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: 3J6ML

Calculation Name: 2NR7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NR7

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MXB3

Base Structure: X-ray

Registration Date: 2023-09-24

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2178359.488312
FMO2-HF: Nuclear repulsion 2102477.105902
FMO2-HF: Total energy -75882.382409
FMO2-MP2: Total energy -76110.065851


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:-1:ASN)


Summations of interaction energy for fragment #1(A:-1:ASN)
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.
4.0656.4980.08-0.745-1.7680.002
Interaction energy analysis for fragmet #1(A:-1:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / 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].
3A1MET0-0.0010.0263.258-0.7071.3050.081-0.682-1.4110.002
4A2ALA0-0.025-0.0016.3720.4420.4420.0000.0000.0000.000
5A3ASN00.018-0.0089.817-0.276-0.2760.0000.0000.0000.000
6A4VAL00.0680.02912.4460.1680.1680.0000.0000.0000.000
7A5LYS10.9220.94915.4560.7550.7550.0000.0000.0000.000
8A6LEU0-0.016-0.00513.4270.0590.0590.0000.0000.0000.000
9A7LEU00.0040.01917.1330.0670.0670.0000.0000.0000.000
10A8LEU00.004-0.00319.0340.0370.0370.0000.0000.0000.000
11A9PRO00.0390.01620.7720.0300.0300.0000.0000.0000.000
12A10TYR0-0.023-0.02522.3530.0210.0210.0000.0000.0000.000
13A11ILE0-0.003-0.00122.8680.0200.0200.0000.0000.0000.000
14A12LEU00.0280.01125.4570.0160.0160.0000.0000.0000.000
15A13LYS10.9270.97827.1970.0650.0650.0000.0000.0000.000
16A14TRP0-0.082-0.05127.0030.0120.0120.0000.0000.0000.000
17A15GLU-1-0.741-0.86728.889-0.069-0.0690.0000.0000.0000.000
18A16GLY00.0030.00331.4250.0030.0030.0000.0000.0000.000
19A17GLY0-0.027-0.02032.7730.0060.0060.0000.0000.0000.000
20A18PHE0-0.015-0.01433.4470.0070.0070.0000.0000.0000.000
21A19VAL0-0.023-0.00932.794-0.002-0.0020.0000.0000.0000.000
22A20HIS00.0350.01631.8660.0050.0050.0000.0000.0000.000
23A21ASP-1-0.875-0.92034.892-0.071-0.0710.0000.0000.0000.000
24A22PRO00.000-0.01934.944-0.010-0.0100.0000.0000.0000.000
25A23ALA00.032-0.00835.6870.0040.0040.0000.0000.0000.000
26A24ASP-1-0.966-0.97537.550-0.082-0.0820.0000.0000.0000.000
27A25ALA0-0.0010.01139.9090.0050.0050.0000.0000.0000.000
28A26GLY0-0.033-0.02141.2430.0040.0040.0000.0000.0000.000
29A27GLY0-0.064-0.02337.990-0.003-0.0030.0000.0000.0000.000
30A28ALA00.0070.02038.227-0.005-0.0050.0000.0000.0000.000
31A29THR0-0.006-0.00436.262-0.001-0.0010.0000.0000.0000.000
32A30ASN0-0.029-0.01237.7750.0070.0070.0000.0000.0000.000
33A31LYS10.8920.95437.4720.0650.0650.0000.0000.0000.000
34A32GLY00.0160.00637.6610.0060.0060.0000.0000.0000.000
35A33VAL0-0.047-0.02935.3940.0000.0000.0000.0000.0000.000
36A34THR0-0.002-0.00234.698-0.007-0.0070.0000.0000.0000.000
37A35ILE0-0.114-0.04132.0620.0080.0080.0000.0000.0000.000
38A36ALA00.0510.03431.704-0.002-0.0020.0000.0000.0000.000
39A37THR0-0.075-0.06329.0720.0090.0090.0000.0000.0000.000
40A38TRP00.0160.01628.3590.0080.0080.0000.0000.0000.000
41A39LYS10.9110.92930.2270.0960.0960.0000.0000.0000.000
42A40ARG10.8570.93632.1460.0650.0650.0000.0000.0000.000
43A41VAL0-0.043-0.01230.8260.0070.0070.0000.0000.0000.000
44A42GLY0-0.006-0.00531.9170.0060.0060.0000.0000.0000.000
45A43TYR0-0.097-0.05228.7430.0040.0040.0000.0000.0000.000
46A44ASP-1-0.883-0.92731.0990.0000.0000.0000.0000.0000.000
47A45LYS11.0000.97030.5360.0420.0420.0000.0000.0000.000
48A46ASP-1-0.894-0.93430.671-0.024-0.0240.0000.0000.0000.000
49A47GLY00.005-0.01127.7630.0030.0030.0000.0000.0000.000
50A48ASP-1-0.869-0.90626.434-0.092-0.0920.0000.0000.0000.000
51A49GLY0-0.004-0.00627.267-0.017-0.0170.0000.0000.0000.000
52A50ASP-1-0.974-0.97528.368-0.087-0.0870.0000.0000.0000.000
53A51ILE0-0.0280.00727.069-0.004-0.0040.0000.0000.0000.000
54A52ASP-1-0.911-0.97330.129-0.083-0.0830.0000.0000.0000.000
55A53VAL0-0.065-0.03031.304-0.011-0.0110.0000.0000.0000.000
56A54GLU-1-0.910-0.94034.189-0.082-0.0820.0000.0000.0000.000
57A55ASP-1-0.808-0.92036.194-0.085-0.0850.0000.0000.0000.000
58A56LEU0-0.015-0.00629.261-0.007-0.0070.0000.0000.0000.000
59A57LYS10.7760.88032.3230.0770.0770.0000.0000.0000.000
60A58LEU0-0.0200.00134.491-0.001-0.0010.0000.0000.0000.000
61A59LEU0-0.0220.00830.053-0.005-0.0050.0000.0000.0000.000
62A60THR00.0470.02129.3330.0000.0000.0000.0000.0000.000
63A61ASP-1-0.832-0.93225.655-0.213-0.2130.0000.0000.0000.000
64A62ASP-1-0.930-0.97024.024-0.363-0.3630.0000.0000.0000.000
65A63ASP-1-0.892-0.94124.539-0.268-0.2680.0000.0000.0000.000
66A64VAL0-0.0070.00225.434-0.002-0.0020.0000.0000.0000.000
67A65LEU0-0.012-0.01518.772-0.014-0.0140.0000.0000.0000.000
68A66ASN0-0.032-0.03721.003-0.059-0.0590.0000.0000.0000.000
69A67ARG10.8850.94022.5080.2500.2500.0000.0000.0000.000
70A68VAL00.0160.02524.8580.0190.0190.0000.0000.0000.000
71A69LEU00.000-0.00620.7320.0000.0000.0000.0000.0000.000
72A70LYS10.7660.84913.9740.7930.7930.0000.0000.0000.000
73A71PRO00.0100.03019.158-0.006-0.0060.0000.0000.0000.000
74A72PHE00.004-0.00220.8810.0130.0130.0000.0000.0000.000
75A73TYR0-0.055-0.02421.5500.0340.0340.0000.0000.0000.000
76A74TRP0-0.021-0.04012.6550.1410.1410.0000.0000.0000.000
77A75ASP-1-0.792-0.90015.799-0.576-0.5760.0000.0000.0000.000
78A76ARG10.8880.97216.9900.0990.0990.0000.0000.0000.000
79A77TRP0-0.029-0.03116.1670.0610.0610.0000.0000.0000.000
80A78LYS10.8630.91612.9010.1820.1820.0000.0000.0000.000
81A79ALA00.0650.02511.988-0.030-0.0300.0000.0000.0000.000
82A80ASP-1-0.822-0.8799.759-1.061-1.0610.0000.0000.0000.000
83A81LEU0-0.035-0.0266.825-0.516-0.5160.0000.0000.0000.000
84A82ILE0-0.057-0.0088.3400.4950.4950.0000.0000.0000.000
85A83GLU-1-0.867-0.9544.2423.7774.198-0.001-0.063-0.3570.000
86A84SER00.0000.0236.5310.1380.1380.0000.0000.0000.000
87A85GLN00.042-0.0049.492-0.266-0.2660.0000.0000.0000.000
88A86LYS10.8630.92511.763-0.483-0.4830.0000.0000.0000.000
89A87VAL00.0350.01712.617-0.047-0.0470.0000.0000.0000.000
90A88ALA00.0410.02112.416-0.041-0.0410.0000.0000.0000.000
91A89ASN00.0140.00114.336-0.084-0.0840.0000.0000.0000.000
92A90ILE0-0.0160.00017.177-0.026-0.0260.0000.0000.0000.000
93A91LEU00.0380.01915.616-0.006-0.0060.0000.0000.0000.000
94A92VAL00.0030.00816.987-0.014-0.0140.0000.0000.0000.000
95A93ASP-1-0.783-0.88719.720-0.037-0.0370.0000.0000.0000.000
96A94TRP0-0.0070.00222.1290.0070.0070.0000.0000.0000.000
97A95VAL0-0.0110.00122.130-0.001-0.0010.0000.0000.0000.000
98A96TRP0-0.045-0.01823.996-0.010-0.0100.0000.0000.0000.000
99A97GLY00.0430.01725.776-0.001-0.0010.0000.0000.0000.000
100A98SER0-0.037-0.05727.5130.0030.0030.0000.0000.0000.000
101A99GLY00.0180.02127.4870.0080.0080.0000.0000.0000.000
102A100LYS10.9240.96126.347-0.011-0.0110.0000.0000.0000.000
103A101TYR00.002-0.00226.6680.0160.0160.0000.0000.0000.000
104A102GLY00.0050.00424.2570.0190.0190.0000.0000.0000.000
105A103ILE0-0.0080.00021.5260.0070.0070.0000.0000.0000.000
106A104VAL00.005-0.00623.1040.0280.0280.0000.0000.0000.000
107A105ILE0-0.032-0.00525.6870.0200.0200.0000.0000.0000.000
108A106PRO00.0320.00720.2320.0230.0230.0000.0000.0000.000
109A107GLN00.0120.00621.2740.0190.0190.0000.0000.0000.000
110A108ARG10.9640.99522.528-0.150-0.1500.0000.0000.0000.000
111A109ILE0-0.078-0.04220.9620.0100.0100.0000.0000.0000.000
112A110LEU0-0.011-0.00217.0280.0210.0210.0000.0000.0000.000
113A111GLY0-0.0050.02420.6120.0340.0340.0000.0000.0000.000
114A112VAL0-0.090-0.04519.2530.0130.0130.0000.0000.0000.000
115A113GLN0-0.025-0.02622.689-0.037-0.0370.0000.0000.0000.000
116A114ALA00.0060.00324.253-0.001-0.0010.0000.0000.0000.000
117A115ASP-1-0.851-0.93624.0440.0890.0890.0000.0000.0000.000
118A116GLY0-0.040-0.02924.969-0.019-0.0190.0000.0000.0000.000
119A117ILE0-0.033-0.00721.066-0.031-0.0310.0000.0000.0000.000
120A118VAL00.0400.03016.1070.0420.0420.0000.0000.0000.000
121A119GLY00.0270.01617.499-0.051-0.0510.0000.0000.0000.000
122A120ASN00.0360.00013.2200.0820.0820.0000.0000.0000.000
123A121LYS10.9710.98414.617-0.300-0.3000.0000.0000.0000.000
124A122THR00.0590.03416.5420.0540.0540.0000.0000.0000.000
125A123LEU00.0390.01311.7450.0350.0350.0000.0000.0000.000
126A124GLN0-0.047-0.01710.9620.1650.1650.0000.0000.0000.000
127A125ALA00.0010.00512.7580.1270.1270.0000.0000.0000.000
128A126VAL0-0.033-0.02611.8700.0210.0210.0000.0000.0000.000
129A127ASN00.014-0.0158.452-0.113-0.1130.0000.0000.0000.000
130A128SER0-0.049-0.00810.0010.2100.2100.0000.0000.0000.000
131A129ALA0-0.037-0.00212.326-0.023-0.0230.0000.0000.0000.000
132A130ASP-1-0.766-0.88112.4330.8360.8360.0000.0000.0000.000
133A131PRO0-0.026-0.02710.348-0.123-0.1230.0000.0000.0000.000
134A132ASP-1-0.844-0.90913.1610.4160.4160.0000.0000.0000.000
135A133GLU-1-0.928-0.96116.3230.4170.4170.0000.0000.0000.000
136A134LEU0-0.0010.00014.476-0.070-0.0700.0000.0000.0000.000
137A135PHE0-0.048-0.03816.405-0.073-0.0730.0000.0000.0000.000
138A136GLU-1-0.811-0.90818.0640.1840.1840.0000.0000.0000.000
139A137SER00.0140.02320.818-0.034-0.0340.0000.0000.0000.000
140A138ILE0-0.053-0.03417.839-0.036-0.0360.0000.0000.0000.000
141A139PHE0-0.005-0.02021.919-0.038-0.0380.0000.0000.0000.000
142A140ASP-1-0.927-0.95523.7790.1670.1670.0000.0000.0000.000
143A141ALA00.0260.01025.030-0.018-0.0180.0000.0000.0000.000
144A142ARG10.7820.89022.746-0.060-0.0600.0000.0000.0000.000
145A143ARG10.9440.97026.996-0.131-0.1310.0000.0000.0000.000
146A144GLU-1-0.914-0.95429.6740.1240.1240.0000.0000.0000.000
147A145PHE0-0.021-0.00729.453-0.010-0.0100.0000.0000.0000.000
148A146LEU0-0.019-0.01229.613-0.011-0.0110.0000.0000.0000.000
149A147GLU-1-0.873-0.94632.8390.0480.0480.0000.0000.0000.000
150A148ASP-1-0.867-0.91434.4980.0540.0540.0000.0000.0000.000
151A149ILE0-0.028-0.02133.565-0.007-0.0070.0000.0000.0000.000
152A150THR0-0.050-0.03936.683-0.010-0.0100.0000.0000.0000.000
153A151ALA00.0250.01538.932-0.004-0.0040.0000.0000.0000.000
154A152ARG10.8930.93337.910-0.056-0.0560.0000.0000.0000.000
155A153SER0-0.059-0.00740.865-0.004-0.0040.0000.0000.0000.000
156A154ILE00.008-0.01442.576-0.003-0.0030.0000.0000.0000.000
157A155LYS10.9150.95844.537-0.035-0.0350.0000.0000.0000.000
158A156LYS10.9410.97341.249-0.019-0.0190.0000.0000.0000.000
159A157TYR00.0090.00046.908-0.002-0.0020.0000.0000.0000.000
160A158GLU-1-0.812-0.92848.8740.0250.0250.0000.0000.0000.000
161A159ASP-1-0.844-0.91749.3200.0270.0270.0000.0000.0000.000
162A160SER0-0.088-0.03751.191-0.001-0.0010.0000.0000.0000.000
163A161ILE0-0.069-0.03052.943-0.001-0.0010.0000.0000.0000.000
164A162GLY00.0120.02354.723-0.001-0.0010.0000.0000.0000.000
165A163ARG10.7790.86055.008-0.011-0.0110.0000.0000.0000.000
166A164LYS10.9020.95849.925-0.024-0.0240.0000.0000.0000.000
167A165ALA00.0080.01250.356-0.002-0.0020.0000.0000.0000.000
168A166THR0-0.020-0.01452.1370.0020.0020.0000.0000.0000.000
169A167GLU-1-0.896-0.96147.8960.0160.0160.0000.0000.0000.000
170A168ARG10.9970.99148.9560.0000.0000.0000.0000.0000.000
171A169GLU-1-0.800-0.87450.0740.0080.0080.0000.0000.0000.000
172A170LEU00.0380.01646.146-0.001-0.0010.0000.0000.0000.000
173A171LEU00.0030.01644.134-0.001-0.0010.0000.0000.0000.000
174A172ARG10.8630.92545.7500.0040.0040.0000.0000.0000.000
175A173HIS0-0.0010.00547.261-0.004-0.0040.0000.0000.0000.000
176A174THR0-0.017-0.00343.9010.0020.0020.0000.0000.0000.000
177A175ASN00.0520.00538.408-0.007-0.0070.0000.0000.0000.000
178A176LYS10.9620.99039.564-0.026-0.0260.0000.0000.0000.000
179A177ARG10.8490.93741.2260.0130.0130.0000.0000.0000.000
180A178PHE0-0.001-0.00836.753-0.004-0.0040.0000.0000.0000.000
181A179LEU00.0220.03834.901-0.002-0.0020.0000.0000.0000.000
182A180ARG10.9830.98835.230-0.010-0.0100.0000.0000.0000.000
183A181GLY00.0020.00434.8270.0020.0020.0000.0000.0000.000
184A182TRP00.0770.01531.9210.0010.0010.0000.0000.0000.000
185A183LEU00.0160.01630.4480.0020.0020.0000.0000.0000.000
186A184ASN0-0.019-0.01630.2700.0110.0110.0000.0000.0000.000
187A185ARG10.8260.90925.9870.0550.0550.0000.0000.0000.000
188A186LEU0-0.0010.01824.733-0.004-0.0040.0000.0000.0000.000
189A187GLU-1-0.878-0.95225.3910.1040.1040.0000.0000.0000.000
190A188ASP-1-0.910-0.96425.756-0.005-0.0050.0000.0000.0000.000
191A189ILE0-0.0120.00420.596-0.005-0.0050.0000.0000.0000.000
192A190ARG10.7740.88420.791-0.148-0.1480.0000.0000.0000.000
193A191LYS10.8880.95020.862-0.023-0.0230.0000.0000.0000.000
194A192LEU0-0.0260.01617.680-0.020-0.0200.0000.0000.0000.000