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: 53RMZ

Calculation Name: 1I8D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1I8D

Chain ID: A

ChEMBL ID:

UniProt ID: P0AFU8

Base Structure: X-ray

Registration Date: 2023-03-13

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2273098.231295
FMO2-HF: Nuclear repulsion 2192354.127991
FMO2-HF: Total energy -80744.103304
FMO2-MP2: Total energy -80976.199464


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.
-7.101-0.647.156-4.131-9.483-0.016
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 : 0.001 / q_NPA : 0.014
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].
3A3THR0-0.024-0.0403.7590.0842.427-0.008-1.245-1.0900.004
4A4GLY00.0370.0036.4230.7180.7180.0000.0000.0000.000
5A5ILE0-0.058-0.0139.0900.3470.3470.0000.0000.0000.000
6A6VAL0-0.030-0.02511.445-0.168-0.1680.0000.0000.0000.000
7A7GLN00.0340.0328.9470.3290.3290.0000.0000.0000.000
8A8GLY00.0450.02413.8830.1280.1280.0000.0000.0000.000
9A9THR0-0.044-0.01315.781-0.038-0.0380.0000.0000.0000.000
10A10ALA00.0040.00316.8620.0120.0120.0000.0000.0000.000
11A11LYS10.8060.89118.6540.3720.3720.0000.0000.0000.000
12A12LEU0-0.006-0.00519.973-0.021-0.0210.0000.0000.0000.000
13A13VAL0-0.001-0.00321.8620.0440.0440.0000.0000.0000.000
14A14SER0-0.034-0.02423.4730.0250.0250.0000.0000.0000.000
15A15ILE00.0090.00422.938-0.025-0.0250.0000.0000.0000.000
16A16ASP-1-0.811-0.88223.890-0.157-0.1570.0000.0000.0000.000
17A17GLU-1-0.804-0.88524.195-0.153-0.1530.0000.0000.0000.000
18A18LYS10.8200.90224.7060.1650.1650.0000.0000.0000.000
19A19PRO0-0.005-0.00726.2010.0050.0050.0000.0000.0000.000
20A20ASN00.0290.00523.0290.0100.0100.0000.0000.0000.000
21A21PHE0-0.002-0.00619.9720.0200.0200.0000.0000.0000.000
22A22ARG10.8060.90220.4220.2120.2120.0000.0000.0000.000
23A23THR00.0210.00419.677-0.016-0.0160.0000.0000.0000.000
24A24HIS0-0.033-0.02417.7560.0750.0750.0000.0000.0000.000
25A25VAL00.0500.02918.598-0.048-0.0480.0000.0000.0000.000
26A26VAL0-0.023-0.02615.9160.0310.0310.0000.0000.0000.000
27A27GLU-1-0.794-0.86219.334-0.388-0.3880.0000.0000.0000.000
28A28LEU0-0.015-0.02114.593-0.016-0.0160.0000.0000.0000.000
29A29PRO00.024-0.00317.0750.0360.0360.0000.0000.0000.000
30A30ASP-1-0.792-0.89118.319-0.561-0.5610.0000.0000.0000.000
31A31HIS0-0.051-0.02616.8040.0450.0450.0000.0000.0000.000
32A32MET0-0.061-0.02712.502-0.036-0.0360.0000.0000.0000.000
33A33LEU00.0300.01714.755-0.118-0.1180.0000.0000.0000.000
34A34ASP-1-0.901-0.93716.923-0.709-0.7090.0000.0000.0000.000
35A35GLY00.0390.02314.828-0.151-0.1510.0000.0000.0000.000
36A36LEU0-0.106-0.03511.983-0.166-0.1660.0000.0000.0000.000
37A37GLU-1-0.867-0.94213.289-0.497-0.4970.0000.0000.0000.000
38A38THR0-0.028-0.01913.567-0.082-0.0820.0000.0000.0000.000
39A39GLY0-0.006-0.00912.6580.0390.0390.0000.0000.0000.000
40A40ALA0-0.041-0.0109.437-0.101-0.1010.0000.0000.0000.000
41A41SER00.0200.0025.0140.2450.2450.0000.0000.0000.000
42A42VAL0-0.030-0.0236.713-0.648-0.6480.0000.0000.0000.000
43A43ALA0-0.0090.0207.0890.4170.4170.0000.0000.0000.000
44A44HIS00.0260.0038.5010.2590.2590.0000.0000.0000.000
45A45ASN0-0.032-0.03812.2780.0890.0890.0000.0000.0000.000
46A46GLY00.0330.0059.0280.1820.1820.0000.0000.0000.000
47A47CYS0-0.038-0.0058.132-0.022-0.0220.0000.0000.0000.000
48A48CYS00.0060.0095.614-0.531-0.468-0.001-0.004-0.0580.000
49A49LEU0-0.042-0.0067.4920.4210.4210.0000.0000.0000.000
50A50THR0-0.002-0.0168.527-0.344-0.3440.0000.0000.0000.000
51A51VAL0-0.027-0.00110.6320.1610.1610.0000.0000.0000.000
52A52THR0-0.049-0.05213.4270.0280.0280.0000.0000.0000.000
53A53GLU-1-0.867-0.90816.748-0.298-0.2980.0000.0000.0000.000
54A54ILE00.001-0.00416.033-0.060-0.0600.0000.0000.0000.000
55A55ASN0-0.061-0.02419.8680.0530.0530.0000.0000.0000.000
56A56GLY00.0190.00823.0500.0200.0200.0000.0000.0000.000
57A57ASN00.000-0.01720.558-0.024-0.0240.0000.0000.0000.000
58A58HIS0-0.055-0.01820.249-0.009-0.0090.0000.0000.0000.000
59A59VAL00.0050.00315.131-0.003-0.0030.0000.0000.0000.000
60A60SER0-0.020-0.02718.088-0.003-0.0030.0000.0000.0000.000
61A61PHE00.0700.03111.190-0.089-0.0890.0000.0000.0000.000
62A62ASP-1-0.796-0.86615.400-0.273-0.2730.0000.0000.0000.000
63A63LEU0-0.012-0.00115.337-0.012-0.0120.0000.0000.0000.000
64A64MET00.0380.01016.3860.0570.0570.0000.0000.0000.000
65A65LYS10.8240.87718.2050.1060.1060.0000.0000.0000.000
66A66GLU-1-0.797-0.84516.1480.1440.1440.0000.0000.0000.000
67A67THR00.0390.01313.5760.0190.0190.0000.0000.0000.000
68A68LEU0-0.0400.00215.928-0.011-0.0110.0000.0000.0000.000
69A69ARG10.8050.87019.041-0.112-0.1120.0000.0000.0000.000
70A70ILE0-0.031-0.01314.3720.0010.0010.0000.0000.0000.000
71A71THR0-0.027-0.02513.690-0.011-0.0110.0000.0000.0000.000
72A72ASN0-0.058-0.05516.910-0.038-0.0380.0000.0000.0000.000
73A73LEU00.011-0.00213.859-0.009-0.0090.0000.0000.0000.000
74A74GLY00.0490.02218.533-0.009-0.0090.0000.0000.0000.000
75A75ASP-1-0.860-0.90021.547-0.084-0.0840.0000.0000.0000.000
76A76LEU0-0.077-0.01318.6180.0000.0000.0000.0000.0000.000
77A77LYS10.8080.86523.0210.1910.1910.0000.0000.0000.000
78A78VAL00.0140.00824.964-0.018-0.0180.0000.0000.0000.000
79A79GLY0-0.0250.00025.4680.0230.0230.0000.0000.0000.000
80A80ASP-1-0.840-0.89322.965-0.223-0.2230.0000.0000.0000.000
81A81TRP0-0.028-0.02521.037-0.028-0.0280.0000.0000.0000.000
82A82VAL0-0.044-0.01015.8760.0400.0400.0000.0000.0000.000
83A83ASN00.0250.00714.0800.0170.0170.0000.0000.0000.000
84A84VAL00.0130.00911.976-0.017-0.0170.0000.0000.0000.000
85A85GLU-1-0.757-0.8677.614-2.675-2.6750.0000.0000.0000.000
86A86ARG10.8000.8837.9131.2131.2130.0000.0000.0000.000
87A87ALA00.0170.0003.025-0.464-0.0210.056-0.168-0.3300.001
88A88ALA0-0.0160.0093.4871.3552.0540.007-0.250-0.4560.000
89A89LYS10.8330.9024.0720.7590.882-0.001-0.071-0.0510.000
90A90PHE0-0.005-0.0296.3630.1530.1530.0000.0000.0000.000
91A91SER0-0.044-0.0288.3720.2100.2100.0000.0000.0000.000
92A92ASP-1-0.811-0.8687.729-1.915-1.9150.0000.0000.0000.000
93A93GLU-1-0.930-0.9628.783-0.591-0.5910.0000.0000.0000.000
94A94ILE0-0.007-0.0156.322-0.197-0.1970.0000.0000.0000.000
95A95GLY0-0.002-0.0058.7760.2250.2250.0000.0000.0000.000
96A96GLY0-0.013-0.0089.8160.0620.0620.0000.0000.0000.000
97A97HIS0-0.070-0.0438.2820.3570.3570.0000.0000.0000.000
98A98LEU0-0.001-0.0042.477-1.847-0.8631.731-0.539-2.1760.000
99A99MET0-0.0380.0154.5271.2971.7440.001-0.065-0.3820.000
100A100SER0-0.011-0.0632.538-3.662-1.2105.194-3.783-3.863-0.013
101A101GLY00.0250.0063.014-2.042-3.2160.1782.003-1.006-0.008
102A102HIS0-0.066-0.0275.447-0.186-0.1860.0000.0000.0000.000
103A103ILE0-0.032-0.0117.1090.1430.1430.0000.0000.0000.000
104A104MET00.0330.01710.342-0.058-0.0580.0000.0000.0000.000
105A105THR0-0.017-0.01412.850-0.053-0.0530.0000.0000.0000.000
106A106THR00.0150.01915.306-0.029-0.0290.0000.0000.0000.000
107A107ALA0-0.035-0.01218.0540.0480.0480.0000.0000.0000.000
108A108GLU-1-0.820-0.89220.675-0.016-0.0160.0000.0000.0000.000
109A109VAL00.0030.00622.9810.0190.0190.0000.0000.0000.000
110A110ALA00.0340.02224.957-0.004-0.0040.0000.0000.0000.000
111A111LYS10.8860.93727.586-0.016-0.0160.0000.0000.0000.000
112A112ILE00.0140.01727.034-0.002-0.0020.0000.0000.0000.000
113A113LEU0-0.0140.00429.3110.0040.0040.0000.0000.0000.000
114A114THR0-0.001-0.00430.110-0.012-0.0120.0000.0000.0000.000
115A115SER0-0.0060.00031.9590.0080.0080.0000.0000.0000.000
116A116GLU-1-0.872-0.94033.106-0.073-0.0730.0000.0000.0000.000
117A117ASN0-0.039-0.01431.501-0.003-0.0030.0000.0000.0000.000
118A118ASN0-0.0060.00428.857-0.006-0.0060.0000.0000.0000.000
119A119ARG10.8920.94026.2470.1310.1310.0000.0000.0000.000
120A120GLN00.0340.03625.8800.0050.0050.0000.0000.0000.000
121A121ILE0-0.023-0.01022.961-0.004-0.0040.0000.0000.0000.000
122A122TRP0-0.018-0.03424.1160.0200.0200.0000.0000.0000.000
123A123PHE00.0220.00620.372-0.024-0.0240.0000.0000.0000.000
124A124LYS10.7830.88323.497-0.020-0.0200.0000.0000.0000.000
125A125VAL00.0340.01019.814-0.018-0.0180.0000.0000.0000.000
126A126GLN0-0.030-0.01120.312-0.032-0.0320.0000.0000.0000.000
127A127ASP-1-0.788-0.90619.6600.3350.3350.0000.0000.0000.000
128A128SER0-0.065-0.03821.0620.0170.0170.0000.0000.0000.000
129A129GLN0-0.012-0.01020.9740.0200.0200.0000.0000.0000.000
130A130LEU00.0540.01214.8060.0310.0310.0000.0000.0000.000
131A131MET0-0.049-0.01618.1290.0290.0290.0000.0000.0000.000
132A132LYS10.7500.88318.218-0.591-0.5910.0000.0000.0000.000
133A133TYR0-0.036-0.05715.0160.0220.0220.0000.0000.0000.000
134A134ILE0-0.054-0.01616.3530.0260.0260.0000.0000.0000.000
135A135LEU00.0240.01018.134-0.068-0.0680.0000.0000.0000.000
136A136TYR0-0.036-0.04719.704-0.021-0.0210.0000.0000.0000.000
137A137LYS10.7750.89320.287-0.090-0.0900.0000.0000.0000.000
138A138GLY00.0470.04216.8520.0010.0010.0000.0000.0000.000
139A139PHE00.0050.00511.804-0.076-0.0760.0000.0000.0000.000
140A140ILE0-0.019-0.01313.2150.1080.1080.0000.0000.0000.000
141A141GLY00.0740.03110.861-0.123-0.1230.0000.0000.0000.000
142A142ILE0-0.049-0.02711.8530.0510.0510.0000.0000.0000.000
143A143ASP-1-0.770-0.87513.944-0.333-0.3330.0000.0000.0000.000
144A144GLY00.0500.0139.875-0.128-0.1280.0000.0000.0000.000
145A145ILE0-0.041-0.00410.653-0.184-0.1840.0000.0000.0000.000
146A146SER00.0100.0249.8840.2250.2250.0000.0000.0000.000
147A147LEU0-0.067-0.03711.867-0.040-0.0400.0000.0000.0000.000
148A148THR00.0320.01815.0420.0650.0650.0000.0000.0000.000
149A149VAL0-0.036-0.01416.844-0.045-0.0450.0000.0000.0000.000
150A150GLY00.0170.00519.2340.0000.0000.0000.0000.0000.000
151A151GLU-1-0.799-0.90922.8680.0960.0960.0000.0000.0000.000
152A152VAL00.0200.00622.324-0.009-0.0090.0000.0000.0000.000
153A153THR0-0.043-0.03325.429-0.014-0.0140.0000.0000.0000.000
154A154PRO00.0770.01925.7860.0130.0130.0000.0000.0000.000
155A155THR00.0040.01825.6510.0110.0110.0000.0000.0000.000
156A156ARG10.9010.94524.860-0.073-0.0730.0000.0000.0000.000
157A157PHE00.0670.05718.3600.0190.0190.0000.0000.0000.000
158A158CYS0-0.052-0.00823.408-0.026-0.0260.0000.0000.0000.000
159A159VAL00.0600.04218.7260.0240.0240.0000.0000.0000.000
160A160HIS0-0.026-0.03321.969-0.021-0.0210.0000.0000.0000.000
161A161LEU0-0.019-0.00920.374-0.011-0.0110.0000.0000.0000.000
162A162ILE00.0570.03520.5210.0170.0170.0000.0000.0000.000
163A163PRO00.0290.00123.278-0.020-0.0200.0000.0000.0000.000
164A164GLU-1-0.729-0.83820.231-0.389-0.3890.0000.0000.0000.000
165A165THR0-0.006-0.00517.934-0.029-0.0290.0000.0000.0000.000
166A166LEU0-0.088-0.03220.249-0.018-0.0180.0000.0000.0000.000
167A167GLU-1-0.949-0.97523.109-0.261-0.2610.0000.0000.0000.000
168A168ARG10.8450.90818.1720.5100.5100.0000.0000.0000.000
169A169THR0-0.041-0.02816.718-0.049-0.0490.0000.0000.0000.000
170A170THR0-0.016-0.03018.2230.0690.0690.0000.0000.0000.000
171A171LEU00.0310.01218.3240.0510.0510.0000.0000.0000.000
172A172GLY00.013-0.00120.7760.0390.0390.0000.0000.0000.000
173A173LYS10.9160.95323.6770.3170.3170.0000.0000.0000.000
174A174LYS10.8350.92719.0560.2550.2550.0000.0000.0000.000
175A175LYS10.9600.97924.4400.1130.1130.0000.0000.0000.000
176A176LEU00.028-0.00326.6230.0020.0020.0000.0000.0000.000
177A177GLY0-0.0030.00127.907-0.007-0.0070.0000.0000.0000.000
178A178ALA0-0.032-0.00623.7260.0010.0010.0000.0000.0000.000
179A179ARG10.8660.91220.2460.0500.0500.0000.0000.0000.000
180A180VAL0-0.064-0.02417.868-0.044-0.0440.0000.0000.0000.000
181A181ASN00.0440.00313.4340.1310.1310.0000.0000.0000.000
182A182ILE0-0.034-0.01614.135-0.045-0.0450.0000.0000.0000.000
183A183GLU-1-0.740-0.8376.5001.8951.8950.0000.0000.0000.000
184A184ILE00.004-0.00111.191-0.138-0.1380.0000.0000.0000.000
185A185ASP-1-0.733-0.8469.7901.6621.6620.0000.0000.0000.000
186A186PRO00.0200.0075.428-0.254-0.173-0.001-0.009-0.0710.000
187A187GLN0-0.042-0.0128.250-0.289-0.2890.0000.0000.0000.000
188A188THR0-0.004-0.03610.188-0.236-0.2360.0000.0000.0000.000
189A189GLN0-0.044-0.02411.234-0.053-0.0530.0000.0000.0000.000
190A190ALA0-0.030-0.00610.360-0.145-0.1450.0000.0000.0000.000
191A191VAL0-0.0100.00712.428-0.176-0.1760.0000.0000.0000.000
192A192VAL00.0160.00815.537-0.097-0.0970.0000.0000.0000.000
193A193ASP-1-0.720-0.84114.8190.8080.8080.0000.0000.0000.000
194A194THR0-0.079-0.06115.504-0.060-0.0600.0000.0000.0000.000
195A195VAL0-0.009-0.00518.229-0.075-0.0750.0000.0000.0000.000
196A196GLU-1-0.825-0.89420.5320.4800.4800.0000.0000.0000.000
197A197ARG10.9230.97114.563-0.956-0.9560.0000.0000.0000.000
198A198VAL0-0.007-0.00321.909-0.048-0.0480.0000.0000.0000.000
199A199LEU0-0.031-0.01824.198-0.041-0.0410.0000.0000.0000.000
200A200ALA00.0790.04525.115-0.028-0.0280.0000.0000.0000.000
201A201ALA0-0.0130.00025.663-0.026-0.0260.0000.0000.0000.000
202A202ARG10.9030.94227.522-0.338-0.3380.0000.0000.0000.000
203A203GLU-1-0.935-0.95729.8870.2500.2500.0000.0000.0000.000
204A204ASN0-0.057-0.04429.502-0.027-0.0270.0000.0000.0000.000
205A205ALA0-0.052-0.02231.668-0.015-0.0150.0000.0000.0000.000
206A206MET0-0.106-0.03133.485-0.030-0.0300.0000.0000.0000.000