Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: X1NVZ

Calculation Name: 1KR4-A-Xray18

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KR4

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0E6

Base Structure: X-ray

Registration Date: 2018-06-04

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 192
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1117672.02246
FMO2-HF: Nuclear repulsion 1065494.826667
FMO2-HF: Total energy -52177.195793
FMO2-MP2: Total energy -52327.737563


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:ACE)


Summations of interaction energy for fragment #1(A:-1:ACE)
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.
1.9263.1820.101-0.627-0.730
Interaction energy analysis for fragmet #1(A:-1:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.008
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].
3A1LEU00.0440.0413.8471.0141.832-0.011-0.404-0.4020.000
4A2TYR00.0110.0136.7860.3780.3780.0000.0000.0000.000
5A3PHE00.0120.0234.855-0.292-0.2920.0000.0000.0000.000
6A4MET00.1020.0507.0210.0490.0490.0000.0000.0000.000
7A5GLY0-0.037-0.0048.5220.0060.0060.0000.0000.0000.000
8A6HIS00.0400.0149.9700.0530.0530.0000.0000.0000.000
9A7MET0-0.018-0.00713.323-0.001-0.0010.0000.0000.0000.000
10A8ILE00.0320.03015.536-0.015-0.0150.0000.0000.0000.000
11A9LEU0-0.027-0.01119.1140.0000.0000.0000.0000.0000.000
12A10VAL00.0150.01321.750-0.003-0.0030.0000.0000.0000.000
13A11TYR00.0150.00325.294-0.002-0.0020.0000.0000.0000.000
14A12SER0-0.013-0.02228.2760.0030.0030.0000.0000.0000.000
15A13THR0-0.0210.00431.851-0.002-0.0020.0000.0000.0000.000
16A14PHE00.001-0.02032.2070.0030.0030.0000.0000.0000.000
17A15PRO00.0540.03137.446-0.002-0.0020.0000.0000.0000.000
18A16ASN0-0.014-0.01239.7170.0000.0000.0000.0000.0000.000
19A17GLU-1-0.806-0.87636.9760.0020.0020.0000.0000.0000.000
20A18GLU-1-0.807-0.90837.2120.0070.0070.0000.0000.0000.000
21A19LYS10.8950.95537.900-0.014-0.0140.0000.0000.0000.000
22A20ALA00.0240.01733.8650.0030.0030.0000.0000.0000.000
23A21LEU0-0.006-0.00433.1710.0030.0030.0000.0000.0000.000
24A22GLU-1-0.892-0.92333.6680.0240.0240.0000.0000.0000.000
25A23ILE00.006-0.00532.1780.0040.0040.0000.0000.0000.000
26A24GLY00.0410.02230.0350.0040.0040.0000.0000.0000.000
27A25ARG10.8710.92629.602-0.026-0.0260.0000.0000.0000.000
28A26LYS10.7960.89131.165-0.024-0.0240.0000.0000.0000.000
29A27LEU00.0220.00927.8120.0050.0050.0000.0000.0000.000
30A28LEU0-0.042-0.01625.0700.0070.0070.0000.0000.0000.000
31A29GLU-1-0.848-0.90527.3680.0470.0470.0000.0000.0000.000
32A30LYS10.8440.92229.097-0.053-0.0530.0000.0000.0000.000
33A31ARG10.9020.93921.994-0.102-0.1020.0000.0000.0000.000
34A32LEU00.0390.01223.9090.0080.0080.0000.0000.0000.000
35A33ILE0-0.0310.02122.6530.0000.0000.0000.0000.0000.000
36A34ALA00.0400.03619.3960.0030.0030.0000.0000.0000.000
37A35CYS0-0.026-0.01021.404-0.010-0.0100.0000.0000.0000.000
38A36PHE00.0970.11223.3010.0010.0010.0000.0000.0000.000
39A37ASN0-0.065-0.03324.196-0.011-0.0110.0000.0000.0000.000
40A38ALA00.0530.02427.1260.0000.0000.0000.0000.0000.000
41A39PHE0-0.023-0.01528.930-0.003-0.0030.0000.0000.0000.000
42A40GLU-1-0.812-0.88033.067-0.007-0.0070.0000.0000.0000.000
43A41ILE0-0.046-0.02434.518-0.003-0.0030.0000.0000.0000.000
44A42ARG10.8840.93137.5100.0130.0130.0000.0000.0000.000
45A43SER0-0.022-0.04839.371-0.002-0.0020.0000.0000.0000.000
46A44GLY00.0480.01540.9050.0000.0000.0000.0000.0000.000
47A45TYR0-0.084-0.03741.9540.0000.0000.0000.0000.0000.000
48A46TRP00.0070.00944.0060.0000.0000.0000.0000.0000.000
49A47TRP00.0370.01746.3790.0010.0010.0000.0000.0000.000
50A48LYS10.9210.96948.912-0.003-0.0030.0000.0000.0000.000
51A49GLY00.0330.01751.4480.0000.0000.0000.0000.0000.000
52A50GLU-1-0.941-0.95951.793-0.003-0.0030.0000.0000.0000.000
53A51ILE0-0.0030.00647.0850.0000.0000.0000.0000.0000.000
54A52VAL0-0.0130.01146.5190.0000.0000.0000.0000.0000.000
55A53GLN00.0210.00644.172-0.001-0.0010.0000.0000.0000.000
56A54ASP-1-0.778-0.88643.1480.0010.0010.0000.0000.0000.000
57A55LYS10.8870.93642.1430.0050.0050.0000.0000.0000.000
58A56GLU-1-0.751-0.81338.5430.0020.0020.0000.0000.0000.000
59A57TRP00.0390.02633.905-0.002-0.0020.0000.0000.0000.000
60A58ALA0-0.0050.00631.9760.0030.0030.0000.0000.0000.000
61A59ALA00.007-0.01429.7240.0000.0000.0000.0000.0000.000
62A60ILE0-0.045-0.00423.3800.0010.0010.0000.0000.0000.000
63A61PHE00.020-0.04124.7520.0010.0010.0000.0000.0000.000
64A62LYS10.9220.96419.2970.0050.0050.0000.0000.0000.000
65A63THR00.046-0.00619.5440.0110.0110.0000.0000.0000.000
66A64THR0-0.037-0.02015.354-0.010-0.0100.0000.0000.0000.000
67A65GLU-1-0.741-0.86216.2450.1090.1090.0000.0000.0000.000
68A66GLU-1-0.807-0.88716.5450.1870.1870.0000.0000.0000.000
69A67LYS10.8740.96920.123-0.128-0.1280.0000.0000.0000.000
70A68GLU-1-0.828-0.90122.1520.0440.0440.0000.0000.0000.000
71A69LYS10.8870.94623.896-0.070-0.0700.0000.0000.0000.000
72A70GLU-1-0.780-0.86425.3210.0890.0890.0000.0000.0000.000
73A71LEU00.0190.02124.596-0.007-0.0070.0000.0000.0000.000
74A72TYR00.009-0.00826.219-0.009-0.0090.0000.0000.0000.000
75A73GLU-1-0.783-0.84429.7850.0520.0520.0000.0000.0000.000
76A74GLU-1-0.695-0.82230.6140.0430.0430.0000.0000.0000.000
77A75LEU0-0.016-0.01229.122-0.004-0.0040.0000.0000.0000.000
78A76ARG10.7860.88132.810-0.026-0.0260.0000.0000.0000.000
79A77LYS10.8800.96235.257-0.043-0.0430.0000.0000.0000.000
80A78LEU0-0.039-0.01833.672-0.003-0.0030.0000.0000.0000.000
81A79HIS00.0170.03134.779-0.002-0.0020.0000.0000.0000.000
82A80PRO0-0.0250.00837.8030.0000.0000.0000.0000.0000.000
83A81TYR0-0.024-0.01838.868-0.001-0.0010.0000.0000.0000.000
84A82GLU-1-0.836-0.91040.7000.0130.0130.0000.0000.0000.000
85A83THR0-0.040-0.03739.6870.0020.0020.0000.0000.0000.000
86A84PRO0-0.044-0.01236.077-0.002-0.0020.0000.0000.0000.000
87A85ALA00.0070.01334.1960.0010.0010.0000.0000.0000.000
88A86ILE00.001-0.00729.7890.0010.0010.0000.0000.0000.000
89A87PHE0-0.0180.00227.7320.0000.0000.0000.0000.0000.000
90A88THR00.0190.00722.702-0.002-0.0020.0000.0000.0000.000
91A89LEU0-0.042-0.01922.974-0.005-0.0050.0000.0000.0000.000
92A90LYS10.8740.93816.7360.0250.0250.0000.0000.0000.000
93A91VAL0-0.028-0.01314.541-0.017-0.0170.0000.0000.0000.000
94A92GLU-1-0.849-0.91215.057-0.057-0.0570.0000.0000.0000.000
95A93ASN0-0.003-0.01810.426-0.062-0.0620.0000.0000.0000.000
96A94ILE0-0.0200.0019.7000.0310.0310.0000.0000.0000.000
97A95LEU0-0.0190.0029.219-0.064-0.0640.0000.0000.0000.000
98A96THR00.015-0.0354.5360.1800.224-0.001-0.008-0.0360.000
99A97GLU-1-0.846-0.8967.5690.1190.1190.0000.0000.0000.000
100A98TYR00.0060.0119.8740.0430.0430.0000.0000.0000.000
101A99MET0-0.0230.0069.2520.0280.0280.0000.0000.0000.000
102A100ASN00.0190.0087.3860.1140.1140.0000.0000.0000.000
103A101TRP00.0450.03011.389-0.013-0.0130.0000.0000.0000.000
104A102LEU0-0.027-0.00714.225-0.010-0.0100.0000.0000.0000.000
105A103ARG10.9520.9898.795-0.590-0.5900.0000.0000.0000.000
106A104GLU-1-0.842-0.90614.4840.2050.2050.0000.0000.0000.000
107A105SER00.0240.00717.071-0.023-0.0230.0000.0000.0000.000
108A106VAL0-0.0070.01318.148-0.015-0.0150.0000.0000.0000.000
109A107LEU0-0.081-0.01218.7970.0020.0020.0000.0000.0000.000
110A108GLY0-0.022-0.01320.772-0.010-0.0100.0000.0000.0000.000
111A109SER-1-0.818-0.89524.4560.0800.0800.0000.0000.0000.000
112A200HOH0-0.040-0.03621.313-0.001-0.0010.0000.0000.0000.000
113A201HOH0-0.008-0.0078.4080.0250.0250.0000.0000.0000.000
114A202HOH00.0450.03722.3120.0000.0000.0000.0000.0000.000
115A204HOH0-0.026-0.01843.3210.0000.0000.0000.0000.0000.000
116A205HOH00.0120.01638.7720.0000.0000.0000.0000.0000.000
117A206HOH0-0.049-0.02637.579-0.001-0.0010.0000.0000.0000.000
118A207HOH0-0.035-0.04124.224-0.004-0.0040.0000.0000.0000.000
119A208HOH0-0.013-0.00136.4340.0000.0000.0000.0000.0000.000
120A209HOH00.0240.01641.3240.0000.0000.0000.0000.0000.000
121A210HOH0-0.026-0.02217.367-0.007-0.0070.0000.0000.0000.000
122A211HOH0-0.062-0.05332.672-0.001-0.0010.0000.0000.0000.000
123A212HOH00.0310.02745.0000.0010.0010.0000.0000.0000.000
124A214HOH0-0.020-0.01639.3370.0000.0000.0000.0000.0000.000
125A215HOH0-0.007-0.00632.5720.0000.0000.0000.0000.0000.000
126A216HOH0-0.040-0.05238.2140.0010.0010.0000.0000.0000.000
127A217HOH0-0.034-0.02434.353-0.001-0.0010.0000.0000.0000.000
128A218HOH0-0.042-0.03019.425-0.005-0.0050.0000.0000.0000.000
129A219HOH00.005-0.00636.6860.0000.0000.0000.0000.0000.000
130A220HOH0-0.053-0.03543.4550.0000.0000.0000.0000.0000.000
131A221HOH00.003-0.00717.431-0.008-0.0080.0000.0000.0000.000
132A222HOH00.002-0.00412.7380.0080.0080.0000.0000.0000.000
133A223HOH00.0350.02042.2410.0010.0010.0000.0000.0000.000
134A224HOH0-0.037-0.01617.657-0.005-0.0050.0000.0000.0000.000
135A225HOH0-0.043-0.03040.3040.0000.0000.0000.0000.0000.000
136A226HOH0-0.066-0.04530.787-0.002-0.0020.0000.0000.0000.000
137A227HOH0-0.039-0.02938.3090.0000.0000.0000.0000.0000.000
138A229HOH0-0.024-0.02012.3840.0010.0010.0000.0000.0000.000
139A230HOH0-0.048-0.03839.7620.0000.0000.0000.0000.0000.000
140A231HOH0-0.038-0.03713.568-0.005-0.0050.0000.0000.0000.000
141A232HOH00.0270.02050.2940.0000.0000.0000.0000.0000.000
142A233HOH0-0.036-0.02919.663-0.003-0.0030.0000.0000.0000.000
143A234HOH0-0.064-0.05421.2690.0020.0020.0000.0000.0000.000
144A235HOH0-0.036-0.02945.6650.0000.0000.0000.0000.0000.000
145A237HOH00.0220.01548.9880.0000.0000.0000.0000.0000.000
146A239HOH0-0.057-0.03638.9420.0000.0000.0000.0000.0000.000
147A241HOH00.0170.00553.0970.0000.0000.0000.0000.0000.000
148A245HOH0-0.037-0.02435.413-0.001-0.0010.0000.0000.0000.000
149A246HOH0-0.032-0.01721.141-0.004-0.0040.0000.0000.0000.000
150A247HOH0-0.0070.0012.9500.6711.0650.113-0.215-0.2920.000
151A248HOH0-0.058-0.06824.335-0.001-0.0010.0000.0000.0000.000
152A250HOH0-0.034-0.01940.3980.0000.0000.0000.0000.0000.000
153A252HOH00.0170.00946.3080.0000.0000.0000.0000.0000.000
154A254HOH0-0.038-0.03238.9730.0000.0000.0000.0000.0000.000
155A255HOH0-0.036-0.02930.320-0.001-0.0010.0000.0000.0000.000
156A258HOH0-0.048-0.03350.2860.0000.0000.0000.0000.0000.000
157A259HOH0-0.031-0.03316.2390.0000.0000.0000.0000.0000.000
158A260HOH0-0.023-0.00945.1500.0000.0000.0000.0000.0000.000
159A264HOH00.0290.01821.8760.0020.0020.0000.0000.0000.000
160A266HOH0-0.022-0.02054.9640.0000.0000.0000.0000.0000.000
161A267HOH0-0.0050.01117.641-0.012-0.0120.0000.0000.0000.000
162A268HOH0-0.036-0.02932.9180.0010.0010.0000.0000.0000.000
163A269HOH0-0.056-0.03313.1250.0270.0270.0000.0000.0000.000
164A270HOH00.005-0.0077.026-0.019-0.0190.0000.0000.0000.000
165A271HOH00.002-0.00853.9680.0000.0000.0000.0000.0000.000
166A273HOH0-0.001-0.02017.716-0.007-0.0070.0000.0000.0000.000
167A274HOH00.0270.01639.3500.0000.0000.0000.0000.0000.000
168A277HOH0-0.035-0.02331.031-0.002-0.0020.0000.0000.0000.000
169A278HOH0-0.030-0.04510.905-0.024-0.0240.0000.0000.0000.000
170A279HOH0-0.045-0.03832.4990.0010.0010.0000.0000.0000.000
171A280HOH0-0.030-0.01822.4490.0020.0020.0000.0000.0000.000
172A281HOH0-0.171-0.08823.7710.0010.0010.0000.0000.0000.000
173A282HOH0-0.0140.00117.179-0.009-0.0090.0000.0000.0000.000
174A283HOH00.000-0.00142.1380.0000.0000.0000.0000.0000.000
175A284HOH0-0.021-0.02441.4010.0000.0000.0000.0000.0000.000
176A285HOH0-0.008-0.01717.5520.0080.0080.0000.0000.0000.000
177A286HOH0-0.021-0.00344.5000.0000.0000.0000.0000.0000.000
178A288HOH00.0170.00533.3030.0000.0000.0000.0000.0000.000
179A290HOH0-0.025-0.01842.1950.0000.0000.0000.0000.0000.000
180A292HOH00.0260.01543.9820.0000.0000.0000.0000.0000.000
181A293HOH0-0.014-0.01612.5930.0300.0300.0000.0000.0000.000
182A294HOH0-0.031-0.03126.0020.0040.0040.0000.0000.0000.000
183A302HOH0-0.073-0.06015.676-0.007-0.0070.0000.0000.0000.000
184A306HOH0-0.041-0.02926.530-0.001-0.0010.0000.0000.0000.000
185A307HOH0-0.024-0.0246.181-0.008-0.0080.0000.0000.0000.000
186A308HOH00.003-0.00831.303-0.001-0.0010.0000.0000.0000.000
187A310HOH00.0090.0029.6350.0020.0020.0000.0000.0000.000
188A312HOH0-0.076-0.04840.199-0.001-0.0010.0000.0000.0000.000
189A313HOH0-0.018-0.02030.237-0.001-0.0010.0000.0000.0000.000
190A315HOH0-0.044-0.03435.369-0.001-0.0010.0000.0000.0000.000
191A318HOH00.0280.02140.9700.0000.0000.0000.0000.0000.000
192A322HOH0-0.018-0.01148.6950.0000.0000.0000.0000.0000.000