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: G5GG1

Calculation Name: 4BJI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4BJI

Chain ID: A

ChEMBL ID:

UniProt ID: O14229

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptHSide
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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2395174.924117
FMO2-HF: Nuclear repulsion 2313480.493235
FMO2-HF: Total energy -81694.430882
FMO2-MP2: Total energy -81933.858344


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:190:ARG)


Summations of interaction energy for fragment #1(A:190:ARG)
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.
120.476127.9784.775-4.258-8.017-0.02
Interaction energy analysis for fragmet #1(A:190:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.975 / q_NPA : 0.990
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].
3A192TRP00.002-0.0092.679-10.826-3.5954.776-4.207-7.799-0.020
4A193ILE00.0380.0324.2643.1823.3390.000-0.034-0.1220.000
5A194ILE00.0130.0127.276-2.058-2.0580.0000.0000.0000.000
6A195THR0-0.024-0.0159.8251.1571.1570.0000.0000.0000.000
7A196THR00.0470.02512.052-0.074-0.0740.0000.0000.0000.000
8A197ASN00.0180.00415.7810.6450.6450.0000.0000.0000.000
9A198MET00.0350.00618.925-0.008-0.0080.0000.0000.0000.000
10A199GLY00.0000.01721.7570.5080.5080.0000.0000.0000.000
11A200VAL0-0.062-0.01217.8290.0370.0370.0000.0000.0000.000
12A201GLU-1-0.871-0.92620.657-11.782-11.7820.0000.0000.0000.000
13A202SER00.005-0.00521.2200.6830.6830.0000.0000.0000.000
14A203VAL0-0.074-0.02618.843-0.724-0.7240.0000.0000.0000.000
15A204PRO00.0230.00314.4130.1460.1460.0000.0000.0000.000
16A205THR00.0380.01116.7020.1610.1610.0000.0000.0000.000
17A206CYS00.0030.00314.6860.6090.6090.0000.0000.0000.000
18A207ARG10.7790.87311.20919.35119.3510.0000.0000.0000.000
19A208HIS00.0410.0096.6970.6840.6840.0000.0000.0000.000
20A209SER00.0480.0229.665-0.813-0.8130.0000.0000.0000.000
21A210LYS10.9310.9585.65839.43639.4360.0000.0000.0000.000
22A211LEU0-0.063-0.0056.667-1.885-1.8850.0000.0000.0000.000
23A212GLY00.0770.0518.6471.9301.9300.0000.0000.0000.000
24A213GLU-1-0.794-0.87011.116-18.407-18.4070.0000.0000.0000.000
25A214PRO0-0.0180.01511.520-1.026-1.0260.0000.0000.0000.000
26A215SER00.0540.01612.1051.2261.2260.0000.0000.0000.000
27A216LYS11.0430.99914.03912.56612.5660.0000.0000.0000.000
28A217THR00.0100.01714.3540.1580.1580.0000.0000.0000.000
29A218ILE0-0.016-0.01310.4630.0870.0870.0000.0000.0000.000
30A219GLN0-0.029-0.02413.907-0.288-0.2880.0000.0000.0000.000
31A220GLU-1-0.852-0.89616.710-12.336-12.3360.0000.0000.0000.000
32A221VAL00.000-0.00214.7670.2510.2510.0000.0000.0000.000
33A222ILE0-0.024-0.01513.3570.2680.2680.0000.0000.0000.000
34A223GLU-1-0.789-0.87517.116-12.848-12.8480.0000.0000.0000.000
35A224ALA00.0120.01620.0260.5410.5410.0000.0000.0000.000
36A225LEU0-0.038-0.03015.3710.2430.2430.0000.0000.0000.000
37A226LYS10.8520.91319.68613.49313.4930.0000.0000.0000.000
38A227PRO00.0440.02421.7060.2770.2770.0000.0000.0000.000
39A228LEU0-0.034-0.01621.2980.3870.3870.0000.0000.0000.000
40A229PHE0-0.002-0.00816.6560.0350.0350.0000.0000.0000.000
41A230GLU-1-0.873-0.92122.533-10.948-10.9480.0000.0000.0000.000
42A231LYS10.8880.95925.87810.31310.3130.0000.0000.0000.000
43A232ARG10.7590.83923.79011.43511.4350.0000.0000.0000.000
44A233PRO00.0250.02822.973-0.487-0.4870.0000.0000.0000.000
45A234VAL00.0230.00620.752-0.633-0.6330.0000.0000.0000.000
46A235TRP00.0200.01119.1020.5680.5680.0000.0000.0000.000
47A236THR00.0540.03518.145-0.838-0.8380.0000.0000.0000.000
48A237ARG10.9200.95512.90717.65417.6540.0000.0000.0000.000
49A238ARG10.8730.94916.55713.21313.2130.0000.0000.0000.000
50A239ALA00.0870.03619.6240.3210.3210.0000.0000.0000.000
51A240LEU00.0420.03217.2500.2360.2360.0000.0000.0000.000
52A241LEU0-0.069-0.02515.9980.1370.1370.0000.0000.0000.000
53A242ASN0-0.081-0.06319.7630.0220.0220.0000.0000.0000.000
54A243HIS0-0.071-0.03922.6250.7970.7970.0000.0000.0000.000
55A244LEU0-0.041-0.01618.094-0.043-0.0430.0000.0000.0000.000
56A245ASP-1-0.746-0.82921.355-11.466-11.4660.0000.0000.0000.000
57A246PRO00.0420.01320.202-0.634-0.6340.0000.0000.0000.000
58A247SER0-0.067-0.04619.246-0.702-0.7020.0000.0000.0000.000
59A248TYR0-0.028-0.05916.200-0.896-0.8960.0000.0000.0000.000
60A249THR0-0.051-0.03714.846-0.974-0.9740.0000.0000.0000.000
61A250HIS0-0.025-0.03811.198-1.250-1.2500.0000.0000.0000.000
62A251TYR00.0670.03010.317-1.858-1.8580.0000.0000.0000.000
63A252LEU00.0310.02911.091-1.207-1.2070.0000.0000.0000.000
64A253LYS10.9050.9516.09726.68226.6820.0000.0000.0000.000
65A254PHE0-0.003-0.0184.175-2.113-1.999-0.001-0.017-0.0960.000
66A255ALA00.0500.0398.360-0.449-0.4490.0000.0000.0000.000
67A256LEU00.0060.00511.1700.3130.3130.0000.0000.0000.000
68A257PRO0-0.011-0.0037.4100.9750.9750.0000.0000.0000.000
69A258TYR0-0.046-0.0469.619-0.451-0.4510.0000.0000.0000.000
70A259LEU0-0.068-0.02212.5651.0041.0040.0000.0000.0000.000
71A260SER0-0.029-0.01613.5750.9320.9320.0000.0000.0000.000
72A261TYR0-0.010-0.01412.438-1.624-1.6240.0000.0000.0000.000
73A262LEU0-0.040-0.02110.5540.7610.7610.0000.0000.0000.000
74A263TRP00.0040.01513.808-0.749-0.7490.0000.0000.0000.000
75A264THR0-0.008-0.02312.984-0.024-0.0240.0000.0000.0000.000
76A265SER0-0.045-0.03515.8940.4160.4160.0000.0000.0000.000
77A266GLY00.0440.03219.648-0.086-0.0860.0000.0000.0000.000
78A267PRO00.0060.00322.803-0.252-0.2520.0000.0000.0000.000
79A268PHE00.0580.02421.2690.2420.2420.0000.0000.0000.000
80A269ARG10.7800.91618.08013.72613.7260.0000.0000.0000.000
81A270ASP-1-0.829-0.91215.900-15.306-15.3060.0000.0000.0000.000
82A271THR0-0.086-0.06116.9760.2430.2430.0000.0000.0000.000
83A272TYR0-0.004-0.01910.495-0.523-0.5230.0000.0000.0000.000
84A273THR00.0050.00516.1991.1271.1270.0000.0000.0000.000
85A274ARG10.8700.93217.12410.69710.6970.0000.0000.0000.000
86A275PHE0-0.012-0.02412.2520.2470.2470.0000.0000.0000.000
87A276GLY00.0150.00718.2630.5510.5510.0000.0000.0000.000
88A277TYR0-0.057-0.03521.1230.4080.4080.0000.0000.0000.000
89A278ASP-1-0.715-0.84521.654-12.639-12.6390.0000.0000.0000.000
90A279PRO00.0190.02122.4860.4900.4900.0000.0000.0000.000
91A280ARG10.7660.83023.22712.82412.8240.0000.0000.0000.000
92A281LYS10.8590.91625.84811.50911.5090.0000.0000.0000.000
93A282ASP-1-0.752-0.83228.575-9.307-9.3070.0000.0000.0000.000
94A283SER00.0570.02429.918-0.147-0.1470.0000.0000.0000.000
95A284ASN0-0.041-0.03031.4360.2340.2340.0000.0000.0000.000
96A285ALA0-0.025-0.01226.666-0.086-0.0860.0000.0000.0000.000
97A286ALA00.0260.01227.987-0.295-0.2950.0000.0000.0000.000
98A287ALA00.0010.01929.957-0.043-0.0430.0000.0000.0000.000
99A288TYR00.015-0.00524.731-0.136-0.1360.0000.0000.0000.000
100A289GLN00.0100.01924.578-0.319-0.3190.0000.0000.0000.000
101A290ALA0-0.014-0.00922.4030.1940.1940.0000.0000.0000.000
102A291LEU00.0000.01324.2910.0180.0180.0000.0000.0000.000
103A292PHE00.0240.00021.215-0.202-0.2020.0000.0000.0000.000
104A293PHE0-0.013-0.01124.1490.3090.3090.0000.0000.0000.000
105A294LYS10.9500.97624.34811.29511.2950.0000.0000.0000.000
106A295LEU00.0360.01625.8360.2940.2940.0000.0000.0000.000
107A296LYS10.9080.95626.0378.8058.8050.0000.0000.0000.000
108A297LEU00.0040.01522.0880.2780.2780.0000.0000.0000.000
109A298ASN0-0.005-0.00925.760-0.344-0.3440.0000.0000.0000.000
110A299GLY00.0470.02226.639-0.097-0.0970.0000.0000.0000.000
111A300LYS10.9450.96027.4369.2009.2000.0000.0000.0000.000
112A301HIS00.0260.03129.4500.3220.3220.0000.0000.0000.000
113A302LYS10.9200.95028.2948.9758.9750.0000.0000.0000.000
114A303GLY00.0840.05428.1040.2810.2810.0000.0000.0000.000
115A304THR00.0120.02927.874-0.367-0.3670.0000.0000.0000.000
116A305LYS10.9580.97422.35511.28411.2840.0000.0000.0000.000
117A306THR00.0380.01924.387-0.464-0.4640.0000.0000.0000.000
118A307HIS00.0380.02323.764-0.424-0.4240.0000.0000.0000.000
119A308VAL0-0.0190.00525.517-0.001-0.0010.0000.0000.0000.000
120A309PHE0-0.019-0.00529.236-0.013-0.0130.0000.0000.0000.000
121A310ASP-1-0.754-0.87931.221-8.168-8.1680.0000.0000.0000.000
122A311GLY00.0010.00734.2380.2270.2270.0000.0000.0000.000
123A312LYS10.9140.94735.8207.6207.6200.0000.0000.0000.000
124A313THR0-0.055-0.05332.7520.0920.0920.0000.0000.0000.000
125A314LEU00.0150.01233.634-0.204-0.2040.0000.0000.0000.000
126A315PHE0-0.027-0.00531.141-0.218-0.2180.0000.0000.0000.000
127A316PRO00.0320.02928.280-0.313-0.3130.0000.0000.0000.000
128A317THR0-0.034-0.03623.873-0.267-0.2670.0000.0000.0000.000
129A318ASN0-0.037-0.02522.398-0.935-0.9350.0000.0000.0000.000
130A319ARG10.8390.90222.19411.15111.1510.0000.0000.0000.000
131A320VAL00.0050.00719.6330.0620.0620.0000.0000.0000.000
132A321TYR00.0020.01822.802-0.132-0.1320.0000.0000.0000.000
133A322GLN00.016-0.01022.609-0.262-0.2620.0000.0000.0000.000
134A323VAL00.0220.00725.9330.2560.2560.0000.0000.0000.000
135A324CYS0-0.029-0.01027.7040.1540.1540.0000.0000.0000.000
136A325ASP-1-0.814-0.85625.848-10.515-10.5150.0000.0000.0000.000
137A326ILE0-0.034-0.02229.4690.0570.0570.0000.0000.0000.000
138A327VAL00.0270.00532.1150.1700.1700.0000.0000.0000.000
139A328ASP-1-0.753-0.83435.061-7.500-7.5000.0000.0000.0000.000
140A329PRO00.0370.01337.105-0.040-0.0400.0000.0000.0000.000
141A330THR0-0.052-0.04239.8850.1160.1160.0000.0000.0000.000
142A331ILE0-0.016-0.01934.8730.0010.0010.0000.0000.0000.000
143A332ALA00.0130.01036.164-0.038-0.0380.0000.0000.0000.000
144A333PRO00.0400.01337.152-0.078-0.0780.0000.0000.0000.000
145A334LEU0-0.0230.00238.1030.0330.0330.0000.0000.0000.000
146A335LEU00.011-0.00432.573-0.034-0.0340.0000.0000.0000.000
147A336LYS10.8630.93336.6247.0717.0710.0000.0000.0000.000
148A337ASP-1-0.843-0.91738.287-7.003-7.0030.0000.0000.0000.000
149A338THR0-0.087-0.02437.3180.1550.1550.0000.0000.0000.000
150A339GLN0-0.0050.00139.2890.0070.0070.0000.0000.0000.000
151A340LEU0-0.033-0.01234.396-0.095-0.0950.0000.0000.0000.000
152A341ARG10.7650.85533.6119.0149.0140.0000.0000.0000.000
153A342SER00.0350.01036.236-0.043-0.0430.0000.0000.0000.000
154A343GLU-1-0.834-0.90032.106-9.141-9.1410.0000.0000.0000.000
155A344CYS0-0.0710.01228.306-0.065-0.0650.0000.0000.0000.000
156A345HIS00.0690.03929.575-0.368-0.3680.0000.0000.0000.000
157A346ARG10.9490.96226.30310.76110.7610.0000.0000.0000.000
158A347ASP-1-0.882-0.94926.167-11.119-11.1190.0000.0000.0000.000
159A348THR0-0.026-0.04527.849-0.164-0.1640.0000.0000.0000.000
160A349GLY00.0230.01428.9420.1280.1280.0000.0000.0000.000
161A350TRP00.013-0.00528.8870.3290.3290.0000.0000.0000.000
162A351TYR0-0.0090.00030.6050.4500.4500.0000.0000.0000.000
163A352ARG10.9090.94434.3577.2667.2660.0000.0000.0000.000
164A353SER00.0380.01135.2650.0250.0250.0000.0000.0000.000
165A354GLY00.0640.02836.322-0.099-0.0990.0000.0000.0000.000
166A355ARG10.8130.89937.2087.4197.4190.0000.0000.0000.000
167A356TYR0-0.013-0.01527.693-0.081-0.0810.0000.0000.0000.000
168A357TYR00.008-0.01831.009-0.259-0.2590.0000.0000.0000.000
169A358LYS10.8960.95935.1487.0047.0040.0000.0000.0000.000
170A359VAL00.0300.01033.0710.0090.0090.0000.0000.0000.000
171A360ARG10.8500.91130.4429.0469.0460.0000.0000.0000.000
172A361ASP-1-0.782-0.87832.903-8.547-8.5470.0000.0000.0000.000
173A362LEU00.0190.01835.6570.0370.0370.0000.0000.0000.000
174A363MET0-0.025-0.00729.538-0.015-0.0150.0000.0000.0000.000
175A364ARG10.7690.87131.6828.3368.3360.0000.0000.0000.000
176A365GLU-1-0.825-0.91132.953-7.954-7.9540.0000.0000.0000.000
177A366LYS10.8390.89935.3257.6777.6770.0000.0000.0000.000
178A367LEU0-0.026-0.01928.938-0.046-0.0460.0000.0000.0000.000
179A368PHE0-0.035-0.02032.879-0.199-0.1990.0000.0000.0000.000
180A369ALA00.0460.03734.5110.0050.0050.0000.0000.0000.000
181A370LEU00.0220.02433.485-0.022-0.0220.0000.0000.0000.000
182A371ILE0-0.135-0.07129.686-0.133-0.1330.0000.0000.0000.000
183A372GLU-1-0.888-0.95532.534-8.830-8.8300.0000.0000.0000.000
184A373GLY0-0.047-0.01935.5600.1500.1500.0000.0000.0000.000
185A374GLU-1-0.946-0.96537.188-7.033-7.0330.0000.0000.0000.000
186A375MET0-0.016-0.02138.570-0.224-0.2240.0000.0000.0000.000
187A376PRO0-0.019-0.01437.9180.0920.0920.0000.0000.0000.000
188A377SER00.0370.02940.7080.1540.1540.0000.0000.0000.000
189A378GLU-1-0.860-0.92943.984-6.382-6.3820.0000.0000.0000.000
190A379VAL00.0450.02245.518-0.014-0.0140.0000.0000.0000.000
191A380ALA00.006-0.00644.048-0.001-0.0010.0000.0000.0000.000
192A381VAL0-0.001-0.01040.393-0.085-0.0850.0000.0000.0000.000
193A382ASN0-0.021-0.02742.919-0.168-0.1680.0000.0000.0000.000
194A383MET0-0.0250.00345.4530.0320.0320.0000.0000.0000.000
195A384ILE0-0.0020.00239.290-0.018-0.0180.0000.0000.0000.000
196A385LEU0-0.040-0.01641.823-0.085-0.0850.0000.0000.0000.000
197A386ASN0-0.035-0.03943.3120.0280.0280.0000.0000.0000.000
198A387ALA00.0000.04043.7780.1080.1080.0000.0000.0000.000
199A388GLU-1-0.889-0.93845.128-6.291-6.2910.0000.0000.0000.000
200A389GLU-1-0.839-0.88841.691-7.492-7.4920.0000.0000.0000.000
201A390VAL00.0100.00240.683-0.007-0.0070.0000.0000.0000.000