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: K9453

Calculation Name: 3HO7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HO7

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MXD3

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2735205.616731
FMO2-HF: Nuclear repulsion 2646117.723635
FMO2-HF: Total energy -89087.893096
FMO2-MP2: Total energy -89344.816975


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:90:THR)


Summations of interaction energy for fragment #1(A:90:THR)
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.
-7.262-0.9323.15-4.667-4.813-0.023
Interaction energy analysis for fragmet #1(A:90:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : 0.008
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].
3A92ARG10.7790.8743.861-1.9911.208-0.022-1.859-1.3170.006
4A93LEU0-0.019-0.0046.989-0.120-0.1200.0000.0000.0000.000
5A94ASN00.0010.0099.9750.2040.2040.0000.0000.0000.000
6A95ILE00.012-0.00413.645-0.010-0.0100.0000.0000.0000.000
7A96ALA00.0420.03516.0290.0400.0400.0000.0000.0000.000
8A97VAL0-0.010-0.01419.608-0.016-0.0160.0000.0000.0000.000
9A98LEU00.0580.03522.1950.0170.0170.0000.0000.0000.000
10A99PRO00.0520.03225.932-0.001-0.0010.0000.0000.0000.000
11A100THR0-0.056-0.01827.7570.0030.0030.0000.0000.0000.000
12A101ILE00.0060.00424.0010.0050.0050.0000.0000.0000.000
13A102ALA00.0220.01723.2720.0000.0000.0000.0000.0000.000
14A103PRO00.0380.01323.920-0.004-0.0040.0000.0000.0000.000
15A104TYR0-0.0020.00926.4450.0080.0080.0000.0000.0000.000
16A105LEU00.0200.01621.3830.0010.0010.0000.0000.0000.000
17A106LEU00.0170.00918.382-0.008-0.0080.0000.0000.0000.000
18A107PRO0-0.007-0.00919.966-0.009-0.0090.0000.0000.0000.000
19A108ARG10.8340.90421.7480.1350.1350.0000.0000.0000.000
20A109VAL00.0030.00416.459-0.002-0.0020.0000.0000.0000.000
21A110PHE00.0000.00715.718-0.025-0.0250.0000.0000.0000.000
22A111PRO0-0.009-0.01015.354-0.009-0.0090.0000.0000.0000.000
23A112ILE00.0260.02314.9160.0150.0150.0000.0000.0000.000
24A113TRP00.0540.00111.818-0.028-0.0280.0000.0000.0000.000
25A114LYS10.8960.96110.7070.0810.0810.0000.0000.0000.000
26A115LYS10.7890.87610.9780.1630.1630.0000.0000.0000.000
27A116GLU-1-0.773-0.87610.764-0.108-0.1080.0000.0000.0000.000
28A117LEU0-0.050-0.0157.390-0.095-0.0950.0000.0000.0000.000
29A118ALA0-0.0050.0026.579-0.246-0.2460.0000.0000.0000.000
30A119GLY00.0110.0042.8880.1320.6230.322-0.303-0.5100.001
31A120LEU0-0.050-0.0192.486-6.113-3.5372.851-2.497-2.930-0.030
32A121GLU-1-0.826-0.8954.7330.4450.509-0.001-0.008-0.0560.000
33A122ILE0-0.002-0.0197.185-0.142-0.1420.0000.0000.0000.000
34A123HIS0-0.026-0.00610.6520.1330.1330.0000.0000.0000.000
35A124VAL00.0080.00313.491-0.020-0.0200.0000.0000.0000.000
36A125SER0-0.012-0.00316.5360.0430.0430.0000.0000.0000.000
37A126GLU-1-0.874-0.95019.914-0.150-0.1500.0000.0000.0000.000
38A127MET0-0.081-0.04621.1930.0130.0130.0000.0000.0000.000
39A128GLN00.0600.03325.430-0.004-0.0040.0000.0000.0000.000
40A129THR00.037-0.01227.136-0.012-0.0120.0000.0000.0000.000
41A130SER0-0.038-0.02327.689-0.007-0.0070.0000.0000.0000.000
42A131ARG10.8710.94526.0120.1270.1270.0000.0000.0000.000
43A132CYS0-0.0100.00323.476-0.012-0.0120.0000.0000.0000.000
44A133LEU00.0160.01023.533-0.020-0.0200.0000.0000.0000.000
45A134ALA00.0530.02725.401-0.008-0.0080.0000.0000.0000.000
46A135SER00.010-0.01821.4730.0020.0020.0000.0000.0000.000
47A136LEU0-0.053-0.01419.174-0.022-0.0220.0000.0000.0000.000
48A137LEU0-0.038-0.02021.399-0.015-0.0150.0000.0000.0000.000
49A138SER0-0.059-0.04423.319-0.005-0.0050.0000.0000.0000.000
50A139GLY0-0.0060.00419.1020.0060.0060.0000.0000.0000.000
51A140GLU-1-0.932-0.92517.736-0.211-0.2110.0000.0000.0000.000
52A141ILE0-0.060-0.04116.513-0.018-0.0180.0000.0000.0000.000
53A142ASP-1-0.761-0.84712.077-0.917-0.9170.0000.0000.0000.000
54A143MET0-0.036-0.01512.6230.0090.0090.0000.0000.0000.000
55A144ALA00.0250.01816.9450.0250.0250.0000.0000.0000.000
56A145ILE0-0.006-0.00117.953-0.005-0.0050.0000.0000.0000.000
57A146ILE00.0180.00121.7410.0200.0200.0000.0000.0000.000
58A147ALA00.0140.00125.498-0.001-0.0010.0000.0000.0000.000
59A148SER00.012-0.01028.5240.0140.0140.0000.0000.0000.000
60A149LYS10.8010.88928.3200.1290.1290.0000.0000.0000.000
61A150ALA00.0200.00626.2300.0100.0100.0000.0000.0000.000
62A151GLU-1-0.888-0.91628.394-0.126-0.1260.0000.0000.0000.000
63A152THR0-0.013-0.00928.6860.0130.0130.0000.0000.0000.000
64A153GLU-1-0.814-0.89828.655-0.180-0.1800.0000.0000.0000.000
65A154GLY0-0.004-0.00926.381-0.002-0.0020.0000.0000.0000.000
66A155LEU0-0.072-0.03223.064-0.029-0.0290.0000.0000.0000.000
67A156GLU-1-0.797-0.87721.834-0.306-0.3060.0000.0000.0000.000
68A157ASP-1-0.794-0.89722.928-0.228-0.2280.0000.0000.0000.000
69A158ASP-1-0.794-0.86520.544-0.329-0.3290.0000.0000.0000.000
70A159LEU0-0.040-0.01923.580-0.001-0.0010.0000.0000.0000.000
71A160LEU0-0.044-0.02020.041-0.013-0.0130.0000.0000.0000.000
72A161TYR0-0.013-0.02523.9290.0040.0040.0000.0000.0000.000
73A162TYR00.0180.01327.321-0.003-0.0030.0000.0000.0000.000
74A163GLU-1-0.770-0.89629.618-0.129-0.1290.0000.0000.0000.000
75A164GLU-1-0.839-0.90632.231-0.078-0.0780.0000.0000.0000.000
76A165PHE0-0.020-0.01034.804-0.002-0.0020.0000.0000.0000.000
77A166LEU0-0.008-0.00836.9100.0040.0040.0000.0000.0000.000
78A167GLY00.0190.00439.575-0.001-0.0010.0000.0000.0000.000
79A168TYR0-0.059-0.05139.9320.0000.0000.0000.0000.0000.000
80A169VAL00.014-0.00742.5340.0000.0000.0000.0000.0000.000
81A170SER00.016-0.01146.2320.0020.0020.0000.0000.0000.000
82A171ARG10.8180.87346.3370.0340.0340.0000.0000.0000.000
83A172CYS0-0.043-0.00850.7600.0020.0020.0000.0000.0000.000
84A173GLU-1-0.778-0.80149.537-0.038-0.0380.0000.0000.0000.000
85A174PRO00.023-0.00252.7250.0000.0000.0000.0000.0000.000
86A175LEU00.013-0.00649.4520.0000.0000.0000.0000.0000.000
87A176PHE0-0.0160.00447.808-0.001-0.0010.0000.0000.0000.000
88A177GLU-1-0.914-0.92951.510-0.031-0.0310.0000.0000.0000.000
89A178GLN0-0.013-0.00252.438-0.001-0.0010.0000.0000.0000.000
90A179ASP-1-0.862-0.93149.902-0.040-0.0400.0000.0000.0000.000
91A180VAL0-0.057-0.03747.076-0.003-0.0030.0000.0000.0000.000
92A181ILE0-0.045-0.02144.6700.0020.0020.0000.0000.0000.000
93A182ARG10.8400.91347.7920.0370.0370.0000.0000.0000.000
94A183THR0-0.002-0.02748.679-0.001-0.0010.0000.0000.0000.000
95A184THR0-0.024-0.01350.097-0.001-0.0010.0000.0000.0000.000
96A185GLU-1-0.818-0.89852.633-0.038-0.0380.0000.0000.0000.000
97A186VAL0-0.0150.00547.4770.0010.0010.0000.0000.0000.000
98A187ASN00.0410.01050.6800.0000.0000.0000.0000.0000.000
99A188PRO00.0390.02550.264-0.001-0.0010.0000.0000.0000.000
100A189HIS10.8160.88050.2650.0360.0360.0000.0000.0000.000
101A190ARG10.7820.85450.0880.0370.0370.0000.0000.0000.000
102A191LEU0-0.0100.03144.354-0.001-0.0010.0000.0000.0000.000
103A192TRP0-0.028-0.01742.7390.0010.0010.0000.0000.0000.000
104A193LEU00.0130.00640.861-0.002-0.0020.0000.0000.0000.000
105A194LEU0-0.0030.00134.6800.0010.0010.0000.0000.0000.000
106A195ASP-1-0.786-0.87837.067-0.076-0.0760.0000.0000.0000.000
107A196GLU-1-0.771-0.88630.642-0.135-0.1350.0000.0000.0000.000
108A197GLY0-0.033-0.02833.269-0.006-0.0060.0000.0000.0000.000
109A198HIS0-0.014-0.00834.2970.0010.0010.0000.0000.0000.000
110A199CYS0-0.016-0.00637.4750.0030.0030.0000.0000.0000.000
111A200PHE00.0460.03531.4570.0020.0020.0000.0000.0000.000
112A201ARG10.8310.89432.1370.1290.1290.0000.0000.0000.000
113A202ASP-1-0.806-0.89338.276-0.072-0.0720.0000.0000.0000.000
114A203GLN00.0010.00733.3040.0040.0040.0000.0000.0000.000
115A204LEU00.0120.00438.7250.0030.0030.0000.0000.0000.000
116A205VAL00.0410.02341.2740.0050.0050.0000.0000.0000.000
117A206ARG10.8630.93243.9570.0680.0680.0000.0000.0000.000
118A207PHE00.017-0.01443.6880.0030.0030.0000.0000.0000.000
119A209GLN0-0.008-0.00144.6830.0050.0050.0000.0000.0000.000
120A210MET0-0.0790.00747.8970.0020.0020.0000.0000.0000.000
121A211LYS10.8940.92250.3640.0500.0500.0000.0000.0000.000
122A212GLY00.0980.03653.4620.0000.0000.0000.0000.0000.000
123A213LEU0-0.066-0.00845.7370.0010.0010.0000.0000.0000.000
124A214HIS00.0620.01346.4230.0010.0010.0000.0000.0000.000
125A215GLU-1-0.899-0.91350.976-0.036-0.0360.0000.0000.0000.000
126A216ARG10.7810.87647.2310.0480.0480.0000.0000.0000.000
127A217GLN0-0.0010.01053.3240.0000.0000.0000.0000.0000.000
128A218THR00.000-0.00647.8160.0000.0000.0000.0000.0000.000
129A219ALA00.0130.00647.690-0.002-0.0020.0000.0000.0000.000
130A220TYR00.009-0.01240.1760.0000.0000.0000.0000.0000.000
131A221SER0-0.063-0.03740.877-0.001-0.0010.0000.0000.0000.000
132A222GLY00.0150.00037.0930.0020.0020.0000.0000.0000.000
133A223GLY0-0.0050.00436.7280.0000.0000.0000.0000.0000.000
134A224SER00.000-0.00133.588-0.005-0.0050.0000.0000.0000.000
135A225MET00.0400.01433.3510.0050.0050.0000.0000.0000.000
136A226GLU-1-0.883-0.93033.851-0.055-0.0550.0000.0000.0000.000
137A227ALA00.0140.01335.7790.0050.0050.0000.0000.0000.000
138A228PHE00.029-0.00538.7620.0040.0040.0000.0000.0000.000
139A229MET0-0.035-0.00335.7450.0000.0000.0000.0000.0000.000
140A230ARG10.8250.87935.9250.0550.0550.0000.0000.0000.000
141A231LEU0-0.0140.00641.3700.0030.0030.0000.0000.0000.000
142A232VAL0-0.0080.00942.7470.0030.0030.0000.0000.0000.000
143A233GLU-1-0.730-0.82939.790-0.048-0.0480.0000.0000.0000.000
144A234SER0-0.098-0.03844.5570.0030.0030.0000.0000.0000.000
145A235GLY00.0310.01347.2290.0020.0020.0000.0000.0000.000
146A236GLN0-0.092-0.06147.5630.0010.0010.0000.0000.0000.000
147A237GLY00.0630.03547.080-0.002-0.0020.0000.0000.0000.000
148A238ILE0-0.011-0.00544.8860.0000.0000.0000.0000.0000.000
149A239THR00.005-0.02039.750-0.002-0.0020.0000.0000.0000.000
150A240PHE0-0.007-0.00739.3120.0020.0020.0000.0000.0000.000
151A241ILE00.0530.02935.632-0.004-0.0040.0000.0000.0000.000
152A242PRO0-0.0040.00231.4780.0010.0010.0000.0000.0000.000
153A243GLN00.0350.01732.5160.0060.0060.0000.0000.0000.000
154A244LEU0-0.024-0.01026.4030.0040.0040.0000.0000.0000.000
155A245THR0-0.030-0.02330.3290.0010.0010.0000.0000.0000.000
156A246VAL00.0050.00132.4100.0070.0070.0000.0000.0000.000
157A247GLU-1-0.839-0.92230.144-0.088-0.0880.0000.0000.0000.000
158A248GLN0-0.027-0.02827.8430.0090.0090.0000.0000.0000.000
159A249LEU0-0.0540.01132.7330.0050.0050.0000.0000.0000.000
160A250SER00.029-0.01236.4190.0030.0030.0000.0000.0000.000
161A251PRO00.019-0.01638.888-0.002-0.0020.0000.0000.0000.000
162A252SER00.009-0.00841.841-0.001-0.0010.0000.0000.0000.000
163A253GLN00.0110.01537.6730.0010.0010.0000.0000.0000.000
164A254LYS10.8290.91135.8760.0540.0540.0000.0000.0000.000
165A255GLU-1-0.774-0.85141.411-0.034-0.0340.0000.0000.0000.000
166A256LEU0-0.0190.01243.0110.0010.0010.0000.0000.0000.000
167A257VAL0-0.032-0.00339.713-0.002-0.0020.0000.0000.0000.000
168A258ARG10.7870.88342.6680.0460.0460.0000.0000.0000.000
169A259PRO00.0430.03242.136-0.003-0.0030.0000.0000.0000.000
170A260PHE00.013-0.00241.3590.0030.0030.0000.0000.0000.000
171A261GLY00.0430.03244.7720.0010.0010.0000.0000.0000.000
172A262MET0-0.042-0.00444.379-0.002-0.0020.0000.0000.0000.000
173A263PRO0-0.038-0.01043.6430.0030.0030.0000.0000.0000.000
174A264ARG0-0.008-0.02441.007-0.001-0.0010.0000.0000.0000.000
175A265PRO0-0.0270.00039.517-0.004-0.0040.0000.0000.0000.000
176A266VAL00.0150.00334.394-0.001-0.0010.0000.0000.0000.000
177A267ARG10.8320.90529.4940.1310.1310.0000.0000.0000.000
178A268GLU-1-0.772-0.87829.814-0.152-0.1520.0000.0000.0000.000
179A269VAL0-0.032-0.01524.515-0.002-0.0020.0000.0000.0000.000
180A270ARG10.8060.87624.3430.1890.1890.0000.0000.0000.000
181A271LEU0-0.0030.00116.579-0.004-0.0040.0000.0000.0000.000
182A272ALA00.0090.00620.7020.0140.0140.0000.0000.0000.000
183A273VAL00.014-0.00816.811-0.043-0.0430.0000.0000.0000.000
184A274ARG10.8640.89019.3040.3200.3200.0000.0000.0000.000
185A275GLN0-0.035-0.02019.929-0.035-0.0350.0000.0000.0000.000
186A276ASP-1-0.823-0.86820.143-0.337-0.3370.0000.0000.0000.000
187A277TYR0-0.039-0.04312.124-0.098-0.0980.0000.0000.0000.000
188A278SER00.0390.00513.604-0.008-0.0080.0000.0000.0000.000
189A279ARG10.8100.9198.4111.2141.2140.0000.0000.0000.000
190A280ARG10.8930.91911.4910.3810.3810.0000.0000.0000.000
191A281LYS10.8550.9129.9370.5940.5940.0000.0000.0000.000
192A282LEU00.0340.0257.6570.0310.0310.0000.0000.0000.000
193A283ARG10.7760.84810.3850.4800.4800.0000.0000.0000.000
194A284GLU-1-0.833-0.89813.888-0.419-0.4190.0000.0000.0000.000
195A285GLN0-0.003-0.0059.301-0.105-0.1050.0000.0000.0000.000
196A286LEU00.004-0.01210.7720.0810.0810.0000.0000.0000.000
197A287ILE00.0120.01114.3070.0710.0710.0000.0000.0000.000
198A288GLY00.0140.01416.9160.0480.0480.0000.0000.0000.000
199A289LEU0-0.037-0.02411.8650.0430.0430.0000.0000.0000.000
200A290LEU00.0020.00016.4820.0450.0450.0000.0000.0000.000
201A291ARG10.8680.94618.7730.2440.2440.0000.0000.0000.000
202A292SER0-0.075-0.04518.7410.0250.0250.0000.0000.0000.000
203A293ALA00.0080.01319.6760.0210.0210.0000.0000.0000.000
204A294VAL0-0.019-0.00421.5610.0180.0180.0000.0000.0000.000
205A295PRO00.0310.00625.181-0.002-0.0020.0000.0000.0000.000
206A296SER00.0380.00627.911-0.006-0.0060.0000.0000.0000.000
207A297ASP-1-0.919-0.93628.788-0.097-0.0970.0000.0000.0000.000
208A298MET00.0380.02828.9530.0030.0030.0000.0000.0000.000
209A299HIS0-0.0180.00324.376-0.011-0.0110.0000.0000.0000.000
210A300LYS10.8990.93928.7160.1100.1100.0000.0000.0000.000
211A301LEU00.0120.02832.2630.0020.0020.0000.0000.0000.000
212A302GLN0-0.004-0.01134.2530.0070.0070.0000.0000.0000.000
213A303THR0-0.009-0.02037.7690.0000.0000.0000.0000.0000.000
214A304GLY00.0580.02441.5730.0030.0030.0000.0000.0000.000
215A305GLN0-0.057-0.03535.901-0.003-0.0030.0000.0000.0000.000
216A306HIS00.007-0.00939.6610.0000.0000.0000.0000.0000.000
217A307LEU0-0.037-0.00533.921-0.001-0.0010.0000.0000.0000.000
218A308ALA0-0.033-0.01237.2380.0040.0040.0000.0000.0000.000
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