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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: VR161

Calculation Name: 4YEQ-U-Xray372

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: 2023-06-20

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2176083.312448
FMO2-HF: Nuclear repulsion 2100030.14355
FMO2-HF: Total energy -76053.168898
FMO2-MP2: Total energy -76275.416021


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:5:GLY)


Summations of interaction energy for fragment #1(U:5:GLY)
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.
0.9340.5779.609-5.122-4.128-0.02
Interaction energy analysis for fragmet #1(U:5:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.013
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].
3U7ILE00.0070.0082.342-1.195-0.0211.008-0.931-1.250-0.001
4U8ARG10.8640.9154.7510.7380.830-0.001-0.006-0.0850.000
5U9THR0-0.0070.0088.294-0.091-0.0910.0000.0000.0000.000
6U10TRP00.013-0.00610.6070.0290.0290.0000.0000.0000.000
7U11VAL0-0.0030.02014.262-0.010-0.0100.0000.0000.0000.000
8U12THR00.0330.00216.463-0.016-0.0160.0000.0000.0000.000
9U13LEU00.0140.01319.9490.0140.0140.0000.0000.0000.000
10U14LYS10.9120.96322.652-0.070-0.0700.0000.0000.0000.000
11U15ALA00.021-0.01323.869-0.004-0.0040.0000.0000.0000.000
12U16GLU-1-0.912-0.97326.1520.0690.0690.0000.0000.0000.000
13U17GLN00.0650.05524.567-0.003-0.0030.0000.0000.0000.000
14U18THR0-0.0140.00128.414-0.001-0.0010.0000.0000.0000.000
15U19ILE0-0.030-0.02431.081-0.004-0.0040.0000.0000.0000.000
16U20LEU00.004-0.00827.5930.0070.0070.0000.0000.0000.000
17U21PRO0-0.0100.00331.076-0.005-0.0050.0000.0000.0000.000
18U22LEU00.0230.00933.3730.0030.0030.0000.0000.0000.000
19U23VAL0-0.016-0.01833.2510.0010.0010.0000.0000.0000.000
20U24ASP-1-0.685-0.81436.3300.0620.0620.0000.0000.0000.000
21U25GLU-1-0.852-0.92135.4150.0730.0730.0000.0000.0000.000
22U26ALA0-0.062-0.03335.4450.0050.0050.0000.0000.0000.000
23U27LEU0-0.026-0.00531.4680.0040.0040.0000.0000.0000.000
24U28GLN0-0.089-0.03236.2170.0010.0010.0000.0000.0000.000
25U29HIS10.8200.88039.420-0.058-0.0580.0000.0000.0000.000
26U30THR00.0110.00935.4390.0020.0020.0000.0000.0000.000
27U31THR0-0.049-0.04038.002-0.003-0.0030.0000.0000.0000.000
28U32THR00.013-0.01636.5980.0020.0020.0000.0000.0000.000
29U33LYS10.8560.90739.120-0.045-0.0450.0000.0000.0000.000
30U34GLY00.0570.03341.188-0.003-0.0030.0000.0000.0000.000
31U35ILE0-0.064-0.02235.434-0.001-0.0010.0000.0000.0000.000
32U36VAL0-0.005-0.00337.997-0.001-0.0010.0000.0000.0000.000
33U37PHE00.0230.00930.7020.0000.0000.0000.0000.0000.000
34U38GLN0-0.020-0.02335.078-0.003-0.0030.0000.0000.0000.000
35U39HIS0-0.0280.03630.359-0.001-0.0010.0000.0000.0000.000
36U40PRO0-0.022-0.02229.707-0.003-0.0030.0000.0000.0000.000
37U41GLU-1-0.849-0.93330.9190.0260.0260.0000.0000.0000.000
38U42ILE0-0.0200.00730.713-0.001-0.0010.0000.0000.0000.000
39U43VAL0-0.033-0.01433.5080.0010.0010.0000.0000.0000.000
40U44ALA00.0250.02636.8500.0010.0010.0000.0000.0000.000
41U45HIS0-0.002-0.01938.764-0.001-0.0010.0000.0000.0000.000
42U46MET00.0700.03840.3520.0020.0020.0000.0000.0000.000
43U47ASP-1-0.868-0.92444.6290.0240.0240.0000.0000.0000.000
44U48LEU0-0.084-0.02843.568-0.001-0.0010.0000.0000.0000.000
45U49MET00.0190.00940.7840.0020.0020.0000.0000.0000.000
46U50ARG10.8400.92045.644-0.023-0.0230.0000.0000.0000.000
47U51GLU-1-0.932-0.96847.2050.0350.0350.0000.0000.0000.000
48U52ASP-1-0.813-0.87444.1470.0440.0440.0000.0000.0000.000
49U53LEU0-0.007-0.01744.6650.0020.0020.0000.0000.0000.000
50U54HIS00.0230.01046.2200.0000.0000.0000.0000.0000.000
51U55LEU0-0.100-0.03842.5860.0010.0010.0000.0000.0000.000
52U56GLU-1-0.912-0.92541.6350.0420.0420.0000.0000.0000.000
53U57PRO0-0.026-0.03138.689-0.001-0.0010.0000.0000.0000.000
54U58PHE00.026-0.00637.5460.0030.0030.0000.0000.0000.000
55U59TYR0-0.042-0.04831.832-0.001-0.0010.0000.0000.0000.000
56U60TRP00.0340.00130.2110.0000.0000.0000.0000.0000.000
57U61LYS10.8180.90027.809-0.119-0.1190.0000.0000.0000.000
58U62LEU0-0.021-0.00623.250-0.003-0.0030.0000.0000.0000.000
59U63PRO00.0120.00923.7860.0020.0020.0000.0000.0000.000
60U64GLU-1-0.843-0.93923.4550.1510.1510.0000.0000.0000.000
61U65GLN0-0.054-0.02219.1920.0190.0190.0000.0000.0000.000
62U66PHE0-0.027-0.03918.5900.0310.0310.0000.0000.0000.000
63U67GLU-1-0.797-0.87619.7360.1670.1670.0000.0000.0000.000
64U68GLY00.0480.03319.6520.0230.0230.0000.0000.0000.000
65U69LYS10.9080.95115.964-0.357-0.3570.0000.0000.0000.000
66U70LYS10.7810.90714.890-0.272-0.2720.0000.0000.0000.000
67U71LEU00.0550.02013.255-0.004-0.0040.0000.0000.0000.000
68U72MET00.011-0.0137.279-0.080-0.0800.0000.0000.0000.000
69U73ALA0-0.0020.00611.2120.0060.0060.0000.0000.0000.000
70U74TYR0-0.122-0.08113.446-0.066-0.0660.0000.0000.0000.000
71U75GLY0-0.0100.01312.327-0.039-0.0390.0000.0000.0000.000
72U76GLY0-0.005-0.02113.170-0.079-0.0790.0000.0000.0000.000
73U77LYS10.8630.91015.810-0.045-0.0450.0000.0000.0000.000
74U78LEU00.0450.04417.6670.0150.0150.0000.0000.0000.000
75U79LYS10.8420.90119.657-0.035-0.0350.0000.0000.0000.000
76U80TYR00.037-0.00422.2240.0100.0100.0000.0000.0000.000
77U81ALA0-0.040-0.01425.535-0.004-0.0040.0000.0000.0000.000
78U82ILE00.0180.00728.9130.0040.0040.0000.0000.0000.000
79U83TYR0-0.031-0.04932.227-0.005-0.0050.0000.0000.0000.000
80U84PHE00.0120.01035.7580.0030.0030.0000.0000.0000.000
81U85GLU-1-0.797-0.86239.0230.0160.0160.0000.0000.0000.000
82U86ALA00.0160.01442.8090.0020.0020.0000.0000.0000.000
83U87ARG10.8170.90945.247-0.023-0.0230.0000.0000.0000.000
84U88GLU-1-0.794-0.86148.1400.0200.0200.0000.0000.0000.000
85U89GLU-1-0.861-0.93742.5900.0210.0210.0000.0000.0000.000
86U90THR0-0.060-0.01843.2150.0020.0020.0000.0000.0000.000
87U91GLY00.061-0.00644.9620.0000.0000.0000.0000.0000.000
88U92PHE00.0430.02740.8360.0010.0010.0000.0000.0000.000
89U93SER0-0.037-0.00837.5270.0020.0020.0000.0000.0000.000
90U94THR0-0.0130.00537.5290.0030.0030.0000.0000.0000.000
91U95TYR0-0.061-0.01939.724-0.003-0.0030.0000.0000.0000.000
92U96ASN00.0620.02337.5690.0020.0020.0000.0000.0000.000
93U97PRO00.0600.05432.462-0.002-0.0020.0000.0000.0000.000
94U98GLN00.0120.01029.811-0.004-0.0040.0000.0000.0000.000
95U99VAL00.011-0.00425.6320.0010.0010.0000.0000.0000.000
96U100ILE0-0.027-0.01028.6260.0010.0010.0000.0000.0000.000
97U101ILE00.0060.00222.5290.0040.0040.0000.0000.0000.000
98U102ARG10.9100.97626.575-0.133-0.1330.0000.0000.0000.000
99U103GLY00.0860.04224.3530.0080.0080.0000.0000.0000.000
100U104GLY00.0600.04724.251-0.008-0.0080.0000.0000.0000.000
101U105THR00.0320.00823.697-0.006-0.0060.0000.0000.0000.000
102U106PRO00.0730.02226.239-0.006-0.0060.0000.0000.0000.000
103U107THR0-0.037-0.03228.268-0.006-0.0060.0000.0000.0000.000
104U108HIS0-0.044-0.01026.082-0.012-0.0120.0000.0000.0000.000
105U109ALA0-0.069-0.00527.4690.0070.0070.0000.0000.0000.000
106U110ARG10.8430.90728.051-0.156-0.1560.0000.0000.0000.000
107U111ILE0-0.014-0.00928.4880.0090.0090.0000.0000.0000.000
108U112ILE0-0.0100.00324.190-0.008-0.0080.0000.0000.0000.000
109U113VAL00.0140.01028.5540.0010.0010.0000.0000.0000.000
110U114ARG10.8230.90326.506-0.080-0.0800.0000.0000.0000.000
111U115HIS00.0290.00429.046-0.005-0.0050.0000.0000.0000.000
112U116MET0-0.011-0.02328.8710.0020.0020.0000.0000.0000.000
113U117ALA0-0.007-0.00632.513-0.001-0.0010.0000.0000.0000.000
114U118ALA00.003-0.00534.5990.0020.0020.0000.0000.0000.000
115U119PRO0-0.0360.00334.402-0.003-0.0030.0000.0000.0000.000
116U120LEU00.0180.00236.2920.0000.0000.0000.0000.0000.000
117U121ILE00.0220.00738.8440.0010.0010.0000.0000.0000.000
118U122GLY0-0.067-0.01840.911-0.002-0.0020.0000.0000.0000.000
119U123GLN0-0.027-0.01636.134-0.002-0.0020.0000.0000.0000.000
120U124LEU0-0.012-0.00131.1340.0020.0020.0000.0000.0000.000
121U125THR0-0.022-0.01432.750-0.002-0.0020.0000.0000.0000.000
122U126ARG10.7860.84826.748-0.004-0.0040.0000.0000.0000.000
123U127HIS00.0420.03726.9600.0040.0040.0000.0000.0000.000
124U128GLU-1-0.828-0.90721.7000.0250.0250.0000.0000.0000.000
125U129ILE0-0.018-0.01022.648-0.005-0.0050.0000.0000.0000.000
126U130GLU-1-0.892-0.93918.6620.1360.1360.0000.0000.0000.000
127U131MET0-0.0180.01916.935-0.016-0.0160.0000.0000.0000.000
128U132THR00.031-0.01317.1540.0300.0300.0000.0000.0000.000
129U133GLU-1-0.755-0.86419.8360.1850.1850.0000.0000.0000.000
130U134LYS10.8040.91319.483-0.177-0.1770.0000.0000.0000.000
131U135GLU-1-0.804-0.90024.5100.0580.0580.0000.0000.0000.000
132U136TRP0-0.070-0.01222.694-0.009-0.0090.0000.0000.0000.000
133U137LYS10.8720.91227.080-0.072-0.0720.0000.0000.0000.000
134U138TYR00.004-0.02428.7050.0070.0070.0000.0000.0000.000
135U139TYR0-0.068-0.05231.852-0.006-0.0060.0000.0000.0000.000
136U140GLY00.0260.01333.8210.0000.0000.0000.0000.0000.000
137U141ASP-1-0.882-0.92435.1800.0720.0720.0000.0000.0000.000
138U142ASP-1-0.799-0.90236.8240.0490.0490.0000.0000.0000.000
139U143PRO00.0320.00436.1400.0020.0020.0000.0000.0000.000
140U144ARG10.8270.90336.594-0.042-0.0420.0000.0000.0000.000
141U145VAL0-0.0190.01735.442-0.003-0.0030.0000.0000.0000.000
142U146HIS00.002-0.00634.9920.0040.0040.0000.0000.0000.000
143U147ARG10.8480.93832.137-0.075-0.0750.0000.0000.0000.000
144U148THR0-0.002-0.00327.965-0.002-0.0020.0000.0000.0000.000
145U149VAL0-0.026-0.00725.5080.0000.0000.0000.0000.0000.000
146U150THR00.0260.01025.8410.0090.0090.0000.0000.0000.000
147U151ARG10.9910.97618.171-0.222-0.2220.0000.0000.0000.000
148U152GLU-1-0.954-0.98221.1880.2050.2050.0000.0000.0000.000
149U153ASP-1-0.733-0.83022.5210.1610.1610.0000.0000.0000.000
150U154PHE00.002-0.00318.9370.0090.0090.0000.0000.0000.000
151U155LEU0-0.031-0.01816.0840.0210.0210.0000.0000.0000.000
152U156ASP-1-0.870-0.93819.3160.2720.2720.0000.0000.0000.000
153U157ILE0-0.079-0.03821.862-0.004-0.0040.0000.0000.0000.000
154U158LEU0-0.016-0.01816.5270.0040.0040.0000.0000.0000.000
155U159TYR0-0.032-0.01416.9470.0410.0410.0000.0000.0000.000
156U160ASP-1-0.936-0.98318.8620.2420.2420.0000.0000.0000.000
157U161ILE0-0.0210.02119.062-0.029-0.0290.0000.0000.0000.000
158U162HIS0-0.030-0.03222.391-0.018-0.0180.0000.0000.0000.000
159U163TYR00.0460.00525.766-0.007-0.0070.0000.0000.0000.000
160U164ILE0-0.023-0.00221.1010.0020.0020.0000.0000.0000.000
161U165LEU0-0.0140.00225.806-0.007-0.0070.0000.0000.0000.000
162U166ILE00.000-0.01125.5300.0020.0020.0000.0000.0000.000
163U167LYS10.8830.96629.807-0.056-0.0560.0000.0000.0000.000
164U168ALA00.0090.00633.344-0.002-0.0020.0000.0000.0000.000
165U169THR0-0.0010.00835.522-0.003-0.0030.0000.0000.0000.000
166U170TYR0-0.054-0.06533.2380.0020.0020.0000.0000.0000.000
167U171GLY00.0050.00339.906-0.001-0.0010.0000.0000.0000.000
168U172ASN0-0.017-0.01043.0960.0030.0030.0000.0000.0000.000
169U173PHE0-0.012-0.01646.490-0.002-0.0020.0000.0000.0000.000
170U174MET00.0280.05339.652-0.001-0.0010.0000.0000.0000.000
171U175ARG10.9250.95444.552-0.019-0.0190.0000.0000.0000.000
172U176GLN0-0.036-0.03541.0100.0020.0020.0000.0000.0000.000
173U177SER00.001-0.02236.705-0.001-0.0010.0000.0000.0000.000
174U178ARG10.8300.90034.707-0.022-0.0220.0000.0000.0000.000
175U179ILE00.0020.02128.2830.0010.0010.0000.0000.0000.000
176U180SER00.017-0.00328.615-0.002-0.0020.0000.0000.0000.000
177U181GLU-1-0.799-0.86424.7650.0150.0150.0000.0000.0000.000
178U182ILE00.0230.01722.7990.0030.0030.0000.0000.0000.000
179U183SER0-0.022-0.02318.337-0.002-0.0020.0000.0000.0000.000
180U184MET0-0.030-0.00916.344-0.007-0.0070.0000.0000.0000.000
181U185GLU-1-0.833-0.88712.5180.0710.0710.0000.0000.0000.000
182U186VAL0-0.024-0.01810.2880.0510.0510.0000.0000.0000.000
183U187ALA0-0.043-0.0286.161-0.043-0.0430.0000.0000.0000.000
184U188GLU-1-0.846-0.8965.1991.2371.344-0.001-0.014-0.0920.000
185U189GLN0-0.074-0.0521.8040.252-1.4788.603-4.171-2.701-0.019