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: 943L2

Calculation Name: 4KD6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KD6

Chain ID: A

ChEMBL ID:

UniProt ID: B1GB42

Base Structure: X-ray

Registration Date: 2023-09-20

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2583975.426645
FMO2-HF: Nuclear repulsion 2498993.839984
FMO2-HF: Total energy -84981.586661
FMO2-MP2: Total energy -85224.783573


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:4:ASP)


Summations of interaction energy for fragment #1(A:4:ASP)
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.
-43.559-39.74824.069-13.813-14.0680.071
Interaction energy analysis for fragmet #1(A:4:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.835 / q_NPA : -0.916
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].
3A6LEU00.0110.0322.948-3.0991.8220.805-2.474-3.2520.018
4A7PHE00.012-0.0104.802-9.315-9.260-0.001-0.018-0.0360.000
5A8SER0-0.027-0.0088.517-0.703-0.7030.0000.0000.0000.000
6A9ASN00.0190.00111.4230.0970.0970.0000.0000.0000.000
7A10HIS00.0200.00913.122-1.517-1.5170.0000.0000.0000.000
8A11GLY00.0340.01917.752-0.912-0.9120.0000.0000.0000.000
9A12ARG10.8470.92619.536-12.535-12.5350.0000.0000.0000.000
10A13VAL00.0020.00717.741-0.375-0.3750.0000.0000.0000.000
11A14ALA00.0370.03514.4050.7400.7400.0000.0000.0000.000
12A15VAL0-0.023-0.02211.530-0.860-0.8600.0000.0000.0000.000
13A16ILE0-0.009-0.0039.0112.5532.5530.0000.0000.0000.000
14A17THR0-0.006-0.0156.873-3.844-3.8440.0000.0000.0000.000
15A18LEU0-0.011-0.0055.8518.6428.6420.0000.0000.0000.000
16A19ASN0-0.066-0.0601.713-36.874-40.44716.086-6.943-5.5700.073
17A20ARG10.8600.9172.001-36.251-34.9497.126-3.948-4.480-0.022
18A21PRO00.0390.0334.110-4.604-4.4060.000-0.058-0.1410.000
19A22GLU-1-0.879-0.9555.72531.34131.3410.0000.0000.0000.000
20A23ARG10.7950.8656.953-24.474-24.4740.0000.0000.0000.000
21A24LEU0-0.016-0.0078.748-0.355-0.3550.0000.0000.0000.000
22A25ASN00.013-0.0166.0981.8841.8840.0000.0000.0000.000
23A26ALA0-0.0010.0317.1630.2350.2350.0000.0000.0000.000
24A27TRP00.0630.0136.7633.9253.9250.0000.0000.0000.000
25A28THR00.039-0.0045.770-1.749-1.7490.0000.0000.0000.000
26A29THR0-0.005-0.0068.2731.0461.0460.0000.0000.0000.000
27A30PRO00.0910.0486.3870.2620.2620.0000.0000.0000.000
28A31MET0-0.0600.0143.581-0.6070.3010.053-0.372-0.5890.002
29A32ARG10.8300.9005.910-22.303-22.3030.0000.0000.0000.000
30A33GLU-1-0.898-0.9649.62122.78822.7880.0000.0000.0000.000
31A34THR0-0.013-0.0176.051-1.280-1.2800.0000.0000.0000.000
32A35ILE00.0030.0017.680-1.001-1.0010.0000.0000.0000.000
33A36ILE0-0.051-0.0169.897-2.160-2.1600.0000.0000.0000.000
34A37ASP-1-0.801-0.87611.88220.87120.8710.0000.0000.0000.000
35A38ALA0-0.0030.00310.336-1.301-1.3010.0000.0000.0000.000
36A39LEU0-0.002-0.00312.481-1.566-1.5660.0000.0000.0000.000
37A40GLU-1-0.811-0.87915.29215.55115.5510.0000.0000.0000.000
38A41ARG10.7900.88513.728-23.079-23.0790.0000.0000.0000.000
39A42PHE00.0480.01011.996-1.037-1.0370.0000.0000.0000.000
40A43ASN00.0160.02817.515-1.226-1.2260.0000.0000.0000.000
41A44ARG10.9130.95020.561-13.374-13.3740.0000.0000.0000.000
42A45ASP-1-0.862-0.92018.02116.52916.5290.0000.0000.0000.000
43A46PRO0-0.004-0.00420.874-0.324-0.3240.0000.0000.0000.000
44A47GLU-1-0.891-0.95920.25312.98612.9860.0000.0000.0000.000
45A48VAL0-0.055-0.01417.042-0.029-0.0290.0000.0000.0000.000
46A49ALA0-0.020-0.00920.278-0.488-0.4880.0000.0000.0000.000
47A50ALA00.000-0.00121.179-0.502-0.5020.0000.0000.0000.000
48A51ILE0-0.014-0.00715.4010.8280.8280.0000.0000.0000.000
49A52ILE00.0120.02315.184-0.920-0.9200.0000.0000.0000.000
50A53MET0-0.026-0.00711.6061.5411.5410.0000.0000.0000.000
51A54THR0-0.032-0.03110.965-1.864-1.8640.0000.0000.0000.000
52A55GLY00.0330.0238.9322.7322.7320.0000.0000.0000.000
53A56ALA00.0040.0126.838-1.588-1.5880.0000.0000.0000.000
54A57GLY0-0.025-0.0118.863-1.394-1.3940.0000.0000.0000.000
55A58ASN0-0.004-0.01212.0120.8120.8120.0000.0000.0000.000
56A59ARG10.9460.98113.084-18.932-18.9320.0000.0000.0000.000
57A60ALA00.001-0.01111.769-1.218-1.2180.0000.0000.0000.000
58A61PHE0-0.0180.03011.5071.7741.7740.0000.0000.0000.000
59A62SER0-0.007-0.0489.3271.3871.3870.0000.0000.0000.000
60A63ALA00.0070.00011.203-1.631-1.6310.0000.0000.0000.000
61A64GLY00.0150.03211.964-1.362-1.3620.0000.0000.0000.000
62A65GLN0-0.016-0.02911.2241.9531.9530.0000.0000.0000.000
63A66ASP-1-0.751-0.8068.76823.57623.5760.0000.0000.0000.000
64A67LEU0-0.0010.01310.902-0.539-0.5390.0000.0000.0000.000
65A68SER0-0.068-0.05811.108-0.930-0.9300.0000.0000.0000.000
66A81TRP00.0470.01513.603-0.207-0.2070.0000.0000.0000.000
67A82VAL00.0730.03818.8430.6920.6920.0000.0000.0000.000
68A83LYS10.9160.96021.172-11.966-11.9660.0000.0000.0000.000
69A84GLU-1-0.821-0.88615.03218.87218.8720.0000.0000.0000.000
70A85TRP00.0280.00013.0411.0641.0640.0000.0000.0000.000
71A86GLN00.0410.03717.6900.1430.1430.0000.0000.0000.000
72A87ARG10.8160.88316.198-17.719-17.7190.0000.0000.0000.000
73A88TYR0-0.004-0.00811.8380.2130.2130.0000.0000.0000.000
74A89TYR00.017-0.02316.4480.2890.2890.0000.0000.0000.000
75A90THR0-0.006-0.02319.525-0.700-0.7000.0000.0000.0000.000
76A91ALA0-0.0050.02416.974-0.435-0.4350.0000.0000.0000.000
77A92LEU00.0070.00415.644-0.167-0.1670.0000.0000.0000.000
78A93ARG10.8130.89519.085-12.334-12.3340.0000.0000.0000.000
79A94SER0-0.048-0.04921.545-0.974-0.9740.0000.0000.0000.000
80A95LEU0-0.0570.00318.122-0.201-0.2010.0000.0000.0000.000
81A96SER0-0.049-0.04422.278-0.561-0.5610.0000.0000.0000.000
82A97LYS10.8120.90521.356-15.228-15.2280.0000.0000.0000.000
83A98PRO00.0320.01722.8600.2570.2570.0000.0000.0000.000
84A99LEU0-0.032-0.01616.1800.7030.7030.0000.0000.0000.000
85A100VAL0-0.014-0.00619.254-0.583-0.5830.0000.0000.0000.000
86A101MET0-0.023-0.00815.9361.6621.6620.0000.0000.0000.000
87A102ALA00.0440.02015.644-1.103-1.1030.0000.0000.0000.000
88A103LEU0-0.016-0.00515.6411.4581.4580.0000.0000.0000.000
89A104ASN00.049-0.00311.956-1.185-1.1850.0000.0000.0000.000
90A105GLY00.0440.01515.923-0.430-0.4300.0000.0000.0000.000
91A106THR0-0.047-0.02215.770-0.210-0.2100.0000.0000.0000.000
92A107ALA00.0210.01114.8291.3581.3580.0000.0000.0000.000
93A108ALA0-0.0050.00415.408-1.110-1.1100.0000.0000.0000.000
94A109GLY00.0370.02315.8680.8950.8950.0000.0000.0000.000
95A110SER00.022-0.00414.4550.0830.0830.0000.0000.0000.000
96A111ALA0-0.0360.00412.7680.3650.3650.0000.0000.0000.000
97A112PHE00.0290.00614.583-0.057-0.0570.0000.0000.0000.000
98A113GLN00.005-0.00318.184-0.387-0.3870.0000.0000.0000.000
99A114VAL0-0.008-0.00413.826-0.289-0.2890.0000.0000.0000.000
100A115ALA00.0240.01616.716-0.190-0.1900.0000.0000.0000.000
101A116LEU0-0.037-0.02117.875-0.453-0.4530.0000.0000.0000.000
102A117LEU0-0.014-0.00819.408-0.603-0.6030.0000.0000.0000.000
103A118GLY00.0050.01919.9360.2220.2220.0000.0000.0000.000
104A119ASP-1-0.795-0.86220.48713.04213.0420.0000.0000.0000.000
105A120ILE00.011-0.00622.710-0.549-0.5490.0000.0000.0000.000
106A121ARG10.7580.87020.237-12.770-12.7700.0000.0000.0000.000
107A122VAL00.0090.00420.827-0.828-0.8280.0000.0000.0000.000
108A123GLY00.0100.00720.2180.8950.8950.0000.0000.0000.000
109A124HIS00.0600.03718.489-1.210-1.2100.0000.0000.0000.000
110A125PRO00.022-0.01123.0630.0870.0870.0000.0000.0000.000
111A126GLY00.0020.01421.655-0.316-0.3160.0000.0000.0000.000
112A127VAL0-0.088-0.03518.8820.4150.4150.0000.0000.0000.000
113A128ARG10.8940.94220.296-12.907-12.9070.0000.0000.0000.000
114A129MET0-0.024-0.02119.5980.7390.7390.0000.0000.0000.000
115A130GLY00.0400.02420.533-0.729-0.7290.0000.0000.0000.000
116A131GLN0-0.013-0.03120.4630.7820.7820.0000.0000.0000.000
117A132PRO00.0340.02819.827-0.438-0.4380.0000.0000.0000.000
118A133GLU-1-0.770-0.90519.94813.72013.7200.0000.0000.0000.000
119A134ILE00.0350.03022.445-0.105-0.1050.0000.0000.0000.000
120A135ASN0-0.068-0.03424.134-0.588-0.5880.0000.0000.0000.000
121A136ALA0-0.053-0.01921.970-0.031-0.0310.0000.0000.0000.000
122A137GLY0-0.014-0.00424.0030.0050.0050.0000.0000.0000.000
123A138ILE0-0.065-0.02121.435-0.113-0.1130.0000.0000.0000.000
124A139ALA00.0400.01924.760-0.072-0.0720.0000.0000.0000.000
125A140SER0-0.027-0.01224.8920.5640.5640.0000.0000.0000.000
126A141THR00.015-0.00125.305-0.263-0.2630.0000.0000.0000.000
127A142THR00.015-0.01022.146-0.155-0.1550.0000.0000.0000.000
128A143GLY00.0350.02623.507-0.019-0.0190.0000.0000.0000.000
129A144PRO0-0.002-0.00324.062-0.173-0.1730.0000.0000.0000.000
130A145TRP00.0190.01424.437-0.131-0.1310.0000.0000.0000.000
131A146ILE0-0.005-0.00522.311-0.248-0.2480.0000.0000.0000.000
132A147MET00.0000.00825.532-0.135-0.1350.0000.0000.0000.000
133A148ASN00.028-0.00127.783-0.439-0.4390.0000.0000.0000.000
134A149ALA0-0.042-0.02328.984-0.298-0.2980.0000.0000.0000.000
135A150MET0-0.040-0.00824.9490.0320.0320.0000.0000.0000.000
136A151LEU0-0.037-0.01027.837-0.154-0.1540.0000.0000.0000.000
137A152GLY00.0190.02431.982-0.306-0.3060.0000.0000.0000.000
138A153MET00.0270.00733.6040.2160.2160.0000.0000.0000.000
139A154SER0-0.045-0.00734.7590.0990.0990.0000.0000.0000.000
140A155ARG11.0290.99831.706-8.944-8.9440.0000.0000.0000.000
141A156THR00.0270.01529.5600.2890.2890.0000.0000.0000.000
142A157ILE0-0.0060.00730.4660.2130.2130.0000.0000.0000.000
143A158GLU-1-0.802-0.87031.1659.7449.7440.0000.0000.0000.000
144A159LEU00.019-0.00127.0870.1240.1240.0000.0000.0000.000
145A160THR0-0.053-0.04227.3500.4320.4320.0000.0000.0000.000
146A161LEU0-0.040-0.02228.5160.0670.0670.0000.0000.0000.000
147A162THR0-0.033-0.02729.4800.0750.0750.0000.0000.0000.000
148A163GLY00.0020.01425.7580.1490.1490.0000.0000.0000.000
149A164ARG10.7210.80624.479-9.555-9.5550.0000.0000.0000.000
150A165LEU0-0.067-0.03219.9580.3570.3570.0000.0000.0000.000
151A166MET0-0.0090.00123.890-0.469-0.4690.0000.0000.0000.000
152A167GLU-1-0.789-0.89424.31712.12112.1210.0000.0000.0000.000
153A168ALA00.0650.05023.977-0.145-0.1450.0000.0000.0000.000
154A169GLU-1-0.822-0.90925.3859.3849.3840.0000.0000.0000.000
155A170GLU-1-0.806-0.87728.6619.8149.8140.0000.0000.0000.000
156A171CYS0-0.014-0.02324.934-0.056-0.0560.0000.0000.0000.000
157A172HIS0-0.068-0.02926.996-0.129-0.1290.0000.0000.0000.000
158A173ARG10.8490.92028.608-9.502-9.5020.0000.0000.0000.000
159A174ILE0-0.107-0.05728.304-0.346-0.3460.0000.0000.0000.000
160A175GLY00.0290.02130.034-0.028-0.0280.0000.0000.0000.000
161A176LEU0-0.033-0.00824.6440.2410.2410.0000.0000.0000.000
162A177ILE0-0.012-0.01122.8500.5210.5210.0000.0000.0000.000
163A178HIS00.0020.00525.307-0.218-0.2180.0000.0000.0000.000
164A179HIS00.0370.00925.417-0.483-0.4830.0000.0000.0000.000
165A180LEU0-0.033-0.00124.7480.5780.5780.0000.0000.0000.000
166A181VAL0-0.038-0.01523.357-0.431-0.4310.0000.0000.0000.000
167A182ASP-1-0.845-0.93724.98311.77411.7740.0000.0000.0000.000
168A183GLU-1-0.864-0.94119.41815.90815.9080.0000.0000.0000.000
169A184ASP-1-0.851-0.92319.52514.33814.3380.0000.0000.0000.000
170A185LYS10.8300.91520.396-13.058-13.0580.0000.0000.0000.000
171A186VAL0-0.024-0.00218.189-0.026-0.0260.0000.0000.0000.000
172A187PHE0-0.002-0.00214.9260.1940.1940.0000.0000.0000.000
173A188ASP-1-0.839-0.92318.00914.71014.7100.0000.0000.0000.000
174A189LYS10.8020.88621.201-12.007-12.0070.0000.0000.0000.000
175A190ALA00.009-0.00118.735-0.362-0.3620.0000.0000.0000.000
176A191LEU00.0280.00918.581-0.050-0.0500.0000.0000.0000.000
177A192GLU-1-0.835-0.88220.64811.27611.2760.0000.0000.0000.000
178A193ILE00.0330.01323.741-0.331-0.3310.0000.0000.0000.000
179A194ALA00.004-0.00420.576-0.289-0.2890.0000.0000.0000.000
180A195THR0-0.034-0.03122.575-0.123-0.1230.0000.0000.0000.000
181A196GLU-1-0.881-0.92424.74110.53210.5320.0000.0000.0000.000
182A197LEU0-0.015-0.01424.512-0.493-0.4930.0000.0000.0000.000
183A198ALA0-0.005-0.00524.077-0.243-0.2430.0000.0000.0000.000
184A199ALA0-0.038-0.00526.129-0.245-0.2450.0000.0000.0000.000
185A200LYS10.7750.87729.422-11.064-11.0640.0000.0000.0000.000
186A201PRO00.026-0.00130.6910.1790.1790.0000.0000.0000.000
187A202PRO00.0420.02228.747-0.011-0.0110.0000.0000.0000.000
188A203VAL0-0.036-0.02630.3210.1380.1380.0000.0000.0000.000
189A204ALA00.0150.01533.013-0.052-0.0520.0000.0000.0000.000
190A205MET00.0600.04227.1820.0900.0900.0000.0000.0000.000
191A206ARG10.9520.98628.526-10.083-10.0830.0000.0000.0000.000
192A207LEU0-0.058-0.03129.5330.0230.0230.0000.0000.0000.000
193A208ASP-1-0.890-0.93831.4289.5949.5940.0000.0000.0000.000
194A209LYS10.8400.89722.734-13.881-13.8810.0000.0000.0000.000
195A210GLN0-0.082-0.04428.7780.2300.2300.0000.0000.0000.000
196A211ARG10.9040.93530.325-8.825-8.8250.0000.0000.0000.000
197A212PHE00.027-0.00228.425-0.180-0.1800.0000.0000.0000.000
198A213ARG10.8150.91924.762-12.116-12.1160.0000.0000.0000.000
199A214GLU-1-0.822-0.90929.2199.0969.0960.0000.0000.0000.000
200A215MET0-0.076-0.03732.753-0.236-0.2360.0000.0000.0000.000
201A216THR00.0200.00329.3880.0900.0900.0000.0000.0000.000
202A217GLU-1-0.787-0.86327.83111.60211.6020.0000.0000.0000.000
203A218PRO0-0.002-0.01130.5340.1040.1040.0000.0000.0000.000
204A219GLY00.0280.02331.634-0.092-0.0920.0000.0000.0000.000
205A220PHE0-0.0010.00022.6900.2500.2500.0000.0000.0000.000
206A221ILE00.0120.00627.8160.2560.2560.0000.0000.0000.000
207A222ASP-1-0.878-0.93029.9629.3229.3220.0000.0000.0000.000
208A223CYS0-0.054-0.02126.5120.2560.2560.0000.0000.0000.000
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210A225GLU-1-0.912-0.96127.0449.4329.4320.0000.0000.0000.000
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