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: VR781

Calculation Name: 3HD0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HD0

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X2H9

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2806108.102905
FMO2-HF: Nuclear repulsion 2719406.600149
FMO2-HF: Total energy -86701.502756
FMO2-MP2: Total energy -86957.835015


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-38.44-24.82318.637-9.976-22.278-0.091
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.085 / q_NPA : -0.037
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].
3A3TYR0-0.078-0.0303.240-3.623-1.3000.044-1.270-1.096-0.002
4A4ARG10.9480.9956.048-0.050-0.0500.0000.0000.0000.000
5A5GLN0-0.020-0.0369.655-0.255-0.2550.0000.0000.0000.000
6A6LEU0-0.062-0.04112.3630.1220.1220.0000.0000.0000.000
7A7HIS10.8070.91414.8110.4590.4590.0000.0000.0000.000
8A8ARG10.9821.00716.1350.1850.1850.0000.0000.0000.000
9A9TRP00.0720.02312.7240.0960.0960.0000.0000.0000.000
10A10ASP-1-0.915-0.93818.186-0.347-0.3470.0000.0000.0000.000
11A11LEU0-0.054-0.03021.2670.0480.0480.0000.0000.0000.000
12A12PRO00.0900.03823.668-0.017-0.0170.0000.0000.0000.000
13A13PRO00.0570.02326.0000.0010.0010.0000.0000.0000.000
14A14GLU-1-0.877-0.94626.908-0.172-0.1720.0000.0000.0000.000
15A15GLU-1-0.893-0.95925.933-0.118-0.1180.0000.0000.0000.000
16A16ALA0-0.024-0.00522.7680.0050.0050.0000.0000.0000.000
17A17ILE0-0.003-0.01823.2830.0020.0020.0000.0000.0000.000
18A18LYS10.9330.97025.5770.1190.1190.0000.0000.0000.000
19A19VAL00.0240.02119.5360.0220.0220.0000.0000.0000.000
20A20GLN00.0160.00120.9140.0480.0480.0000.0000.0000.000
21A21ASN00.0250.01521.8910.0210.0210.0000.0000.0000.000
22A22GLU-1-0.867-0.93222.2710.0030.0030.0000.0000.0000.000
23A23LEU0-0.044-0.03316.5600.0340.0340.0000.0000.0000.000
24A24ARG10.9340.97119.2680.0930.0930.0000.0000.0000.000
25A25LYS10.8850.95321.4190.0030.0030.0000.0000.0000.000
26A26LYS10.9210.95316.517-0.100-0.1000.0000.0000.0000.000
27A27ILE00.0040.01816.5090.0510.0510.0000.0000.0000.000
28A28LYS10.8520.93217.265-0.216-0.2160.0000.0000.0000.000
29A29LEU0-0.0080.00918.1080.0230.0230.0000.0000.0000.000
30A30THR0-0.004-0.01718.2580.0010.0010.0000.0000.0000.000
31A31PRO00.0320.02718.9540.0100.0100.0000.0000.0000.000
32A32TYR00.002-0.01013.2420.0680.0680.0000.0000.0000.000
33A33GLU-1-0.952-0.98918.3120.2930.2930.0000.0000.0000.000
34A34GLY00.0240.02718.6670.0570.0570.0000.0000.0000.000
35A35GLU-1-0.896-0.96317.8220.2030.2030.0000.0000.0000.000
36A36PRO0-0.066-0.01912.3960.0550.0550.0000.0000.0000.000
37A37GLU-1-0.891-0.94311.0160.5430.5430.0000.0000.0000.000
38A38TYR0-0.019-0.0207.303-0.343-0.3430.0000.0000.0000.000
39A39VAL00.0020.0049.7870.1780.1780.0000.0000.0000.000
40A40ALA00.0170.0087.378-0.182-0.1820.0000.0000.0000.000
41A41GLY0-0.041-0.0209.5050.2000.2000.0000.0000.0000.000
42A42VAL0-0.035-0.0209.681-0.240-0.2400.0000.0000.0000.000
43A43ASP-1-0.808-0.87812.305-0.537-0.5370.0000.0000.0000.000
44A44LEU0-0.034-0.00512.198-0.151-0.1510.0000.0000.0000.000
45A45SER00.0110.00415.8920.1320.1320.0000.0000.0000.000
46A46PHE00.031-0.01218.426-0.056-0.0560.0000.0000.0000.000
47A47PRO0-0.0080.01020.2480.0590.0590.0000.0000.0000.000
48A48GLY0-0.021-0.02023.2920.0510.0510.0000.0000.0000.000
49A49LYS10.8980.95025.0810.3690.3690.0000.0000.0000.000
50A50GLU-1-0.899-0.95523.851-0.380-0.3800.0000.0000.0000.000
51A51GLU-1-0.884-0.91620.125-0.736-0.7360.0000.0000.0000.000
52A52GLY00.018-0.01917.9100.0340.0340.0000.0000.0000.000
53A53LEU0-0.041-0.02615.178-0.029-0.0290.0000.0000.0000.000
54A54ALA0-0.0240.00911.1090.0710.0710.0000.0000.0000.000
55A55VAL00.0200.01012.172-0.178-0.1780.0000.0000.0000.000
56A56ILE0-0.0120.0006.2600.1400.1400.0000.0000.0000.000
57A57VAL0-0.044-0.01610.141-0.075-0.0750.0000.0000.0000.000
58A58VAL00.0360.0135.7570.1130.1130.0000.0000.0000.000
59A59LEU0-0.038-0.0209.0600.0640.0640.0000.0000.0000.000
60A60GLU-1-0.877-0.93911.0490.0620.0620.0000.0000.0000.000
61A61TYR0-0.044-0.00413.153-0.057-0.0570.0000.0000.0000.000
62A62PRO00.0510.00815.7150.0420.0420.0000.0000.0000.000
63A63SER0-0.040-0.02616.765-0.053-0.0530.0000.0000.0000.000
64A64PHE0-0.006-0.02316.066-0.023-0.0230.0000.0000.0000.000
65A65LYS10.8990.96414.4620.1570.1570.0000.0000.0000.000
66A66ILE00.0160.00013.042-0.004-0.0040.0000.0000.0000.000
67A67LEU0-0.053-0.0129.2130.0330.0330.0000.0000.0000.000
68A68GLU-1-0.807-0.9175.754-3.795-3.7950.0000.0000.0000.000
69A69VAL0-0.023-0.0139.6790.0840.0840.0000.0000.0000.000
70A70VAL0-0.0090.0186.6060.1850.1850.0000.0000.0000.000
71A71SER0-0.034-0.0409.8190.2340.2340.0000.0000.0000.000
72A72GLU-1-0.843-0.92310.150-1.727-1.7270.0000.0000.0000.000
73A73ARG10.9430.97112.2600.8920.8920.0000.0000.0000.000
74A74GLY00.017-0.00214.636-0.088-0.0880.0000.0000.0000.000
75A75GLU-1-0.889-0.93016.374-0.457-0.4570.0000.0000.0000.000
76A76ILE0-0.123-0.06917.747-0.048-0.0480.0000.0000.0000.000
77A77THR00.0360.02120.3670.0500.0500.0000.0000.0000.000
78A78PHE00.0200.01021.2090.0450.0450.0000.0000.0000.000
79A79PRO00.0860.03622.973-0.017-0.0170.0000.0000.0000.000
80A80TYR0-0.034-0.02424.2800.0000.0000.0000.0000.0000.000
81A81ILE00.0520.01925.0370.0300.0300.0000.0000.0000.000
82A82PRO00.0560.02825.288-0.019-0.0190.0000.0000.0000.000
83A83GLY00.0020.00024.7430.0220.0220.0000.0000.0000.000
84A84LEU0-0.009-0.02622.6760.0060.0060.0000.0000.0000.000
85A85LEU00.0200.02620.678-0.026-0.0260.0000.0000.0000.000
86A86ALA00.0350.01516.455-0.049-0.0490.0000.0000.0000.000
87A87PHE0-0.047-0.03016.553-0.080-0.0800.0000.0000.0000.000
88A88ARG10.9010.96818.5640.4630.4630.0000.0000.0000.000
89A89GLU-1-0.924-0.96815.951-0.694-0.6940.0000.0000.0000.000
90A90GLY00.003-0.00212.872-0.153-0.1530.0000.0000.0000.000
91A91PRO0-0.013-0.00911.512-0.261-0.2610.0000.0000.0000.000
92A92LEU00.0170.04011.313-0.249-0.2490.0000.0000.0000.000
93A93PHE00.0630.0217.041-0.305-0.3050.0000.0000.0000.000
94A94LEU0-0.046-0.0176.908-0.494-0.4940.0000.0000.0000.000
95A95LYS10.8800.9526.5050.9750.9750.0000.0000.0000.000
96A96ALA00.0080.0046.892-0.410-0.4100.0000.0000.0000.000
97A97TRP0-0.022-0.0402.633-4.174-1.4362.384-1.080-4.042-0.009
98A98GLU-1-0.893-0.9632.355-8.572-6.6742.163-1.564-2.497-0.015
99A99LYS10.8220.9292.2510.4661.1073.057-1.684-2.014-0.023
100A100LEU0-0.056-0.0152.1790.2211.6111.961-0.944-2.4070.000
101A101ARG10.9360.9612.266-7.978-4.6172.758-2.660-3.459-0.035
102A102THR0-0.044-0.0103.005-0.5390.7550.351-0.597-1.048-0.006
103A103LYS10.9650.9742.468-13.758-12.3125.748-2.211-4.9830.000
104A104PRO0-0.029-0.0203.2390.560-0.9140.1712.034-0.732-0.001
105A105ASP-1-0.741-0.8656.1972.3592.3590.0000.0000.0000.000
106A106VAL0-0.038-0.0319.334-0.101-0.1010.0000.0000.0000.000
107A107VAL0-0.044-0.0236.574-0.199-0.1990.0000.0000.0000.000
108A108VAL0-0.022-0.0039.8320.0930.0930.0000.0000.0000.000
109A109PHE00.011-0.0189.428-0.118-0.1180.0000.0000.0000.000
110A110ASP-1-0.897-0.94914.221-0.385-0.3850.0000.0000.0000.000
111A111GLY00.0410.01417.589-0.027-0.0270.0000.0000.0000.000
112A112GLN0-0.110-0.06819.3300.0750.0750.0000.0000.0000.000
113A113GLY00.0400.01318.152-0.051-0.0510.0000.0000.0000.000
114A114LEU00.0100.01919.228-0.003-0.0030.0000.0000.0000.000
115A115ALA0-0.008-0.00522.0990.0070.0070.0000.0000.0000.000
116A116HIS00.0050.01022.613-0.009-0.0090.0000.0000.0000.000
117A117PRO00.0120.01624.8190.0190.0190.0000.0000.0000.000
118A118ARG10.8410.91625.0230.2010.2010.0000.0000.0000.000
119A119LYS10.9040.94623.6180.0610.0610.0000.0000.0000.000
120A120LEU00.002-0.02018.2140.0150.0150.0000.0000.0000.000
121A121GLY0-0.0170.00019.560-0.046-0.0460.0000.0000.0000.000
122A122ILE00.0220.00314.3860.0320.0320.0000.0000.0000.000
123A123ALA00.0540.03013.854-0.069-0.0690.0000.0000.0000.000
124A124SER00.0240.03313.6890.0200.0200.0000.0000.0000.000
125A125HIS0-0.0040.00614.3370.0170.0170.0000.0000.0000.000
126A126MET00.0020.02010.228-0.051-0.0510.0000.0000.0000.000
127A127GLY00.0610.0419.720-0.076-0.0760.0000.0000.0000.000
128A128LEU0-0.072-0.04410.3620.1740.1740.0000.0000.0000.000
129A129PHE0-0.030-0.0178.8870.1800.1800.0000.0000.0000.000
130A130ILE0-0.002-0.0125.1040.0780.0780.0000.0000.0000.000
131A131GLU-1-0.918-0.9465.8551.5861.5860.0000.0000.0000.000
132A132ILE0-0.0050.0075.7020.4580.4580.0000.0000.0000.000
133A133PRO00.0010.0088.861-0.401-0.4010.0000.0000.0000.000
134A134THR0-0.020-0.0209.927-0.057-0.0570.0000.0000.0000.000
135A135ILE0-0.036-0.02812.4360.0460.0460.0000.0000.0000.000
136A136GLY0-0.0050.00514.906-0.099-0.0990.0000.0000.0000.000
137A137VAL0-0.026-0.01617.4660.0640.0640.0000.0000.0000.000
138A138ALA00.0810.04419.720-0.048-0.0480.0000.0000.0000.000
139A139LYS10.9150.94322.4180.4170.4170.0000.0000.0000.000
140A140SER00.0250.00025.1640.0290.0290.0000.0000.0000.000
141A141ARG10.9260.97626.0480.1350.1350.0000.0000.0000.000
142A142LEU0-0.023-0.00222.481-0.004-0.0040.0000.0000.0000.000
143A143TYR0-0.039-0.03826.462-0.003-0.0030.0000.0000.0000.000
144A144GLY00.0750.03828.1790.0030.0030.0000.0000.0000.000
145A145THR0-0.055-0.03230.426-0.009-0.0090.0000.0000.0000.000
146A146PHE00.0840.02531.9790.0020.0020.0000.0000.0000.000
147A147LYS10.9890.99834.1060.0570.0570.0000.0000.0000.000
148A148MET0-0.0050.00834.080-0.002-0.0020.0000.0000.0000.000
149A149PRO00.0230.03532.1370.0060.0060.0000.0000.0000.000
150A150GLU-1-0.859-0.93635.453-0.049-0.0490.0000.0000.0000.000
151A151ASP-1-0.868-0.91936.060-0.105-0.1050.0000.0000.0000.000
152A152LYS10.9981.00036.2220.0390.0390.0000.0000.0000.000
153A153ARG10.9140.94730.9300.0820.0820.0000.0000.0000.000
154A154CYS0-0.050-0.04129.5850.0080.0080.0000.0000.0000.000
155A155SER00.0360.02831.3560.0140.0140.0000.0000.0000.000
156A156TRP0-0.051-0.03929.788-0.012-0.0120.0000.0000.0000.000
157A157SER00.0130.00331.0550.0100.0100.0000.0000.0000.000
158A158TYR00.0000.00028.723-0.010-0.0100.0000.0000.0000.000
159A159LEU0-0.079-0.03126.332-0.007-0.0070.0000.0000.0000.000
160A160TYR00.0180.00129.6570.0080.0080.0000.0000.0000.000
161A161ASP-1-0.862-0.92429.869-0.096-0.0960.0000.0000.0000.000
162A162GLY0-0.0130.00031.8650.0090.0090.0000.0000.0000.000
163A163GLU-1-0.919-0.96835.268-0.012-0.0120.0000.0000.0000.000
164A164GLU-1-0.917-0.94430.5710.0120.0120.0000.0000.0000.000
165A165ILE0-0.010-0.00527.712-0.016-0.0160.0000.0000.0000.000
166A166ILE0-0.064-0.03826.1260.0050.0050.0000.0000.0000.000
167A167GLY00.0410.00324.690-0.015-0.0150.0000.0000.0000.000
168A168CYS0-0.066-0.02024.7840.0150.0150.0000.0000.0000.000
169A169VAL00.0210.01726.184-0.019-0.0190.0000.0000.0000.000
170A170ILE00.0350.00824.8740.0160.0160.0000.0000.0000.000
171A171ARG10.8190.89628.6030.0830.0830.0000.0000.0000.000
172A172THR0-0.0310.00026.6230.0080.0080.0000.0000.0000.000
173A173LYS10.9140.95728.7390.1510.1510.0000.0000.0000.000
174A174GLU-1-0.816-0.89431.236-0.102-0.1020.0000.0000.0000.000
175A175GLY00.010-0.00234.961-0.006-0.0060.0000.0000.0000.000
176A176SER0-0.090-0.03931.545-0.015-0.0150.0000.0000.0000.000
177A177ALA00.0220.01731.2130.0090.0090.0000.0000.0000.000
178A178PRO0-0.0010.00829.572-0.008-0.0080.0000.0000.0000.000
179A179ILE0-0.026-0.00822.766-0.018-0.0180.0000.0000.0000.000
180A180PHE0-0.001-0.00724.6850.0290.0290.0000.0000.0000.000
181A181VAL00.0390.02720.461-0.034-0.0340.0000.0000.0000.000
182A182SER00.004-0.00220.6730.0270.0270.0000.0000.0000.000
183A183PRO00.0180.02918.490-0.035-0.0350.0000.0000.0000.000
184A184GLY00.0260.01015.436-0.044-0.0440.0000.0000.0000.000
185A185HIS00.0020.00312.135-0.054-0.0540.0000.0000.0000.000
186A186LEU0-0.0060.00611.8580.0490.0490.0000.0000.0000.000
187A187MET00.0100.01815.1480.0020.0020.0000.0000.0000.000
188A188ASP-1-0.783-0.88917.7950.1240.1240.0000.0000.0000.000
189A189VAL00.058-0.00121.121-0.013-0.0130.0000.0000.0000.000
190A190GLU-1-0.868-0.92623.4620.0300.0300.0000.0000.0000.000
191A191SER00.0280.01919.7170.0000.0000.0000.0000.0000.000
192A192SER0-0.022-0.01119.213-0.019-0.0190.0000.0000.0000.000
193A193LYS10.9040.95420.183-0.038-0.0380.0000.0000.0000.000
194A194ARG10.8010.90020.113-0.223-0.2230.0000.0000.0000.000
195A195LEU00.0680.03016.163-0.021-0.0210.0000.0000.0000.000
196A196ILE00.0210.01217.535-0.033-0.0330.0000.0000.0000.000
197A197LYS10.8120.91420.3220.0030.0030.0000.0000.0000.000
198A198ALA00.0000.01220.282-0.016-0.0160.0000.0000.0000.000
199A199PHE00.0220.00915.193-0.023-0.0230.0000.0000.0000.000
200A200THR0-0.019-0.01119.723-0.064-0.0640.0000.0000.0000.000
201A201LEU00.0040.02022.3180.0240.0240.0000.0000.0000.000
202A202PRO0-0.0040.03124.951-0.007-0.0070.0000.0000.0000.000
203A203GLY00.028-0.01128.6230.0000.0000.0000.0000.0000.000
204A204ARG10.8560.91323.6320.2120.2120.0000.0000.0000.000
205A205ARG10.8590.90426.6960.2270.2270.0000.0000.0000.000
206A206ILE0-0.027-0.02820.7790.0100.0100.0000.0000.0000.000
207A207PRO00.0530.03218.7370.0010.0010.0000.0000.0000.000
208A208GLU-1-0.711-0.85718.212-0.346-0.3460.0000.0000.0000.000
209A209PRO00.0370.03113.575-0.057-0.0570.0000.0000.0000.000
210A210THR00.0580.01215.346-0.076-0.0760.0000.0000.0000.000
211A211ARG10.7810.88416.9710.3110.3110.0000.0000.0000.000
212A212LEU0-0.013-0.01016.396-0.014-0.0140.0000.0000.0000.000
213A213ALA00.0510.02814.183-0.033-0.0330.0000.0000.0000.000
214A214HIS0-0.053-0.01715.8840.0350.0350.0000.0000.0000.000
215A215ILE0-0.049-0.02119.2240.0120.0120.0000.0000.0000.000
216A216TYR0-0.030-0.03016.2540.0240.0240.0000.0000.0000.000
217A217THR0-0.008-0.03817.395-0.055-0.0550.0000.0000.0000.000
218A218GLN00.013-0.00318.6120.0280.0280.0000.0000.0000.000
219A219ARG10.8160.93519.6270.5760.5760.0000.0000.0000.000
220A220LEU0-0.044-0.01416.4790.0180.0180.0000.0000.0000.000