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: 5JRQZ

Calculation Name: 3F5D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F5D

Chain ID: A

ChEMBL ID:

UniProt ID: P96658

Base Structure: X-ray

Registration Date: 2023-09-22

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2209800.826496
FMO2-HF: Nuclear repulsion 2132824.906795
FMO2-HF: Total energy -76975.919701
FMO2-MP2: Total energy -77201.057023


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:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
-11.211-3.0194.489-4.604-8.079-0.041
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.042 / q_NPA : -0.023
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].
3A5LYS10.9440.9623.249-1.8910.6050.071-1.034-1.5340.000
4A6ALA00.0310.0105.0950.2360.299-0.001-0.004-0.0580.000
5A7LEU0-0.016-0.0178.479-0.059-0.0590.0000.0000.0000.000
6A8PHE00.011-0.00911.1650.0660.0660.0000.0000.0000.000
7A9LEU0-0.030-0.02214.2710.0030.0030.0000.0000.0000.000
8A10ILE00.0100.01617.3480.0170.0170.0000.0000.0000.000
9A11LEU0-0.0040.01520.0050.0010.0010.0000.0000.0000.000
10A12ASP-1-0.794-0.91923.444-0.118-0.1180.0000.0000.0000.000
11A13GLN0-0.0190.02726.1200.0100.0100.0000.0000.0000.000
12A14TYR0-0.030-0.02220.7540.0060.0060.0000.0000.0000.000
13A15ALA00.0240.00524.4620.0000.0000.0000.0000.0000.000
14A16ASP-1-0.787-0.86622.624-0.144-0.1440.0000.0000.0000.000
15A17TRP0-0.012-0.03521.644-0.018-0.0180.0000.0000.0000.000
16A18GLU-1-0.782-0.90721.968-0.099-0.0990.0000.0000.0000.000
17A19GLY00.0350.01017.6950.0070.0070.0000.0000.0000.000
18A20VAL00.0080.00616.235-0.034-0.0340.0000.0000.0000.000
19A21TYR00.0210.01216.432-0.023-0.0230.0000.0000.0000.000
20A22LEU00.0100.01413.168-0.008-0.0080.0000.0000.0000.000
21A23ALA00.0100.00311.921-0.043-0.0430.0000.0000.0000.000
22A24SER0-0.004-0.01411.029-0.089-0.0890.0000.0000.0000.000
23A25ALA0-0.015-0.00411.653-0.046-0.0460.0000.0000.0000.000
24A26LEU0-0.012-0.0168.2430.0050.0050.0000.0000.0000.000
25A27ASN00.0290.0006.718-0.363-0.3630.0000.0000.0000.000
26A28GLN0-0.053-0.0177.008-0.145-0.1450.0000.0000.0000.000
27A29ARG10.7750.8915.878-0.312-0.3120.0000.0000.0000.000
28A30GLU-1-0.895-0.9414.640-1.762-1.618-0.001-0.017-0.1260.000
29A31ASP-1-0.829-0.9042.588-1.859-0.1661.553-1.106-2.141-0.011
30A32TRP0-0.025-0.0262.616-1.994-0.2892.606-1.748-2.562-0.024
31A33SER00.0500.0332.841-3.299-1.2510.261-0.684-1.625-0.006
32A34VAL0-0.039-0.0084.1620.4970.5400.000-0.011-0.0330.000
33A35HIS00.0020.0055.768-0.140-0.1400.0000.0000.0000.000
34A36THR0-0.0080.00110.0100.0680.0680.0000.0000.0000.000
35A37VAL0-0.007-0.00913.7220.0060.0060.0000.0000.0000.000
36A38SER00.010-0.02615.8020.0200.0200.0000.0000.0000.000
37A39LEU0-0.064-0.03419.5620.0030.0030.0000.0000.0000.000
38A40ASP-1-0.874-0.93222.385-0.111-0.1110.0000.0000.0000.000
39A41PRO0-0.025-0.02720.205-0.014-0.0140.0000.0000.0000.000
40A42ILE0-0.005-0.01720.374-0.015-0.0150.0000.0000.0000.000
41A43VAL0-0.0080.02720.9440.0120.0120.0000.0000.0000.000
42A44SER0-0.012-0.02023.193-0.012-0.0120.0000.0000.0000.000
43A45SER0-0.039-0.02623.4460.0050.0050.0000.0000.0000.000
44A46ILE00.019-0.00625.2170.0060.0060.0000.0000.0000.000
45A47GLY0-0.052-0.03026.9620.0070.0070.0000.0000.0000.000
46A48GLY0-0.037-0.01627.8260.0030.0030.0000.0000.0000.000
47A49PHE0-0.066-0.03022.162-0.002-0.0020.0000.0000.0000.000
48A50LYS10.9350.97324.0520.1240.1240.0000.0000.0000.000
49A51THR00.0280.02017.734-0.003-0.0030.0000.0000.0000.000
50A52SER0-0.006-0.00717.8630.0220.0220.0000.0000.0000.000
51A53VAL0-0.042-0.02416.305-0.030-0.0300.0000.0000.0000.000
52A54ASP-1-0.858-0.90311.563-0.473-0.4730.0000.0000.0000.000
53A55TYR0-0.034-0.0287.9670.0460.0460.0000.0000.0000.000
54A56ILE00.0260.03314.7900.0050.0050.0000.0000.0000.000
55A57ILE0-0.001-0.02117.8150.0050.0050.0000.0000.0000.000
56A58GLY0-0.116-0.06718.1920.0160.0160.0000.0000.0000.000
57A59LEU0-0.070-0.03616.6700.0110.0110.0000.0000.0000.000
58A60GLU-1-0.848-0.89913.175-0.183-0.1830.0000.0000.0000.000
59A61PRO0-0.043-0.0158.8050.0250.0250.0000.0000.0000.000
60A62ALA00.0470.01611.324-0.006-0.0060.0000.0000.0000.000
61A63ASN0-0.078-0.05710.268-0.012-0.0120.0000.0000.0000.000
62A64PHE0-0.020-0.0017.956-0.052-0.0520.0000.0000.0000.000
63A65ASN00.0260.0076.176-0.442-0.4420.0000.0000.0000.000
64A66LEU00.0460.0419.0760.1090.1090.0000.0000.0000.000
65A67LEU0-0.0080.01011.100-0.077-0.0770.0000.0000.0000.000
66A68VAL00.0010.00813.1660.0440.0440.0000.0000.0000.000
67A69MET0-0.046-0.01315.648-0.016-0.0160.0000.0000.0000.000
68A70ILE00.0240.01118.1070.0150.0150.0000.0000.0000.000
69A71GLY00.0030.00720.6760.0060.0060.0000.0000.0000.000
70A72GLY00.001-0.00824.237-0.013-0.0130.0000.0000.0000.000
71A73ASP-1-0.914-0.94326.956-0.072-0.0720.0000.0000.0000.000
72A74SER0-0.028-0.04927.1330.0070.0070.0000.0000.0000.000
73A75TRP0-0.023-0.03021.4590.0040.0040.0000.0000.0000.000
74A76SER0-0.063-0.00728.1830.0060.0060.0000.0000.0000.000
75A77ASN00.011-0.01527.7930.0030.0030.0000.0000.0000.000
76A78ASP-1-0.893-0.94029.409-0.049-0.0490.0000.0000.0000.000
77A79ASN00.0120.00226.2860.0000.0000.0000.0000.0000.000
78A80LYS11.0241.00025.8030.0640.0640.0000.0000.0000.000
79A81LYS10.8730.93323.5690.0810.0810.0000.0000.0000.000
80A82LEU00.1040.06921.767-0.004-0.0040.0000.0000.0000.000
81A83LEU00.0090.01422.518-0.002-0.0020.0000.0000.0000.000
82A84HIS0-0.027-0.01821.7140.0060.0060.0000.0000.0000.000
83A85PHE00.0290.03714.7560.0090.0090.0000.0000.0000.000
84A86VAL00.0550.02418.892-0.002-0.0020.0000.0000.0000.000
85A87LYS10.9650.98020.1910.0390.0390.0000.0000.0000.000
86A88THR0-0.023-0.03418.2680.0130.0130.0000.0000.0000.000
87A89ALA0-0.009-0.00916.3770.0080.0080.0000.0000.0000.000
88A90PHE00.0550.01117.6680.0130.0130.0000.0000.0000.000
89A91GLN0-0.062-0.02520.4900.0110.0110.0000.0000.0000.000
90A92LYS10.8280.93414.8030.1230.1230.0000.0000.0000.000
91A93ASN0-0.026-0.01916.6320.0070.0070.0000.0000.0000.000
92A94ILE0-0.0330.00912.9650.0250.0250.0000.0000.0000.000
93A95PRO00.0180.00512.956-0.011-0.0110.0000.0000.0000.000
94A96ILE00.010-0.00314.668-0.049-0.0490.0000.0000.0000.000
95A97ALA00.0080.01317.0360.0250.0250.0000.0000.0000.000
96A98ALA0-0.032-0.02418.504-0.023-0.0230.0000.0000.0000.000
97A99ILE0-0.0010.00421.3340.0140.0140.0000.0000.0000.000
98A100CYS0-0.0050.01123.567-0.003-0.0030.0000.0000.0000.000
99A101GLY00.0310.00526.8760.0050.0050.0000.0000.0000.000
100A102ALA00.0070.01722.5640.0040.0040.0000.0000.0000.000
101A103VAL0-0.022-0.01624.5790.0060.0060.0000.0000.0000.000
102A104ASP-1-0.797-0.88826.367-0.043-0.0430.0000.0000.0000.000
103A105PHE0-0.025-0.00924.7970.0040.0040.0000.0000.0000.000
104A106LEU0-0.012-0.00622.6550.0050.0050.0000.0000.0000.000
105A107ALA00.0260.01526.6640.0060.0060.0000.0000.0000.000
106A108LYS10.9350.96630.2630.0450.0450.0000.0000.0000.000
107A109ASN0-0.120-0.08527.9010.0030.0030.0000.0000.0000.000
108A110GLY00.0040.00829.1910.0010.0010.0000.0000.0000.000
109A111LEU0-0.065-0.02823.7950.0040.0040.0000.0000.0000.000
110A112LEU00.0000.01126.3330.0020.0020.0000.0000.0000.000
111A113ASN0-0.011-0.02128.6080.0030.0030.0000.0000.0000.000
112A114ASN00.005-0.00628.4290.0050.0050.0000.0000.0000.000
113A115HIS00.0030.01023.3580.0040.0040.0000.0000.0000.000
114A116SER00.0310.00528.176-0.006-0.0060.0000.0000.0000.000
115A117HIS0-0.039-0.02527.589-0.004-0.0040.0000.0000.0000.000
116A118THR00.0290.01727.7450.0010.0010.0000.0000.0000.000
117A119GLY00.042-0.00228.483-0.004-0.0040.0000.0000.0000.000
118A120ASN00.0380.01829.5840.0030.0030.0000.0000.0000.000
119A121PHE00.0400.00331.8550.0030.0030.0000.0000.0000.000
120A122VAL00.0710.04935.086-0.002-0.0020.0000.0000.0000.000
121A123TYR00.001-0.00735.9920.0000.0000.0000.0000.0000.000
122A124LEU0-0.040-0.00533.7360.0010.0010.0000.0000.0000.000
123A125TRP0-0.022-0.05430.4430.0010.0010.0000.0000.0000.000
124A126LYS10.8450.92036.4000.0210.0210.0000.0000.0000.000
125A127ASP-1-0.836-0.89139.613-0.017-0.0170.0000.0000.0000.000
126A128TYR0-0.038-0.00932.566-0.001-0.0010.0000.0000.0000.000
127A129LYS10.9740.97337.1220.0210.0210.0000.0000.0000.000
128A130GLN0-0.080-0.05832.2800.0050.0050.0000.0000.0000.000
129A131TYR00.0260.02132.2760.0010.0010.0000.0000.0000.000
130A132LYS10.8470.91834.5060.0090.0090.0000.0000.0000.000
131A133PRO0-0.0160.02033.2880.0020.0020.0000.0000.0000.000
132A134ILE0-0.0350.00931.6620.0010.0010.0000.0000.0000.000
133A135SER0-0.042-0.01931.8410.0030.0030.0000.0000.0000.000
134A136SER00.011-0.00433.738-0.004-0.0040.0000.0000.0000.000
135A137PHE0-0.0200.01132.1050.0020.0020.0000.0000.0000.000
136A138VAL0-0.003-0.01731.5990.0020.0020.0000.0000.0000.000
137A139GLU-1-0.932-0.96232.674-0.011-0.0110.0000.0000.0000.000
138A140LYS10.9090.94830.868-0.009-0.0090.0000.0000.0000.000
139A141GLN0-0.0070.01828.0800.0000.0000.0000.0000.0000.000
140A142ALA00.0230.00224.442-0.008-0.0080.0000.0000.0000.000
141A143VAL0-0.040-0.00925.7440.0090.0090.0000.0000.0000.000
142A144ARG10.9750.98619.024-0.126-0.1260.0000.0000.0000.000
143A145ASP-1-0.787-0.86123.5050.0510.0510.0000.0000.0000.000
144A146LYS10.8570.91321.972-0.060-0.0600.0000.0000.0000.000
145A147ASN00.0320.01116.7900.0190.0190.0000.0000.0000.000
146A148LEU00.0230.02219.032-0.020-0.0200.0000.0000.0000.000
147A149VAL00.0130.00319.3360.0110.0110.0000.0000.0000.000
148A150THR0-0.014-0.00221.535-0.015-0.0150.0000.0000.0000.000
149A151ALA00.0530.00324.1690.0080.0080.0000.0000.0000.000
150A152ASN00.0460.07825.880-0.011-0.0110.0000.0000.0000.000
151A153GLY00.0730.00026.714-0.003-0.0030.0000.0000.0000.000
152A154THR0-0.082-0.05627.312-0.004-0.0040.0000.0000.0000.000
153A155ALA0-0.0020.00326.0010.0030.0030.0000.0000.0000.000
154A156PRO00.0420.03922.3620.0010.0010.0000.0000.0000.000
155A157ILE00.0210.01521.339-0.003-0.0030.0000.0000.0000.000
156A158GLU-1-0.827-0.93121.833-0.026-0.0260.0000.0000.0000.000
157A159PHE0-0.001-0.00618.8790.0120.0120.0000.0000.0000.000
158A160THR0-0.013-0.03616.322-0.006-0.0060.0000.0000.0000.000
159A161ASN00.0140.00617.5970.0130.0130.0000.0000.0000.000
160A162LEU0-0.015-0.01118.9930.0210.0210.0000.0000.0000.000
161A163ILE0-0.016-0.00114.3160.0200.0200.0000.0000.0000.000
162A164LEU0-0.004-0.01013.0870.0210.0210.0000.0000.0000.000
163A165GLU-1-0.916-0.95814.7990.1470.1470.0000.0000.0000.000
164A166MET0-0.129-0.04315.8410.0370.0370.0000.0000.0000.000
165A167ILE0-0.094-0.04210.141-0.002-0.0020.0000.0000.0000.000
166A168ASP-1-0.934-0.94811.4740.4790.4790.0000.0000.0000.000
167A169PHE0-0.051-0.0278.8960.1240.1240.0000.0000.0000.000
168A170ASP-1-0.867-0.92111.7660.3240.3240.0000.0000.0000.000
169A171THR0-0.018-0.01714.473-0.014-0.0140.0000.0000.0000.000
170A172PRO00.1000.02818.045-0.026-0.0260.0000.0000.0000.000
171A173GLU-1-0.888-0.94320.6720.1400.1400.0000.0000.0000.000
172A174ASN0-0.083-0.03417.806-0.032-0.0320.0000.0000.0000.000
173A175ILE00.0230.01015.979-0.034-0.0340.0000.0000.0000.000
174A176GLU-1-0.932-0.96718.8590.0260.0260.0000.0000.0000.000
175A177LYS10.9320.97021.421-0.077-0.0770.0000.0000.0000.000
176A178MET00.0130.00814.224-0.009-0.0090.0000.0000.0000.000
177A179MET0-0.015-0.00517.860-0.027-0.0270.0000.0000.0000.000
178A180TYR0-0.024-0.00521.920-0.007-0.0070.0000.0000.0000.000
179A181MET0-0.001-0.00122.052-0.007-0.0070.0000.0000.0000.000
180A182ASN0-0.037-0.02218.811-0.013-0.0130.0000.0000.0000.000
181A183ARG10.8890.95623.1050.0230.0230.0000.0000.0000.000
182A184TYR0-0.057-0.03726.3690.0010.0010.0000.0000.0000.000
183A185GLY00.0430.04326.9760.0000.0000.0000.0000.0000.000
184A186PHE00.036-0.00826.5760.0070.0070.0000.0000.0000.000
185A187TYR00.0160.00328.1620.0040.0040.0000.0000.0000.000
186A188HIS00.0880.05930.9250.0050.0050.0000.0000.0000.000
187A189PHE0-0.053-0.02723.9920.0070.0070.0000.0000.0000.000
188A190CYS0-0.016-0.03828.8150.0050.0050.0000.0000.0000.000
189A191ASP-1-0.917-0.92130.472-0.002-0.0020.0000.0000.0000.000
190A192LYS10.8660.94429.864-0.017-0.0170.0000.0000.0000.000
191A193TYR0-0.048-0.04226.5220.0070.0070.0000.0000.0000.000
192A194GLY0-0.0250.02729.6010.0050.0050.0000.0000.0000.000
193A195ASN0-0.033-0.04125.243-0.006-0.0060.0000.0000.0000.000