Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 49MJN

Calculation Name: 4K3J-A-Xray372

Preferred Name: Hepatocyte growth factor

Target Type: SINGLE PROTEIN

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 4K3J

Chain ID: A

ChEMBL ID: CHEMBL5479

UniProt ID: P14210

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2809385.704118
FMO2-HF: Nuclear repulsion 2719508.844409
FMO2-HF: Total energy -89876.859708
FMO2-MP2: Total energy -90133.041362


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(A:495:VAL)


Summations of interaction energy for fragment #1(A:495: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.
-30.664-14.36218.462-12.608-22.151-0.092
Interaction energy analysis for fragmet #1(A:495:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.009
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].
3A497ASN0-0.060-0.0473.435-0.7211.0200.029-0.815-0.9550.001
4A498GLY00.0170.0262.442-0.9530.0241.038-0.939-1.0760.000
5A499ILE0-0.035-0.0143.2030.387-0.1410.0410.716-0.2300.000
6A500PRO00.0260.0155.3560.2390.2390.0000.0000.0000.000
7A501THR00.004-0.0206.545-0.196-0.1960.0000.0000.0000.000
8A502ARG10.9610.9698.946-0.280-0.2800.0000.0000.0000.000
9A503THR0-0.029-0.01211.929-0.034-0.0340.0000.0000.0000.000
10A504ASN00.0630.02511.3890.0300.0300.0000.0000.0000.000
11A505ILE0-0.027-0.0118.8620.0070.0070.0000.0000.0000.000
12A506GLY00.0540.03711.967-0.028-0.0280.0000.0000.0000.000
13A507TRP00.0540.0389.7220.0070.0070.0000.0000.0000.000
14A508MET0-0.060-0.0206.683-0.056-0.0560.0000.0000.0000.000
15A509VAL00.000-0.00610.9720.0380.0380.0000.0000.0000.000
16A510SER0-0.018-0.01010.424-0.063-0.0630.0000.0000.0000.000
17A511LEU0-0.010-0.00611.3340.0620.0620.0000.0000.0000.000
18A512ARG10.8390.89612.434-0.015-0.0150.0000.0000.0000.000
19A513TYR0-0.008-0.03515.4790.0010.0010.0000.0000.0000.000
20A514ARG10.8480.89517.3000.1070.1070.0000.0000.0000.000
21A515ASN00.0170.01119.002-0.006-0.0060.0000.0000.0000.000
22A516LYS10.8840.95214.3420.1510.1510.0000.0000.0000.000
23A517HIS00.0380.0367.2420.2320.2320.0000.0000.0000.000
24A518ILE0-0.054-0.02511.278-0.006-0.0060.0000.0000.0000.000
25A519CYS0-0.087-0.0159.245-0.167-0.1670.0000.0000.0000.000
26A520GLY00.0410.0358.0690.0930.0930.0000.0000.0000.000
27A521GLY00.0310.0118.9340.0340.0340.0000.0000.0000.000
28A522SER0-0.014-0.00611.1390.0270.0270.0000.0000.0000.000
29A523LEU0-0.030-0.00413.216-0.003-0.0030.0000.0000.0000.000
30A524ILE0-0.029-0.02316.4760.0120.0120.0000.0000.0000.000
31A525LYS10.8600.92918.7490.0460.0460.0000.0000.0000.000
32A526GLU-1-0.789-0.90521.415-0.036-0.0360.0000.0000.0000.000
33A527SER0-0.033-0.01823.4770.0030.0030.0000.0000.0000.000
34A528TRP0-0.004-0.00321.336-0.009-0.0090.0000.0000.0000.000
35A529VAL00.0440.02215.1150.0060.0060.0000.0000.0000.000
36A530LEU0-0.023-0.00114.995-0.006-0.0060.0000.0000.0000.000
37A531THR00.019-0.00412.340-0.028-0.0280.0000.0000.0000.000
38A532ALA00.0420.01912.6300.0300.0300.0000.0000.0000.000
39A533ARG10.8120.86614.4050.2360.2360.0000.0000.0000.000
40A534GLN0-0.026-0.04213.7890.0100.0100.0000.0000.0000.000
41A536PHE00.027-0.00414.9400.0280.0280.0000.0000.0000.000
42A537PRO00.0030.01017.0800.0160.0160.0000.0000.0000.000
43A538SER0-0.0240.00219.9510.0220.0220.0000.0000.0000.000
44A539ARG10.9920.99722.9870.1010.1010.0000.0000.0000.000
45A540ASP-1-0.808-0.87425.638-0.072-0.0720.0000.0000.0000.000
46A541LEU00.0440.00323.887-0.006-0.0060.0000.0000.0000.000
47A542LYS10.8300.88824.1440.0690.0690.0000.0000.0000.000
48A543ASP-1-0.789-0.84521.674-0.108-0.1080.0000.0000.0000.000
49A544TYR0-0.081-0.05018.112-0.019-0.0190.0000.0000.0000.000
50A545GLU-1-0.905-0.93718.419-0.029-0.0290.0000.0000.0000.000
51A546ALA0-0.005-0.00316.125-0.031-0.0310.0000.0000.0000.000
52A547TRP0-0.042-0.04114.2830.0310.0310.0000.0000.0000.000
53A548LEU00.014-0.01014.028-0.023-0.0230.0000.0000.0000.000
54A549GLY00.0590.04415.1010.0100.0100.0000.0000.0000.000
55A550ILE0-0.044-0.01511.6430.0050.0050.0000.0000.0000.000
56A551HIS0-0.009-0.01310.096-0.064-0.0640.0000.0000.0000.000
57A552ASP-1-0.715-0.8369.8690.5250.5250.0000.0000.0000.000
58A553VAL00.0120.0268.654-0.113-0.1130.0000.0000.0000.000
59A554HIS0-0.019-0.01310.542-0.137-0.1370.0000.0000.0000.000
60A555GLY00.0190.00713.646-0.030-0.0300.0000.0000.0000.000
61A556ARG10.7330.82412.969-0.406-0.4060.0000.0000.0000.000
62A557GLY00.0340.02016.9460.0340.0340.0000.0000.0000.000
63A558ASP-1-0.805-0.89814.7920.2230.2230.0000.0000.0000.000
64A559GLU-1-0.806-0.90718.2160.0940.0940.0000.0000.0000.000
65A560LYS10.9100.96121.735-0.087-0.0870.0000.0000.0000.000
66A561CYS0-0.066-0.02817.659-0.002-0.0020.0000.0000.0000.000
67A562LYS10.8390.90117.689-0.114-0.1140.0000.0000.0000.000
68A563GLN0-0.0210.00118.861-0.021-0.0210.0000.0000.0000.000
69A564VAL00.008-0.00318.484-0.007-0.0070.0000.0000.0000.000
70A565LEU0-0.030-0.00720.0470.0020.0020.0000.0000.0000.000
71A566ASN00.0390.01920.761-0.008-0.0080.0000.0000.0000.000
72A567VAL00.0340.01820.4900.0000.0000.0000.0000.0000.000
73A568SER0-0.035-0.02523.3110.0050.0050.0000.0000.0000.000
74A569GLN0-0.011-0.01525.0370.0080.0080.0000.0000.0000.000
75A570LEU00.0320.03120.404-0.005-0.0050.0000.0000.0000.000
76A571VAL0-0.034-0.00923.0720.0040.0040.0000.0000.0000.000
77A572TYR00.0250.00120.871-0.003-0.0030.0000.0000.0000.000
78A573GLY00.0140.00321.3650.0140.0140.0000.0000.0000.000
79A574PRO0-0.018-0.01522.7050.0000.0000.0000.0000.0000.000
80A575GLU-1-0.901-0.93023.381-0.135-0.1350.0000.0000.0000.000
81A576GLY00.0270.01422.3490.0060.0060.0000.0000.0000.000
82A577SER0-0.075-0.05620.366-0.008-0.0080.0000.0000.0000.000
83A578ASP-1-0.780-0.86716.548-0.275-0.2750.0000.0000.0000.000
84A579LEU00.0030.02015.872-0.031-0.0310.0000.0000.0000.000
85A580VAL0-0.029-0.01517.1390.0170.0170.0000.0000.0000.000
86A581LEU0-0.0260.00317.701-0.010-0.0100.0000.0000.0000.000
87A582MET00.0220.01316.1480.0090.0090.0000.0000.0000.000
88A583LYS10.8900.95820.1910.0670.0670.0000.0000.0000.000
89A584LEU00.0480.01619.138-0.003-0.0030.0000.0000.0000.000
90A585ALA0-0.063-0.04023.0790.0040.0040.0000.0000.0000.000
91A586ARG10.9460.97225.4140.0160.0160.0000.0000.0000.000
92A587PRO0-0.033-0.00924.966-0.004-0.0040.0000.0000.0000.000
93A588ALA00.0320.01321.4100.0050.0050.0000.0000.0000.000
94A589VAL0-0.056-0.02123.408-0.001-0.0010.0000.0000.0000.000
95A590LEU0-0.026-0.00721.390-0.001-0.0010.0000.0000.0000.000
96A591ASP-1-0.885-0.93421.0050.0410.0410.0000.0000.0000.000
97A592ASP-1-0.928-0.97521.1460.0720.0720.0000.0000.0000.000
98A593PHE0-0.049-0.03717.4860.0140.0140.0000.0000.0000.000
99A594VAL0-0.0300.00416.5110.0000.0000.0000.0000.0000.000
100A595SER0-0.009-0.02016.9170.0040.0040.0000.0000.0000.000
101A596THR00.0140.01517.161-0.008-0.0080.0000.0000.0000.000
102A597ILE0-0.023-0.01113.2050.0120.0120.0000.0000.0000.000
103A598ASP-1-0.885-0.92716.836-0.021-0.0210.0000.0000.0000.000
104A599LEU0-0.011-0.02317.753-0.012-0.0120.0000.0000.0000.000
105A600PRO0-0.012-0.00418.0290.0110.0110.0000.0000.0000.000
106A601ASN00.0310.01320.904-0.007-0.0070.0000.0000.0000.000
107A602TYR0-0.0060.00124.098-0.001-0.0010.0000.0000.0000.000
108A603GLY00.0050.01325.1390.0060.0060.0000.0000.0000.000
109A604SER0-0.068-0.04322.9060.0020.0020.0000.0000.0000.000
110A605THR00.0220.00722.051-0.011-0.0110.0000.0000.0000.000
111A606ILE0-0.0070.00117.5380.0060.0060.0000.0000.0000.000
112A607PRO00.0390.01720.759-0.005-0.0050.0000.0000.0000.000
113A608GLU-1-0.768-0.85018.830-0.010-0.0100.0000.0000.0000.000
114A609LYS10.8930.94617.454-0.013-0.0130.0000.0000.0000.000
115A610THR0-0.010-0.01416.1530.0130.0130.0000.0000.0000.000
116A611SER0-0.002-0.00912.944-0.007-0.0070.0000.0000.0000.000
117A612CYS0-0.069-0.03410.699-0.004-0.0040.0000.0000.0000.000
118A613SER0-0.002-0.0167.0410.0500.0500.0000.0000.0000.000
119A614VAL0-0.0230.0053.039-0.622-0.1240.176-0.125-0.5480.001
120A615TYR00.023-0.0153.304-0.3130.2070.028-0.152-0.3950.000
121A616GLY00.0160.0042.810-1.060-0.2440.369-0.374-0.811-0.002
122A617TRP0-0.027-0.0123.1850.2020.7920.199-0.163-0.626-0.003
123A618GLY00.0050.0132.8860.6351.1550.050-0.194-0.3760.000
124A619TYR0-0.005-0.0163.3441.6902.8560.157-0.484-0.839-0.002
125A620THR00.0470.0122.086-7.797-7.3395.498-2.878-3.079-0.017
126A621GLY0-0.013-0.0103.592-0.512-0.3870.014-0.014-0.1250.000
127A622LEU0-0.068-0.0236.891-0.012-0.0120.0000.0000.0000.000
128A623ILE00.004-0.0048.961-0.025-0.0250.0000.0000.0000.000
129A624ASN0-0.010-0.00811.881-0.060-0.0600.0000.0000.0000.000
130A625TYR0-0.054-0.0365.7210.3640.3640.0000.0000.0000.000
131A626ASP-1-0.775-0.8738.9761.3151.3150.0000.0000.0000.000
132A627GLY00.0330.0179.067-0.231-0.2310.0000.0000.0000.000
133A628LEU0-0.018-0.0018.943-0.144-0.1440.0000.0000.0000.000
134A629LEU0-0.0210.0175.3510.6060.6060.0000.0000.0000.000
135A630ARG10.8240.8982.480-3.523-2.6211.320-0.600-1.6220.000
136A631VAL00.0230.0052.794-3.192-1.3970.629-0.847-1.578-0.010
137A632ALA0-0.004-0.0022.413-0.0200.1342.248-0.618-1.7840.000
138A633HIS00.0050.0213.627-0.348-0.2920.0120.076-0.1430.000
139A634LEU0-0.064-0.0256.128-0.017-0.0170.0000.0000.0000.000
140A635TYR00.005-0.0019.5060.0020.0020.0000.0000.0000.000
141A636ILE00.0340.01512.801-0.020-0.0200.0000.0000.0000.000
142A637MET0-0.057-0.03214.8450.0080.0080.0000.0000.0000.000
143A638GLY00.0420.02816.896-0.013-0.0130.0000.0000.0000.000
144A639ASN00.022-0.01619.2180.0010.0010.0000.0000.0000.000
145A640GLU-1-0.884-0.93220.375-0.060-0.0600.0000.0000.0000.000
146A641LYS10.8720.91220.7000.0210.0210.0000.0000.0000.000
147A642CYS0-0.056-0.01313.415-0.041-0.0410.0000.0000.0000.000
148A643SER00.007-0.01918.179-0.008-0.0080.0000.0000.0000.000
149A644GLN00.013-0.00420.778-0.001-0.0010.0000.0000.0000.000
150A645HIS0-0.0070.00016.8750.0060.0060.0000.0000.0000.000
151A646HIS0-0.082-0.04614.020-0.011-0.0110.0000.0000.0000.000
152A647ARG10.8720.93418.9580.0980.0980.0000.0000.0000.000
153A648GLY00.0660.04122.6350.0030.0030.0000.0000.0000.000
154A649LYS10.9100.96520.0470.1640.1640.0000.0000.0000.000
155A650VAL00.012-0.00918.197-0.015-0.0150.0000.0000.0000.000
156A651THR00.0050.02621.7220.0080.0080.0000.0000.0000.000
157A652LEU0-0.038-0.00516.874-0.001-0.0010.0000.0000.0000.000
158A653ASN0-0.009-0.01121.3000.0230.0230.0000.0000.0000.000
159A654GLU-1-0.828-0.90621.862-0.079-0.0790.0000.0000.0000.000
160A655SER00.0140.01521.3990.0040.0040.0000.0000.0000.000
161A656GLU-1-0.828-0.89817.673-0.191-0.1910.0000.0000.0000.000
162A657ILE0-0.0110.00114.2790.0250.0250.0000.0000.0000.000
163A659ALA00.0410.0259.9830.0270.0270.0000.0000.0000.000
164A660GLY00.0440.0099.601-0.045-0.0450.0000.0000.0000.000
165A661ALA00.0410.0368.6690.0340.0340.0000.0000.0000.000
166A662GLU-1-0.864-0.93810.6650.0020.0020.0000.0000.0000.000
167A663LYS10.8670.92313.217-0.047-0.0470.0000.0000.0000.000
168A664ILE00.0140.0099.035-0.029-0.0290.0000.0000.0000.000
169A665GLY00.0280.0199.592-0.004-0.0040.0000.0000.0000.000
170A666SER0-0.002-0.0034.634-0.103-0.062-0.001-0.006-0.0330.000
171A667GLY00.005-0.0013.618-0.3060.0290.009-0.080-0.2640.000
172A668PRO0-0.0060.0102.451-2.218-0.2212.345-1.959-2.382-0.015
173A669CYS0-0.100-0.0483.3950.5410.8360.0200.198-0.512-0.001
174A670GLU-1-0.792-0.8934.860-1.213-1.098-0.001-0.002-0.1120.000
175A671GLY00.0450.0315.504-0.463-0.4630.0000.0000.0000.000
176A672ASP-1-0.754-0.8832.333-14.006-10.3854.284-3.341-4.564-0.044
177A673TYR0-0.080-0.0755.2000.4740.506-0.001-0.003-0.0270.000
178A674GLY00.0400.0068.5010.0460.0460.0000.0000.0000.000
179A675GLY00.0030.0086.9460.1240.1240.0000.0000.0000.000
180A676PRO0-0.021-0.0097.4590.0220.0220.0000.0000.0000.000
181A677LEU0-0.016-0.0087.540-0.015-0.0150.0000.0000.0000.000
182A678VAL0-0.016-0.0169.3540.0070.0070.0000.0000.0000.000
183A680GLU-1-0.773-0.84813.7920.0940.0940.0000.0000.0000.000
184A681GLN0-0.0010.00916.7570.0070.0070.0000.0000.0000.000
185A682HIS00.0380.02119.9900.0060.0060.0000.0000.0000.000
186A683LYS10.9400.96020.571-0.042-0.0420.0000.0000.0000.000
187A684MET00.000-0.00320.1590.0020.0020.0000.0000.0000.000
188A685ARG10.8050.87513.716-0.094-0.0940.0000.0000.0000.000
189A686MET00.0320.01616.050-0.010-0.0100.0000.0000.0000.000
190A687VAL00.0150.01512.3280.0040.0040.0000.0000.0000.000
191A688LEU00.015-0.02214.224-0.009-0.0090.0000.0000.0000.000
192A689GLY0-0.007-0.00713.1970.0010.0010.0000.0000.0000.000
193A690VAL0-0.0270.00210.9100.0020.0020.0000.0000.0000.000
194A691ILE0-0.034-0.0034.537-0.0490.027-0.001-0.004-0.0700.000
195A692VAL00.0420.0208.802-0.009-0.0090.0000.0000.0000.000
196A693PRO00.0170.00310.161-0.065-0.0650.0000.0000.0000.000
197A694GLY00.0480.04510.4270.0940.0940.0000.0000.0000.000
198A695ARG10.8570.91511.7190.2310.2310.0000.0000.0000.000
199A696GLY00.0130.00511.4530.0570.0570.0000.0000.0000.000
200A698ALA00.0060.0185.8080.0810.0810.0000.0000.0000.000
201A699ILE00.0170.0207.8070.0860.0860.0000.0000.0000.000
202A700PRO00.027-0.00311.6670.0320.0320.0000.0000.0000.000
203A701ASN0-0.040-0.01913.0120.0000.0000.0000.0000.0000.000
204A702ARG10.8660.94313.0040.1680.1680.0000.0000.0000.000
205A703PRO00.0240.01011.276-0.021-0.0210.0000.0000.0000.000
206A704GLY00.0220.0319.394-0.043-0.0430.0000.0000.0000.000
207A705ILE00.009-0.01410.3750.0510.0510.0000.0000.0000.000
208A706PHE0-0.033-0.0157.489-0.066-0.0660.0000.0000.0000.000
209A707VAL00.0440.02812.9170.0410.0410.0000.0000.0000.000
210A708ARG10.8410.91115.1630.0850.0850.0000.0000.0000.000
211A709VAL00.0350.01915.4430.0090.0090.0000.0000.0000.000
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