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

tag_button

FMODB ID: MVMJZ

Calculation Name: 1HU3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1HU3

Chain ID: A

ChEMBL ID:

UniProt ID: O43432

Base Structure: X-ray

Registration Date: 2023-06-21

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2449645.266384
FMO2-HF: Nuclear repulsion 2363681.238467
FMO2-HF: Total energy -85964.027916
FMO2-MP2: Total energy -86207.698641


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:1:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
-2.3522.2753.732-3.576-4.785-0.022
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.007
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].
3A746PRO00.0190.0113.8510.3022.067-0.016-0.795-0.9550.001
4A747GLU-1-0.883-0.9462.262-1.971-1.5251.399-0.676-1.1690.003
5A748ASN0-0.024-0.0232.434-5.730-3.4272.349-2.075-2.577-0.026
6A749ILE00.0600.0384.3060.8010.9140.000-0.030-0.0840.000
7A750LYS11.0411.0177.4341.6691.6690.0000.0000.0000.000
8A751THR0-0.0100.0025.9960.1840.1840.0000.0000.0000.000
9A752GLN0-0.0260.0118.3970.4820.4820.0000.0000.0000.000
10A753GLU-1-0.894-0.95910.179-0.780-0.7800.0000.0000.0000.000
11A754LEU0-0.035-0.00211.5320.1410.1410.0000.0000.0000.000
12A755PHE00.0240.00010.7110.0880.0880.0000.0000.0000.000
13A756ARG10.9560.98314.0900.5550.5550.0000.0000.0000.000
14A757LYS10.9210.97815.9160.4690.4690.0000.0000.0000.000
15A758VAL00.022-0.00216.0560.0450.0450.0000.0000.0000.000
16A759ARG10.9560.97416.5240.1790.1790.0000.0000.0000.000
17A760SER0-0.048-0.01120.0430.0330.0330.0000.0000.0000.000
18A761ILE0-0.032-0.02321.0830.0200.0200.0000.0000.0000.000
19A762LEU0-0.027-0.02020.9140.0180.0180.0000.0000.0000.000
20A763ASN0-0.024-0.01622.4100.0320.0320.0000.0000.0000.000
21A764LYS10.9180.98725.7190.1810.1810.0000.0000.0000.000
22A765LEU00.0340.01228.5520.0070.0070.0000.0000.0000.000
23A766THR0-0.0170.00031.5280.0110.0110.0000.0000.0000.000
24A767PRO0-0.032-0.01030.974-0.008-0.0080.0000.0000.0000.000
25A768GLN00.0380.03527.707-0.004-0.0040.0000.0000.0000.000
26A769MET0-0.016-0.01631.1450.0050.0050.0000.0000.0000.000
27A770PHE00.0770.00930.018-0.008-0.0080.0000.0000.0000.000
28A771ASN00.0580.02430.633-0.007-0.0070.0000.0000.0000.000
29A772GLN00.003-0.00629.839-0.015-0.0150.0000.0000.0000.000
30A773LEU00.0450.02326.935-0.014-0.0140.0000.0000.0000.000
31A774MET00.0310.00926.083-0.012-0.0120.0000.0000.0000.000
32A775LYS10.9230.97526.2670.1390.1390.0000.0000.0000.000
33A776GLN00.0170.00324.080-0.012-0.0120.0000.0000.0000.000
34A777VAL00.0310.00121.171-0.028-0.0280.0000.0000.0000.000
35A778SER0-0.072-0.02721.186-0.017-0.0170.0000.0000.0000.000
36A779GLY00.0050.00821.149-0.013-0.0130.0000.0000.0000.000
37A780LEU0-0.091-0.05317.250-0.053-0.0530.0000.0000.0000.000
38A781THR00.0120.00713.3140.0210.0210.0000.0000.0000.000
39A782VAL0-0.029-0.00413.229-0.068-0.0680.0000.0000.0000.000
40A783ASP-1-0.780-0.88010.211-0.666-0.6660.0000.0000.0000.000
41A784THR00.0360.0237.2740.0460.0460.0000.0000.0000.000
42A785GLU-1-0.883-0.94910.2340.2970.2970.0000.0000.0000.000
43A786GLU-1-0.864-0.9517.5000.8700.8700.0000.0000.0000.000
44A787ARG10.7720.8516.0961.4191.4190.0000.0000.0000.000
45A788LEU00.012-0.00911.0650.0030.0030.0000.0000.0000.000
46A789LYS10.8730.93213.430-0.314-0.3140.0000.0000.0000.000
47A790GLY00.0530.03813.0780.0100.0100.0000.0000.0000.000
48A791VAL0-0.008-0.00614.065-0.021-0.0210.0000.0000.0000.000
49A792ILE0-0.001-0.01016.4870.0050.0050.0000.0000.0000.000
50A793ASP-1-0.841-0.92316.4420.1900.1900.0000.0000.0000.000
51A794LEU0-0.028-0.01315.353-0.015-0.0150.0000.0000.0000.000
52A795VAL0-0.023-0.01019.107-0.005-0.0050.0000.0000.0000.000
53A796PHE0-0.029-0.02322.0660.0050.0050.0000.0000.0000.000
54A797GLU-1-0.949-0.97719.0890.0320.0320.0000.0000.0000.000
55A798LYS10.8630.94623.3150.0770.0770.0000.0000.0000.000
56A799ALA0-0.013-0.01125.1150.0010.0010.0000.0000.0000.000
57A800ILE0-0.128-0.06726.1740.0070.0070.0000.0000.0000.000
58A801ASP-1-0.926-0.95727.299-0.033-0.0330.0000.0000.0000.000
59A802GLU-1-0.855-0.92429.073-0.065-0.0650.0000.0000.0000.000
60A803PRO00.0360.02331.351-0.002-0.0020.0000.0000.0000.000
61A804SER0-0.016-0.01032.7730.0020.0020.0000.0000.0000.000
62A805PHE00.0200.02631.3670.0010.0010.0000.0000.0000.000
63A806SER0-0.021-0.03730.772-0.004-0.0040.0000.0000.0000.000
64A807VAL00.0490.02531.4600.0010.0010.0000.0000.0000.000
65A808ALA0-0.0180.00030.603-0.002-0.0020.0000.0000.0000.000
66A809TYR00.0690.02426.607-0.003-0.0030.0000.0000.0000.000
67A810ALA00.0220.02226.9810.0000.0000.0000.0000.0000.000
68A811ASN00.000-0.01228.6360.0020.0020.0000.0000.0000.000
69A812MET0-0.018-0.00921.314-0.005-0.0050.0000.0000.0000.000
70A813CYS0-0.017-0.00724.018-0.002-0.0020.0000.0000.0000.000
71A814ARG10.9260.95424.9950.0360.0360.0000.0000.0000.000
72A815CYS0-0.0340.00025.184-0.001-0.0010.0000.0000.0000.000
73A816LEU00.0160.00519.939-0.008-0.0080.0000.0000.0000.000
74A817VAL0-0.089-0.02321.5130.0040.0040.0000.0000.0000.000
75A818THR0-0.049-0.01623.6830.0150.0150.0000.0000.0000.000
76A819LEU00.022-0.00118.293-0.021-0.0210.0000.0000.0000.000
77A820LYS10.8810.96017.787-0.040-0.0400.0000.0000.0000.000
78A821VAL00.0190.00113.195-0.025-0.0250.0000.0000.0000.000
79A822PRO00.0230.03212.1760.0730.0730.0000.0000.0000.000
80A832ASN00.015-0.00117.056-0.027-0.0270.0000.0000.0000.000
81A833PHE00.1130.04720.0350.0220.0220.0000.0000.0000.000
82A834ARG11.0280.99421.437-0.014-0.0140.0000.0000.0000.000
83A835LYS10.9120.99217.262-0.237-0.2370.0000.0000.0000.000
84A836LEU00.0040.00216.4720.0190.0190.0000.0000.0000.000
85A837LEU00.0470.02620.5060.0070.0070.0000.0000.0000.000
86A838LEU00.0240.02123.3340.0020.0020.0000.0000.0000.000
87A839ASN00.003-0.00620.337-0.014-0.0140.0000.0000.0000.000
88A840ARG10.8480.93620.134-0.105-0.1050.0000.0000.0000.000
89A841CYS0-0.022-0.00922.744-0.009-0.0090.0000.0000.0000.000
90A842GLN00.046-0.00426.503-0.014-0.0140.0000.0000.0000.000
91A843LYS10.9761.02320.182-0.223-0.2230.0000.0000.0000.000
92A844GLU-1-0.879-0.96225.3580.0960.0960.0000.0000.0000.000
93A845PHE00.0540.01327.961-0.005-0.0050.0000.0000.0000.000
94A846GLU-1-0.858-0.92227.2150.1520.1520.0000.0000.0000.000
95A847LYS10.8210.92726.333-0.108-0.1080.0000.0000.0000.000
96A848ASP-1-0.924-0.97029.0200.0760.0760.0000.0000.0000.000
97A849LYS10.8260.91131.612-0.142-0.1420.0000.0000.0000.000
98A850ALA0-0.0340.00031.082-0.004-0.0040.0000.0000.0000.000
99A881ALA00.0740.02338.9410.0000.0000.0000.0000.0000.000
100A882LYS10.9470.97836.338-0.074-0.0740.0000.0000.0000.000
101A883ASP-1-0.819-0.91538.7280.0480.0480.0000.0000.0000.000
102A884LYS10.9740.98735.515-0.036-0.0360.0000.0000.0000.000
103A885ALA0-0.016-0.01435.058-0.002-0.0020.0000.0000.0000.000
104A886ARG10.9220.95735.666-0.044-0.0440.0000.0000.0000.000
105A887ARG10.9010.96137.236-0.024-0.0240.0000.0000.0000.000
106A888ARG10.9470.96926.427-0.077-0.0770.0000.0000.0000.000
107A889SER0-0.038-0.02733.2090.0010.0010.0000.0000.0000.000
108A890ILE00.0150.01134.8410.0010.0010.0000.0000.0000.000
109A891GLY00.0270.01033.731-0.003-0.0030.0000.0000.0000.000
110A892ASN00.0260.00029.134-0.005-0.0050.0000.0000.0000.000
111A893ILE00.0200.00431.768-0.001-0.0010.0000.0000.0000.000
112A894LYS10.9410.99634.3660.0030.0030.0000.0000.0000.000
113A895PHE00.003-0.00926.050-0.005-0.0050.0000.0000.0000.000
114A896ILE00.014-0.00629.566-0.002-0.0020.0000.0000.0000.000
115A897GLY00.0430.01131.4780.0010.0010.0000.0000.0000.000
116A898GLU-1-0.911-0.96032.274-0.009-0.0090.0000.0000.0000.000
117A899LEU0-0.033-0.03126.825-0.003-0.0030.0000.0000.0000.000
118A900PHE0-0.012-0.01130.980-0.001-0.0010.0000.0000.0000.000
119A901LYS10.9280.97333.469-0.002-0.0020.0000.0000.0000.000
120A902LEU0-0.041-0.01131.328-0.005-0.0050.0000.0000.0000.000
121A903LYS10.9170.95132.106-0.023-0.0230.0000.0000.0000.000
122A904MET0-0.095-0.01727.5460.0040.0040.0000.0000.0000.000
123A905LEU00.006-0.00127.5720.0100.0100.0000.0000.0000.000
124A906THR00.0370.01330.569-0.006-0.0060.0000.0000.0000.000
125A907GLU-1-0.832-0.93733.0700.0450.0450.0000.0000.0000.000
126A908ALA0-0.051-0.02334.106-0.001-0.0010.0000.0000.0000.000
127A909ILE00.0410.02830.3350.0020.0020.0000.0000.0000.000
128A910MET00.0080.01233.734-0.001-0.0010.0000.0000.0000.000
129A911HIS00.0290.03136.624-0.002-0.0020.0000.0000.0000.000
130A912ASP-1-0.879-0.92133.7070.0920.0920.0000.0000.0000.000
131A913CYS0-0.112-0.05834.858-0.002-0.0020.0000.0000.0000.000
132A914VAL00.0340.02237.210-0.003-0.0030.0000.0000.0000.000
133A915VAL00.0380.02339.687-0.002-0.0020.0000.0000.0000.000
134A916LYS10.7770.89336.299-0.068-0.0680.0000.0000.0000.000
135A917LEU0-0.051-0.03739.463-0.002-0.0020.0000.0000.0000.000
136A918LEU0-0.0020.00341.751-0.003-0.0030.0000.0000.0000.000
137A919LYS10.8430.96037.626-0.077-0.0770.0000.0000.0000.000
138A920ASN0-0.065-0.03739.7720.0030.0030.0000.0000.0000.000
139A921HIS00.0810.04643.995-0.001-0.0010.0000.0000.0000.000
140A922ASP-1-0.774-0.86644.1580.0280.0280.0000.0000.0000.000
141A923GLU-1-0.855-0.95946.6320.0130.0130.0000.0000.0000.000
142A924GLU-1-0.892-0.95441.6670.0150.0150.0000.0000.0000.000
143A925SER0-0.051-0.04042.3940.0000.0000.0000.0000.0000.000
144A926LEU00.0580.02343.4470.0000.0000.0000.0000.0000.000
145A927GLU-1-0.768-0.86245.6540.0050.0050.0000.0000.0000.000
146A928CYS0-0.049-0.02439.977-0.002-0.0020.0000.0000.0000.000
147A929LEU0-0.001-0.00442.5010.0000.0000.0000.0000.0000.000
148A930CYS00.0250.01243.9400.0000.0000.0000.0000.0000.000
149A931ARG10.8610.94943.467-0.004-0.0040.0000.0000.0000.000
150A932LEU0-0.032-0.01438.160-0.001-0.0010.0000.0000.0000.000
151A933LEU00.025-0.00842.125-0.001-0.0010.0000.0000.0000.000
152A934THR0-0.013-0.00844.719-0.001-0.0010.0000.0000.0000.000
153A935THR0-0.082-0.03941.138-0.003-0.0030.0000.0000.0000.000
154A936ILE0-0.019-0.01538.930-0.001-0.0010.0000.0000.0000.000
155A937GLY00.0170.01942.4340.0030.0030.0000.0000.0000.000
156A938LYS10.9990.97945.261-0.009-0.0090.0000.0000.0000.000
157A939ASP-1-0.985-0.97241.1300.0190.0190.0000.0000.0000.000
158A940LEU0-0.021-0.01838.9430.0040.0040.0000.0000.0000.000
159A941ASP-1-0.803-0.88242.6100.0350.0350.0000.0000.0000.000
160A942PHE00.0790.03543.050-0.001-0.0010.0000.0000.0000.000
161A943GLU-1-0.792-0.92745.8570.0340.0340.0000.0000.0000.000
162A944LYS10.8180.91144.442-0.044-0.0440.0000.0000.0000.000
163A945ALA0-0.059-0.03543.3950.0040.0040.0000.0000.0000.000
164A946LYS10.8910.97345.354-0.030-0.0300.0000.0000.0000.000
165A947PRO00.0780.04547.411-0.001-0.0010.0000.0000.0000.000
166A948ARG10.9680.97639.957-0.062-0.0620.0000.0000.0000.000
167A949MET00.0040.03044.2520.0000.0000.0000.0000.0000.000
168A950ASP-1-0.852-0.91247.5760.0340.0340.0000.0000.0000.000
169A951GLN0-0.055-0.01547.6680.0000.0000.0000.0000.0000.000
170A952TYR0-0.019-0.03441.9410.0000.0000.0000.0000.0000.000
171A953PHE00.014-0.02647.643-0.001-0.0010.0000.0000.0000.000
172A954ASN00.0390.03651.245-0.003-0.0030.0000.0000.0000.000
173A955GLN0-0.046-0.03147.1540.0000.0000.0000.0000.0000.000
174A956MET0-0.019-0.01147.512-0.001-0.0010.0000.0000.0000.000
175A957GLU-1-0.880-0.92751.9090.0240.0240.0000.0000.0000.000
176A958LYS10.9490.98954.230-0.032-0.0320.0000.0000.0000.000
177A959ILE0-0.064-0.05449.759-0.001-0.0010.0000.0000.0000.000
178A960VAL00.016-0.00354.225-0.002-0.0020.0000.0000.0000.000
179A961LYS10.9510.96856.808-0.026-0.0260.0000.0000.0000.000
180A962GLU-1-0.930-0.95657.2500.0260.0260.0000.0000.0000.000
181A963ARG10.9890.99557.420-0.015-0.0150.0000.0000.0000.000
182A964LYS10.8210.94453.536-0.028-0.0280.0000.0000.0000.000
183A965THR00.0160.00652.4210.0000.0000.0000.0000.0000.000
184A966SER00.0820.04753.321-0.001-0.0010.0000.0000.0000.000
185A967SER00.021-0.01455.9800.0010.0010.0000.0000.0000.000
186A968ARG10.9400.95948.906-0.007-0.0070.0000.0000.0000.000
187A969ILE00.0330.01249.5700.0000.0000.0000.0000.0000.000
188A970ARG10.8590.93553.042-0.015-0.0150.0000.0000.0000.000
189A971PHE00.0340.01955.7840.0010.0010.0000.0000.0000.000
190A972MET0-0.048-0.01849.3030.0000.0000.0000.0000.0000.000
191A973LEU0-0.011-0.02649.8730.0010.0010.0000.0000.0000.000
192A974GLN0-0.026-0.02952.6840.0000.0000.0000.0000.0000.000
193A975ASP-1-0.828-0.88353.1370.0080.0080.0000.0000.0000.000
194A976VAL0-0.063-0.02848.5680.0000.0000.0000.0000.0000.000
195A977ILE0-0.050-0.04251.6740.0010.0010.0000.0000.0000.000
196A978ASP-1-0.870-0.92454.1860.0140.0140.0000.0000.0000.000
197A979LEU0-0.022-0.02050.0100.0000.0000.0000.0000.0000.000
198A980ARG10.8130.89950.649-0.030-0.0300.0000.0000.0000.000
199A981LEU0-0.043-0.01653.0710.0000.0000.0000.0000.0000.000
200A982CYS0-0.0110.00655.955-0.001-0.0010.0000.0000.0000.000
201A983ASN0-0.052-0.03454.0280.0000.0000.0000.0000.0000.000
202A984TRP0-0.094-0.07648.172-0.001-0.0010.0000.0000.0000.000
203A985VAL0-0.0300.00151.608-0.002-0.0020.0000.0000.0000.000
204A986SER00.002-0.00153.4100.0000.0000.0000.0000.0000.000