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: 397RL

Calculation Name: 4J1J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J1J

Chain ID: A

ChEMBL ID:

UniProt ID: F2WAD7

Base Structure: X-ray

Registration Date: 2023-06-22

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 OptHSide
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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2739777.101343
FMO2-HF: Nuclear repulsion 2648997.117799
FMO2-HF: Total energy -90779.983544
FMO2-MP2: Total energy -91046.418394


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:THR)


Summations of interaction energy for fragment #1(A:3:THR)
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.
6.344-3.2880.44510.34-1.152-0.001
Interaction energy analysis for fragmet #1(A:3:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.017
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].
3A5PRO0-0.046-0.0172.9636.910-2.7580.44610.342-1.120-0.001
4A6ASP-1-0.894-0.9374.982-0.640-0.604-0.001-0.002-0.0320.000
5A7PHE0-0.043-0.0288.3990.0340.0340.0000.0000.0000.000
6A8ILE0-0.006-0.0098.7170.1570.1570.0000.0000.0000.000
7A9TYR0-0.034-0.03010.818-0.122-0.1220.0000.0000.0000.000
8A10ASP-1-0.832-0.91113.8500.5350.5350.0000.0000.0000.000
9A11ASP-1-0.947-0.95516.3940.1800.1800.0000.0000.0000.000
10A12ARG10.8430.90715.940-0.428-0.4280.0000.0000.0000.000
11A13PRO00.0370.02521.522-0.010-0.0100.0000.0000.0000.000
12A14ALA0-0.063-0.03325.1930.0020.0020.0000.0000.0000.000
13A15ALA0-0.0020.00527.0850.0010.0010.0000.0000.0000.000
14A16VAL00.008-0.01428.409-0.006-0.0060.0000.0000.0000.000
15A17SER0-0.033-0.01532.1020.0020.0020.0000.0000.0000.000
16A18SER00.0330.02633.9560.0020.0020.0000.0000.0000.000
17A19THR0-0.051-0.03136.160-0.003-0.0030.0000.0000.0000.000
18A20PHE00.0450.03138.717-0.001-0.0010.0000.0000.0000.000
19A21ASN0-0.016-0.01540.412-0.004-0.0040.0000.0000.0000.000
20A22PRO00.0300.00243.9910.0000.0000.0000.0000.0000.000
21A23GLU-1-0.828-0.91745.2030.0400.0400.0000.0000.0000.000
22A24LYS10.8270.90142.777-0.060-0.0600.0000.0000.0000.000
23A25GLY00.0160.00542.9750.0000.0000.0000.0000.0000.000
24A26TYR0-0.050-0.05243.6830.0000.0000.0000.0000.0000.000
25A27MET00.0480.02446.719-0.002-0.0020.0000.0000.0000.000
26A28ASP-1-0.845-0.89043.1970.0560.0560.0000.0000.0000.000
27A29PHE0-0.017-0.01143.053-0.001-0.0010.0000.0000.0000.000
28A30ILE00.0320.01144.750-0.002-0.0020.0000.0000.0000.000
29A31THR0-0.046-0.03447.130-0.003-0.0030.0000.0000.0000.000
30A32ALA0-0.078-0.04243.193-0.002-0.0020.0000.0000.0000.000
31A33TYR0-0.022-0.02139.286-0.001-0.0010.0000.0000.0000.000
32A34GLY00.0290.02046.125-0.002-0.0020.0000.0000.0000.000
33A35LYS10.9140.96049.147-0.033-0.0330.0000.0000.0000.000
34A36ASN00.0120.01347.473-0.003-0.0030.0000.0000.0000.000
35A37ILE0-0.0440.00547.339-0.001-0.0010.0000.0000.0000.000
36A38ASN00.0780.04950.469-0.001-0.0010.0000.0000.0000.000
37A39ALA00.1060.04052.3750.0010.0010.0000.0000.0000.000
38A40ASP-1-0.845-0.89753.2130.0120.0120.0000.0000.0000.000
39A41ASN0-0.009-0.03048.201-0.002-0.0020.0000.0000.0000.000
40A42VAL0-0.0010.01348.3660.0010.0010.0000.0000.0000.000
41A43ARG10.9120.95449.573-0.010-0.0100.0000.0000.0000.000
42A44ILE0-0.030-0.01646.2160.0000.0000.0000.0000.0000.000
43A45PHE00.0070.00941.9530.0000.0000.0000.0000.0000.000
44A46PHE00.012-0.00445.6310.0000.0000.0000.0000.0000.000
45A47LEU0-0.037-0.00447.854-0.001-0.0010.0000.0000.0000.000
46A48ASN0-0.108-0.06843.318-0.003-0.0030.0000.0000.0000.000
47A49HIS00.0800.05741.4340.0000.0000.0000.0000.0000.000
48A50LYS10.9000.92440.069-0.011-0.0110.0000.0000.0000.000
49A51LYS10.9410.97139.695-0.009-0.0090.0000.0000.0000.000
50A52ALA00.0480.03938.3140.0000.0000.0000.0000.0000.000
51A53LYS10.9340.96636.397-0.035-0.0350.0000.0000.0000.000
52A54ASP-1-0.872-0.93434.9920.0150.0150.0000.0000.0000.000
53A55SER00.0390.00633.801-0.002-0.0020.0000.0000.0000.000
54A56LEU0-0.047-0.02532.2810.0010.0010.0000.0000.0000.000
55A57LYS10.8070.91329.985-0.037-0.0370.0000.0000.0000.000
56A58GLY00.0120.01029.3270.0000.0000.0000.0000.0000.000
57A59SER0-0.0300.00328.245-0.003-0.0030.0000.0000.0000.000
58A60PRO00.0240.01223.0270.0070.0070.0000.0000.0000.000
59A61LYS10.8990.95224.087-0.035-0.0350.0000.0000.0000.000
60A62VAL00.0980.04624.063-0.004-0.0040.0000.0000.0000.000
61A63GLU-1-0.850-0.90226.7290.0780.0780.0000.0000.0000.000
62A64VAL0-0.070-0.05729.971-0.005-0.0050.0000.0000.0000.000
63A65ASP-1-0.846-0.90232.1440.0330.0330.0000.0000.0000.000
64A66LEU0-0.020-0.00835.197-0.005-0.0050.0000.0000.0000.000
65A67GLN0-0.004-0.02838.1090.0010.0010.0000.0000.0000.000
66A68PHE0-0.022-0.00540.655-0.002-0.0020.0000.0000.0000.000
67A69GLY00.0660.03744.7370.0010.0010.0000.0000.0000.000
68A70THR0-0.030-0.02645.9190.0000.0000.0000.0000.0000.000
69A71LEU0-0.0090.00444.1800.0020.0020.0000.0000.0000.000
70A72ARG10.8550.93036.991-0.024-0.0240.0000.0000.0000.000
71A73VAL00.0180.00039.1210.0020.0020.0000.0000.0000.000
72A74LYS10.9030.95332.051-0.064-0.0640.0000.0000.0000.000
73A75VAL0-0.051-0.02034.9310.0030.0030.0000.0000.0000.000
74A76VAL00.0160.00130.1700.0010.0010.0000.0000.0000.000
75A77ASN0-0.032-0.02528.400-0.006-0.0060.0000.0000.0000.000
76A78ASN00.0160.00029.1610.0050.0050.0000.0000.0000.000
77A79HIS00.012-0.00330.560-0.003-0.0030.0000.0000.0000.000
78A80ASN00.002-0.00425.726-0.005-0.0050.0000.0000.0000.000
79A81PRO00.0150.00925.5680.0060.0060.0000.0000.0000.000
80A82ARG10.9260.97119.851-0.091-0.0910.0000.0000.0000.000
81A83ASN00.028-0.00522.141-0.022-0.0220.0000.0000.0000.000
82A84ARG10.9161.00823.528-0.105-0.1050.0000.0000.0000.000
83A85ASP-1-0.764-0.90823.0960.1560.1560.0000.0000.0000.000
84A86ASN0-0.123-0.07324.885-0.011-0.0110.0000.0000.0000.000
85A87PRO0-0.0130.02125.899-0.007-0.0070.0000.0000.0000.000
86A88VAL0-0.003-0.01329.015-0.005-0.0050.0000.0000.0000.000
87A89ALA00.0450.02632.243-0.001-0.0010.0000.0000.0000.000
88A90ASP-1-0.840-0.93533.7680.0810.0810.0000.0000.0000.000
89A91ASN0-0.030-0.01835.637-0.004-0.0040.0000.0000.0000.000
90A92ALA00.0080.02134.047-0.003-0.0030.0000.0000.0000.000
91A93ILE00.0270.02436.105-0.002-0.0020.0000.0000.0000.000
92A94THR00.0410.01434.5840.0000.0000.0000.0000.0000.000
93A95LEU00.0540.01237.060-0.002-0.0020.0000.0000.0000.000
94A96HIS0-0.070-0.03838.952-0.003-0.0030.0000.0000.0000.000
95A97ARG10.8380.90436.795-0.074-0.0740.0000.0000.0000.000
96A98LEU00.0030.01940.921-0.001-0.0010.0000.0000.0000.000
97A99SER00.001-0.02842.806-0.003-0.0030.0000.0000.0000.000
98A100GLY00.0170.00644.706-0.002-0.0020.0000.0000.0000.000
99A101TYR0-0.003-0.01541.6600.0000.0000.0000.0000.0000.000
100A102LEU00.0240.01046.041-0.002-0.0020.0000.0000.0000.000
101A103ALA00.0110.02048.878-0.002-0.0020.0000.0000.0000.000
102A104LYS10.8040.88350.327-0.034-0.0340.0000.0000.0000.000
103A105TRP00.0670.02450.896-0.001-0.0010.0000.0000.0000.000
104A106CYS0-0.064-0.03452.472-0.002-0.0020.0000.0000.0000.000
105A107PHE0-0.047-0.02954.723-0.001-0.0010.0000.0000.0000.000
106A108ASP-1-0.739-0.83554.6040.0300.0300.0000.0000.0000.000
107A109GLU-1-0.882-0.93356.4110.0200.0200.0000.0000.0000.000
108A110ILE0-0.075-0.05858.323-0.001-0.0010.0000.0000.0000.000
109A111ASP-1-0.944-0.97360.5980.0220.0220.0000.0000.0000.000
110A112HIS0-0.108-0.05157.6100.0010.0010.0000.0000.0000.000
111A113GLY00.0330.02962.8570.0000.0000.0000.0000.0000.000
112A114GLN00.012-0.00565.1640.0000.0000.0000.0000.0000.000
113A115ILE0-0.023-0.00764.739-0.001-0.0010.0000.0000.0000.000
114A116GLU-1-0.829-0.91661.1250.0160.0160.0000.0000.0000.000
115A117GLU-1-0.823-0.88861.3380.0160.0160.0000.0000.0000.000
116A118ALA0-0.064-0.03362.5800.0000.0000.0000.0000.0000.000
117A119GLU-1-0.801-0.89258.6830.0130.0130.0000.0000.0000.000
118A120VAL0-0.003-0.01556.6540.0000.0000.0000.0000.0000.000
119A121LYS10.8010.88358.358-0.016-0.0160.0000.0000.0000.000
120A122SER0-0.051-0.00160.854-0.001-0.0010.0000.0000.0000.000
121A123LYS10.7380.84756.302-0.013-0.0130.0000.0000.0000.000
122A124VAL0-0.024-0.00653.0500.0000.0000.0000.0000.0000.000
123A125VAL0-0.015-0.00553.7610.0000.0000.0000.0000.0000.000
124A126ILE00.0230.01450.7230.0010.0010.0000.0000.0000.000
125A127PRO00.002-0.00949.4770.0000.0000.0000.0000.0000.000
126A128LEU0-0.029-0.02046.811-0.001-0.0010.0000.0000.0000.000
127A129ALA00.0530.03551.2730.0000.0000.0000.0000.0000.000
128A130GLU-1-0.763-0.86154.7310.0120.0120.0000.0000.0000.000
129A131ALA0-0.073-0.02252.873-0.001-0.0010.0000.0000.0000.000
130A132LYS10.7680.89252.779-0.016-0.0160.0000.0000.0000.000
131A133GLY0-0.037-0.03356.8610.0000.0000.0000.0000.0000.000
132A134CYS0-0.091-0.01657.6700.0000.0000.0000.0000.0000.000
133A135LYS10.8910.91258.971-0.011-0.0110.0000.0000.0000.000
134A136TRP00.0980.01856.7690.0010.0010.0000.0000.0000.000
135A137GLY0-0.061-0.01961.8260.0010.0010.0000.0000.0000.000
136A138ASP-1-0.833-0.90162.0260.0140.0140.0000.0000.0000.000
137A139GLY00.0070.00563.0100.0010.0010.0000.0000.0000.000
138A140VAL00.006-0.00159.1240.0000.0000.0000.0000.0000.000
139A141ALA00.0580.04057.8360.0010.0010.0000.0000.0000.000
140A142LEU00.007-0.00656.8380.0010.0010.0000.0000.0000.000
141A143TYR0-0.023-0.04056.2590.0010.0010.0000.0000.0000.000
142A144LEU0-0.006-0.01053.6980.0000.0000.0000.0000.0000.000
143A145ALA0-0.0060.00352.5980.0020.0020.0000.0000.0000.000
144A146PHE0-0.033-0.02351.5650.0010.0010.0000.0000.0000.000
145A147ALA0-0.0250.00748.9660.0000.0000.0000.0000.0000.000
146A148PRO0-0.005-0.01644.0410.0020.0020.0000.0000.0000.000
147A149GLY00.0230.01944.6460.0000.0000.0000.0000.0000.000
148A150ALA00.0480.02945.3390.0020.0020.0000.0000.0000.000
149A151GLU-1-0.746-0.84944.3540.0440.0440.0000.0000.0000.000
150A152MET0-0.133-0.05343.5800.0040.0040.0000.0000.0000.000
151A153PHE00.0110.00547.2160.0010.0010.0000.0000.0000.000
152A154LEU00.0290.01550.572-0.002-0.0020.0000.0000.0000.000
153A155LYS10.9690.98052.854-0.032-0.0320.0000.0000.0000.000
154A156ASP-1-0.861-0.91154.6030.0310.0310.0000.0000.0000.000
155A157PHE0-0.017-0.01251.246-0.002-0.0020.0000.0000.0000.000
156A158GLU-1-0.861-0.93256.1600.0230.0230.0000.0000.0000.000
157A159PHE0-0.020-0.02854.510-0.001-0.0010.0000.0000.0000.000
158A160TYR0-0.042-0.02755.6070.0000.0000.0000.0000.0000.000
159A161PRO00.0120.00950.3950.0000.0000.0000.0000.0000.000
160A162LEU00.0150.01551.2260.0000.0000.0000.0000.0000.000
161A163ALA00.0110.00752.3820.0000.0000.0000.0000.0000.000
162A164ILE0-0.003-0.00351.571-0.001-0.0010.0000.0000.0000.000
163A165ASP-1-0.849-0.93448.0890.0330.0330.0000.0000.0000.000
164A166ILE0-0.008-0.01450.559-0.001-0.0010.0000.0000.0000.000
165A167GLN00.0070.01252.871-0.002-0.0020.0000.0000.0000.000
166A168ARG10.8600.91046.961-0.024-0.0240.0000.0000.0000.000
167A169VAL0-0.045-0.01148.258-0.001-0.0010.0000.0000.0000.000
168A170VAL0-0.025-0.01650.736-0.001-0.0010.0000.0000.0000.000
169A171LYS10.8550.92954.276-0.019-0.0190.0000.0000.0000.000
170A172ASP-1-0.796-0.86151.0520.0160.0160.0000.0000.0000.000
171A173GLY00.0330.03150.0620.0000.0000.0000.0000.0000.000
172A174MET0-0.105-0.03545.7010.0000.0000.0000.0000.0000.000
173A175ASP-1-0.762-0.86942.1370.0380.0380.0000.0000.0000.000
174A176ILE00.0540.01144.7910.0010.0010.0000.0000.0000.000
175A177THR0-0.088-0.06539.8840.0030.0030.0000.0000.0000.000
176A178PHE0-0.032-0.02439.8900.0040.0040.0000.0000.0000.000
177A179MET00.0130.01242.8420.0000.0000.0000.0000.0000.000
178A180ARG10.9330.96337.280-0.058-0.0580.0000.0000.0000.000
179A181LYS10.8170.90240.688-0.051-0.0510.0000.0000.0000.000
180A182VAL00.0630.02942.9890.0020.0020.0000.0000.0000.000
181A183LEU0-0.013-0.00146.175-0.001-0.0010.0000.0000.0000.000
182A184LYS10.9580.98439.559-0.073-0.0730.0000.0000.0000.000
183A185GLN0-0.069-0.02843.2930.0020.0020.0000.0000.0000.000
184A186ARG10.9280.95347.245-0.052-0.0520.0000.0000.0000.000
185A187TYR00.0060.01049.983-0.001-0.0010.0000.0000.0000.000
186A188GLY00.0440.02053.485-0.001-0.0010.0000.0000.0000.000
187A189THR0-0.016-0.01052.6710.0020.0020.0000.0000.0000.000
188A190LYS10.8700.95453.112-0.033-0.0330.0000.0000.0000.000
189A191THR00.029-0.00149.5870.0000.0000.0000.0000.0000.000
190A192ALA00.0530.02148.718-0.002-0.0020.0000.0000.0000.000
191A193ASP-1-0.899-0.96249.3180.0510.0510.0000.0000.0000.000
192A194ASP-1-0.883-0.91652.0500.0370.0370.0000.0000.0000.000
193A195TRP0-0.012-0.02850.338-0.003-0.0030.0000.0000.0000.000
194A196MET0-0.043-0.02449.319-0.002-0.0020.0000.0000.0000.000
195A197ILE0-0.035-0.00755.281-0.002-0.0020.0000.0000.0000.000
196A198SER0-0.052-0.04858.325-0.002-0.0020.0000.0000.0000.000
197A199GLU-1-0.841-0.90457.9720.0310.0310.0000.0000.0000.000
198A200VAL00.0280.01359.248-0.001-0.0010.0000.0000.0000.000
199A201THR00.0440.02660.927-0.001-0.0010.0000.0000.0000.000
200A202ALA00.0480.03360.741-0.001-0.0010.0000.0000.0000.000
201A203ILE00.0260.02056.197-0.001-0.0010.0000.0000.0000.000
202A204GLN0-0.012-0.01159.449-0.001-0.0010.0000.0000.0000.000
203A205SER0-0.045-0.02962.053-0.001-0.0010.0000.0000.0000.000
204A206ALA00.0500.02858.664-0.001-0.0010.0000.0000.0000.000
205A207VAL0-0.002-0.01257.636-0.001-0.0010.0000.0000.0000.000
206A208LYS10.9080.95760.029-0.018-0.0180.0000.0000.0000.000
207A209VAL00.0130.00261.783-0.001-0.0010.0000.0000.0000.000
208A210VAL00.0280.00556.740-0.001-0.0010.0000.0000.0000.000
209A211ALA0-0.066-0.03360.109-0.001-0.0010.0000.0000.0000.000
210A212LYS10.8590.93661.843-0.015-0.0150.0000.0000.0000.000
211A213LEU00.0170.03458.866-0.001-0.0010.0000.0000.0000.000
212A214PRO0-0.009-0.00961.7390.0000.0000.0000.0000.0000.000
213A215TRP00.019-0.02353.605-0.001-0.0010.0000.0000.0000.000
214A216ALA00.0260.01257.102-0.001-0.0010.0000.0000.0000.000
215A217LYS10.8510.93258.151-0.010-0.0100.0000.0000.0000.000
216A218ALA00.0290.02858.575-0.001-0.0010.0000.0000.0000.000
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