Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 5N22Z

Calculation Name: 4KI5-F-Xray372

Preferred Name: Coagulation factor VIII

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4KI5

Chain ID: F

ChEMBL ID: CHEMBL3143

UniProt ID: P00451

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2183428.063311
FMO2-HF: Nuclear repulsion 2099761.999032
FMO2-HF: Total energy -83666.064279
FMO2-MP2: Total energy -83908.489422


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(F:1:ASP)


Summations of interaction energy for fragment #1(F:1: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.
-33.03-27.2832.604-3.278-5.0720.031
Interaction energy analysis for fragmet #1(F:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.905 / q_NPA : -0.964
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].
3F3GLN00.0360.0293.863-4.048-2.477-0.011-0.657-0.9030.005
4F4MET0-0.0130.0055.431-3.102-3.1020.0000.0000.0000.000
5F5THR00.0140.0108.567-0.834-0.8340.0000.0000.0000.000
6F6GLN00.017-0.01411.4390.1520.1520.0000.0000.0000.000
7F7SER0-0.0470.00214.391-0.465-0.4650.0000.0000.0000.000
8F8PRO00.0590.01318.016-0.019-0.0190.0000.0000.0000.000
9F9SER0-0.038-0.01517.330-0.072-0.0720.0000.0000.0000.000
10F10SER00.001-0.00918.933-0.077-0.0770.0000.0000.0000.000
11F11LEU00.0140.00722.626-0.158-0.1580.0000.0000.0000.000
12F12SER0-0.011-0.01325.494-0.156-0.1560.0000.0000.0000.000
13F13ALA0-0.008-0.00129.165-0.139-0.1390.0000.0000.0000.000
14F14SER0-0.017-0.01031.326-0.067-0.0670.0000.0000.0000.000
15F15LEU00.0450.01834.1190.1770.1770.0000.0000.0000.000
16F16GLY0-0.0030.00235.671-0.203-0.2030.0000.0000.0000.000
17F17GLU-1-0.791-0.85532.2449.2249.2240.0000.0000.0000.000
18F18ARG10.9020.95028.122-10.205-10.2050.0000.0000.0000.000
19F19VAL00.0350.02225.6140.0680.0680.0000.0000.0000.000
20F20SER0-0.038-0.01224.371-0.139-0.1390.0000.0000.0000.000
21F21LEU00.0140.02619.854-0.028-0.0280.0000.0000.0000.000
22F22THR00.0110.02317.702-0.211-0.2110.0000.0000.0000.000
23F23CYS0-0.084-0.02012.7190.5080.5080.0000.0000.0000.000
24F24ARG10.8590.89513.059-17.483-17.4830.0000.0000.0000.000
25F25ALA00.0310.0169.1981.2671.2670.0000.0000.0000.000
26F26SER0-0.022-0.0236.071-1.132-1.1320.0000.0000.0000.000
27F27GLN00.0470.0334.282-1.642-1.548-0.001-0.057-0.0360.000
28F28GLU-1-0.701-0.8219.38417.77317.7730.0000.0000.0000.000
29F29ILE0-0.009-0.0168.6311.7831.7830.0000.0000.0000.000
30F30SER0-0.061-0.04611.388-0.430-0.4300.0000.0000.0000.000
31F31GLY00.0180.00915.103-0.729-0.7290.0000.0000.0000.000
32F32TYR0-0.042-0.00112.382-0.720-0.7200.0000.0000.0000.000
33F33LEU0-0.003-0.00512.0421.8781.8780.0000.0000.0000.000
34F34SER0-0.086-0.05913.999-1.461-1.4610.0000.0000.0000.000
35F35TRP00.005-0.00415.4951.0211.0210.0000.0000.0000.000
36F36LEU00.0190.00415.664-0.750-0.7500.0000.0000.0000.000
37F37GLN0-0.013-0.01119.113-0.094-0.0940.0000.0000.0000.000
38F38GLN0-0.021-0.01319.7160.5330.5330.0000.0000.0000.000
39F39LYS10.8370.91922.288-11.072-11.0720.0000.0000.0000.000
40F40PRO00.017-0.00925.1500.3260.3260.0000.0000.0000.000
41F41ASP-1-0.842-0.89126.92011.42911.4290.0000.0000.0000.000
42F42GLY00.0290.02323.5190.0660.0660.0000.0000.0000.000
43F43THR0-0.047-0.04422.8370.7320.7320.0000.0000.0000.000
44F44ILE00.0070.00518.2370.0450.0450.0000.0000.0000.000
45F45LYS10.8830.93922.297-12.640-12.6400.0000.0000.0000.000
46F46ARG10.8880.93319.924-13.203-13.2030.0000.0000.0000.000
47F47LEU0-0.014-0.00621.290-0.629-0.6290.0000.0000.0000.000
48F48ILE0-0.0130.00020.073-0.518-0.5180.0000.0000.0000.000
49F49TYR0-0.0140.00018.4651.0751.0750.0000.0000.0000.000
50F50ALA00.0400.01817.864-0.688-0.6880.0000.0000.0000.000
51F51ALA00.0070.01217.272-0.630-0.6300.0000.0000.0000.000
52F52SER0-0.031-0.03118.604-0.094-0.0940.0000.0000.0000.000
53F53THR0-0.048-0.00222.018-0.814-0.8140.0000.0000.0000.000
54F54LEU00.0250.00423.1860.4740.4740.0000.0000.0000.000
55F55ASP-1-0.788-0.84624.28112.24012.2400.0000.0000.0000.000
56F56SER00.003-0.01225.877-0.250-0.2500.0000.0000.0000.000
57F57SER0-0.103-0.06127.925-0.391-0.3910.0000.0000.0000.000
58F58VAL0-0.0030.00526.059-0.094-0.0940.0000.0000.0000.000
59F59PRO00.0040.00029.390-0.181-0.1810.0000.0000.0000.000
60F60LYS10.9790.96630.285-8.528-8.5280.0000.0000.0000.000
61F61ARG10.8150.91230.471-9.617-9.6170.0000.0000.0000.000
62F62PHE0-0.0010.00625.6350.1890.1890.0000.0000.0000.000
63F63SER00.003-0.00626.147-0.135-0.1350.0000.0000.0000.000
64F64GLY00.0280.01322.1990.3240.3240.0000.0000.0000.000
65F65SER0-0.024-0.01621.301-0.515-0.5150.0000.0000.0000.000
66F66ARG10.8410.88115.479-16.364-16.3640.0000.0000.0000.000
67F67SER0-0.022-0.01619.518-0.992-0.9920.0000.0000.0000.000
68F68GLY0-0.0130.01117.7040.4180.4180.0000.0000.0000.000
69F69SER00.014-0.00113.049-0.742-0.7420.0000.0000.0000.000
70F70ASP-1-0.770-0.83714.70517.18017.1800.0000.0000.0000.000
71F71TYR00.011-0.00913.784-0.770-0.7700.0000.0000.0000.000
72F72SER0-0.004-0.03617.5920.3280.3280.0000.0000.0000.000
73F73LEU0-0.0030.03520.216-0.392-0.3920.0000.0000.0000.000
74F74THR0-0.076-0.07021.866-0.282-0.2820.0000.0000.0000.000
75F75ILE00.0410.01725.4930.0010.0010.0000.0000.0000.000
76F76SER0-0.047-0.02828.433-0.175-0.1750.0000.0000.0000.000
77F77SER0-0.055-0.04932.082-0.055-0.0550.0000.0000.0000.000
78F78LEU0-0.0410.00228.994-0.077-0.0770.0000.0000.0000.000
79F79ASP-1-0.763-0.88032.2758.5028.5020.0000.0000.0000.000
80F80SER00.011-0.02732.5200.2090.2090.0000.0000.0000.000
81F81GLU-1-0.843-0.90332.3149.1189.1180.0000.0000.0000.000
82F82ASP-1-0.806-0.88028.53410.54810.5480.0000.0000.0000.000
83F83PHE00.0210.03427.3130.5230.5230.0000.0000.0000.000
84F84ALA0-0.0050.00623.869-0.028-0.0280.0000.0000.0000.000
85F85VAL00.0210.01618.610-0.062-0.0620.0000.0000.0000.000
86F86TYR0-0.021-0.03119.6800.1140.1140.0000.0000.0000.000
87F87TYR0-0.006-0.00714.3420.6280.6280.0000.0000.0000.000
88F89LEU0-0.004-0.00310.1781.1701.1700.0000.0000.0000.000
89F90GLN00.0470.0075.353-5.154-5.1540.0000.0000.0000.000
90F91TYR0-0.018-0.0298.8731.3741.3740.0000.0000.0000.000
91F92ALA00.0090.0118.997-1.375-1.3750.0000.0000.0000.000
92F93SER0-0.070-0.0275.8890.6990.6990.0000.0000.0000.000
93F94TYR0-0.017-0.0026.347-0.097-0.0970.0000.0000.0000.000
94F95PRO00.0430.0212.577-7.913-4.3482.592-2.462-3.6940.026
95F96TYR00.0030.0024.532-1.009-0.956-0.001-0.010-0.0430.000
96F97THR0-0.021-0.0163.2250.8241.2880.025-0.092-0.3960.000
97F98PHE00.0260.0016.608-3.901-3.9010.0000.0000.0000.000
98F99GLY00.0150.0108.3802.0572.0570.0000.0000.0000.000
99F100GLY0-0.029-0.02710.832-0.388-0.3880.0000.0000.0000.000
100F101GLY00.0240.02712.438-0.961-0.9610.0000.0000.0000.000
101F102THR0-0.065-0.06015.730-0.311-0.3110.0000.0000.0000.000
102F103LYS10.7810.91919.174-11.597-11.5970.0000.0000.0000.000
103F104VAL0-0.010-0.00722.427-0.139-0.1390.0000.0000.0000.000
104F105GLU-1-0.748-0.84825.60810.61210.6120.0000.0000.0000.000
105F106ILE00.005-0.00529.050-0.066-0.0660.0000.0000.0000.000
106F107LYS10.8070.89732.024-9.448-9.4480.0000.0000.0000.000
107F108ARG10.8230.88834.777-7.908-7.9080.0000.0000.0000.000
108F109ALA00.0130.00738.3440.0230.0230.0000.0000.0000.000
109F110ASP-1-0.840-0.92240.7707.6787.6780.0000.0000.0000.000
110F111ALA0-0.049-0.02041.827-0.154-0.1540.0000.0000.0000.000
111F112ALA00.0210.01242.5940.1340.1340.0000.0000.0000.000
112F113PRO00.0000.01542.870-0.009-0.0090.0000.0000.0000.000
113F114THR00.0160.00344.476-0.233-0.2330.0000.0000.0000.000
114F115VAL0-0.024-0.01446.0710.0760.0760.0000.0000.0000.000
115F116SER0-0.044-0.01147.232-0.244-0.2440.0000.0000.0000.000
116F117ILE0-0.017-0.00647.7740.1500.1500.0000.0000.0000.000
117F118PHE00.001-0.00547.157-0.118-0.1180.0000.0000.0000.000
118F119PRO00.0180.02250.1380.1040.1040.0000.0000.0000.000
119F120PRO00.0040.00550.2880.0680.0680.0000.0000.0000.000
120F121SER0-0.015-0.02251.026-0.100-0.1000.0000.0000.0000.000
121F122SER00.0480.00952.9450.0190.0190.0000.0000.0000.000
122F123GLU-1-0.815-0.87751.7216.0326.0320.0000.0000.0000.000
123F124GLN00.0350.03146.264-0.029-0.0290.0000.0000.0000.000
124F125LEU00.0220.00750.9550.0100.0100.0000.0000.0000.000
125F126THR0-0.060-0.04753.910-0.083-0.0830.0000.0000.0000.000
126F127SER0-0.074-0.04150.117-0.014-0.0140.0000.0000.0000.000
127F128GLY0-0.020-0.00250.8200.0960.0960.0000.0000.0000.000
128F129GLY0-0.023-0.01148.7830.0470.0470.0000.0000.0000.000
129F130ALA00.006-0.02048.899-0.116-0.1160.0000.0000.0000.000
130F131SER0-0.029-0.01944.5410.0510.0510.0000.0000.0000.000
131F132VAL00.0030.01646.881-0.072-0.0720.0000.0000.0000.000
132F133VAL0-0.0040.00243.9230.1710.1710.0000.0000.0000.000
133F134CYS0-0.066-0.01944.632-0.061-0.0610.0000.0000.0000.000
134F135PHE0-0.0130.00542.8300.2010.2010.0000.0000.0000.000
135F136LEU00.030-0.00241.463-0.212-0.2120.0000.0000.0000.000
136F137ASN00.0330.00641.2010.3160.3160.0000.0000.0000.000
137F138ASN0-0.020-0.02940.698-0.210-0.2100.0000.0000.0000.000
138F139PHE00.0050.01836.957-0.160-0.1600.0000.0000.0000.000
139F140TYR00.028-0.01033.9350.2190.2190.0000.0000.0000.000
140F141PRO00.0200.02435.326-0.234-0.2340.0000.0000.0000.000
141F142LYS10.8600.89428.344-10.722-10.7220.0000.0000.0000.000
142F143ASP-1-0.939-0.95633.1689.3369.3360.0000.0000.0000.000
143F144ILE0-0.021-0.00935.521-0.271-0.2710.0000.0000.0000.000
144F145ASN0-0.057-0.02037.9330.2310.2310.0000.0000.0000.000
145F146VAL00.033-0.00140.528-0.163-0.1630.0000.0000.0000.000
146F147LYS10.8080.90642.586-6.663-6.6630.0000.0000.0000.000
147F148TRP00.0370.00143.778-0.165-0.1650.0000.0000.0000.000
148F149LYS10.8110.88147.858-6.143-6.1430.0000.0000.0000.000
149F150ILE00.0130.00250.6680.0100.0100.0000.0000.0000.000
150F151ASP-1-0.733-0.82853.9995.4445.4440.0000.0000.0000.000
151F152GLY0-0.0020.00856.174-0.056-0.0560.0000.0000.0000.000
152F153SER0-0.034-0.01154.3240.0440.0440.0000.0000.0000.000
153F154GLU-1-0.805-0.88946.8316.7736.7730.0000.0000.0000.000
154F155ARG10.7500.85547.161-6.638-6.6380.0000.0000.0000.000
155F156GLN0-0.005-0.00242.7980.2320.2320.0000.0000.0000.000
156F157ASN00.000-0.01343.1290.1500.1500.0000.0000.0000.000
157F158GLY00.0940.04442.343-0.186-0.1860.0000.0000.0000.000
158F159VAL0-0.0360.00340.6040.0010.0010.0000.0000.0000.000
159F160LEU0-0.0130.00936.5640.2220.2220.0000.0000.0000.000
160F161ASN00.0120.00636.414-0.363-0.3630.0000.0000.0000.000
161F162SER0-0.0050.00034.0910.3390.3390.0000.0000.0000.000
162F163TRP00.0290.01032.458-0.267-0.2670.0000.0000.0000.000
163F164THR0-0.013-0.01032.6060.1460.1460.0000.0000.0000.000
164F165ASP-1-0.778-0.88728.03011.11711.1170.0000.0000.0000.000
165F166GLN0-0.0040.00330.652-0.038-0.0380.0000.0000.0000.000
166F167ASP-1-0.750-0.87632.5738.5728.5720.0000.0000.0000.000
167F168SER0-0.055-0.02933.9370.0250.0250.0000.0000.0000.000
168F169LYS10.8050.87734.957-8.358-8.3580.0000.0000.0000.000
169F170ASP-1-0.784-0.82638.1457.4727.4720.0000.0000.0000.000
170F171SER0-0.067-0.02635.009-0.059-0.0590.0000.0000.0000.000
171F172THR0-0.087-0.04735.9450.1660.1660.0000.0000.0000.000
172F173TYR0-0.009-0.02730.9540.2180.2180.0000.0000.0000.000
173F174SER00.0170.00936.384-0.389-0.3890.0000.0000.0000.000
174F175MET0-0.0420.00236.6480.2270.2270.0000.0000.0000.000
175F176SER0-0.019-0.00238.199-0.325-0.3250.0000.0000.0000.000
176F177SER00.0500.01038.9010.1460.1460.0000.0000.0000.000
177F178THR0-0.032-0.03741.337-0.163-0.1630.0000.0000.0000.000
178F179LEU00.0050.03242.4250.1410.1410.0000.0000.0000.000
179F180THR00.0110.00243.023-0.150-0.1500.0000.0000.0000.000
180F181LEU0-0.061-0.01845.2590.0210.0210.0000.0000.0000.000
181F182THR00.001-0.03248.331-0.020-0.0200.0000.0000.0000.000
182F183LYS10.8600.91250.481-5.800-5.8000.0000.0000.0000.000
183F184ASP-1-0.813-0.89753.4775.6715.6710.0000.0000.0000.000
184F185GLU-1-0.807-0.87250.2116.3366.3360.0000.0000.0000.000
185F186TYR00.0300.01352.628-0.029-0.0290.0000.0000.0000.000
186F187GLU-1-0.784-0.88454.5415.4115.4110.0000.0000.0000.000
187F188ARG10.8480.93657.345-5.548-5.5480.0000.0000.0000.000
188F189HIS10.8290.91055.712-5.694-5.6940.0000.0000.0000.000
189F190ASN00.007-0.00458.634-0.005-0.0050.0000.0000.0000.000
190F191SER0-0.016-0.01357.9620.0370.0370.0000.0000.0000.000
191F192TYR00.004-0.00551.9990.1220.1220.0000.0000.0000.000
192F193THR0-0.044-0.04051.727-0.101-0.1010.0000.0000.0000.000
193F195GLU-1-0.812-0.90847.4686.1436.1430.0000.0000.0000.000
194F196ALA00.0570.03644.5160.1650.1650.0000.0000.0000.000
195F197THR0-0.056-0.04543.721-0.225-0.2250.0000.0000.0000.000
196F198HIS00.030-0.00139.2490.1350.1350.0000.0000.0000.000
197F199LYS10.8760.93541.568-7.321-7.3210.0000.0000.0000.000
198F200THR00.0120.00243.5880.0060.0060.0000.0000.0000.000
199F201SER00.0150.00746.288-0.072-0.0720.0000.0000.0000.000
200F202THR0-0.025-0.01349.150-0.061-0.0610.0000.0000.0000.000
201F203SER00.0210.00747.406-0.098-0.0980.0000.0000.0000.000
202F204PRO0-0.0280.00448.3280.1110.1110.0000.0000.0000.000
203F205ILE00.0050.00547.143-0.122-0.1220.0000.0000.0000.000
204F206VAL00.0100.00448.8580.1280.1280.0000.0000.0000.000
205F207LYS10.8620.91950.802-6.240-6.2400.0000.0000.0000.000
206F208SER00.0150.00052.1360.0910.0910.0000.0000.0000.000
207F209PHE0-0.0080.00551.991-0.017-0.0170.0000.0000.0000.000
208F210ASN0-0.002-0.01656.8860.1110.1110.0000.0000.0000.000
209F211ARG10.7900.86957.217-5.401-5.4010.0000.0000.0000.000
210F212ASN0-0.052-0.02360.2170.0270.0270.0000.0000.0000.000
211F213GLU-1-0.868-0.91362.6874.8744.8740.0000.0000.0000.000
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