Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: VKRJ1

Calculation Name: 3KB5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KB5

Chain ID: A

ChEMBL ID:

UniProt ID: Q6ZMU5

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptH
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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2184493.728525
FMO2-HF: Nuclear repulsion 2109730.710724
FMO2-HF: Total energy -74763.017801
FMO2-MP2: Total energy -74984.438986


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:278:ARG)


Summations of interaction energy for fragment #1(A:278: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.
-117.7-103.3699.195-9.348-14.178-0.09
Interaction energy analysis for fragmet #1(A:278:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.934 / q_NPA : 0.962
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].
3A280MET00.0260.0153.176-0.7541.4670.003-0.950-1.2740.001
4A281PHE00.0160.0082.3500.3621.6240.787-0.781-1.269-0.004
5A282ARG10.8490.9254.44631.88832.033-0.001-0.020-0.1240.000
6A283ALA0-0.001-0.0066.4532.2462.2460.0000.0000.0000.000
7A284LEU0-0.056-0.0277.1901.4931.4930.0000.0000.0000.000
8A285MET0-0.0490.0038.0591.1671.1670.0000.0000.0000.000
9A286PRO00.0100.01610.9110.5610.5610.0000.0000.0000.000
10A287ALA00.003-0.01114.312-0.603-0.6030.0000.0000.0000.000
11A288LEU0-0.043-0.02414.524-0.024-0.0240.0000.0000.0000.000
12A289GLU-1-0.857-0.92316.990-12.475-12.4750.0000.0000.0000.000
13A290GLU-1-0.983-0.97919.722-11.274-11.2740.0000.0000.0000.000
14A291LEU0-0.049-0.03220.7260.3500.3500.0000.0000.0000.000
15A292THR0-0.023-0.02624.076-0.059-0.0590.0000.0000.0000.000
16A293PHE0-0.048-0.02723.1820.1310.1310.0000.0000.0000.000
17A294ASP-1-0.791-0.88928.025-9.020-9.0200.0000.0000.0000.000
18A295PRO0-0.036-0.04431.4050.0280.0280.0000.0000.0000.000
19A296SER0-0.083-0.04333.9000.1590.1590.0000.0000.0000.000
20A297SER00.003-0.00132.2860.0330.0330.0000.0000.0000.000
21A298ALA0-0.016-0.00932.263-0.133-0.1330.0000.0000.0000.000
22A299HIS00.0730.07332.8890.2820.2820.0000.0000.0000.000
23A300PRO00.0080.00034.750-0.075-0.0750.0000.0000.0000.000
24A301SER0-0.083-0.04934.3820.0110.0110.0000.0000.0000.000
25A302LEU0-0.042-0.01530.026-0.169-0.1690.0000.0000.0000.000
26A303VAL00.0040.01432.3610.3340.3340.0000.0000.0000.000
27A304VAL00.0050.00729.563-0.366-0.3660.0000.0000.0000.000
28A305SER0-0.002-0.01229.8980.2730.2730.0000.0000.0000.000
29A306SER0-0.002-0.01627.521-0.312-0.3120.0000.0000.0000.000
30A307SER0-0.038-0.02928.007-0.230-0.2300.0000.0000.0000.000
31A308GLY00.0580.03128.702-0.108-0.1080.0000.0000.0000.000
32A309ARG11.0101.02123.38911.84711.8470.0000.0000.0000.000
33A310ARG10.8060.89724.09910.99010.9900.0000.0000.0000.000
34A311VAL00.0200.02125.6360.5440.5440.0000.0000.0000.000
35A312GLU-1-0.800-0.87826.785-11.596-11.5960.0000.0000.0000.000
36A313CYS0-0.0120.00729.1140.2320.2320.0000.0000.0000.000
37A314SER0-0.0070.00931.8960.1130.1130.0000.0000.0000.000
38A315GLU-1-0.853-0.95033.469-9.363-9.3630.0000.0000.0000.000
39A316GLN0-0.076-0.03436.6250.4040.4040.0000.0000.0000.000
40A317LYS10.9010.92640.2817.4037.4030.0000.0000.0000.000
41A318ALA00.0180.01239.0940.0270.0270.0000.0000.0000.000
42A319PRO00.0050.02340.0050.1720.1720.0000.0000.0000.000
43A320PRO0-0.014-0.01141.667-0.167-0.1670.0000.0000.0000.000
44A321ALA00.004-0.00340.267-0.061-0.0610.0000.0000.0000.000
45A322GLY00.0140.00941.3920.2010.2010.0000.0000.0000.000
46A323GLU-1-0.938-0.99243.005-7.116-7.1160.0000.0000.0000.000
47A324ASP-1-0.828-0.90739.881-7.998-7.9980.0000.0000.0000.000
48A325PRO0-0.013-0.01739.408-0.193-0.1930.0000.0000.0000.000
49A326ARG10.8970.95135.0658.2818.2810.0000.0000.0000.000
50A327GLN0-0.0030.01734.985-0.115-0.1150.0000.0000.0000.000
51A328PHE0-0.0080.00929.9710.1570.1570.0000.0000.0000.000
52A329ASP-1-0.797-0.90835.104-8.394-8.3940.0000.0000.0000.000
53A330LYS10.8120.91536.0148.3098.3090.0000.0000.0000.000
54A331ALA00.0310.02530.595-0.100-0.1000.0000.0000.0000.000
55A332VAL00.000-0.00430.1440.2120.2120.0000.0000.0000.000
56A333ALA00.0280.00728.249-0.450-0.4500.0000.0000.0000.000
57A334VAL00.0080.00327.0940.4780.4780.0000.0000.0000.000
58A335VAL00.0150.01626.969-0.465-0.4650.0000.0000.0000.000
59A336ALA00.0160.00324.9230.1780.1780.0000.0000.0000.000
60A337HIS00.0170.01627.0650.0440.0440.0000.0000.0000.000
61A338GLN00.0350.01125.5860.0700.0700.0000.0000.0000.000
62A339GLN00.0200.01726.340-0.260-0.2600.0000.0000.0000.000
63A340LEU0-0.020-0.00721.283-0.046-0.0460.0000.0000.0000.000
64A341SER00.033-0.01225.3540.0600.0600.0000.0000.0000.000
65A342GLU-1-0.897-0.96924.701-10.267-10.2670.0000.0000.0000.000
66A343GLY00.0340.03222.067-0.108-0.1080.0000.0000.0000.000
67A344GLU-1-0.922-0.96716.438-13.813-13.8130.0000.0000.0000.000
68A345HIS10.7990.87117.27113.51613.5160.0000.0000.0000.000
69A346TYR00.022-0.03410.353-1.424-1.4240.0000.0000.0000.000
70A347TRP00.0180.02815.0870.6990.6990.0000.0000.0000.000
71A348GLU-1-0.769-0.86511.000-24.623-24.6230.0000.0000.0000.000
72A349VAL0-0.018-0.00715.0121.3561.3560.0000.0000.0000.000
73A350ASP-1-0.804-0.87915.728-20.493-20.4930.0000.0000.0000.000
74A351VAL0-0.033-0.03115.3951.1301.1300.0000.0000.0000.000
75A352GLY0-0.005-0.00216.6340.8590.8590.0000.0000.0000.000
76A353ASP-1-0.906-0.99516.289-16.270-16.2700.0000.0000.0000.000
77A354LYS10.8090.93018.22313.92913.9290.0000.0000.0000.000
78A355PRO0-0.063-0.03219.212-0.991-0.9910.0000.0000.0000.000
79A356ARG10.8620.90720.64011.92311.9230.0000.0000.0000.000
80A357TRP00.0780.03415.2960.4200.4200.0000.0000.0000.000
81A358ALA00.014-0.00620.867-0.479-0.4790.0000.0000.0000.000
82A359LEU0-0.0100.00117.0650.5050.5050.0000.0000.0000.000
83A360GLY00.0690.01719.279-0.570-0.5700.0000.0000.0000.000
84A361VAL0-0.0230.01120.3100.1710.1710.0000.0000.0000.000
85A362ILE0-0.024-0.00722.954-0.021-0.0210.0000.0000.0000.000
86A363ALA00.014-0.00126.6260.0630.0630.0000.0000.0000.000
87A364ALA0-0.022-0.02028.6550.1440.1440.0000.0000.0000.000
88A365GLU-1-0.942-0.96831.347-8.344-8.3440.0000.0000.0000.000
89A366ALA0-0.052-0.00330.9530.1600.1600.0000.0000.0000.000
90A367PRO0-0.018-0.00132.9200.1080.1080.0000.0000.0000.000
91A368ARG10.9590.96431.2389.4999.4990.0000.0000.0000.000
92A369ARG10.8400.93534.6118.0718.0710.0000.0000.0000.000
93A370GLY0-0.008-0.00737.6180.0400.0400.0000.0000.0000.000
94A371ARG10.8950.93034.3138.6078.6070.0000.0000.0000.000
95A372LEU00.0450.02831.0100.0970.0970.0000.0000.0000.000
96A373HIS0-0.037-0.02030.858-0.248-0.2480.0000.0000.0000.000
97A374ALA0-0.002-0.00325.4480.0130.0130.0000.0000.0000.000
98A375VAL0-0.0070.00325.958-0.376-0.3760.0000.0000.0000.000
99A376PRO00.0400.01323.7670.2940.2940.0000.0000.0000.000
100A377SER0-0.055-0.05026.3670.3600.3600.0000.0000.0000.000
101A378GLN0-0.067-0.03829.7620.4260.4260.0000.0000.0000.000
102A379GLY00.0080.00928.5590.1790.1790.0000.0000.0000.000
103A380LEU0-0.013-0.00526.046-0.179-0.1790.0000.0000.0000.000
104A381TRP0-0.033-0.01521.048-0.062-0.0620.0000.0000.0000.000
105A382LEU0-0.017-0.01420.474-0.393-0.3930.0000.0000.0000.000
106A383LEU00.0080.02213.962-0.216-0.2160.0000.0000.0000.000
107A384GLY00.012-0.00418.1240.5440.5440.0000.0000.0000.000
108A385LEU0-0.062-0.00715.235-1.069-1.0690.0000.0000.0000.000
109A386ARG10.9030.92518.36515.32315.3230.0000.0000.0000.000
110A387GLU-1-0.890-0.95319.530-13.639-13.6390.0000.0000.0000.000
111A388GLY0-0.036-0.03318.548-0.137-0.1370.0000.0000.0000.000
112A389LYS10.8550.92215.46216.61816.6180.0000.0000.0000.000
113A390ILE0-0.0040.01715.091-0.952-0.9520.0000.0000.0000.000
114A391LEU00.0450.03511.4280.6970.6970.0000.0000.0000.000
115A392GLU-1-0.827-0.91215.239-14.954-14.9540.0000.0000.0000.000
116A393ALA00.0180.01116.369-0.003-0.0030.0000.0000.0000.000
117A394HIS0-0.021-0.01218.1260.9880.9880.0000.0000.0000.000
118A395VAL0-0.015-0.01719.9000.1610.1610.0000.0000.0000.000
119A396GLU-1-0.760-0.85022.543-10.822-10.8220.0000.0000.0000.000
120A397ALA0-0.031-0.01925.1170.1110.1110.0000.0000.0000.000
121A398LYS10.9410.97527.05110.25010.2500.0000.0000.0000.000
122A399GLU-1-0.963-0.99024.899-11.538-11.5380.0000.0000.0000.000
123A400PRO00.0000.01321.482-0.258-0.2580.0000.0000.0000.000
124A401ARG10.9570.99516.24717.06317.0630.0000.0000.0000.000
125A402ALA00.0330.01817.050-0.837-0.8370.0000.0000.0000.000
126A403LEU0-0.032-0.02211.877-0.377-0.3770.0000.0000.0000.000
127A404ARG10.8990.9468.94424.92424.9240.0000.0000.0000.000
128A405SER0-0.0020.0399.345-1.040-1.0400.0000.0000.0000.000
129A406PRO00.001-0.0234.794-0.733-0.667-0.0010.000-0.0650.000
130A407GLU-1-0.893-0.9612.527-90.125-83.9140.937-3.846-3.301-0.052
131A408ARG10.9750.9715.16846.87946.8790.0000.0000.0000.000
132A409ARG10.8030.9288.40117.64817.6480.0000.0000.0000.000
133A410PRO00.0190.0278.9080.8290.8290.0000.0000.0000.000
134A411THR0-0.039-0.01510.6002.6372.6370.0000.0000.0000.000
135A412ARG10.8940.93311.61523.03723.0370.0000.0000.0000.000
136A413ILE0-0.0350.00211.115-2.643-2.6430.0000.0000.0000.000
137A414GLY00.0330.01910.9971.6551.6550.0000.0000.0000.000
138A415LEU0-0.056-0.02911.943-0.859-0.8590.0000.0000.0000.000
139A416TYR00.0230.00811.6530.5410.5410.0000.0000.0000.000
140A417LEU0-0.013-0.00413.6800.1010.1010.0000.0000.0000.000
141A418SER00.0160.00316.3700.5560.5560.0000.0000.0000.000
142A419PHE0-0.024-0.01018.2330.1390.1390.0000.0000.0000.000
143A420GLY0-0.046-0.01621.3040.3280.3280.0000.0000.0000.000
144A421ASP-1-0.877-0.93117.390-14.460-14.4600.0000.0000.0000.000
145A422GLY0-0.086-0.02819.662-0.078-0.0780.0000.0000.0000.000
146A423VAL00.0260.00414.744-0.376-0.3760.0000.0000.0000.000
147A424LEU00.0070.01016.4720.2900.2900.0000.0000.0000.000
148A425SER0-0.030-0.02211.1600.0800.0800.0000.0000.0000.000
149A426PHE00.0100.00412.1010.4250.4250.0000.0000.0000.000
150A427TYR00.005-0.0176.074-1.524-1.5240.0000.0000.0000.000
151A428ASP-1-0.825-0.9016.285-36.973-36.9730.0000.0000.0000.000
152A429ALA00.017-0.0276.476-4.709-4.7090.0000.0000.0000.000
153A430SER0-0.036-0.0338.1433.5233.5230.0000.0000.0000.000
154A431ASP-1-0.930-0.9485.573-37.633-37.6330.0000.0000.0000.000
155A432ALA00.0440.0107.144-0.516-0.5160.0000.0000.0000.000
156A433ASP-1-0.950-0.9707.308-29.019-29.0190.0000.0000.0000.000
157A434ALA0-0.064-0.0422.337-4.480-4.0840.934-0.401-0.929-0.003
158A435LEU0-0.0040.0192.5921.8263.0070.219-0.459-0.941-0.005
159A436VAL0-0.055-0.0312.103-14.778-12.3006.312-2.841-5.949-0.027
160A437PRO0-0.0130.0063.7235.5145.8850.005-0.050-0.3260.000
161A438LEU0-0.027-0.0076.707-2.115-2.1150.0000.0000.0000.000
162A439PHE0-0.009-0.0349.5641.5501.5500.0000.0000.0000.000
163A440ALA0-0.006-0.00212.684-0.531-0.5310.0000.0000.0000.000
164A441PHE0-0.0260.00614.6180.4870.4870.0000.0000.0000.000
165A442HIS00.042-0.01214.5890.2760.2760.0000.0000.0000.000
166A443GLU-1-0.861-0.89619.319-11.848-11.8480.0000.0000.0000.000
167A444ARG10.9860.97922.34510.33810.3380.0000.0000.0000.000
168A445LEU00.0160.01219.8420.2390.2390.0000.0000.0000.000
169A446PRO0-0.049-0.00524.3900.2610.2610.0000.0000.0000.000
170A447ARG10.8960.98926.5419.5269.5260.0000.0000.0000.000
171A448PRO0-0.022-0.01827.8670.2860.2860.0000.0000.0000.000
172A449VAL00.027-0.00523.3220.0620.0620.0000.0000.0000.000
173A450TYR00.002-0.00526.0710.1210.1210.0000.0000.0000.000
174A451PRO00.0170.01821.695-0.214-0.2140.0000.0000.0000.000
175A452PHE00.001-0.01022.7870.5600.5600.0000.0000.0000.000
176A453PHE0-0.009-0.01920.608-0.827-0.8270.0000.0000.0000.000
177A454ASP-1-0.823-0.91723.881-11.310-11.3100.0000.0000.0000.000
178A455VAL00.007-0.00724.310-0.691-0.6910.0000.0000.0000.000
179A456CYS0-0.081-0.03425.360-0.295-0.2950.0000.0000.0000.000
180A457TRP00.0200.02327.8420.2270.2270.0000.0000.0000.000
181A458HIS00.1070.04928.834-0.451-0.4510.0000.0000.0000.000
182A459ASP-1-0.832-0.91727.234-11.695-11.6950.0000.0000.0000.000
183A460LYS10.8980.93630.4779.1099.1090.0000.0000.0000.000
184A461GLY00.0370.02431.3930.0890.0890.0000.0000.0000.000
185A462LYS10.9000.95527.03010.56810.5680.0000.0000.0000.000
186A463ASN00.011-0.00924.410-1.058-1.0580.0000.0000.0000.000
187A464ALA00.0130.00426.4970.0930.0930.0000.0000.0000.000
188A465GLN00.0260.02022.5260.5580.5580.0000.0000.0000.000
189A466PRO00.0130.01123.9400.0450.0450.0000.0000.0000.000
190A467LEU0-0.0190.01220.572-0.707-0.7070.0000.0000.0000.000
191A468LEU0-0.018-0.03320.6150.8340.8340.0000.0000.0000.000
192A469LEU0-0.0180.00719.667-0.901-0.9010.0000.0000.0000.000
193A470VAL0-0.034-0.01015.3420.7530.7530.0000.0000.0000.000