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

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FMODB ID: GN9L1

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2805710.56232
FMO2-HF: Nuclear repulsion 2719006.480573
FMO2-HF: Total energy -86704.081747
FMO2-MP2: Total energy -86960.272348


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.
-40.527-32.4229.469-12.373-25.202-0.094
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 : -0.077 / q_NPA : -0.031
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].
3A3TYR0-0.100-0.0742.864-5.217-1.9820.267-1.787-1.714-0.008
4A4ARG10.8610.8955.711-0.154-0.1540.0000.0000.0000.000
5A5GLN00.017-0.0169.534-0.268-0.2680.0000.0000.0000.000
6A6LEU0-0.046-0.02712.0920.0880.0880.0000.0000.0000.000
7A7HIS10.7760.88014.6770.3540.3540.0000.0000.0000.000
8A8ARG10.8910.94316.3920.1040.1040.0000.0000.0000.000
9A9TRP00.0530.03612.3410.0720.0720.0000.0000.0000.000
10A10ASP-1-0.802-0.88017.925-0.207-0.2070.0000.0000.0000.000
11A11LEU0-0.046-0.03621.1980.0400.0400.0000.0000.0000.000
12A12PRO00.0800.04723.912-0.018-0.0180.0000.0000.0000.000
13A13PRO00.0450.01225.950-0.006-0.0060.0000.0000.0000.000
14A14GLU-1-0.840-0.92626.761-0.142-0.1420.0000.0000.0000.000
15A15GLU-1-0.806-0.89025.774-0.070-0.0700.0000.0000.0000.000
16A16ALA00.0150.01222.5890.0050.0050.0000.0000.0000.000
17A17ILE0-0.011-0.01623.076-0.005-0.0050.0000.0000.0000.000
18A18LYS10.7920.87325.3810.0780.0780.0000.0000.0000.000
19A19VAL00.0240.01019.6600.0180.0180.0000.0000.0000.000
20A20GLN00.0160.01120.6260.0300.0300.0000.0000.0000.000
21A21ASN00.0410.02021.9100.0100.0100.0000.0000.0000.000
22A22GLU-1-0.819-0.88622.0530.0400.0400.0000.0000.0000.000
23A23LEU0-0.0240.00116.1050.0360.0360.0000.0000.0000.000
24A24ARG10.9230.95919.2550.0980.0980.0000.0000.0000.000
25A25LYS10.8320.90121.646-0.003-0.0030.0000.0000.0000.000
26A26LYS10.8780.93417.143-0.040-0.0400.0000.0000.0000.000
27A27ILE00.0160.02216.5260.0480.0480.0000.0000.0000.000
28A28LYS10.8060.89717.476-0.156-0.1560.0000.0000.0000.000
29A29LEU00.0020.00918.0360.0110.0110.0000.0000.0000.000
30A30THR00.0170.00917.7980.0040.0040.0000.0000.0000.000
31A31PRO00.0200.00919.167-0.015-0.0150.0000.0000.0000.000
32A32TYR0-0.003-0.00613.1620.0480.0480.0000.0000.0000.000
33A33GLU-1-0.943-0.96818.3830.1770.1770.0000.0000.0000.000
34A34GLY00.0330.02718.8440.0430.0430.0000.0000.0000.000
35A35GLU-1-0.861-0.93017.8550.0370.0370.0000.0000.0000.000
36A36PRO0-0.074-0.02412.5130.0660.0660.0000.0000.0000.000
37A37GLU-1-0.838-0.88511.5350.1650.1650.0000.0000.0000.000
38A38TYR0-0.066-0.0718.150-0.356-0.3560.0000.0000.0000.000
39A39VAL0-0.013-0.0079.9690.1380.1380.0000.0000.0000.000
40A40ALA00.0130.0087.467-0.197-0.1970.0000.0000.0000.000
41A41GLY0-0.041-0.0229.5820.2730.2730.0000.0000.0000.000
42A42VAL0-0.037-0.0119.931-0.214-0.2140.0000.0000.0000.000
43A43ASP-1-0.803-0.87912.642-0.552-0.5520.0000.0000.0000.000
44A44LEU0-0.032-0.01512.222-0.159-0.1590.0000.0000.0000.000
45A45SER0-0.0180.00116.1010.1260.1260.0000.0000.0000.000
46A46PHE00.039-0.00618.852-0.032-0.0320.0000.0000.0000.000
47A47PRO00.0150.02020.5490.0520.0520.0000.0000.0000.000
48A48GLY00.0040.01222.7910.0480.0480.0000.0000.0000.000
49A49LYS10.8190.90424.5660.3630.3630.0000.0000.0000.000
50A50GLU-1-0.843-0.92423.420-0.323-0.3230.0000.0000.0000.000
51A51GLU-1-0.805-0.89318.727-0.653-0.6530.0000.0000.0000.000
52A52GLY0-0.009-0.00718.1070.0290.0290.0000.0000.0000.000
53A53LEU0-0.028-0.01114.986-0.017-0.0170.0000.0000.0000.000
54A54ALA0-0.0070.01711.4840.0510.0510.0000.0000.0000.000
55A55VAL00.007-0.01312.276-0.114-0.1140.0000.0000.0000.000
56A56ILE00.003-0.0016.5970.1340.1340.0000.0000.0000.000
57A57VAL0-0.025-0.00210.197-0.108-0.1080.0000.0000.0000.000
58A58VAL00.0310.0005.872-0.029-0.0290.0000.0000.0000.000
59A59LEU0-0.041-0.0199.2820.0970.0970.0000.0000.0000.000
60A60GLU-1-0.698-0.80011.369-0.258-0.2580.0000.0000.0000.000
61A61TYR0-0.104-0.04313.127-0.013-0.0130.0000.0000.0000.000
62A62PRO00.0460.01115.6800.0480.0480.0000.0000.0000.000
63A63SER0-0.071-0.08817.175-0.040-0.0400.0000.0000.0000.000
64A64PHE0-0.031-0.02516.373-0.012-0.0120.0000.0000.0000.000
65A65LYS10.8220.91815.5930.2920.2920.0000.0000.0000.000
66A66ILE00.012-0.00312.998-0.035-0.0350.0000.0000.0000.000
67A67LEU0-0.0010.0089.9050.0810.0810.0000.0000.0000.000
68A68GLU-1-0.782-0.8525.782-4.060-4.0600.0000.0000.0000.000
69A69VAL0-0.027-0.0209.9150.1020.1020.0000.0000.0000.000
70A70VAL0-0.0050.0176.6740.1640.1640.0000.0000.0000.000
71A71SER0-0.008-0.0079.9890.0820.0820.0000.0000.0000.000
72A72GLU-1-0.819-0.8819.727-1.305-1.3050.0000.0000.0000.000
73A73ARG10.8660.91211.8490.7230.7230.0000.0000.0000.000
74A74GLY00.008-0.00613.993-0.061-0.0610.0000.0000.0000.000
75A75GLU-1-0.893-0.94516.290-0.351-0.3510.0000.0000.0000.000
76A76ILE0-0.099-0.04817.341-0.023-0.0230.0000.0000.0000.000
77A77THR00.0180.00320.1550.0440.0440.0000.0000.0000.000
78A78PHE00.0070.01421.0110.0310.0310.0000.0000.0000.000
79A79PRO00.0720.03222.864-0.018-0.0180.0000.0000.0000.000
80A80TYR0-0.015-0.01923.840-0.007-0.0070.0000.0000.0000.000
81A81ILE00.0470.02324.9540.0280.0280.0000.0000.0000.000
82A82PRO00.0630.01825.032-0.021-0.0210.0000.0000.0000.000
83A83GLY0-0.005-0.00224.3000.0190.0190.0000.0000.0000.000
84A84LEU0-0.024-0.00522.4410.0060.0060.0000.0000.0000.000
85A85LEU00.0070.01620.848-0.015-0.0150.0000.0000.0000.000
86A86ALA00.0410.02016.390-0.044-0.0440.0000.0000.0000.000
87A87PHE0-0.015-0.01216.222-0.069-0.0690.0000.0000.0000.000
88A88ARG10.8570.94818.3930.4260.4260.0000.0000.0000.000
89A89GLU-1-0.905-0.96215.471-0.631-0.6310.0000.0000.0000.000
90A90GLY00.008-0.00912.420-0.156-0.1560.0000.0000.0000.000
91A91PRO0-0.031-0.01911.419-0.230-0.2300.0000.0000.0000.000
92A92LEU00.0190.01811.458-0.134-0.1340.0000.0000.0000.000
93A93PHE00.0310.0037.213-0.286-0.2860.0000.0000.0000.000
94A94LEU0-0.005-0.0036.489-0.603-0.6030.0000.0000.0000.000
95A95LYS10.8120.9036.0930.6900.6900.0000.0000.0000.000
96A96ALA00.0120.0066.884-0.051-0.0510.0000.0000.0000.000
97A97TRP0-0.012-0.0352.571-4.588-1.9163.811-1.451-5.031-0.010
98A98GLU-1-0.775-0.8632.251-11.269-9.7624.633-2.694-3.446-0.029
99A99LYS10.7970.8822.8015.9336.0450.7090.370-1.191-0.004
100A100LEU0-0.058-0.0082.1890.3881.7711.759-0.971-2.1720.001
101A101ARG10.8750.9082.027-8.915-7.0856.110-3.745-4.194-0.046
102A102THR0-0.043-0.0372.767-1.0340.2120.791-0.768-1.271-0.009
103A103LYS10.9550.9752.506-14.270-17.60611.252-2.268-5.6480.011
104A104PRO0-0.025-0.0133.1160.401-0.1410.1370.941-0.5350.000
105A105ASP-1-0.781-0.8826.4261.6941.6940.0000.0000.0000.000
106A106VAL0-0.040-0.0279.329-0.012-0.0120.0000.0000.0000.000
107A107VAL0-0.0110.0037.045-0.256-0.2560.0000.0000.0000.000
108A108VAL0-0.040-0.02010.0820.1560.1560.0000.0000.0000.000
109A109PHE00.0460.0069.525-0.112-0.1120.0000.0000.0000.000
110A110ASP-1-0.804-0.89314.492-0.397-0.3970.0000.0000.0000.000
111A111GLY00.0120.00417.919-0.024-0.0240.0000.0000.0000.000
112A112GLN0-0.063-0.05919.4850.0750.0750.0000.0000.0000.000
113A113GLY00.0050.00018.504-0.056-0.0560.0000.0000.0000.000
114A114LEU00.0530.04019.2370.0100.0100.0000.0000.0000.000
115A115ALA0-0.008-0.00622.1130.0160.0160.0000.0000.0000.000
116A116HIS0-0.027-0.01622.742-0.010-0.0100.0000.0000.0000.000
117A117PRO00.0140.01724.8920.0190.0190.0000.0000.0000.000
118A118ARG10.8240.90624.8070.1980.1980.0000.0000.0000.000
119A119LYS10.8230.90323.6360.0840.0840.0000.0000.0000.000
120A120LEU00.0270.01417.6070.0140.0140.0000.0000.0000.000
121A121GLY00.0000.00419.807-0.032-0.0320.0000.0000.0000.000
122A122ILE00.0310.01114.0450.0200.0200.0000.0000.0000.000
123A123ALA00.0580.03713.865-0.070-0.0700.0000.0000.0000.000
124A124SER00.0070.00513.5690.0000.0000.0000.0000.0000.000
125A125HIS0-0.031-0.00214.2850.0320.0320.0000.0000.0000.000
126A126MET0-0.0200.01510.107-0.051-0.0510.0000.0000.0000.000
127A127GLY00.0610.0369.677-0.092-0.0920.0000.0000.0000.000
128A128LEU0-0.074-0.04810.4200.1510.1510.0000.0000.0000.000
129A129PHE0-0.021-0.0078.7660.1840.1840.0000.0000.0000.000
130A130ILE00.0150.0055.0890.0630.0630.0000.0000.0000.000
131A131GLU-1-0.892-0.8935.7891.4411.4410.0000.0000.0000.000
132A132ILE00.0320.0285.4340.3590.3590.0000.0000.0000.000
133A133PRO00.0020.0028.793-0.352-0.3520.0000.0000.0000.000
134A134THR0-0.020-0.0109.985-0.108-0.1080.0000.0000.0000.000
135A135ILE0-0.011-0.00912.4670.0830.0830.0000.0000.0000.000
136A136GLY0-0.0120.00114.886-0.115-0.1150.0000.0000.0000.000
137A137VAL0-0.011-0.01017.5160.0730.0730.0000.0000.0000.000
138A138ALA00.0210.02119.959-0.047-0.0470.0000.0000.0000.000
139A139LYS10.8430.89821.4260.5320.5320.0000.0000.0000.000
140A140SER00.0010.00025.1770.0300.0300.0000.0000.0000.000
141A141ARG10.8790.95326.3360.1600.1600.0000.0000.0000.000
142A142LEU00.0250.01922.5760.0100.0100.0000.0000.0000.000
143A143TYR0-0.065-0.05926.5050.0030.0030.0000.0000.0000.000
144A144GLY00.0780.04228.2310.0000.0000.0000.0000.0000.000
145A145THR0-0.068-0.02430.410-0.004-0.0040.0000.0000.0000.000
146A146PHE00.1060.03432.1070.0010.0010.0000.0000.0000.000
147A147LYS10.9400.96834.2440.0910.0910.0000.0000.0000.000
148A148MET00.0250.02434.144-0.006-0.0060.0000.0000.0000.000
149A149PRO00.0250.03832.1660.0080.0080.0000.0000.0000.000
150A150GLU-1-0.717-0.83035.498-0.089-0.0890.0000.0000.0000.000
151A151ASP-1-0.809-0.90936.268-0.145-0.1450.0000.0000.0000.000
152A152LYS10.8720.93636.1910.0840.0840.0000.0000.0000.000
153A153ARG10.9060.93930.8270.1440.1440.0000.0000.0000.000
154A154CYS0-0.009-0.00829.0640.0130.0130.0000.0000.0000.000
155A155SER0-0.031-0.03131.3740.0090.0090.0000.0000.0000.000
156A156TRP0-0.030-0.02829.972-0.016-0.0160.0000.0000.0000.000
157A157SER00.0060.00831.2620.0120.0120.0000.0000.0000.000
158A158TYR00.003-0.03128.270-0.012-0.0120.0000.0000.0000.000
159A159LEU0-0.090-0.03626.475-0.005-0.0050.0000.0000.0000.000
160A160TYR00.0260.00829.4520.0020.0020.0000.0000.0000.000
161A161ASP-1-0.804-0.89629.706-0.105-0.1050.0000.0000.0000.000
162A162GLY00.0250.01531.8000.0090.0090.0000.0000.0000.000
163A163GLU-1-0.918-0.96134.889-0.031-0.0310.0000.0000.0000.000
164A164GLU-1-0.933-0.95730.168-0.015-0.0150.0000.0000.0000.000
165A165ILE0-0.019-0.00927.787-0.017-0.0170.0000.0000.0000.000
166A166ILE0-0.019-0.01525.9320.0040.0040.0000.0000.0000.000
167A167GLY00.0420.00524.427-0.023-0.0230.0000.0000.0000.000
168A168CYS0-0.069-0.01424.8640.0190.0190.0000.0000.0000.000
169A169VAL00.0120.01526.381-0.023-0.0230.0000.0000.0000.000
170A170ILE00.0340.00825.0250.0190.0190.0000.0000.0000.000
171A171ARG10.7680.88628.8950.1180.1180.0000.0000.0000.000
172A172THR0-0.047-0.03726.0980.0160.0160.0000.0000.0000.000
173A173LYS10.8660.92228.7020.1770.1770.0000.0000.0000.000
174A174GLU-1-0.781-0.86531.518-0.155-0.1550.0000.0000.0000.000
175A175GLY00.0470.02635.326-0.007-0.0070.0000.0000.0000.000
176A176SER0-0.068-0.04532.025-0.015-0.0150.0000.0000.0000.000
177A177ALA00.0380.03531.4120.0080.0080.0000.0000.0000.000
178A178PRO00.0020.01429.790-0.012-0.0120.0000.0000.0000.000
179A179ILE0-0.0090.01023.105-0.018-0.0180.0000.0000.0000.000
180A180PHE00.0110.00625.0450.0300.0300.0000.0000.0000.000
181A181VAL00.0190.01120.608-0.039-0.0390.0000.0000.0000.000
182A182SER00.009-0.00720.6890.0330.0330.0000.0000.0000.000
183A183PRO00.0130.03018.175-0.046-0.0460.0000.0000.0000.000
184A184GLY00.013-0.00615.308-0.028-0.0280.0000.0000.0000.000
185A185HIS00.0520.01812.166-0.032-0.0320.0000.0000.0000.000
186A186LEU00.0270.01811.751-0.003-0.0030.0000.0000.0000.000
187A187MET00.0080.02614.9830.0020.0020.0000.0000.0000.000
188A188ASP-1-0.752-0.85917.4390.0330.0330.0000.0000.0000.000
189A189VAL00.0210.00220.983-0.028-0.0280.0000.0000.0000.000
190A190GLU-1-0.741-0.83023.470-0.055-0.0550.0000.0000.0000.000
191A191SER00.020-0.00519.7170.0010.0010.0000.0000.0000.000
192A192SER00.007-0.02518.843-0.025-0.0250.0000.0000.0000.000
193A193LYS10.7190.85219.9040.0220.0220.0000.0000.0000.000
194A194ARG10.7660.85720.096-0.082-0.0820.0000.0000.0000.000
195A195LEU00.0220.01316.142-0.017-0.0170.0000.0000.0000.000
196A196ILE00.012-0.00517.277-0.038-0.0380.0000.0000.0000.000
197A197LYS10.8200.91120.3070.0850.0850.0000.0000.0000.000
198A198ALA00.0410.03620.567-0.011-0.0110.0000.0000.0000.000
199A199PHE00.0150.01215.156-0.027-0.0270.0000.0000.0000.000
200A200THR0-0.027-0.03619.753-0.066-0.0660.0000.0000.0000.000
201A201LEU00.0230.02822.3170.0300.0300.0000.0000.0000.000
202A202PRO0-0.0140.01125.165-0.005-0.0050.0000.0000.0000.000
203A203GLY0-0.001-0.02428.9150.0040.0040.0000.0000.0000.000
204A204ARG10.8620.91123.5660.3050.3050.0000.0000.0000.000
205A205ARG10.8520.89826.5230.2640.2640.0000.0000.0000.000
206A206ILE0-0.023-0.01921.0670.0080.0080.0000.0000.0000.000
207A207PRO00.0480.02518.868-0.002-0.0020.0000.0000.0000.000
208A208GLU-1-0.721-0.81418.358-0.435-0.4350.0000.0000.0000.000
209A209PRO00.0570.03113.650-0.049-0.0490.0000.0000.0000.000
210A210THR00.0420.01315.452-0.083-0.0830.0000.0000.0000.000
211A211ARG10.7950.87816.9680.4170.4170.0000.0000.0000.000
212A212LEU00.001-0.00416.6110.0110.0110.0000.0000.0000.000
213A213ALA00.0280.02014.361-0.029-0.0290.0000.0000.0000.000
214A214HIS0-0.046-0.02915.8650.0610.0610.0000.0000.0000.000
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