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: LZ1Q9

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2577686.789351
FMO2-HF: Nuclear repulsion 2492705.875623
FMO2-HF: Total energy -84980.913728
FMO2-MP2: Total energy -85224.105599


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.
-30.411-24.58116.981-10.944-11.8680.068
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 : -0.882 / q_NPA : -0.940
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].
3A6LEU0-0.0200.0012.6984.1187.9631.225-2.036-3.0340.017
4A7PHE00.0300.0005.403-7.434-7.405-0.001-0.003-0.0240.000
5A8SER0-0.024-0.0078.636-0.427-0.4270.0000.0000.0000.000
6A9ASN00.0180.00011.622-0.318-0.3180.0000.0000.0000.000
7A10HIS00.0270.01113.645-1.165-1.1650.0000.0000.0000.000
8A11GLY00.0260.00417.922-0.742-0.7420.0000.0000.0000.000
9A12ARG10.8780.92819.786-12.674-12.6740.0000.0000.0000.000
10A13VAL0-0.0050.02417.690-0.185-0.1850.0000.0000.0000.000
11A14ALA00.0640.05014.5510.7190.7190.0000.0000.0000.000
12A15VAL0-0.025-0.02311.555-0.782-0.7820.0000.0000.0000.000
13A16ILE0-0.017-0.0088.9462.5252.5250.0000.0000.0000.000
14A17THR0-0.003-0.0047.238-3.532-3.5320.0000.0000.0000.000
15A18LEU0-0.028-0.0075.9387.7797.7790.0000.0000.0000.000
16A19ASN0-0.038-0.0481.784-34.054-35.69812.085-5.668-4.7740.067
17A20ARG10.8760.9312.108-33.017-30.5143.616-2.786-3.334-0.019
18A21PRO00.0560.0344.220-4.540-4.3720.000-0.033-0.1350.000
19A22GLU-1-0.925-0.9666.41330.47230.4720.0000.0000.0000.000
20A23ARG10.8330.8957.231-24.227-24.2270.0000.0000.0000.000
21A24LEU0-0.023-0.0189.081-0.656-0.6560.0000.0000.0000.000
22A25ASN0-0.012-0.0246.2511.8091.8090.0000.0000.0000.000
23A26ALA00.0050.0367.3160.0770.0770.0000.0000.0000.000
24A27TRP00.0400.0046.9043.7053.7050.0000.0000.0000.000
25A28THR00.0310.0015.817-1.485-1.4850.0000.0000.0000.000
26A29THR00.0340.0038.3661.1791.1790.0000.0000.0000.000
27A30PRO00.0720.0446.5210.0190.0190.0000.0000.0000.000
28A31MET0-0.0440.0163.515-0.998-0.0690.056-0.418-0.5670.003
29A32ARG10.8080.8736.101-21.879-21.8790.0000.0000.0000.000
30A33GLU-1-0.914-0.9559.57522.30722.3070.0000.0000.0000.000
31A34THR00.002-0.0135.669-0.694-0.6940.0000.0000.0000.000
32A35ILE0-0.0070.0027.504-0.893-0.8930.0000.0000.0000.000
33A36ILE0-0.036-0.0109.659-2.097-2.0970.0000.0000.0000.000
34A37ASP-1-0.829-0.89311.73920.39820.3980.0000.0000.0000.000
35A38ALA00.0080.00010.526-1.374-1.3740.0000.0000.0000.000
36A39LEU0-0.032-0.01012.555-1.570-1.5700.0000.0000.0000.000
37A40GLU-1-0.811-0.87515.13015.38715.3870.0000.0000.0000.000
38A41ARG10.8070.89413.739-23.116-23.1160.0000.0000.0000.000
39A42PHE00.0730.02711.973-0.861-0.8610.0000.0000.0000.000
40A43ASN00.0350.04217.678-1.312-1.3120.0000.0000.0000.000
41A44ARG10.9080.94620.771-13.261-13.2610.0000.0000.0000.000
42A45ASP-1-0.853-0.91917.92616.48516.4850.0000.0000.0000.000
43A46PRO0-0.030-0.02121.043-0.216-0.2160.0000.0000.0000.000
44A47GLU-1-0.879-0.93819.92913.38313.3830.0000.0000.0000.000
45A48VAL0-0.054-0.00817.5020.2390.2390.0000.0000.0000.000
46A49ALA0-0.053-0.04020.697-0.556-0.5560.0000.0000.0000.000
47A50ALA00.0030.00120.977-0.551-0.5510.0000.0000.0000.000
48A51ILE0-0.006-0.00115.4640.7620.7620.0000.0000.0000.000
49A52ILE00.0020.01915.125-0.881-0.8810.0000.0000.0000.000
50A53MET0-0.0020.00811.6411.4591.4590.0000.0000.0000.000
51A54THR0-0.037-0.03611.467-1.856-1.8560.0000.0000.0000.000
52A55GLY00.0330.0279.3022.6452.6450.0000.0000.0000.000
53A56ALA00.0020.0167.194-1.528-1.5280.0000.0000.0000.000
54A57GLY0-0.022-0.0179.162-1.224-1.2240.0000.0000.0000.000
55A58ASN0-0.027-0.02011.8780.2210.2210.0000.0000.0000.000
56A59ARG10.9590.99313.762-18.521-18.5210.0000.0000.0000.000
57A60ALA0-0.012-0.02211.953-1.050-1.0500.0000.0000.0000.000
58A61PHE00.0010.03811.6941.5251.5250.0000.0000.0000.000
59A62SER0-0.017-0.0559.4831.4191.4190.0000.0000.0000.000
60A63ALA00.0050.00011.351-1.547-1.5470.0000.0000.0000.000
61A64GLY00.0010.02511.992-1.197-1.1970.0000.0000.0000.000
62A65GLN0-0.004-0.01011.3241.7561.7560.0000.0000.0000.000
63A66ASP-1-0.749-0.8179.28422.84622.8460.0000.0000.0000.000
64A67LEU00.010-0.00311.398-0.558-0.5580.0000.0000.0000.000
65A68SER0-0.067-0.04111.645-0.879-0.8790.0000.0000.0000.000
66A81TRP00.029-0.00113.941-0.129-0.1290.0000.0000.0000.000
67A82VAL00.0910.03518.8460.7350.7350.0000.0000.0000.000
68A83LYS11.0091.00921.255-12.095-12.0950.0000.0000.0000.000
69A84GLU-1-0.829-0.89215.31118.23818.2380.0000.0000.0000.000
70A85TRP00.0460.01213.1640.9480.9480.0000.0000.0000.000
71A86GLN00.0520.03517.5470.3440.3440.0000.0000.0000.000
72A87ARG10.7830.86016.621-17.207-17.2070.0000.0000.0000.000
73A88TYR00.010-0.00111.5440.3120.3120.0000.0000.0000.000
74A89TYR0-0.002-0.02916.3440.2300.2300.0000.0000.0000.000
75A90THR00.000-0.01619.442-0.592-0.5920.0000.0000.0000.000
76A91ALA0-0.0080.01516.667-0.470-0.4700.0000.0000.0000.000
77A92LEU0-0.037-0.01615.3880.0320.0320.0000.0000.0000.000
78A93ARG10.8160.88518.895-12.184-12.1840.0000.0000.0000.000
79A94SER0-0.060-0.05221.469-0.878-0.8780.0000.0000.0000.000
80A95LEU0-0.0420.00818.121-0.243-0.2430.0000.0000.0000.000
81A96SER0-0.047-0.04222.198-0.629-0.6290.0000.0000.0000.000
82A97LYS10.8110.90721.745-14.957-14.9570.0000.0000.0000.000
83A98PRO00.0270.01122.6020.3400.3400.0000.0000.0000.000
84A99LEU0-0.025-0.01116.3910.6950.6950.0000.0000.0000.000
85A100VAL0-0.001-0.00919.433-0.665-0.6650.0000.0000.0000.000
86A101MET0-0.042-0.00915.7511.6341.6340.0000.0000.0000.000
87A102ALA00.0130.00715.989-1.037-1.0370.0000.0000.0000.000
88A103LEU00.005-0.01215.6051.3871.3870.0000.0000.0000.000
89A104ASN00.0460.01312.172-1.115-1.1150.0000.0000.0000.000
90A105GLY00.0620.00916.028-0.394-0.3940.0000.0000.0000.000
91A106THR0-0.021-0.01216.636-0.203-0.2030.0000.0000.0000.000
92A107ALA0-0.0060.00815.0741.2271.2270.0000.0000.0000.000
93A108ALA00.0120.00915.862-1.044-1.0440.0000.0000.0000.000
94A109GLY00.0320.02216.0950.9020.9020.0000.0000.0000.000
95A110SER00.025-0.00314.5960.0250.0250.0000.0000.0000.000
96A111ALA0-0.011-0.00113.0640.2500.2500.0000.0000.0000.000
97A112PHE00.0130.00614.824-0.053-0.0530.0000.0000.0000.000
98A113GLN00.0530.02818.446-0.144-0.1440.0000.0000.0000.000
99A114VAL0-0.009-0.00513.781-0.290-0.2900.0000.0000.0000.000
100A115ALA00.0240.00516.866-0.134-0.1340.0000.0000.0000.000
101A116LEU0-0.043-0.02017.938-0.424-0.4240.0000.0000.0000.000
102A117LEU0-0.024-0.01119.178-0.593-0.5930.0000.0000.0000.000
103A118GLY0-0.0240.00220.0320.1200.1200.0000.0000.0000.000
104A119ASP-1-0.792-0.84920.65812.77512.7750.0000.0000.0000.000
105A120ILE0-0.011-0.02522.685-0.548-0.5480.0000.0000.0000.000
106A121ARG10.8270.91520.406-12.493-12.4930.0000.0000.0000.000
107A122VAL0-0.010-0.00321.004-0.794-0.7940.0000.0000.0000.000
108A123GLY00.0290.01620.3500.8590.8590.0000.0000.0000.000
109A124HIS00.0530.03718.661-1.149-1.1490.0000.0000.0000.000
110A125PRO00.026-0.01123.1820.1150.1150.0000.0000.0000.000
111A126GLY0-0.0010.01722.493-0.346-0.3460.0000.0000.0000.000
112A127VAL0-0.104-0.03319.0060.3560.3560.0000.0000.0000.000
113A128ARG10.8890.93020.271-12.838-12.8380.0000.0000.0000.000
114A129MET0-0.008-0.01319.6600.6570.6570.0000.0000.0000.000
115A130GLY00.0290.01820.651-0.691-0.6910.0000.0000.0000.000
116A131GLN0-0.022-0.03920.6790.8300.8300.0000.0000.0000.000
117A132PRO00.0340.03120.268-0.481-0.4810.0000.0000.0000.000
118A133GLU-1-0.775-0.90920.17813.39013.3900.0000.0000.0000.000
119A134ILE00.0180.02222.931-0.109-0.1090.0000.0000.0000.000
120A135ASN0-0.056-0.02624.697-0.571-0.5710.0000.0000.0000.000
121A136ALA0-0.063-0.02022.264-0.071-0.0710.0000.0000.0000.000
122A137GLY0-0.0070.00124.2820.0230.0230.0000.0000.0000.000
123A138ILE0-0.032-0.00921.701-0.019-0.0190.0000.0000.0000.000
124A139ALA00.0130.00925.100-0.157-0.1570.0000.0000.0000.000
125A140SER0-0.021-0.00825.2220.4980.4980.0000.0000.0000.000
126A141THR00.0410.00925.388-0.249-0.2490.0000.0000.0000.000
127A142THR00.0330.00221.815-0.144-0.1440.0000.0000.0000.000
128A143GLY00.0360.02523.752-0.001-0.0010.0000.0000.0000.000
129A144PRO0-0.010-0.00924.442-0.135-0.1350.0000.0000.0000.000
130A145TRP00.0340.03124.199-0.053-0.0530.0000.0000.0000.000
131A146ILE00.0160.00422.476-0.228-0.2280.0000.0000.0000.000
132A147MET0-0.023-0.00825.479-0.135-0.1350.0000.0000.0000.000
133A148ASN00.029-0.00127.697-0.398-0.3980.0000.0000.0000.000
134A149ALA0-0.0140.00129.244-0.300-0.3000.0000.0000.0000.000
135A150MET0-0.058-0.01825.032-0.045-0.0450.0000.0000.0000.000
136A151LEU0-0.024-0.00128.097-0.150-0.1500.0000.0000.0000.000
137A152GLY00.0060.01832.170-0.303-0.3030.0000.0000.0000.000
138A153MET00.025-0.00133.6110.2440.2440.0000.0000.0000.000
139A154SER0-0.041-0.01234.8420.1330.1330.0000.0000.0000.000
140A155ARG11.0141.00031.808-8.819-8.8190.0000.0000.0000.000
141A156THR00.0470.01529.5070.2620.2620.0000.0000.0000.000
142A157ILE0-0.0120.00930.5380.2270.2270.0000.0000.0000.000
143A158GLU-1-0.791-0.87131.8959.5059.5050.0000.0000.0000.000
144A159LEU00.002-0.00827.3330.1370.1370.0000.0000.0000.000
145A160THR0-0.048-0.03827.6300.3620.3620.0000.0000.0000.000
146A161LEU0-0.045-0.03928.5320.1040.1040.0000.0000.0000.000
147A162THR0-0.035-0.01030.0030.0770.0770.0000.0000.0000.000
148A163GLY00.0010.01726.1120.1030.1030.0000.0000.0000.000
149A164ARG10.7090.80125.132-9.369-9.3690.0000.0000.0000.000
150A165LEU0-0.075-0.03820.6390.3220.3220.0000.0000.0000.000
151A166MET0-0.0040.00624.374-0.466-0.4660.0000.0000.0000.000
152A167GLU-1-0.771-0.89224.57611.98711.9870.0000.0000.0000.000
153A168ALA00.0470.04524.317-0.226-0.2260.0000.0000.0000.000
154A169GLU-1-0.816-0.91125.6719.3039.3030.0000.0000.0000.000
155A170GLU-1-0.786-0.85829.0099.5809.5800.0000.0000.0000.000
156A171CYS0-0.052-0.03625.139-0.026-0.0260.0000.0000.0000.000
157A172HIS0-0.066-0.03127.248-0.223-0.2230.0000.0000.0000.000
158A173ARG10.8670.92928.788-9.310-9.3100.0000.0000.0000.000
159A174ILE0-0.123-0.07328.632-0.308-0.3080.0000.0000.0000.000
160A175GLY00.0400.03130.235-0.061-0.0610.0000.0000.0000.000
161A176LEU0-0.052-0.01624.9010.2290.2290.0000.0000.0000.000
162A177ILE0-0.025-0.02322.8630.5210.5210.0000.0000.0000.000
163A178HIS00.0280.03125.428-0.116-0.1160.0000.0000.0000.000
164A179HIS00.015-0.00125.659-0.505-0.5050.0000.0000.0000.000
165A180LEU0-0.0120.00524.9420.5620.5620.0000.0000.0000.000
166A181VAL0-0.035-0.02323.654-0.408-0.4080.0000.0000.0000.000
167A182ASP-1-0.863-0.93424.87111.63411.6340.0000.0000.0000.000
168A183GLU-1-0.844-0.94519.41715.68515.6850.0000.0000.0000.000
169A184ASP-1-0.870-0.93420.07914.01114.0110.0000.0000.0000.000
170A185LYS10.8440.91621.029-12.859-12.8590.0000.0000.0000.000
171A186VAL0-0.039-0.00718.5550.0100.0100.0000.0000.0000.000
172A187PHE00.0000.00214.7780.1220.1220.0000.0000.0000.000
173A188ASP-1-0.829-0.92518.27514.95014.9500.0000.0000.0000.000
174A189LYS10.8130.90221.217-12.003-12.0030.0000.0000.0000.000
175A190ALA00.0060.00018.921-0.331-0.3310.0000.0000.0000.000
176A191LEU00.0230.00318.828-0.168-0.1680.0000.0000.0000.000
177A192GLU-1-0.833-0.87720.89411.22911.2290.0000.0000.0000.000
178A193ILE00.0290.00623.941-0.404-0.4040.0000.0000.0000.000
179A194ALA0-0.001-0.00421.022-0.324-0.3240.0000.0000.0000.000
180A195THR0-0.043-0.04323.009-0.185-0.1850.0000.0000.0000.000
181A196GLU-1-0.873-0.90824.85510.31010.3100.0000.0000.0000.000
182A197LEU0-0.035-0.04124.899-0.442-0.4420.0000.0000.0000.000
183A198ALA0-0.027-0.01324.213-0.212-0.2120.0000.0000.0000.000
184A199ALA0-0.054-0.01426.213-0.249-0.2490.0000.0000.0000.000
185A200LYS10.8160.90729.614-10.771-10.7710.0000.0000.0000.000
186A201PRO00.009-0.01230.8380.1820.1820.0000.0000.0000.000
187A202PRO00.0620.02329.173-0.032-0.0320.0000.0000.0000.000
188A203VAL0-0.033-0.01530.5260.1740.1740.0000.0000.0000.000
189A204ALA00.0210.01833.150-0.009-0.0090.0000.0000.0000.000
190A205MET00.0730.05527.6390.0630.0630.0000.0000.0000.000
191A206ARG10.9630.98628.605-10.088-10.0880.0000.0000.0000.000
192A207LEU0-0.064-0.04029.6160.0050.0050.0000.0000.0000.000
193A208ASP-1-0.895-0.94631.4429.4799.4790.0000.0000.0000.000
194A209LYS10.8050.87922.756-13.592-13.5920.0000.0000.0000.000
195A210GLN0-0.073-0.03728.7670.2430.2430.0000.0000.0000.000
196A211ARG10.8990.93730.200-8.843-8.8430.0000.0000.0000.000
197A212PHE00.0470.01028.276-0.157-0.1570.0000.0000.0000.000
198A213ARG10.8470.94024.918-11.889-11.8890.0000.0000.0000.000
199A214GLU-1-0.832-0.91029.0869.0569.0560.0000.0000.0000.000
200A215MET0-0.065-0.03432.564-0.249-0.2490.0000.0000.0000.000
201A216THR00.002-0.00329.1550.1060.1060.0000.0000.0000.000
202A217GLU-1-0.792-0.86328.03811.38711.3870.0000.0000.0000.000
203A218PRO00.001-0.00130.7810.0940.0940.0000.0000.0000.000
204A219GLY00.0250.01631.777-0.065-0.0650.0000.0000.0000.000
205A220PHE00.0120.00422.9350.2710.2710.0000.0000.0000.000
206A221ILE0-0.024-0.02328.1370.2240.2240.0000.0000.0000.000
207A222ASP-1-0.903-0.93530.1549.1529.1520.0000.0000.0000.000
208A223CYS0-0.067-0.02726.9970.1810.1810.0000.0000.0000.000
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