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: 4JQNN

Calculation Name: 3R3H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R3H

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZT85

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2661984.159995
FMO2-HF: Nuclear repulsion 2576037.429039
FMO2-HF: Total energy -85946.730956
FMO2-MP2: Total energy -86198.628201


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:LYS)


Summations of interaction energy for fragment #1(A:4:LYS)
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.
-85.681-82.9828.565-5.883-5.381-0.061
Interaction energy analysis for fragmet #1(A:4:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.956 / q_NPA : 0.973
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].
3A6LEU00.001-0.0021.844-47.561-45.3058.560-5.807-5.010-0.061
4A7SER00.0100.0063.24111.34711.7360.006-0.076-0.3190.000
5A8LEU00.004-0.0015.134-0.0180.036-0.0010.000-0.0520.000
6A9THR00.005-0.0047.3722.0652.0650.0000.0000.0000.000
7A10PRO00.0470.0189.7331.0821.0820.0000.0000.0000.000
8A11GLU-1-0.793-0.88411.387-24.101-24.1010.0000.0000.0000.000
9A12LEU00.0000.0087.4180.7600.7600.0000.0000.0000.000
10A13TYR0-0.037-0.04611.3021.1131.1130.0000.0000.0000.000
11A14LYS10.8620.92113.62419.83519.8350.0000.0000.0000.000
12A15TYR00.0150.01412.9400.5220.5220.0000.0000.0000.000
13A16LEU00.0080.00612.3900.6410.6410.0000.0000.0000.000
14A17LEU0-0.013-0.00115.2641.0821.0820.0000.0000.0000.000
15A18ASP-1-0.947-0.96218.567-14.446-14.4460.0000.0000.0000.000
16A19ILE0-0.033-0.00715.3160.6890.6890.0000.0000.0000.000
17A20SER0-0.094-0.06618.4790.3540.3540.0000.0000.0000.000
18A21LEU0-0.0490.00520.7780.6590.6590.0000.0000.0000.000
19A22ARG10.9140.94022.73112.54312.5430.0000.0000.0000.000
20A23GLU-1-0.731-0.81026.330-11.688-11.6880.0000.0000.0000.000
21A24HIS00.0810.04128.0050.1190.1190.0000.0000.0000.000
22A25PRO00.0220.00031.644-0.149-0.1490.0000.0000.0000.000
23A26ALA00.0760.04133.632-0.042-0.0420.0000.0000.0000.000
24A27LEU0-0.057-0.01929.2480.0240.0240.0000.0000.0000.000
25A28ALA00.0260.01829.387-0.144-0.1440.0000.0000.0000.000
26A29ALA0-0.057-0.02830.376-0.045-0.0450.0000.0000.0000.000
27A30LEU0-0.0100.00131.7940.0050.0050.0000.0000.0000.000
28A31ARG10.8500.90125.34512.35912.3590.0000.0000.0000.000
29A32LYS10.9620.98529.8989.6279.6270.0000.0000.0000.000
30A33GLU-1-0.875-0.92530.852-8.684-8.6840.0000.0000.0000.000
31A34THR0-0.025-0.03231.4120.1610.1610.0000.0000.0000.000
32A35SER0-0.029-0.01827.916-0.252-0.2520.0000.0000.0000.000
33A36THR0-0.041-0.01628.457-0.281-0.2810.0000.0000.0000.000
34A37MET0-0.0380.00931.0510.2290.2290.0000.0000.0000.000
35A38GLU-1-0.843-0.93329.329-11.118-11.1180.0000.0000.0000.000
36A39LEU0-0.010-0.01129.357-0.291-0.2910.0000.0000.0000.000
37A40ALA0-0.036-0.01627.104-0.187-0.1870.0000.0000.0000.000
38A41ASN0-0.044-0.02224.766-0.899-0.8990.0000.0000.0000.000
39A42MET0-0.068-0.01624.838-0.527-0.5270.0000.0000.0000.000
40A43GLN00.0210.00125.7820.5650.5650.0000.0000.0000.000
41A44VAL00.0040.01023.131-0.517-0.5170.0000.0000.0000.000
42A45ALA00.0380.02319.9460.2560.2560.0000.0000.0000.000
43A46PRO00.0340.00421.1920.1360.1360.0000.0000.0000.000
44A47GLU-1-0.765-0.87217.323-17.141-17.1410.0000.0000.0000.000
45A48GLN00.0310.00617.625-0.094-0.0940.0000.0000.0000.000
46A49ALA00.0160.01821.2650.5500.5500.0000.0000.0000.000
47A50GLN0-0.012-0.01822.8700.7330.7330.0000.0000.0000.000
48A51PHE0-0.013-0.00820.2250.2710.2710.0000.0000.0000.000
49A52MET00.0390.01822.8550.4680.4680.0000.0000.0000.000
50A53GLN0-0.050-0.02625.8060.2670.2670.0000.0000.0000.000
51A54MET0-0.035-0.01224.1800.5730.5730.0000.0000.0000.000
52A55LEU00.0180.01523.1200.3520.3520.0000.0000.0000.000
53A56ILE00.0250.03427.0090.4150.4150.0000.0000.0000.000
54A57ARG10.8990.94227.27311.62911.6290.0000.0000.0000.000
55A58LEU0-0.026-0.01624.9510.3480.3480.0000.0000.0000.000
56A59THR0-0.043-0.02529.3560.2270.2270.0000.0000.0000.000
57A60ARG10.8150.90130.98210.00210.0020.0000.0000.0000.000
58A61ALA0-0.0030.01033.8280.3150.3150.0000.0000.0000.000
59A62LYS10.8270.91635.6918.3698.3690.0000.0000.0000.000
60A63LYS10.8860.96038.1027.7667.7660.0000.0000.0000.000
61A64VAL0-0.022-0.01132.993-0.195-0.1950.0000.0000.0000.000
62A65LEU0-0.0020.00434.4590.2700.2700.0000.0000.0000.000
63A66GLU-1-0.767-0.83831.366-10.548-10.5480.0000.0000.0000.000
64A67LEU00.004-0.00132.1510.3970.3970.0000.0000.0000.000
65A68GLY00.0280.01031.284-0.431-0.4310.0000.0000.0000.000
66A69THR00.0150.02130.8470.3570.3570.0000.0000.0000.000
67A70PHE00.0060.01029.822-0.304-0.3040.0000.0000.0000.000
68A71THR00.0440.01331.1320.2190.2190.0000.0000.0000.000
69A72GLY00.013-0.01033.6420.2240.2240.0000.0000.0000.000
70A73TYR0-0.041-0.04425.9030.0480.0480.0000.0000.0000.000
71A74SER00.028-0.02028.726-0.040-0.0400.0000.0000.0000.000
72A75ALA00.0520.03630.2110.0360.0360.0000.0000.0000.000
73A76LEU0-0.0130.00133.2810.1630.1630.0000.0000.0000.000
74A77ALA00.0250.02028.9180.0870.0870.0000.0000.0000.000
75A78MET00.0150.00229.1840.0810.0810.0000.0000.0000.000
76A79SER0-0.009-0.01732.2330.2120.2120.0000.0000.0000.000
77A80LEU0-0.029-0.02132.9010.1750.1750.0000.0000.0000.000
78A81ALA0-0.076-0.02430.872-0.123-0.1230.0000.0000.0000.000
79A82LEU0-0.0300.00432.870-0.004-0.0040.0000.0000.0000.000
80A83PRO00.000-0.00136.1350.0340.0340.0000.0000.0000.000
81A84ASP-1-0.913-0.96139.137-7.795-7.7950.0000.0000.0000.000
82A85ASP-1-0.891-0.95242.299-7.610-7.6100.0000.0000.0000.000
83A86GLY0-0.035-0.00239.7210.0350.0350.0000.0000.0000.000
84A87GLN0-0.020-0.02440.0730.0520.0520.0000.0000.0000.000
85A88VAL0-0.013-0.01334.645-0.185-0.1850.0000.0000.0000.000
86A89ILE0-0.062-0.02237.6410.2420.2420.0000.0000.0000.000
87A90THR0-0.050-0.05234.722-0.166-0.1660.0000.0000.0000.000
88A91CYS0-0.035-0.02836.1030.3670.3670.0000.0000.0000.000
89A92ASP-1-0.798-0.90535.918-9.295-9.2950.0000.0000.0000.000
90A93ILE0-0.013-0.02334.0700.2700.2700.0000.0000.0000.000
91A94ASN0-0.022-0.01735.5840.1330.1330.0000.0000.0000.000
92A95GLU-1-1.002-0.98337.476-7.632-7.6320.0000.0000.0000.000
93A96GLY00.0110.01038.9340.1710.1710.0000.0000.0000.000
94A97TRP0-0.049-0.03437.8530.1240.1240.0000.0000.0000.000
95A98THR00.0510.02237.322-0.214-0.2140.0000.0000.0000.000
96A99LYS10.7910.87436.3238.8958.8950.0000.0000.0000.000
97A100HIS00.0070.00938.635-0.227-0.2270.0000.0000.0000.000
98A101ALA00.0540.03136.9060.0240.0240.0000.0000.0000.000
99A102HIS00.037-0.00138.659-0.079-0.0790.0000.0000.0000.000
100A103PRO0-0.037-0.01440.5650.1140.1140.0000.0000.0000.000
101A104TYR00.0900.04636.4850.0620.0620.0000.0000.0000.000
102A105TRP0-0.015-0.01036.0160.0820.0820.0000.0000.0000.000
103A106ARG10.9570.99439.5397.1787.1780.0000.0000.0000.000
104A107GLU-1-0.951-0.98537.651-8.535-8.5350.0000.0000.0000.000
105A108ALA0-0.029-0.02337.1540.0250.0250.0000.0000.0000.000
106A109LYS10.8760.96139.0717.3537.3530.0000.0000.0000.000
107A110GLN00.0480.00637.346-0.007-0.0070.0000.0000.0000.000
108A111GLU-1-0.851-0.94240.663-7.469-7.4690.0000.0000.0000.000
109A112HIS0-0.071-0.03842.5270.1080.1080.0000.0000.0000.000
110A113LYS10.8150.92638.0988.5048.5040.0000.0000.0000.000
111A114ILE0-0.021-0.00437.598-0.167-0.1670.0000.0000.0000.000
112A115LYS10.9140.96340.3447.2997.2990.0000.0000.0000.000
113A116LEU0-0.002-0.00539.270-0.119-0.1190.0000.0000.0000.000
114A117ARG10.8380.90940.4297.6027.6020.0000.0000.0000.000
115A118LEU00.0120.00840.248-0.183-0.1830.0000.0000.0000.000
116A119GLY00.0430.03440.8510.2180.2180.0000.0000.0000.000
117A120PRO00.0320.00240.085-0.219-0.2190.0000.0000.0000.000
118A121ALA00.0660.02736.8370.1290.1290.0000.0000.0000.000
119A122LEU0-0.0040.01138.4240.0370.0370.0000.0000.0000.000
120A123ASP-1-0.838-0.91840.054-7.310-7.3100.0000.0000.0000.000
121A124THR0-0.012-0.01340.6680.1910.1910.0000.0000.0000.000
122A125LEU0-0.005-0.00436.0750.0740.0740.0000.0000.0000.000
123A126HIS0-0.023-0.01940.7950.0970.0970.0000.0000.0000.000
124A127SER0-0.063-0.03143.7230.0980.0980.0000.0000.0000.000
125A128LEU0-0.016-0.02140.5330.0890.0890.0000.0000.0000.000
126A129LEU0-0.0120.00740.5610.0240.0240.0000.0000.0000.000
127A130ASN0-0.052-0.01743.9920.0750.0750.0000.0000.0000.000
128A131GLU-1-0.888-0.93847.325-6.499-6.4990.0000.0000.0000.000
129A132GLY0-0.042-0.01545.6340.0770.0770.0000.0000.0000.000
130A133GLY0-0.0120.01145.346-0.031-0.0310.0000.0000.0000.000
131A134GLU-1-0.863-0.95240.922-7.674-7.6740.0000.0000.0000.000
132A135HIS0-0.073-0.04638.045-0.043-0.0430.0000.0000.0000.000
133A136GLN0-0.033-0.01339.1130.1580.1580.0000.0000.0000.000
134A137PHE0-0.013-0.00935.8300.0450.0450.0000.0000.0000.000
135A138ASP-1-0.746-0.85434.479-8.806-8.8060.0000.0000.0000.000
136A139PHE0-0.005-0.01426.825-0.333-0.3330.0000.0000.0000.000
137A140ILE00.0200.01830.6150.3070.3070.0000.0000.0000.000
138A141PHE00.0170.00324.834-0.346-0.3460.0000.0000.0000.000
139A142ILE0-0.031-0.02428.1640.4440.4440.0000.0000.0000.000
140A143ASP-1-0.802-0.90826.667-12.712-12.7120.0000.0000.0000.000
141A144ALA0-0.0190.00328.2960.1730.1730.0000.0000.0000.000
142A145ASP-1-0.729-0.83630.279-9.580-9.5800.0000.0000.0000.000
143A146LYS10.8500.92426.31112.01012.0100.0000.0000.0000.000
144A147THR0-0.063-0.05330.116-0.079-0.0790.0000.0000.0000.000
145A148ASN0-0.030-0.02133.2840.3870.3870.0000.0000.0000.000
146A149TYR0-0.010-0.01525.8440.2980.2980.0000.0000.0000.000
147A150LEU0-0.010-0.00130.059-0.060-0.0600.0000.0000.0000.000
148A151ASN00.0150.00732.156-0.050-0.0500.0000.0000.0000.000
149A152TYR0-0.019-0.04732.2930.2360.2360.0000.0000.0000.000
150A153TYR0-0.035-0.02627.327-0.134-0.1340.0000.0000.0000.000
151A154GLU-1-0.769-0.86031.628-8.914-8.9140.0000.0000.0000.000
152A155LEU0-0.079-0.02534.7280.2520.2520.0000.0000.0000.000
153A156ALA00.0410.01532.0800.1390.1390.0000.0000.0000.000
154A157LEU0-0.021-0.02230.0680.0500.0500.0000.0000.0000.000
155A158LYS10.8280.93833.7158.0898.0890.0000.0000.0000.000
156A159LEU00.0210.00836.5190.1040.1040.0000.0000.0000.000
157A160VAL0-0.0240.00631.6890.0450.0450.0000.0000.0000.000
158A161THR0-0.013-0.02735.0730.2510.2510.0000.0000.0000.000
159A162PRO00.014-0.00334.254-0.276-0.2760.0000.0000.0000.000
160A163LYS10.9130.95632.4898.5538.5530.0000.0000.0000.000
161A164GLY00.0260.01631.737-0.180-0.1800.0000.0000.0000.000
162A165LEU0-0.062-0.03124.865-0.184-0.1840.0000.0000.0000.000
163A166ILE00.0210.00927.7950.2060.2060.0000.0000.0000.000
164A167ALA0-0.007-0.00824.938-0.474-0.4740.0000.0000.0000.000
165A168ILE0-0.033-0.01624.1990.4700.4700.0000.0000.0000.000
166A169ASP-1-0.767-0.89421.101-15.954-15.9540.0000.0000.0000.000
167A170ASN0-0.029-0.04321.3801.0971.0970.0000.0000.0000.000
168A171ILE0-0.057-0.01919.0360.2510.2510.0000.0000.0000.000
169A172PHE0-0.024-0.03414.201-0.245-0.2450.0000.0000.0000.000
170A173TRP0-0.0060.00218.813-0.065-0.0650.0000.0000.0000.000
171A174ASP-1-0.881-0.94618.160-16.426-16.4260.0000.0000.0000.000
172A175GLY0-0.0170.00417.374-0.354-0.3540.0000.0000.0000.000
173A176LYS10.8000.86718.02813.75013.7500.0000.0000.0000.000
174A177VAL0-0.045-0.02818.7600.7390.7390.0000.0000.0000.000
175A178ILE0-0.050-0.03215.8050.3960.3960.0000.0000.0000.000
176A179ASP-1-0.767-0.86119.191-13.246-13.2460.0000.0000.0000.000
177A180PRO0-0.042-0.03221.1480.5550.5550.0000.0000.0000.000
178A181ASN0-0.066-0.04023.8250.9270.9270.0000.0000.0000.000
179A182ASP-1-0.810-0.86725.247-11.361-11.3610.0000.0000.0000.000
180A183THR00.006-0.00727.0560.0780.0780.0000.0000.0000.000
181A184SER0-0.056-0.03028.8710.3760.3760.0000.0000.0000.000
182A185GLY00.014-0.02029.920-0.219-0.2190.0000.0000.0000.000
183A186GLN00.0330.01328.777-0.229-0.2290.0000.0000.0000.000
184A187THR00.0550.03924.915-0.307-0.3070.0000.0000.0000.000
185A188ARG10.9330.97826.2309.2169.2160.0000.0000.0000.000
186A189GLU-1-0.768-0.87528.649-9.586-9.5860.0000.0000.0000.000
187A190ILE00.0310.04023.1140.0450.0450.0000.0000.0000.000
188A191LYS10.8240.92823.36912.38612.3860.0000.0000.0000.000
189A192LYS10.7450.86125.0479.4359.4350.0000.0000.0000.000
190A193LEU00.0390.02025.8820.0580.0580.0000.0000.0000.000
191A194ASN0-0.001-0.01720.6490.2440.2440.0000.0000.0000.000
192A195GLN0-0.015-0.00222.984-0.154-0.1540.0000.0000.0000.000
193A196VAL0-0.001-0.00124.9850.2250.2250.0000.0000.0000.000
194A197ILE00.0400.01722.6680.1230.1230.0000.0000.0000.000
195A198LYS10.8420.93121.26212.04412.0440.0000.0000.0000.000
196A199ASN0-0.076-0.04522.986-0.100-0.1000.0000.0000.0000.000
197A200ASP-1-0.746-0.81726.167-9.433-9.4330.0000.0000.0000.000
198A201SER0-0.015-0.01527.493-0.161-0.1610.0000.0000.0000.000
199A202ARG10.7280.80429.3339.3709.3700.0000.0000.0000.000
200A203VAL0-0.017-0.00526.3950.1420.1420.0000.0000.0000.000
201A204PHE00.0050.01424.485-0.198-0.1980.0000.0000.0000.000
202A205VAL00.012-0.00620.313-0.045-0.0450.0000.0000.0000.000
203A206SER0-0.045-0.01418.000-0.479-0.4790.0000.0000.0000.000
204A207LEU0-0.004-0.00615.4680.4260.4260.0000.0000.0000.000
205A208LEU0-0.0010.00814.768-1.217-1.2170.0000.0000.0000.000
206A209ALA0-0.018-0.01411.6190.7130.7130.0000.0000.0000.000
207A210ILE0-0.037-0.02112.365-1.902-1.9020.0000.0000.0000.000
208A211ALA00.0320.02714.6830.1960.1960.0000.0000.0000.000
209A212ASP-1-0.749-0.84015.928-17.291-17.2910.0000.0000.0000.000
210A213GLY0-0.012-0.01216.7920.5070.5070.0000.0000.0000.000
211A214MET00.0060.00217.7600.9950.9950.0000.0000.0000.000
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