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: QY9VY

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 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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2809115.486331
FMO2-HF: Nuclear repulsion 2719240.549723
FMO2-HF: Total energy -89874.936609
FMO2-MP2: Total energy -90131.20866


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.
-29.35-27.73343.429-20.569-24.472-0.118
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 : -0.032 / q_NPA : -0.036
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].
3A497ASN0-0.045-0.0433.089-0.8811.3360.161-1.092-1.2860.000
4A498GLY00.0330.0282.671-0.6220.2050.385-0.465-0.7480.001
5A499ILE0-0.053-0.0373.444-0.310-0.4060.0180.231-0.1530.000
6A500PRO00.0290.0165.7710.2500.2500.0000.0000.0000.000
7A501THR0-0.007-0.0076.850-0.132-0.1320.0000.0000.0000.000
8A502ARG10.9610.9749.305-0.361-0.3610.0000.0000.0000.000
9A503THR00.0100.00412.482-0.034-0.0340.0000.0000.0000.000
10A504ASN00.0390.02811.7900.0330.0330.0000.0000.0000.000
11A505ILE0-0.023-0.0118.9370.0090.0090.0000.0000.0000.000
12A506GLY00.0590.02711.914-0.026-0.0260.0000.0000.0000.000
13A507TRP00.0490.03310.066-0.007-0.0070.0000.0000.0000.000
14A508MET0-0.047-0.0256.775-0.043-0.0430.0000.0000.0000.000
15A509VAL0-0.0100.00011.0740.0140.0140.0000.0000.0000.000
16A510SER0-0.032-0.01010.545-0.055-0.0550.0000.0000.0000.000
17A511LEU0-0.010-0.00611.4920.0500.0500.0000.0000.0000.000
18A512ARG10.8650.91012.6870.0090.0090.0000.0000.0000.000
19A513TYR00.0580.02315.6030.0190.0190.0000.0000.0000.000
20A514ARG10.9240.95717.3260.1230.1230.0000.0000.0000.000
21A515ASN0-0.009-0.00918.8490.0020.0020.0000.0000.0000.000
22A516LYS10.9430.98114.2370.1910.1910.0000.0000.0000.000
23A517HIS00.0330.0407.2210.2210.2210.0000.0000.0000.000
24A518ILE0-0.048-0.03211.332-0.040-0.0400.0000.0000.0000.000
25A519CYS0-0.082-0.0189.090-0.188-0.1880.0000.0000.0000.000
26A520GLY00.0470.0427.9560.0880.0880.0000.0000.0000.000
27A521GLY00.0310.0088.8710.0120.0120.0000.0000.0000.000
28A522SER0-0.0130.00011.4790.0560.0560.0000.0000.0000.000
29A523LEU0-0.0170.00813.291-0.014-0.0140.0000.0000.0000.000
30A524ILE0-0.013-0.01416.4900.0160.0160.0000.0000.0000.000
31A525LYS10.9130.95118.6470.0110.0110.0000.0000.0000.000
32A526GLU-1-0.827-0.89721.3470.0020.0020.0000.0000.0000.000
33A527SER00.0140.00622.9850.0000.0000.0000.0000.0000.000
34A528TRP0-0.040-0.02621.370-0.012-0.0120.0000.0000.0000.000
35A529VAL00.0450.02615.1440.0090.0090.0000.0000.0000.000
36A530LEU0-0.029-0.00715.085-0.007-0.0070.0000.0000.0000.000
37A531THR00.008-0.00712.468-0.024-0.0240.0000.0000.0000.000
38A532ALA00.0500.02612.5530.0290.0290.0000.0000.0000.000
39A533ARG10.8470.89814.3400.1920.1920.0000.0000.0000.000
40A534GLN0-0.045-0.04413.8040.0080.0080.0000.0000.0000.000
41A536PHE00.008-0.01214.7940.0190.0190.0000.0000.0000.000
42A537PRO0-0.0120.00616.9670.0150.0150.0000.0000.0000.000
43A538SER0-0.0210.01219.7600.0220.0220.0000.0000.0000.000
44A539ARG10.9950.98922.5850.0920.0920.0000.0000.0000.000
45A540ASP-1-0.860-0.93725.305-0.078-0.0780.0000.0000.0000.000
46A541LEU00.006-0.02023.410-0.007-0.0070.0000.0000.0000.000
47A542LYS10.9060.96224.2530.0690.0690.0000.0000.0000.000
48A543ASP-1-0.930-0.94721.731-0.114-0.1140.0000.0000.0000.000
49A544TYR0-0.079-0.05317.790-0.026-0.0260.0000.0000.0000.000
50A545GLU-1-0.881-0.93518.667-0.040-0.0400.0000.0000.0000.000
51A546ALA0-0.033-0.01316.396-0.025-0.0250.0000.0000.0000.000
52A547TRP0-0.029-0.02814.5400.0230.0230.0000.0000.0000.000
53A548LEU00.008-0.01114.389-0.009-0.0090.0000.0000.0000.000
54A549GLY00.0680.04015.4060.0030.0030.0000.0000.0000.000
55A550ILE0-0.020-0.00111.910-0.007-0.0070.0000.0000.0000.000
56A551HIS0-0.020-0.01110.500-0.027-0.0270.0000.0000.0000.000
57A552ASP-1-0.655-0.79810.3780.3910.3910.0000.0000.0000.000
58A553VAL0-0.0200.0069.154-0.085-0.0850.0000.0000.0000.000
59A554HIS0-0.050-0.04111.143-0.117-0.1170.0000.0000.0000.000
60A555GLY0-0.035-0.01814.357-0.030-0.0300.0000.0000.0000.000
61A556ARG10.7490.83513.750-0.240-0.2400.0000.0000.0000.000
62A557GLY00.0030.00816.8650.0340.0340.0000.0000.0000.000
63A558ASP-1-0.858-0.94615.3860.1980.1980.0000.0000.0000.000
64A559GLU-1-0.890-0.94618.7260.0700.0700.0000.0000.0000.000
65A560LYS10.8640.92322.282-0.083-0.0830.0000.0000.0000.000
66A561CYS0-0.013-0.00218.164-0.001-0.0010.0000.0000.0000.000
67A562LYS10.9861.01318.025-0.040-0.0400.0000.0000.0000.000
68A563GLN0-0.045-0.02918.830-0.019-0.0190.0000.0000.0000.000
69A564VAL00.0100.00018.974-0.005-0.0050.0000.0000.0000.000
70A565LEU0-0.034-0.00620.2940.0010.0010.0000.0000.0000.000
71A566ASN00.0710.03321.194-0.015-0.0150.0000.0000.0000.000
72A567VAL00.0210.01220.1880.0040.0040.0000.0000.0000.000
73A568SER0-0.037-0.02023.2840.0020.0020.0000.0000.0000.000
74A569GLN0-0.034-0.03224.7730.0080.0080.0000.0000.0000.000
75A570LEU00.0330.03120.620-0.004-0.0040.0000.0000.0000.000
76A571VAL0-0.032-0.01423.0910.0050.0050.0000.0000.0000.000
77A572TYR00.008-0.00621.626-0.010-0.0100.0000.0000.0000.000
78A573GLY00.007-0.01421.3140.0130.0130.0000.0000.0000.000
79A574PRO0-0.042-0.03022.473-0.003-0.0030.0000.0000.0000.000
80A575GLU-1-0.895-0.94623.349-0.105-0.1050.0000.0000.0000.000
81A576GLY00.0130.00522.4310.0060.0060.0000.0000.0000.000
82A577SER0-0.023-0.00919.988-0.006-0.0060.0000.0000.0000.000
83A578ASP-1-0.825-0.90216.151-0.229-0.2290.0000.0000.0000.000
84A579LEU00.0070.02715.770-0.026-0.0260.0000.0000.0000.000
85A580VAL0-0.022-0.01017.2160.0100.0100.0000.0000.0000.000
86A581LEU0-0.0370.00017.928-0.002-0.0020.0000.0000.0000.000
87A582MET00.0310.01016.426-0.004-0.0040.0000.0000.0000.000
88A583LYS10.9570.98320.5250.0480.0480.0000.0000.0000.000
89A584LEU00.0210.00419.258-0.006-0.0060.0000.0000.0000.000
90A585ALA0-0.090-0.05523.3030.0060.0060.0000.0000.0000.000
91A586ARG10.9710.97525.4860.0060.0060.0000.0000.0000.000
92A587PRO0-0.0420.00424.997-0.002-0.0020.0000.0000.0000.000
93A588ALA00.020-0.01021.4160.0020.0020.0000.0000.0000.000
94A589VAL0-0.045-0.01723.3520.0000.0000.0000.0000.0000.000
95A590LEU0-0.024-0.00921.6810.0040.0040.0000.0000.0000.000
96A591ASP-1-0.906-0.93521.2170.0620.0620.0000.0000.0000.000
97A592ASP-1-0.918-0.96721.4650.0890.0890.0000.0000.0000.000
98A593PHE0-0.047-0.03917.9110.0160.0160.0000.0000.0000.000
99A594VAL0-0.0080.00316.7720.0060.0060.0000.0000.0000.000
100A595SER0-0.0030.00017.3490.0030.0030.0000.0000.0000.000
101A596THR00.0170.00716.961-0.003-0.0030.0000.0000.0000.000
102A597ILE0-0.044-0.02612.9930.0140.0140.0000.0000.0000.000
103A598ASP-1-0.889-0.93116.7920.0350.0350.0000.0000.0000.000
104A599LEU0-0.017-0.02517.621-0.002-0.0020.0000.0000.0000.000
105A600PRO00.0090.00518.3140.0060.0060.0000.0000.0000.000
106A601ASN00.0130.00521.006-0.009-0.0090.0000.0000.0000.000
107A602TYR0-0.013-0.04023.9580.0010.0010.0000.0000.0000.000
108A603GLY0-0.015-0.00724.4700.0030.0030.0000.0000.0000.000
109A604SER0-0.064-0.01622.7190.0040.0040.0000.0000.0000.000
110A605THR00.0530.02622.565-0.006-0.0060.0000.0000.0000.000
111A606ILE0-0.021-0.01117.4770.0030.0030.0000.0000.0000.000
112A607PRO00.0170.00320.588-0.004-0.0040.0000.0000.0000.000
113A608GLU-1-0.866-0.92318.6820.0560.0560.0000.0000.0000.000
114A609LYS10.9770.98217.264-0.067-0.0670.0000.0000.0000.000
115A610THR0-0.021-0.02915.7630.0120.0120.0000.0000.0000.000
116A611SER00.0350.01013.3170.0010.0010.0000.0000.0000.000
117A612CYS0-0.034-0.02310.774-0.002-0.0020.0000.0000.0000.000
118A613SER00.006-0.0047.1590.0510.0510.0000.0000.0000.000
119A614VAL0-0.0270.0092.968-0.816-0.1830.195-0.163-0.6650.001
120A615TYR00.016-0.0133.379-0.3560.2480.034-0.211-0.426-0.001
121A616GLY00.0160.0042.857-1.025-0.2920.393-0.345-0.7820.000
122A617TRP0-0.051-0.0433.0260.5571.1680.201-0.126-0.684-0.005
123A618GLY0-0.0050.0012.9730.4931.0520.072-0.202-0.4300.000
124A619TYR00.013-0.0123.0310.8043.1520.554-1.281-1.621-0.007
125A620THR00.0290.0161.671-5.092-15.78922.370-8.046-3.627-0.025
126A621GLY0-0.017-0.0123.825-0.0910.1090.004-0.080-0.1230.000
127A622LEU0-0.067-0.0267.0040.1320.1320.0000.0000.0000.000
128A623ILE0-0.008-0.0019.001-0.049-0.0490.0000.0000.0000.000
129A624ASN0-0.006-0.01412.208-0.046-0.0460.0000.0000.0000.000
130A625TYR0-0.075-0.0536.2560.2190.2190.0000.0000.0000.000
131A626ASP-1-0.830-0.9219.3940.7890.7890.0000.0000.0000.000
132A627GLY00.0300.0119.012-0.144-0.1440.0000.0000.0000.000
133A628LEU0-0.0010.0259.215-0.108-0.1080.0000.0000.0000.000
134A629LEU0-0.0180.0335.6390.5250.5250.0000.0000.0000.000
135A630ARG10.9230.9672.367-2.975-2.2191.083-0.486-1.353-0.001
136A631VAL00.014-0.0073.233-2.023-0.7010.110-0.498-0.933-0.004
137A632ALA00.0020.0112.452-0.394-0.0591.601-0.531-1.4040.000
138A633HIS0-0.0060.0043.722-0.357-0.2710.0080.035-0.1270.000
139A634LEU0-0.073-0.0336.212-0.040-0.0400.0000.0000.0000.000
140A635TYR00.002-0.0019.203-0.013-0.0130.0000.0000.0000.000
141A636ILE00.0010.00612.825-0.015-0.0150.0000.0000.0000.000
142A637MET0-0.018-0.01114.8500.0000.0000.0000.0000.0000.000
143A638GLY00.0340.03016.895-0.011-0.0110.0000.0000.0000.000
144A639ASN00.0710.00919.0690.0010.0010.0000.0000.0000.000
145A640GLU-1-0.895-0.94220.331-0.017-0.0170.0000.0000.0000.000
146A641LYS10.9820.97620.277-0.026-0.0260.0000.0000.0000.000
147A642CYS0-0.0500.01113.723-0.026-0.0260.0000.0000.0000.000
148A643SER00.015-0.03218.081-0.011-0.0110.0000.0000.0000.000
149A644GLN0-0.042-0.02920.465-0.002-0.0020.0000.0000.0000.000
150A645HIS0-0.0310.00216.6280.0010.0010.0000.0000.0000.000
151A646HIS0-0.074-0.04314.028-0.019-0.0190.0000.0000.0000.000
152A647ARG10.8550.93018.9190.0730.0730.0000.0000.0000.000
153A648GLY00.0430.03322.528-0.002-0.0020.0000.0000.0000.000
154A649LYS10.9200.96918.8100.1470.1470.0000.0000.0000.000
155A650VAL0-0.021-0.01818.470-0.010-0.0100.0000.0000.0000.000
156A651THR00.0100.02521.6410.0060.0060.0000.0000.0000.000
157A652LEU00.0010.00817.526-0.005-0.0050.0000.0000.0000.000
158A653ASN00.0450.04021.7400.0150.0150.0000.0000.0000.000
159A654GLU-1-0.910-0.96621.713-0.035-0.0350.0000.0000.0000.000
160A655SER0-0.005-0.00220.3460.0090.0090.0000.0000.0000.000
161A656GLU-1-0.917-0.95917.220-0.132-0.1320.0000.0000.0000.000
162A657ILE0-0.033-0.02814.0920.0190.0190.0000.0000.0000.000
163A659ALA00.0360.02510.2620.0210.0210.0000.0000.0000.000
164A660GLY00.0400.0109.265-0.029-0.0290.0000.0000.0000.000
165A661ALA00.0140.0298.5110.0170.0170.0000.0000.0000.000
166A662GLU-1-0.929-0.96010.3340.0730.0730.0000.0000.0000.000
167A663LYS10.9550.96513.681-0.115-0.1150.0000.0000.0000.000
168A664ILE0-0.0040.0108.452-0.036-0.0360.0000.0000.0000.000
169A665GLY00.0160.0119.4870.0070.0070.0000.0000.0000.000
170A666SER0-0.048-0.0324.470-0.0220.032-0.001-0.009-0.0440.000
171A667GLY00.0240.0123.427-0.557-0.1080.026-0.104-0.3710.001
172A668PRO00.0040.0122.408-1.477-0.1214.467-2.545-3.279-0.023
173A669CYS0-0.078-0.0203.3980.4480.8710.0250.194-0.6430.000
174A670GLU-1-0.822-0.9534.781-1.348-1.221-0.001-0.004-0.1220.000
175A671GLY00.0060.0154.922-0.969-0.928-0.001-0.003-0.0360.000
176A672ASP-1-0.732-0.8661.917-14.988-16.37911.727-4.826-5.510-0.055
177A673TYR0-0.045-0.0214.9840.5630.611-0.001-0.008-0.0390.000
178A674GLY00.0370.0008.3620.0440.0440.0000.0000.0000.000
179A675GLY00.0000.0087.4070.1150.1150.0000.0000.0000.000
180A676PRO0-0.023-0.0077.1060.0170.0170.0000.0000.0000.000
181A677LEU0-0.008-0.0027.2550.0720.0720.0000.0000.0000.000
182A678VAL0-0.054-0.0409.201-0.045-0.0450.0000.0000.0000.000
183A680GLU-1-0.883-0.94814.1140.1700.1700.0000.0000.0000.000
184A681GLN0-0.0080.01517.1210.0070.0070.0000.0000.0000.000
185A682HIS00.013-0.00720.0900.0040.0040.0000.0000.0000.000
186A683LYS10.9650.96620.573-0.075-0.0750.0000.0000.0000.000
187A684MET0-0.0080.00720.0720.0040.0040.0000.0000.0000.000
188A685ARG10.9601.00513.272-0.202-0.2020.0000.0000.0000.000
189A686MET0-0.0040.00915.928-0.020-0.0200.0000.0000.0000.000
190A687VAL00.0070.00812.0850.0200.0200.0000.0000.0000.000
191A688LEU00.016-0.02013.571-0.021-0.0210.0000.0000.0000.000
192A689GLY0-0.015-0.00912.519-0.014-0.0140.0000.0000.0000.000
193A690VAL0-0.0100.00610.8540.0170.0170.0000.0000.0000.000
194A691ILE0-0.025-0.0024.601-0.0590.013-0.001-0.004-0.0660.000
195A692VAL00.0430.0248.670-0.060-0.0600.0000.0000.0000.000
196A693PRO00.0140.01110.162-0.030-0.0300.0000.0000.0000.000
197A694GLY00.0530.03410.2030.1000.1000.0000.0000.0000.000
198A695ARG10.8890.93311.4560.1900.1900.0000.0000.0000.000
199A696GLY00.0310.01011.2320.0480.0480.0000.0000.0000.000
200A698ALA00.0110.0285.9620.0630.0630.0000.0000.0000.000
201A699ILE00.0010.0097.7910.0320.0320.0000.0000.0000.000
202A700PRO00.0440.00411.3800.0440.0440.0000.0000.0000.000
203A701ASN0-0.022-0.01312.979-0.011-0.0110.0000.0000.0000.000
204A702ARG10.9250.97312.7570.1120.1120.0000.0000.0000.000
205A703PRO00.0260.01911.248-0.001-0.0010.0000.0000.0000.000
206A704GLY0-0.011-0.0109.504-0.052-0.0520.0000.0000.0000.000
207A705ILE00.012-0.01310.4760.0370.0370.0000.0000.0000.000
208A706PHE0-0.043-0.0197.279-0.045-0.0450.0000.0000.0000.000
209A707VAL00.0620.03812.5030.0250.0250.0000.0000.0000.000
210A708ARG10.8590.91114.7880.0330.0330.0000.0000.0000.000
211A709VAL00.0590.03015.189-0.004-0.0040.0000.0000.0000.000
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