FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: N1RRQ

Calculation Name: 3D5N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D5N

Chain ID: A

ChEMBL ID:

UniProt ID: Q97W15

Base Structure: X-ray

Registration Date: 2023-06-21

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1937441.836315
FMO2-HF: Nuclear repulsion 1867436.775144
FMO2-HF: Total energy -70005.061171
FMO2-MP2: Total energy -70208.473922


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.
-10.591-5.3338.947-4.357-9.849-0.017
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 : 0.005 / q_NPA : 0.010
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].
3A3ILE00.007-0.0093.0730.1202.8341.960-1.406-3.2670.004
4A4GLY00.0570.0435.553-0.805-0.767-0.001-0.018-0.0190.000
5A5VAL0-0.058-0.0239.2630.2870.2870.0000.0000.0000.000
6A6ILE00.007-0.00111.811-0.061-0.0610.0000.0000.0000.000
7A7ILE0-0.023-0.01714.8490.0410.0410.0000.0000.0000.000
8A8LEU0-0.002-0.00417.805-0.016-0.0160.0000.0000.0000.000
9A9ALA00.028-0.00220.4580.0050.0050.0000.0000.0000.000
10A10ALA0-0.0420.00123.866-0.006-0.0060.0000.0000.0000.000
11A11GLY00.055-0.01026.1870.0040.0040.0000.0000.0000.000
12A12GLU-1-0.855-0.88224.2830.0040.0040.0000.0000.0000.000
13A13GLY00.0390.01728.8010.0050.0050.0000.0000.0000.000
14A14LYS10.8920.94130.939-0.015-0.0150.0000.0000.0000.000
15A15ARG10.8190.88725.710-0.030-0.0300.0000.0000.0000.000
16A16PHE00.0310.00927.841-0.005-0.0050.0000.0000.0000.000
17A17GLY00.0660.00428.5230.0000.0000.0000.0000.0000.000
18A18GLY0-0.013-0.01929.1370.0000.0000.0000.0000.0000.000
19A19ASP-1-0.762-0.87731.042-0.009-0.0090.0000.0000.0000.000
20A20LYS10.8600.93131.454-0.010-0.0100.0000.0000.0000.000
21A21LEU0-0.063-0.02326.0780.0000.0000.0000.0000.0000.000
22A22LEU00.0360.02229.063-0.005-0.0050.0000.0000.0000.000
23A23ALA0-0.0230.00731.668-0.001-0.0010.0000.0000.0000.000
24A24LYS10.8570.91931.0510.0230.0230.0000.0000.0000.000
25A25ILE00.0400.01928.0060.0040.0040.0000.0000.0000.000
26A26ASP-1-0.820-0.88529.518-0.004-0.0040.0000.0000.0000.000
27A27ASN0-0.022-0.02431.248-0.003-0.0030.0000.0000.0000.000
28A28THR00.0140.00627.690-0.004-0.0040.0000.0000.0000.000
29A29PRO00.0270.01028.2850.0050.0050.0000.0000.0000.000
30A30ILE00.0180.01626.237-0.004-0.0040.0000.0000.0000.000
31A31ILE00.0330.02322.844-0.001-0.0010.0000.0000.0000.000
32A32MET00.0180.00822.888-0.004-0.0040.0000.0000.0000.000
33A33ARG10.8000.89722.442-0.005-0.0050.0000.0000.0000.000
34A34THR0-0.022-0.04819.735-0.007-0.0070.0000.0000.0000.000
35A35ILE00.0240.01618.271-0.003-0.0030.0000.0000.0000.000
36A36ARG10.9580.99417.3130.0240.0240.0000.0000.0000.000
37A37ILE0-0.030-0.01615.809-0.028-0.0280.0000.0000.0000.000
38A38TYR00.0310.00912.5450.0190.0190.0000.0000.0000.000
39A39GLY0-0.077-0.04212.392-0.085-0.0850.0000.0000.0000.000
40A40ASP-1-0.920-0.9539.785-0.532-0.5320.0000.0000.0000.000
41A41LEU00.0140.0297.091-0.132-0.1320.0000.0000.0000.000
42A42GLU-1-0.806-0.8908.066-1.071-1.0710.0000.0000.0000.000
43A43LYS10.8300.92710.8300.3920.3920.0000.0000.0000.000
44A44ILE00.0520.02814.140-0.014-0.0140.0000.0000.0000.000
45A45ILE0-0.034-0.00417.0600.0340.0340.0000.0000.0000.000
46A46ILE0-0.0180.00318.904-0.004-0.0040.0000.0000.0000.000
47A47VAL00.007-0.00721.9710.0120.0120.0000.0000.0000.000
48A48GLY00.0740.01925.659-0.002-0.0020.0000.0000.0000.000
49A49LYS10.7930.91828.5260.0050.0050.0000.0000.0000.000
50A50TYR00.0220.02430.7130.0020.0020.0000.0000.0000.000
51A51VAL00.0310.01228.755-0.003-0.0030.0000.0000.0000.000
52A52ASN0-0.044-0.02030.810-0.004-0.0040.0000.0000.0000.000
53A53GLU-1-0.839-0.91833.116-0.030-0.0300.0000.0000.0000.000
54A54MET0-0.037-0.00527.706-0.001-0.0010.0000.0000.0000.000
55A55LEU00.0500.01226.693-0.005-0.0050.0000.0000.0000.000
56A56PRO00.0060.01328.110-0.008-0.0080.0000.0000.0000.000
57A57LEU0-0.038-0.02627.4770.0000.0000.0000.0000.0000.000
58A58LEU0-0.061-0.04222.978-0.005-0.0050.0000.0000.0000.000
59A59MET0-0.026-0.00524.076-0.009-0.0090.0000.0000.0000.000
60A60ASP-1-0.879-0.91421.705-0.144-0.1440.0000.0000.0000.000
61A61GLN0-0.047-0.02918.456-0.046-0.0460.0000.0000.0000.000
62A62ILE00.0250.02316.3710.0130.0130.0000.0000.0000.000
63A63VAL0-0.017-0.01620.0200.0060.0060.0000.0000.0000.000
64A64ILE0-0.013-0.00219.7020.0010.0010.0000.0000.0000.000
65A65TYR00.003-0.00323.5100.0110.0110.0000.0000.0000.000
66A66ASN00.041-0.00924.812-0.006-0.0060.0000.0000.0000.000
67A67PRO0-0.030-0.00926.7810.0060.0060.0000.0000.0000.000
68A68PHE00.022-0.00227.9030.0030.0030.0000.0000.0000.000
69A69TRP00.0600.03027.5970.0060.0060.0000.0000.0000.000
70A70ASN0-0.044-0.02328.5970.0060.0060.0000.0000.0000.000
71A71GLU-1-0.984-0.98229.005-0.007-0.0070.0000.0000.0000.000
72A72GLY0-0.009-0.02328.0030.0040.0040.0000.0000.0000.000
73A73ILE00.016-0.01322.018-0.002-0.0020.0000.0000.0000.000
74A74SER0-0.102-0.05121.7530.0000.0000.0000.0000.0000.000
75A75THR00.0480.01821.859-0.005-0.0050.0000.0000.0000.000
76A76SER0-0.036-0.04322.166-0.013-0.0130.0000.0000.0000.000
77A77LEU0-0.049-0.02715.868-0.007-0.0070.0000.0000.0000.000
78A78LYS10.8840.95317.6090.0020.0020.0000.0000.0000.000
79A79LEU0-0.059-0.00818.889-0.017-0.0170.0000.0000.0000.000
80A80GLY00.025-0.00517.242-0.020-0.0200.0000.0000.0000.000
81A81LEU0-0.0050.00012.001-0.018-0.0180.0000.0000.0000.000
82A82ARG10.9120.95214.4270.0640.0640.0000.0000.0000.000
83A83PHE0-0.015-0.00713.866-0.010-0.0100.0000.0000.0000.000
84A84PHE00.0370.03210.339-0.017-0.0170.0000.0000.0000.000
85A85LYS10.9370.98410.6100.1840.1840.0000.0000.0000.000
86A86ASP-1-0.927-0.97310.668-0.395-0.3950.0000.0000.0000.000
87A87TYR0-0.031-0.0366.939-0.138-0.1380.0000.0000.0000.000
88A88ASP-1-0.871-0.9492.252-6.365-4.4033.625-2.137-3.450-0.022
89A89ALA0-0.042-0.0274.262-0.423-0.1140.001-0.033-0.2780.000
90A90VAL00.0100.0126.012-0.117-0.1170.0000.0000.0000.000
91A91LEU0-0.006-0.0148.9490.0910.0910.0000.0000.0000.000
92A92VAL0-0.034-0.02110.527-0.141-0.1410.0000.0000.0000.000
93A93ALA00.0000.00414.1260.0060.0060.0000.0000.0000.000
94A94LEU00.0060.00116.480-0.016-0.0160.0000.0000.0000.000
95A95GLY00.0710.02120.265-0.006-0.0060.0000.0000.0000.000
96A96ASP-1-0.902-0.94022.5530.0230.0230.0000.0000.0000.000
97A97MET00.0030.00421.1370.0120.0120.0000.0000.0000.000
98A98PRO0-0.029-0.00421.2740.0020.0020.0000.0000.0000.000
99A99PHE0-0.017-0.02723.082-0.007-0.0070.0000.0000.0000.000
100A100VAL0-0.0120.03016.7840.0060.0060.0000.0000.0000.000
101A101THR0-0.001-0.03618.760-0.021-0.0210.0000.0000.0000.000
102A102LYS10.9170.92714.4350.1630.1630.0000.0000.0000.000
103A103GLU-1-0.802-0.89913.9660.1200.1200.0000.0000.0000.000
104A104ASP-1-0.760-0.82314.4290.1470.1470.0000.0000.0000.000
105A105VAL00.0380.00910.6170.0650.0650.0000.0000.0000.000
106A106ASN0-0.024-0.01010.0560.0490.0490.0000.0000.0000.000
107A107LYS10.8920.9449.762-0.075-0.0750.0000.0000.0000.000
108A108ILE00.0010.0049.8320.0970.0970.0000.0000.0000.000
109A109ILE00.0280.0104.6570.1750.284-0.001-0.004-0.1040.000
110A110ASN0-0.036-0.0195.8990.5560.5560.0000.0000.0000.000
111A111THR0-0.057-0.0247.939-0.031-0.0310.0000.0000.0000.000
112A112PHE0-0.037-0.0132.303-1.880-1.8153.364-0.756-2.6740.001
113A113LYS10.8820.9175.397-0.830-0.8300.0000.0000.0000.000
114A114PRO00.0480.0095.2360.0550.0550.0000.0000.0000.000
115A115ASN0-0.0010.0026.5910.0160.0160.0000.0000.0000.000
116A116CYS0-0.102-0.0247.770-0.020-0.0200.0000.0000.0000.000
117A117LYS10.9110.9497.886-0.052-0.0520.0000.0000.0000.000
118A118ALA00.001-0.0069.5990.0350.0350.0000.0000.0000.000
119A119VAL0-0.0190.0108.372-0.066-0.0660.0000.0000.0000.000
120A120ILE0-0.058-0.04511.184-0.032-0.0320.0000.0000.0000.000
121A121PRO00.0430.04114.111-0.015-0.0150.0000.0000.0000.000
122A122THR0-0.053-0.04716.245-0.026-0.0260.0000.0000.0000.000
123A123HIS00.0340.02419.747-0.012-0.0120.0000.0000.0000.000
124A124LYS10.9040.93922.893-0.090-0.0900.0000.0000.0000.000
125A125GLY00.0090.01624.920-0.009-0.0090.0000.0000.0000.000
126A126GLU-1-0.911-0.95524.5190.0930.0930.0000.0000.0000.000
127A127ARG10.9430.96419.218-0.156-0.1560.0000.0000.0000.000
128A128GLY00.010-0.00519.461-0.020-0.0200.0000.0000.0000.000
129A129ASN0-0.103-0.03517.0840.0400.0400.0000.0000.0000.000
130A130PRO00.0450.00913.750-0.021-0.0210.0000.0000.0000.000
131A131VAL00.024-0.01113.1530.0410.0410.0000.0000.0000.000
132A132LEU0-0.0190.0085.780-0.183-0.122-0.001-0.003-0.0570.000
133A133ILE0-0.001-0.0029.7930.0010.0010.0000.0000.0000.000
134A134SER00.0470.0115.9570.0810.0810.0000.0000.0000.000
135A135LYS10.8970.9306.1920.4940.4940.0000.0000.0000.000
136A136SER0-0.079-0.0408.245-0.038-0.0380.0000.0000.0000.000
137A137LEU00.003-0.01910.285-0.022-0.0220.0000.0000.0000.000
138A138PHE0-0.0100.0208.271-0.019-0.0190.0000.0000.0000.000
139A139ASN0-0.001-0.00612.960-0.010-0.0100.0000.0000.0000.000
140A140GLU-1-0.823-0.90615.5380.0280.0280.0000.0000.0000.000
141A141ILE0-0.022-0.00514.468-0.006-0.0060.0000.0000.0000.000
142A142GLU-1-0.869-0.96016.892-0.028-0.0280.0000.0000.0000.000
143A143LYS10.7870.88219.144-0.013-0.0130.0000.0000.0000.000
144A144LEU0-0.072-0.00919.599-0.002-0.0020.0000.0000.0000.000
145A145ARG10.9680.97722.524-0.014-0.0140.0000.0000.0000.000
146A146GLY00.1110.05725.9940.0060.0060.0000.0000.0000.000
147A147ASP-1-0.762-0.82726.2590.0250.0250.0000.0000.0000.000
148A148VAL0-0.077-0.01423.7020.0070.0070.0000.0000.0000.000
149A149GLY00.0800.02921.718-0.001-0.0010.0000.0000.0000.000
150A150ALA00.0920.02316.522-0.004-0.0040.0000.0000.0000.000
151A151ARG10.9530.97618.412-0.083-0.0830.0000.0000.0000.000
152A152VAL0-0.011-0.00620.242-0.001-0.0010.0000.0000.0000.000
153A153ILE00.0060.00216.265-0.005-0.0050.0000.0000.0000.000
154A154LEU00.0380.02414.2420.0010.0010.0000.0000.0000.000
155A155ASN0-0.087-0.04417.793-0.001-0.0010.0000.0000.0000.000
156A156LYS10.9330.97119.970-0.069-0.0690.0000.0000.0000.000
157A157ILE00.0140.02314.581-0.007-0.0070.0000.0000.0000.000
158A158LYS10.8830.92818.302-0.065-0.0650.0000.0000.0000.000
159A159ILE00.0600.02917.1980.0170.0170.0000.0000.0000.000
160A160GLU-1-0.846-0.90617.6700.1070.1070.0000.0000.0000.000
161A161GLU-1-0.872-0.93913.5020.0790.0790.0000.0000.0000.000
162A162LEU0-0.057-0.00412.5350.0450.0450.0000.0000.0000.000
163A164PHE00.0250.02013.3620.0500.0500.0000.0000.0000.000
164A165ILE00.0250.00312.9270.0160.0160.0000.0000.0000.000
165A166GLU-1-0.850-0.91416.4820.1380.1380.0000.0000.0000.000
166A167CYS0-0.078-0.01416.0940.0140.0140.0000.0000.0000.000
167A168SER0-0.009-0.04718.746-0.016-0.0160.0000.0000.0000.000
168A169GLU-1-0.830-0.93521.7000.0640.0640.0000.0000.0000.000
169A170GLY00.0160.00822.436-0.002-0.0020.0000.0000.0000.000
170A171VAL0-0.042-0.01617.881-0.001-0.0010.0000.0000.0000.000
171A172LEU0-0.065-0.02220.6380.0100.0100.0000.0000.0000.000
172A173ILE0-0.048-0.01423.823-0.008-0.0080.0000.0000.0000.000
173A174ASP-1-0.823-0.91024.5560.0490.0490.0000.0000.0000.000
174A175ILE0-0.037-0.04626.383-0.003-0.0030.0000.0000.0000.000
175A176ASP-1-0.825-0.92029.3310.0170.0170.0000.0000.0000.000
176A177LYS10.7590.90626.452-0.073-0.0730.0000.0000.0000.000
177A178LYS10.8790.95929.151-0.043-0.0430.0000.0000.0000.000