Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: J3MV9

Calculation Name: 4RL9-A-Xray322

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RL9

Chain ID: A

ChEMBL ID:

UniProt ID: A6XB80

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 208
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2058812.572303
FMO2-HF: Nuclear repulsion 1980937.679356
FMO2-HF: Total energy -77874.892947
FMO2-MP2: Total energy -78105.291893


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:16:ACE )


Summations of interaction energy for fragment #1(A:16:ACE )
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.
0.531.745-0.002-0.584-0.629-0.001
Interaction energy analysis for fragmet #1(A:16:ACE )
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 : -0.009
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].
3A18PRO 0-0.0160.0233.8840.4641.547-0.005-0.523-0.555-0.001
4A19VAL 0-0.0070.0056.7430.0470.0470.0000.0000.0000.000
5A20GLY 00.024-0.0019.7080.0880.0880.0000.0000.0000.000
6A21ALA 0-0.033-0.01611.636-0.057-0.0570.0000.0000.0000.000
7A22ARG 10.8120.89414.2570.1030.1030.0000.0000.0000.000
8A23ALA 00.0110.02417.514-0.007-0.0070.0000.0000.0000.000
9A24GLU -1-0.799-0.88019.339-0.072-0.0720.0000.0000.0000.000
10A25VAL 00.0500.01322.783-0.003-0.0030.0000.0000.0000.000
11A26GLY 0-0.002-0.01926.1220.0040.0040.0000.0000.0000.000
12A27THR 00.0400.03027.711-0.002-0.0020.0000.0000.0000.000
13A28THR 00.0390.04324.4930.0040.0040.0000.0000.0000.000
14A29GLY 00.0490.02725.962-0.004-0.0040.0000.0000.0000.000
15A30TYR 0-0.042-0.03424.7950.0010.0010.0000.0000.0000.000
16A31GLY 00.0260.01821.603-0.001-0.0010.0000.0000.0000.000
17A32GLY 0-0.026-0.01318.643-0.003-0.0030.0000.0000.0000.000
18A33ALA 0-0.0070.00414.4070.0050.0050.0000.0000.0000.000
19A34LEU 0-0.007-0.0019.485-0.042-0.0420.0000.0000.0000.000
20A35LEU 00.0250.01710.3690.0770.0770.0000.0000.0000.000
21A36TRP 0-0.0120.0003.7970.1420.2740.003-0.061-0.0740.000
22A37GLN 00.002-0.0197.5450.0630.0630.0000.0000.0000.000
23A38ALA 0-0.0160.0127.6150.0660.0660.0000.0000.0000.000
24A39ASN 00.028-0.0028.567-0.071-0.0710.0000.0000.0000.000
25A40PRO 00.000-0.01011.983-0.026-0.0260.0000.0000.0000.000
26A41TYR 0-0.020-0.00115.138-0.032-0.0320.0000.0000.0000.000
27A42VAL 0-0.0120.02211.126-0.014-0.0140.0000.0000.0000.000
28A43GLY 00.0140.00210.0840.0520.0520.0000.0000.0000.000
29A44LEU 0-0.030-0.0147.4990.0370.0370.0000.0000.0000.000
30A45ALA 00.0600.03610.429-0.082-0.0820.0000.0000.0000.000
31A46LEU 0-0.011-0.00110.5490.0350.0350.0000.0000.0000.000
32A47GLY 00.003-0.00812.488-0.058-0.0580.0000.0000.0000.000
33A48TYR 0-0.040-0.02815.8410.0130.0130.0000.0000.0000.000
34A49ASN 0-0.133-0.08219.0290.0050.0050.0000.0000.0000.000
35A50GLY 00.0720.01922.4990.0060.0060.0000.0000.0000.000
36A51GLY 0-0.019-0.01325.555-0.003-0.0030.0000.0000.0000.000
37A52ASP -1-0.863-0.92729.025-0.044-0.0440.0000.0000.0000.000
38A53ILE 0-0.101-0.03530.523-0.002-0.0020.0000.0000.0000.000
39A54SER 00.0580.02434.5850.0020.0020.0000.0000.0000.000
40A55TRP 0-0.105-0.05033.964-0.002-0.0020.0000.0000.0000.000
41A56THR 0-0.0020.00740.4920.0010.0010.0000.0000.0000.000
42A57ASP -1-0.961-0.98543.889-0.023-0.0230.0000.0000.0000.000
43A58NME 0-0.043-0.01546.6010.0020.0020.0000.0000.0000.000
44A64ACE 00.015-0.01950.3650.0000.0000.0000.0000.0000.000
45A65LYS 10.8580.94049.5600.0130.0130.0000.0000.0000.000
46A66TYR 0-0.001-0.00845.1340.0020.0020.0000.0000.0000.000
47A67ASP -1-0.842-0.90243.659-0.021-0.0210.0000.0000.0000.000
48A68LEU 0-0.038-0.02537.1940.0020.0020.0000.0000.0000.000
49A69ASP -1-0.828-0.91337.492-0.027-0.0270.0000.0000.0000.000
50A70MET 0-0.066-0.01931.7580.0020.0020.0000.0000.0000.000
51A71ASP -1-0.853-0.89732.001-0.034-0.0340.0000.0000.0000.000
52A72ASN 0-0.008-0.02827.2590.0070.0070.0000.0000.0000.000
53A73ASN 00.0200.02224.825-0.015-0.0150.0000.0000.0000.000
54A74ASN 00.0020.00022.5380.0120.0120.0000.0000.0000.000
55A75VAL 00.0010.00816.703-0.015-0.0150.0000.0000.0000.000
56A76TYR 0-0.034-0.02516.2230.0140.0140.0000.0000.0000.000
57A77LEU 0-0.005-0.00510.663-0.021-0.0210.0000.0000.0000.000
58A78ASN 00.0230.00914.0580.0280.0280.0000.0000.0000.000
59A79ALA 0-0.019-0.01412.9370.0030.0030.0000.0000.0000.000
60A80GLU -1-0.879-0.94913.642-0.043-0.0430.0000.0000.0000.000
61A81ILE 0-0.015-0.01914.8960.0260.0260.0000.0000.0000.000
62A82ARG 10.9200.98016.393-0.024-0.0240.0000.0000.0000.000
63A83PRO 00.0290.00719.0880.0120.0120.0000.0000.0000.000
64A84TRP 00.010-0.00221.8190.0040.0040.0000.0000.0000.000
65A85GLY 00.0220.00418.431-0.013-0.0130.0000.0000.0000.000
66A86ALA 0-0.029-0.02518.963-0.010-0.0100.0000.0000.0000.000
67A87SER 0-0.0340.00320.152-0.008-0.0080.0000.0000.0000.000
68A88THR 00.008-0.00622.805-0.005-0.0050.0000.0000.0000.000
69A89ASN 00.0200.00925.066-0.010-0.0100.0000.0000.0000.000
70A90PRO 00.031-0.00924.4650.0050.0050.0000.0000.0000.000
71A91TRP 00.0260.02424.8720.0000.0000.0000.0000.0000.000
72A92ALA 00.0130.00126.0440.0020.0020.0000.0000.0000.000
73A93GLN 0-0.035-0.02218.340-0.010-0.0100.0000.0000.0000.000
74A94GLY 00.0180.01520.7380.0010.0010.0000.0000.0000.000
75A95LEU 0-0.048-0.02021.803-0.002-0.0020.0000.0000.0000.000
76A96TYR 0-0.076-0.08618.8690.0080.0080.0000.0000.0000.000
77A97ILE 00.0160.02220.342-0.008-0.0080.0000.0000.0000.000
78A98ALA 0-0.0140.00018.2990.0120.0120.0000.0000.0000.000
79A99ALA 00.0200.01117.803-0.005-0.0050.0000.0000.0000.000
80A100GLY 00.0010.00216.8720.0210.0210.0000.0000.0000.000
81A101ALA 0-0.0260.00117.402-0.003-0.0030.0000.0000.0000.000
82A102ALA 00.0090.00218.105-0.006-0.0060.0000.0000.0000.000
83A103TYR 0-0.0220.02020.3050.0080.0080.0000.0000.0000.000
84A104LEU 0-0.033-0.04022.257-0.009-0.0090.0000.0000.0000.000
85A105ASP -1-0.907-0.96225.263-0.017-0.0170.0000.0000.0000.000
86A106ASN 0-0.003-0.01626.807-0.009-0.0090.0000.0000.0000.000
87A107ASP -1-0.836-0.90330.344-0.012-0.0120.0000.0000.0000.000
88A108TYR 0-0.051-0.04230.165-0.001-0.0010.0000.0000.0000.000
89A109ASP -1-0.828-0.91636.134-0.015-0.0150.0000.0000.0000.000
90A110LEU 0-0.030-0.01539.667-0.001-0.0010.0000.0000.0000.000
91A111ALA 0-0.018-0.01442.4700.0010.0010.0000.0000.0000.000
92A112LYS 10.8790.95245.9130.0080.0080.0000.0000.0000.000
93A113ARG 10.9310.96248.9330.0150.0150.0000.0000.0000.000
94A114ILE 0-0.070-0.04052.0250.0000.0000.0000.0000.0000.000
95A115GLY 00.0270.01155.4130.0000.0000.0000.0000.0000.000
96A116ASN 00.031-0.01258.4160.0010.0010.0000.0000.0000.000
97A117GLY 0-0.0250.00061.7540.0000.0000.0000.0000.0000.000
98A118ASP -1-0.916-0.93256.930-0.011-0.0110.0000.0000.0000.000
99A119THR 0-0.047-0.04556.4270.0010.0010.0000.0000.0000.000
100A120LEU 0-0.025-0.01951.782-0.001-0.0010.0000.0000.0000.000
101A121SER 0-0.006-0.01351.2030.0010.0010.0000.0000.0000.000
102A122ILE 00.011-0.00549.571-0.001-0.0010.0000.0000.0000.000
103A123ASP -1-0.795-0.87348.7360.0010.0010.0000.0000.0000.000
104A124GLY 0-0.035-0.01749.7400.0010.0010.0000.0000.0000.000
105A125LYS 10.8740.94651.7340.0000.0000.0000.0000.0000.000
106A126ASN 00.0010.00354.108-0.001-0.0010.0000.0000.0000.000
107A127TYR 0-0.022-0.02854.8800.0010.0010.0000.0000.0000.000
108A128GLN 00.0080.00757.679-0.001-0.0010.0000.0000.0000.000
109A129GLN 00.0510.02659.7960.0010.0010.0000.0000.0000.000
110A130ALA 0-0.049-0.00560.8810.0000.0000.0000.0000.0000.000
111A131VAL 0-0.028-0.03662.6790.0000.0000.0000.0000.0000.000
112A132PRO 0-0.002-0.01063.3400.0000.0000.0000.0000.0000.000
113A133GLY 0-0.046-0.00364.5350.0000.0000.0000.0000.0000.000
114A134GLN 0-0.0110.00559.947-0.001-0.0010.0000.0000.0000.000
115A135GLU -1-0.900-0.95254.092-0.011-0.0110.0000.0000.0000.000
116A136GLY 00.0790.05556.4640.0010.0010.0000.0000.0000.000
117A137GLY 00.011-0.01152.412-0.001-0.0010.0000.0000.0000.000
118A138VAL 0-0.030-0.01448.2040.0010.0010.0000.0000.0000.000
119A139ARG 10.9220.97542.6420.0140.0140.0000.0000.0000.000
120A140GLY 0-0.007-0.00843.9280.0010.0010.0000.0000.0000.000
121A141LYS 10.9651.00237.9150.0130.0130.0000.0000.0000.000
122A142MET 0-0.033-0.02136.4930.0030.0030.0000.0000.0000.000
123A143SER 0-0.005-0.00134.428-0.002-0.0020.0000.0000.0000.000
124A144TYR 0-0.019-0.01530.2060.0040.0040.0000.0000.0000.000
125A145LYS 10.9430.97827.4610.0000.0000.0000.0000.0000.000
126A146ASN 0-0.081-0.04926.6890.0010.0010.0000.0000.0000.000
127A147ASP -1-0.892-0.94624.7250.0070.0070.0000.0000.0000.000
128A148ILE 0-0.037-0.03120.8410.0030.0030.0000.0000.0000.000
129A149ALA 00.0040.02023.0270.0010.0010.0000.0000.0000.000
130A150PRO 0-0.022-0.01522.0440.0010.0010.0000.0000.0000.000
131A151TYR 0-0.041-0.04119.918-0.009-0.0090.0000.0000.0000.000
132A152LEU 0-0.034-0.02621.8250.0130.0130.0000.0000.0000.000
133A153GLY 00.0270.01922.560-0.009-0.0090.0000.0000.0000.000
134A154PHE 0-0.049-0.03123.1150.0100.0100.0000.0000.0000.000
135A155GLY 00.0630.03822.386-0.008-0.0080.0000.0000.0000.000
136A156PHE 0-0.083-0.04023.3650.0060.0060.0000.0000.0000.000
137A157ALA 00.0390.01119.927-0.008-0.0080.0000.0000.0000.000
138A158PRO 0-0.0270.01020.981-0.001-0.0010.0000.0000.0000.000
139A159LYS 10.9450.96816.5670.0450.0450.0000.0000.0000.000
140A160ILE 0-0.019-0.00422.2540.0080.0080.0000.0000.0000.000
141A161SER 0-0.013-0.01923.0880.0010.0010.0000.0000.0000.000
142A162LYS 10.9310.95218.6750.0620.0620.0000.0000.0000.000
143A163ASN 00.0100.01518.2820.0170.0170.0000.0000.0000.000
144A164TRP 00.0690.05019.196-0.018-0.0180.0000.0000.0000.000
145A165GLY 00.006-0.01221.1760.0130.0130.0000.0000.0000.000
146A166VAL 0-0.0060.02321.934-0.009-0.0090.0000.0000.0000.000
147A167PHE 0-0.033-0.02520.7680.0050.0050.0000.0000.0000.000
148A168GLY 00.0280.02723.321-0.004-0.0040.0000.0000.0000.000
149A169GLU -1-0.840-0.87620.223-0.003-0.0030.0000.0000.0000.000
150A170VAL 00.004-0.00724.373-0.004-0.0040.0000.0000.0000.000
151A171GLY 00.0210.00925.3530.0070.0070.0000.0000.0000.000
152A172ALA 0-0.032-0.00725.924-0.005-0.0050.0000.0000.0000.000
153A173TYR 00.0280.01521.5830.0070.0070.0000.0000.0000.000
154A174TYR 0-0.051-0.01126.334-0.001-0.0010.0000.0000.0000.000
155A175THR 0-0.036-0.04328.0070.0020.0020.0000.0000.0000.000
156A176GLY 00.0110.01629.8930.0000.0000.0000.0000.0000.000
157A177ASN 0-0.051-0.02633.4310.0000.0000.0000.0000.0000.000
158A178PRO 00.0090.03334.8280.0000.0000.0000.0000.0000.000
159A179LYS 10.9150.94836.020-0.001-0.0010.0000.0000.0000.000
160A180VAL 00.0340.01038.481-0.001-0.0010.0000.0000.0000.000
161A181GLU -1-0.998-0.98741.266-0.007-0.0070.0000.0000.0000.000
162A182LEU 00.0220.00343.889-0.001-0.0010.0000.0000.0000.000
163A183THR 0-0.045-0.00346.5570.0000.0000.0000.0000.0000.000
164A184GLN 00.004-0.02849.693-0.001-0.0010.0000.0000.0000.000
165A185TYR 00.0170.02149.1830.0000.0000.0000.0000.0000.000
166A186ASN 0-0.031-0.04455.2180.0000.0000.0000.0000.0000.000
167A187LEU 00.0340.01853.9280.0000.0000.0000.0000.0000.000
168A188ALA 0-0.015-0.01358.5160.0010.0010.0000.0000.0000.000
169A189PRO 00.0200.01659.8130.0000.0000.0000.0000.0000.000
170A190VAL 0-0.0020.01559.7790.0000.0000.0000.0000.0000.000
171A191THR 0-0.039-0.03562.4210.0010.0010.0000.0000.0000.000
172A192GLY 00.0620.01764.5140.0000.0000.0000.0000.0000.000
173A193ASN 0-0.052-0.00557.6880.0010.0010.0000.0000.0000.000
174A194PRO 0-0.010-0.01460.8130.0000.0000.0000.0000.0000.000
175A195THR 0-0.024-0.00756.1420.0000.0000.0000.0000.0000.000
176A196SER 00.0630.04058.851-0.001-0.0010.0000.0000.0000.000
177A197ALA 00.0720.02855.3500.0000.0000.0000.0000.0000.000
178A198GLN 00.010-0.00252.890-0.001-0.0010.0000.0000.0000.000
179A199ASP -1-0.859-0.92253.8630.0010.0010.0000.0000.0000.000
180A200ALA 0-0.082-0.03153.0120.0010.0010.0000.0000.0000.000
181A201VAL 00.009-0.00649.6470.0000.0000.0000.0000.0000.000
182A202ASP -1-0.879-0.94349.0160.0000.0000.0000.0000.0000.000
183A203LYS 10.7950.89349.347-0.002-0.0020.0000.0000.0000.000
184A204GLU -1-0.857-0.93545.574-0.002-0.0020.0000.0000.0000.000
185A205ALA 00.009-0.00644.7200.0000.0000.0000.0000.0000.000
186A206ASN 0-0.028-0.03144.1910.0010.0010.0000.0000.0000.000
187A207GLU -1-0.937-0.95344.6830.0050.0050.0000.0000.0000.000
188A208ILE 00.0420.00839.3190.0010.0010.0000.0000.0000.000
189A209ARG 10.8720.94139.963-0.001-0.0010.0000.0000.0000.000
190A210ASN 0-0.038-0.01640.7940.0020.0020.0000.0000.0000.000
191A211ASP -1-0.871-0.92941.8060.0130.0130.0000.0000.0000.000
192A212ASN 00.0260.02438.1830.0000.0000.0000.0000.0000.000
193A213LYS 10.8550.92637.004-0.012-0.0120.0000.0000.0000.000
194A214TYR 0-0.023-0.01135.9680.0000.0000.0000.0000.0000.000
195A215GLU -1-0.890-0.93933.8270.0220.0220.0000.0000.0000.000
196A216TRP 0-0.030-0.02127.0360.0040.0040.0000.0000.0000.000
197A217MET 00.0210.02627.617-0.002-0.0020.0000.0000.0000.000
198A218PRO 0-0.031-0.00428.8740.0010.0010.0000.0000.0000.000
199A219VAL 0-0.002-0.01524.889-0.004-0.0040.0000.0000.0000.000
200A220GLY 00.015-0.00827.2910.0040.0040.0000.0000.0000.000
201A221LYS 10.8870.96820.8190.0380.0380.0000.0000.0000.000
202A222VAL 00.001-0.00925.1670.0050.0050.0000.0000.0000.000
203A223GLY 00.0360.01923.038-0.005-0.0050.0000.0000.0000.000
204A224VAL 0-0.069-0.03321.6360.0070.0070.0000.0000.0000.000
205A225ASN 00.004-0.00517.344-0.016-0.0160.0000.0000.0000.000
206A226PHE 0-0.006-0.01216.7020.0170.0170.0000.0000.0000.000
207A227TYR 0-0.060-0.04013.624-0.008-0.0080.0000.0000.0000.000
208A228TRP -1-0.938-0.9789.777-0.205-0.2050.0000.0000.0000.000