.0000.0000.0000.000
97A99VAL0-0.040-0.02916.007-0.456-0.4560.0000.0000.0000.000
98A100LYS10.8650.91617.10112.71512.7150.0000.0000.0000.000
99A101LYS10.9090.96318.43312.12212.1220.0000.0000.0000.000
100A102ALA0-0.032-0.02217.1130.3110.3110.0000.0000.0000.000
101A103GLY0-0.021-0.00715.467-0.417-0.4170.0000.0000.0000.000
102A104VAL0-0.0390.00312.032-0.949-0.9490.0000.0000.0000.000
103A105ASN00.020-0.0069.4702.0312.0310.0000.0000.0000.000
104A106ARG10.7850.8658.94927.55527.5550.0000.0000.0000.000
105A107PHE00.002-0.00511.259-0.617-0.6170.0000.0000.0000.000
106A108LEU00.0140.01210.7320.4130.4130.0000.0000.0000.000
107A109MET0-0.019-0.01114.7440.2170.2170.0000.0000.0000.000
108A110VAL00.0060.00817.634-0.024-0.0240.0000.0000.0000.000
109A111GLY00.0170.00719.2830.6310.6310.0000.0000.0000.000
110A112GLY00.029-0.01422.3390.1230.1230.0000.0000.0000.000
111A113ALA00.0240.00725.458-0.179-0.1790.0000.0000.0000.000
112A114GLY00.0330.01127.5470.2610.2610.0000.0000.0000.000
113A115SER00.0640.02226.9960.2180.2180.0000.0000.0000.000
114A116LEU0-0.0440.00225.103-0.029-0.0290.0000.0000.0000.000
115A117PHE0-0.021-0.00129.1010.3800.3800.0000.0000.0000.000
116A118ILE00.0310.00631.512-0.256-0.2560.0000.0000.0000.000
117A119ALA00.0070.00234.0860.1950.1950.0000.0000.0000.000
118A120PRO00.005-0.01035.899-0.163-0.1630.0000.0000.0000.000
119A121GLY0-0.0100.00136.0230.2050.2050.0000.0000.0000.000
120A122LEU00.0150.02136.6680.1230.1230.0000.0000.0000.000
121A123ARG10.9300.95329.9239.9079.9070.0000.0000.0000.000
122A124LEU00.0270.01531.2670.2330.2330.0000.0000.0000.000
123A125MET0-0.042-0.01432.4390.0140.0140.0000.0000.0000.000
124A126ASP-1-0.958-0.97335.020-8.556-8.5560.0000.0000.0000.000
125A127SER0-0.036-0.01336.9830.2500.2500.0000.0000.0000.000
126A128GLY0-0.0010.00639.0490.2010.2010.0000.0000.0000.000
127A129GLU-1-0.941-0.97036.773-8.133-8.1330.0000.0000.0000.000
128A130VAL0-0.086-0.03134.212-0.209-0.2090.0000.0000.0000.000
129A131PRO00.0210.00335.2700.2350.2350.0000.0000.0000.000
130A132GLU-1-0.873-0.95037.807-7.444-7.4440.0000.0000.0000.000
131A133ASN0-0.033-0.02837.063-0.170-0.1700.0000.0000.0000.000
132A134ILE0-0.0110.00032.302-0.125-0.1250.0000.0000.0000.000
133A135LEU00.0180.01834.380-0.278-0.2780.0000.0000.0000.000
134A136PRO00.000-0.00835.380-0.203-0.2030.0000.0000.0000.000
135A137GLY00.0680.03332.473-0.126-0.1260.0000.0000.0000.000
136A138VAL0-0.047-0.02030.736-0.397-0.3970.0000.0000.0000.000
137A139LYS10.9880.98331.1908.1388.1380.0000.0000.0000.000
138A140ALA00.0350.03531.860-0.115-0.1150.0000.0000.0000.000
139A141LEU0-0.041-0.01824.629-0.213-0.2130.0000.0000.0000.000
140A142GLY0-0.002-0.01927.793-0.372-0.3720.0000.0000.0000.000
141A143GLU-1-0.884-0.95729.650-9.493-9.4930.0000.0000.0000.000
142A144PHE0-0.0040.00423.410-0.031-0.0310.0000.0000.0000.000
143A145TYR00.035-0.00223.432-0.019-0.0190.0000.0000.0000.000
144A146LEU00.021-0.00526.305-0.088-0.0880.0000.0000.0000.000
145A147ASN0-0.085-0.04229.1270.2580.2580.0000.0000.0000.000
146A148PHE00.0120.00326.7210.2650.2650.0000.0000.0000.000
147A149LEU00.0190.02621.181-0.124-0.1240.0000.0000.0000.000
148A150MET0-0.038-0.00423.241-0.481-0.4810.0000.0000.0000.000
149A151LYS10.8280.90925.40710.33410.3340.0000.0000.0000.000
150A152GLU-1-0.793-0.85920.347-13.282-13.2820.0000.0000.0000.000
151A153LYS10.9100.93720.40211.50511.5050.0000.0000.0000.000
152A154GLU-1-0.996-0.98419.283-12.668-12.6680.0000.0000.0000.000
153A155ILE00.0090.00814.909-0.500-0.5000.0000.0000.0000.000
154A156ASP-1-0.822-0.88711.461-21.244-21.2440.0000.0000.0000.000
155A157TRP0-0.006-0.00313.542-1.533-1.5330.0000.0000.0000.000
156A158VAL00.0270.01313.5500.2510.2510.0000.0000.0000.000
157A159PHE0-0.033-0.00516.527-0.194-0.1940.0000.0000.0000.000
158A160PHE00.0090.00115.7850.3560.3560.0000.0000.0000.000
159A161SER00.0120.01118.8430.1900.1900.0000.0000.0000.000
160A162PRO0-0.0160.01721.638-0.129-0.1290.0000.0000.0000.000
161A163ALA00.0100.01422.5500.4240.4240.0000.0000.0000.000
162A164ALA0-0.012-0.02525.537-0.037-0.0370.0000.0000.0000.000
163A165ASP-1-0.931-0.95228.584-10.359-10.3590.0000.0000.0000.000
164A166MET0-0.021-0.00721.686-0.513-0.5130.0000.0000.0000.000
165A167ARG10.9400.96525.78210.35410.3540.0000.0000.0000.000
166A168PRO0-0.033-0.01424.010-0.414-0.4140.0000.0000.0000.000
167A169GLY0-0.001-0.01023.7070.6160.6160.0000.0000.0000.000
168A170VAL00.0030.00822.684-0.147-0.1470.0000.0000.0000.000
169A171ARG10.8860.96312.54721.40921.4090.0000.0000.0000.000
170A172THR0-0.039-0.04819.676-0.053-0.0530.0000.0000.0000.000
171A173GLY0-0.053-0.02717.205-0.104-0.1040.0000.0000.0000.000
172A174ARG10.8270.89718.08912.59512.5950.0000.0000.0000.000
173A175TYR00.0360.00515.0750.5190.5190.0000.0000.0000.000
174A176ARG10.9210.97121.02012.22012.2200.0000.0000.0000.000
175A177LEU00.0370.01616.011-0.037-0.0370.0000.0000.0000.000
176A178GLY0-0.021-0.01720.5550.5500.5500.0000.0000.0000.000
177A179LYS10.9610.98021.51312.69612.6960.0000.0000.0000.000
178A180ASP-1-0.833-0.92123.650-12.578-12.5780.0000.0000.0000.000
179A181ASP-1-0.906-0.93526.657-10.174-10.1740.0000.0000.0000.000
180A182MET0-0.037-0.02327.239-0.398-0.3980.0000.0000.0000.000
181A183ILE0-0.040-0.00724.4230.2410.2410.0000.0000.0000.000
182A184VAL00.001-0.00727.747-0.068-0.0680.0000.0000.0000.000
183A185ASP-1-0.804-0.90130.277-9.898-9.8980.0000.0000.0000.000
184A186ILE0-0.038-0.03531.4260.2340.2340.0000.0000.0000.000
185A187VAL0-0.075-0.04334.6050.2880.2880.0000.0000.0000.000
186A188GLY00.0220.03234.6950.2420.2420.0000.0000.0000.000
187A189ASN0-0.037-0.02232.6940.1330.1330.0000.0000.0000.000
188A190SER00.0440.03328.070-0.328-0.3280.0000.0000.0000.000
189A191HIS0-0.042-0.03127.489-0.107-0.1070.0000.0000.0000.000
190A192ILE0-0.014-0.01420.927-0.259-0.2590.0000.0000.0000.000
191A193SER00.0330.03221.4540.0790.0790.0000.0000.0000.000
192A194VAL00.022-0.00819.937-0.591-0.5910.0000.0000.0000.000
193A195GLU-1-0.831-0.93018.067-15.471-15.4710.0000.0000.0000.000
194A196ASP-1-0.732-0.83316.665-17.278-17.2780.0000.0000.0000.000
195A197TYR0-0.020-0.00716.580-1.141-1.1410.0000.0000.0000.000
196A198ALA0-0.007-0.01314.325-1.025-1.0250.0000.0000.0000.000
197A199ALA0-0.011-0.00912.277-1.986-1.9860.0000.0000.0000.000
198A200ALA00.0280.02511.500-1.980-1.9800.0000.0000.0000.000
199A201MET0-0.018-0.00412.007-1.509-1.5090.0000.0000.0000.000
200A202ILE0-0.041-0.0276.783-1.856-1.8560.0000.0000.0000.000
201A203ASP-1-0.805-0.8727.078-34.506-34.5060.0000.0000.0000.000
202A204GLU-1-0.756-0.8538.332-27.132-27.1320.0000.0000.0000.000
203A205LEU0-0.055-0.0255.658-0.132-0.1320.0000.0000.0000.000
204A206GLU-1-0.992-1.0082.564-67.101-66.0060.181-0.406-0.869-0.004
205A207HIS0-0.065-0.0294.245-3.680-3.368-0.001-0.046-0.2660.000
206A208PRO0-0.043-0.0166.3294.8144.8140.0000.0000.0000.000
207A209LYS10.8760.9379.22024.60124.6010.0000.0000.0000.000
208A210HIS0-0.058-0.00912.8032.7082.7080.0000.0000.0000.000
209A211HIS10.8130.8829.99020.34720.3470.0000.0000.0000.000
210A212GLN0-0.0150.01514.8531.1051.1050.0000.0000.0000.000
211A213GLU-1-0.883-0.94517.561-15.037-15.0370.0000.0000.0000.000
212A214ARG10.8020.88518.75811.90411.9040.0000.0000.0000.000
213A215PHE0-0.039-0.00814.6350.3450.3450.0000.0000.0000.000
214A216THR0-0.004-0.02320.4140.1680.1680.0000.0000.0000.000
215A217ILE0-0.017-0.01217.985-0.480-0.4800.0000.0000.0000.000
216A218GLY00.0300.01721.5160.5070.5070.0000.0000.0000.000
217A219TYR0-0.054-0.04122.168-0.130-0.1300.0000.0000.0000.000
218A220LEU00.0090.00625.7310.2700.2700.0000.0000.0000.000
219A221GLU-1-0.867-0.92227.729-11.040-11.0400.0000.0000.0000.000
220A222HIS10.9500.97929.8159.0829.0820.0000.0000.0000.000
221A223HIS00.0220.01731.1650.0920.0920.0000.0000.0000.000
222A224HIS0-0.028-0.02132.7360.3400.3400.0000.0000.0000.000