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: 89MMY

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2397871.760988
FMO2-HF: Nuclear repulsion 2316177.015026
FMO2-HF: Total energy -81694.745961
FMO2-MP2: Total energy -81934.119682


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.
117.064124.1744.758-3.923-7.945-0.024
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 : 0.978 / 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].
3A192TRP00.008-0.0092.456-10.206-3.4174.756-3.849-7.696-0.024
4A193ILE00.0320.0274.0682.9863.2060.003-0.060-0.1640.000
5A194ILE00.0310.0267.325-1.858-1.8580.0000.0000.0000.000
6A195THR0-0.024-0.0119.6171.2031.2030.0000.0000.0000.000
7A196THR00.0450.02711.9870.0840.0840.0000.0000.0000.000
8A197ASN00.0290.01815.7430.4990.4990.0000.0000.0000.000
9A198MET00.0320.01018.915-0.017-0.0170.0000.0000.0000.000
10A199GLY00.0110.02621.8390.5360.5360.0000.0000.0000.000
11A200VAL0-0.052-0.01217.846-0.044-0.0440.0000.0000.0000.000
12A201GLU-1-0.841-0.88920.619-11.970-11.9700.0000.0000.0000.000
13A202SER0-0.014-0.03321.6500.6010.6010.0000.0000.0000.000
14A203VAL0-0.070-0.02618.926-0.725-0.7250.0000.0000.0000.000
15A204PRO00.010-0.00514.4790.1030.1030.0000.0000.0000.000
16A205THR00.0400.01216.6610.1910.1910.0000.0000.0000.000
17A206CYS0-0.025-0.01114.3290.6540.6540.0000.0000.0000.000
18A207ARG10.7670.85711.35119.12919.1290.0000.0000.0000.000
19A208HIS00.0470.0186.8150.7860.7860.0000.0000.0000.000
20A209SER00.0460.0189.678-0.960-0.9600.0000.0000.0000.000
21A210LYS10.9330.9675.77638.00638.0060.0000.0000.0000.000
22A211LEU0-0.072-0.0096.447-2.412-2.4120.0000.0000.0000.000
23A212GLY00.0850.0508.6152.2532.2530.0000.0000.0000.000
24A213GLU-1-0.769-0.85111.254-18.379-18.3790.0000.0000.0000.000
25A214PRO0-0.0150.01611.397-1.051-1.0510.0000.0000.0000.000
26A215SER00.0320.01011.9751.1531.1530.0000.0000.0000.000
27A216LYS11.0230.98913.90612.36412.3640.0000.0000.0000.000
28A217THR00.0360.02414.2950.2770.2770.0000.0000.0000.000
29A218ILE0-0.028-0.00710.391-0.066-0.0660.0000.0000.0000.000
30A219GLN0-0.021-0.02713.733-0.300-0.3000.0000.0000.0000.000
31A220GLU-1-0.858-0.90016.592-12.388-12.3880.0000.0000.0000.000
32A221VAL00.007-0.00415.1230.3070.3070.0000.0000.0000.000
33A222ILE0-0.027-0.00913.1780.1610.1610.0000.0000.0000.000
34A223GLU-1-0.794-0.87617.119-12.892-12.8920.0000.0000.0000.000
35A224ALA00.0090.00820.0680.4930.4930.0000.0000.0000.000
36A225LEU0-0.025-0.01815.3740.2360.2360.0000.0000.0000.000
37A226LYS10.8580.92119.66813.56313.5630.0000.0000.0000.000
38A227PRO00.0340.01521.9600.2950.2950.0000.0000.0000.000
39A228LEU0-0.048-0.02421.2900.4310.4310.0000.0000.0000.000
40A229PHE00.004-0.00916.7940.0530.0530.0000.0000.0000.000
41A230GLU-1-0.843-0.91022.624-10.878-10.8780.0000.0000.0000.000
42A231LYS10.8970.96926.06510.40910.4090.0000.0000.0000.000
43A232ARG10.7730.84923.88911.48511.4850.0000.0000.0000.000
44A233PRO00.0180.02523.021-0.494-0.4940.0000.0000.0000.000
45A234VAL00.012-0.00120.826-0.625-0.6250.0000.0000.0000.000
46A235TRP00.0150.00919.1660.5340.5340.0000.0000.0000.000
47A236THR00.0510.03918.257-0.826-0.8260.0000.0000.0000.000
48A237ARG10.8990.93812.80017.78617.7860.0000.0000.0000.000
49A238ARG10.8610.92916.57313.01313.0130.0000.0000.0000.000
50A239ALA00.0800.03419.6640.3510.3510.0000.0000.0000.000
51A240LEU00.0330.02917.3370.2520.2520.0000.0000.0000.000
52A241LEU0-0.091-0.04216.2630.1040.1040.0000.0000.0000.000
53A242ASN0-0.062-0.03519.748-0.053-0.0530.0000.0000.0000.000
54A243HIS0-0.056-0.03422.5430.8080.8080.0000.0000.0000.000
55A244LEU0-0.022-0.00718.365-0.079-0.0790.0000.0000.0000.000
56A245ASP-1-0.746-0.83521.211-11.516-11.5160.0000.0000.0000.000
57A246PRO00.0190.00820.173-0.651-0.6510.0000.0000.0000.000
58A247SER0-0.045-0.03119.024-0.761-0.7610.0000.0000.0000.000
59A248TYR0-0.024-0.05416.188-0.938-0.9380.0000.0000.0000.000
60A249THR0-0.047-0.03914.953-0.986-0.9860.0000.0000.0000.000
61A250HIS0-0.008-0.02611.259-1.340-1.3400.0000.0000.0000.000
62A251TYR00.0780.03710.330-2.026-2.0260.0000.0000.0000.000
63A252LEU00.0390.02111.168-1.297-1.2970.0000.0000.0000.000
64A253LYS10.8890.9546.67625.62525.6250.0000.0000.0000.000
65A254PHE0-0.002-0.0154.186-2.249-2.148-0.001-0.014-0.0850.000
66A255ALA00.0320.0268.604-0.258-0.2580.0000.0000.0000.000
67A256LEU00.0160.00611.4660.2020.2020.0000.0000.0000.000
68A257PRO00.0000.0017.6170.9310.9310.0000.0000.0000.000
69A258TYR0-0.029-0.0399.511-0.387-0.3870.0000.0000.0000.000
70A259LEU0-0.068-0.02312.6871.0431.0430.0000.0000.0000.000
71A260SER0-0.040-0.02513.5830.9090.9090.0000.0000.0000.000
72A261TYR0-0.013-0.02412.450-1.632-1.6320.0000.0000.0000.000
73A262LEU0-0.041-0.02410.8020.8190.8190.0000.0000.0000.000
74A263TRP00.0160.01613.832-0.847-0.8470.0000.0000.0000.000
75A264THR0-0.009-0.03013.5550.2600.2600.0000.0000.0000.000
76A265SER0-0.045-0.03816.2630.4960.4960.0000.0000.0000.000
77A266GLY00.0460.03120.0030.0040.0040.0000.0000.0000.000
78A267PRO0-0.016-0.00423.292-0.266-0.2660.0000.0000.0000.000
79A268PHE00.0610.02721.5910.2950.2950.0000.0000.0000.000
80A269ARG10.7660.89318.25714.00214.0020.0000.0000.0000.000
81A270ASP-1-0.820-0.88716.216-15.317-15.3170.0000.0000.0000.000
82A271THR0-0.068-0.05717.2740.1590.1590.0000.0000.0000.000
83A272TYR0-0.005-0.01210.474-0.460-0.4600.0000.0000.0000.000
84A273THR00.0060.00416.2871.1621.1620.0000.0000.0000.000
85A274ARG10.8360.90717.01610.73710.7370.0000.0000.0000.000
86A275PHE00.000-0.00912.3650.3210.3210.0000.0000.0000.000
87A276GLY00.0030.00318.3510.5780.5780.0000.0000.0000.000
88A277TYR0-0.049-0.04121.4660.3430.3430.0000.0000.0000.000
89A278ASP-1-0.705-0.83421.524-12.796-12.7960.0000.0000.0000.000
90A279PRO00.0210.01722.3920.4880.4880.0000.0000.0000.000
91A280ARG10.7480.81323.00112.91012.9100.0000.0000.0000.000
92A281LYS10.8480.91725.52511.64511.6450.0000.0000.0000.000
93A282ASP-1-0.754-0.83528.452-9.379-9.3790.0000.0000.0000.000
94A283SER00.0630.02629.934-0.145-0.1450.0000.0000.0000.000
95A284ASN0-0.053-0.04031.3420.2480.2480.0000.0000.0000.000
96A285ALA0-0.0120.00526.801-0.081-0.0810.0000.0000.0000.000
97A286ALA00.0350.01828.369-0.267-0.2670.0000.0000.0000.000
98A287ALA00.0100.02030.630-0.025-0.0250.0000.0000.0000.000
99A288TYR00.002-0.01625.183-0.147-0.1470.0000.0000.0000.000
100A289GLN00.0120.01425.007-0.306-0.3060.0000.0000.0000.000
101A290ALA0-0.022-0.01622.7740.1770.1770.0000.0000.0000.000
102A291LEU0-0.0050.01024.733-0.053-0.0530.0000.0000.0000.000
103A292PHE00.020-0.00321.618-0.182-0.1820.0000.0000.0000.000
104A293PHE00.006-0.00224.4220.3180.3180.0000.0000.0000.000
105A294LYS10.9420.97624.68311.34611.3460.0000.0000.0000.000
106A295LEU00.0280.01326.0660.2770.2770.0000.0000.0000.000
107A296LYS10.8700.90126.5428.8528.8520.0000.0000.0000.000
108A297LEU00.0360.05922.0640.2080.2080.0000.0000.0000.000
109A298ASN0-0.040-0.03125.640-0.258-0.2580.0000.0000.0000.000
110A299GLY00.0560.02627.067-0.014-0.0140.0000.0000.0000.000
111A300LYS10.9540.96827.7199.1839.1830.0000.0000.0000.000
112A301HIS00.0150.02529.7790.3020.3020.0000.0000.0000.000
113A302LYS10.9180.94929.0508.9498.9490.0000.0000.0000.000
114A303GLY00.0660.03928.8700.2930.2930.0000.0000.0000.000
115A304THR00.0290.04428.380-0.422-0.4220.0000.0000.0000.000
116A305LYS10.9760.99523.16011.12311.1230.0000.0000.0000.000
117A306THR00.0280.02024.809-0.434-0.4340.0000.0000.0000.000
118A307HIS00.0460.03024.080-0.453-0.4530.0000.0000.0000.000
119A308VAL0-0.0240.00125.801-0.021-0.0210.0000.0000.0000.000
120A309PHE0-0.012-0.00829.531-0.025-0.0250.0000.0000.0000.000
121A310ASP-1-0.760-0.87631.582-8.130-8.1300.0000.0000.0000.000
122A311GLY00.0100.00934.6660.2250.2250.0000.0000.0000.000
123A312LYS10.9010.94236.1957.7077.7070.0000.0000.0000.000
124A313THR0-0.046-0.05433.0040.0860.0860.0000.0000.0000.000
125A314LEU00.0180.01033.807-0.227-0.2270.0000.0000.0000.000
126A315PHE0-0.0180.00931.356-0.203-0.2030.0000.0000.0000.000
127A316PRO00.0210.01528.643-0.287-0.2870.0000.0000.0000.000
128A317THR0-0.046-0.04724.017-0.311-0.3110.0000.0000.0000.000
129A318ASN0-0.033-0.02522.695-0.893-0.8930.0000.0000.0000.000
130A319ARG10.7920.85922.33811.17411.1740.0000.0000.0000.000
131A320VAL00.0000.00019.983-0.010-0.0100.0000.0000.0000.000
132A321TYR00.0000.02223.057-0.158-0.1580.0000.0000.0000.000
133A322GLN00.018-0.00722.778-0.284-0.2840.0000.0000.0000.000
134A323VAL00.0120.00526.2140.2460.2460.0000.0000.0000.000
135A324CYS0-0.024-0.00427.6780.1440.1440.0000.0000.0000.000
136A325ASP-1-0.805-0.86025.897-10.645-10.6450.0000.0000.0000.000
137A326ILE0-0.050-0.02429.5510.1030.1030.0000.0000.0000.000
138A327VAL00.016-0.00432.4500.1520.1520.0000.0000.0000.000
139A328ASP-1-0.722-0.82335.396-7.562-7.5620.0000.0000.0000.000
140A329PRO00.0230.01337.370-0.028-0.0280.0000.0000.0000.000
141A330THR0-0.046-0.03940.1250.1270.1270.0000.0000.0000.000
142A331ILE0-0.023-0.02535.091-0.016-0.0160.0000.0000.0000.000
143A332ALA00.0180.01136.192-0.059-0.0590.0000.0000.0000.000
144A333PRO00.0320.00337.177-0.066-0.0660.0000.0000.0000.000
145A334LEU0-0.0140.01538.2930.0250.0250.0000.0000.0000.000
146A335LEU0-0.013-0.00932.734-0.031-0.0310.0000.0000.0000.000
147A336LYS10.8390.91636.7167.0257.0250.0000.0000.0000.000
148A337ASP-1-0.816-0.88138.563-6.998-6.9980.0000.0000.0000.000
149A338THR0-0.040-0.03838.0040.1450.1450.0000.0000.0000.000
150A339GLN0-0.0160.01339.8410.0340.0340.0000.0000.0000.000
151A340LEU00.0010.00434.631-0.102-0.1020.0000.0000.0000.000
152A341ARG10.7570.84633.7989.0429.0420.0000.0000.0000.000
153A342SER00.0240.00836.322-0.051-0.0510.0000.0000.0000.000
154A343GLU-1-0.808-0.88532.296-9.130-9.1300.0000.0000.0000.000
155A344CYS0-0.0590.01328.402-0.064-0.0640.0000.0000.0000.000
156A345HIS00.0650.04329.454-0.415-0.4150.0000.0000.0000.000
157A346ARG10.8660.89526.20410.84210.8420.0000.0000.0000.000
158A347ASP-1-0.827-0.90226.243-11.299-11.2990.0000.0000.0000.000
159A348THR0-0.013-0.03828.285-0.105-0.1050.0000.0000.0000.000
160A349GLY00.0240.01829.1720.1280.1280.0000.0000.0000.000
161A350TRP00.0260.00829.0830.3420.3420.0000.0000.0000.000
162A351TYR0-0.014-0.00531.2110.4380.4380.0000.0000.0000.000
163A352ARG10.8670.91334.6977.3087.3080.0000.0000.0000.000
164A353SER00.0390.01135.4330.0280.0280.0000.0000.0000.000
165A354GLY00.0820.04536.493-0.107-0.1070.0000.0000.0000.000
166A355ARG10.7740.87737.6127.3877.3870.0000.0000.0000.000
167A356TYR0-0.006-0.00328.090-0.092-0.0920.0000.0000.0000.000
168A357TYR0-0.007-0.02731.318-0.283-0.2830.0000.0000.0000.000
169A358LYS10.8750.94035.3387.0107.0100.0000.0000.0000.000
170A359VAL00.0280.01333.2260.0130.0130.0000.0000.0000.000
171A360ARG10.8560.91330.6169.0769.0760.0000.0000.0000.000
172A361ASP-1-0.789-0.87733.038-8.589-8.5890.0000.0000.0000.000
173A362LEU00.0180.01535.8390.0240.0240.0000.0000.0000.000
174A363MET0-0.035-0.01329.727-0.016-0.0160.0000.0000.0000.000
175A364ARG10.7510.85632.3588.3358.3350.0000.0000.0000.000
176A365GLU-1-0.798-0.89833.328-8.053-8.0530.0000.0000.0000.000
177A366LYS10.8110.89535.5897.7517.7510.0000.0000.0000.000
178A367LEU0-0.020-0.01529.264-0.039-0.0390.0000.0000.0000.000
179A368PHE0-0.037-0.02733.157-0.193-0.1930.0000.0000.0000.000
180A369ALA00.0550.04634.9850.0040.0040.0000.0000.0000.000
181A370LEU00.0050.01433.774-0.039-0.0390.0000.0000.0000.000
182A371ILE0-0.124-0.06929.867-0.125-0.1250.0000.0000.0000.000
183A372GLU-1-0.802-0.88332.470-9.015-9.0150.0000.0000.0000.000
184A373GLY0-0.032-0.01535.4060.1040.1040.0000.0000.0000.000
185A374GLU-1-0.949-0.96937.140-7.060-7.0600.0000.0000.0000.000
186A375MET0-0.002-0.01638.707-0.224-0.2240.0000.0000.0000.000
187A376PRO0-0.028-0.01638.0780.1040.1040.0000.0000.0000.000
188A377SER00.0200.02040.8820.1510.1510.0000.0000.0000.000
189A378GLU-1-0.858-0.91944.311-6.415-6.4150.0000.0000.0000.000
190A379VAL00.0360.01245.453-0.030-0.0300.0000.0000.0000.000
191A380ALA00.0240.01744.2160.0290.0290.0000.0000.0000.000
192A381VAL0-0.009-0.01340.562-0.083-0.0830.0000.0000.0000.000
193A382ASN0-0.012-0.03442.969-0.168-0.1680.0000.0000.0000.000
194A383MET0-0.0170.00745.5540.0420.0420.0000.0000.0000.000
195A384ILE0-0.0020.00139.472-0.009-0.0090.0000.0000.0000.000
196A385LEU0-0.036-0.01642.149-0.066-0.0660.0000.0000.0000.000
197A386ASN0-0.035-0.02943.7130.0420.0420.0000.0000.0000.000
198A387ALA00.0280.04644.5170.1080.1080.0000.0000.0000.000
199A388GLU-1-0.897-0.94145.713-6.332-6.3320.0000.0000.0000.000
200A389GLU-1-0.829-0.89041.944-7.509-7.5090.0000.0000.0000.000
201A390VAL0-0.0020.00341.104-0.065-0.0650.0000.0000.0000.000