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: P9ML2

Calculation Name: 1KMZ-A-Xray30

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KMZ

Chain ID: A

ChEMBL ID:

UniProt ID: O05205

Base Structure: X-ray

Registration Date: 2018-09-06

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 233
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1340060.905876
FMO2-HF: Nuclear repulsion 1283240.882669
FMO2-HF: Total energy -56820.023207
FMO2-MP2: Total energy -56986.533613


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:2:ACE)


Summations of interaction energy for fragment #1(A:2: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.
13.032-1.77619.491-1.329-3.355-0.012
Interaction energy analysis for fragmet #1(A:2:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : -0.055
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].
3A4ARG10.8080.9083.6301.2051.785-0.027-0.012-0.541-0.002
4A5ILE00.0250.0206.7820.0940.0940.0000.0000.0000.000
5A6SER0-0.0150.00210.3660.1230.1230.0000.0000.0000.000
6A7LEU00.020-0.00211.8780.0800.0800.0000.0000.0000.000
7A8PHE00.0100.02415.260-0.057-0.0570.0000.0000.0000.000
8A9ALA0-0.014-0.00318.0120.0290.0290.0000.0000.0000.000
9A10VAL00.0130.00120.531-0.006-0.0060.0000.0000.0000.000
10A11VAL00.0280.02824.1520.0090.0090.0000.0000.0000.000
11A12VAL0-0.055-0.01726.2200.0040.0040.0000.0000.0000.000
12A13GLU-1-0.789-0.89629.578-0.070-0.0700.0000.0000.0000.000
13A14ASP-1-0.843-0.90232.925-0.044-0.0440.0000.0000.0000.000
14A15MET00.0140.01827.088-0.004-0.0040.0000.0000.0000.000
15A16ALA00.0400.02331.850-0.002-0.0020.0000.0000.0000.000
16A17LYS10.9000.94534.6840.0530.0530.0000.0000.0000.000
17A18SER00.0050.00529.398-0.001-0.0010.0000.0000.0000.000
18A19LEU00.0430.01328.348-0.002-0.0020.0000.0000.0000.000
19A20GLU-1-0.858-0.87031.510-0.041-0.0410.0000.0000.0000.000
20A21PHE0-0.013-0.00331.2760.0030.0030.0000.0000.0000.000
21A22TYR00.0650.02828.102-0.002-0.0020.0000.0000.0000.000
22A23ARG10.8630.92130.9080.0450.0450.0000.0000.0000.000
23A24LYS10.7910.90432.6640.0480.0480.0000.0000.0000.000
24A25LEU0-0.048-0.01230.9070.0020.0020.0000.0000.0000.000
25A26GLY00.0050.02330.808-0.004-0.0040.0000.0000.0000.000
26A27VAL0-0.0280.00625.8340.0000.0000.0000.0000.0000.000
27A28GLU-1-0.854-0.87526.831-0.032-0.0320.0000.0000.0000.000
28A29ILE00.0010.00226.679-0.004-0.0040.0000.0000.0000.000
29A30PRO00.0390.06126.2850.0050.0050.0000.0000.0000.000
30A31ALA00.054-0.00429.192-0.002-0.0020.0000.0000.0000.000
31A32GLU-1-0.908-0.96831.834-0.018-0.0180.0000.0000.0000.000
32A33ALA00.0210.01329.0120.0000.0000.0000.0000.0000.000
33A34ASP-1-0.860-0.94230.850-0.045-0.0450.0000.0000.0000.000
34A35SER0-0.028-0.01833.186-0.001-0.0010.0000.0000.0000.000
35A36ALA0-0.0020.02227.7880.0020.0020.0000.0000.0000.000
36A37PRO0-0.0010.01526.459-0.003-0.0030.0000.0000.0000.000
37A38HIS10.8310.83819.7280.1020.1020.0000.0000.0000.000
38A39THR00.0150.01724.6790.0110.0110.0000.0000.0000.000
39A40GLU-1-0.777-0.87118.881-0.114-0.1140.0000.0000.0000.000
40A41ALA00.0130.01522.2240.0130.0130.0000.0000.0000.000
41A42VAL0-0.052-0.03019.315-0.016-0.0160.0000.0000.0000.000
42A43LEU00.0360.01519.0760.0080.0080.0000.0000.0000.000
43A44ASP-1-0.744-0.82919.307-0.088-0.0880.0000.0000.0000.000
44A45GLY0-0.0320.02316.536-0.021-0.0210.0000.0000.0000.000
45A46GLY0-0.0120.00814.9300.0010.0010.0000.0000.0000.000
46A47ILE0-0.051-0.01313.443-0.009-0.0090.0000.0000.0000.000
47A48ARG10.8580.93115.5920.1030.1030.0000.0000.0000.000
48A49LEU00.0080.01617.944-0.030-0.0300.0000.0000.0000.000
49A50ALA00.000-0.01219.7400.0190.0190.0000.0000.0000.000
50A51TRP0-0.001-0.00221.609-0.007-0.0070.0000.0000.0000.000
51A52ASP-1-0.716-0.78821.798-0.122-0.1220.0000.0000.0000.000
52A53THR0-0.028-0.02325.119-0.004-0.0040.0000.0000.0000.000
53A54VAL00.0600.03227.424-0.005-0.0050.0000.0000.0000.000
54A55GLU-1-0.859-0.85428.899-0.061-0.0610.0000.0000.0000.000
55A56THR00.0430.02924.1840.0050.0050.0000.0000.0000.000
56A57VAL00.0400.05723.628-0.001-0.0010.0000.0000.0000.000
57A58ARG10.8410.90625.1330.0690.0690.0000.0000.0000.000
58A59SER0-0.110-0.06425.8170.0050.0050.0000.0000.0000.000
59A60TYR0-0.003-0.00720.2260.0110.0110.0000.0000.0000.000
60A61ASP-1-0.736-0.77922.585-0.143-0.1430.0000.0000.0000.000
61A62PRO00.0260.01924.5020.0010.0010.0000.0000.0000.000
62A63GLU-1-0.787-0.82225.757-0.107-0.1070.0000.0000.0000.000
63A64TRP0-0.052-0.00925.4090.0080.0080.0000.0000.0000.000
64A65GLN00.0480.01628.1100.0130.0130.0000.0000.0000.000
65A66ALA00.0420.02330.078-0.007-0.0070.0000.0000.0000.000
66A67PRO0-0.060-0.04429.8830.0010.0010.0000.0000.0000.000
67A68THR0-0.085-0.03031.6160.0030.0030.0000.0000.0000.000
68A69GLY00.0360.02130.1830.0000.0000.0000.0000.0000.000
69A70GLY00.0570.03027.068-0.009-0.0090.0000.0000.0000.000
70A71HIS0-0.0030.01622.0210.0050.0050.0000.0000.0000.000
71A72ARG10.8980.92625.1130.1120.1120.0000.0000.0000.000
72A73PHE0-0.0040.02119.9840.0090.0090.0000.0000.0000.000
73A74ALA00.0860.08117.894-0.001-0.0010.0000.0000.0000.000
74A75ILE0-0.028-0.01113.3640.0150.0150.0000.0000.0000.000
75A76ALA00.0550.03913.021-0.029-0.0290.0000.0000.0000.000
76A77PHE0-0.015-0.0237.757-0.018-0.0180.0000.0000.0000.000
77A78GLU-1-0.869-0.9327.091-0.013-0.0130.0000.0000.0000.000
78A79PHE0-0.045-0.0403.429-1.205-1.0110.024-0.150-0.0680.000
79A80PRO00.0000.0192.1231.818-1.1097.348-3.036-1.386-0.001
80A81ASP-1-0.828-0.8874.7450.7300.815-0.001-0.027-0.0570.000
81A82THR00.0930.0266.893-0.139-0.1390.0000.0000.0000.000
82A83ALA0-0.026-0.0119.456-0.097-0.0970.0000.0000.0000.000
83A84SER00.010-0.0354.465-0.0400.018-0.001-0.005-0.0520.000
84A85VAL0-0.0230.0106.548-0.292-0.2920.0000.0000.0000.000
85A86ASP-1-0.789-0.8618.552-0.097-0.0970.0000.0000.0000.000
86A87LYS10.8560.9568.2280.1180.1180.0000.0000.0000.000
87A88LYS10.9470.9776.5811.2071.2070.0000.0000.0000.000
88A89TYR00.0430.0169.0210.0170.0170.0000.0000.0000.000
89A90ALA0-0.009-0.00412.2980.0220.0220.0000.0000.0000.000
90A91GLU-1-0.809-0.8918.843-0.359-0.3590.0000.0000.0000.000
91A92LEU0-0.023-0.01111.0750.0090.0090.0000.0000.0000.000
92A93VAL00.0260.01414.1750.0400.0400.0000.0000.0000.000
93A94ASP-1-0.784-0.80416.248-0.139-0.1390.0000.0000.0000.000
94A95ALA0-0.065-0.01615.9440.0180.0180.0000.0000.0000.000
95A96GLY0-0.053-0.02917.9070.0090.0090.0000.0000.0000.000
96A97TYR0-0.058-0.01815.751-0.007-0.0070.0000.0000.0000.000
97A98GLU-1-0.830-0.89119.224-0.147-0.1470.0000.0000.0000.000
98A99GLY0-0.010-0.00618.023-0.030-0.0300.0000.0000.0000.000
99A100HIS0-0.039-0.03918.6420.0160.0160.0000.0000.0000.000
100A101LEU0-0.001-0.00418.7570.0240.0240.0000.0000.0000.000
101A102LYS10.8970.95117.3020.0530.0530.0000.0000.0000.000
102A103PRO00.0430.02313.5700.0120.0120.0000.0000.0000.000
103A104TRP0-0.0500.01815.6540.0290.0290.0000.0000.0000.000
104A105ASN00.0230.02416.255-0.011-0.0110.0000.0000.0000.000
105A106ALA00.0400.03017.2470.0040.0040.0000.0000.0000.000
106A107VAL00.010-0.00919.0990.0140.0140.0000.0000.0000.000
107A108TRP00.0240.01516.3660.0240.0240.0000.0000.0000.000
108A109GLY00.0130.01318.0240.0030.0030.0000.0000.0000.000
109A110GLN00.0620.03013.352-0.005-0.0050.0000.0000.0000.000
110A111ARG10.8310.91711.4290.0280.0280.0000.0000.0000.000
111A112TYR0-0.0220.01012.084-0.046-0.0460.0000.0000.0000.000
112A113ALA00.0150.00512.7700.0380.0380.0000.0000.0000.000
113A114ILE0-0.0210.00914.048-0.042-0.0420.0000.0000.0000.000
114A115VAL00.0170.01613.9860.0250.0250.0000.0000.0000.000
115A116LYS10.9040.96516.6080.1570.1570.0000.0000.0000.000
116A117ASP-1-0.776-0.83917.573-0.273-0.2730.0000.0000.0000.000
117A118PRO00.020-0.01718.5580.0260.0260.0000.0000.0000.000
118A119ASP-1-0.895-0.92021.757-0.166-0.1660.0000.0000.0000.000
119A120GLY0-0.0160.00422.6890.0150.0150.0000.0000.0000.000
120A121ASN0-0.080-0.06119.7620.0280.0280.0000.0000.0000.000
121A122VAL0-0.023-0.01018.319-0.017-0.0170.0000.0000.0000.000
122A123VAL0-0.009-0.01012.728-0.023-0.0230.0000.0000.0000.000
123A124ASP-1-0.733-0.84613.828-0.258-0.2580.0000.0000.0000.000
124A125LEU0-0.049-0.0339.128-0.138-0.1380.0000.0000.0000.000
125A126PHE00.0110.0029.1420.1120.1120.0000.0000.0000.000
126A127ALA00.0460.0157.636-0.087-0.0870.0000.0000.0000.000
127A128PRO0-0.0260.0029.355-0.026-0.0260.0000.0000.0000.000
128A129LEU0-0.081-0.04412.0320.0450.0450.0000.0000.0000.000
129A130PRO-1-0.941-0.95313.8800.1260.1260.0000.0000.0000.000
130A2001HOH00.0410.02325.6970.0000.0000.0000.0000.0000.000
131A2002HOH0-0.039-0.02528.1690.0020.0020.0000.0000.0000.000
132A2003HOH00.0600.03821.9040.0010.0010.0000.0000.0000.000
133A2004HOH0-0.068-0.05720.529-0.008-0.0080.0000.0000.0000.000
134A2005HOH0-0.030-0.02721.0770.0040.0040.0000.0000.0000.000
135A2006HOH0-0.059-0.03623.7440.0010.0010.0000.0000.0000.000
136A2007HOH0-0.025-0.02528.3170.0020.0020.0000.0000.0000.000
137A2009HOH0-0.030-0.03719.7460.0000.0000.0000.0000.0000.000
138A2010HOH0-0.0010.00013.4910.0000.0000.0000.0000.0000.000
139A2011HOH0-0.020-0.02624.821-0.002-0.0020.0000.0000.0000.000
140A2012HOH00.0340.03431.010-0.001-0.0010.0000.0000.0000.000
141A2013HOH0-0.054-0.02926.8940.0010.0010.0000.0000.0000.000
142A2014HOH00.0080.02118.3730.0060.0060.0000.0000.0000.000
143A2015HOH0-0.033-0.02719.6660.0050.0050.0000.0000.0000.000
144A2017HOH0-0.017-0.01524.7810.0000.0000.0000.0000.0000.000
145A2018HOH0-0.050-0.04318.8670.0030.0030.0000.0000.0000.000
146A2019HOH0-0.0050.00431.3160.0010.0010.0000.0000.0000.000
147A2020HOH0-0.045-0.05219.0270.0060.0060.0000.0000.0000.000
148A2021HOH0-0.040-0.02723.0080.0040.0040.0000.0000.0000.000
149A2022HOH0-0.042-0.03232.9900.0020.0020.0000.0000.0000.000
150A2023HOH0-0.017-0.02222.095-0.006-0.0060.0000.0000.0000.000
151A2025HOH00.001-0.00115.211-0.013-0.0130.0000.0000.0000.000
152A2027HOH0-0.016-0.03024.8690.0050.0050.0000.0000.0000.000
153A2028HOH00.0080.00021.262-0.008-0.0080.0000.0000.0000.000
154A2030HOH0-0.064-0.0397.1380.0820.0820.0000.0000.0000.000
155A2031HOH00.000-0.00332.8470.0000.0000.0000.0000.0000.000
156A2032HOH0-0.054-0.05028.745-0.002-0.0020.0000.0000.0000.000
157A2033HOH0-0.087-0.08036.5680.0000.0000.0000.0000.0000.000
158A2034HOH0-0.009-0.00627.9190.0010.0010.0000.0000.0000.000
159A2035HOH0-0.032-0.01921.320-0.002-0.0020.0000.0000.0000.000
160A2036HOH00.0260.0149.884-0.032-0.0320.0000.0000.0000.000
161A2037HOH0-0.0060.00234.5460.0000.0000.0000.0000.0000.000
162A2038HOH0-0.035-0.0309.322-0.063-0.0630.0000.0000.0000.000
163A2039HOH0-0.0210.01423.5940.0030.0030.0000.0000.0000.000
164A2040HOH0-0.034-0.02223.3770.0000.0000.0000.0000.0000.000
165A2042HOH00.0100.0119.392-0.072-0.0720.0000.0000.0000.000
166A2043HOH0-0.053-0.04015.8230.0050.0050.0000.0000.0000.000
167A2044HOH0-0.016-0.00322.4710.0020.0020.0000.0000.0000.000
168A2045HOH00.0150.00515.968-0.002-0.0020.0000.0000.0000.000
169A2048HOH0-0.0020.00431.1790.0000.0000.0000.0000.0000.000
170A2049HOH0-0.062-0.07118.4710.0100.0100.0000.0000.0000.000
171A2050HOH0-0.013-0.00921.667-0.001-0.0010.0000.0000.0000.000
172A2052HOH0-0.074-0.07213.727-0.004-0.0040.0000.0000.0000.000
173A2053HOH00.0490.01837.133-0.001-0.0010.0000.0000.0000.000
174A2054HOH0-0.040-0.02240.9010.0000.0000.0000.0000.0000.000
175A2055HOH0-0.014-0.01133.4190.0010.0010.0000.0000.0000.000
176A2056HOH0-0.081-0.07223.9390.0000.0000.0000.0000.0000.000
177A2058HOH0-0.0070.0362.31610.997-1.80112.1481.901-1.251-0.009
178A2059HOH0-0.048-0.03816.3660.0080.0080.0000.0000.0000.000
179A2060HOH0-0.015-0.02210.790-0.010-0.0100.0000.0000.0000.000
180A2061HOH00.0370.02733.144-0.002-0.0020.0000.0000.0000.000
181A2062HOH0-0.020-0.02813.716-0.002-0.0020.0000.0000.0000.000
182A2063HOH0-0.030-0.02936.3880.0010.0010.0000.0000.0000.000
183A2065HOH0-0.035-0.04514.9790.0050.0050.0000.0000.0000.000
184A2068HOH0-0.035-0.02121.0430.0030.0030.0000.0000.0000.000
185A2069HOH0-0.038-0.03017.3250.0050.0050.0000.0000.0000.000
186A2070HOH00.0200.01324.6270.0010.0010.0000.0000.0000.000
187A2072HOH00.0320.01831.509-0.001-0.0010.0000.0000.0000.000
188A2073HOH0-0.056-0.04736.1360.0020.0020.0000.0000.0000.000
189A2076HOH0-0.023-0.05424.8620.0000.0000.0000.0000.0000.000
190A2077HOH0-0.002-0.00713.047-0.011-0.0110.0000.0000.0000.000
191A2078HOH00.0310.02013.457-0.014-0.0140.0000.0000.0000.000
192A2080HOH0-0.014-0.03217.0930.0120.0120.0000.0000.0000.000
193A2084HOH00.007-0.00132.9980.0000.0000.0000.0000.0000.000
194A2085HOH0-0.062-0.04030.8100.0010.0010.0000.0000.0000.000
195A2086HOH0-0.029-0.02124.2620.0000.0000.0000.0000.0000.000
196A2087HOH0-0.044-0.02414.921-0.003-0.0030.0000.0000.0000.000
197A2090HOH0-0.021-0.01216.4700.0110.0110.0000.0000.0000.000
198A2092HOH00.0710.09434.1430.0000.0000.0000.0000.0000.000
199A2095HOH0-0.035-0.03016.039-0.004-0.0040.0000.0000.0000.000
200A2096HOH0-0.029-0.0166.134-0.098-0.0980.0000.0000.0000.000
201A2097HOH0-0.051-0.03410.9100.0240.0240.0000.0000.0000.000
202A2098HOH00.0420.03524.023-0.001-0.0010.0000.0000.0000.000
203A2099HOH00.004-0.02034.1710.0000.0000.0000.0000.0000.000
204A2103HOH0-0.024-0.02020.654-0.002-0.0020.0000.0000.0000.000
205A2105HOH0-0.055-0.04229.9950.0020.0020.0000.0000.0000.000
206A2108HOH0-0.089-0.06134.0920.0000.0000.0000.0000.0000.000
207A2113HOH00.0340.02828.3070.0010.0010.0000.0000.0000.000
208A2115HOH0-0.060-0.08816.244-0.001-0.0010.0000.0000.0000.000
209A2116HOH0-0.001-0.01822.4080.0000.0000.0000.0000.0000.000
210A2117HOH00.0360.02718.654-0.004-0.0040.0000.0000.0000.000
211A2119HOH0-0.034-0.02116.263-0.001-0.0010.0000.0000.0000.000
212A2123HOH00.0100.00329.1790.0010.0010.0000.0000.0000.000
213A2129HOH0-0.053-0.05020.5090.0090.0090.0000.0000.0000.000
214A2130HOH0-0.064-0.06223.6150.0030.0030.0000.0000.0000.000
215A2131HOH0-0.094-0.08823.4970.0030.0030.0000.0000.0000.000
216A2132HOH0-0.009-0.00734.1320.0000.0000.0000.0000.0000.000
217A2135HOH0-0.042-0.02538.2280.0010.0010.0000.0000.0000.000
218A2137HOH00.0220.00631.5790.0000.0000.0000.0000.0000.000
219A2138HOH00.0280.02021.989-0.003-0.0030.0000.0000.0000.000
220A2139HOH00.0340.02333.545-0.002-0.0020.0000.0000.0000.000
221A2140HOH00.003-0.00612.585-0.009-0.0090.0000.0000.0000.000
222A2142HOH0-0.0070.00533.162-0.001-0.0010.0000.0000.0000.000
223A2143HOH0-0.048-0.07232.166-0.002-0.0020.0000.0000.0000.000
224A2147HOH0-0.046-0.05032.8770.0010.0010.0000.0000.0000.000
225A2154HOH0-0.033-0.01835.8550.0000.0000.0000.0000.0000.000
226A2155HOH0-0.005-0.00733.0750.0000.0000.0000.0000.0000.000
227A2156HOH0-0.073-0.08129.894-0.001-0.0010.0000.0000.0000.000
228A2158HOH00.0070.0099.411-0.022-0.0220.0000.0000.0000.000
229A2159HOH0-0.067-0.09925.9200.0000.0000.0000.0000.0000.000
230A2160HOH0-0.055-0.08318.2290.0080.0080.0000.0000.0000.000
231A2162HOH0-0.061-0.06125.640-0.002-0.0020.0000.0000.0000.000
232A2165HOH0-0.045-0.05631.692-0.001-0.0010.0000.0000.0000.000
233A2168HOH0-0.031-0.03715.4360.0040.0040.0000.0000.0000.000