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

tag_button

FMODB ID: K2993

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 OptH
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 -2181124.267792
FMO2-HF: Nuclear repulsion 2097460.02226
FMO2-HF: Total energy -83664.245532
FMO2-MP2: Total energy -83906.594906


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.
-20.911-14.611.985-3.226-5.0590.031
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 : -0.906 / q_NPA : -0.958
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].
3F3GLN00.0240.0013.796-2.994-1.219-0.008-0.779-0.9880.006
4F4MET0-0.0250.0015.694-3.145-3.1450.0000.0000.0000.000
5F5THR00.0200.0138.947-0.232-0.2320.0000.0000.0000.000
6F6GLN00.008-0.01811.8330.0360.0360.0000.0000.0000.000
7F7SER0-0.0260.02315.071-0.418-0.4180.0000.0000.0000.000
8F8PRO00.037-0.00618.498-0.029-0.0290.0000.0000.0000.000
9F9SER0-0.012-0.00418.073-0.136-0.1360.0000.0000.0000.000
10F10SER00.0070.00219.376-0.161-0.1610.0000.0000.0000.000
11F11LEU00.0150.00023.048-0.155-0.1550.0000.0000.0000.000
12F12SER00.0100.00925.833-0.182-0.1820.0000.0000.0000.000
13F13ALA0-0.0060.00129.513-0.124-0.1240.0000.0000.0000.000
14F14SER00.0030.01531.700-0.097-0.0970.0000.0000.0000.000
15F15LEU00.0490.01334.1490.1700.1700.0000.0000.0000.000
16F16GLY0-0.0110.00135.573-0.166-0.1660.0000.0000.0000.000
17F17GLU-1-0.899-0.89732.5559.0929.0920.0000.0000.0000.000
18F18ARG10.9210.96628.915-9.858-9.8580.0000.0000.0000.000
19F19VAL00.0440.01925.6470.0710.0710.0000.0000.0000.000
20F20SER0-0.054-0.04224.3260.0040.0040.0000.0000.0000.000
21F21LEU0-0.0200.01119.8850.1100.1100.0000.0000.0000.000
22F22THR00.0400.01217.517-0.184-0.1840.0000.0000.0000.000
23F23CYS0-0.088-0.00112.2940.1330.1330.0000.0000.0000.000
24F24ARG10.8760.93813.126-17.226-17.2260.0000.0000.0000.000
25F25ALA00.0150.0149.3611.2321.2320.0000.0000.0000.000
26F26SER00.0020.0125.946-0.854-0.8540.0000.0000.0000.000
27F27GLN0-0.010-0.0084.9954.4094.473-0.001-0.006-0.0560.000
28F28GLU-1-0.839-0.9298.88217.72217.7220.0000.0000.0000.000
29F29ILE00.003-0.0108.6381.4841.4840.0000.0000.0000.000
30F30SER0-0.021-0.02111.121-0.412-0.4120.0000.0000.0000.000
31F31GLY0-0.027-0.02314.785-0.685-0.6850.0000.0000.0000.000
32F32TYR0-0.0220.01512.468-0.922-0.9220.0000.0000.0000.000
33F33LEU0-0.019-0.01312.3501.5931.5930.0000.0000.0000.000
34F34SER0-0.073-0.04113.734-1.321-1.3210.0000.0000.0000.000
35F35TRP00.0210.00915.0580.9660.9660.0000.0000.0000.000
36F36LEU00.015-0.00115.034-0.662-0.6620.0000.0000.0000.000
37F37GLN0-0.001-0.01518.496-0.027-0.0270.0000.0000.0000.000
38F38GLN00.0090.00519.5680.0930.0930.0000.0000.0000.000
39F39LYS10.8210.89921.962-10.878-10.8780.0000.0000.0000.000
40F40PRO00.012-0.00324.9010.3080.3080.0000.0000.0000.000
41F41ASP-1-0.849-0.89626.87511.14611.1460.0000.0000.0000.000
42F42GLY00.0150.02023.6210.0430.0430.0000.0000.0000.000
43F43THR0-0.069-0.06123.0170.5630.5630.0000.0000.0000.000
44F44ILE0-0.004-0.00817.9580.1410.1410.0000.0000.0000.000
45F45LYS10.9120.96621.837-11.684-11.6840.0000.0000.0000.000
46F46ARG10.8940.94619.213-13.281-13.2810.0000.0000.0000.000
47F47LEU0-0.0020.00220.649-0.561-0.5610.0000.0000.0000.000
48F48ILE0-0.022-0.00219.697-0.465-0.4650.0000.0000.0000.000
49F49TYR0-0.022-0.01818.5031.0171.0170.0000.0000.0000.000
50F50ALA00.0510.01617.781-0.501-0.5010.0000.0000.0000.000
51F51ALA0-0.0030.01217.679-0.561-0.5610.0000.0000.0000.000
52F52SER0-0.059-0.05018.779-0.119-0.1190.0000.0000.0000.000
53F53THR00.0090.03022.170-0.719-0.7190.0000.0000.0000.000
54F54LEU00.0150.00023.1430.4540.4540.0000.0000.0000.000
55F55ASP-1-0.821-0.90123.73211.94311.9430.0000.0000.0000.000
56F56SER00.006-0.01525.458-0.215-0.2150.0000.0000.0000.000
57F57SER0-0.091-0.02727.722-0.428-0.4280.0000.0000.0000.000
58F58VAL00.0120.00425.3160.0120.0120.0000.0000.0000.000
59F59PRO0-0.011-0.00328.696-0.167-0.1670.0000.0000.0000.000
60F60LYS11.0050.97529.517-8.290-8.2900.0000.0000.0000.000
61F61ARG10.8500.92530.207-9.493-9.4930.0000.0000.0000.000
62F62PHE0-0.0010.00824.9450.1940.1940.0000.0000.0000.000
63F63SER0-0.006-0.01025.566-0.112-0.1120.0000.0000.0000.000
64F64GLY00.0440.02821.7410.2550.2550.0000.0000.0000.000
65F65SER0-0.010-0.01521.412-0.456-0.4560.0000.0000.0000.000
66F66ARG10.8830.91216.799-15.498-15.4980.0000.0000.0000.000
67F67SER00.0150.03020.188-0.677-0.6770.0000.0000.0000.000
68F68GLY0-0.0780.01717.4480.4160.4160.0000.0000.0000.000
69F69SER00.0570.01312.602-0.796-0.7960.0000.0000.0000.000
70F70ASP-1-0.799-0.91314.79317.07217.0720.0000.0000.0000.000
71F71TYR00.0380.01014.101-1.085-1.0850.0000.0000.0000.000
72F72SER00.0120.00417.5070.2150.2150.0000.0000.0000.000
73F73LEU0-0.0260.01020.116-0.203-0.2030.0000.0000.0000.000
74F74THR0-0.068-0.04521.687-0.321-0.3210.0000.0000.0000.000
75F75ILE00.0440.02825.359-0.046-0.0460.0000.0000.0000.000
76F76SER0-0.030-0.02328.086-0.195-0.1950.0000.0000.0000.000
77F77SER0-0.096-0.11431.550-0.080-0.0800.0000.0000.0000.000
78F78LEU0-0.0440.00929.429-0.189-0.1890.0000.0000.0000.000
79F79ASP-1-0.813-0.90131.8348.5318.5310.0000.0000.0000.000
80F80SER00.005-0.00832.3340.1820.1820.0000.0000.0000.000
81F81GLU-1-0.953-0.98532.2188.9858.9850.0000.0000.0000.000
82F82ASP-1-0.760-0.85228.36110.38710.3870.0000.0000.0000.000
83F83PHE00.0390.05227.3290.4890.4890.0000.0000.0000.000
84F84ALA0-0.037-0.01523.926-0.081-0.0810.0000.0000.0000.000
85F85VAL00.0200.01818.701-0.104-0.1040.0000.0000.0000.000
86F86TYR0-0.043-0.03419.4450.2170.2170.0000.0000.0000.000
87F87TYR00.0330.02413.9060.5680.5680.0000.0000.0000.000
88F89LEU0-0.004-0.0139.6271.3131.3130.0000.0000.0000.000
89F90GLN00.0630.0255.577-4.118-4.1180.0000.0000.0000.000
90F91TYR0-0.031-0.0438.5521.2361.2360.0000.0000.0000.000
91F92ALA00.0130.0128.999-1.318-1.3180.0000.0000.0000.000
92F93SER0-0.065-0.0345.8470.3940.3940.0000.0000.0000.000
93F94TYR0-0.049-0.0026.4410.2900.2900.0000.0000.0000.000
94F95PRO00.0630.0292.669-6.734-2.8121.886-2.293-3.5160.025
95F96TYR00.003-0.0064.194-0.461-0.341-0.001-0.029-0.0900.000
96F97THR0-0.0040.0082.987-0.0890.3310.109-0.119-0.4090.000
97F98PHE00.013-0.0026.032-3.234-3.2340.0000.0000.0000.000
98F99GLY00.001-0.0208.8261.5121.5120.0000.0000.0000.000
99F100GLY0-0.010-0.01511.277-0.046-0.0460.0000.0000.0000.000
100F101GLY00.0190.01413.017-0.650-0.6500.0000.0000.0000.000
101F102THR0-0.056-0.04116.272-0.072-0.0720.0000.0000.0000.000
102F103LYS10.9110.97419.667-11.706-11.7060.0000.0000.0000.000
103F104VAL0-0.006-0.00322.793-0.208-0.2080.0000.0000.0000.000
104F105GLU-1-0.942-0.98425.73010.60410.6040.0000.0000.0000.000
105F106ILE0-0.017-0.01029.088-0.049-0.0490.0000.0000.0000.000
106F107LYS10.9210.97132.465-9.150-9.1500.0000.0000.0000.000
107F108ARG10.8660.92534.924-7.775-7.7750.0000.0000.0000.000
108F109ALA0-0.011-0.00138.4290.0080.0080.0000.0000.0000.000
109F110ASP-1-0.885-0.94940.6627.6327.6320.0000.0000.0000.000
110F111ALA0-0.043-0.02742.115-0.152-0.1520.0000.0000.0000.000
111F112ALA00.0070.00143.0150.1280.1280.0000.0000.0000.000
112F113PRO0-0.0110.01843.037-0.014-0.0140.0000.0000.0000.000
113F114THR00.0160.00044.727-0.224-0.2240.0000.0000.0000.000
114F115VAL0-0.005-0.00946.3270.1120.1120.0000.0000.0000.000
115F116SER0-0.059-0.03147.609-0.216-0.2160.0000.0000.0000.000
116F117ILE0-0.0160.00448.1800.1440.1440.0000.0000.0000.000
117F118PHE0-0.015-0.01147.893-0.114-0.1140.0000.0000.0000.000
118F119PRO00.0130.01150.7460.1040.1040.0000.0000.0000.000
119F120PRO00.013-0.00151.2260.0570.0570.0000.0000.0000.000
120F121SER00.0320.02951.568-0.103-0.1030.0000.0000.0000.000
121F122SER00.042-0.00153.6640.0150.0150.0000.0000.0000.000
122F123GLU-1-0.871-0.94052.5725.9095.9090.0000.0000.0000.000
123F124GLN0-0.011-0.02047.071-0.009-0.0090.0000.0000.0000.000
124F125LEU00.0120.00051.6080.0200.0200.0000.0000.0000.000
125F126THR0-0.044-0.01854.409-0.069-0.0690.0000.0000.0000.000
126F127SER0-0.051-0.01650.910-0.030-0.0300.0000.0000.0000.000
127F128GLY0-0.028-0.01251.4220.0970.0970.0000.0000.0000.000
128F129GLY0-0.010-0.00349.3750.0660.0660.0000.0000.0000.000
129F130ALA00.015-0.01049.517-0.116-0.1160.0000.0000.0000.000
130F131SER0-0.0310.01345.4910.0810.0810.0000.0000.0000.000
131F132VAL0-0.0120.00547.814-0.091-0.0910.0000.0000.0000.000
132F133VAL00.0170.01644.2980.1570.1570.0000.0000.0000.000
133F134CYS0-0.074-0.04044.994-0.050-0.0500.0000.0000.0000.000
134F135PHE0-0.027-0.00142.5730.1950.1950.0000.0000.0000.000
135F136LEU00.014-0.01341.712-0.199-0.1990.0000.0000.0000.000
136F137ASN00.036-0.00141.4140.3430.3430.0000.0000.0000.000
137F138ASN00.0210.00540.978-0.224-0.2240.0000.0000.0000.000
138F139PHE0-0.0280.00537.366-0.164-0.1640.0000.0000.0000.000
139F140TYR00.0260.01633.8050.2190.2190.0000.0000.0000.000
140F141PRO00.0510.01935.617-0.220-0.2200.0000.0000.0000.000
141F142LYS10.9930.98129.220-10.394-10.3940.0000.0000.0000.000
142F143ASP-1-0.926-0.94633.6259.1489.1480.0000.0000.0000.000
143F144ILE0-0.027-0.01936.016-0.259-0.2590.0000.0000.0000.000
144F145ASN0-0.045-0.01738.4980.2670.2670.0000.0000.0000.000
145F146VAL00.0450.00341.035-0.157-0.1570.0000.0000.0000.000
146F147LYS10.8860.96743.232-6.496-6.4960.0000.0000.0000.000
147F148TRP00.0340.00943.937-0.209-0.2090.0000.0000.0000.000
148F149LYS10.8650.93148.050-6.044-6.0440.0000.0000.0000.000
149F150ILE0-0.003-0.00550.885-0.017-0.0170.0000.0000.0000.000
150F151ASP-1-0.773-0.89654.0735.4155.4150.0000.0000.0000.000
151F152GLY0-0.0030.00856.254-0.068-0.0680.0000.0000.0000.000
152F153SER0-0.037-0.02054.3410.0090.0090.0000.0000.0000.000
153F154GLU-1-0.913-0.95846.6946.7566.7560.0000.0000.0000.000
154F155ARG10.8190.91347.451-6.549-6.5490.0000.0000.0000.000
155F156GLN0-0.004-0.00943.2260.2270.2270.0000.0000.0000.000
156F157ASN00.010-0.00643.2680.2610.2610.0000.0000.0000.000
157F158GLY00.0570.01842.611-0.155-0.1550.0000.0000.0000.000
158F159VAL00.0040.01540.715-0.041-0.0410.0000.0000.0000.000
159F160LEU0-0.023-0.00236.4770.2250.2250.0000.0000.0000.000
160F161ASN00.0260.00936.493-0.322-0.3220.0000.0000.0000.000
161F162SER0-0.0090.00034.4010.3110.3110.0000.0000.0000.000
162F163TRP00.0170.00832.669-0.183-0.1830.0000.0000.0000.000
163F164THR0-0.025-0.00932.8630.2060.2060.0000.0000.0000.000
164F165ASP-1-0.872-0.94628.16010.82210.8220.0000.0000.0000.000
165F166GLN0-0.053-0.05231.3830.0250.0250.0000.0000.0000.000
166F167ASP-1-0.878-0.94033.0608.3068.3060.0000.0000.0000.000
167F168SER0-0.010-0.02334.104-0.007-0.0070.0000.0000.0000.000
168F169LYS10.8940.94335.054-7.958-7.9580.0000.0000.0000.000
169F170ASP-1-0.719-0.80537.7907.5317.5310.0000.0000.0000.000
170F171SER0-0.055-0.02635.599-0.107-0.1070.0000.0000.0000.000
171F172THR0-0.123-0.10336.2840.1100.1100.0000.0000.0000.000
172F173TYR00.0120.00330.6760.1430.1430.0000.0000.0000.000
173F174SER00.0490.02536.603-0.357-0.3570.0000.0000.0000.000
174F175MET0-0.0270.00336.8610.2720.2720.0000.0000.0000.000
175F176SER0-0.0200.00738.445-0.316-0.3160.0000.0000.0000.000
176F177SER00.0160.00139.3560.1260.1260.0000.0000.0000.000
177F178THR00.013-0.00241.483-0.228-0.2280.0000.0000.0000.000
178F179LEU00.0030.01642.8140.1310.1310.0000.0000.0000.000
179F180THR00.003-0.00943.722-0.137-0.1370.0000.0000.0000.000
180F181LEU0-0.075-0.02946.0330.0210.0210.0000.0000.0000.000
181F182THR00.0410.01749.077-0.040-0.0400.0000.0000.0000.000
182F183LYS10.9220.95351.051-5.679-5.6790.0000.0000.0000.000
183F184ASP-1-0.840-0.92154.0615.6225.6220.0000.0000.0000.000
184F185GLU-1-0.882-0.95950.4536.2566.2560.0000.0000.0000.000
185F186TYR00.0360.01553.178-0.046-0.0460.0000.0000.0000.000
186F187GLU-1-0.917-0.95054.9175.3725.3720.0000.0000.0000.000
187F188ARG10.8720.95557.174-5.551-5.5510.0000.0000.0000.000
188F189HIS10.8330.92555.803-5.690-5.6900.0000.0000.0000.000
189F190ASN00.0390.01959.055-0.006-0.0060.0000.0000.0000.000
190F191SER00.0030.03158.1190.0260.0260.0000.0000.0000.000
191F192TYR0-0.009-0.03552.3340.1090.1090.0000.0000.0000.000
192F193THR0-0.015-0.02152.122-0.077-0.0770.0000.0000.0000.000
193F195GLU-1-0.861-0.94348.0826.1496.1490.0000.0000.0000.000
194F196ALA00.0490.02544.7390.1700.1700.0000.0000.0000.000
195F197THR0-0.038-0.02443.377-0.199-0.1990.0000.0000.0000.000
196F198HIS00.0370.03339.5990.1420.1420.0000.0000.0000.000
197F199LYS10.9120.93842.606-7.177-7.1770.0000.0000.0000.000
198F200THR00.0160.00144.1420.0090.0090.0000.0000.0000.000
199F201SER00.0060.00146.745-0.083-0.0830.0000.0000.0000.000
200F202THR0-0.017-0.00749.587-0.064-0.0640.0000.0000.0000.000
201F203SER00.012-0.00448.147-0.090-0.0900.0000.0000.0000.000
202F204PRO0-0.0410.00948.8540.0910.0910.0000.0000.0000.000
203F205ILE00.0290.01847.297-0.131-0.1310.0000.0000.0000.000
204F206VAL00.0040.00149.5400.1080.1080.0000.0000.0000.000
205F207LYS10.9150.96150.991-6.105-6.1050.0000.0000.0000.000
206F208SER00.003-0.00752.4640.0740.0740.0000.0000.0000.000
207F209PHE00.0050.01752.587-0.032-0.0320.0000.0000.0000.000
208F210ASN00.015-0.00557.1160.0500.0500.0000.0000.0000.000
209F211ARG10.8430.91857.394-5.401-5.4010.0000.0000.0000.000
210F212ASN0-0.029-0.00760.5000.0360.0360.0000.0000.0000.000
211F213GLU-1-0.924-0.95263.1384.7684.7680.0000.0000.0000.000
212F214CYS0-0.0090.00061.4770.0810.0810.0000.0000.0000.000