FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 53M6Z

Calculation Name: 4HNM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HNM

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WYA6

Base Structure: X-ray

Registration Date: 2023-06-20

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 489
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -9190083.432772
FMO2-HF: Nuclear repulsion 8989777.841902
FMO2-HF: Total energy -200305.59087
FMO2-MP2: Total energy -200879.13101


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:75:GLU)


Summations of interaction energy for fragment #1(A:75:GLU)
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.
262.648265.1150.217-1.365-1.318-0.006
Interaction energy analysis for fragmet #1(A:75:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -1.025 / q_NPA : -1.026
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].
3A77LEU00.0320.0132.936-0.4881.9790.217-1.365-1.318-0.006
4A78ASP-1-0.778-0.8685.57433.01933.0190.0000.0000.0000.000
5A79GLU-1-0.794-0.9077.54822.63122.6310.0000.0000.0000.000
6A80SER0-0.148-0.0888.887-2.920-2.9200.0000.0000.0000.000
7A81SER0-0.089-0.0906.688-1.666-1.6660.0000.0000.0000.000
8A82VAL00.1570.0968.867-1.394-1.3940.0000.0000.0000.000
9A83LYS10.9741.00311.725-22.040-22.0400.0000.0000.0000.000
10A84LYS10.8110.9027.603-29.268-29.2680.0000.0000.0000.000
11A85MET0-0.0100.01312.038-0.191-0.1910.0000.0000.0000.000
12A86ILE00.0790.04514.054-0.931-0.9310.0000.0000.0000.000
13A87LEU0-0.018-0.01416.905-0.913-0.9130.0000.0000.0000.000
14A88THR0-0.065-0.03715.324-0.805-0.8050.0000.0000.0000.000
15A89PHE00.0970.05018.249-0.577-0.5770.0000.0000.0000.000
16A90GLU-1-0.827-0.91020.09611.18511.1850.0000.0000.0000.000
17A91LYS10.8110.92519.332-14.574-14.5740.0000.0000.0000.000
18A92ARG10.8230.88817.128-14.710-14.7100.0000.0000.0000.000
19A93SER00.1000.07123.606-0.457-0.4570.0000.0000.0000.000
20A94TYR0-0.055-0.04925.926-0.543-0.5430.0000.0000.0000.000
21A95LYS10.7900.88125.564-11.255-11.2550.0000.0000.0000.000
22A96ASN0-0.007-0.00627.363-0.414-0.4140.0000.0000.0000.000
23A97GLN00.0250.01529.111-0.233-0.2330.0000.0000.0000.000
24A98GLU-1-0.925-0.95430.5679.1399.1390.0000.0000.0000.000
25A99LEU0-0.0520.01332.207-0.385-0.3850.0000.0000.0000.000
26A100ARG10.8450.92234.471-8.314-8.3140.0000.0000.0000.000
27A101ILE0-0.067-0.03637.198-0.271-0.2710.0000.0000.0000.000
28A102LYS10.9791.01037.314-7.406-7.4060.0000.0000.0000.000
29A103PHE0-0.006-0.03838.174-0.250-0.2500.0000.0000.0000.000
30A104PRO0-0.048-0.02636.6120.0390.0390.0000.0000.0000.000
31A105ASP-1-0.712-0.89231.5799.2049.2040.0000.0000.0000.000
32A106ASN0-0.089-0.02532.746-0.171-0.1710.0000.0000.0000.000
33A107PRO0-0.026-0.01533.686-0.233-0.2330.0000.0000.0000.000
34A108GLU-1-0.837-0.90727.11510.63410.6340.0000.0000.0000.000
35A109LYS10.7500.84626.882-10.367-10.3670.0000.0000.0000.000
36A110PHE00.0280.02330.353-0.041-0.0410.0000.0000.0000.000
37A111MET00.0070.02329.8570.1850.1850.0000.0000.0000.000
38A112GLU-1-0.793-0.90325.27010.94910.9490.0000.0000.0000.000
39A113SER00.0000.00225.6270.2410.2410.0000.0000.0000.000
40A114GLU-1-0.818-0.88726.0989.5319.5310.0000.0000.0000.000
41A115LEU0-0.064-0.02623.8080.2520.2520.0000.0000.0000.000
42A116ASP-1-0.788-0.86521.61713.18213.1820.0000.0000.0000.000
43A117LEU0-0.045-0.03021.1230.5730.5730.0000.0000.0000.000
44A118ASN00.0310.01022.4550.1870.1870.0000.0000.0000.000
45A119ASP-1-0.892-0.95317.93014.14814.1480.0000.0000.0000.000
46A120ILE00.0150.02815.5600.7260.7260.0000.0000.0000.000
47A121ILE00.005-0.00117.2290.6300.6300.0000.0000.0000.000
48A122GLN0-0.052-0.01916.9360.5080.5080.0000.0000.0000.000
49A123GLU-1-0.952-0.99113.11718.40418.4040.0000.0000.0000.000
50A124MET0-0.079-0.06013.5510.9720.9720.0000.0000.0000.000
51A125HIS00.0790.04415.3580.6290.6290.0000.0000.0000.000
52A126VAL0-0.046-0.0199.0890.3210.3210.0000.0000.0000.000
53A127VAL0-0.032-0.01112.4051.3301.3300.0000.0000.0000.000
54A128ALA00.0730.04614.0640.2690.2690.0000.0000.0000.000
55A129THR0-0.098-0.05811.3210.6900.6900.0000.0000.0000.000
56A130MET0-0.100-0.0488.8352.1162.1160.0000.0000.0000.000
57A131PRO00.1010.05313.3990.0190.0190.0000.0000.0000.000
58A132ASP-1-0.877-0.90915.70416.07116.0710.0000.0000.0000.000
59A133LEU0-0.084-0.04311.503-0.309-0.3090.0000.0000.0000.000
60A134TYR00.0230.00115.7320.2910.2910.0000.0000.0000.000
61A135HIS0-0.040-0.03317.2630.0250.0250.0000.0000.0000.000
62A136LEU0-0.051-0.02114.202-0.334-0.3340.0000.0000.0000.000
63A137LEU00.008-0.00517.828-0.337-0.3370.0000.0000.0000.000
64A138VAL00.0110.01120.204-0.597-0.5970.0000.0000.0000.000
65A139GLU-1-0.892-0.92820.07013.76113.7610.0000.0000.0000.000
66A140LEU0-0.094-0.05118.006-0.026-0.0260.0000.0000.0000.000
67A141ASN0-0.079-0.04422.415-0.187-0.1870.0000.0000.0000.000
68A142ALA00.0610.03921.113-0.208-0.2080.0000.0000.0000.000
69A143VAL00.0800.03723.108-0.261-0.2610.0000.0000.0000.000
70A144GLN00.009-0.00225.008-0.255-0.2550.0000.0000.0000.000
71A145SER0-0.097-0.06225.471-0.516-0.5160.0000.0000.0000.000
72A146LEU0-0.004-0.00921.945-0.194-0.1940.0000.0000.0000.000
73A147LEU00.0120.01826.469-0.224-0.2240.0000.0000.0000.000
74A148GLY0-0.027-0.00930.002-0.285-0.2850.0000.0000.0000.000
75A149LEU0-0.027-0.01125.647-0.219-0.2190.0000.0000.0000.000
76A150LEU00.0110.01329.478-0.094-0.0940.0000.0000.0000.000
77A151GLY0-0.070-0.02931.562-0.237-0.2370.0000.0000.0000.000
78A152HIS0-0.083-0.05031.349-0.248-0.2480.0000.0000.0000.000
79A153ASP-1-0.979-0.99733.3747.8807.8800.0000.0000.0000.000
80A154ASN0-0.104-0.06631.957-0.329-0.3290.0000.0000.0000.000
81A155THR00.034-0.00931.9360.2370.2370.0000.0000.0000.000
82A156ASP-1-0.920-0.96528.4759.4479.4470.0000.0000.0000.000
83A157VAL0-0.020-0.01726.8430.3530.3530.0000.0000.0000.000
84A158SER0-0.0170.01527.2910.1350.1350.0000.0000.0000.000
85A159ILE00.0500.01926.9420.1590.1590.0000.0000.0000.000
86A160ALA0-0.0060.01923.4880.2740.2740.0000.0000.0000.000
87A161VAL00.0060.00023.4990.4830.4830.0000.0000.0000.000
88A162VAL0-0.034-0.01625.0290.2240.2240.0000.0000.0000.000
89A163ASP-1-0.853-0.93822.02212.38712.3870.0000.0000.0000.000
90A164LEU0-0.0010.00718.7160.3180.3180.0000.0000.0000.000
91A165LEU0-0.031-0.02521.8730.2720.2720.0000.0000.0000.000
92A166GLN0-0.0160.00723.411-0.166-0.1660.0000.0000.0000.000
93A167GLU-1-0.935-0.95717.97814.82914.8290.0000.0000.0000.000
94A168LEU0-0.085-0.05718.4530.4230.4230.0000.0000.0000.000
95A169THR0-0.066-0.06321.271-0.104-0.1040.0000.0000.0000.000
96A170ASP-1-0.817-0.89822.17312.11212.1120.0000.0000.0000.000
97A171ILE00.0270.00223.9390.3440.3440.0000.0000.0000.000
98A172ASP-1-0.911-0.95122.71712.17112.1710.0000.0000.0000.000
99A173THR0-0.055-0.02919.0830.4050.4050.0000.0000.0000.000
100A174LEU0-0.074-0.04521.0050.3780.3780.0000.0000.0000.000
101A175HIS0-0.029-0.00523.581-0.260-0.2600.0000.0000.0000.000
102A176GLU-1-1.048-1.01417.28917.13217.1320.0000.0000.0000.000
103A177SER0-0.075-0.06719.3060.3300.3300.0000.0000.0000.000
104A178GLU-1-0.910-0.95521.16810.97210.9720.0000.0000.0000.000
105A179GLU-1-1.021-1.02623.08712.06812.0680.0000.0000.0000.000
106A180GLY0-0.0180.00320.5000.0130.0130.0000.0000.0000.000
107A181ALA00.0420.01521.475-0.070-0.0700.0000.0000.0000.000
108A182GLU-1-0.824-0.90323.49910.07510.0750.0000.0000.0000.000
109A183VAL0-0.032-0.01422.650-0.255-0.2550.0000.0000.0000.000
110A184LEU00.0070.01021.680-0.185-0.1850.0000.0000.0000.000
111A185ILE00.0490.03224.877-0.405-0.4050.0000.0000.0000.000
112A186ASP-1-0.840-0.91227.9989.6729.6720.0000.0000.0000.000
113A187ALA0-0.024-0.01826.731-0.310-0.3100.0000.0000.0000.000
114A188LEU0-0.039-0.02725.870-0.279-0.2790.0000.0000.0000.000
115A189VAL0-0.024-0.02029.429-0.272-0.2720.0000.0000.0000.000
116A190ASP-1-0.977-0.96731.9458.6468.6460.0000.0000.0000.000
117A191GLY0-0.056-0.02832.000-0.260-0.2600.0000.0000.0000.000
118A192GLN0-0.086-0.05133.126-0.238-0.2380.0000.0000.0000.000
119A193VAL00.0770.03329.727-0.140-0.1400.0000.0000.0000.000
120A194VAL00.0350.01432.812-0.069-0.0690.0000.0000.0000.000
121A195ALA00.0140.01135.399-0.135-0.1350.0000.0000.0000.000
122A196LEU0-0.014-0.00633.562-0.183-0.1830.0000.0000.0000.000
123A197LEU00.0230.01830.335-0.057-0.0570.0000.0000.0000.000
124A198VAL00.0130.01134.438-0.081-0.0810.0000.0000.0000.000
125A199GLN0-0.060-0.01337.777-0.163-0.1630.0000.0000.0000.000
126A200ASN0-0.011-0.01732.949-0.053-0.0530.0000.0000.0000.000
127A201LEU00.0550.03434.895-0.030-0.0300.0000.0000.0000.000
128A202GLU-1-1.016-0.99437.1036.7226.7220.0000.0000.0000.000
129A203ARG10.7570.86133.702-8.666-8.6660.0000.0000.0000.000
130A204LEU0-0.0070.03033.9320.0610.0610.0000.0000.0000.000
131A205ASP-1-0.851-0.91937.3927.0567.0560.0000.0000.0000.000
132A206GLU-1-0.793-0.85037.1497.7997.7990.0000.0000.0000.000
133A207SER0-0.160-0.09738.2330.0190.0190.0000.0000.0000.000
134A208VAL0-0.0080.00233.732-0.003-0.0030.0000.0000.0000.000
135A209LYS10.8680.91429.263-9.372-9.3720.0000.0000.0000.000
136A210GLU-1-0.798-0.88528.7209.3379.3370.0000.0000.0000.000
137A211GLU-1-0.758-0.88230.7098.4588.4580.0000.0000.0000.000
138A212ALA0-0.102-0.04833.211-0.049-0.0490.0000.0000.0000.000
139A213ASP-1-0.876-0.95229.0379.3929.3920.0000.0000.0000.000
140A214GLY00.0390.03030.0090.2390.2390.0000.0000.0000.000
141A215VAL0-0.007-0.00931.0730.0750.0750.0000.0000.0000.000
142A216HIS0-0.077-0.03630.2910.0900.0900.0000.0000.0000.000
143A217ASN00.033-0.00325.590-0.219-0.2190.0000.0000.0000.000
144A218THR0-0.047-0.02929.0500.1760.1760.0000.0000.0000.000
145A219LEU0-0.080-0.05531.442-0.069-0.0690.0000.0000.0000.000
146A220ALA00.0580.03828.650-0.081-0.0810.0000.0000.0000.000
147A221ILE00.0010.02127.4390.0440.0440.0000.0000.0000.000
148A222VAL0-0.071-0.04629.594-0.044-0.0440.0000.0000.0000.000
149A223GLU-1-0.887-0.92431.9859.0449.0440.0000.0000.0000.000
150A224ASN00.0660.04526.800-0.305-0.3050.0000.0000.0000.000
151A225MET0-0.001-0.00529.554-0.044-0.0440.0000.0000.0000.000
152A226ALA0-0.043-0.01631.422-0.163-0.1630.0000.0000.0000.000
153A227GLU-1-0.975-0.99331.8529.5909.5900.0000.0000.0000.000
154A228PHE0-0.042-0.01227.362-0.065-0.0650.0000.0000.0000.000
155A229ARG10.7770.86630.703-9.784-9.7840.0000.0000.0000.000
156A230PRO00.0480.02434.170-0.199-0.1990.0000.0000.0000.000
157A231GLU-1-0.948-0.98036.5688.2948.2940.0000.0000.0000.000
158A232MET0-0.0160.00133.579-0.182-0.1820.0000.0000.0000.000
159A233CYS0-0.0010.00337.411-0.044-0.0440.0000.0000.0000.000
160A234THR0-0.001-0.01239.735-0.085-0.0850.0000.0000.0000.000
161A235GLU-1-0.881-0.92636.7648.2678.2670.0000.0000.0000.000
162A236GLY00.0790.02938.266-0.101-0.1010.0000.0000.0000.000
163A237ALA0-0.039-0.01939.124-0.059-0.0590.0000.0000.0000.000
164A238GLN0-0.045-0.04042.303-0.107-0.1070.0000.0000.0000.000
165A239GLN0-0.051-0.02537.784-0.025-0.0250.0000.0000.0000.000
166A240GLY00.0120.00641.4430.0540.0540.0000.0000.0000.000
167A241LEU00.0600.04237.605-0.057-0.0570.0000.0000.0000.000
168A242LEU00.0290.01141.035-0.073-0.0730.0000.0000.0000.000
169A243GLN0-0.023-0.02343.942-0.156-0.1560.0000.0000.0000.000
170A244TRP00.0420.01539.336-0.138-0.1380.0000.0000.0000.000
171A245LEU00.0670.03239.328-0.077-0.0770.0000.0000.0000.000
172A246LEU0-0.040-0.01143.158-0.118-0.1180.0000.0000.0000.000
173A247LYS10.8390.90944.984-6.827-6.8270.0000.0000.0000.000
174A248ARG10.7870.84939.926-7.458-7.4580.0000.0000.0000.000
175A249LEU0-0.0050.00444.123-0.088-0.0880.0000.0000.0000.000
176A250LYS10.8330.90246.189-5.866-5.8660.0000.0000.0000.000
177A251ALA0-0.0080.00946.002-0.153-0.1530.0000.0000.0000.000
178A252LYS10.8860.94147.956-5.840-5.8400.0000.0000.0000.000
179A253MET00.0390.02642.921-0.036-0.0360.0000.0000.0000.000
180A254PRO0-0.073-0.04644.111-0.135-0.1350.0000.0000.0000.000
181A255PHE00.012-0.01342.6430.0430.0430.0000.0000.0000.000
182A256ASP-1-0.786-0.86239.0767.3767.3760.0000.0000.0000.000
183A257ALA00.035-0.00836.222-0.086-0.0860.0000.0000.0000.000
184A258ASN00.0700.03735.3100.2230.2230.0000.0000.0000.000
185A259LYS10.8270.91637.819-6.577-6.5770.0000.0000.0000.000
186A260LEU0-0.053-0.04038.572-0.180-0.1800.0000.0000.0000.000
187A261TYR00.0430.01631.690-0.171-0.1710.0000.0000.0000.000
188A262CYS0-0.048-0.02737.783-0.011-0.0110.0000.0000.0000.000
189A263SER0-0.111-0.07140.110-0.200-0.2000.0000.0000.0000.000
190A264GLU-1-0.859-0.92337.3127.9687.9680.0000.0000.0000.000
191A265VAL00.0720.04436.224-0.054-0.0540.0000.0000.0000.000
192A266LEU0-0.061-0.04139.004-0.106-0.1060.0000.0000.0000.000
193A267ALA0-0.042-0.02842.322-0.133-0.1330.0000.0000.0000.000
194A268ILE00.0510.02636.586-0.148-0.1480.0000.0000.0000.000
195A269LEU0-0.029-0.00539.512-0.075-0.0750.0000.0000.0000.000
196A270LEU0-0.038-0.02642.140-0.167-0.1670.0000.0000.0000.000
197A271GLN0-0.028-0.01141.421-0.133-0.1330.0000.0000.0000.000
198A272ASP-1-0.925-0.97544.3166.8366.8360.0000.0000.0000.000
199A273ASN00.0680.03143.791-0.031-0.0310.0000.0000.0000.000
200A274ASP-1-0.841-0.92546.8776.0616.0610.0000.0000.0000.000
201A275GLU-1-0.894-0.94947.0376.5026.5020.0000.0000.0000.000
202A276ASN00.0290.00343.193-0.147-0.1470.0000.0000.0000.000
203A277ARG10.7530.88447.677-6.474-6.4740.0000.0000.0000.000
204A278GLU-1-0.759-0.84950.5825.5295.5290.0000.0000.0000.000
205A279LEU0-0.0120.01346.606-0.109-0.1090.0000.0000.0000.000
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