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: 14G3Z

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 OptAll
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 -2177524.735548
FMO2-HF: Nuclear repulsion 2101470.481195
FMO2-HF: Total energy -76054.254353
FMO2-MP2: Total energy -76276.474487


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.
0.5122.3822.927-1.9-2.896-0.002
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 : 0.031 / q_NPA : -0.004
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].
3U7ILE00.0240.0222.817-1.3090.0890.180-0.612-0.9650.000
4U8ARG10.8440.9115.2600.8160.903-0.001-0.005-0.0810.000
5U9THR0-0.022-0.0088.668-0.132-0.1320.0000.0000.0000.000
6U10TRP0-0.026-0.02211.1020.0440.0440.0000.0000.0000.000
7U11VAL00.0040.01314.865-0.006-0.0060.0000.0000.0000.000
8U12THR00.008-0.01316.946-0.021-0.0210.0000.0000.0000.000
9U13LEU00.0380.03020.4520.0150.0150.0000.0000.0000.000
10U14LYS10.9150.97922.854-0.074-0.0740.0000.0000.0000.000
11U15ALA0-0.007-0.02724.034-0.004-0.0040.0000.0000.0000.000
12U16GLU-1-0.864-0.93626.5860.0690.0690.0000.0000.0000.000
13U17GLN00.0520.05324.955-0.001-0.0010.0000.0000.0000.000
14U18THR0-0.061-0.04629.1530.0000.0000.0000.0000.0000.000
15U19ILE0-0.014-0.01131.860-0.004-0.0040.0000.0000.0000.000
16U20LEU00.0210.00428.2310.0060.0060.0000.0000.0000.000
17U21PRO0-0.0140.00131.760-0.005-0.0050.0000.0000.0000.000
18U22LEU00.0170.01233.7690.0040.0040.0000.0000.0000.000
19U23VAL0-0.021-0.02034.1720.0000.0000.0000.0000.0000.000
20U24ASP-1-0.727-0.84837.0500.0590.0590.0000.0000.0000.000
21U25GLU-1-0.802-0.90136.1090.0660.0660.0000.0000.0000.000
22U26ALA0-0.050-0.01435.9780.0050.0050.0000.0000.0000.000
23U27LEU0-0.049-0.02132.0310.0040.0040.0000.0000.0000.000
24U28GLN0-0.083-0.02936.7460.0000.0000.0000.0000.0000.000
25U29HIS10.8560.90339.709-0.057-0.0570.0000.0000.0000.000
26U30THR00.0190.01935.8960.0030.0030.0000.0000.0000.000
27U31THR0-0.072-0.06738.552-0.003-0.0030.0000.0000.0000.000
28U32THR00.035-0.01437.2090.0020.0020.0000.0000.0000.000
29U33LYS10.7810.87239.867-0.042-0.0420.0000.0000.0000.000
30U34GLY00.0540.02742.486-0.002-0.0020.0000.0000.0000.000
31U35ILE0-0.054-0.01936.165-0.001-0.0010.0000.0000.0000.000
32U36VAL0-0.011-0.00638.6090.0000.0000.0000.0000.0000.000
33U37PHE00.0230.00731.1540.0000.0000.0000.0000.0000.000
34U38GLN00.001-0.01335.680-0.003-0.0030.0000.0000.0000.000
35U39HIS00.0130.04030.7530.0000.0000.0000.0000.0000.000
36U40PRO0-0.035-0.02630.082-0.003-0.0030.0000.0000.0000.000
37U41GLU-1-0.869-0.93530.9080.0230.0230.0000.0000.0000.000
38U42ILE0-0.0340.00431.5450.0000.0000.0000.0000.0000.000
39U43VAL0-0.033-0.01534.1060.0000.0000.0000.0000.0000.000
40U44ALA00.0330.01737.4850.0020.0020.0000.0000.0000.000
41U45HIS00.000-0.01139.442-0.001-0.0010.0000.0000.0000.000
42U46MET00.0440.02541.2910.0010.0010.0000.0000.0000.000
43U47ASP-1-0.821-0.90145.4180.0210.0210.0000.0000.0000.000
44U48LEU0-0.077-0.01744.443-0.001-0.0010.0000.0000.0000.000
45U49MET00.0200.00341.1180.0020.0020.0000.0000.0000.000
46U50ARG10.8430.91846.118-0.021-0.0210.0000.0000.0000.000
47U51GLU-1-0.873-0.91247.8360.0340.0340.0000.0000.0000.000
48U52ASP-1-0.785-0.86044.6610.0420.0420.0000.0000.0000.000
49U53LEU0-0.002-0.00345.6060.0020.0020.0000.0000.0000.000
50U54HIS0-0.006-0.00446.5390.0000.0000.0000.0000.0000.000
51U55LEU0-0.065-0.03743.0350.0010.0010.0000.0000.0000.000
52U56GLU-1-0.912-0.89642.2050.0390.0390.0000.0000.0000.000
53U57PRO0-0.017-0.02639.494-0.001-0.0010.0000.0000.0000.000
54U58PHE00.012-0.01038.3840.0030.0030.0000.0000.0000.000
55U59TYR0-0.036-0.04532.717-0.002-0.0020.0000.0000.0000.000
56U60TRP00.0440.00731.0550.0010.0010.0000.0000.0000.000
57U61LYS10.8350.90228.169-0.119-0.1190.0000.0000.0000.000
58U62LEU0-0.019-0.00824.015-0.004-0.0040.0000.0000.0000.000
59U63PRO0-0.0160.00224.3840.0020.0020.0000.0000.0000.000
60U64GLU-1-0.863-0.94724.0670.1520.1520.0000.0000.0000.000
61U65GLN0-0.021-0.02019.5890.0210.0210.0000.0000.0000.000
62U66PHE0-0.036-0.03419.1310.0360.0360.0000.0000.0000.000
63U67GLU-1-0.802-0.88320.5770.1610.1610.0000.0000.0000.000
64U68GLY00.0570.03820.3520.0260.0260.0000.0000.0000.000
65U69LYS10.8720.92816.606-0.360-0.3600.0000.0000.0000.000
66U70LYS10.8210.91115.546-0.289-0.2890.0000.0000.0000.000
67U71LEU00.0190.01813.5700.0120.0120.0000.0000.0000.000
68U72MET00.006-0.0077.276-0.106-0.1060.0000.0000.0000.000
69U73ALA00.0080.00511.4190.0070.0070.0000.0000.0000.000
70U74TYR0-0.093-0.06813.240-0.073-0.0730.0000.0000.0000.000
71U75GLY0-0.0200.00312.028-0.037-0.0370.0000.0000.0000.000
72U76GLY0-0.008-0.01512.725-0.091-0.0910.0000.0000.0000.000
73U77LYS10.8490.90516.359-0.018-0.0180.0000.0000.0000.000
74U78LEU00.0650.04518.4070.0100.0100.0000.0000.0000.000
75U79LYS10.8080.88319.995-0.022-0.0220.0000.0000.0000.000
76U80TYR00.018-0.00822.7580.0110.0110.0000.0000.0000.000
77U81ALA0-0.013-0.00426.018-0.006-0.0060.0000.0000.0000.000
78U82ILE00.0170.00229.4910.0060.0060.0000.0000.0000.000
79U83TYR0-0.027-0.03332.966-0.005-0.0050.0000.0000.0000.000
80U84PHE00.001-0.00636.5870.0040.0040.0000.0000.0000.000
81U85GLU-1-0.778-0.85539.7960.0130.0130.0000.0000.0000.000
82U86ALA0-0.0030.00143.6200.0020.0020.0000.0000.0000.000
83U87ARG10.8080.88646.034-0.020-0.0200.0000.0000.0000.000
84U88GLU-1-0.774-0.84248.4410.0170.0170.0000.0000.0000.000
85U89GLU-1-0.820-0.91643.0470.0160.0160.0000.0000.0000.000
86U90THR0-0.064-0.03443.7130.0010.0010.0000.0000.0000.000
87U91GLY00.0440.00945.024-0.001-0.0010.0000.0000.0000.000
88U92PHE00.0430.02441.0250.0010.0010.0000.0000.0000.000
89U93SER0-0.031-0.00637.3730.0020.0020.0000.0000.0000.000
90U94THR0-0.0410.00837.6710.0030.0030.0000.0000.0000.000
91U95TYR0-0.081-0.05940.052-0.002-0.0020.0000.0000.0000.000
92U96ASN00.015-0.00538.073-0.001-0.0010.0000.0000.0000.000
93U97PRO00.0500.04932.548-0.003-0.0030.0000.0000.0000.000
94U98GLN00.0200.00930.361-0.005-0.0050.0000.0000.0000.000
95U99VAL0-0.009-0.01126.3620.0010.0010.0000.0000.0000.000
96U100ILE0-0.0080.00429.5830.0010.0010.0000.0000.0000.000
97U101ILE00.0000.00223.0130.0050.0050.0000.0000.0000.000
98U102ARG10.8840.95426.960-0.133-0.1330.0000.0000.0000.000
99U103GLY00.0620.02324.3600.0110.0110.0000.0000.0000.000
100U104GLY0-0.0030.01924.016-0.014-0.0140.0000.0000.0000.000
101U105THR0-0.012-0.02523.663-0.014-0.0140.0000.0000.0000.000
102U106PRO00.008-0.01626.158-0.009-0.0090.0000.0000.0000.000
103U107THR0-0.031-0.00828.110-0.008-0.0080.0000.0000.0000.000
104U108HIS0-0.016-0.02125.827-0.016-0.0160.0000.0000.0000.000
105U109ALA0-0.063-0.00227.9980.0020.0020.0000.0000.0000.000
106U110ARG10.8220.91228.063-0.146-0.1460.0000.0000.0000.000
107U111ILE00.0220.00628.3900.0090.0090.0000.0000.0000.000
108U112ILE0-0.030-0.00624.278-0.007-0.0070.0000.0000.0000.000
109U113VAL00.002-0.00528.9840.0000.0000.0000.0000.0000.000
110U114ARG10.8160.89527.021-0.064-0.0640.0000.0000.0000.000
111U115HIS00.0460.01729.289-0.004-0.0040.0000.0000.0000.000
112U116MET0-0.021-0.02529.0770.0020.0020.0000.0000.0000.000
113U117ALA0-0.004-0.00332.838-0.001-0.0010.0000.0000.0000.000
114U118ALA00.0070.00134.6770.0020.0020.0000.0000.0000.000
115U119PRO0-0.0390.00235.262-0.003-0.0030.0000.0000.0000.000
116U120LEU00.000-0.00236.9570.0000.0000.0000.0000.0000.000
117U121ILE0-0.017-0.01839.7670.0010.0010.0000.0000.0000.000
118U122GLY0-0.043-0.01441.774-0.002-0.0020.0000.0000.0000.000
119U123GLN0-0.038-0.01236.814-0.002-0.0020.0000.0000.0000.000
120U124LEU0-0.020-0.00231.7270.0020.0020.0000.0000.0000.000
121U125THR0-0.048-0.02533.287-0.003-0.0030.0000.0000.0000.000
122U126ARG10.8120.85127.2480.0010.0010.0000.0000.0000.000
123U127HIS00.0300.03527.4260.0030.0030.0000.0000.0000.000
124U128GLU-1-0.816-0.90222.0350.0030.0030.0000.0000.0000.000
125U129ILE00.0080.01823.107-0.004-0.0040.0000.0000.0000.000
126U130GLU-1-0.875-0.91318.6090.1060.1060.0000.0000.0000.000
127U131MET0-0.0100.01617.324-0.015-0.0150.0000.0000.0000.000
128U132THR00.004-0.03016.8750.0310.0310.0000.0000.0000.000
129U133GLU-1-0.756-0.84719.5870.1510.1510.0000.0000.0000.000
130U134LYS10.8250.88319.271-0.138-0.1380.0000.0000.0000.000
131U135GLU-1-0.812-0.87624.3730.0430.0430.0000.0000.0000.000
132U136TRP0-0.045-0.01122.919-0.005-0.0050.0000.0000.0000.000
133U137LYS10.8440.90227.124-0.059-0.0590.0000.0000.0000.000
134U138TYR00.014-0.02128.5210.0060.0060.0000.0000.0000.000
135U139TYR0-0.061-0.05131.738-0.006-0.0060.0000.0000.0000.000
136U140GLY00.0260.01333.8250.0000.0000.0000.0000.0000.000
137U141ASP-1-0.853-0.91334.5490.0640.0640.0000.0000.0000.000
138U142ASP-1-0.780-0.87936.4020.0420.0420.0000.0000.0000.000
139U143PRO00.017-0.00536.0700.0000.0000.0000.0000.0000.000
140U144ARG10.8580.92236.370-0.035-0.0350.0000.0000.0000.000
141U145VAL0-0.0360.00735.334-0.002-0.0020.0000.0000.0000.000
142U146HIS00.0210.00134.9350.0040.0040.0000.0000.0000.000
143U147ARG10.8280.92231.802-0.066-0.0660.0000.0000.0000.000
144U148THR00.002-0.00427.626-0.002-0.0020.0000.0000.0000.000
145U149VAL0-0.029-0.00525.0800.0000.0000.0000.0000.0000.000
146U150THR00.002-0.01125.6760.0060.0060.0000.0000.0000.000
147U151ARG10.9020.91818.034-0.181-0.1810.0000.0000.0000.000
148U152GLU-1-0.807-0.89121.0060.2040.2040.0000.0000.0000.000
149U153ASP-1-0.771-0.83722.5220.1490.1490.0000.0000.0000.000
150U154PHE00.0160.00819.0840.0090.0090.0000.0000.0000.000
151U155LEU0-0.006-0.00115.9180.0270.0270.0000.0000.0000.000
152U156ASP-1-0.818-0.91519.1300.2520.2520.0000.0000.0000.000
153U157ILE0-0.038-0.02421.7130.0060.0060.0000.0000.0000.000
154U158LEU00.005-0.00216.2560.0040.0040.0000.0000.0000.000
155U159TYR0-0.033-0.01816.9140.0500.0500.0000.0000.0000.000
156U160ASP-1-0.917-0.96418.8170.2340.2340.0000.0000.0000.000
157U161ILE00.0080.03419.644-0.028-0.0280.0000.0000.0000.000
158U162HIS0-0.020-0.02022.925-0.018-0.0180.0000.0000.0000.000
159U163TYR00.023-0.00226.339-0.010-0.0100.0000.0000.0000.000
160U164ILE0-0.0050.00521.8500.0040.0040.0000.0000.0000.000
161U165LEU0-0.0010.00826.568-0.006-0.0060.0000.0000.0000.000
162U166ILE00.0120.00526.0840.0000.0000.0000.0000.0000.000
163U167LYS10.8730.94830.288-0.049-0.0490.0000.0000.0000.000
164U168ALA0-0.0220.00533.820-0.002-0.0020.0000.0000.0000.000
165U169THR00.019-0.00936.230-0.003-0.0030.0000.0000.0000.000
166U170TYR0-0.032-0.04833.8130.0020.0020.0000.0000.0000.000
167U171GLY00.0120.01540.524-0.002-0.0020.0000.0000.0000.000
168U172ASN0-0.035-0.02743.8860.0030.0030.0000.0000.0000.000
169U173PHE0-0.013-0.02447.158-0.002-0.0020.0000.0000.0000.000
170U174MET00.0230.04640.466-0.001-0.0010.0000.0000.0000.000
171U175ARG10.8720.93445.302-0.018-0.0180.0000.0000.0000.000
172U176GLN0-0.029-0.04041.7300.0020.0020.0000.0000.0000.000
173U177SER0-0.009-0.02437.291-0.001-0.0010.0000.0000.0000.000
174U178ARG10.7960.89035.608-0.020-0.0200.0000.0000.0000.000
175U179ILE00.0120.02128.9930.0010.0010.0000.0000.0000.000
176U180SER00.0350.00829.232-0.001-0.0010.0000.0000.0000.000
177U181GLU-1-0.793-0.86725.1350.0100.0100.0000.0000.0000.000
178U182ILE00.0050.01623.7980.0020.0020.0000.0000.0000.000
179U183SER0-0.013-0.01919.1870.0000.0000.0000.0000.0000.000
180U184MET0-0.020-0.00917.217-0.007-0.0070.0000.0000.0000.000
181U185GLU-1-0.843-0.88813.5150.0370.0370.0000.0000.0000.000
182U186VAL0-0.0020.00010.9600.0460.0460.0000.0000.0000.000
183U187ALA0-0.033-0.0196.472-0.137-0.1370.0000.0000.0000.000
184U188GLU-1-0.814-0.8745.8221.5701.5700.0000.0000.0000.000
185U189GLN0-0.121-0.0872.142-0.2640.1212.748-1.283-1.850-0.002