Manual

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: YYKM2

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2176663.603683
FMO2-HF: Nuclear repulsion 2100612.270749
FMO2-HF: Total energy -76051.332935
FMO2-MP2: Total energy -76273.715652


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.
1.1940.60810.188-5.345-4.256-0.02
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 : 0.017 / q_NPA : -0.014
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].
3U7ILE0-0.0010.0072.237-1.143-0.0791.451-1.158-1.356-0.002
4U8ARG10.9670.9814.7550.7860.874-0.001-0.006-0.0810.000
5U9THR0-0.0080.0098.306-0.082-0.0820.0000.0000.0000.000
6U10TRP00.011-0.00810.6100.0150.0150.0000.0000.0000.000
7U11VAL00.0020.02314.265-0.009-0.0090.0000.0000.0000.000
8U12THR00.0360.00216.465-0.019-0.0190.0000.0000.0000.000
9U13LEU00.0150.01019.9510.0150.0150.0000.0000.0000.000
10U14LYS10.9100.98122.654-0.075-0.0750.0000.0000.0000.000
11U15ALA00.025-0.02423.871-0.005-0.0050.0000.0000.0000.000
12U16GLU-1-0.941-0.98426.1540.0750.0750.0000.0000.0000.000
13U17GLN00.0820.05224.829-0.003-0.0030.0000.0000.0000.000
14U18THR0-0.025-0.00228.416-0.001-0.0010.0000.0000.0000.000
15U19ILE0-0.021-0.01331.083-0.004-0.0040.0000.0000.0000.000
16U20LEU00.011-0.01027.4930.0070.0070.0000.0000.0000.000
17U21PRO0-0.0280.00230.995-0.005-0.0050.0000.0000.0000.000
18U22LEU00.0270.01133.3750.0020.0020.0000.0000.0000.000
19U23VAL0-0.032-0.03133.2310.0010.0010.0000.0000.0000.000
20U24ASP-1-0.676-0.83136.3300.0670.0670.0000.0000.0000.000
21U25GLU-1-0.846-0.91135.3990.0750.0750.0000.0000.0000.000
22U26ALA0-0.073-0.03235.4450.0050.0050.0000.0000.0000.000
23U27LEU0-0.029-0.00431.5790.0050.0050.0000.0000.0000.000
24U28GLN0-0.046-0.01136.2160.0040.0040.0000.0000.0000.000
25U29HIS10.8140.89939.364-0.061-0.0610.0000.0000.0000.000
26U30THR00.0140.01835.5610.0020.0020.0000.0000.0000.000
27U31THR0-0.041-0.03738.017-0.003-0.0030.0000.0000.0000.000
28U32THR0-0.026-0.04136.9340.0020.0020.0000.0000.0000.000
29U33LYS10.9830.99839.121-0.053-0.0530.0000.0000.0000.000
30U34GLY00.0700.03941.200-0.003-0.0030.0000.0000.0000.000
31U35ILE0-0.085-0.02335.483-0.001-0.0010.0000.0000.0000.000
32U36VAL0-0.007-0.00338.0060.0000.0000.0000.0000.0000.000
33U37PHE0-0.002-0.00130.8120.0000.0000.0000.0000.0000.000
34U38GLN0-0.042-0.03535.086-0.003-0.0030.0000.0000.0000.000
35U39HIS0-0.0400.03230.3280.0000.0000.0000.0000.0000.000
36U40PRO0-0.014-0.02529.706-0.003-0.0030.0000.0000.0000.000
37U41GLU-1-0.851-0.92530.9220.0270.0270.0000.0000.0000.000
38U42ILE00.0040.01130.7490.0000.0000.0000.0000.0000.000
39U43VAL0-0.033-0.01733.5110.0010.0010.0000.0000.0000.000
40U44ALA00.0290.02636.8520.0010.0010.0000.0000.0000.000
41U45HIS0-0.010-0.02138.766-0.001-0.0010.0000.0000.0000.000
42U46MET00.0670.03940.5190.0020.0020.0000.0000.0000.000
43U47ASP-1-0.891-0.95544.6310.0260.0260.0000.0000.0000.000
44U48LEU0-0.083-0.03143.460-0.001-0.0010.0000.0000.0000.000
45U49MET00.0230.01141.5280.0030.0030.0000.0000.0000.000
46U50ARG10.8510.94245.646-0.025-0.0250.0000.0000.0000.000
47U51GLU-1-0.945-0.97247.3900.0360.0360.0000.0000.0000.000
48U52ASP-1-0.861-0.93144.2180.0450.0450.0000.0000.0000.000
49U53LEU0-0.035-0.03144.8520.0020.0020.0000.0000.0000.000
50U54HIS00.0230.01446.222-0.001-0.0010.0000.0000.0000.000
51U55LEU0-0.102-0.04142.6200.0010.0010.0000.0000.0000.000
52U56GLU-1-0.959-0.93841.6410.0430.0430.0000.0000.0000.000
53U57PRO0-0.025-0.03938.726-0.001-0.0010.0000.0000.0000.000
54U58PHE00.013-0.01537.4510.0030.0030.0000.0000.0000.000
55U59TYR0-0.030-0.02731.982-0.001-0.0010.0000.0000.0000.000
56U60TRP00.0340.00030.1760.0000.0000.0000.0000.0000.000
57U61LYS10.9170.97128.495-0.119-0.1190.0000.0000.0000.000
58U62LEU0-0.026-0.01323.281-0.003-0.0030.0000.0000.0000.000
59U63PRO00.0000.00423.8010.0030.0030.0000.0000.0000.000
60U64GLU-1-0.828-0.92823.4920.1630.1630.0000.0000.0000.000
61U65GLN0-0.070-0.02519.2780.0200.0200.0000.0000.0000.000
62U66PHE0-0.057-0.05018.5900.0300.0300.0000.0000.0000.000
63U67GLU-1-0.908-0.95019.7360.1850.1850.0000.0000.0000.000
64U68GLY00.0330.00519.6520.0260.0260.0000.0000.0000.000
65U69LYS10.9390.95615.871-0.375-0.3750.0000.0000.0000.000
66U70LYS10.8270.95014.888-0.321-0.3210.0000.0000.0000.000
67U71LEU00.0700.02813.160-0.007-0.0070.0000.0000.0000.000
68U72MET00.016-0.0107.276-0.053-0.0530.0000.0000.0000.000
69U73ALA0-0.0130.00211.2120.0000.0000.0000.0000.0000.000
70U74TYR0-0.144-0.08713.552-0.070-0.0700.0000.0000.0000.000
71U75GLY0-0.0070.01512.329-0.042-0.0420.0000.0000.0000.000
72U76GLY00.002-0.01813.170-0.081-0.0810.0000.0000.0000.000
73U77LYS10.9110.94615.812-0.045-0.0450.0000.0000.0000.000
74U78LEU00.0500.04717.6700.0170.0170.0000.0000.0000.000
75U79LYS10.8920.93319.603-0.026-0.0260.0000.0000.0000.000
76U80TYR00.011-0.03422.2270.0110.0110.0000.0000.0000.000
77U81ALA0-0.031-0.00825.538-0.005-0.0050.0000.0000.0000.000
78U82ILE00.0230.00628.9160.0040.0040.0000.0000.0000.000
79U83TYR0-0.091-0.11632.230-0.005-0.0050.0000.0000.0000.000
80U84PHE00.0160.00735.7610.0030.0030.0000.0000.0000.000
81U85GLU-1-0.775-0.81539.0260.0160.0160.0000.0000.0000.000
82U86ALA00.0130.01442.8120.0020.0020.0000.0000.0000.000
83U87ARG10.8820.97445.249-0.023-0.0230.0000.0000.0000.000
84U88GLU-1-0.853-0.90348.1030.0200.0200.0000.0000.0000.000
85U89GLU-1-0.839-0.92942.1460.0210.0210.0000.0000.0000.000
86U90THR0-0.0530.00043.2170.0020.0020.0000.0000.0000.000
87U91GLY00.055-0.01544.9500.0000.0000.0000.0000.0000.000
88U92PHE00.0390.01440.7340.0020.0020.0000.0000.0000.000
89U93SER0-0.033-0.00337.4920.0020.0020.0000.0000.0000.000
90U94THR0-0.0050.00937.4510.0030.0030.0000.0000.0000.000
91U95TYR0-0.057-0.02139.720-0.003-0.0030.0000.0000.0000.000
92U96ASN00.0590.01237.4370.0050.0050.0000.0000.0000.000
93U97PRO00.0220.03432.536-0.002-0.0020.0000.0000.0000.000
94U98GLN00.0000.00929.624-0.005-0.0050.0000.0000.0000.000
95U99VAL00.021-0.00525.6630.0010.0010.0000.0000.0000.000
96U100ILE0-0.012-0.00628.6410.0010.0010.0000.0000.0000.000
97U101ILE00.005-0.00322.7590.0040.0040.0000.0000.0000.000
98U102ARG10.9100.96726.575-0.139-0.1390.0000.0000.0000.000
99U103GLY00.0940.04024.3520.0080.0080.0000.0000.0000.000
100U104GLY00.0520.04524.295-0.009-0.0090.0000.0000.0000.000
101U105THR00.0300.00923.873-0.005-0.0050.0000.0000.0000.000
102U106PRO00.0680.01426.304-0.008-0.0080.0000.0000.0000.000
103U107THR0-0.027-0.03028.853-0.004-0.0040.0000.0000.0000.000
104U108HIS0-0.062-0.02026.491-0.008-0.0080.0000.0000.0000.000
105U109ALA0-0.069-0.00727.4690.0070.0070.0000.0000.0000.000
106U110ARG10.9440.98228.245-0.153-0.1530.0000.0000.0000.000
107U111ILE00.003-0.00328.4880.0090.0090.0000.0000.0000.000
108U112ILE0-0.0100.00124.286-0.008-0.0080.0000.0000.0000.000
109U113VAL00.0140.00828.5540.0020.0020.0000.0000.0000.000
110U114ARG10.9470.99225.879-0.082-0.0820.0000.0000.0000.000
111U115HIS00.0450.01829.047-0.005-0.0050.0000.0000.0000.000
112U116MET0-0.016-0.03928.9770.0020.0020.0000.0000.0000.000
113U117ALA0-0.0010.00132.515-0.001-0.0010.0000.0000.0000.000
114U118ALA0-0.013-0.00834.6020.0020.0020.0000.0000.0000.000
115U119PRO0-0.026-0.00833.900-0.003-0.0030.0000.0000.0000.000
116U120LEU00.0340.01536.2950.0000.0000.0000.0000.0000.000
117U121ILE0-0.012-0.01238.8470.0010.0010.0000.0000.0000.000
118U122GLY0-0.049-0.00840.929-0.002-0.0020.0000.0000.0000.000
119U123GLN0-0.018-0.01536.438-0.002-0.0020.0000.0000.0000.000
120U124LEU0-0.010-0.00231.3420.0020.0020.0000.0000.0000.000
121U125THR0-0.033-0.01332.754-0.002-0.0020.0000.0000.0000.000
122U126ARG10.7960.84226.503-0.005-0.0050.0000.0000.0000.000
123U127HIS00.0370.06026.8440.0030.0030.0000.0000.0000.000
124U128GLU-1-0.891-0.96621.6280.0170.0170.0000.0000.0000.000
125U129ILE0-0.028-0.01622.675-0.006-0.0060.0000.0000.0000.000
126U130GLU-1-0.951-0.97818.7390.1180.1180.0000.0000.0000.000
127U131MET0-0.0150.02016.913-0.016-0.0160.0000.0000.0000.000
128U132THR00.037-0.01217.2320.0300.0300.0000.0000.0000.000
129U133GLU-1-0.776-0.89819.8360.1810.1810.0000.0000.0000.000
130U134LYS10.8700.95919.638-0.145-0.1450.0000.0000.0000.000
131U135GLU-1-0.884-0.95224.4940.0570.0570.0000.0000.0000.000
132U136TRP0-0.101-0.02722.777-0.007-0.0070.0000.0000.0000.000
133U137LYS10.8660.91627.080-0.071-0.0710.0000.0000.0000.000
134U138TYR0-0.031-0.06528.5910.0080.0080.0000.0000.0000.000
135U139TYR0-0.090-0.07531.852-0.006-0.0060.0000.0000.0000.000
136U140GLY00.0180.01133.8210.0000.0000.0000.0000.0000.000
137U141ASP-1-0.950-0.96635.3090.0740.0740.0000.0000.0000.000
138U142ASP-1-0.805-0.89536.8240.0480.0480.0000.0000.0000.000
139U143PRO00.0330.00036.1410.0020.0020.0000.0000.0000.000
140U144ARG10.8080.88336.594-0.041-0.0410.0000.0000.0000.000
141U145VAL0-0.0280.01335.427-0.003-0.0030.0000.0000.0000.000
142U146HIS00.001-0.01534.9400.0040.0040.0000.0000.0000.000
143U147ARG10.9440.99132.262-0.074-0.0740.0000.0000.0000.000
144U148THR00.0070.00127.408-0.001-0.0010.0000.0000.0000.000
145U149VAL0-0.018-0.00425.221-0.001-0.0010.0000.0000.0000.000
146U150THR00.0400.02725.8410.0080.0080.0000.0000.0000.000
147U151ARG10.9750.96718.095-0.212-0.2120.0000.0000.0000.000
148U152GLU-1-0.967-0.98821.1880.1980.1980.0000.0000.0000.000
149U153ASP-1-0.755-0.82922.5210.1650.1650.0000.0000.0000.000
150U154PHE0-0.0110.00018.8530.0100.0100.0000.0000.0000.000
151U155LEU0-0.040-0.02716.1230.0260.0260.0000.0000.0000.000
152U156ASP-1-0.894-0.94119.3160.2800.2800.0000.0000.0000.000
153U157ILE0-0.082-0.03721.862-0.003-0.0030.0000.0000.0000.000
154U158LEU0-0.023-0.02216.5990.0060.0060.0000.0000.0000.000
155U159TYR0-0.074-0.02517.0900.0470.0470.0000.0000.0000.000
156U160ASP-1-0.939-1.00118.9190.2540.2540.0000.0000.0000.000
157U161ILE0-0.0290.02419.319-0.030-0.0300.0000.0000.0000.000
158U162HIS00.0070.00022.390-0.017-0.0170.0000.0000.0000.000
159U163TYR00.027-0.00825.785-0.008-0.0080.0000.0000.0000.000
160U164ILE00.0020.01221.2310.0010.0010.0000.0000.0000.000
161U165LEU0-0.011-0.00325.806-0.007-0.0070.0000.0000.0000.000
162U166ILE00.001-0.00525.5940.0010.0010.0000.0000.0000.000
163U167LYS10.9150.98329.809-0.055-0.0550.0000.0000.0000.000
164U168ALA00.0040.01133.345-0.003-0.0030.0000.0000.0000.000
165U169THR00.0400.01735.524-0.003-0.0030.0000.0000.0000.000
166U170TYR0-0.058-0.06633.3340.0020.0020.0000.0000.0000.000
167U171GLY00.0060.00439.908-0.001-0.0010.0000.0000.0000.000
168U172ASN0-0.034-0.03143.0980.0030.0030.0000.0000.0000.000
169U173PHE00.002-0.01046.492-0.002-0.0020.0000.0000.0000.000
170U174MET00.0170.03639.908-0.001-0.0010.0000.0000.0000.000
171U175ARG10.9450.96544.568-0.019-0.0190.0000.0000.0000.000
172U176GLN0-0.037-0.03840.8790.0030.0030.0000.0000.0000.000
173U177SER0-0.005-0.01436.500-0.001-0.0010.0000.0000.0000.000
174U178ARG10.8900.93134.614-0.023-0.0230.0000.0000.0000.000
175U179ILE00.0040.02428.1170.0000.0000.0000.0000.0000.000
176U180SER00.009-0.00928.600-0.003-0.0030.0000.0000.0000.000
177U181GLU-1-0.803-0.85824.8450.0160.0160.0000.0000.0000.000
178U182ILE00.0190.02322.7170.0020.0020.0000.0000.0000.000
179U183SER0-0.036-0.03118.391-0.001-0.0010.0000.0000.0000.000
180U184MET0-0.022-0.00616.375-0.007-0.0070.0000.0000.0000.000
181U185GLU-1-0.930-0.95612.6730.0890.0890.0000.0000.0000.000
182U186VAL0-0.018-0.00710.0880.0530.0530.0000.0000.0000.000
183U187ALA0-0.043-0.0356.172-0.057-0.0570.0000.0000.0000.000
184U188GLU-1-0.840-0.8925.1991.4171.520-0.001-0.013-0.0890.000
185U189GLN0-0.076-0.0531.8080.194-1.6478.739-4.168-2.730-0.018