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: N1K4Q

Calculation Name: 3KR9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KR9

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

Base Structure: X-ray

Registration Date: 2023-06-19

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2569180.435515
FMO2-HF: Nuclear repulsion 2484256.321336
FMO2-HF: Total energy -84924.114179
FMO2-MP2: Total energy -85176.840956


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.
-23.594-16.55415.142-6.913-15.269-0.057
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 : -0.034 / 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].
3A3SER0-0.044-0.0313.8841.5883.099-0.016-0.798-0.6970.002
4A4LYS10.9460.9607.053-0.166-0.1660.0000.0000.0000.000
5A5ARG10.8510.9159.8200.3780.3780.0000.0000.0000.000
6A6LEU00.0090.0027.598-0.005-0.0050.0000.0000.0000.000
7A7GLU-1-0.786-0.8566.092-1.048-1.0480.0000.0000.0000.000
8A8LEU00.010-0.0048.3040.0090.0090.0000.0000.0000.000
9A9VAL0-0.0170.00211.4970.0270.0270.0000.0000.0000.000
10A10ALA00.0340.0098.3530.0410.0410.0000.0000.0000.000
11A11SER0-0.063-0.03510.3870.1010.1010.0000.0000.0000.000
12A12PHE00.0180.01212.5810.0730.0730.0000.0000.0000.000
13A13VAL0-0.044-0.01412.1310.0580.0580.0000.0000.0000.000
14A14SER0-0.008-0.01514.961-0.009-0.0090.0000.0000.0000.000
15A15GLN0-0.003-0.00915.156-0.066-0.0660.0000.0000.0000.000
16A16GLY0-0.043-0.02916.1490.0470.0470.0000.0000.0000.000
17A17ALA00.0050.01116.1370.0290.0290.0000.0000.0000.000
18A18ILE0-0.034-0.00516.006-0.011-0.0110.0000.0000.0000.000
19A19LEU00.0080.00610.6020.0020.0020.0000.0000.0000.000
20A20LEU0-0.0110.00014.2670.0190.0190.0000.0000.0000.000
21A21ASP-1-0.751-0.8309.330-1.334-1.3340.0000.0000.0000.000
22A22VAL0-0.007-0.01412.4810.0200.0200.0000.0000.0000.000
23A23GLY0-0.027-0.01413.7460.0030.0030.0000.0000.0000.000
24A24SER0-0.075-0.0508.181-0.153-0.1530.0000.0000.0000.000
25A25ASP-1-0.802-0.9057.927-1.295-1.2950.0000.0000.0000.000
26A26HIS10.7940.8945.3690.8030.8030.0000.0000.0000.000
27A27ALA00.0410.0185.2850.0020.0020.0000.0000.0000.000
28A28TYR0-0.038-0.0262.170-1.551-1.1735.798-1.646-4.529-0.004
29A29LEU00.0480.0362.958-1.514-1.4310.0940.719-0.896-0.009
30A30PRO00.0260.0005.7190.1620.1620.0000.0000.0000.000
31A31ILE0-0.031-0.0212.652-0.895-0.0731.439-0.386-1.875-0.003
32A32GLU-1-0.823-0.9032.170-17.438-13.4383.567-3.350-4.217-0.046
33A33LEU0-0.007-0.0054.3330.5990.7880.001-0.025-0.1650.000
34A34VAL0-0.019-0.0097.8240.3040.3040.0000.0000.0000.000
35A35GLU-1-0.852-0.9124.5054.1224.6990.022-0.140-0.460-0.001
36A36ARG10.6740.8065.4081.7401.7400.0000.0000.0000.000
37A37GLY0-0.0120.0028.8550.0730.0730.0000.0000.0000.000
38A38GLN00.0080.00310.500-0.081-0.0810.0000.0000.0000.000
39A39ILE0-0.024-0.00510.2650.0440.0440.0000.0000.0000.000
40A40LYS10.9060.96313.5920.2060.2060.0000.0000.0000.000
41A41SER0-0.041-0.03713.2320.0890.0890.0000.0000.0000.000
42A42ALA0-0.0050.00910.556-0.057-0.0570.0000.0000.0000.000
43A43ILE0-0.0060.00812.6870.0770.0770.0000.0000.0000.000
44A44ALA00.0280.0219.475-0.086-0.0860.0000.0000.0000.000
45A45GLY00.0310.00711.5440.1020.1020.0000.0000.0000.000
46A46GLH0-0.076-0.06510.440-0.042-0.0420.0000.0000.0000.000
47A47VAL00.0310.02415.2710.0480.0480.0000.0000.0000.000
48A48VAL0-0.005-0.00816.9540.0380.0380.0000.0000.0000.000
49A49GLU-1-0.757-0.88816.469-0.196-0.1960.0000.0000.0000.000
50A50GLY0-0.0090.00915.7770.0030.0030.0000.0000.0000.000
51A51PRO00.014-0.01312.192-0.004-0.0040.0000.0000.0000.000
52A52TYR00.0200.02711.488-0.067-0.0670.0000.0000.0000.000
53A53GLN00.005-0.01712.1800.0100.0100.0000.0000.0000.000
54A54SER0-0.040-0.0059.337-0.033-0.0330.0000.0000.0000.000
55A55ALA00.0470.0277.603-0.020-0.0200.0000.0000.0000.000
56A56VAL0-0.0010.0038.0040.0670.0670.0000.0000.0000.000
57A57LYS10.8820.9519.7280.1070.1070.0000.0000.0000.000
58A58ASN0-0.018-0.0174.1400.2450.396-0.001-0.010-0.1400.000
59A59VAL00.0440.0245.7270.4050.4050.0000.0000.0000.000
60A60GLU-1-0.903-0.9567.3960.2650.2650.0000.0000.0000.000
61A61ALA0-0.042-0.0137.0900.0580.0580.0000.0000.0000.000
62A62HIS10.8000.8732.635-8.040-8.7114.238-1.277-2.2900.004
63A63GLY00.0140.0237.206-0.084-0.0840.0000.0000.0000.000
64A64LEU0-0.038-0.0246.471-0.150-0.1500.0000.0000.0000.000
65A65LYS10.9080.93410.255-0.289-0.2890.0000.0000.0000.000
66A66GLU-1-0.921-0.95712.8820.0080.0080.0000.0000.0000.000
67A67LYS10.8630.92911.763-0.082-0.0820.0000.0000.0000.000
68A68ILE00.0070.0187.406-0.077-0.0770.0000.0000.0000.000
69A69GLN00.0680.05411.5440.0520.0520.0000.0000.0000.000
70A70VAL0-0.008-0.00710.286-0.088-0.0880.0000.0000.0000.000
71A71ARG10.7000.80613.2330.2880.2880.0000.0000.0000.000
72A72LEU00.0100.01016.579-0.040-0.0400.0000.0000.0000.000
73A73ALA00.0100.00618.4120.0310.0310.0000.0000.0000.000
74A74ASN0-0.007-0.01518.977-0.053-0.0530.0000.0000.0000.000
75A75GLY00.0300.00519.6510.0130.0130.0000.0000.0000.000
76A76LEU00.0200.02119.559-0.021-0.0210.0000.0000.0000.000
77A77ALA0-0.0120.00021.6790.0180.0180.0000.0000.0000.000
78A78ALA0-0.047-0.01417.2220.0110.0110.0000.0000.0000.000
79A79PHE00.005-0.00618.842-0.012-0.0120.0000.0000.0000.000
80A80GLU-1-0.800-0.89220.764-0.156-0.1560.0000.0000.0000.000
81A81GLU-1-0.816-0.91223.415-0.180-0.1800.0000.0000.0000.000
82A82THR0-0.045-0.02424.4270.0040.0040.0000.0000.0000.000
83A83ASP-1-0.790-0.86219.772-0.200-0.2000.0000.0000.0000.000
84A84GLN0-0.072-0.03920.665-0.005-0.0050.0000.0000.0000.000
85A85VAL0-0.021-0.01217.618-0.007-0.0070.0000.0000.0000.000
86A86SER00.0080.00419.2520.0010.0010.0000.0000.0000.000
87A87VAL0-0.003-0.00516.3610.0000.0000.0000.0000.0000.000
88A88ILE00.003-0.00216.368-0.027-0.0270.0000.0000.0000.000
89A89THR0-0.021-0.03512.1300.0200.0200.0000.0000.0000.000
90A90ILE00.0160.00014.806-0.004-0.0040.0000.0000.0000.000
91A91ALA00.0280.00613.0740.0420.0420.0000.0000.0000.000
92A92GLY00.0210.02615.171-0.018-0.0180.0000.0000.0000.000
93A93MET00.0050.01816.0730.0520.0520.0000.0000.0000.000
94A94GLY00.0140.01319.4130.0110.0110.0000.0000.0000.000
95A95GLY00.0560.01723.100-0.009-0.0090.0000.0000.0000.000
96A96ARG10.8940.92424.4880.1480.1480.0000.0000.0000.000
97A97LEU0-0.031-0.00521.5990.0110.0110.0000.0000.0000.000
98A98ILE00.0220.01319.624-0.003-0.0030.0000.0000.0000.000
99A99ALA00.0370.01722.4480.0010.0010.0000.0000.0000.000
100A100ARG10.7930.88025.8990.1950.1950.0000.0000.0000.000
101A101ILE0-0.009-0.01220.0190.0070.0070.0000.0000.0000.000
102A102LEU00.0050.00221.751-0.001-0.0010.0000.0000.0000.000
103A103GLU-1-0.816-0.91224.667-0.145-0.1450.0000.0000.0000.000
104A104GLU-1-0.857-0.91525.991-0.185-0.1850.0000.0000.0000.000
105A105GLY00.0040.00325.4480.0050.0050.0000.0000.0000.000
106A106LEU00.0100.01526.485-0.004-0.0040.0000.0000.0000.000
107A107GLY0-0.049-0.03028.3260.0020.0020.0000.0000.0000.000
108A108LYS10.8020.89324.4840.2030.2030.0000.0000.0000.000
109A109LEU0-0.030-0.02023.021-0.012-0.0120.0000.0000.0000.000
110A110ALA0-0.027-0.00925.967-0.003-0.0030.0000.0000.0000.000
111A111ASN0-0.072-0.03426.5140.0100.0100.0000.0000.0000.000
112A112VAL0-0.0250.00521.166-0.011-0.0110.0000.0000.0000.000
113A113GLU-1-0.871-0.90121.506-0.272-0.2720.0000.0000.0000.000
114A114ARG10.7880.86518.6630.3190.3190.0000.0000.0000.000
115A115LEU00.0020.00519.720-0.032-0.0320.0000.0000.0000.000
116A116ILE0-0.012-0.00715.4900.0220.0220.0000.0000.0000.000
117A117LEU00.003-0.00217.071-0.053-0.0530.0000.0000.0000.000
118A118GLN0-0.004-0.00215.123-0.010-0.0100.0000.0000.0000.000
119A119PRO00.0210.01017.929-0.022-0.0220.0000.0000.0000.000
120A120ASN0-0.063-0.06018.507-0.012-0.0120.0000.0000.0000.000
121A121ASN0-0.022-0.01620.9460.0240.0240.0000.0000.0000.000
122A122ARG10.7500.84224.7470.1280.1280.0000.0000.0000.000
123A123GLU-1-0.719-0.85924.102-0.181-0.1810.0000.0000.0000.000
124A124ASP-1-0.728-0.84526.362-0.145-0.1450.0000.0000.0000.000
125A125ASP-1-0.772-0.85829.337-0.143-0.1430.0000.0000.0000.000
126A126LEU0-0.024-0.00423.1020.0020.0020.0000.0000.0000.000
127A127ARG10.7960.88625.4130.1750.1750.0000.0000.0000.000
128A128ILE0-0.021-0.00529.2280.0050.0050.0000.0000.0000.000
129A129TRP0-0.058-0.04326.826-0.002-0.0020.0000.0000.0000.000
130A130LEU00.009-0.00825.1310.0010.0010.0000.0000.0000.000
131A131GLN00.009-0.00329.3470.0100.0100.0000.0000.0000.000
132A132ASP-1-0.908-0.94532.722-0.113-0.1130.0000.0000.0000.000
133A133HIS10.7820.89430.6910.1540.1540.0000.0000.0000.000
134A134GLY0-0.0040.01831.658-0.003-0.0030.0000.0000.0000.000
135A135PHE0-0.028-0.00826.527-0.006-0.0060.0000.0000.0000.000
136A136GLN0-0.020-0.02628.7620.0160.0160.0000.0000.0000.000
137A137ILE0-0.017-0.03624.795-0.015-0.0150.0000.0000.0000.000
138A138VAL0-0.017-0.00923.5390.0160.0160.0000.0000.0000.000
139A139ALA00.0120.00721.7380.0090.0090.0000.0000.0000.000
140A140GLU-1-0.737-0.86021.563-0.190-0.1900.0000.0000.0000.000
141A141SER0-0.015-0.01418.0330.0100.0100.0000.0000.0000.000
142A142ILE0-0.017-0.00119.636-0.024-0.0240.0000.0000.0000.000
143A143LEU0-0.0140.01013.9830.0230.0230.0000.0000.0000.000
144A144GLU-1-0.829-0.92317.253-0.053-0.0530.0000.0000.0000.000
145A145GLU-1-0.839-0.92211.017-0.250-0.2500.0000.0000.0000.000
146A146ALA0-0.001-0.01314.501-0.028-0.0280.0000.0000.0000.000
147A147GLY00.0350.03016.192-0.009-0.0090.0000.0000.0000.000
148A148LYS10.8870.95218.1430.1650.1650.0000.0000.0000.000
149A149PHE00.0550.03018.393-0.006-0.0060.0000.0000.0000.000
150A150TYR0-0.048-0.03116.190-0.032-0.0320.0000.0000.0000.000
151A151GLU-1-0.746-0.84718.949-0.165-0.1650.0000.0000.0000.000
152A152ILE0-0.007-0.00614.493-0.041-0.0410.0000.0000.0000.000
153A153LEU0-0.0070.00218.8300.0360.0360.0000.0000.0000.000
154A154VAL00.0150.01018.635-0.044-0.0440.0000.0000.0000.000
155A155VAL0-0.015-0.01021.1600.0350.0350.0000.0000.0000.000
156A156GLU-1-0.746-0.85423.213-0.253-0.2530.0000.0000.0000.000
157A157ALA00.0620.03425.8150.0110.0110.0000.0000.0000.000
158A158GLY0-0.007-0.00729.0190.0060.0060.0000.0000.0000.000
159A159GLN0-0.032-0.01232.3200.0000.0000.0000.0000.0000.000
160A160MET00.0240.04529.919-0.004-0.0040.0000.0000.0000.000
161A161LYS10.8630.91834.4580.1050.1050.0000.0000.0000.000
162A162LEU0-0.0030.01231.0550.0010.0010.0000.0000.0000.000
163A163SER0-0.022-0.04035.5110.0060.0060.0000.0000.0000.000
164A164ALA00.029-0.01435.655-0.006-0.0060.0000.0000.0000.000
165A165SER00.0580.03234.621-0.003-0.0030.0000.0000.0000.000
166A166ASP-1-0.793-0.86532.027-0.108-0.1080.0000.0000.0000.000
167A167VAL0-0.015-0.00530.752-0.012-0.0120.0000.0000.0000.000
168A168ARG10.7480.85027.5390.1310.1310.0000.0000.0000.000
169A169PHE0-0.0050.00229.366-0.004-0.0040.0000.0000.0000.000
170A170GLY00.0900.04927.470-0.002-0.0020.0000.0000.0000.000
171A171PRO0-0.0260.00528.1430.0090.0090.0000.0000.0000.000
172A172PHE0-0.051-0.02525.5600.0070.0070.0000.0000.0000.000
173A173LEU0-0.002-0.01222.4890.0080.0080.0000.0000.0000.000
174A174SER0-0.035-0.03226.4790.0120.0120.0000.0000.0000.000
175A175LYS10.9260.96529.1940.0980.0980.0000.0000.0000.000
176A176GLU-1-0.880-0.91123.492-0.108-0.1080.0000.0000.0000.000
177A177VAL0-0.017-0.00527.6950.0090.0090.0000.0000.0000.000
178A178SER0-0.020-0.02723.5780.0120.0120.0000.0000.0000.000
179A179PRO00.005-0.02023.9550.0000.0000.0000.0000.0000.000
180A180VAL00.0280.02219.9290.0010.0010.0000.0000.0000.000
181A181PHE00.0030.01723.303-0.007-0.0070.0000.0000.0000.000
182A182VAL00.0290.01225.8360.0000.0000.0000.0000.0000.000
183A183GLN0-0.092-0.05022.2580.0020.0020.0000.0000.0000.000
184A184LYS10.7880.88623.9090.1620.1620.0000.0000.0000.000
185A185TRP00.022-0.00126.3520.0010.0010.0000.0000.0000.000
186A186GLN00.0420.02529.9710.0010.0010.0000.0000.0000.000
187A187LYS10.8340.89826.6850.0530.0530.0000.0000.0000.000
188A188GLU-1-0.842-0.91329.047-0.104-0.1040.0000.0000.0000.000
189A189ALA00.0360.02031.3710.0020.0020.0000.0000.0000.000
190A190GLU-1-0.837-0.90031.681-0.045-0.0450.0000.0000.0000.000
191A191LYS10.7810.87927.9170.1020.1020.0000.0000.0000.000
192A192LEU0-0.0060.00334.3240.0010.0010.0000.0000.0000.000
193A193GLU-1-0.797-0.89336.930-0.044-0.0440.0000.0000.0000.000
194A194PHE0-0.022-0.00137.0850.0030.0030.0000.0000.0000.000
195A195ALA0-0.044-0.03037.5670.0020.0020.0000.0000.0000.000
196A196LEU00.000-0.00939.5200.0010.0010.0000.0000.0000.000
197A197GLY0-0.0030.00942.0440.0020.0020.0000.0000.0000.000
198A198GLN0-0.084-0.02639.1360.0030.0030.0000.0000.0000.000
199A199ILE00.0100.01543.0980.0020.0020.0000.0000.0000.000
200A200PRO00.0230.03445.8380.0000.0000.0000.0000.0000.000
201A201GLU-1-0.852-0.94149.442-0.036-0.0360.0000.0000.0000.000
202A202LYS10.8470.91651.7150.0340.0340.0000.0000.0000.000
203A203ASN00.010-0.00148.3140.0000.0000.0000.0000.0000.000
204A204LEU00.0350.01749.302-0.001-0.0010.0000.0000.0000.000
205A205GLU-1-0.856-0.93348.782-0.046-0.0460.0000.0000.0000.000
206A206GLU-1-0.928-0.95144.429-0.056-0.0560.0000.0000.0000.000
207A207ARG10.7940.86444.2830.0380.0380.0000.0000.0000.000
208A208GLN0-0.026-0.02344.6060.0010.0010.0000.0000.0000.000
209A209VAL00.0250.02440.806-0.003-0.0030.0000.0000.0000.000
210A210LEU0-0.040-0.01539.239-0.006-0.0060.0000.0000.0000.000
211A211VAL00.0330.01240.370-0.001-0.0010.0000.0000.0000.000
212A212ASP-1-0.839-0.91041.783-0.060-0.0600.0000.0000.0000.000
213A213LYS10.8210.90336.1200.0780.0780.0000.0000.0000.000
214A214ILE0-0.0010.00537.376-0.002-0.0020.0000.0000.0000.000
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