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: K91G3

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 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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2807997.438672
FMO2-HF: Nuclear repulsion 2718121.254202
FMO2-HF: Total energy -89876.184471
FMO2-MP2: Total energy -90132.389151


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.
-28.759-24.44838.81-19.139-23.986-0.115
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 : -0.042 / q_NPA : -0.034
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].
3A497ASN0-0.050-0.0443.198-0.7111.4220.094-1.039-1.1890.001
4A498GLY00.0330.0262.655-0.5630.2250.385-0.460-0.7130.001
5A499ILE0-0.068-0.0373.454-0.378-0.4640.0170.220-0.1510.000
6A500PRO00.0380.0245.6960.2260.2260.0000.0000.0000.000
7A501THR00.0140.0026.597-0.115-0.1150.0000.0000.0000.000
8A502ARG10.9510.9679.109-0.338-0.3380.0000.0000.0000.000
9A503THR00.0060.00112.304-0.029-0.0290.0000.0000.0000.000
10A504ASN00.0490.02411.5870.0270.0270.0000.0000.0000.000
11A505ILE0-0.037-0.0158.6040.0110.0110.0000.0000.0000.000
12A506GLY00.0740.03811.771-0.030-0.0300.0000.0000.0000.000
13A507TRP00.0380.02610.000-0.004-0.0040.0000.0000.0000.000
14A508MET0-0.054-0.0256.919-0.042-0.0420.0000.0000.0000.000
15A509VAL0-0.007-0.00310.9820.0220.0220.0000.0000.0000.000
16A510SER0-0.021-0.00810.499-0.063-0.0630.0000.0000.0000.000
17A511LEU0-0.014-0.00911.4180.0620.0620.0000.0000.0000.000
18A512ARG10.8520.89912.6450.0430.0430.0000.0000.0000.000
19A513TYR00.021-0.00315.5930.0170.0170.0000.0000.0000.000
20A514ARG10.8110.87817.3320.1300.1300.0000.0000.0000.000
21A515ASN0-0.005-0.00918.814-0.005-0.0050.0000.0000.0000.000
22A516LYS10.9010.96414.2760.2010.2010.0000.0000.0000.000
23A517HIS00.0240.0387.1120.2460.2460.0000.0000.0000.000
24A518ILE0-0.039-0.02911.308-0.032-0.0320.0000.0000.0000.000
25A519CYS0-0.072-0.0169.092-0.183-0.1830.0000.0000.0000.000
26A520GLY00.0470.0437.9590.0820.0820.0000.0000.0000.000
27A521GLY00.0280.0098.8670.0290.0290.0000.0000.0000.000
28A522SER0-0.0120.00011.4540.0460.0460.0000.0000.0000.000
29A523LEU0-0.0250.00313.294-0.008-0.0080.0000.0000.0000.000
30A524ILE0-0.022-0.01816.4610.0170.0170.0000.0000.0000.000
31A525LYS10.8870.93618.6540.0310.0310.0000.0000.0000.000
32A526GLU-1-0.811-0.89621.315-0.022-0.0220.0000.0000.0000.000
33A527SER00.0120.00322.926-0.001-0.0010.0000.0000.0000.000
34A528TRP0-0.032-0.02821.366-0.011-0.0110.0000.0000.0000.000
35A529VAL00.0440.02415.1300.0070.0070.0000.0000.0000.000
36A530LEU0-0.030-0.00515.147-0.005-0.0050.0000.0000.0000.000
37A531THR00.011-0.00812.401-0.028-0.0280.0000.0000.0000.000
38A532ALA00.0510.02912.5350.0350.0350.0000.0000.0000.000
39A533ARG10.8260.87114.3370.2090.2090.0000.0000.0000.000
40A534GLN0-0.050-0.05713.8220.0090.0090.0000.0000.0000.000
41A536PHE00.008-0.01014.8130.0200.0200.0000.0000.0000.000
42A537PRO00.0010.01416.9680.0180.0180.0000.0000.0000.000
43A538SER0-0.0070.01219.7870.0260.0260.0000.0000.0000.000
44A539ARG11.0041.00722.6000.1010.1010.0000.0000.0000.000
45A540ASP-1-0.830-0.90125.320-0.085-0.0850.0000.0000.0000.000
46A541LEU00.040-0.00223.569-0.008-0.0080.0000.0000.0000.000
47A542LYS10.8330.90424.2210.0840.0840.0000.0000.0000.000
48A543ASP-1-0.812-0.86821.565-0.133-0.1330.0000.0000.0000.000
49A544TYR0-0.063-0.05017.874-0.024-0.0240.0000.0000.0000.000
50A545GLU-1-0.865-0.91218.613-0.060-0.0600.0000.0000.0000.000
51A546ALA0-0.024-0.01416.335-0.029-0.0290.0000.0000.0000.000
52A547TRP0-0.032-0.04214.4610.0270.0270.0000.0000.0000.000
53A548LEU00.014-0.00914.301-0.016-0.0160.0000.0000.0000.000
54A549GLY00.0740.04515.2930.0070.0070.0000.0000.0000.000
55A550ILE0-0.029-0.00511.7970.0000.0000.0000.0000.0000.000
56A551HIS0-0.037-0.02310.179-0.045-0.0450.0000.0000.0000.000
57A552ASP-1-0.661-0.81710.2180.3350.3350.0000.0000.0000.000
58A553VAL0-0.0200.0099.048-0.081-0.0810.0000.0000.0000.000
59A554HIS0-0.026-0.02110.994-0.109-0.1090.0000.0000.0000.000
60A555GLY0-0.015-0.00614.199-0.025-0.0250.0000.0000.0000.000
61A556ARG10.7610.84313.515-0.223-0.2230.0000.0000.0000.000
62A557GLY00.0020.01016.6970.0320.0320.0000.0000.0000.000
63A558ASP-1-0.823-0.91315.0930.1620.1620.0000.0000.0000.000
64A559GLU-1-0.861-0.95518.5710.0490.0490.0000.0000.0000.000
65A560LYS10.8960.94622.130-0.068-0.0680.0000.0000.0000.000
66A561CYS0-0.031-0.00617.9160.0000.0000.0000.0000.0000.000
67A562LYS10.8680.95518.047-0.055-0.0550.0000.0000.0000.000
68A563GLN0-0.036-0.02618.716-0.016-0.0160.0000.0000.0000.000
69A564VAL00.0190.00718.875-0.009-0.0090.0000.0000.0000.000
70A565LEU0-0.042-0.00620.2150.0040.0040.0000.0000.0000.000
71A566ASN00.0640.02821.129-0.013-0.0130.0000.0000.0000.000
72A567VAL00.0300.01820.1690.0020.0020.0000.0000.0000.000
73A568SER0-0.033-0.02023.2550.0040.0040.0000.0000.0000.000
74A569GLN0-0.008-0.01624.7690.0100.0100.0000.0000.0000.000
75A570LEU00.0250.03020.581-0.005-0.0050.0000.0000.0000.000
76A571VAL0-0.031-0.01623.0250.0070.0070.0000.0000.0000.000
77A572TYR0-0.002-0.00821.246-0.009-0.0090.0000.0000.0000.000
78A573GLY00.0190.00021.3030.0130.0130.0000.0000.0000.000
79A574PRO0-0.031-0.02122.474-0.002-0.0020.0000.0000.0000.000
80A575GLU-1-0.899-0.93623.390-0.114-0.1140.0000.0000.0000.000
81A576GLY00.0270.01622.5190.0070.0070.0000.0000.0000.000
82A577SER0-0.054-0.04220.058-0.007-0.0070.0000.0000.0000.000
83A578ASP-1-0.792-0.86816.300-0.244-0.2440.0000.0000.0000.000
84A579LEU00.0120.03415.703-0.030-0.0300.0000.0000.0000.000
85A580VAL0-0.027-0.01217.1850.0130.0130.0000.0000.0000.000
86A581LEU0-0.0310.00217.871-0.006-0.0060.0000.0000.0000.000
87A582MET00.0160.00516.3510.0010.0010.0000.0000.0000.000
88A583LYS10.9340.97320.5390.0620.0620.0000.0000.0000.000
89A584LEU00.0220.00319.196-0.006-0.0060.0000.0000.0000.000
90A585ALA0-0.094-0.05823.2720.0070.0070.0000.0000.0000.000
91A586ARG10.9690.97825.4370.0210.0210.0000.0000.0000.000
92A587PRO0-0.045-0.00524.943-0.003-0.0030.0000.0000.0000.000
93A588ALA00.0330.00421.3070.0030.0030.0000.0000.0000.000
94A589VAL0-0.054-0.02023.2890.0010.0010.0000.0000.0000.000
95A590LEU0-0.021-0.00921.5040.0020.0020.0000.0000.0000.000
96A591ASP-1-0.918-0.95821.2040.0390.0390.0000.0000.0000.000
97A592ASP-1-0.914-0.95221.3120.0740.0740.0000.0000.0000.000
98A593PHE0-0.053-0.04117.6410.0130.0130.0000.0000.0000.000
99A594VAL00.0100.01716.6220.0010.0010.0000.0000.0000.000
100A595SER00.005-0.00417.0960.0060.0060.0000.0000.0000.000
101A596THR00.0190.01616.888-0.007-0.0070.0000.0000.0000.000
102A597ILE0-0.068-0.03213.0220.0140.0140.0000.0000.0000.000
103A598ASP-1-0.885-0.92916.7880.0170.0170.0000.0000.0000.000
104A599LEU0-0.013-0.02217.676-0.004-0.0040.0000.0000.0000.000
105A600PRO00.008-0.00118.3840.0080.0080.0000.0000.0000.000
106A601ASN00.0200.00921.114-0.010-0.0100.0000.0000.0000.000
107A602TYR0-0.007-0.01523.9450.0010.0010.0000.0000.0000.000
108A603GLY0-0.005-0.00324.4600.0030.0030.0000.0000.0000.000
109A604SER0-0.067-0.03922.9780.0050.0050.0000.0000.0000.000
110A605THR00.0200.00922.478-0.006-0.0060.0000.0000.0000.000
111A606ILE0-0.024-0.00817.3760.0040.0040.0000.0000.0000.000
112A607PRO00.0380.01320.542-0.004-0.0040.0000.0000.0000.000
113A608GLU-1-0.823-0.90018.8750.0650.0650.0000.0000.0000.000
114A609LYS10.9220.95117.247-0.075-0.0750.0000.0000.0000.000
115A610THR0-0.027-0.02615.8880.0130.0130.0000.0000.0000.000
116A611SER00.010-0.00113.2220.0040.0040.0000.0000.0000.000
117A612CYS0-0.020-0.01810.812-0.001-0.0010.0000.0000.0000.000
118A613SER0-0.008-0.0057.1430.0580.0580.0000.0000.0000.000
119A614VAL0-0.0180.0102.947-0.797-0.2060.221-0.161-0.6520.001
120A615TYR00.024-0.0103.312-0.3160.2990.037-0.208-0.445-0.001
121A616GLY00.0220.0062.853-1.029-0.2720.528-0.387-0.898-0.001
122A617TRP0-0.057-0.0442.8710.3730.9560.397-0.123-0.857-0.006
123A618GLY0-0.0050.0042.9440.5871.1790.075-0.215-0.4520.000
124A619TYR00.002-0.0213.0461.0953.2590.554-1.169-1.549-0.006
125A620THR00.0320.0161.682-4.483-14.96421.331-7.415-3.435-0.027
126A621GLY0-0.009-0.0053.867-0.1340.0530.003-0.074-0.1170.000
127A622LEU0-0.064-0.0227.0570.1210.1210.0000.0000.0000.000
128A623ILE0-0.003-0.0029.046-0.053-0.0530.0000.0000.0000.000
129A624ASN0-0.016-0.01712.249-0.049-0.0490.0000.0000.0000.000
130A625TYR0-0.044-0.0286.2820.1700.1700.0000.0000.0000.000
131A626ASP-1-0.775-0.8779.2370.8570.8570.0000.0000.0000.000
132A627GLY00.0360.0129.013-0.148-0.1480.0000.0000.0000.000
133A628LEU0-0.0070.0219.042-0.131-0.1310.0000.0000.0000.000
134A629LEU0-0.0270.0225.2860.4880.4880.0000.0000.0000.000
135A630ARG10.8580.9222.379-2.815-1.9920.912-0.464-1.272-0.001
136A631VAL00.0270.0023.042-2.513-0.9320.221-0.667-1.135-0.006
137A632ALA0-0.0020.0072.567-0.3500.0701.572-0.527-1.4650.000
138A633HIS00.0060.0113.761-0.418-0.3210.0070.025-0.1300.000
139A634LEU0-0.073-0.0285.765-0.032-0.0320.0000.0000.0000.000
140A635TYR00.000-0.0029.192-0.021-0.0210.0000.0000.0000.000
141A636ILE00.0020.00712.829-0.014-0.0140.0000.0000.0000.000
142A637MET0-0.025-0.01714.8460.0030.0030.0000.0000.0000.000
143A638GLY00.0350.02616.912-0.013-0.0130.0000.0000.0000.000
144A639ASN00.0550.00219.0440.0050.0050.0000.0000.0000.000
145A640GLU-1-0.886-0.93520.355-0.014-0.0140.0000.0000.0000.000
146A641LYS10.9750.97320.477-0.035-0.0350.0000.0000.0000.000
147A642CYS0-0.0500.00213.732-0.024-0.0240.0000.0000.0000.000
148A643SER00.018-0.01718.166-0.008-0.0080.0000.0000.0000.000
149A644GLN0-0.032-0.02620.543-0.001-0.0010.0000.0000.0000.000
150A645HIS0-0.045-0.01216.8300.0030.0030.0000.0000.0000.000
151A646HIS0-0.087-0.06013.979-0.020-0.0200.0000.0000.0000.000
152A647ARG10.8680.93719.0320.0550.0550.0000.0000.0000.000
153A648GLY00.0460.03422.650-0.002-0.0020.0000.0000.0000.000
154A649LYS10.9170.97219.5420.1270.1270.0000.0000.0000.000
155A650VAL0-0.017-0.01918.484-0.010-0.0100.0000.0000.0000.000
156A651THR00.0230.02821.7170.0100.0100.0000.0000.0000.000
157A652LEU0-0.038-0.01717.338-0.006-0.0060.0000.0000.0000.000
158A653ASN0-0.0080.00021.7670.0160.0160.0000.0000.0000.000
159A654GLU-1-0.849-0.91321.829-0.041-0.0410.0000.0000.0000.000
160A655SER00.0040.00220.8560.0070.0070.0000.0000.0000.000
161A656GLU-1-0.837-0.90817.432-0.130-0.1300.0000.0000.0000.000
162A657ILE0-0.023-0.01814.2710.0210.0210.0000.0000.0000.000
163A659ALA00.0320.02510.2750.0200.0200.0000.0000.0000.000
164A660GLY00.0370.0089.329-0.027-0.0270.0000.0000.0000.000
165A661ALA00.0290.0358.5290.0080.0080.0000.0000.0000.000
166A662GLU-1-0.873-0.92710.4110.0780.0780.0000.0000.0000.000
167A663LYS10.8920.92513.682-0.142-0.1420.0000.0000.0000.000
168A664ILE0-0.0030.0078.849-0.038-0.0380.0000.0000.0000.000
169A665GLY00.0070.0079.5630.0030.0030.0000.0000.0000.000
170A666SER0-0.012-0.0174.510-0.132-0.083-0.001-0.009-0.0380.000
171A667GLY00.0050.0073.576-0.557-0.1610.018-0.098-0.3150.001
172A668PRO00.0000.0112.521-1.4970.3143.344-2.260-2.895-0.020
173A669CYS0-0.107-0.0453.4080.3730.9250.0270.039-0.6180.000
174A670GLU-1-0.754-0.8744.780-1.413-1.284-0.001-0.004-0.1240.000
175A671GLY00.0110.0164.884-0.934-0.897-0.001-0.003-0.0340.000
176A672ASP-1-0.728-0.8652.037-14.729-14.2799.072-4.128-5.395-0.051
177A673TYR0-0.088-0.0764.9940.5670.613-0.001-0.007-0.0370.000
178A674GLY00.038-0.0028.3810.0440.0440.0000.0000.0000.000
179A675GLY00.0010.0097.3050.1230.1230.0000.0000.0000.000
180A676PRO0-0.018-0.0047.2220.0300.0300.0000.0000.0000.000
181A677LEU0-0.013-0.0037.3670.0510.0510.0000.0000.0000.000
182A678VAL0-0.047-0.0379.310-0.036-0.0360.0000.0000.0000.000
183A680GLU-1-0.779-0.85814.1100.1670.1670.0000.0000.0000.000
184A681GLN0-0.0140.00617.0740.0070.0070.0000.0000.0000.000
185A682HIS00.0230.00420.0650.0050.0050.0000.0000.0000.000
186A683LYS10.9590.96220.514-0.069-0.0690.0000.0000.0000.000
187A684MET00.0010.01220.1120.0040.0040.0000.0000.0000.000
188A685ARG10.8320.89913.483-0.166-0.1660.0000.0000.0000.000
189A686MET00.0120.01315.994-0.019-0.0190.0000.0000.0000.000
190A687VAL00.0050.00912.1160.0190.0190.0000.0000.0000.000
191A688LEU00.011-0.02013.691-0.017-0.0170.0000.0000.0000.000
192A689GLY0-0.016-0.01012.551-0.009-0.0090.0000.0000.0000.000
193A690VAL0-0.0140.00410.8410.0080.0080.0000.0000.0000.000
194A691ILE0-0.029-0.0054.504-0.0490.028-0.001-0.005-0.0700.000
195A692VAL00.0430.0238.725-0.056-0.0560.0000.0000.0000.000
196A693PRO00.0150.01510.291-0.020-0.0200.0000.0000.0000.000
197A694GLY00.0440.03110.1990.1020.1020.0000.0000.0000.000
198A695ARG10.8910.93211.4560.1940.1940.0000.0000.0000.000
199A696GLY00.0360.01211.2420.0480.0480.0000.0000.0000.000
200A698ALA00.0090.0255.9060.0650.0650.0000.0000.0000.000
201A699ILE00.0140.0087.8120.0280.0280.0000.0000.0000.000
202A700PRO00.0460.00711.5420.0440.0440.0000.0000.0000.000
203A701ASN0-0.039-0.01513.085-0.017-0.0170.0000.0000.0000.000
204A702ARG10.9260.97812.8970.0790.0790.0000.0000.0000.000
205A703PRO00.0220.01711.3710.0030.0030.0000.0000.0000.000
206A704GLY00.0030.0059.552-0.053-0.0530.0000.0000.0000.000
207A705ILE00.007-0.01310.5340.0340.0340.0000.0000.0000.000
208A706PHE0-0.038-0.0177.246-0.052-0.0520.0000.0000.0000.000
209A707VAL00.0510.03012.6040.0300.0300.0000.0000.0000.000
210A708ARG10.8660.92014.8300.0380.0380.0000.0000.0000.000
211A709VAL00.0480.02615.167-0.002-0.0020.0000.0000.0000.000
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