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: P37KL

Calculation Name: 1LMI-A-Xray30

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1LMI

Chain ID: A

ChEMBL ID:

UniProt ID: P9WIP1

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 230
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1288568.672096
FMO2-HF: Nuclear repulsion 1232972.140816
FMO2-HF: Total energy -55596.53128
FMO2-MP2: Total energy -55756.874347


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:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
-44.189-37.9214.818-11.372-9.719-0.051
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.046
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].
3A3TYR0-0.120-0.0392.094-9.508-6.2224.575-3.616-4.2450.037
4A4PRO00.1480.1123.630-3.111-2.9080.015-0.207-0.0110.000
5A5ILE0-0.0500.0056.4310.2920.2920.0000.0000.0000.000
6A6THR00.029-0.0099.423-0.209-0.2090.0000.0000.0000.000
7A7GLY0-0.017-0.01412.4840.1320.1320.0000.0000.0000.000
8A8LYS10.9731.00216.0880.0260.0260.0000.0000.0000.000
9A9LEU00.0420.01319.4610.0150.0150.0000.0000.0000.000
10A10GLY0-0.045-0.03321.0800.0240.0240.0000.0000.0000.000
11A11SER0-0.049-0.03919.3280.0340.0340.0000.0000.0000.000
12A12GLU-1-0.822-0.90218.851-0.050-0.0500.0000.0000.0000.000
13A13LEU0-0.0160.01713.2950.0530.0530.0000.0000.0000.000
14A14THR00.003-0.00314.680-0.039-0.0390.0000.0000.0000.000
15A15MET0-0.004-0.0039.7830.0300.0300.0000.0000.0000.000
16A16THR00.0210.01210.944-0.124-0.1240.0000.0000.0000.000
17A17ASP-1-0.838-0.91810.3260.3210.3210.0000.0000.0000.000
18A18THR00.014-0.00611.702-0.117-0.1170.0000.0000.0000.000
19A19VAL0-0.0230.00811.237-0.035-0.0350.0000.0000.0000.000
20A20GLY00.0610.05513.555-0.056-0.0560.0000.0000.0000.000
21A21GLN0-0.0270.04715.4240.0170.0170.0000.0000.0000.000
22A22VAL00.0320.04814.843-0.028-0.0280.0000.0000.0000.000
23A23VAL0-0.012-0.01114.8890.0760.0760.0000.0000.0000.000
24A24LEU0-0.034-0.00613.586-0.048-0.0480.0000.0000.0000.000
25A25GLY00.0370.03415.4260.0370.0370.0000.0000.0000.000
26A26TRP00.016-0.01314.612-0.034-0.0340.0000.0000.0000.000
27A27LYS10.8590.93317.4300.0990.0990.0000.0000.0000.000
28A28VAL00.0380.02517.903-0.013-0.0130.0000.0000.0000.000
29A29SER0-0.011-0.02220.4910.0130.0130.0000.0000.0000.000
30A30ASP-1-0.819-0.87523.697-0.149-0.1490.0000.0000.0000.000
31A31LEU00.0310.02421.598-0.002-0.0020.0000.0000.0000.000
32A32LYS10.7910.89425.0830.1610.1610.0000.0000.0000.000
33A33SER00.0320.01228.286-0.008-0.0080.0000.0000.0000.000
34A34SER00.011-0.01530.0650.0150.0150.0000.0000.0000.000
35A35THR0-0.036-0.02831.953-0.002-0.0020.0000.0000.0000.000
36A36ALA00.0040.00832.0910.0070.0070.0000.0000.0000.000
37A37VAL00.0190.01434.144-0.008-0.0080.0000.0000.0000.000
38A38ILE0-0.013-0.01729.2160.0050.0050.0000.0000.0000.000
39A39PRO00.025-0.02733.1050.0040.0040.0000.0000.0000.000
40A40GLY00.0570.02234.4750.0080.0080.0000.0000.0000.000
41A41TYR0-0.118-0.02027.666-0.002-0.0020.0000.0000.0000.000
42A42PRO0-0.004-0.00331.3670.0100.0100.0000.0000.0000.000
43A43VAL0-0.004-0.00431.287-0.014-0.0140.0000.0000.0000.000
44A44ALA00.0090.00430.6110.0140.0140.0000.0000.0000.000
45A45GLY0-0.0180.00330.9490.0090.0090.0000.0000.0000.000
46A46GLN0-0.0240.02230.7020.0240.0240.0000.0000.0000.000
47A47VAL00.0080.00629.163-0.020-0.0200.0000.0000.0000.000
48A48TRP0-0.0040.00225.9540.0110.0110.0000.0000.0000.000
49A49GLU-1-0.736-0.85226.274-0.177-0.1770.0000.0000.0000.000
50A50ALA00.0250.01822.562-0.008-0.0080.0000.0000.0000.000
51A51THR0-0.016-0.01324.6450.0090.0090.0000.0000.0000.000
52A52ALA0-0.027-0.00720.502-0.004-0.0040.0000.0000.0000.000
53A53THR00.0250.00321.5100.0150.0150.0000.0000.0000.000
54A54VAL0-0.0200.00918.432-0.006-0.0060.0000.0000.0000.000
55A55ASN00.0400.01419.8140.0170.0170.0000.0000.0000.000
56A56ALA00.0500.03219.7420.0090.0090.0000.0000.0000.000
57A57ILE00.0130.00818.1130.0160.0160.0000.0000.0000.000
58A58ARG10.7840.84417.952-0.261-0.2610.0000.0000.0000.000
59A59GLY00.0590.02319.461-0.003-0.0030.0000.0000.0000.000
60A60SER00.0060.04721.822-0.005-0.0050.0000.0000.0000.000
61A61VAL00.0410.03018.042-0.001-0.0010.0000.0000.0000.000
62A62THR00.0350.03619.6370.0060.0060.0000.0000.0000.000
63A63PRO0-0.0400.00718.317-0.032-0.0320.0000.0000.0000.000
64A64ALA00.0430.02314.967-0.001-0.0010.0000.0000.0000.000
65A65VAL00.0440.01316.407-0.071-0.0710.0000.0000.0000.000
66A66SER00.0080.00618.156-0.043-0.0430.0000.0000.0000.000
67A67GLN00.0180.01411.428-0.041-0.0410.0000.0000.0000.000
68A68PHE00.0020.01414.130-0.112-0.1120.0000.0000.0000.000
69A69ASN00.009-0.00114.2690.0520.0520.0000.0000.0000.000
70A70ALA00.0180.03017.2810.0050.0050.0000.0000.0000.000
71A71ARG10.8310.86311.3541.2341.2340.0000.0000.0000.000
72A72THR00.0080.00818.9820.0370.0370.0000.0000.0000.000
73A73ALA00.0190.00618.504-0.061-0.0610.0000.0000.0000.000
74A74ASP-1-0.801-0.88117.756-0.501-0.5010.0000.0000.0000.000
75A75GLY00.0130.01716.655-0.060-0.0600.0000.0000.0000.000
76A76ILE0-0.0100.01317.282-0.053-0.0530.0000.0000.0000.000
77A77ASN0-0.014-0.01116.178-0.074-0.0740.0000.0000.0000.000
78A78TYR0-0.010-0.02819.0280.0330.0330.0000.0000.0000.000
79A79ARG10.8530.92617.1820.6240.6240.0000.0000.0000.000
80A80VAL00.0080.01119.1090.0520.0520.0000.0000.0000.000
81A81LEU0-0.069-0.03121.252-0.006-0.0060.0000.0000.0000.000
82A82TRP0-0.189-0.22021.3570.0120.0120.0000.0000.0000.000
83A83GLN00.2500.29123.408-0.028-0.0280.0000.0000.0000.000
84A84ALA00.0200.01525.743-0.012-0.0120.0000.0000.0000.000
85A85ALA0-0.0080.01028.6070.0130.0130.0000.0000.0000.000
86A86GLY00.0460.01330.1040.0000.0000.0000.0000.0000.000
87A87PRO0-0.0150.02631.1790.0050.0050.0000.0000.0000.000
88A88ASP-1-0.853-0.92431.125-0.135-0.1350.0000.0000.0000.000
89A89THR0-0.055-0.00826.319-0.011-0.0110.0000.0000.0000.000
90A90ILE0-0.068-0.01022.2120.0120.0120.0000.0000.0000.000
91A91SER00.001-0.05126.221-0.013-0.0130.0000.0000.0000.000
92A92GLY00.0250.00323.702-0.010-0.0100.0000.0000.0000.000
93A93ALA00.0000.01524.191-0.003-0.0030.0000.0000.0000.000
94A94THR0-0.011-0.03323.526-0.006-0.0060.0000.0000.0000.000
95A95ILE0-0.0030.01022.3920.0090.0090.0000.0000.0000.000
96A96PRO00.0260.00724.2140.0080.0080.0000.0000.0000.000
97A97GLN00.0750.03923.5500.0020.0020.0000.0000.0000.000
98A98GLY0-0.051-0.02324.4800.0010.0010.0000.0000.0000.000
99A99GLU-1-0.879-0.91726.079-0.026-0.0260.0000.0000.0000.000
100A100GLN00.010-0.00824.454-0.014-0.0140.0000.0000.0000.000
101A101SER0-0.024-0.00924.1800.0000.0000.0000.0000.0000.000
102A102THR00.013-0.01324.216-0.015-0.0150.0000.0000.0000.000
103A103GLY00.0660.03825.7310.0080.0080.0000.0000.0000.000
104A104LYS10.8210.92525.5810.1400.1400.0000.0000.0000.000
105A105ILE0-0.0160.00220.410-0.007-0.0070.0000.0000.0000.000
106A106TYR0-0.002-0.05424.3500.0110.0110.0000.0000.0000.000
107A107PHE00.0240.01219.755-0.029-0.0290.0000.0000.0000.000
108A108ASP-1-0.701-0.79124.833-0.243-0.2430.0000.0000.0000.000
109A109VAL0-0.016-0.00425.171-0.026-0.0260.0000.0000.0000.000
110A110THR00.0390.03326.8220.0150.0150.0000.0000.0000.000
111A111GLY0-0.011-0.00626.9490.0100.0100.0000.0000.0000.000
112A112PRO0-0.0190.00025.4030.0200.0200.0000.0000.0000.000
113A113SER00.0280.02225.759-0.021-0.0210.0000.0000.0000.000
114A114PRO0-0.0260.01022.082-0.009-0.0090.0000.0000.0000.000
115A115THR0-0.032-0.04321.6720.0250.0250.0000.0000.0000.000
116A116ILE00.0240.01615.8750.0220.0220.0000.0000.0000.000
117A117VAL0-0.036-0.00416.5850.0020.0020.0000.0000.0000.000
118A118ALA00.0200.01012.056-0.012-0.0120.0000.0000.0000.000
119A119MET0-0.081-0.03211.6500.0860.0860.0000.0000.0000.000
120A120ASN0-0.004-0.0269.344-0.022-0.0220.0000.0000.0000.000
121A121ASN00.0580.0407.006-0.029-0.0290.0000.0000.0000.000
122A122GLY0-0.044-0.02110.4510.1660.1660.0000.0000.0000.000
123A123MET0-0.067-0.0367.1970.2050.2050.0000.0000.0000.000
124A124GLU-1-0.858-0.9181.790-30.306-30.1649.572-5.784-3.931-0.075
125A125ASP-1-0.749-0.8256.166-0.945-0.9450.0000.0000.0000.000
126A126LEU0-0.018-0.0165.132-0.538-0.5380.0000.0000.0000.000
127A127LEU0-0.011-0.0207.1160.4450.4450.0000.0000.0000.000
128A128ILE00.0170.01810.003-0.133-0.1330.0000.0000.0000.000
129A129TRP0-0.034-0.03212.7750.0770.0770.0000.0000.0000.000
130A130GLU-1-0.937-0.97316.180-0.440-0.4400.0000.0000.0000.000
131A131PRO-1-0.829-0.85218.606-0.169-0.1690.0000.0000.0000.000
132A132HOH0-0.037-0.02125.547-0.004-0.0040.0000.0000.0000.000
133A134HOH00.0420.03027.6940.0010.0010.0000.0000.0000.000
134A135HOH00.0020.00322.451-0.019-0.0190.0000.0000.0000.000
135A136HOH0-0.033-0.02917.468-0.002-0.0020.0000.0000.0000.000
136A137HOH00.0440.03520.2250.0010.0010.0000.0000.0000.000
137A138HOH0-0.037-0.03327.5090.0030.0030.0000.0000.0000.000
138A139HOH00.0030.00331.088-0.006-0.0060.0000.0000.0000.000
139A140HOH0-0.017-0.01230.203-0.002-0.0020.0000.0000.0000.000
140A141HOH00.0220.01623.5480.0060.0060.0000.0000.0000.000
141A142HOH0-0.032-0.01524.8650.0050.0050.0000.0000.0000.000
142A143HOH0-0.043-0.03027.5990.0030.0030.0000.0000.0000.000
143A144HOH0-0.005-0.01714.372-0.030-0.0300.0000.0000.0000.000
144A146HOH00.0310.01729.070-0.001-0.0010.0000.0000.0000.000
145A147HOH0-0.018-0.02023.6700.0030.0030.0000.0000.0000.000
146A148HOH00.0350.02527.5060.0020.0020.0000.0000.0000.000
147A149HOH00.0260.01626.179-0.002-0.0020.0000.0000.0000.000
148A150HOH0-0.010-0.01010.0270.0270.0270.0000.0000.0000.000
149A151HOH0-0.021-0.01827.008-0.001-0.0010.0000.0000.0000.000
150A152HOH00.0020.00215.344-0.020-0.0200.0000.0000.0000.000
151A153HOH00.0230.02515.676-0.027-0.0270.0000.0000.0000.000
152A154HOH0-0.031-0.02128.8030.0030.0030.0000.0000.0000.000
153A155HOH00.0090.01313.934-0.046-0.0460.0000.0000.0000.000
154A156HOH0-0.001-0.00629.9450.0050.0050.0000.0000.0000.000
155A158HOH0-0.046-0.04016.434-0.010-0.0100.0000.0000.0000.000
156A160HOH00.000-0.00232.440-0.001-0.0010.0000.0000.0000.000
157A163HOH00.0140.0008.633-0.134-0.1340.0000.0000.0000.000
158A164HOH00.0360.02114.5120.0070.0070.0000.0000.0000.000
159A165HOH0-0.012-0.01932.5150.0010.0010.0000.0000.0000.000
160A166HOH0-0.076-0.07023.2450.0060.0060.0000.0000.0000.000
161A167HOH00.0150.0084.6660.4450.462-0.001-0.001-0.0160.000
162A168HOH0-0.057-0.04021.173-0.005-0.0050.0000.0000.0000.000
163A169HOH00.0290.0168.8860.1710.1710.0000.0000.0000.000
164A170HOH0-0.045-0.03322.5810.0090.0090.0000.0000.0000.000
165A171HOH00.0090.00919.867-0.023-0.0230.0000.0000.0000.000
166A172HOH0-0.034-0.02528.0980.0050.0050.0000.0000.0000.000
167A173HOH0-0.058-0.08224.965-0.012-0.0120.0000.0000.0000.000
168A174HOH0-0.020-0.01718.5630.0180.0180.0000.0000.0000.000
169A175HOH0-0.043-0.02328.068-0.004-0.0040.0000.0000.0000.000
170A176HOH0-0.043-0.02933.9040.0040.0040.0000.0000.0000.000
171A177HOH0-0.025-0.0308.736-0.121-0.1210.0000.0000.0000.000
172A178HOH0-0.027-0.0302.594-0.9800.9660.628-1.429-1.146-0.011
173A179HOH00.0310.01934.329-0.002-0.0020.0000.0000.0000.000
174A180HOH0-0.021-0.02223.2870.0110.0110.0000.0000.0000.000
175A181HOH0-0.030-0.06034.071-0.005-0.0050.0000.0000.0000.000
176A182HOH0-0.042-0.03719.070-0.004-0.0040.0000.0000.0000.000
177A183HOH00.0040.01934.2170.0010.0010.0000.0000.0000.000
178A185HOH0-0.019-0.00323.5980.0110.0110.0000.0000.0000.000
179A186HOH0-0.0080.00923.0310.0040.0040.0000.0000.0000.000
180A188HOH00.002-0.00331.7060.0040.0040.0000.0000.0000.000
181A189HOH0-0.038-0.06328.567-0.008-0.0080.0000.0000.0000.000
182A191HOH0-0.039-0.05420.482-0.009-0.0090.0000.0000.0000.000
183A193HOH00.0130.00322.0970.0010.0010.0000.0000.0000.000
184A197HOH00.037-0.00812.6970.0140.0140.0000.0000.0000.000
185A198HOH0-0.041-0.03231.6600.0060.0060.0000.0000.0000.000
186A201HOH0-0.010-0.02325.094-0.003-0.0030.0000.0000.0000.000
187A206HOH0-0.027-0.02119.314-0.007-0.0070.0000.0000.0000.000
188A207HOH0-0.033-0.02122.2550.0020.0020.0000.0000.0000.000
189A210HOH00.0100.02012.352-0.034-0.0340.0000.0000.0000.000
190A211HOH00.0190.0317.9320.1850.1850.0000.0000.0000.000
191A212HOH00.0340.02433.223-0.001-0.0010.0000.0000.0000.000
192A213HOH0-0.008-0.00618.502-0.010-0.0100.0000.0000.0000.000
193A216HOH0-0.021-0.01922.853-0.009-0.0090.0000.0000.0000.000
194A217HOH0-0.0020.01435.0370.0030.0030.0000.0000.0000.000
195A218HOH0-0.013-0.0138.7890.0270.0270.0000.0000.0000.000
196A219HOH0-0.0050.02819.299-0.017-0.0170.0000.0000.0000.000
197A220HOH0-0.055-0.04434.7890.0010.0010.0000.0000.0000.000
198A222HOH0-0.062-0.06722.9220.0040.0040.0000.0000.0000.000
199A223HOH0-0.030-0.02715.154-0.029-0.0290.0000.0000.0000.000
200A224HOH00.0110.02727.621-0.001-0.0010.0000.0000.0000.000
201A225HOH0-0.032-0.02114.415-0.021-0.0210.0000.0000.0000.000
202A232HOH0-0.037-0.01928.374-0.001-0.0010.0000.0000.0000.000
203A235HOH0-0.070-0.08123.8100.0060.0060.0000.0000.0000.000
204A239HOH0-0.022-0.02031.976-0.008-0.0080.0000.0000.0000.000
205A240HOH0-0.0110.01632.6000.0020.0020.0000.0000.0000.000
206A241HOH00.0110.00631.5700.0030.0030.0000.0000.0000.000
207A247HOH00.0120.0009.555-0.105-0.1050.0000.0000.0000.000
208A252HOH0-0.087-0.0803.081-0.1040.5710.029-0.335-0.370-0.002
209A253HOH0-0.0120.00536.6650.0020.0020.0000.0000.0000.000
210A254HOH00.0630.06326.524-0.012-0.0120.0000.0000.0000.000
211A258HOH00.0110.00024.3480.0090.0090.0000.0000.0000.000
212A266HOH0-0.029-0.03820.090-0.003-0.0030.0000.0000.0000.000
213A273HOH0-0.058-0.03132.0930.0010.0010.0000.0000.0000.000
214A274HOH00.0030.00435.115-0.003-0.0030.0000.0000.0000.000
215A276HOH00.0250.01320.566-0.013-0.0130.0000.0000.0000.000
216A279HOH0-0.021-0.03819.483-0.007-0.0070.0000.0000.0000.000
217A283HOH0-0.028-0.01811.9060.0980.0980.0000.0000.0000.000
218A286HOH0-0.017-0.01125.4220.0000.0000.0000.0000.0000.000
219A287HOH00.0540.07930.293-0.005-0.0050.0000.0000.0000.000
220A288HOH0-0.023-0.02124.8340.0030.0030.0000.0000.0000.000
221A289HOH0-0.060-0.04935.4730.0040.0040.0000.0000.0000.000
222A290HOH0-0.045-0.05027.3040.0010.0010.0000.0000.0000.000
223A291HOH00.0000.00835.235-0.001-0.0010.0000.0000.0000.000
224A292HOH0-0.045-0.04815.7280.0100.0100.0000.0000.0000.000
225A294HOH00.0040.01523.0780.0080.0080.0000.0000.0000.000
226A295HOH0-0.039-0.05724.2600.0040.0040.0000.0000.0000.000
227A297HOH00.0190.01911.490-0.011-0.0110.0000.0000.0000.000
228A298HOH0-0.033-0.04928.227-0.007-0.0070.0000.0000.0000.000
229A301HOH00.0450.03622.6980.0120.0120.0000.0000.0000.000
230A303HOH0-0.004-0.00232.508-0.002-0.0020.0000.0000.0000.000