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: YZLM2

Calculation Name: 2ASU-B-Xray372

Preferred Name: Hepatocyte growth factor-like protein

Target Type: SINGLE PROTEIN

Ligand Name:
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ligand 3-letter code:
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PDB ID: 2ASU

Chain ID: B

ChEMBL ID: CHEMBL6042

UniProt ID: P26927

Base Structure: X-ray

Registration Date: 2023-09-20

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2762465.323635
FMO2-HF: Nuclear repulsion 2673648.109087
FMO2-HF: Total energy -88817.214547
FMO2-MP2: Total energy -89069.312372


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(B:484:VAL)


Summations of interaction energy for fragment #1(B:484:VAL)
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.
-28.12-9.98313.057-11.076-20.113-0.085
Interaction energy analysis for fragmet #1(B:484:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.010
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].
3B486GLY00.008-0.0053.008-1.1440.9300.212-1.073-1.213-0.002
4B487GLY0-0.0130.0072.735-0.7050.1610.258-0.431-0.693-0.001
5B488HIS0-0.064-0.0333.492-0.075-0.0680.0160.141-0.1620.000
6B489PRO00.0330.0115.6740.1000.1000.0000.0000.0000.000
7B490GLY00.0080.0177.608-0.179-0.1790.0000.0000.0000.000
8B491ASN0-0.069-0.0468.925-0.011-0.0110.0000.0000.0000.000
9B492SER00.0710.0117.696-0.035-0.0350.0000.0000.0000.000
10B493PRO00.0100.0179.679-0.024-0.0240.0000.0000.0000.000
11B494TRP00.0520.0389.669-0.011-0.0110.0000.0000.0000.000
12B495THR0-0.044-0.0306.297-0.061-0.0610.0000.0000.0000.000
13B496VAL0-0.046-0.0189.7180.0440.0440.0000.0000.0000.000
14B497SER0-0.009-0.0249.907-0.055-0.0550.0000.0000.0000.000
15B498LEU0-0.007-0.00411.0150.0580.0580.0000.0000.0000.000
16B499ARG10.8130.88811.690-0.031-0.0310.0000.0000.0000.000
17B500ASN00.025-0.01115.7230.0220.0220.0000.0000.0000.000
18B501ARG10.8620.91817.8870.0920.0920.0000.0000.0000.000
19B502GLN0-0.040-0.01619.2630.0130.0130.0000.0000.0000.000
20B503GLY00.0080.01118.2850.0130.0130.0000.0000.0000.000
21B504GLN00.0320.02514.3790.0070.0070.0000.0000.0000.000
22B505HIS00.0290.0307.0690.2160.2160.0000.0000.0000.000
23B506PHE0-0.041-0.02911.055-0.015-0.0150.0000.0000.0000.000
24B507CYS0-0.0430.0169.258-0.122-0.1220.0000.0000.0000.000
25B508GLY00.0490.0407.9810.0630.0630.0000.0000.0000.000
26B509GLY00.018-0.0028.8240.0420.0420.0000.0000.0000.000
27B510SER00.0110.00510.5280.0170.0170.0000.0000.0000.000
28B511LEU0-0.042-0.02112.6900.0000.0000.0000.0000.0000.000
29B512VAL00.0170.00715.7060.0100.0100.0000.0000.0000.000
30B513LYS10.8560.90218.3860.0170.0170.0000.0000.0000.000
31B514GLU-1-0.766-0.87520.597-0.013-0.0130.0000.0000.0000.000
32B515GLN00.0170.00922.210-0.001-0.0010.0000.0000.0000.000
33B516TRP00.010-0.00221.047-0.007-0.0070.0000.0000.0000.000
34B517ILE00.0050.00814.8340.0050.0050.0000.0000.0000.000
35B518LEU00.0210.02215.261-0.007-0.0070.0000.0000.0000.000
36B519THR00.006-0.00912.391-0.022-0.0220.0000.0000.0000.000
37B520ALA00.0720.04111.7630.0270.0270.0000.0000.0000.000
38B521ARG10.8240.89313.7080.1540.1540.0000.0000.0000.000
39B522GLN00.018-0.02113.9850.0140.0140.0000.0000.0000.000
40B524PHE00.0450.00714.9010.0220.0220.0000.0000.0000.000
41B525SER00.0160.00318.6850.0020.0020.0000.0000.0000.000
42B526SER0-0.015-0.02121.5420.0090.0090.0000.0000.0000.000
43B527CYS0-0.061-0.04821.655-0.018-0.0180.0000.0000.0000.000
44B528HIS00.0600.03424.5520.0060.0060.0000.0000.0000.000
45B529MET0-0.0090.03619.069-0.002-0.0020.0000.0000.0000.000
46B530PRO00.0530.02524.4550.0040.0040.0000.0000.0000.000
47B531LEU00.007-0.00420.170-0.002-0.0020.0000.0000.0000.000
48B532THR00.0190.00923.5200.0020.0020.0000.0000.0000.000
49B533GLY00.0440.01724.383-0.003-0.0030.0000.0000.0000.000
50B534TYR00.0020.01917.8730.0050.0050.0000.0000.0000.000
51B535GLU-1-0.796-0.88118.695-0.003-0.0030.0000.0000.0000.000
52B536VAL00.0020.00414.438-0.024-0.0240.0000.0000.0000.000
53B537TRP0-0.088-0.05914.3040.0230.0230.0000.0000.0000.000
54B538LEU00.0340.00913.593-0.013-0.0130.0000.0000.0000.000
55B539GLY00.0880.03714.4910.0090.0090.0000.0000.0000.000
56B540THR0-0.025-0.01313.6680.0250.0250.0000.0000.0000.000
57B541LEU00.0430.01610.700-0.017-0.0170.0000.0000.0000.000
58B542PHE00.0020.0119.9420.1370.1370.0000.0000.0000.000
59B543GLN0-0.0040.0077.406-0.169-0.1690.0000.0000.0000.000
60B544ASN0-0.041-0.02710.811-0.139-0.1390.0000.0000.0000.000
61B545PRO00.0030.02114.1410.0120.0120.0000.0000.0000.000
62B546GLN00.010-0.00416.653-0.033-0.0330.0000.0000.0000.000
63B547HIS0-0.017-0.03919.464-0.006-0.0060.0000.0000.0000.000
64B548GLY00.0260.02221.925-0.009-0.0090.0000.0000.0000.000
65B549GLU-1-0.909-0.94317.7470.1540.1540.0000.0000.0000.000
66B550PRO00.0180.00321.204-0.006-0.0060.0000.0000.0000.000
67B551SER0-0.033-0.02417.969-0.003-0.0030.0000.0000.0000.000
68B552LEU0-0.081-0.02316.460-0.001-0.0010.0000.0000.0000.000
69B553GLN0-0.015-0.00917.931-0.018-0.0180.0000.0000.0000.000
70B554ARG10.8560.91118.038-0.013-0.0130.0000.0000.0000.000
71B555VAL0-0.010-0.00919.6960.0030.0030.0000.0000.0000.000
72B556PRO00.0370.03320.353-0.011-0.0110.0000.0000.0000.000
73B557VAL0-0.014-0.00919.3440.0010.0010.0000.0000.0000.000
74B558ALA0-0.0020.00822.1510.0020.0020.0000.0000.0000.000
75B559LYS10.9340.96324.1420.0530.0530.0000.0000.0000.000
76B560MET00.0070.02620.496-0.004-0.0040.0000.0000.0000.000
77B561VAL0-0.017-0.01222.1760.0090.0090.0000.0000.0000.000
78B563GLY00.0840.05021.2670.0100.0100.0000.0000.0000.000
79B564PRO00.004-0.00122.496-0.002-0.0020.0000.0000.0000.000
80B565SER00.0190.02223.193-0.012-0.0120.0000.0000.0000.000
81B566GLY00.0050.00022.2280.0050.0050.0000.0000.0000.000
82B567SER00.002-0.01920.355-0.009-0.0090.0000.0000.0000.000
83B568GLN0-0.051-0.02016.015-0.028-0.0280.0000.0000.0000.000
84B569LEU00.0400.04215.287-0.024-0.0240.0000.0000.0000.000
85B570VAL0-0.031-0.02116.9660.0090.0090.0000.0000.0000.000
86B571LEU0-0.0010.02017.448-0.006-0.0060.0000.0000.0000.000
87B572LEU0-0.024-0.01616.7600.0010.0010.0000.0000.0000.000
88B573LYS10.8860.95820.1450.0390.0390.0000.0000.0000.000
89B574LEU00.0050.00018.734-0.004-0.0040.0000.0000.0000.000
90B575GLU-1-0.883-0.95122.783-0.021-0.0210.0000.0000.0000.000
91B576ARG10.8540.92124.2100.0110.0110.0000.0000.0000.000
92B577SER0-0.016-0.00923.931-0.004-0.0040.0000.0000.0000.000
93B578VAL00.0100.01619.2840.0040.0040.0000.0000.0000.000
94B579THR0-0.040-0.01922.4360.0000.0000.0000.0000.0000.000
95B580LEU00.0200.01120.1130.0050.0050.0000.0000.0000.000
96B581ASN00.0340.00719.8140.0070.0070.0000.0000.0000.000
97B582GLN00.0320.00719.375-0.002-0.0020.0000.0000.0000.000
98B583ARG10.8830.95614.547-0.152-0.1520.0000.0000.0000.000
99B584VAL0-0.0200.00615.2250.0040.0040.0000.0000.0000.000
100B585ALA00.0140.00615.951-0.004-0.0040.0000.0000.0000.000
101B586LEU0-0.0010.00215.993-0.006-0.0060.0000.0000.0000.000
102B587ILE0-0.0090.00512.7440.0090.0090.0000.0000.0000.000
103B588CYS0-0.029-0.00516.476-0.007-0.0070.0000.0000.0000.000
104B589LEU00.0340.01017.921-0.004-0.0040.0000.0000.0000.000
105B590PRO0-0.0160.01318.2390.0050.0050.0000.0000.0000.000
106B591PRO00.016-0.00620.943-0.003-0.0030.0000.0000.0000.000
107B592GLU-1-0.850-0.94523.740-0.035-0.0350.0000.0000.0000.000
108B593TRP0-0.074-0.04625.0490.0010.0010.0000.0000.0000.000
109B594TYR0-0.0270.00820.0220.0020.0020.0000.0000.0000.000
110B595VAL0-0.0020.00421.486-0.006-0.0060.0000.0000.0000.000
111B596VAL00.0110.00416.3950.0040.0040.0000.0000.0000.000
112B597PRO00.0270.02319.624-0.002-0.0020.0000.0000.0000.000
113B598PRO00.0260.00818.6270.0050.0050.0000.0000.0000.000
114B599GLY0-0.0080.01117.8720.0010.0010.0000.0000.0000.000
115B600THR0-0.034-0.03215.6470.0090.0090.0000.0000.0000.000
116B601LYS10.8460.91412.957-0.060-0.0600.0000.0000.0000.000
117B602CYS0-0.039-0.01710.5090.0080.0080.0000.0000.0000.000
118B603GLU-1-0.809-0.8796.4630.1680.1680.0000.0000.0000.000
119B604ILE0-0.053-0.0112.447-0.744-0.1490.671-0.240-1.0260.002
120B605ALA00.016-0.0042.775-0.927-0.1640.223-0.351-0.636-0.001
121B606GLY00.001-0.0012.848-0.799-0.2350.809-0.278-1.095-0.002
122B607TRP0-0.063-0.0323.2771.0501.2310.0850.228-0.494-0.002
123B608GLY00.0300.0242.9800.6641.0970.030-0.157-0.3060.000
124B609GLU-1-0.938-0.9883.1560.1191.3490.212-0.581-0.861-0.004
125B610THR0-0.011-0.0192.206-5.400-4.5573.209-1.948-2.103-0.018
126B611LYS10.8820.9363.7880.7430.8940.003-0.017-0.1370.000
127B612GLY00.0200.0197.1030.0730.0730.0000.0000.0000.000
128B613THR0-0.057-0.0396.3800.0780.0780.0000.0000.0000.000
129B614GLY00.0930.0436.9440.0440.0440.0000.0000.0000.000
130B615ASN00.0170.0397.4260.0030.0030.0000.0000.0000.000
131B616DAS00.010-0.0034.6290.6220.787-0.001-0.010-0.1530.000
132B617THR0-0.001-0.0176.775-0.412-0.4120.0000.0000.0000.000
133B618VAL0-0.017-0.0047.521-0.308-0.3080.0000.0000.0000.000
134B619LEU0-0.0140.0185.0920.6660.6660.0000.0000.0000.000
135B620ASN0-0.027-0.0182.555-2.655-1.7090.801-0.545-1.2020.002
136B621VAL00.0300.0022.972-2.716-0.9080.355-0.753-1.410-0.007
137B622ALA00.0220.0052.721-0.5910.1680.905-0.418-1.246-0.002
138B623LEU00.0000.0103.858-0.186-0.0980.0020.023-0.1130.000
139B624LEU0-0.030-0.0145.9820.0010.0010.0000.0000.0000.000
140B625ASN00.024-0.0019.203-0.018-0.0180.0000.0000.0000.000
141B626VAL00.0290.01912.972-0.007-0.0070.0000.0000.0000.000
142B627ILE0-0.0190.00614.8950.0010.0010.0000.0000.0000.000
143B628SER00.0220.01417.287-0.006-0.0060.0000.0000.0000.000
144B629ASN00.028-0.01019.6650.0020.0020.0000.0000.0000.000
145B630GLN00.0190.00920.656-0.005-0.0050.0000.0000.0000.000
146B631GLU-1-0.838-0.92519.689-0.013-0.0130.0000.0000.0000.000
147B632CYS0-0.074-0.03613.409-0.029-0.0290.0000.0000.0000.000
148B633ASN00.001-0.01318.868-0.015-0.0150.0000.0000.0000.000
149B634ILE00.0390.04021.821-0.002-0.0020.0000.0000.0000.000
150B635LYS10.8710.93117.2490.0400.0400.0000.0000.0000.000
151B636HIS0-0.036-0.02814.785-0.012-0.0120.0000.0000.0000.000
152B637ARG10.9290.96920.2710.0590.0590.0000.0000.0000.000
153B638GLY00.0280.01523.792-0.002-0.0020.0000.0000.0000.000
154B639ARG10.8120.90517.9710.1150.1150.0000.0000.0000.000
155B640VAL0-0.040-0.00717.654-0.010-0.0100.0000.0000.0000.000
156B641ARG10.8980.92820.3610.1120.1120.0000.0000.0000.000
157B642GLU-1-0.839-0.93521.026-0.045-0.0450.0000.0000.0000.000
158B643SER0-0.0010.00320.9100.0050.0050.0000.0000.0000.000
159B644GLU-1-0.835-0.88517.135-0.129-0.1290.0000.0000.0000.000
160B645MET00.0230.03014.0950.0130.0130.0000.0000.0000.000
161B647THR00.0570.0379.8640.0140.0140.0000.0000.0000.000
162B648GLU-1-0.882-0.94112.2760.0180.0180.0000.0000.0000.000
163B649GLY0-0.036-0.01211.1700.0070.0070.0000.0000.0000.000
164B650LEU00.0310.0198.131-0.007-0.0070.0000.0000.0000.000
165B651LEU00.0560.01611.612-0.031-0.0310.0000.0000.0000.000
166B652ALA00.0300.03910.143-0.017-0.0170.0000.0000.0000.000
167B653PRO0-0.020-0.0299.0480.0160.0160.0000.0000.0000.000
168B654VAL00.0240.0214.435-0.118-0.060-0.001-0.007-0.0500.000
169B655GLY0-0.031-0.0273.773-0.358-0.0390.005-0.080-0.2430.000
170B656ALA00.0290.0282.348-2.254-0.2171.791-1.798-2.030-0.009
171B657CYS0-0.057-0.0233.3730.4250.4500.0220.416-0.4630.000
172B658GLU-1-0.748-0.8495.067-1.022-0.924-0.001-0.001-0.0960.000
173B659GLY00.0450.0265.522-0.582-0.5820.0000.0000.0000.000
174B660ASP-1-0.759-0.8882.397-12.777-8.8103.452-3.179-4.240-0.041
175B661TYR0-0.088-0.0795.3060.4370.473-0.001-0.002-0.0330.000
176B662GLY00.012-0.0118.3840.0320.0320.0000.0000.0000.000
177B663GLY00.0100.0136.6760.0850.0850.0000.0000.0000.000
178B664PRO00.0060.0026.8150.0190.0190.0000.0000.0000.000
179B665LEU0-0.037-0.0167.3570.0190.0190.0000.0000.0000.000
180B666ALA0-0.0010.0019.267-0.008-0.0080.0000.0000.0000.000
181B668PHE00.0270.01913.680-0.004-0.0040.0000.0000.0000.000
182B669THR00.013-0.00516.0180.0010.0010.0000.0000.0000.000
183B670HIS0-0.003-0.00719.5880.0010.0010.0000.0000.0000.000
184B671ASN0-0.0200.00421.7130.0010.0010.0000.0000.0000.000
185B672SER0-0.008-0.01219.916-0.001-0.0010.0000.0000.0000.000
186B673TRP00.0200.01711.3700.0010.0010.0000.0000.0000.000
187B674VAL00.0110.00015.661-0.007-0.0070.0000.0000.0000.000
188B675LEU0-0.025-0.00512.3400.0040.0040.0000.0000.0000.000
189B676GLU-1-0.801-0.94114.642-0.026-0.0260.0000.0000.0000.000
190B677GLY00.008-0.00413.097-0.006-0.0060.0000.0000.0000.000
191B678ILE0-0.053-0.01010.5220.0040.0040.0000.0000.0000.000
192B679ILE0-0.0280.0044.043-0.1090.0150.000-0.015-0.1080.000
193B680ILE00.0230.0138.286-0.044-0.0440.0000.0000.0000.000
194B681PRO00.0160.0219.887-0.024-0.0240.0000.0000.0000.000
195B682ASN0-0.043-0.03010.5240.1140.1140.0000.0000.0000.000
196B683ARG10.8990.95412.4900.1270.1270.0000.0000.0000.000
197B684VAL0-0.049-0.03312.3950.0060.0060.0000.0000.0000.000
198B686ALA00.0610.0365.741-0.062-0.0620.0000.0000.0000.000
199B687ARG10.9260.9677.8460.2070.2070.0000.0000.0000.000
200B688SER00.012-0.01111.6930.0330.0330.0000.0000.0000.000
201B689ARG10.9330.96113.1400.0520.0520.0000.0000.0000.000
202B690TRP0-0.032-0.02813.4270.0090.0090.0000.0000.0000.000
203B691PRO00.0030.00612.119-0.004-0.0040.0000.0000.0000.000
204B692ALA00.0310.0368.668-0.030-0.0300.0000.0000.0000.000
205B693VAL0-0.002-0.01410.6360.0300.0300.0000.0000.0000.000
206B694PHE00.0420.0197.469-0.041-0.0410.0000.0000.0000.000
207B695THR0-0.012-0.01812.6870.0240.0240.0000.0000.0000.000
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