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: 66KRZ

Calculation Name: 3H25-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H25

Chain ID: A

ChEMBL ID:

UniProt ID: Q52349

Base Structure: X-ray

Registration Date: 2023-06-19

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2027765.422347
FMO2-HF: Nuclear repulsion 1953757.426995
FMO2-HF: Total energy -74007.995352
FMO2-MP2: Total energy -74223.087642


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:4:ASP)


Summations of interaction energy for fragment #1(A:4:ASP)
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.
-58.545-54.3260.047-1.655-2.610.004
Interaction energy analysis for fragmet #1(A:4:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.899 / q_NPA : -0.953
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].
3A6THR0-0.020-0.0193.015-6.445-3.5900.026-1.299-1.5810.004
4A7LEU00.0080.0013.256-4.863-4.1680.014-0.153-0.5560.000
5A8GLN00.0440.0123.724-3.446-2.9490.008-0.169-0.3360.000
6A9ALA0-0.033-0.0016.179-3.373-3.3730.0000.0000.0000.000
7A10ILE00.0600.0327.841-2.109-2.1090.0000.0000.0000.000
8A11GLY00.0320.0198.743-1.927-1.9270.0000.0000.0000.000
9A12ARG10.8640.93410.164-22.849-22.8490.0000.0000.0000.000
10A13GLN00.0600.03712.196-0.444-0.4440.0000.0000.0000.000
11A14LEU0-0.012-0.01013.015-1.163-1.1630.0000.0000.0000.000
12A15LYS10.9440.97814.482-17.257-17.2570.0000.0000.0000.000
13A16ALA0-0.053-0.02416.198-0.793-0.7930.0000.0000.0000.000
14A17MET0-0.059-0.03417.959-0.446-0.4460.0000.0000.0000.000
15A18GLY0-0.008-0.00119.001-0.661-0.6610.0000.0000.0000.000
16A19CYS0-0.060-0.00520.694-0.356-0.3560.0000.0000.0000.000
17A20GLU-1-0.919-0.95520.15811.99311.9930.0000.0000.0000.000
18A21ARG10.8230.89920.909-11.445-11.4450.0000.0000.0000.000
19A22PHE0-0.010-0.02317.727-0.066-0.0660.0000.0000.0000.000
20A23ASP-1-0.855-0.92021.06111.82811.8280.0000.0000.0000.000
21A24ILE0-0.048-0.04716.0180.5750.5750.0000.0000.0000.000
22A25GLY00.0320.01719.162-0.431-0.4310.0000.0000.0000.000
23A26VAL0-0.049-0.03917.3070.8810.8810.0000.0000.0000.000
24A27ARG10.9790.97719.548-12.418-12.4180.0000.0000.0000.000
25A28ASP-1-0.781-0.87020.78213.30113.3010.0000.0000.0000.000
26A29ALA0-0.054-0.03921.031-0.580-0.5800.0000.0000.0000.000
27A30THR0-0.003-0.00323.024-0.371-0.3710.0000.0000.0000.000
28A31THR0-0.025-0.04526.258-0.397-0.3970.0000.0000.0000.000
29A32GLY0-0.052-0.01026.128-0.365-0.3650.0000.0000.0000.000
30A33GLN0-0.016-0.01226.8130.0810.0810.0000.0000.0000.000
31A34MET0-0.0320.01222.9030.7780.7780.0000.0000.0000.000
32A35MET00.0040.01721.625-0.175-0.1750.0000.0000.0000.000
33A36ASN00.0720.03022.0310.9480.9480.0000.0000.0000.000
34A37ARG10.9240.96719.788-14.735-14.7350.0000.0000.0000.000
35A38GLU-1-0.815-0.88821.13011.64911.6490.0000.0000.0000.000
36A39TRP0-0.058-0.03616.1500.4160.4160.0000.0000.0000.000
37A40SER00.0450.02819.7130.0920.0920.0000.0000.0000.000
38A41ALA00.0580.01416.1860.8020.8020.0000.0000.0000.000
39A42ALA0-0.001-0.01014.7241.1581.1580.0000.0000.0000.000
40A43GLU-1-0.830-0.91714.62014.87514.8750.0000.0000.0000.000
41A44VAL0-0.024-0.00413.1290.8830.8830.0000.0000.0000.000
42A45LEU0-0.020-0.0138.9271.4541.4540.0000.0000.0000.000
43A46GLN00.0020.03310.5041.8821.8820.0000.0000.0000.000
44A47ASN0-0.055-0.03012.5440.7320.7320.0000.0000.0000.000
45A48THR00.023-0.0106.7970.4490.4490.0000.0000.0000.000
46A49PRO0-0.001-0.0118.9051.3581.3580.0000.0000.0000.000
47A50TRP00.0250.0129.822-0.010-0.0100.0000.0000.0000.000
48A51LEU00.0310.01611.047-0.449-0.4490.0000.0000.0000.000
49A52LYS10.9350.9663.890-48.566-48.394-0.001-0.034-0.1370.000
50A53ARG10.9530.9909.944-19.059-19.0590.0000.0000.0000.000
51A54MET00.000-0.00213.006-1.194-1.1940.0000.0000.0000.000
52A55ASN00.0420.04011.2501.3201.3200.0000.0000.0000.000
53A56ALA0-0.025-0.02311.882-0.861-0.8610.0000.0000.0000.000
54A57GLN0-0.075-0.04313.706-0.246-0.2460.0000.0000.0000.000
55A58GLY0-0.0100.01216.480-0.992-0.9920.0000.0000.0000.000
56A59ASN0-0.001-0.00416.753-1.494-1.4940.0000.0000.0000.000
57A60ASP-1-0.800-0.88716.07816.94816.9480.0000.0000.0000.000
58A61VAL00.0060.00013.264-0.543-0.5430.0000.0000.0000.000
59A62TYR0-0.028-0.02516.1980.2350.2350.0000.0000.0000.000
60A63ILE0-0.030-0.02615.9260.3590.3590.0000.0000.0000.000
61A64ARG10.9020.94818.992-11.814-11.8140.0000.0000.0000.000
62A65PRO00.0180.00821.9790.3210.3210.0000.0000.0000.000
63A66ALA00.0430.03323.725-0.217-0.2170.0000.0000.0000.000
64A67GLU-1-0.788-0.89225.4479.5259.5250.0000.0000.0000.000
65A68GLN0-0.036-0.02429.087-0.294-0.2940.0000.0000.0000.000
66A69GLU-1-0.816-0.89224.87711.60511.6050.0000.0000.0000.000
67A70ARG10.8710.93127.940-9.342-9.3420.0000.0000.0000.000
68A71HIS00.0640.02426.3190.1280.1280.0000.0000.0000.000
69A72GLY00.0320.01027.864-0.370-0.3700.0000.0000.0000.000
70A73LEU0-0.058-0.02022.041-0.058-0.0580.0000.0000.0000.000
71A74VAL00.0220.00926.709-0.156-0.1560.0000.0000.0000.000
72A75LEU0-0.048-0.00822.9520.2880.2880.0000.0000.0000.000
73A76VAL00.0290.02125.816-0.391-0.3910.0000.0000.0000.000
74A77ASP-1-0.838-0.93724.19612.68712.6870.0000.0000.0000.000
75A78ASP-1-0.943-0.95425.07310.32610.3260.0000.0000.0000.000
76A79LEU00.0540.03125.276-0.217-0.2170.0000.0000.0000.000
77A80SER00.001-0.00525.2310.5190.5190.0000.0000.0000.000
78A81GLU-1-0.929-1.01624.30012.61212.6120.0000.0000.0000.000
79A82PHE0-0.028-0.00526.1000.0010.0010.0000.0000.0000.000
80A83ASP-1-0.723-0.85528.6009.7389.7380.0000.0000.0000.000
81A84LEU0-0.110-0.06123.2490.0730.0730.0000.0000.0000.000
82A85ASP-1-0.973-0.98827.50710.64810.6480.0000.0000.0000.000
83A86ASP-1-0.836-0.91029.7248.8888.8880.0000.0000.0000.000
84A87MET0-0.062-0.02827.4070.0070.0070.0000.0000.0000.000
85A88LYS10.7490.84823.496-12.159-12.1590.0000.0000.0000.000
86A89ALA0-0.0110.01130.137-0.120-0.1200.0000.0000.0000.000
87A90GLU-1-0.848-0.89433.5798.2208.2200.0000.0000.0000.000
88A91GLY0-0.067-0.01633.283-0.183-0.1830.0000.0000.0000.000
89A92ARG10.8010.87431.042-8.437-8.4370.0000.0000.0000.000
90A93GLU-1-0.777-0.89327.13710.13210.1320.0000.0000.0000.000
91A94PRO00.0260.01123.3480.0340.0340.0000.0000.0000.000
92A95ALA0-0.067-0.03222.2740.1270.1270.0000.0000.0000.000
93A96LEU0-0.048-0.05517.2780.7850.7850.0000.0000.0000.000
94A97VAL00.0020.02218.897-0.426-0.4260.0000.0000.0000.000
95A98VAL0-0.023-0.02915.6651.1521.1520.0000.0000.0000.000
96A99GLU-1-0.824-0.91815.94315.86515.8650.0000.0000.0000.000
97A100THR00.006-0.00315.9761.1921.1920.0000.0000.0000.000
98A101SER00.0450.02817.2590.6730.6730.0000.0000.0000.000
99A102PRO0-0.026-0.01217.194-0.236-0.2360.0000.0000.0000.000
100A103LYS10.9150.95919.273-13.377-13.3770.0000.0000.0000.000
101A104ASN00.0060.02320.852-1.011-1.0110.0000.0000.0000.000
102A105TYR0-0.011-0.02019.3431.2921.2920.0000.0000.0000.000
103A106GLN00.0470.04920.0690.2420.2420.0000.0000.0000.000
104A107ALA0-0.001-0.01721.3170.6810.6810.0000.0000.0000.000
105A108TRP00.0360.03220.180-0.488-0.4880.0000.0000.0000.000
106A109VAL00.0580.02623.9490.1960.1960.0000.0000.0000.000
107A110LYS10.8990.96625.179-11.114-11.1140.0000.0000.0000.000
108A111VAL00.0170.01027.393-0.156-0.1560.0000.0000.0000.000
109A112ALA00.012-0.01030.196-0.282-0.2820.0000.0000.0000.000
110A113ASP-1-0.881-0.94328.70010.33610.3360.0000.0000.0000.000
111A114ALA0-0.030-0.02129.1410.2100.2100.0000.0000.0000.000
112A115ALA00.0220.01531.619-0.279-0.2790.0000.0000.0000.000
113A116GLY0-0.0100.00432.8140.2180.2180.0000.0000.0000.000
114A117GLY00.0500.01233.6930.0830.0830.0000.0000.0000.000
115A118GLU-1-0.893-0.94734.6947.5117.5110.0000.0000.0000.000
116A119LEU0-0.0110.00136.359-0.043-0.0430.0000.0000.0000.000
117A120ARG10.8920.93730.018-9.764-9.7640.0000.0000.0000.000
118A121GLY00.0060.00933.3700.1710.1710.0000.0000.0000.000
119A122GLN00.0000.00535.2040.0120.0120.0000.0000.0000.000
120A123ILE00.015-0.00933.105-0.018-0.0180.0000.0000.0000.000
121A124ALA00.0180.01331.8130.0690.0690.0000.0000.0000.000
122A125ARG10.9440.97733.080-8.003-8.0030.0000.0000.0000.000
123A126THR0-0.060-0.02136.032-0.164-0.1640.0000.0000.0000.000
124A127LEU0-0.017-0.02230.5500.0050.0050.0000.0000.0000.000
125A128ALA00.0140.00732.4130.1130.1130.0000.0000.0000.000
126A129SER0-0.048-0.01133.351-0.034-0.0340.0000.0000.0000.000
127A130GLU-1-0.835-0.92335.2038.3448.3440.0000.0000.0000.000
128A131TYR0-0.039-0.04331.6740.0880.0880.0000.0000.0000.000
129A132ASP-1-0.942-0.95132.2478.6088.6080.0000.0000.0000.000
130A133ALA00.0110.00929.5670.2020.2020.0000.0000.0000.000
131A134ASP-1-0.875-0.95029.3179.6169.6160.0000.0000.0000.000
132A135PRO0-0.027-0.02631.1700.0640.0640.0000.0000.0000.000
133A136ALA0-0.057-0.02631.521-0.118-0.1180.0000.0000.0000.000
134A137SER0-0.011-0.00627.6510.1670.1670.0000.0000.0000.000
135A138ALA0-0.0260.00229.4040.2120.2120.0000.0000.0000.000
136A139ASP-1-0.876-0.95430.9259.4849.4840.0000.0000.0000.000
137A140SER0-0.076-0.04630.3070.3660.3660.0000.0000.0000.000
138A141ARG10.7500.87327.677-10.049-10.0490.0000.0000.0000.000
139A142HIS00.0630.07425.8410.1750.1750.0000.0000.0000.000
140A143TYR0-0.103-0.07321.3740.3690.3690.0000.0000.0000.000
141A144GLY00.0380.03221.074-0.213-0.2130.0000.0000.0000.000
142A145ARG10.8310.88916.531-15.387-15.3870.0000.0000.0000.000
143A146LEU0-0.037-0.00412.3930.0400.0400.0000.0000.0000.000
144A147ALA00.014-0.00111.6820.7450.7450.0000.0000.0000.000
145A148GLY0-0.043-0.0237.8521.1271.1270.0000.0000.0000.000
146A149PHE0-0.0010.0037.7643.6033.6030.0000.0000.0000.000
147A150THR0-0.033-0.01210.385-0.833-0.8330.0000.0000.0000.000
148A151ASN0-0.024-0.04712.417-0.962-0.9620.0000.0000.0000.000
149A152ARG10.8770.92614.071-19.177-19.1770.0000.0000.0000.000
150A153LYS10.8670.96818.206-13.208-13.2080.0000.0000.0000.000
151A154ASP-1-0.840-0.93219.49313.23413.2340.0000.0000.0000.000
152A155LYS10.9480.99319.710-10.445-10.4450.0000.0000.0000.000
153A163GLN0-0.094-0.05515.066-0.113-0.1130.0000.0000.0000.000
154A164PRO00.0450.03913.5871.4621.4620.0000.0000.0000.000
155A165TRP0-0.006-0.0147.2040.7180.7180.0000.0000.0000.000
156A166VAL00.0240.02711.572-0.967-0.9670.0000.0000.0000.000
157A167LEU0-0.058-0.02010.4182.5832.5830.0000.0000.0000.000
158A168LEU0-0.024-0.00311.987-1.214-1.2140.0000.0000.0000.000
159A169ARG10.9210.97913.667-13.098-13.0980.0000.0000.0000.000
160A170GLU-1-0.844-0.92316.32913.30213.3020.0000.0000.0000.000
161A171SER00.016-0.00415.4480.3390.3390.0000.0000.0000.000
162A172LYS10.8910.94317.753-12.379-12.3790.0000.0000.0000.000
163A173GLY00.0370.01720.455-0.147-0.1470.0000.0000.0000.000
164A174LYS10.7690.93621.607-10.585-10.5850.0000.0000.0000.000
165A175THR0-0.008-0.02225.1840.2030.2030.0000.0000.0000.000
166A176ALA0-0.0090.00528.297-0.056-0.0560.0000.0000.0000.000
167A177THR0-0.027-0.04030.045-0.190-0.1900.0000.0000.0000.000
168A178ALA0-0.0020.00333.254-0.273-0.2730.0000.0000.0000.000
169A179GLY0-0.017-0.00132.752-0.109-0.1090.0000.0000.0000.000
170A180PRO00.043-0.00233.525-0.117-0.1170.0000.0000.0000.000
171A181ALA00.0070.00736.506-0.191-0.1910.0000.0000.0000.000
172A182LEU00.0360.00933.618-0.172-0.1720.0000.0000.0000.000
173A183VAL0-0.035-0.01435.255-0.078-0.0780.0000.0000.0000.000
174A184GLN0-0.034-0.02237.801-0.085-0.0850.0000.0000.0000.000
175A185GLN0-0.0050.00540.735-0.041-0.0410.0000.0000.0000.000
176A186ALA00.0340.01638.820-0.137-0.1370.0000.0000.0000.000
177A187GLY00.0130.00240.861-0.088-0.0880.0000.0000.0000.000
178A188GLN00.0220.01442.829-0.155-0.1550.0000.0000.0000.000
179A189GLN0-0.025-0.02742.217-0.021-0.0210.0000.0000.0000.000
180A190ILE00.0060.01140.290-0.069-0.0690.0000.0000.0000.000
181A191GLU-1-0.836-0.91044.8816.1936.1930.0000.0000.0000.000
182A192GLN0-0.031-0.01147.979-0.235-0.2350.0000.0000.0000.000
183A193ALA0-0.006-0.01047.041-0.128-0.1280.0000.0000.0000.000
184A194GLN0-0.035-0.01048.087-0.022-0.0220.0000.0000.0000.000
185A195ARG10.8310.90349.918-6.055-6.0550.0000.0000.0000.000
186A196GLN0-0.091-0.03052.226-0.197-0.1970.0000.0000.0000.000
187A197GLN0-0.040-0.00753.0510.1440.1440.0000.0000.0000.000
188A198GLU-1-0.963-0.98154.5645.3815.3810.0000.0000.0000.000