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: 1648Z

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2185380.660647
FMO2-HF: Nuclear repulsion 2110616.74546
FMO2-HF: Total energy -74763.915186
FMO2-MP2: Total energy -74985.32604


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.
-147.635-138.42722.405-13.487-18.127-0.145
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 : 0.889 / q_NPA : 0.922
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].
3A280MET00.0200.0153.107-0.5741.5860.007-0.921-1.2450.001
4A281PHE00.0130.0022.2660.3101.5711.066-0.968-1.359-0.005
5A282ARG10.8270.9064.46432.01532.168-0.001-0.021-0.1310.000
6A283ALA0-0.001-0.0026.4732.1012.1010.0000.0000.0000.000
7A284LEU0-0.048-0.0237.0151.4611.4610.0000.0000.0000.000
8A285MET0-0.0450.0098.3461.1151.1150.0000.0000.0000.000
9A286PRO00.0140.01810.9260.5310.5310.0000.0000.0000.000
10A287ALA0-0.009-0.01714.330-0.609-0.6090.0000.0000.0000.000
11A288LEU0-0.049-0.02414.414-0.011-0.0110.0000.0000.0000.000
12A289GLU-1-0.841-0.90617.011-12.633-12.6330.0000.0000.0000.000
13A290GLU-1-0.980-0.98119.742-11.356-11.3560.0000.0000.0000.000
14A291LEU0-0.049-0.03220.6850.3710.3710.0000.0000.0000.000
15A292THR0-0.025-0.03424.096-0.083-0.0830.0000.0000.0000.000
16A293PHE0-0.041-0.02123.2100.1430.1430.0000.0000.0000.000
17A294ASP-1-0.756-0.86628.062-8.989-8.9890.0000.0000.0000.000
18A295PRO0-0.030-0.03731.4460.0160.0160.0000.0000.0000.000
19A296SER0-0.101-0.05633.9410.1720.1720.0000.0000.0000.000
20A297SER00.0180.00232.2420.0650.0650.0000.0000.0000.000
21A298ALA0-0.026-0.01132.387-0.132-0.1320.0000.0000.0000.000
22A299HIS00.0610.06632.8540.2480.2480.0000.0000.0000.000
23A300PRO00.0130.00034.721-0.083-0.0830.0000.0000.0000.000
24A301SER0-0.083-0.04333.8980.0070.0070.0000.0000.0000.000
25A302LEU0-0.049-0.01729.730-0.173-0.1730.0000.0000.0000.000
26A303VAL0-0.0030.00532.2090.3390.3390.0000.0000.0000.000
27A304VAL00.0080.00829.594-0.372-0.3720.0000.0000.0000.000
28A305SER00.005-0.00929.9200.2920.2920.0000.0000.0000.000
29A306SER0-0.002-0.01327.513-0.322-0.3220.0000.0000.0000.000
30A307SER0-0.024-0.02528.010-0.367-0.3670.0000.0000.0000.000
31A308GLY00.0620.03328.711-0.105-0.1050.0000.0000.0000.000
32A309ARG10.9931.01423.54711.80111.8010.0000.0000.0000.000
33A310ARG10.7970.88224.11711.05811.0580.0000.0000.0000.000
34A311VAL00.0220.01725.7160.5510.5510.0000.0000.0000.000
35A312GLU-1-0.782-0.85626.626-11.817-11.8170.0000.0000.0000.000
36A313CYS0-0.0020.00928.7310.2460.2460.0000.0000.0000.000
37A314SER0-0.0030.00631.3130.1070.1070.0000.0000.0000.000
38A315GLU-1-0.868-0.96333.378-9.328-9.3280.0000.0000.0000.000
39A316GLN0-0.045-0.02536.0300.3860.3860.0000.0000.0000.000
40A317LYS10.9140.93939.6887.4367.4360.0000.0000.0000.000
41A318ALA00.0150.01338.4780.0310.0310.0000.0000.0000.000
42A319PRO00.0110.02839.5960.1790.1790.0000.0000.0000.000
43A320PRO0-0.012-0.01341.335-0.165-0.1650.0000.0000.0000.000
44A321ALA00.000-0.00340.146-0.060-0.0600.0000.0000.0000.000
45A322GLY00.0240.01741.3550.2050.2050.0000.0000.0000.000
46A323GLU-1-0.911-0.96542.849-7.201-7.2010.0000.0000.0000.000
47A324ASP-1-0.825-0.89039.858-8.048-8.0480.0000.0000.0000.000
48A325PRO0-0.006-0.01239.365-0.188-0.1880.0000.0000.0000.000
49A326ARG10.8510.90335.1838.3608.3600.0000.0000.0000.000
50A327GLN0-0.0230.00035.000-0.106-0.1060.0000.0000.0000.000
51A328PHE00.0160.01630.0370.1620.1620.0000.0000.0000.000
52A329ASP-1-0.745-0.87034.918-8.383-8.3830.0000.0000.0000.000
53A330LYS10.7440.86035.6948.3618.3610.0000.0000.0000.000
54A331ALA00.0390.03530.335-0.104-0.1040.0000.0000.0000.000
55A332VAL00.003-0.00329.7930.1960.1960.0000.0000.0000.000
56A333ALA00.0210.00428.089-0.461-0.4610.0000.0000.0000.000
57A334VAL00.0070.00027.2330.4880.4880.0000.0000.0000.000
58A335VAL00.0100.01526.977-0.454-0.4540.0000.0000.0000.000
59A336ALA00.0140.00424.9300.1770.1770.0000.0000.0000.000
60A337HIS00.0080.01827.0830.0520.0520.0000.0000.0000.000
61A338GLN00.0330.01225.5980.1400.1400.0000.0000.0000.000
62A339GLN00.0290.03626.356-0.249-0.2490.0000.0000.0000.000
63A340LEU0-0.013-0.00621.282-0.041-0.0410.0000.0000.0000.000
64A341SER0-0.003-0.04725.3670.1180.1180.0000.0000.0000.000
65A342GLU-1-0.816-0.88324.709-10.071-10.0710.0000.0000.0000.000
66A343GLY00.0260.03222.076-0.100-0.1000.0000.0000.0000.000
67A344GLU-1-0.908-0.96316.461-13.433-13.4330.0000.0000.0000.000
68A345HIS10.7870.85817.27113.44513.4450.0000.0000.0000.000
69A346TYR00.027-0.02710.376-1.450-1.4500.0000.0000.0000.000
70A347TRP00.0210.02815.1150.7130.7130.0000.0000.0000.000
71A348GLU-1-0.743-0.85110.975-24.799-24.7990.0000.0000.0000.000
72A349VAL0-0.018-0.01015.0431.3681.3680.0000.0000.0000.000
73A350ASP-1-0.784-0.85815.498-21.026-21.0260.0000.0000.0000.000
74A351VAL0-0.029-0.02714.8541.1631.1630.0000.0000.0000.000
75A352GLY00.0030.00416.0760.8730.8730.0000.0000.0000.000
76A353ASP-1-0.878-0.96215.692-16.613-16.6130.0000.0000.0000.000
77A354LYS10.8120.93817.62414.03414.0340.0000.0000.0000.000
78A355PRO0-0.058-0.01918.610-1.039-1.0390.0000.0000.0000.000
79A356ARG10.8230.87320.13612.08912.0890.0000.0000.0000.000
80A357TRP00.0740.03614.6570.3660.3660.0000.0000.0000.000
81A358ALA00.015-0.00220.420-0.474-0.4740.0000.0000.0000.000
82A359LEU0-0.0080.00316.9150.4990.4990.0000.0000.0000.000
83A360GLY00.0680.01719.255-0.566-0.5660.0000.0000.0000.000
84A361VAL0-0.0260.00520.2360.1690.1690.0000.0000.0000.000
85A362ILE0-0.019-0.00422.965-0.017-0.0170.0000.0000.0000.000
86A363ALA00.0150.00226.6360.0700.0700.0000.0000.0000.000
87A364ALA0-0.028-0.02428.6640.1380.1380.0000.0000.0000.000
88A365GLU-1-0.933-0.96031.358-8.410-8.4100.0000.0000.0000.000
89A366ALA0-0.053-0.00530.9030.1650.1650.0000.0000.0000.000
90A367PRO0-0.0140.00132.9290.1120.1120.0000.0000.0000.000
91A368ARG10.9550.96431.7279.4559.4550.0000.0000.0000.000
92A369ARG10.8170.90534.4628.0448.0440.0000.0000.0000.000
93A370GLY0-0.010-0.00537.4680.0410.0410.0000.0000.0000.000
94A371ARG10.9010.93334.0238.6878.6870.0000.0000.0000.000
95A372LEU00.0370.02830.9880.0890.0890.0000.0000.0000.000
96A373HIS0-0.026-0.01530.663-0.297-0.2970.0000.0000.0000.000
97A374ALA00.000-0.00325.2530.0070.0070.0000.0000.0000.000
98A375VAL0-0.0100.00025.799-0.370-0.3700.0000.0000.0000.000
99A376PRO00.0420.01523.6460.2890.2890.0000.0000.0000.000
100A377SER0-0.063-0.05326.3130.3650.3650.0000.0000.0000.000
101A378GLN0-0.072-0.04129.6990.5160.5160.0000.0000.0000.000
102A379GLY00.0060.00828.5700.1780.1780.0000.0000.0000.000
103A380LEU0-0.015-0.00125.968-0.170-0.1700.0000.0000.0000.000
104A381TRP0-0.025-0.01221.071-0.056-0.0560.0000.0000.0000.000
105A382LEU0-0.015-0.01620.301-0.400-0.4000.0000.0000.0000.000
106A383LEU0-0.0090.01413.549-0.210-0.2100.0000.0000.0000.000
107A384GLY00.019-0.00117.8920.5320.5320.0000.0000.0000.000
108A385LEU0-0.068-0.01414.583-1.122-1.1220.0000.0000.0000.000
109A386ARG10.8560.89217.92315.34115.3410.0000.0000.0000.000
110A387GLU-1-0.846-0.94019.100-14.092-14.0920.0000.0000.0000.000
111A388GLY0-0.030-0.02018.023-0.118-0.1180.0000.0000.0000.000
112A389LYS10.8470.91615.01416.23916.2390.0000.0000.0000.000
113A390ILE0-0.0180.00914.710-1.049-1.0490.0000.0000.0000.000
114A391LEU00.0400.03511.0280.6570.6570.0000.0000.0000.000
115A392GLU-1-0.812-0.89414.888-14.966-14.9660.0000.0000.0000.000
116A393ALA00.0230.01616.2430.0020.0020.0000.0000.0000.000
117A394HIS0-0.023-0.01117.9780.9900.9900.0000.0000.0000.000
118A395VAL0-0.017-0.01919.7420.1850.1850.0000.0000.0000.000
119A396GLU-1-0.753-0.84622.477-10.797-10.7970.0000.0000.0000.000
120A397ALA0-0.026-0.01425.0310.1160.1160.0000.0000.0000.000
121A398LYS10.9270.96327.00110.62210.6220.0000.0000.0000.000
122A399GLU-1-0.962-0.98724.809-11.407-11.4070.0000.0000.0000.000
123A400PRO00.0100.02021.302-0.214-0.2140.0000.0000.0000.000
124A401ARG10.9500.98616.61416.74616.7460.0000.0000.0000.000
125A402ALA00.0360.01916.937-0.844-0.8440.0000.0000.0000.000
126A403LEU0-0.037-0.02111.759-0.309-0.3090.0000.0000.0000.000
127A404ARG10.9060.9458.90824.37424.3740.0000.0000.0000.000
128A405SER00.0080.0409.108-1.241-1.2410.0000.0000.0000.000
129A406PRO0-0.006-0.0174.447-1.017-0.932-0.001-0.001-0.0820.000
130A407GLU-1-0.803-0.9001.823-118.624-119.28015.026-7.983-6.388-0.115
131A408ARG10.7960.8503.26558.60758.8590.003-0.038-0.2180.000
132A409ARG10.8290.9157.80518.11418.1140.0000.0000.0000.000
133A410PRO00.0230.0278.3660.8100.8100.0000.0000.0000.000
134A411THR0-0.043-0.02010.0042.8662.8660.0000.0000.0000.000
135A412ARG10.8450.89611.48423.18523.1850.0000.0000.0000.000
136A413ILE0-0.0370.00011.065-2.706-2.7060.0000.0000.0000.000
137A414GLY00.0360.02011.0511.7021.7020.0000.0000.0000.000
138A415LEU0-0.057-0.02811.999-0.836-0.8360.0000.0000.0000.000
139A416TYR00.0290.00811.6710.5070.5070.0000.0000.0000.000
140A417LEU0-0.017-0.00713.6920.0980.0980.0000.0000.0000.000
141A418SER00.000-0.02816.5500.5300.5300.0000.0000.0000.000
142A419PHE0-0.021-0.00818.2390.1440.1440.0000.0000.0000.000
143A420GLY0-0.044-0.01521.3160.3290.3290.0000.0000.0000.000
144A421ASP-1-0.870-0.90417.103-14.533-14.5330.0000.0000.0000.000
145A422GLY0-0.082-0.02719.662-0.072-0.0720.0000.0000.0000.000
146A423VAL00.0130.00114.782-0.364-0.3640.0000.0000.0000.000
147A424LEU00.0220.01216.1810.2880.2880.0000.0000.0000.000
148A425SER0-0.033-0.02510.9950.1890.1890.0000.0000.0000.000
149A426PHE00.0060.00111.9870.3920.3920.0000.0000.0000.000
150A427TYR00.005-0.0126.016-1.529-1.5290.0000.0000.0000.000
151A428ASP-1-0.801-0.8746.220-39.249-39.2490.0000.0000.0000.000
152A429ALA0-0.005-0.0336.460-4.623-4.6230.0000.0000.0000.000
153A430SER0-0.015-0.0377.5773.7223.7220.0000.0000.0000.000
154A431ASP-1-0.821-0.8694.314-48.392-48.206-0.001-0.022-0.1630.000
155A432ALA00.028-0.0017.106-0.373-0.3730.0000.0000.0000.000
156A433ASP-1-0.855-0.9167.255-29.664-29.6640.0000.0000.0000.000
157A434ALA0-0.041-0.0342.288-3.179-2.8051.042-0.425-0.991-0.002
158A435LEU00.0050.0292.5901.6022.7110.226-0.401-0.934-0.004
159A436VAL0-0.027-0.0192.215-13.423-9.4735.030-2.687-6.294-0.020
160A437PRO0-0.0020.0123.7095.0375.3710.008-0.020-0.3220.000
161A438LEU0-0.040-0.0086.652-2.097-2.0970.0000.0000.0000.000
162A439PHE0-0.015-0.0319.4341.5891.5890.0000.0000.0000.000
163A440ALA0-0.004-0.00212.635-0.520-0.5200.0000.0000.0000.000
164A441PHE0-0.0200.00614.6150.4860.4860.0000.0000.0000.000
165A442HIS00.034-0.01414.5430.3180.3180.0000.0000.0000.000
166A443GLU-1-0.871-0.89619.316-11.878-11.8780.0000.0000.0000.000
167A444ARG10.9830.97522.34410.30510.3050.0000.0000.0000.000
168A445LEU00.0270.02019.8760.2170.2170.0000.0000.0000.000
169A446PRO0-0.041-0.00324.3930.2640.2640.0000.0000.0000.000
170A447ARG10.8310.93826.5489.5019.5010.0000.0000.0000.000
171A448PRO00.011-0.01627.8900.2860.2860.0000.0000.0000.000
172A449VAL00.008-0.00823.2820.0630.0630.0000.0000.0000.000
173A450TYR0-0.017-0.02226.0830.1260.1260.0000.0000.0000.000
174A451PRO00.0290.02321.596-0.219-0.2190.0000.0000.0000.000
175A452PHE0-0.002-0.01322.8000.5600.5600.0000.0000.0000.000
176A453PHE0-0.009-0.01820.597-0.834-0.8340.0000.0000.0000.000
177A454ASP-1-0.798-0.89523.726-11.370-11.3700.0000.0000.0000.000
178A455VAL00.000-0.01023.950-0.693-0.6930.0000.0000.0000.000
179A456CYS0-0.074-0.05025.239-0.274-0.2740.0000.0000.0000.000
180A457TRP00.0210.01827.3430.2340.2340.0000.0000.0000.000
181A458HIS00.0760.04428.310-0.538-0.5380.0000.0000.0000.000
182A459ASP-1-0.814-0.87726.752-11.837-11.8370.0000.0000.0000.000
183A460LYS10.9020.93829.9549.0979.0970.0000.0000.0000.000
184A461GLY00.0260.01530.7880.0920.0920.0000.0000.0000.000
185A462LYS10.8980.95726.40810.50210.5020.0000.0000.0000.000
186A463ASN00.012-0.01023.770-1.094-1.0940.0000.0000.0000.000
187A464ALA00.0090.00125.8920.1090.1090.0000.0000.0000.000
188A465GLN0-0.008-0.00421.8860.5970.5970.0000.0000.0000.000
189A466PRO00.0160.01023.3790.0740.0740.0000.0000.0000.000
190A467LEU0-0.0240.00320.524-0.732-0.7320.0000.0000.0000.000
191A468LEU0-0.017-0.03020.5210.8450.8450.0000.0000.0000.000
192A469LEU0-0.0160.00619.693-0.923-0.9230.0000.0000.0000.000
193A470VAL0-0.046-0.01415.1010.7260.7260.0000.0000.0000.000