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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: M3M2Z

Calculation Name: 4YEQ-U-Xray323

Preferred Name: Laminin

Target Type: PROTEIN COMPLEX GROUP

Ligand Name:

ligand 3-letter code:

PDB ID: 4YEQ

Chain ID: U

ChEMBL ID: CHEMBL2364187

UniProt ID: P24043

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 187
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2186046.886066
FMO2-HF: Nuclear repulsion 2109824.48126
FMO2-HF: Total energy -76222.404806
FMO2-MP2: Total energy -76445.300869


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(U:4:ACE )


Summations of interaction energy for fragment #1(U:4:ACE )
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.
0.2831.5840.508-0.279-1.53-0.004
Interaction energy analysis for fragmet #1(U:4:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.002
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].
3U6LEU 0-0.055-0.0073.7970.6231.798-0.008-0.570-0.597-0.002
4U7ILE 0-0.0240.0146.4120.2290.2290.0000.0000.0000.000
5U8ARG 10.9640.9808.5300.2920.2920.0000.0000.0000.000
6U9THR 0-0.0100.00711.363-0.004-0.0040.0000.0000.0000.000
7U10TRP 00.014-0.00713.6230.0290.0290.0000.0000.0000.000
8U11VAL 0-0.0040.02116.373-0.011-0.0110.0000.0000.0000.000
9U12THR 00.0410.00318.6880.0100.0100.0000.0000.0000.000
10U13LEU 00.0110.00922.382-0.002-0.0020.0000.0000.0000.000
11U14LYS 10.9120.98225.3570.0850.0850.0000.0000.0000.000
12U15ALA 00.026-0.02426.4730.0060.0060.0000.0000.0000.000
13U16GLU -1-0.941-0.98329.113-0.053-0.0530.0000.0000.0000.000
14U17GLN 00.0820.05226.5940.0020.0020.0000.0000.0000.000
15U18THR 0-0.028-0.00230.8270.0010.0010.0000.0000.0000.000
16U19ILE 0-0.020-0.01233.4640.0030.0030.0000.0000.0000.000
17U20LEU 00.010-0.01129.229-0.001-0.0010.0000.0000.0000.000
18U21PRO 0-0.0290.00232.3610.0020.0020.0000.0000.0000.000
19U22LEU 00.0290.01234.5840.0010.0010.0000.0000.0000.000
20U23VAL 0-0.033-0.03233.7140.0000.0000.0000.0000.0000.000
21U24ASP -1-0.675-0.83036.9710.0020.0020.0000.0000.0000.000
22U25GLU -1-0.846-0.91035.3430.0130.0130.0000.0000.0000.000
23U26ALA 0-0.072-0.03235.2760.0010.0010.0000.0000.0000.000
24U27LEU 0-0.032-0.00531.6760.0000.0000.0000.0000.0000.000
25U28GLN 0-0.042-0.01036.2400.0010.0010.0000.0000.0000.000
26U29HIS 10.8120.89939.594-0.001-0.0010.0000.0000.0000.000
27U30THR 00.0170.01936.2240.0000.0000.0000.0000.0000.000
28U31THR 0-0.051-0.04039.0050.0000.0000.0000.0000.0000.000
29U32THR 0-0.015-0.03938.3270.0000.0000.0000.0000.0000.000
30U33LYS 10.9790.99840.6050.0110.0110.0000.0000.0000.000
31U34GLY 00.0720.03942.8040.0000.0000.0000.0000.0000.000
32U35ILE 0-0.084-0.02237.2850.0000.0000.0000.0000.0000.000
33U36VAL 0-0.008-0.00540.133-0.001-0.0010.0000.0000.0000.000
34U37PHE 0-0.003-0.00133.740-0.001-0.0010.0000.0000.0000.000
35U38GLN 0-0.042-0.03537.7560.0010.0010.0000.0000.0000.000
36U39HIS 0-0.0400.03133.625-0.003-0.0030.0000.0000.0000.000
37U40PRO 0-0.012-0.02432.6490.0010.0010.0000.0000.0000.000
38U41GLU -1-0.852-0.92533.660-0.030-0.0300.0000.0000.0000.000
39U42ILE 00.0040.01232.8770.0000.0000.0000.0000.0000.000
40U43VAL 0-0.034-0.01835.8360.0020.0020.0000.0000.0000.000
41U44ALA 00.0370.02939.0100.0000.0000.0000.0000.0000.000
42U45HIS 0-0.013-0.02240.6010.0010.0010.0000.0000.0000.000
43U46MET 00.0630.03741.9420.0010.0010.0000.0000.0000.000
44U47ASP -1-0.892-0.95446.210-0.010-0.0100.0000.0000.0000.000
45U48LEU 0-0.081-0.02945.4530.0000.0000.0000.0000.0000.000
46U49MET 00.0220.01142.867-0.001-0.0010.0000.0000.0000.000
47U50ARG 10.8510.94247.0600.0100.0100.0000.0000.0000.000
48U51GLU -1-0.944-0.97148.628-0.009-0.0090.0000.0000.0000.000
49U52ASP -1-0.860-0.93245.127-0.007-0.0070.0000.0000.0000.000
50U53LEU 0-0.034-0.03145.8500.0000.0000.0000.0000.0000.000
51U54HIS 00.0210.01247.0200.0010.0010.0000.0000.0000.000
52U55LEU 0-0.103-0.04143.0920.0010.0010.0000.0000.0000.000
53U56GLU -1-0.960-0.93942.272-0.002-0.0020.0000.0000.0000.000
54U57PRO 0-0.025-0.04039.2900.0010.0010.0000.0000.0000.000
55U58PHE 00.013-0.01538.4240.0000.0000.0000.0000.0000.000
56U59TYR 0-0.029-0.02632.5980.0000.0000.0000.0000.0000.000
57U60TRP 00.0350.00031.427-0.002-0.0020.0000.0000.0000.000
58U61LYS 10.9220.97329.1040.0120.0120.0000.0000.0000.000
59U62LEU 0-0.031-0.01524.386-0.005-0.0050.0000.0000.0000.000
60U63PRO 00.0050.00525.3810.0040.0040.0000.0000.0000.000
61U64GLU -1-0.830-0.92924.592-0.044-0.0440.0000.0000.0000.000
62U65GLN 0-0.070-0.02420.8390.0060.0060.0000.0000.0000.000
63U66PHE 0-0.057-0.05119.712-0.011-0.0110.0000.0000.0000.000
64U67GLU -1-0.906-0.94920.163-0.004-0.0040.0000.0000.0000.000
65U68GLY 00.0330.00519.826-0.011-0.0110.0000.0000.0000.000
66U69LYS 10.9380.95615.004-0.052-0.0520.0000.0000.0000.000
67U70LYS 10.8260.94914.6050.0230.0230.0000.0000.0000.000
68U71LEU 00.0710.02811.6930.0050.0050.0000.0000.0000.000
69U72MET 00.011-0.0136.5990.0770.0770.0000.0000.0000.000
70U73ALA 0-0.0110.00310.760-0.023-0.0230.0000.0000.0000.000
71U74TYR 0-0.146-0.08812.6880.0050.0050.0000.0000.0000.000
72U75GLY 0-0.0100.01512.6050.0140.0140.0000.0000.0000.000
73U76GLY 00.004-0.01713.2190.0040.0040.0000.0000.0000.000
74U77LYS 10.9100.94516.715-0.013-0.0130.0000.0000.0000.000
75U78LEU 00.0540.04819.094-0.013-0.0130.0000.0000.0000.000
76U79LYS 10.8970.93621.6120.0650.0650.0000.0000.0000.000
77U80TYR 00.007-0.03524.034-0.003-0.0030.0000.0000.0000.000
78U81ALA 0-0.026-0.00627.4920.0040.0040.0000.0000.0000.000
79U82ILE 00.0230.00631.034-0.001-0.0010.0000.0000.0000.000
80U83TYR 0-0.098-0.11634.1270.0010.0010.0000.0000.0000.000
81U84PHE 00.0240.01037.7850.0000.0000.0000.0000.0000.000
82U85GLU -1-0.780-0.81740.870-0.015-0.0150.0000.0000.0000.000
83U86ALA 00.0160.01444.6340.0000.0000.0000.0000.0000.000
84U87ARG 10.8800.97446.8000.0020.0020.0000.0000.0000.000
85U88GLU -1-0.842-0.89649.4020.0000.0000.0000.0000.0000.000
86U89GLU -1-0.813-0.91343.596-0.005-0.0050.0000.0000.0000.000
87U90THR 0-0.001-0.00244.2660.0000.0000.0000.0000.0000.000
88U91GLY 00.0500.02345.807-0.001-0.0010.0000.0000.0000.000
89U92PHE 00.0070.00042.8970.0010.0010.0000.0000.0000.000
90U93SER 0-0.035-0.03440.6230.0000.0000.0000.0000.0000.000
91U94THR 0-0.038-0.02339.4240.0000.0000.0000.0000.0000.000
92U95TYR 0-0.015-0.01839.6330.0020.0020.0000.0000.0000.000
93U96ASN 00.0380.02637.7380.0030.0030.0000.0000.0000.000
94U97PRO 00.0130.03132.511-0.001-0.0010.0000.0000.0000.000
95U98GLN 00.0000.00830.393-0.001-0.0010.0000.0000.0000.000
96U99VAL 00.018-0.00626.163-0.004-0.0040.0000.0000.0000.000
97U100ILE 0-0.016-0.00628.9040.0060.0060.0000.0000.0000.000
98U101ILE 00.006-0.00422.706-0.005-0.0050.0000.0000.0000.000
99U102ARG 10.9190.97026.220-0.025-0.0250.0000.0000.0000.000
100U103GLY 00.0900.03823.260-0.007-0.0070.0000.0000.0000.000
101U104GLY 00.0540.04622.6890.0060.0060.0000.0000.0000.000
102U105THR 00.0300.00722.132-0.006-0.0060.0000.0000.0000.000
103U106PRO 00.0660.01424.5910.0020.0020.0000.0000.0000.000
104U107THR 0-0.027-0.02826.879-0.003-0.0030.0000.0000.0000.000
105U108HIS 0-0.063-0.02124.613-0.001-0.0010.0000.0000.0000.000
106U109ALA 0-0.071-0.00825.8100.0010.0010.0000.0000.0000.000
107U110ARG 10.9460.98226.843-0.073-0.0730.0000.0000.0000.000
108U111ILE 00.000-0.00427.259-0.001-0.0010.0000.0000.0000.000
109U112ILE 0-0.0100.00023.4210.0020.0020.0000.0000.0000.000
110U113VAL 00.0190.01027.994-0.006-0.0060.0000.0000.0000.000
111U114ARG 10.9430.99025.951-0.022-0.0220.0000.0000.0000.000
112U115HIS 00.0520.02328.921-0.006-0.0060.0000.0000.0000.000
113U116MET 0-0.021-0.04129.6960.0010.0010.0000.0000.0000.000
114U117ALA 0-0.0040.00832.9770.0000.0000.0000.0000.0000.000
115U118ALA 0-0.005-0.00235.542-0.002-0.0020.0000.0000.0000.000
116U119PRO 0-0.016-0.00235.1960.0000.0000.0000.0000.0000.000
117U120LEU 00.0360.01637.6570.0010.0010.0000.0000.0000.000
118U121ILE 0-0.020-0.01440.562-0.002-0.0020.0000.0000.0000.000
119U122GLY 0-0.045-0.00742.8400.0000.0000.0000.0000.0000.000
120U123GLN 0-0.017-0.01338.625-0.001-0.0010.0000.0000.0000.000
121U124LEU 0-0.011-0.00333.8530.0010.0010.0000.0000.0000.000
122U125THR 0-0.032-0.01234.5840.0000.0000.0000.0000.0000.000
123U126ARG 10.7950.84228.8900.0390.0390.0000.0000.0000.000
124U127HIS 00.0360.05928.1170.0040.0040.0000.0000.0000.000
125U128GLU -1-0.891-0.96623.270-0.037-0.0370.0000.0000.0000.000
126U129ILE 0-0.027-0.01623.6170.0070.0070.0000.0000.0000.000
127U130GLU -1-0.951-0.97819.0020.0530.0530.0000.0000.0000.000
128U131MET 0-0.0130.02217.0380.0060.0060.0000.0000.0000.000
129U132THR 00.034-0.01416.7620.0190.0190.0000.0000.0000.000
130U133GLU -1-0.777-0.89919.2650.1360.1360.0000.0000.0000.000
131U134LYS 10.8740.96119.370-0.131-0.1310.0000.0000.0000.000
132U135GLU -1-0.887-0.95223.9050.0360.0360.0000.0000.0000.000
133U136TRP 0-0.102-0.02922.546-0.009-0.0090.0000.0000.0000.000
134U137LYS 10.8670.91626.490-0.033-0.0330.0000.0000.0000.000
135U138TYR 0-0.028-0.06427.1190.0000.0000.0000.0000.0000.000
136U139TYR 0-0.092-0.07530.835-0.002-0.0020.0000.0000.0000.000
137U140GLY 00.0160.01132.8790.0010.0010.0000.0000.0000.000
138U141ASP -1-0.953-0.96934.3810.0410.0410.0000.0000.0000.000
139U142ASP -1-0.803-0.89436.0410.0210.0210.0000.0000.0000.000
140U143PRO 00.0400.00535.5690.0030.0030.0000.0000.0000.000
141U144ARG 10.8110.88536.085-0.019-0.0190.0000.0000.0000.000
142U145VAL 0-0.0310.01134.5590.0010.0010.0000.0000.0000.000
143U146HIS 00.000-0.01534.2790.0020.0020.0000.0000.0000.000
144U147ARG 10.9420.99031.102-0.049-0.0490.0000.0000.0000.000
145U148THR 00.0080.00126.629-0.003-0.0030.0000.0000.0000.000
146U149VAL 0-0.018-0.00423.9870.0030.0030.0000.0000.0000.000
147U150THR 00.0390.02624.4800.0100.0100.0000.0000.0000.000
148U151ARG 10.9710.96616.821-0.220-0.2200.0000.0000.0000.000
149U152GLU -1-0.966-0.98719.6700.1540.1540.0000.0000.0000.000
150U153ASP -1-0.753-0.82920.7700.0890.0890.0000.0000.0000.000
151U154PHE 0-0.017-0.00118.073-0.005-0.0050.0000.0000.0000.000
152U155LEU 0-0.041-0.02714.515-0.002-0.0020.0000.0000.0000.000
153U156ASP -1-0.887-0.93917.7290.1380.1380.0000.0000.0000.000
154U157ILE 0-0.081-0.03720.150-0.013-0.0130.0000.0000.0000.000
155U158LEU 0-0.027-0.02315.702-0.011-0.0110.0000.0000.0000.000
156U159TYR 0-0.072-0.02415.303-0.006-0.0060.0000.0000.0000.000
157U160ASP -1-0.941-1.00117.3590.0260.0260.0000.0000.0000.000
158U161ILE 0-0.0280.02418.963-0.001-0.0010.0000.0000.0000.000
159U162HIS 00.0070.00021.742-0.009-0.0090.0000.0000.0000.000
160U163TYR 00.025-0.00825.312-0.006-0.0060.0000.0000.0000.000
161U164ILE 00.0040.01221.5330.0060.0060.0000.0000.0000.000
162U165LEU 0-0.011-0.00326.135-0.006-0.0060.0000.0000.0000.000
163U166ILE 0-0.002-0.00626.7970.0030.0030.0000.0000.0000.000
164U167LYS 10.8690.96830.696-0.004-0.0040.0000.0000.0000.000
165U168ALA 00.0090.01434.229-0.003-0.0030.0000.0000.0000.000
166U169THR 00.0370.01736.713-0.001-0.0010.0000.0000.0000.000
167U170TYR 0-0.047-0.06134.5650.0020.0020.0000.0000.0000.000
168U171GLY 00.0020.00441.0060.0000.0000.0000.0000.0000.000
169U172ASN 0-0.049-0.04744.1920.0010.0010.0000.0000.0000.000
170U173PHE 00.009-0.00747.524-0.001-0.0010.0000.0000.0000.000
171U174MET 00.0200.03941.365-0.001-0.0010.0000.0000.0000.000
172U175ARG 10.9430.96546.0030.0120.0120.0000.0000.0000.000
173U176GLN 0-0.035-0.03642.897-0.002-0.0020.0000.0000.0000.000
174U177SER 0-0.003-0.01438.0680.0000.0000.0000.0000.0000.000
175U178ARG 10.8890.93136.8980.0230.0230.0000.0000.0000.000
176U179ILE 00.0090.02629.7600.0010.0010.0000.0000.0000.000
177U180SER 00.007-0.01031.007-0.004-0.0040.0000.0000.0000.000
178U181GLU -1-0.801-0.85827.506-0.048-0.0480.0000.0000.0000.000
179U182ILE 00.0150.02224.6590.0000.0000.0000.0000.0000.000
180U183SER 0-0.036-0.03120.862-0.011-0.0110.0000.0000.0000.000
181U184MET 0-0.022-0.00617.6060.0160.0160.0000.0000.0000.000
182U185GLU -1-0.931-0.95614.408-0.112-0.1120.0000.0000.0000.000
183U186VAL 0-0.016-0.00612.0740.0280.0280.0000.0000.0000.000
184U187ALA 0-0.041-0.0347.1370.0030.0030.0000.0000.0000.000
185U188GLU -1-0.801-0.8907.362-0.965-0.9650.0000.0000.0000.000
186U189GLN 0-0.130-0.1002.9160.2490.2520.5160.309-0.828-0.002
187U190NME 00.0240.0314.782-0.209-0.0860.000-0.018-0.1050.000