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: LN769

Calculation Name: 4M98-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M98

Chain ID: A

ChEMBL ID:

UniProt ID: Q5FAE1

Base Structure: X-ray

Registration Date: 2023-09-22

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2014463.15926
FMO2-HF: Nuclear repulsion 1941786.572821
FMO2-HF: Total energy -72676.586438
FMO2-MP2: Total energy -72889.53747


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:199:ASN)


Summations of interaction energy for fragment #1(A:199:ASN)
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.
-43.009-31.74320.303-12.647-18.919-0.093
Interaction energy analysis for fragmet #1(A:199:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.048 / q_NPA : -0.035
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].
3A201LYS10.8410.9322.379-2.7400.1390.300-1.429-1.7510.004
4A202LEU00.0150.0223.365-3.464-2.8520.085-0.330-0.367-0.002
5A203ALA0-0.012-0.0055.9161.2251.2250.0000.0000.0000.000
6A204VAL0-0.010-0.0108.691-0.359-0.3590.0000.0000.0000.000
7A205ILE00.0180.00111.0420.3410.3410.0000.0000.0000.000
8A206GLY00.0200.01113.7840.0430.0430.0000.0000.0000.000
9A207ALA0-0.006-0.01416.775-0.073-0.0730.0000.0000.0000.000
10A208GLY00.0250.01318.6800.1000.1000.0000.0000.0000.000
11A209GLY0-0.005-0.01720.622-0.036-0.0360.0000.0000.0000.000
12A210HIS00.011-0.00217.7320.0100.0100.0000.0000.0000.000
13A211GLY00.1110.04116.658-0.069-0.0690.0000.0000.0000.000
14A212LYS10.8610.92716.4890.4880.4880.0000.0000.0000.000
15A213VAL00.0120.01418.083-0.012-0.0120.0000.0000.0000.000
16A214VAL00.0160.00612.884-0.018-0.0180.0000.0000.0000.000
17A215ALA0-0.0020.00613.117-0.158-0.1580.0000.0000.0000.000
18A216GLU-1-0.889-0.94313.960-0.677-0.6770.0000.0000.0000.000
19A217LEU0-0.064-0.02113.0360.0720.0720.0000.0000.0000.000
20A218ALA00.0230.0019.9300.0080.0080.0000.0000.0000.000
21A219ALA0-0.019-0.02111.1740.0210.0210.0000.0000.0000.000
22A220ALA0-0.044-0.02013.3580.1340.1340.0000.0000.0000.000
23A221LEU0-0.042-0.0159.1110.1130.1130.0000.0000.0000.000
24A222GLY0-0.0260.00411.8950.1510.1510.0000.0000.0000.000
25A223THR0-0.017-0.0116.6970.3340.3340.0000.0000.0000.000
26A224TYR0-0.083-0.0543.1641.9102.4000.019-0.125-0.3830.000
27A225GLY0-0.050-0.0286.8170.5450.5450.0000.0000.0000.000
28A226GLU-1-0.886-0.9587.4000.0940.0940.0000.0000.0000.000
29A227ILE00.0300.0247.493-0.635-0.6350.0000.0000.0000.000
30A228VAL0-0.012-0.0039.1320.3870.3870.0000.0000.0000.000
31A229PHE0-0.019-0.00811.381-0.283-0.2830.0000.0000.0000.000
32A230LEU0-0.0060.00811.9610.1030.1030.0000.0000.0000.000
33A231ASP-1-0.766-0.89314.953-0.805-0.8050.0000.0000.0000.000
34A232ASP-1-0.743-0.85918.616-0.716-0.7160.0000.0000.0000.000
35A233ARG10.7110.84619.8780.7740.7740.0000.0000.0000.000
36A234THR0-0.047-0.00820.9880.0610.0610.0000.0000.0000.000
37A235GLN00.0370.01221.409-0.021-0.0210.0000.0000.0000.000
38A236GLY00.0210.02221.3740.0120.0120.0000.0000.0000.000
39A237SER0-0.034-0.01319.204-0.035-0.0350.0000.0000.0000.000
40A238VAL00.0270.01219.0120.0450.0450.0000.0000.0000.000
41A239ASN0-0.041-0.03919.043-0.019-0.0190.0000.0000.0000.000
42A240GLY00.0350.02219.674-0.018-0.0180.0000.0000.0000.000
43A241PHE00.0070.01813.7300.0120.0120.0000.0000.0000.000
44A242PRO0-0.0010.00113.6920.0400.0400.0000.0000.0000.000
45A243VAL0-0.007-0.01314.741-0.158-0.1580.0000.0000.0000.000
46A244ILE0-0.022-0.01010.8820.1110.1110.0000.0000.0000.000
47A245GLY00.0320.01315.1980.1040.1040.0000.0000.0000.000
48A246THR00.0000.00616.920-0.095-0.0950.0000.0000.0000.000
49A247THR0-0.002-0.05215.571-0.047-0.0470.0000.0000.0000.000
50A248LEU00.0230.02815.723-0.054-0.0540.0000.0000.0000.000
51A249LEU0-0.0030.00113.3620.0400.0400.0000.0000.0000.000
52A250LEU0-0.042-0.0029.788-0.028-0.0280.0000.0000.0000.000
53A251GLU-1-0.818-0.90811.360-0.937-0.9370.0000.0000.0000.000
54A252ASN0-0.106-0.05613.9790.1830.1830.0000.0000.0000.000
55A253SER0-0.066-0.03613.0870.1280.1280.0000.0000.0000.000
56A254LEU0-0.034-0.0088.0500.2430.2430.0000.0000.0000.000
57A255SER00.0620.0317.049-0.037-0.0370.0000.0000.0000.000
58A256PRO00.0610.0243.9220.2950.4430.000-0.070-0.0760.000
59A257GLU-1-0.886-0.9422.157-8.138-6.4272.380-1.888-2.203-0.024
60A258GLN0-0.065-0.0272.8914.1235.9151.841-0.988-2.6440.005
61A259PHE0-0.023-0.0262.540-5.206-2.8371.563-1.461-2.471-0.016
62A260ASP-1-0.748-0.8431.824-38.805-38.88213.359-5.891-7.391-0.064
63A261ILE0-0.024-0.0143.2503.8023.9500.0470.076-0.2710.000
64A262THR00.0340.0136.8280.1780.1780.0000.0000.0000.000
65A263VAL00.0330.0159.9680.2450.2450.0000.0000.0000.000
66A264ALA0-0.0330.00713.3180.1490.1490.0000.0000.0000.000
67A265VAL00.012-0.00116.0170.1690.1690.0000.0000.0000.000
68A266GLY00.0340.01118.974-0.005-0.0050.0000.0000.0000.000
69A267ASN0-0.030-0.02121.8700.0070.0070.0000.0000.0000.000
70A268ASN00.0550.00721.642-0.106-0.1060.0000.0000.0000.000
71A269ARG10.8730.92821.4130.5080.5080.0000.0000.0000.000
72A270ILE00.016-0.00819.814-0.030-0.0300.0000.0000.0000.000
73A271ARG10.7780.89316.3400.9730.9730.0000.0000.0000.000
74A272ARG10.8250.91516.7460.5810.5810.0000.0000.0000.000
75A273GLN0-0.021-0.02217.597-0.062-0.0620.0000.0000.0000.000
76A274ILE00.0190.00313.725-0.023-0.0230.0000.0000.0000.000
77A275THR0-0.019-0.02412.302-0.215-0.2150.0000.0000.0000.000
78A276GLU-1-0.836-0.90812.837-1.005-1.0050.0000.0000.0000.000
79A277ASN0-0.078-0.04314.114-0.101-0.1010.0000.0000.0000.000
80A278ALA00.0490.0139.388-0.005-0.0050.0000.0000.0000.000
81A279ALA00.008-0.0069.687-0.224-0.2240.0000.0000.0000.000
82A280ALA0-0.044-0.01510.9880.0770.0770.0000.0000.0000.000
83A281LEU0-0.049-0.01210.3980.1970.1970.0000.0000.0000.000
84A282GLY00.0090.0108.4080.1180.1180.0000.0000.0000.000
85A283PHE0-0.064-0.0324.930-0.655-0.6550.0000.0000.0000.000
86A284LYS10.8560.9402.5084.5775.7440.710-0.541-1.3370.004
87A285LEU00.0150.0014.895-1.036-1.009-0.0010.000-0.0250.000
88A286PRO00.0110.0115.1801.1771.1770.0000.0000.0000.000
89A287VAL0-0.0130.0027.9420.3650.3650.0000.0000.0000.000
90A288LEU0-0.043-0.0138.2400.0400.0400.0000.0000.0000.000
91A289ILE00.023-0.00411.6830.2000.2000.0000.0000.0000.000
92A290HIS00.0560.02514.3060.0360.0360.0000.0000.0000.000
93A291PRO00.0380.01215.2960.0600.0600.0000.0000.0000.000
94A292ASP-1-0.809-0.88617.561-0.341-0.3410.0000.0000.0000.000
95A293ALA0-0.072-0.01418.7830.0320.0320.0000.0000.0000.000
96A294THR0-0.026-0.01620.5440.0450.0450.0000.0000.0000.000
97A295VAL00.010-0.00218.116-0.011-0.0110.0000.0000.0000.000
98A296SER00.0090.00120.7290.0430.0430.0000.0000.0000.000
99A297PRO00.0210.00520.445-0.039-0.0390.0000.0000.0000.000
100A298SER0-0.019-0.01321.3220.0070.0070.0000.0000.0000.000
101A299ALA0-0.0360.00220.7020.0040.0040.0000.0000.0000.000
102A300ILE0-0.010-0.00418.951-0.017-0.0170.0000.0000.0000.000
103A301ILE0-0.014-0.02115.9690.0080.0080.0000.0000.0000.000
104A302GLY00.0300.03315.449-0.069-0.0690.0000.0000.0000.000
105A303GLN00.003-0.00310.387-0.389-0.3890.0000.0000.0000.000
106A304GLY00.0330.00610.7110.2370.2370.0000.0000.0000.000
107A305SER0-0.068-0.02711.8550.2100.2100.0000.0000.0000.000
108A306VAL0-0.035-0.01913.682-0.178-0.1780.0000.0000.0000.000
109A307VAL0-0.0040.00015.7510.1640.1640.0000.0000.0000.000
110A308MET0-0.0030.00117.411-0.036-0.0360.0000.0000.0000.000
111A309ALA00.0610.02519.6050.0490.0490.0000.0000.0000.000
112A310LYS10.8160.86221.4070.3980.3980.0000.0000.0000.000
113A311ALA0-0.0560.01021.4980.0380.0380.0000.0000.0000.000
114A312VAL00.008-0.00722.9800.0080.0080.0000.0000.0000.000
115A313VAL0-0.010-0.00121.000-0.008-0.0080.0000.0000.0000.000
116A314GLN00.0400.02323.6930.0080.0080.0000.0000.0000.000
117A315ALA0-0.039-0.03525.508-0.023-0.0230.0000.0000.0000.000
118A316GLY00.0870.04825.7430.0060.0060.0000.0000.0000.000
119A317SER0-0.0060.01824.466-0.003-0.0030.0000.0000.0000.000
120A318VAL0-0.049-0.02222.209-0.025-0.0250.0000.0000.0000.000
121A319LEU0-0.017-0.01119.7110.0180.0180.0000.0000.0000.000
122A320LYS10.9290.97719.3090.5100.5100.0000.0000.0000.000
123A321ASP-1-0.803-0.90515.155-1.340-1.3400.0000.0000.0000.000
124A322GLY00.0170.01015.0570.1180.1180.0000.0000.0000.000
125A323VAL0-0.0130.00516.1660.1060.1060.0000.0000.0000.000
126A324ILE0-0.036-0.00717.644-0.113-0.1130.0000.0000.0000.000
127A325VAL00.0330.01819.8640.1030.1030.0000.0000.0000.000
128A326ASN0-0.001-0.01721.047-0.036-0.0360.0000.0000.0000.000
129A327THR00.035-0.01222.9990.0250.0250.0000.0000.0000.000
130A328ALA00.0020.00024.4060.0380.0380.0000.0000.0000.000
131A329ALA0-0.076-0.00725.0690.0430.0430.0000.0000.0000.000
132A330THR00.0220.00725.609-0.010-0.0100.0000.0000.0000.000
133A331VAL0-0.0070.00124.5630.0090.0090.0000.0000.0000.000
134A332ASP-1-0.826-0.91926.888-0.303-0.3030.0000.0000.0000.000
135A333HIS0-0.062-0.05428.454-0.017-0.0170.0000.0000.0000.000
136A334ASP-1-0.866-0.93028.665-0.265-0.2650.0000.0000.0000.000
137A335CYS0-0.080-0.01527.4240.0140.0140.0000.0000.0000.000
138A336LEU0-0.025-0.01225.047-0.014-0.0140.0000.0000.0000.000
139A337LEU0-0.023-0.01223.5790.0170.0170.0000.0000.0000.000
140A338ASP-1-0.824-0.94122.982-0.563-0.5630.0000.0000.0000.000
141A339ALA0-0.008-0.01319.848-0.036-0.0360.0000.0000.0000.000
142A340PHE00.018-0.00415.9540.0710.0710.0000.0000.0000.000
143A341VAL00.0190.03320.5400.0420.0420.0000.0000.0000.000
144A342HIS0-0.044-0.01221.796-0.071-0.0710.0000.0000.0000.000
145A343ILE00.0180.01123.7570.0630.0630.0000.0000.0000.000
146A344SER0-0.038-0.03924.997-0.044-0.0440.0000.0000.0000.000
147A345PRO0-0.005-0.01325.8370.0160.0160.0000.0000.0000.000
148A346GLY00.0170.00427.6000.0310.0310.0000.0000.0000.000
149A347ALA0-0.052-0.00329.1230.0310.0310.0000.0000.0000.000
150A348HIS10.8470.90229.4520.3420.3420.0000.0000.0000.000
151A349LEU0-0.0020.00128.1850.0170.0170.0000.0000.0000.000
152A350SER0-0.001-0.01031.4230.0060.0060.0000.0000.0000.000
153A351GLY00.0710.05132.347-0.017-0.0170.0000.0000.0000.000
154A352ASN0-0.046-0.03432.1550.0230.0230.0000.0000.0000.000
155A353THR0-0.016-0.00631.2640.0150.0150.0000.0000.0000.000
156A354ARG10.8830.93129.7980.2670.2670.0000.0000.0000.000
157A355ILE0-0.025-0.01627.3180.0180.0180.0000.0000.0000.000
158A356GLY00.0620.03327.216-0.032-0.0320.0000.0000.0000.000
159A357GLU-1-0.848-0.93923.866-0.581-0.5810.0000.0000.0000.000
160A358GLU-1-0.770-0.86323.217-0.595-0.5950.0000.0000.0000.000
161A359SER0-0.0100.03025.0560.0140.0140.0000.0000.0000.000
162A360ARG10.9170.96026.2810.4200.4200.0000.0000.0000.000
163A361ILE00.0420.02027.8800.0430.0430.0000.0000.0000.000
164A362GLY00.0090.02129.062-0.028-0.0280.0000.0000.0000.000
165A363THR00.040-0.01630.536-0.006-0.0060.0000.0000.0000.000
166A364GLY00.0020.01231.4390.0250.0250.0000.0000.0000.000
167A365ALA0-0.060-0.00132.7270.0210.0210.0000.0000.0000.000
168A366CYS0-0.011-0.01233.491-0.003-0.0030.0000.0000.0000.000
169A367SER00.0370.02333.8580.0030.0030.0000.0000.0000.000
170A368ARG10.8980.96135.8430.2220.2220.0000.0000.0000.000
171A369GLN00.003-0.00836.358-0.011-0.0110.0000.0000.0000.000
172A370GLN0-0.021-0.01436.1580.0170.0170.0000.0000.0000.000
173A371THR0-0.048-0.00636.0340.0020.0020.0000.0000.0000.000
174A372THR0-0.012-0.01133.603-0.021-0.0210.0000.0000.0000.000
175A373VAL0-0.046-0.02631.7980.0160.0160.0000.0000.0000.000
176A374GLY00.0550.03431.768-0.018-0.0180.0000.0000.0000.000
177A375SER0-0.046-0.04829.018-0.023-0.0230.0000.0000.0000.000
178A376GLY00.0550.01628.7920.0270.0270.0000.0000.0000.000
179A377VAL0-0.0360.00030.1580.0230.0230.0000.0000.0000.000
180A378THR0-0.066-0.03030.648-0.040-0.0400.0000.0000.0000.000
181A379ALA00.0170.01132.1770.0280.0280.0000.0000.0000.000
182A380GLY0-0.016-0.01533.021-0.020-0.0200.0000.0000.0000.000
183A381ALA00.006-0.02134.066-0.002-0.0020.0000.0000.0000.000
184A382GLY0-0.034-0.01134.9530.0180.0180.0000.0000.0000.000
185A383ALA0-0.071-0.01635.8730.0170.0170.0000.0000.0000.000
186A384VAL00.0200.01136.844-0.010-0.0100.0000.0000.0000.000
187A385ILE00.0210.00634.1280.0140.0140.0000.0000.0000.000
188A386VAL00.0330.01138.2700.0000.0000.0000.0000.0000.000
189A387CYS0-0.035-0.01840.2500.0150.0150.0000.0000.0000.000
190A388ASP-1-0.769-0.87338.000-0.264-0.2640.0000.0000.0000.000
191A389ILE0-0.063-0.03335.8120.0100.0100.0000.0000.0000.000
192A390PRO00.0350.00536.060-0.015-0.0150.0000.0000.0000.000
193A391ASP-1-0.785-0.87633.083-0.338-0.3380.0000.0000.0000.000
194A392GLY0-0.0280.00133.5260.0180.0180.0000.0000.0000.000
195A393MET0-0.0560.00334.7530.0100.0100.0000.0000.0000.000
196A394THR00.0330.00635.290-0.025-0.0250.0000.0000.0000.000
197A395VAL0-0.002-0.00636.4700.0190.0190.0000.0000.0000.000
198A396ALA00.025-0.00137.338-0.019-0.0190.0000.0000.0000.000
199A397GLY00.0270.02239.5520.0130.0130.0000.0000.0000.000
200A398ASN00.0090.02141.164-0.009-0.0090.0000.0000.0000.000
201A399PRO00.0490.00642.9720.0100.0100.0000.0000.0000.000
202A400ALA0-0.053-0.02739.1180.0030.0030.0000.0000.0000.000
203A401LYS10.8990.94641.1210.2090.2090.0000.0000.0000.000
204A402PRO00.0610.00941.213-0.010-0.0100.0000.0000.0000.000
205A403LEU0-0.041-0.00139.1280.0130.0130.0000.0000.0000.000