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: 49GZN

Calculation Name: 3HKM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HKM

Chain ID: A

ChEMBL ID:

UniProt ID: Q84T68

Base Structure: X-ray

Registration Date: 2023-06-26

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2315592.735827
FMO2-HF: Nuclear repulsion 2235248.707593
FMO2-HF: Total energy -80344.028234
FMO2-MP2: Total energy -80573.996867


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:5:ARG)


Summations of interaction energy for fragment #1(A:5:ARG)
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.
-240.518-220.18147.215-27.991-39.555-0.294
Interaction energy analysis for fragmet #1(A:5:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.777 / q_NPA : 0.864
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].
3A7ASP-1-0.920-0.9723.197-64.350-60.9020.169-1.519-2.0970.000
4A8GLY00.0090.0063.3044.2005.0850.014-0.357-0.5420.000
5A9ARG10.8560.9592.31969.92873.5303.950-2.308-5.2440.012
6A10ASN00.0490.0162.060-12.349-12.3257.843-3.344-4.523-0.044
7A11PRO00.0510.0112.335-18.255-14.6242.212-2.192-3.651-0.021
8A12ASN00.009-0.0073.136-2.051-1.9530.2990.430-0.826-0.004
9A13GLN0-0.048-0.0173.1185.2625.8570.015-0.166-0.4440.000
10A14LEU00.0110.0102.731-13.597-12.4320.310-0.558-0.917-0.006
11A15ARG10.7850.8965.29341.83741.917-0.001-0.001-0.0780.000
12A16PRO00.008-0.0116.8772.5622.5620.0000.0000.0000.000
13A17PHE00.0120.00210.0450.4010.4010.0000.0000.0000.000
14A18SER0-0.052-0.01912.4691.6231.6230.0000.0000.0000.000
15A19CYS0-0.009-0.02116.1510.0520.0520.0000.0000.0000.000
16A20THR0-0.0050.02819.0850.6440.6440.0000.0000.0000.000
17A21ARG10.8930.93722.61812.57212.5720.0000.0000.0000.000
18A22ASN0-0.008-0.01525.0110.0840.0840.0000.0000.0000.000
19A23PRO0-0.0140.00624.3790.2490.2490.0000.0000.0000.000
20A24LEU0-0.052-0.02527.1590.3260.3260.0000.0000.0000.000
21A25ASP-1-0.816-0.90629.806-9.393-9.3930.0000.0000.0000.000
22A26ARG10.8640.93033.2388.4768.4760.0000.0000.0000.000
23A27ALA0-0.045-0.02429.6530.1220.1220.0000.0000.0000.000
24A28HIS00.0200.02131.675-0.053-0.0530.0000.0000.0000.000
25A29GLY00.059-0.01228.2760.0040.0040.0000.0000.0000.000
26A30SER00.016-0.00325.424-0.156-0.1560.0000.0000.0000.000
27A31ALA00.0210.00320.6330.0530.0530.0000.0000.0000.000
28A32ARG10.9581.00519.50514.16814.1680.0000.0000.0000.000
29A33TRP0-0.020-0.04112.5530.9730.9730.0000.0000.0000.000
30A34ALA00.011-0.00414.055-0.065-0.0650.0000.0000.0000.000
31A35GLN00.0820.0528.4512.5172.5170.0000.0000.0000.000
32A36GLY00.0120.0159.234-1.597-1.5970.0000.0000.0000.000
33A37ASP-1-0.860-0.93210.134-21.363-21.3630.0000.0000.0000.000
34A38THR0-0.113-0.0739.8562.2132.2130.0000.0000.0000.000
35A39ILE00.0140.00012.1060.1100.1100.0000.0000.0000.000
36A40VAL00.0160.00415.2750.8110.8110.0000.0000.0000.000
37A41LEU0-0.050-0.02617.7180.1030.1030.0000.0000.0000.000
38A42ALA00.0170.01220.7580.2470.2470.0000.0000.0000.000
39A43ALA0-0.018-0.01122.5700.2360.2360.0000.0000.0000.000
40A44VAL00.0290.00925.9290.0170.0170.0000.0000.0000.000
41A45TYR0-0.061-0.03828.4120.2170.2170.0000.0000.0000.000
42A46GLY00.0810.03732.0850.2280.2280.0000.0000.0000.000
43A47PRO0-0.0120.00533.677-0.067-0.0670.0000.0000.0000.000
44A48LYS10.9560.99135.5558.2588.2580.0000.0000.0000.000
45A49PRO00.0090.00938.129-0.024-0.0240.0000.0000.0000.000
46A50GLY0-0.020-0.00341.3690.0480.0480.0000.0000.0000.000
47A51THR00.0280.00238.533-0.255-0.2550.0000.0000.0000.000
48A52ARG10.9490.98335.8988.8318.8310.0000.0000.0000.000
49A53LYS10.9660.96639.8596.7656.7650.0000.0000.0000.000
50A54GLY0-0.0180.00140.1890.1380.1380.0000.0000.0000.000
51A55GLU-1-0.891-0.93235.808-8.874-8.8740.0000.0000.0000.000
52A56ASN00.068-0.01438.7090.0430.0430.0000.0000.0000.000
53A57PRO0-0.0340.00240.6000.0890.0890.0000.0000.0000.000
54A58GLU-1-0.953-0.96741.455-6.984-6.9840.0000.0000.0000.000
55A59LYS10.8560.93635.9998.1248.1240.0000.0000.0000.000
56A60ALA0-0.043-0.01534.4560.0530.0530.0000.0000.0000.000
57A61SER00.0060.00433.929-0.148-0.1480.0000.0000.0000.000
58A62ILE00.005-0.00527.336-0.055-0.0550.0000.0000.0000.000
59A63GLU-1-0.932-0.98329.875-9.163-9.1630.0000.0000.0000.000
60A64VAL0-0.018-0.02523.715-0.216-0.2160.0000.0000.0000.000
61A65VAL00.0090.02226.7860.1650.1650.0000.0000.0000.000
62A66TRP0-0.015-0.01217.188-0.295-0.2950.0000.0000.0000.000
63A67LYS10.9140.95123.37211.35211.3520.0000.0000.0000.000
64A68PRO00.0470.03121.786-0.578-0.5780.0000.0000.0000.000
65A69MET0-0.044-0.01317.1590.2760.2760.0000.0000.0000.000
66A70THR0-0.002-0.01022.3030.5510.5510.0000.0000.0000.000
67A71GLY00.0130.02324.897-0.186-0.1860.0000.0000.0000.000
68A72GLN00.002-0.01927.4010.0910.0910.0000.0000.0000.000
69A73ILE0-0.033-0.00123.646-0.173-0.1730.0000.0000.0000.000
70A74GLY00.0680.04523.7920.5180.5180.0000.0000.0000.000
71A75LYS10.9120.92222.25213.28913.2890.0000.0000.0000.000
72A76GLN00.0630.03715.897-0.675-0.6750.0000.0000.0000.000
73A77GLU-1-0.812-0.92219.495-14.285-14.2850.0000.0000.0000.000
74A78LYS10.9550.96920.73511.62911.6290.0000.0000.0000.000
75A79GLU-1-0.915-0.95019.142-14.745-14.7450.0000.0000.0000.000
76A80TYR0-0.017-0.01114.416-0.243-0.2430.0000.0000.0000.000
77A81GLU-1-0.860-0.93819.556-11.733-11.7330.0000.0000.0000.000
78A82MET0-0.0100.01822.6750.2920.2920.0000.0000.0000.000
79A83THR00.011-0.03118.0440.2180.2180.0000.0000.0000.000
80A84LEU00.0180.01318.8380.0420.0420.0000.0000.0000.000
81A85LYN00.0510.03520.9600.0990.0990.0000.0000.0000.000
82A86ARG10.9400.98020.75313.92013.9200.0000.0000.0000.000
83A87THR0-0.044-0.03518.9300.0290.0290.0000.0000.0000.000
84A88LEU0-0.005-0.00821.6290.1600.1600.0000.0000.0000.000
85A89GLN0-0.028-0.02024.0320.1940.1940.0000.0000.0000.000
86A90SER0-0.047-0.00324.0300.3860.3860.0000.0000.0000.000
87A91ILE00.0220.01021.9710.2090.2090.0000.0000.0000.000
88A92CYS0-0.0180.02425.3040.2420.2420.0000.0000.0000.000
89A93LEU0-0.033-0.02128.2430.1890.1890.0000.0000.0000.000
90A94LEU00.0310.00431.5280.2190.2190.0000.0000.0000.000
91A95THR0-0.002-0.02733.8780.2510.2510.0000.0000.0000.000
92A96VAL0-0.0190.01334.9890.2010.2010.0000.0000.0000.000
93A97HIS00.0010.00335.5010.3180.3180.0000.0000.0000.000
94A98PRO00.0510.01637.941-0.139-0.1390.0000.0000.0000.000
95A99ASN00.0180.01940.027-0.022-0.0220.0000.0000.0000.000
96A100THR00.0080.01835.9710.0580.0580.0000.0000.0000.000
97A101THR0-0.018-0.02634.265-0.164-0.1640.0000.0000.0000.000
98A102THR0-0.014-0.00329.7740.0880.0880.0000.0000.0000.000
99A103SER0-0.035-0.02030.539-0.095-0.0950.0000.0000.0000.000
100A104VAL00.027-0.00123.957-0.033-0.0330.0000.0000.0000.000
101A105ILE0-0.042-0.01925.8580.0800.0800.0000.0000.0000.000
102A106LEU00.0050.01418.551-0.259-0.2590.0000.0000.0000.000
103A107GLN0-0.049-0.02622.2710.7510.7510.0000.0000.0000.000
104A108VAL00.0170.00617.077-0.529-0.5290.0000.0000.0000.000
105A109VAL0-0.067-0.02818.2950.8800.8800.0000.0000.0000.000
106A110GLY00.0470.01916.1680.5030.5030.0000.0000.0000.000
107A111ASN0-0.043-0.03312.471-1.772-1.7720.0000.0000.0000.000
108A112ASP-1-0.796-0.9199.140-31.067-31.0670.0000.0000.0000.000
109A113GLY00.0890.0777.805-4.077-4.0770.0000.0000.0000.000
110A114SER00.001-0.0016.0361.2171.2170.0000.0000.0000.000
111A115LEU0-0.016-0.0078.7051.6411.6410.0000.0000.0000.000
112A116LEU0-0.0230.00112.3631.2671.2670.0000.0000.0000.000
113A117PRO00.0600.0149.5451.2001.2000.0000.0000.0000.000
114A118CYS00.0110.03511.0651.0061.0060.0000.0000.0000.000
115A119ALA0-0.016-0.02112.5081.3611.3610.0000.0000.0000.000
116A120ILE00.002-0.00214.9411.2351.2350.0000.0000.0000.000
117A121ASN00.0330.03311.8402.4752.4750.0000.0000.0000.000
118A122ALA00.009-0.00315.8630.9670.9670.0000.0000.0000.000
119A123CYS0-0.044-0.02117.8531.1631.1630.0000.0000.0000.000
120A124CYS0-0.0070.01618.9620.8400.8400.0000.0000.0000.000
121A125ALA00.0200.01719.5190.6310.6310.0000.0000.0000.000
122A126ALA0-0.039-0.01821.3490.6520.6520.0000.0000.0000.000
123A127LEU00.006-0.00323.4940.6020.6020.0000.0000.0000.000
124A128VAL00.0160.01423.6160.4830.4830.0000.0000.0000.000
125A129PHE0-0.0500.00425.6430.3130.3130.0000.0000.0000.000
126A130ALA0-0.0120.00427.4120.3530.3530.0000.0000.0000.000
127A131GLY0-0.0270.00529.4860.3870.3870.0000.0000.0000.000
128A132ILE0-0.061-0.02828.5380.3510.3510.0000.0000.0000.000
129A133PRO00.006-0.00329.167-0.296-0.2960.0000.0000.0000.000
130A134LEU00.0140.00924.119-0.065-0.0650.0000.0000.0000.000
131A135LYS10.8710.93827.13810.51010.5100.0000.0000.0000.000
132A136HIS0-0.038-0.01822.7640.3680.3680.0000.0000.0000.000
133A137LEU00.018-0.00119.560-0.002-0.0020.0000.0000.0000.000
134A138ALA00.008-0.00818.5750.0450.0450.0000.0000.0000.000
135A139VAL0-0.0050.00113.214-0.141-0.1410.0000.0000.0000.000
136A140ALA0-0.018-0.01612.950-0.052-0.0520.0000.0000.0000.000
137A141ILE0-0.022-0.0247.017-1.188-1.1880.0000.0000.0000.000
138A142GLY00.0250.0237.4252.2482.2480.0000.0000.0000.000
139A143CYS0-0.057-0.0205.587-6.846-6.8460.0000.0000.0000.000
140A144GLY00.0550.0095.9073.7353.7350.0000.0000.0000.000
141A145VAL0-0.029-0.0237.171-1.953-1.9530.0000.0000.0000.000
142A146LEU0-0.017-0.0164.294-0.796-0.653-0.001-0.010-0.1320.000
143A147GLU-1-0.948-0.9738.573-24.499-24.4990.0000.0000.0000.000
144A148ASP-1-0.950-0.96811.294-16.054-16.0540.0000.0000.0000.000
145A149GLY00.0280.01611.9440.6120.6120.0000.0000.0000.000
146A150GLU-1-0.954-0.9827.480-25.785-25.7850.0000.0000.0000.000
147A151VAL00.0400.0217.054-2.841-2.8410.0000.0000.0000.000
148A152ILE0-0.045-0.0272.350-6.312-5.6084.777-1.240-4.2400.001
149A153LEU0-0.043-0.0142.7745.3586.5320.238-0.415-0.9960.002
150A154ASP-1-0.842-0.9442.060-78.762-77.0457.287-4.390-4.614-0.066
151A155THR0-0.0050.0072.375-13.173-11.2781.651-1.638-1.907-0.016
152A156ASN0-0.014-0.0073.4318.4748.5520.0090.175-0.2610.000
153A157LYS10.9650.9805.45922.95022.9500.0000.0000.0000.000
154A158ALA0-0.044-0.0287.1372.0732.0730.0000.0000.0000.000
155A159GLU-1-0.718-0.8521.836-128.037-126.93918.443-10.458-9.083-0.152
156A160GLU-1-0.827-0.9096.035-29.858-29.8580.0000.0000.0000.000
157A161GLN0-0.057-0.0178.3573.1503.1500.0000.0000.0000.000
158A162GLN0-0.074-0.0286.791-1.468-1.4680.0000.0000.0000.000
159A163LEU0-0.0030.0186.1861.6261.6260.0000.0000.0000.000
160A164LYS10.9750.98110.12319.34919.3490.0000.0000.0000.000
161A165SER0-0.054-0.03811.6501.7661.7660.0000.0000.0000.000
162A166PHE00.0280.0029.115-2.522-2.5220.0000.0000.0000.000
163A167ALA00.0090.01110.1842.8652.8650.0000.0000.0000.000
164A168HIS0-0.0290.00010.292-3.259-3.2590.0000.0000.0000.000
165A169LEU00.0190.01311.5092.2792.2790.0000.0000.0000.000
166A170VAL00.0250.00912.915-0.973-0.9730.0000.0000.0000.000
167A171PHE00.0210.01011.8641.2741.2740.0000.0000.0000.000
168A172PRO00.0170.02117.0700.0100.0100.0000.0000.0000.000
169A173ASN00.0500.03218.0780.8210.8210.0000.0000.0000.000
170A194LEU00.0190.00716.839-0.121-0.1210.0000.0000.0000.000
171A195ILE0-0.096-0.04219.3610.7640.7640.0000.0000.0000.000
172A196THR0-0.040-0.02618.7450.3360.3360.0000.0000.0000.000
173A197SER00.0140.00216.149-0.921-0.9210.0000.0000.0000.000
174A198ILE0-0.023-0.00415.7491.0421.0420.0000.0000.0000.000
175A199THR00.0260.01514.692-1.189-1.1890.0000.0000.0000.000
176A200HIS0-0.015-0.00613.9231.6031.6030.0000.0000.0000.000
177A201GLY00.0350.02514.338-1.110-1.1100.0000.0000.0000.000
178A202VAL0-0.032-0.02316.2010.5560.5560.0000.0000.0000.000
179A203MET00.0130.03512.804-1.542-1.5420.0000.0000.0000.000
180A204SER00.0320.04917.5310.7340.7340.0000.0000.0000.000
181A205GLU-1-0.915-0.97418.411-13.789-13.7890.0000.0000.0000.000
182A206GLU-1-0.897-0.96418.478-15.078-15.0780.0000.0000.0000.000
183A207ASP-1-0.866-0.93414.682-20.878-20.8780.0000.0000.0000.000
184A208TYR0-0.048-0.05414.201-1.250-1.2500.0000.0000.0000.000
185A209PHE00.039-0.00615.250-0.658-0.6580.0000.0000.0000.000
186A210SER00.0770.06012.319-1.142-1.1420.0000.0000.0000.000
187A211CYS0-0.036-0.01710.565-2.259-2.2590.0000.0000.0000.000
188A212ILE0-0.044-0.01611.231-1.192-1.1920.0000.0000.0000.000
189A213GLU-1-0.964-0.97713.087-21.319-21.3190.0000.0000.0000.000
190A214ARG10.8930.9426.49633.77433.7740.0000.0000.0000.000
191A215GLY00.012-0.0169.138-1.026-1.0260.0000.0000.0000.000
192A216LEU00.0130.01510.1230.2700.2700.0000.0000.0000.000
193A217ALA00.0070.01912.2210.5340.5340.0000.0000.0000.000
194A218ALA0-0.0070.0068.101-0.171-0.1710.0000.0000.0000.000
195A219SER0-0.042-0.05410.1150.7570.7570.0000.0000.0000.000
196A220SER00.0310.01412.1940.2750.2750.0000.0000.0000.000
197A221ARG10.9901.0009.68225.46625.4660.0000.0000.0000.000
198A222ILE00.0030.00710.0430.7840.7840.0000.0000.0000.000
199A223SER00.015-0.01313.6320.9670.9670.0000.0000.0000.000
200A224ASP-1-0.906-0.94116.565-15.586-15.5860.0000.0000.0000.000
201A225PHE0-0.052-0.02415.6910.7680.7680.0000.0000.0000.000
202A226MET0-0.070-0.04916.3111.0491.0490.0000.0000.0000.000
203A227ARG10.8740.93119.76014.19914.1990.0000.0000.0000.000
204A228THR00.0160.02621.2030.8730.8730.0000.0000.0000.000
205A229THR00.002-0.00119.5360.4610.4610.0000.0000.0000.000
206A230LEU0-0.087-0.02419.0130.4150.4150.0000.0000.0000.000
207A231GLN0-0.035-0.01022.6770.6120.6120.0000.0000.0000.000