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: 4J5LN

Calculation Name: 4YZE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YZE

Chain ID: A

ChEMBL ID:

UniProt ID: P67430

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2024911.446608
FMO2-HF: Nuclear repulsion 1949852.263991
FMO2-HF: Total energy -75059.182617
FMO2-MP2: Total energy -75279.318371


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:7:HIS)


Summations of interaction energy for fragment #1(A:7:HIS)
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.
-23.726-21.8367.403-4.51-4.7830.039
Interaction energy analysis for fragmet #1(A:7:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.011
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].
3A9THR00.004-0.0073.178-0.1811.4980.034-0.632-1.0810.003
4A10ARG10.9480.9893.531-6.609-5.6390.026-0.283-0.7120.001
5A11GLU-1-0.790-0.8814.850-0.941-0.9410.0000.0000.0000.000
6A12HIS0-0.0100.0016.841-0.406-0.4060.0000.0000.0000.000
7A13LEU0-0.0090.0047.608-0.142-0.1420.0000.0000.0000.000
8A14LEU0-0.003-0.0057.678-0.290-0.2900.0000.0000.0000.000
9A15ALA00.0130.01110.725-0.189-0.1890.0000.0000.0000.000
10A16THR0-0.031-0.02112.582-0.137-0.1370.0000.0000.0000.000
11A17GLY00.010-0.01913.752-0.056-0.0560.0000.0000.0000.000
12A18GLU-1-0.824-0.89314.141-0.059-0.0590.0000.0000.0000.000
13A19GLN00.0340.02716.669-0.037-0.0370.0000.0000.0000.000
14A20LEU0-0.009-0.01517.980-0.023-0.0230.0000.0000.0000.000
15A21SER00.002-0.01918.585-0.005-0.0050.0000.0000.0000.000
16A22LEU0-0.057-0.01820.881-0.023-0.0230.0000.0000.0000.000
17A23GLN0-0.047-0.02722.6340.0130.0130.0000.0000.0000.000
18A24ARG10.8200.89623.335-0.210-0.2100.0000.0000.0000.000
19A25GLY00.0120.01424.4320.0000.0000.0000.0000.0000.000
20A26PHE00.0140.01217.5260.0390.0390.0000.0000.0000.000
21A27THR0-0.024-0.04622.1260.0510.0510.0000.0000.0000.000
22A28GLY0-0.0080.00024.8260.0240.0240.0000.0000.0000.000
23A29MET0-0.0300.02317.4720.0190.0190.0000.0000.0000.000
24A30GLY00.0420.02421.7680.0580.0580.0000.0000.0000.000
25A31LEU0-0.006-0.01415.6280.0130.0130.0000.0000.0000.000
26A32SER00.010-0.00217.6980.0670.0670.0000.0000.0000.000
27A33GLU-1-0.794-0.88719.3090.3460.3460.0000.0000.0000.000
28A34LEU00.0390.03313.243-0.046-0.0460.0000.0000.0000.000
29A35LEU0-0.031-0.01913.3020.0070.0070.0000.0000.0000.000
30A36LYS10.8980.95115.133-0.331-0.3310.0000.0000.0000.000
31A37THR0-0.060-0.05417.173-0.115-0.1150.0000.0000.0000.000
32A38ALA00.0040.01211.473-0.089-0.0890.0000.0000.0000.000
33A39GLU-1-0.923-0.93912.2440.0630.0630.0000.0000.0000.000
34A40VAL0-0.0230.0009.1400.1510.1510.0000.0000.0000.000
35A41PRO00.0330.01410.689-0.075-0.0750.0000.0000.0000.000
36A42LYS10.9900.96912.224-0.612-0.6120.0000.0000.0000.000
37A43GLY00.0100.00113.3580.1240.1240.0000.0000.0000.000
38A44SER00.0490.0187.990-0.040-0.0400.0000.0000.0000.000
39A45PHE00.0180.0138.5530.7680.7680.0000.0000.0000.000
40A46TYR0-0.022-0.02810.6020.1690.1690.0000.0000.0000.000
41A47HIS0-0.0530.0014.833-0.945-0.9450.0000.0000.0000.000
42A48TYR0-0.043-0.0312.027-12.821-13.5807.343-3.595-2.9900.035
43A49PHE0-0.020-0.0178.076-0.126-0.1260.0000.0000.0000.000
44A50ARG10.9050.93611.648-1.324-1.3240.0000.0000.0000.000
45A51SER00.013-0.00115.154-0.149-0.1490.0000.0000.0000.000
46A52LYS10.8720.92315.525-0.473-0.4730.0000.0000.0000.000
47A53GLU-1-0.758-0.84216.9590.9410.9410.0000.0000.0000.000
48A54ALA00.0180.01114.799-0.013-0.0130.0000.0000.0000.000
49A55PHE0-0.029-0.01510.9330.0420.0420.0000.0000.0000.000
50A56GLY00.0640.00913.571-0.032-0.0320.0000.0000.0000.000
51A57VAL00.0020.00315.813-0.093-0.0930.0000.0000.0000.000
52A58ALA00.0080.00410.706-0.057-0.0570.0000.0000.0000.000
53A59MET0-0.050-0.00412.519-0.115-0.1150.0000.0000.0000.000
54A60LEU0-0.024-0.00613.878-0.199-0.1990.0000.0000.0000.000
55A61GLU-1-0.852-0.92113.7620.6760.6760.0000.0000.0000.000
56A62ARG10.7990.8768.9200.1280.1280.0000.0000.0000.000
57A63HIS0-0.063-0.04311.966-0.238-0.2380.0000.0000.0000.000
58A64TYR00.011-0.02915.073-0.115-0.1150.0000.0000.0000.000
59A65ALA00.0090.01912.292-0.068-0.0680.0000.0000.0000.000
60A66ALA00.005-0.00112.586-0.126-0.1260.0000.0000.0000.000
61A67TYR0-0.079-0.05014.182-0.065-0.0650.0000.0000.0000.000
62A68HIS00.0370.02117.2880.0040.0040.0000.0000.0000.000
63A69GLN00.0140.03014.5110.0920.0920.0000.0000.0000.000
64A70ARG10.9941.00515.5180.4960.4960.0000.0000.0000.000
65A71LEU0-0.042-0.00719.0830.0140.0140.0000.0000.0000.000
66A72THR00.004-0.02619.8700.0390.0390.0000.0000.0000.000
67A73GLU-1-0.922-0.97017.934-0.709-0.7090.0000.0000.0000.000
68A74LEU0-0.043-0.01621.8180.0200.0200.0000.0000.0000.000
69A75LEU00.013-0.00524.7470.0170.0170.0000.0000.0000.000
70A76GLN0-0.006-0.00824.0290.0010.0010.0000.0000.0000.000
71A77SER0-0.082-0.05324.157-0.001-0.0010.0000.0000.0000.000
72A78GLY00.0130.03426.227-0.027-0.0270.0000.0000.0000.000
73A79GLU-1-0.897-0.94627.364-0.276-0.2760.0000.0000.0000.000
74A80GLY0-0.012-0.00430.6560.0150.0150.0000.0000.0000.000
75A81ASN0-0.046-0.03332.838-0.001-0.0010.0000.0000.0000.000
76A82TYR00.0540.01329.794-0.009-0.0090.0000.0000.0000.000
77A83ARG10.8560.93233.0450.1120.1120.0000.0000.0000.000
78A84ASP-1-0.821-0.91034.096-0.171-0.1710.0000.0000.0000.000
79A85ARG10.8430.93828.8270.2510.2510.0000.0000.0000.000
80A86ILE00.0080.00030.215-0.001-0.0010.0000.0000.0000.000
81A87LEU0-0.046-0.02732.0000.0090.0090.0000.0000.0000.000
82A88ALA00.0190.00330.0510.0030.0030.0000.0000.0000.000
83A89TYR00.0280.02925.368-0.015-0.0150.0000.0000.0000.000
84A90TYR0-0.018-0.01428.9340.0000.0000.0000.0000.0000.000
85A91GLN0-0.020-0.00531.6740.0140.0140.0000.0000.0000.000
86A92GLN00.0450.01925.2280.0060.0060.0000.0000.0000.000
87A93THR0-0.041-0.02727.8360.0020.0020.0000.0000.0000.000
88A94LEU0-0.023-0.01728.9380.0080.0080.0000.0000.0000.000
89A95ASN0-0.038-0.02028.5830.0190.0190.0000.0000.0000.000
90A96GLN0-0.031-0.02022.562-0.031-0.0310.0000.0000.0000.000
91A97PHE00.0130.02127.1890.0120.0120.0000.0000.0000.000
92A98SER0-0.040-0.02129.4200.0220.0220.0000.0000.0000.000
93A99GLN0-0.001-0.00325.371-0.053-0.0530.0000.0000.0000.000
94A100HIS00.007-0.00125.7500.0340.0340.0000.0000.0000.000
95A101GLY00.0210.02930.7910.0120.0120.0000.0000.0000.000
96A102THR0-0.047-0.02429.0650.0180.0180.0000.0000.0000.000
97A103ILE00.007-0.00629.689-0.017-0.0170.0000.0000.0000.000
98A104SER0-0.0240.00424.6680.0040.0040.0000.0000.0000.000
99A105GLY0-0.021-0.00925.6220.0160.0160.0000.0000.0000.000
100A106CYS00.0290.00323.577-0.027-0.0270.0000.0000.0000.000
101A107LEU00.0470.02618.4680.0270.0270.0000.0000.0000.000
102A108THR00.0630.03322.5140.0380.0380.0000.0000.0000.000
103A109VAL00.0310.02024.5740.0170.0170.0000.0000.0000.000
104A110LYS10.7730.91125.038-0.203-0.2030.0000.0000.0000.000
105A111LEU00.0380.00121.5610.0170.0170.0000.0000.0000.000
106A112SER0-0.020-0.01026.0280.0180.0180.0000.0000.0000.000
107A113ALA0-0.025-0.01529.0930.0070.0070.0000.0000.0000.000
108A114GLU-1-0.753-0.85625.5730.3240.3240.0000.0000.0000.000
109A115VAL0-0.025-0.01526.9810.0290.0290.0000.0000.0000.000
110A116SER0-0.042-0.00728.4900.0080.0080.0000.0000.0000.000
111A117ASP-1-0.925-0.95428.9040.3020.3020.0000.0000.0000.000
112A118LEU0-0.056-0.03622.7780.0440.0440.0000.0000.0000.000
113A119SER0-0.019-0.02621.116-0.033-0.0330.0000.0000.0000.000
114A120GLU-1-0.741-0.84524.3070.3480.3480.0000.0000.0000.000
115A121ASP-1-0.901-0.94719.9330.6910.6910.0000.0000.0000.000
116A122MET0-0.037-0.00719.1870.0110.0110.0000.0000.0000.000
117A123ARG10.7930.85621.292-0.353-0.3530.0000.0000.0000.000
118A124SER00.001-0.00722.923-0.054-0.0540.0000.0000.0000.000
119A125ALA0-0.042-0.02118.455-0.032-0.0320.0000.0000.0000.000
120A126MET0-0.027-0.01620.323-0.047-0.0470.0000.0000.0000.000
121A127ASP-1-0.821-0.87622.4960.1760.1760.0000.0000.0000.000
122A128LYS10.8340.90017.755-0.514-0.5140.0000.0000.0000.000
123A129GLY00.0260.01220.382-0.041-0.0410.0000.0000.0000.000
124A130ALA0-0.030-0.01421.151-0.052-0.0520.0000.0000.0000.000
125A131ARG10.8930.92624.280-0.247-0.2470.0000.0000.0000.000
126A132GLY00.0220.02521.911-0.019-0.0190.0000.0000.0000.000
127A133VAL00.011-0.00422.593-0.035-0.0350.0000.0000.0000.000
128A134ILE0-0.0110.00124.508-0.019-0.0190.0000.0000.0000.000
129A135ALA00.0060.00125.280-0.011-0.0110.0000.0000.0000.000
130A136LEU0-0.018-0.00221.447-0.011-0.0110.0000.0000.0000.000
131A137LEU00.004-0.00526.111-0.014-0.0140.0000.0000.0000.000
132A138SER00.003-0.00529.2780.0010.0010.0000.0000.0000.000
133A139GLN0-0.049-0.02928.2940.0110.0110.0000.0000.0000.000
134A140ALA00.0050.00529.102-0.007-0.0070.0000.0000.0000.000
135A141LEU0-0.041-0.02130.911-0.003-0.0030.0000.0000.0000.000
136A142GLU-1-0.789-0.90233.890-0.045-0.0450.0000.0000.0000.000
137A143ASN00.0170.01130.3380.0110.0110.0000.0000.0000.000
138A144GLY00.005-0.00734.199-0.006-0.0060.0000.0000.0000.000
139A145ARG10.8010.88936.2440.0490.0490.0000.0000.0000.000
140A146GLU-1-0.949-0.97336.087-0.086-0.0860.0000.0000.0000.000
141A147ASN0-0.0080.01636.1450.0030.0030.0000.0000.0000.000
142A148HIS0-0.042-0.03038.991-0.003-0.0030.0000.0000.0000.000
143A149SER0-0.037-0.03037.112-0.006-0.0060.0000.0000.0000.000
144A150LEU0-0.100-0.05135.682-0.001-0.0010.0000.0000.0000.000
145A151THR0-0.040-0.01440.2350.0060.0060.0000.0000.0000.000
146A152PHE00.0290.01037.572-0.002-0.0020.0000.0000.0000.000
147A153SER00.0000.00742.1230.0030.0030.0000.0000.0000.000
148A154GLY00.0600.02641.6210.0010.0010.0000.0000.0000.000
149A155GLU-1-0.844-0.91738.0940.0120.0120.0000.0000.0000.000
150A156PRO00.0110.00634.5540.0020.0020.0000.0000.0000.000
151A157LEU00.0590.03431.622-0.002-0.0020.0000.0000.0000.000
152A158GLN0-0.067-0.02634.3440.0040.0040.0000.0000.0000.000
153A159GLN00.0140.01036.5590.0010.0010.0000.0000.0000.000
154A160ALA00.0230.01331.095-0.003-0.0030.0000.0000.0000.000
155A161GLN0-0.037-0.02832.0900.0130.0130.0000.0000.0000.000
156A162VAL0-0.0080.00533.3260.0040.0040.0000.0000.0000.000
157A163LEU00.0200.01132.921-0.001-0.0010.0000.0000.0000.000
158A164TYR00.0440.01524.8840.0070.0070.0000.0000.0000.000
159A165ALA00.007-0.00131.0760.0050.0050.0000.0000.0000.000
160A166LEU0-0.0070.00233.5280.0030.0030.0000.0000.0000.000
161A167TRP00.000-0.01025.2860.0130.0130.0000.0000.0000.000
162A168LEU0-0.0020.00928.914-0.002-0.0020.0000.0000.0000.000
163A169GLY00.0080.00231.2340.0050.0050.0000.0000.0000.000
164A170ALA00.0300.01434.3780.0020.0020.0000.0000.0000.000
165A171ASN0-0.013-0.02629.632-0.012-0.0120.0000.0000.0000.000
166A172LEU0-0.045-0.01431.8810.0020.0020.0000.0000.0000.000
167A173GLN00.0180.01133.9030.0050.0050.0000.0000.0000.000
168A174ALA00.0280.03334.1600.0000.0000.0000.0000.0000.000
169A175LYS10.9680.97529.824-0.067-0.0670.0000.0000.0000.000
170A176ILE0-0.071-0.03734.2820.0020.0020.0000.0000.0000.000
171A177SER0-0.053-0.04837.391-0.002-0.0020.0000.0000.0000.000
172A178ARG10.8930.94636.1800.0030.0030.0000.0000.0000.000
173A179SER00.0240.02437.688-0.012-0.0120.0000.0000.0000.000
174A180PHE00.0410.01935.4510.0050.0050.0000.0000.0000.000
175A181GLU-1-0.826-0.90436.913-0.039-0.0390.0000.0000.0000.000
176A182PRO0-0.0010.00037.177-0.002-0.0020.0000.0000.0000.000
177A183LEU0-0.030-0.01732.3000.0010.0010.0000.0000.0000.000
178A184GLU-1-0.904-0.95535.923-0.101-0.1010.0000.0000.0000.000
179A185ASN0-0.077-0.03438.547-0.003-0.0030.0000.0000.0000.000
180A186ALA00.0190.01136.3020.0010.0010.0000.0000.0000.000
181A187LEU00.000-0.00135.282-0.001-0.0010.0000.0000.0000.000
182A188ALA0-0.021-0.01937.419-0.004-0.0040.0000.0000.0000.000
183A189HIS00.0270.01439.971-0.001-0.0010.0000.0000.0000.000
184A190VAL00.001-0.00835.4690.0020.0020.0000.0000.0000.000
185A191LYS10.9020.95338.1870.1190.1190.0000.0000.0000.000
186A192ASN0-0.042-0.01040.606-0.003-0.0030.0000.0000.0000.000
187A193ILE0-0.031-0.01940.5950.0020.0020.0000.0000.0000.000
188A194ILE0-0.0170.00136.7940.0030.0030.0000.0000.0000.000
189A195ALA00.0540.05340.079-0.011-0.0110.0000.0000.0000.000
190A196THR00.0480.01041.878-0.005-0.0050.0000.0000.0000.000
191A197PRO0-0.030-0.01242.6800.0080.0080.0000.0000.0000.000
192A198ALA0-0.018-0.00945.921-0.003-0.0030.0000.0000.0000.000
193A199VAL00.0190.02947.4110.0000.0000.0000.0000.0000.000