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: 1N6JZ

Calculation Name: 4N0V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4N0V

Chain ID: A

ChEMBL ID:

UniProt ID: A1TY67

Base Structure: X-ray

Registration Date: 2023-09-21

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2414608.301361
FMO2-HF: Nuclear repulsion 2332282.89701
FMO2-HF: Total energy -82325.404351
FMO2-MP2: Total energy -82563.524187


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-32.286-20.70221.237-12.315-20.504-0.074
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : 0.001
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].
3A3ILE00.0010.0063.797-1.1082.101-0.029-1.624-1.5550.010
4A4TYR0-0.059-0.0455.927-0.274-0.2740.0000.0000.0000.000
5A5ASP-1-0.801-0.8969.5350.0920.0920.0000.0000.0000.000
6A6THR00.0290.00411.901-0.085-0.0850.0000.0000.0000.000
7A7GLU-1-0.823-0.90414.693-0.226-0.2260.0000.0000.0000.000
8A8GLY00.0390.02916.6030.0030.0030.0000.0000.0000.000
9A9PHE00.003-0.00517.2370.0280.0280.0000.0000.0000.000
10A10PRO00.0320.00917.2540.0240.0240.0000.0000.0000.000
11A11ASN00.0540.00515.4490.0770.0770.0000.0000.0000.000
12A12PRO00.000-0.00912.5330.1110.1110.0000.0000.0000.000
13A13LEU00.0220.03012.6440.0600.0600.0000.0000.0000.000
14A14ARG10.8130.87414.336-0.506-0.5060.0000.0000.0000.000
15A15VAL00.0220.0158.3160.0850.0850.0000.0000.0000.000
16A16ARG10.7700.8379.6560.4310.4310.0000.0000.0000.000
17A17ILE00.0240.01710.755-0.013-0.0130.0000.0000.0000.000
18A18ALA0-0.002-0.00610.178-0.004-0.0040.0000.0000.0000.000
19A19LEU00.0050.0093.7160.0270.2260.002-0.029-0.1720.000
20A20ALA00.0100.0127.507-0.130-0.1300.0000.0000.0000.000
21A21GLU-1-0.817-0.85210.1010.4300.4300.0000.0000.0000.000
22A22LYS10.7120.8767.113-1.498-1.4980.0000.0000.0000.000
23A23GLY0-0.0170.0018.1390.0260.0260.0000.0000.0000.000
24A24ALA0-0.023-0.0233.574-0.314-0.1590.004-0.034-0.1240.000
25A25THR00.027-0.0054.590-0.416-0.366-0.001-0.005-0.0440.000
26A26ASP-1-0.912-0.9566.309-1.063-1.0630.0000.0000.0000.000
27A27LYS10.8410.9272.522-0.679-0.2041.186-0.389-1.2720.000
28A28VAL00.0080.0162.273-6.229-3.8844.135-2.186-4.294-0.018
29A29VAL0-0.018-0.0013.6080.9431.6210.015-0.152-0.5400.000
30A30PHE00.0210.0006.092-0.076-0.0760.0000.0000.0000.000
31A31VAL0-0.041-0.0227.9960.0140.0140.0000.0000.0000.000
32A32PRO0-0.010-0.01210.5480.1910.1910.0000.0000.0000.000
33A33VAL00.0160.01812.854-0.024-0.0240.0000.0000.0000.000
34A34ASP-1-0.853-0.93415.531-0.174-0.1740.0000.0000.0000.000
35A35VAL0-0.040-0.02717.6350.0290.0290.0000.0000.0000.000
36A36MET0-0.077-0.02720.1960.0270.0270.0000.0000.0000.000
37A37GLY00.0270.03322.7540.0160.0160.0000.0000.0000.000
38A38GLY0-0.061-0.03822.969-0.002-0.0020.0000.0000.0000.000
39A39GLU-1-0.834-0.90916.813-0.464-0.4640.0000.0000.0000.000
40A40HIS00.0030.00717.309-0.039-0.0390.0000.0000.0000.000
41A41ARG10.8410.91118.3260.0630.0630.0000.0000.0000.000
42A42THR0-0.009-0.00619.0480.0090.0090.0000.0000.0000.000
43A43THR00.003-0.01919.8030.0200.0200.0000.0000.0000.000
44A44ASP-1-0.883-0.93516.662-0.344-0.3440.0000.0000.0000.000
45A45PHE0-0.0220.00013.018-0.022-0.0220.0000.0000.0000.000
46A46ARG10.9060.94215.1490.0700.0700.0000.0000.0000.000
47A47ALA0-0.051-0.01116.0980.0500.0500.0000.0000.0000.000
48A48LYS10.8600.9289.8330.8780.8780.0000.0000.0000.000
49A49ASN0-0.011-0.02412.7610.1600.1600.0000.0000.0000.000
50A50PRO00.0300.02114.684-0.036-0.0360.0000.0000.0000.000
51A51ASP-1-0.901-0.94117.2390.3230.3230.0000.0000.0000.000
52A52ALA0-0.079-0.04017.759-0.015-0.0150.0000.0000.0000.000
53A53THR0-0.040-0.01716.314-0.001-0.0010.0000.0000.0000.000
54A54VAL00.0460.03713.241-0.016-0.0160.0000.0000.0000.000
55A55PRO0-0.056-0.0429.4730.0120.0120.0000.0000.0000.000
56A56VAL0-0.013-0.0138.7350.1130.1130.0000.0000.0000.000
57A57LEU00.0050.0142.532-1.392-0.4820.790-0.318-1.3830.000
58A58GLU-1-0.771-0.8444.485-1.780-1.565-0.001-0.043-0.1710.000
59A59LEU00.009-0.0102.526-4.248-1.6791.933-1.938-2.563-0.020
60A60ASP-1-0.849-0.9271.925-13.998-14.5078.128-4.084-3.536-0.050
61A61ASP-1-0.914-0.9464.1730.5380.6460.000-0.043-0.0650.000
62A62GLY0-0.018-0.0056.6780.1160.1160.0000.0000.0000.000
63A63THR0-0.055-0.0317.7760.0450.0450.0000.0000.0000.000
64A64CYS0-0.068-0.0286.863-0.055-0.0550.0000.0000.0000.000
65A65ILE0-0.021-0.0087.7630.0320.0320.0000.0000.0000.000
66A66ALA00.0520.0249.4460.0160.0160.0000.0000.0000.000
67A67GLN0-0.003-0.01112.1650.1320.1320.0000.0000.0000.000
68A68CYS00.0120.02112.5490.1420.1420.0000.0000.0000.000
69A69ASN0-0.012-0.01412.5290.2260.2260.0000.0000.0000.000
70A70ALA00.0350.02912.5610.1210.1210.0000.0000.0000.000
71A71ILE00.0130.0037.1710.3270.3270.0000.0000.0000.000
72A72THR0-0.026-0.0428.1470.6320.6320.0000.0000.0000.000
73A73GLU-1-0.858-0.91510.0611.3701.3700.0000.0000.0000.000
74A74TYR0-0.0050.0052.818-3.446-3.0332.266-0.811-1.8680.007
75A75LEU00.002-0.0113.806-0.0360.5730.173-0.148-0.6340.000
76A76ASP-1-0.735-0.8486.4550.8380.8380.0000.0000.0000.000
77A77GLY0-0.0190.0069.414-0.292-0.2920.0000.0000.0000.000
78A78VAL0-0.042-0.0225.077-0.432-0.2960.000-0.020-0.1150.000
79A79PHE0-0.019-0.0042.271-1.254-1.2322.636-0.491-2.168-0.003
80A80ASP-1-0.882-0.9317.5850.9410.9410.0000.0000.0000.000
81A81GLY0-0.005-0.00710.7190.0000.0000.0000.0000.0000.000
82A82PRO0-0.034-0.03213.2910.0280.0280.0000.0000.0000.000
83A83SER00.0290.03413.3620.0710.0710.0000.0000.0000.000
84A84LEU00.025-0.00611.060-0.132-0.1320.0000.0000.0000.000
85A85THR0-0.023-0.04013.561-0.104-0.1040.0000.0000.0000.000
86A86GLY0-0.0080.00516.170-0.077-0.0770.0000.0000.0000.000
87A87ALA00.020-0.00417.7450.0780.0780.0000.0000.0000.000
88A88SER0-0.009-0.00619.592-0.050-0.0500.0000.0000.0000.000
89A89PRO00.0590.01222.6660.0170.0170.0000.0000.0000.000
90A90LYS10.9840.99724.379-0.298-0.2980.0000.0000.0000.000
91A91GLU-1-0.793-0.88021.2850.5380.5380.0000.0000.0000.000
92A92ARG10.8620.91715.272-1.004-1.0040.0000.0000.0000.000
93A93ALA0-0.030-0.00521.3770.0080.0080.0000.0000.0000.000
94A94VAL0-0.032-0.02324.262-0.016-0.0160.0000.0000.0000.000
95A95ILE00.0560.03218.687-0.020-0.0200.0000.0000.0000.000
96A96ALA00.0040.00820.887-0.004-0.0040.0000.0000.0000.000
97A97MET0-0.029-0.00321.800-0.032-0.0320.0000.0000.0000.000
98A98MET0-0.032-0.01124.093-0.030-0.0300.0000.0000.0000.000
99A99ASN00.0430.02518.384-0.031-0.0310.0000.0000.0000.000
100A100ILE00.0180.01021.181-0.019-0.0190.0000.0000.0000.000
101A101ARG10.8860.94323.681-0.312-0.3120.0000.0000.0000.000
102A102ALA00.0420.02823.068-0.028-0.0280.0000.0000.0000.000
103A103GLU-1-0.788-0.88518.9910.5170.5170.0000.0000.0000.000
104A104SER0-0.067-0.04623.174-0.031-0.0310.0000.0000.0000.000
105A105GLY00.0150.01526.166-0.025-0.0250.0000.0000.0000.000
106A106LEU00.004-0.00125.944-0.023-0.0230.0000.0000.0000.000
107A107MET0-0.0110.01120.155-0.026-0.0260.0000.0000.0000.000
108A108ASN0-0.006-0.02622.247-0.026-0.0260.0000.0000.0000.000
109A109ALA0-0.0080.03225.027-0.022-0.0220.0000.0000.0000.000
110A110VAL00.0400.00526.612-0.022-0.0220.0000.0000.0000.000
111A111GLY00.0100.00325.265-0.020-0.0200.0000.0000.0000.000
112A112ALA0-0.049-0.02626.140-0.022-0.0220.0000.0000.0000.000
113A113TYR00.0180.00429.022-0.016-0.0160.0000.0000.0000.000
114A114PHE00.0050.00026.105-0.014-0.0140.0000.0000.0000.000
115A115HIS10.8360.88623.528-0.087-0.0870.0000.0000.0000.000
116A116HIS00.0100.02129.073-0.015-0.0150.0000.0000.0000.000
117A117ALA0-0.026-0.00732.410-0.006-0.0060.0000.0000.0000.000
118A118THR0-0.050-0.01231.649-0.009-0.0090.0000.0000.0000.000
119A119ARG10.9740.97732.6320.0290.0290.0000.0000.0000.000
120A120GLY00.0350.03229.388-0.004-0.0040.0000.0000.0000.000
121A121LEU0-0.064-0.05523.436-0.007-0.0070.0000.0000.0000.000
122A122GLY0-0.013-0.00127.847-0.016-0.0160.0000.0000.0000.000
123A123PRO00.005-0.00530.3920.0040.0040.0000.0000.0000.000
124A124ASP-1-0.903-0.94029.696-0.062-0.0620.0000.0000.0000.000
125A125LEU0-0.016-0.02024.3010.0020.0020.0000.0000.0000.000
126A126GLU-1-0.800-0.85127.7890.0500.0500.0000.0000.0000.000
127A127THR0-0.015-0.00729.4010.0000.0000.0000.0000.0000.000
128A128TRP0-0.026-0.02431.3770.0030.0030.0000.0000.0000.000
129A129GLN0-0.058-0.02232.0230.0020.0020.0000.0000.0000.000
130A130CYS0-0.023-0.01334.054-0.003-0.0030.0000.0000.0000.000
131A131PRO00.0820.02535.5300.0090.0090.0000.0000.0000.000
132A132ASP-1-0.910-0.94137.1270.0640.0640.0000.0000.0000.000
133A133TRP0-0.005-0.00430.7100.0060.0060.0000.0000.0000.000
134A134GLY00.0480.01432.9880.0090.0090.0000.0000.0000.000
135A135ASN0-0.029-0.04133.9870.0050.0050.0000.0000.0000.000
136A136LYS10.8400.93036.405-0.105-0.1050.0000.0000.0000.000
137A137GLN00.004-0.01331.2600.0160.0160.0000.0000.0000.000
138A138LYS10.9030.97832.629-0.068-0.0680.0000.0000.0000.000
139A139GLU-1-0.824-0.90834.0760.1030.1030.0000.0000.0000.000
140A140VAL0-0.055-0.01031.6200.0050.0050.0000.0000.0000.000
141A141ALA00.0210.01230.6700.0100.0100.0000.0000.0000.000
142A142GLN0-0.025-0.04131.8090.0040.0040.0000.0000.0000.000
143A143SER0-0.040-0.02534.717-0.002-0.0020.0000.0000.0000.000
144A144THR0-0.028-0.01228.9230.0080.0080.0000.0000.0000.000
145A145MET0-0.074-0.01430.4000.0060.0060.0000.0000.0000.000
146A146ALA00.0380.01832.0890.0020.0020.0000.0000.0000.000
147A147TYR00.0230.01329.5670.0110.0110.0000.0000.0000.000
148A148LEU00.004-0.01426.9220.0080.0080.0000.0000.0000.000
149A149ASN00.0010.00130.7090.0040.0040.0000.0000.0000.000
150A150GLU-1-0.888-0.94633.1430.1410.1410.0000.0000.0000.000
151A151VAL0-0.050-0.02128.8800.0030.0030.0000.0000.0000.000
152A152LEU0-0.046-0.02127.0400.0040.0040.0000.0000.0000.000
153A153ALA0-0.0030.01931.081-0.005-0.0050.0000.0000.0000.000
154A154GLU-1-1.012-0.99833.6550.1680.1680.0000.0000.0000.000
155A155ASN0-0.103-0.05128.7500.0180.0180.0000.0000.0000.000
156A156GLU-1-0.878-0.91526.3890.2080.2080.0000.0000.0000.000
157A157PHE0-0.001-0.01723.020-0.002-0.0020.0000.0000.0000.000
158A158LEU0-0.007-0.01523.658-0.006-0.0060.0000.0000.0000.000
159A159ALA0-0.036-0.02922.901-0.008-0.0080.0000.0000.0000.000
160A160GLY00.0080.01424.9620.0050.0050.0000.0000.0000.000
161A161ASP-1-0.908-0.95525.7450.3150.3150.0000.0000.0000.000
162A162ARG10.7840.87817.859-0.562-0.5620.0000.0000.0000.000
163A163PHE0-0.0230.00115.9800.0000.0000.0000.0000.0000.000
164A164THR0-0.059-0.03717.2940.0560.0560.0000.0000.0000.000
165A165VAL00.0570.00615.041-0.035-0.0350.0000.0000.0000.000
166A166ALA00.0000.00916.654-0.042-0.0420.0000.0000.0000.000
167A167ASP-1-0.746-0.87719.7430.3530.3530.0000.0000.0000.000
168A168ILE00.0330.02513.764-0.046-0.0460.0000.0000.0000.000
169A169THR0-0.061-0.03817.994-0.037-0.0370.0000.0000.0000.000
170A170ALA00.0210.01019.657-0.046-0.0460.0000.0000.0000.000
171A171TYR0-0.042-0.03119.569-0.036-0.0360.0000.0000.0000.000
172A172ALA00.0360.01218.919-0.040-0.0400.0000.0000.0000.000
173A173GLY00.006-0.00321.060-0.036-0.0360.0000.0000.0000.000
174A174LEU0-0.004-0.00424.125-0.030-0.0300.0000.0000.0000.000
175A175VAL00.0530.03422.365-0.024-0.0240.0000.0000.0000.000
176A176PHE0-0.010-0.01123.266-0.029-0.0290.0000.0000.0000.000
177A177ALA0-0.017-0.01725.090-0.020-0.0200.0000.0000.0000.000
178A178GLU-1-0.764-0.83828.3180.0700.0700.0000.0000.0000.000
179A179PHE0-0.031-0.01026.297-0.017-0.0170.0000.0000.0000.000
180A180ALA0-0.026-0.01628.319-0.015-0.0150.0000.0000.0000.000
181A181LYS10.7870.89530.027-0.038-0.0380.0000.0000.0000.000
182A182VAL0-0.044-0.01931.378-0.002-0.0020.0000.0000.0000.000
183A183ASP-1-0.853-0.93332.7860.0740.0740.0000.0000.0000.000
184A184ILE00.0470.02129.7410.0090.0090.0000.0000.0000.000
185A185PRO0-0.032-0.01534.101-0.007-0.0070.0000.0000.0000.000
186A186GLY00.0330.01136.4290.0060.0060.0000.0000.0000.000
187A187HIS0-0.012-0.01438.194-0.005-0.0050.0000.0000.0000.000
188A188LEU0-0.053-0.00834.3110.0030.0030.0000.0000.0000.000
189A189ASP-1-0.833-0.93134.4760.1240.1240.0000.0000.0000.000
190A190HIS00.0490.02932.9070.0080.0080.0000.0000.0000.000
191A191LEU0-0.016-0.01628.6990.0120.0120.0000.0000.0000.000
192A192LEU0-0.032-0.02129.5850.0060.0060.0000.0000.0000.000
193A193ALA0-0.0090.00230.396-0.002-0.0020.0000.0000.0000.000
194A194TRP0-0.046-0.02522.881-0.008-0.0080.0000.0000.0000.000
195A195ARG10.8340.88225.759-0.110-0.1100.0000.0000.0000.000
196A196ALA0-0.036-0.01025.5050.0000.0000.0000.0000.0000.000
197A197ARG10.8290.89725.806-0.189-0.1890.0000.0000.0000.000
198A198VAL0-0.018-0.01220.3650.0130.0130.0000.0000.0000.000
199A199ALA0-0.007-0.00721.1490.0080.0080.0000.0000.0000.000
200A200ALA0-0.0160.00122.154-0.016-0.0160.0000.0000.0000.000
201A201ARG10.8020.87516.684-0.386-0.3860.0000.0000.0000.000
202A202PRO00.000-0.00516.850-0.009-0.0090.0000.0000.0000.000
203A203SER0-0.080-0.06113.942-0.052-0.0520.0000.0000.0000.000
204A204ILE0-0.052-0.02114.9490.0100.0100.0000.0000.0000.000
205A205THR0-0.0090.01017.478-0.045-0.0450.0000.0000.0000.000
206A206GLY00.012-0.00219.514-0.010-0.0100.0000.0000.0000.000
207A207ALA0-0.050-0.03622.510-0.006-0.0060.0000.0000.0000.000
208A208GLU-1-0.809-0.88119.0220.0920.0920.0000.0000.0000.000
209A209ASN0-0.052-0.02221.3490.0220.0220.0000.0000.0000.000
210A210LEU0-0.024-0.00320.372-0.009-0.0090.0000.0000.0000.000
211A211TYR0-0.019-0.03019.849-0.015-0.0150.0000.0000.0000.000
212A212PHE00.0170.00322.360-0.003-0.0030.0000.0000.0000.000
213A213GLN00.0110.01224.2510.0080.0080.0000.0000.0000.000