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: 4L99N

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2182100.271687
FMO2-HF: Nuclear repulsion 2098434.930006
FMO2-HF: Total energy -83665.341681
FMO2-MP2: Total energy -83907.703525


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.
-25.12-18.6772.219-3.343-5.320.033
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 : -0.909 / q_NPA : -0.961
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].
3F3GLN00.0200.0133.796-2.914-1.128-0.007-0.773-1.0060.006
4F4MET0-0.0230.0035.720-3.230-3.2300.0000.0000.0000.000
5F5THR00.0260.0138.860-0.290-0.2900.0000.0000.0000.000
6F6GLN0-0.006-0.03511.8610.1110.1110.0000.0000.0000.000
7F7SER0-0.0360.01715.112-0.409-0.4090.0000.0000.0000.000
8F8PRO00.0470.00018.530-0.037-0.0370.0000.0000.0000.000
9F9SER0-0.022-0.01117.775-0.091-0.0910.0000.0000.0000.000
10F10SER00.0060.00019.411-0.146-0.1460.0000.0000.0000.000
11F11LEU00.0190.00323.083-0.177-0.1770.0000.0000.0000.000
12F12SER00.0230.02225.875-0.163-0.1630.0000.0000.0000.000
13F13ALA00.0010.00729.557-0.158-0.1580.0000.0000.0000.000
14F14SER0-0.0020.00331.633-0.068-0.0680.0000.0000.0000.000
15F15LEU00.0510.01534.0600.1780.1780.0000.0000.0000.000
16F16GLY0-0.0080.00335.482-0.168-0.1680.0000.0000.0000.000
17F17GLU-1-0.860-0.86732.7399.0949.0940.0000.0000.0000.000
18F18ARG10.9180.96528.115-10.081-10.0810.0000.0000.0000.000
19F19VAL00.0340.01625.6510.0710.0710.0000.0000.0000.000
20F20SER0-0.074-0.05424.300-0.068-0.0680.0000.0000.0000.000
21F21LEU00.0130.02719.8560.0600.0600.0000.0000.0000.000
22F22THR00.0370.02317.630-0.234-0.2340.0000.0000.0000.000
23F23CYS0-0.093-0.03012.2210.5570.5570.0000.0000.0000.000
24F24ARG10.8540.91013.112-17.277-17.2770.0000.0000.0000.000
25F25ALA00.0160.0109.4471.2381.2380.0000.0000.0000.000
26F26SER00.0000.0136.002-0.879-0.8790.0000.0000.0000.000
27F27GLN00.011-0.0044.7192.0912.141-0.001-0.010-0.0390.000
28F28GLU-1-0.736-0.8748.90517.82317.8230.0000.0000.0000.000
29F29ILE0-0.004-0.0098.5731.5521.5520.0000.0000.0000.000
30F30SER0-0.056-0.03011.143-0.438-0.4380.0000.0000.0000.000
31F31GLY0-0.021-0.01414.808-0.663-0.6630.0000.0000.0000.000
32F32TYR0-0.0270.01112.541-0.906-0.9060.0000.0000.0000.000
33F33LEU0-0.017-0.01412.2621.6061.6060.0000.0000.0000.000
34F34SER0-0.082-0.05313.727-1.354-1.3540.0000.0000.0000.000
35F35TRP00.0220.00715.0310.9850.9850.0000.0000.0000.000
36F36LEU00.011-0.00215.017-0.679-0.6790.0000.0000.0000.000
37F37GLN00.002-0.00918.464-0.053-0.0530.0000.0000.0000.000
38F38GLN00.0020.00219.5090.2970.2970.0000.0000.0000.000
39F39LYS10.8000.89521.913-10.881-10.8810.0000.0000.0000.000
40F40PRO00.0280.00024.8480.3170.3170.0000.0000.0000.000
41F41ASP-1-0.828-0.88826.81311.26911.2690.0000.0000.0000.000
42F42GLY00.0130.01723.5790.0470.0470.0000.0000.0000.000
43F43THR0-0.088-0.06422.9890.6100.6100.0000.0000.0000.000
44F44ILE0-0.004-0.00917.9680.1470.1470.0000.0000.0000.000
45F45LYS10.9250.96721.817-11.878-11.8780.0000.0000.0000.000
46F46ARG10.8740.92319.252-13.157-13.1570.0000.0000.0000.000
47F47LEU00.0010.00320.629-0.579-0.5790.0000.0000.0000.000
48F48ILE0-0.024-0.00619.748-0.483-0.4830.0000.0000.0000.000
49F49TYR0-0.023-0.00718.5150.9580.9580.0000.0000.0000.000
50F50ALA00.0530.01417.782-0.533-0.5330.0000.0000.0000.000
51F51ALA00.0090.01917.684-0.572-0.5720.0000.0000.0000.000
52F52SER0-0.021-0.03418.772-0.075-0.0750.0000.0000.0000.000
53F53THR0-0.0400.00922.175-0.764-0.7640.0000.0000.0000.000
54F54LEU00.0150.00423.1460.4630.4630.0000.0000.0000.000
55F55ASP-1-0.787-0.85623.72011.95511.9550.0000.0000.0000.000
56F56SER00.021-0.00225.465-0.256-0.2560.0000.0000.0000.000
57F57SER0-0.134-0.06327.612-0.401-0.4010.0000.0000.0000.000
58F58VAL00.0100.00225.3610.0140.0140.0000.0000.0000.000
59F59PRO00.0080.00328.683-0.150-0.1500.0000.0000.0000.000
60F60LYS11.0040.97829.489-8.359-8.3590.0000.0000.0000.000
61F61ARG10.7900.89330.057-9.527-9.5270.0000.0000.0000.000
62F62PHE0-0.0060.00225.2080.2030.2030.0000.0000.0000.000
63F63SER00.016-0.00425.534-0.137-0.1370.0000.0000.0000.000
64F64GLY00.0240.02021.7080.2500.2500.0000.0000.0000.000
65F65SER0-0.022-0.02221.364-0.461-0.4610.0000.0000.0000.000
66F66ARG10.8560.89915.741-16.071-16.0710.0000.0000.0000.000
67F67SER00.0000.01520.194-0.685-0.6850.0000.0000.0000.000
68F68GLY0-0.0690.02317.4740.4340.4340.0000.0000.0000.000
69F69SER00.0490.00012.675-0.822-0.8220.0000.0000.0000.000
70F70ASP-1-0.764-0.87114.79317.17417.1740.0000.0000.0000.000
71F71TYR00.025-0.00413.826-1.123-1.1230.0000.0000.0000.000
72F72SER00.006-0.01717.4480.2120.2120.0000.0000.0000.000
73F73LEU0-0.0220.01920.063-0.221-0.2210.0000.0000.0000.000
74F74THR0-0.072-0.04921.626-0.319-0.3190.0000.0000.0000.000
75F75ILE00.0350.02125.294-0.052-0.0520.0000.0000.0000.000
76F76SER00.0100.00928.021-0.157-0.1570.0000.0000.0000.000
77F77SER0-0.084-0.11031.486-0.089-0.0890.0000.0000.0000.000
78F78LEU0-0.049-0.00229.205-0.190-0.1900.0000.0000.0000.000
79F79ASP-1-0.770-0.88231.7498.4448.4440.0000.0000.0000.000
80F80SER0-0.016-0.02532.2620.2040.2040.0000.0000.0000.000
81F81GLU-1-0.874-0.92832.1098.9608.9600.0000.0000.0000.000
82F82ASP-1-0.787-0.87028.31310.48410.4840.0000.0000.0000.000
83F83PHE00.0340.03927.2570.4600.4600.0000.0000.0000.000
84F84ALA0-0.0090.00223.825-0.074-0.0740.0000.0000.0000.000
85F85VAL00.0170.01118.668-0.089-0.0890.0000.0000.0000.000
86F86TYR0-0.037-0.03119.3730.2390.2390.0000.0000.0000.000
87F87TYR00.0290.02614.0050.5770.5770.0000.0000.0000.000
88F89LEU0-0.009-0.0059.5931.3431.3430.0000.0000.0000.000
89F90GLN00.0620.0285.427-4.617-4.6170.0000.0000.0000.000
90F91TYR0-0.029-0.0378.5801.3451.3450.0000.0000.0000.000
91F92ALA00.0140.0208.956-1.397-1.3970.0000.0000.0000.000
92F93SER0-0.066-0.0355.9270.3200.3200.0000.0000.0000.000
93F94TYR0-0.0380.0006.4700.6090.6090.0000.0000.0000.000
94F95PRO00.0510.0252.774-7.266-3.2442.087-2.405-3.7040.027
95F96TYR00.004-0.0104.278-0.413-0.309-0.001-0.021-0.0820.000
96F97THR0-0.003-0.0072.8910.1740.6550.141-0.134-0.4890.000
97F98PHE00.014-0.0026.005-3.472-3.4720.0000.0000.0000.000
98F99GLY00.0110.0008.7341.5701.5700.0000.0000.0000.000
99F100GLY0-0.019-0.01511.181-0.054-0.0540.0000.0000.0000.000
100F101GLY00.0220.02113.063-0.686-0.6860.0000.0000.0000.000
101F102THR0-0.092-0.06016.188-0.394-0.3940.0000.0000.0000.000
102F103LYS10.8180.91119.612-11.476-11.4760.0000.0000.0000.000
103F104VAL0-0.012-0.00622.765-0.227-0.2270.0000.0000.0000.000
104F105GLU-1-0.845-0.91225.63510.47810.4780.0000.0000.0000.000
105F106ILE0-0.005-0.01729.024-0.056-0.0560.0000.0000.0000.000
106F107LYS10.8410.92232.371-9.312-9.3120.0000.0000.0000.000
107F108ARG10.8110.88434.907-7.802-7.8020.0000.0000.0000.000
108F109ALA0-0.0090.00138.3870.0140.0140.0000.0000.0000.000
109F110ASP-1-0.849-0.94040.7557.6357.6350.0000.0000.0000.000
110F111ALA0-0.054-0.02942.157-0.152-0.1520.0000.0000.0000.000
111F112ALA00.0090.00643.0560.1240.1240.0000.0000.0000.000
112F113PRO0-0.0050.02143.074-0.009-0.0090.0000.0000.0000.000
113F114THR00.009-0.00644.769-0.228-0.2280.0000.0000.0000.000
114F115VAL00.003-0.00246.3730.1110.1110.0000.0000.0000.000
115F116SER0-0.035-0.00747.650-0.235-0.2350.0000.0000.0000.000
116F117ILE0-0.0150.00648.2210.1470.1470.0000.0000.0000.000
117F118PHE0-0.010-0.00947.776-0.117-0.1170.0000.0000.0000.000
118F119PRO00.0150.01450.5970.1060.1060.0000.0000.0000.000
119F120PRO00.010-0.00451.0120.0530.0530.0000.0000.0000.000
120F121SER0-0.009-0.00951.592-0.095-0.0950.0000.0000.0000.000
121F122SER00.0560.01053.4430.0150.0150.0000.0000.0000.000
122F123GLU-1-0.837-0.89952.1805.9795.9790.0000.0000.0000.000
123F124GLN00.0230.00946.835-0.021-0.0210.0000.0000.0000.000
124F125LEU00.0210.00851.4060.0160.0160.0000.0000.0000.000
125F126THR0-0.066-0.04354.223-0.074-0.0740.0000.0000.0000.000
126F127SER0-0.056-0.01950.760-0.032-0.0320.0000.0000.0000.000
127F128GLY0-0.031-0.01451.2560.0960.0960.0000.0000.0000.000
128F129GLY0-0.011-0.00449.2060.0630.0630.0000.0000.0000.000
129F130ALA00.003-0.01349.342-0.117-0.1170.0000.0000.0000.000
130F131SER0-0.027-0.00345.2690.0800.0800.0000.0000.0000.000
131F132VAL0-0.0160.00547.631-0.090-0.0900.0000.0000.0000.000
132F133VAL00.0060.01044.1190.1620.1620.0000.0000.0000.000
133F134CYS0-0.061-0.03544.989-0.053-0.0530.0000.0000.0000.000
134F135PHE0-0.034-0.00143.1590.1960.1960.0000.0000.0000.000
135F136LEU00.030-0.00141.734-0.203-0.2030.0000.0000.0000.000
136F137ASN00.029-0.00641.4590.3250.3250.0000.0000.0000.000
137F138ASN0-0.002-0.01440.916-0.249-0.2490.0000.0000.0000.000
138F139PHE0-0.0270.00837.650-0.167-0.1670.0000.0000.0000.000
139F140TYR00.0160.00933.9270.2360.2360.0000.0000.0000.000
140F141PRO00.0450.02335.583-0.229-0.2290.0000.0000.0000.000
141F142LYS10.9630.97029.326-10.400-10.4000.0000.0000.0000.000
142F143ASP-1-0.933-0.95033.7219.1529.1520.0000.0000.0000.000
143F144ILE0-0.020-0.01536.041-0.262-0.2620.0000.0000.0000.000
144F145ASN0-0.057-0.02538.5190.2290.2290.0000.0000.0000.000
145F146VAL00.0510.00941.054-0.160-0.1600.0000.0000.0000.000
146F147LYS10.7950.90043.248-6.603-6.6030.0000.0000.0000.000
147F148TRP00.0390.01444.027-0.203-0.2030.0000.0000.0000.000
148F149LYS10.8020.88148.067-6.108-6.1080.0000.0000.0000.000
149F150ILE00.003-0.00350.724-0.015-0.0150.0000.0000.0000.000
150F151ASP-1-0.743-0.85254.0885.4215.4210.0000.0000.0000.000
151F152GLY00.0000.00956.254-0.071-0.0710.0000.0000.0000.000
152F153SER0-0.035-0.01454.3110.0080.0080.0000.0000.0000.000
153F154GLU-1-0.813-0.88946.7786.7516.7510.0000.0000.0000.000
154F155ARG10.7800.88247.398-6.591-6.5910.0000.0000.0000.000
155F156GLN0-0.025-0.02343.0600.2280.2280.0000.0000.0000.000
156F157ASN00.0160.00043.1890.2240.2240.0000.0000.0000.000
157F158GLY00.0550.01942.507-0.158-0.1580.0000.0000.0000.000
158F159VAL00.0020.01440.839-0.040-0.0400.0000.0000.0000.000
159F160LEU0-0.027-0.00236.4900.2250.2250.0000.0000.0000.000
160F161ASN00.0200.01236.499-0.332-0.3320.0000.0000.0000.000
161F162SER00.0010.00534.4310.3330.3330.0000.0000.0000.000
162F163TRP00.0280.01032.730-0.216-0.2160.0000.0000.0000.000
163F164THR00.0090.00832.9100.1710.1710.0000.0000.0000.000
164F165ASP-1-0.831-0.93128.30610.87010.8700.0000.0000.0000.000
165F166GLN0-0.029-0.02331.205-0.001-0.0010.0000.0000.0000.000
166F167ASP-1-0.869-0.93532.9848.3988.3980.0000.0000.0000.000
167F168SER0-0.012-0.01134.0140.0080.0080.0000.0000.0000.000
168F169LYS10.8490.91734.988-8.177-8.1770.0000.0000.0000.000
169F170ASP-1-0.711-0.83237.7217.4047.4040.0000.0000.0000.000
170F171SER0-0.037-0.00835.225-0.115-0.1150.0000.0000.0000.000
171F172THR0-0.084-0.04036.2050.1500.1500.0000.0000.0000.000
172F173TYR0-0.017-0.03131.0000.1540.1540.0000.0000.0000.000
173F174SER00.0530.02436.655-0.373-0.3730.0000.0000.0000.000
174F175MET0-0.0470.00336.9080.2390.2390.0000.0000.0000.000
175F176SER0-0.0120.00738.485-0.321-0.3210.0000.0000.0000.000
176F177SER00.019-0.00939.3920.1330.1330.0000.0000.0000.000
177F178THR00.010-0.00541.412-0.231-0.2310.0000.0000.0000.000
178F179LEU00.0010.01742.6520.1330.1330.0000.0000.0000.000
179F180THR0-0.007-0.01043.650-0.131-0.1310.0000.0000.0000.000
180F181LEU0-0.075-0.02745.8820.0210.0210.0000.0000.0000.000
181F182THR00.022-0.01048.942-0.033-0.0330.0000.0000.0000.000
182F183LYS10.8850.92750.919-5.743-5.7430.0000.0000.0000.000
183F184ASP-1-0.837-0.91753.9115.6295.6290.0000.0000.0000.000
184F185GLU-1-0.800-0.88750.6236.2836.2830.0000.0000.0000.000
185F186TYR00.0260.01352.954-0.035-0.0350.0000.0000.0000.000
186F187GLU-1-0.806-0.89354.7755.3855.3850.0000.0000.0000.000
187F188ARG10.8640.94557.412-5.526-5.5260.0000.0000.0000.000
188F189HIS10.8210.90555.776-5.680-5.6800.0000.0000.0000.000
189F190ASN00.0280.00158.9210.0090.0090.0000.0000.0000.000
190F191SER0-0.0070.01458.1420.0200.0200.0000.0000.0000.000
191F192TYR0-0.015-0.02152.2500.1140.1140.0000.0000.0000.000
192F193THR0-0.018-0.02652.170-0.072-0.0720.0000.0000.0000.000
193F195GLU-1-0.815-0.90248.1036.1286.1280.0000.0000.0000.000
194F196ALA00.0420.02944.8600.1730.1730.0000.0000.0000.000
195F197THR0-0.044-0.03143.766-0.200-0.2000.0000.0000.0000.000
196F198HIS00.0430.03039.8890.1590.1590.0000.0000.0000.000
197F199LYS10.8960.94142.420-7.248-7.2480.0000.0000.0000.000
198F200THR00.005-0.00744.0240.0200.0200.0000.0000.0000.000
199F201SER00.0190.00846.612-0.078-0.0780.0000.0000.0000.000
200F202THR0-0.019-0.00749.458-0.060-0.0600.0000.0000.0000.000
201F203SER00.0330.00648.154-0.094-0.0940.0000.0000.0000.000
202F204PRO0-0.062-0.00448.8780.0900.0900.0000.0000.0000.000
203F205ILE00.0220.01547.431-0.129-0.1290.0000.0000.0000.000
204F206VAL00.0070.00249.5680.1120.1120.0000.0000.0000.000
205F207LYS10.8750.92951.041-6.174-6.1740.0000.0000.0000.000
206F208SER00.013-0.00352.4940.0800.0800.0000.0000.0000.000
207F209PHE00.0060.01452.380-0.029-0.0290.0000.0000.0000.000
208F210ASN00.0230.00157.1490.0880.0880.0000.0000.0000.000
209F211ARG10.7890.87957.389-5.395-5.3950.0000.0000.0000.000
210F212ASN0-0.060-0.03060.3300.0290.0290.0000.0000.0000.000
211F213GLU-1-0.914-0.93363.0574.7904.7900.0000.0000.0000.000
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