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: 37QZL

Calculation Name: 3D9H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D9H

Chain ID: A

ChEMBL ID:

UniProt ID: Q96DX5

Base Structure: X-ray

Registration Date: 2023-09-26

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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2574781.614715
FMO2-HF: Nuclear repulsion 2484947.562724
FMO2-HF: Total energy -89834.051991
FMO2-MP2: Total energy -90092.678495


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:19:PHE)


Summations of interaction energy for fragment #1(A:19:PHE)
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.
-11.362-4.76817.595-5.403-18.783-0.011
Interaction energy analysis for fragmet #1(A:19:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.028
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].
3A21GLY0-0.027-0.0322.163-1.9450.2554.213-2.891-3.5210.007
4A22ILE0-0.0070.0053.0202.1510.4180.7253.004-1.996-0.003
5A23ARG10.8060.8912.338-4.043-2.3963.316-1.432-3.531-0.010
6A24LEU0-0.0060.0154.0340.3680.5190.002-0.049-0.1030.000
7A25LEU0-0.026-0.0256.1410.0670.0670.0000.0000.0000.000
8A26SER00.0490.0099.3550.0340.0340.0000.0000.0000.000
9A27ASN00.0080.00012.7760.0380.0380.0000.0000.0000.000
10A28PRO00.016-0.00215.4010.0080.0080.0000.0000.0000.000
11A29LEU0-0.045-0.01118.5050.0140.0140.0000.0000.0000.000
12A30MET0-0.058-0.03319.1770.0000.0000.0000.0000.0000.000
13A31GLY00.0400.02118.790-0.021-0.0210.0000.0000.0000.000
14A32ASP-1-0.901-0.94418.826-0.124-0.1240.0000.0000.0000.000
15A33ALA0-0.078-0.03415.876-0.023-0.0230.0000.0000.0000.000
16A34VAL00.0050.01013.374-0.005-0.0050.0000.0000.0000.000
17A35SER0-0.052-0.02711.102-0.049-0.0490.0000.0000.0000.000
18A36ASP-1-0.852-0.92710.405-0.252-0.2520.0000.0000.0000.000
19A37TRP00.018-0.01712.2430.0140.0140.0000.0000.0000.000
20A38SER0-0.013-0.04310.337-0.096-0.0960.0000.0000.0000.000
21A39PRO00.0370.00412.4700.0450.0450.0000.0000.0000.000
22A40MET0-0.0030.0089.9470.0850.0850.0000.0000.0000.000
23A41HIS0-0.0120.0128.012-0.013-0.0130.0000.0000.0000.000
24A42GLU-1-0.808-0.87113.024-0.127-0.1270.0000.0000.0000.000
25A43ALA0-0.016-0.02515.7020.0310.0310.0000.0000.0000.000
26A44ALA0-0.056-0.03113.5130.0250.0250.0000.0000.0000.000
27A45ILE00.0450.02215.6280.0310.0310.0000.0000.0000.000
28A46HIS0-0.057-0.01918.0350.0350.0350.0000.0000.0000.000
29A47GLY00.012-0.00119.4930.0080.0080.0000.0000.0000.000
30A48HIS0-0.034-0.01319.552-0.016-0.0160.0000.0000.0000.000
31A49GLN00.1000.02618.259-0.036-0.0360.0000.0000.0000.000
32A50LEU0-0.039-0.02618.923-0.028-0.0280.0000.0000.0000.000
33A51SER00.0160.00719.103-0.009-0.0090.0000.0000.0000.000
34A52LEU00.0550.03113.265-0.035-0.0350.0000.0000.0000.000
35A53ARG10.8790.93715.5740.1990.1990.0000.0000.0000.000
36A54ASN0-0.0140.00417.954-0.008-0.0080.0000.0000.0000.000
37A55LEU00.0410.03614.011-0.009-0.0090.0000.0000.0000.000
38A56ILE00.0350.00512.173-0.037-0.0370.0000.0000.0000.000
39A57SER0-0.131-0.07314.287-0.004-0.0040.0000.0000.0000.000
40A58GLN0-0.016-0.01616.6260.0000.0000.0000.0000.0000.000
41A59GLY00.0080.01614.0660.0030.0030.0000.0000.0000.000
42A60TRP0-0.062-0.01710.950-0.120-0.1200.0000.0000.0000.000
43A61ALA00.0240.0026.6250.0470.0470.0000.0000.0000.000
44A62VAL00.0270.0067.423-0.025-0.0250.0000.0000.0000.000
45A63ASN0-0.030-0.0042.5440.0270.6660.235-0.140-0.7350.001
46A64ILE00.0080.0123.081-2.725-1.3550.127-0.766-0.731-0.008
47A65ILE0-0.040-0.0242.280-0.946-0.2544.025-0.821-3.8950.007
48A66THR0-0.013-0.0064.780-0.463-0.406-0.001-0.001-0.0540.000
49A67ALA00.0590.0306.6200.0760.0760.0000.0000.0000.000
50A68ASP-1-0.821-0.9008.2740.2130.2130.0000.0000.0000.000
51A69HIS0-0.034-0.0205.132-0.329-0.3290.0000.0000.0000.000
52A70VAL00.0590.0537.1150.2250.2250.0000.0000.0000.000
53A71SER00.019-0.0056.438-0.298-0.2980.0000.0000.0000.000
54A72PRO00.0470.0077.3860.0800.0800.0000.0000.0000.000
55A73LEU00.0130.0109.1450.0400.0400.0000.0000.0000.000
56A74HIS00.0270.0378.566-0.112-0.1120.0000.0000.0000.000
57A75GLU-1-0.808-0.91412.164-0.011-0.0110.0000.0000.0000.000
58A76ALA0-0.053-0.02713.7260.0070.0070.0000.0000.0000.000
59A77CYS0-0.081-0.03314.2210.0100.0100.0000.0000.0000.000
60A78LEU00.0030.01716.3390.0160.0160.0000.0000.0000.000
61A79GLY00.0180.01118.2270.0020.0020.0000.0000.0000.000
62A80GLY00.003-0.00319.744-0.003-0.0030.0000.0000.0000.000
63A81HIS00.0190.01718.520-0.007-0.0070.0000.0000.0000.000
64A82LEU00.0330.00318.750-0.027-0.0270.0000.0000.0000.000
65A83SER0-0.035-0.03119.371-0.011-0.0110.0000.0000.0000.000
66A84CYS0-0.0380.00815.850-0.027-0.0270.0000.0000.0000.000
67A85VAL00.0700.03414.720-0.044-0.0440.0000.0000.0000.000
68A86LYS10.9640.98314.9070.0580.0580.0000.0000.0000.000
69A87ILE0-0.063-0.02015.272-0.022-0.0220.0000.0000.0000.000
70A88LEU00.0340.01810.181-0.062-0.0620.0000.0000.0000.000
71A89LEU00.0230.00911.383-0.086-0.0860.0000.0000.0000.000
72A90LYS10.8660.94212.7960.2560.2560.0000.0000.0000.000
73A91HIS0-0.066-0.04411.8920.0490.0490.0000.0000.0000.000
74A92GLY00.0420.0259.181-0.131-0.1310.0000.0000.0000.000
75A93ALA0-0.034-0.0017.352-0.227-0.2270.0000.0000.0000.000
76A94GLN0-0.006-0.0242.130-4.705-3.1344.953-2.307-4.217-0.005
77A95VAL00.0150.0016.7600.2470.2470.0000.0000.0000.000
78A96ASN0-0.028-0.0028.7590.0330.0330.0000.0000.0000.000
79A97GLY00.0190.0206.6440.2220.2220.0000.0000.0000.000
80A98VAL0-0.027-0.0237.291-0.263-0.2630.0000.0000.0000.000
81A99THR0-0.048-0.0388.4020.2940.2940.0000.0000.0000.000
82A100ALA00.0370.00510.8200.0780.0780.0000.0000.0000.000
83A101ASP-1-0.864-0.90612.0370.3380.3380.0000.0000.0000.000
84A102TRP0-0.021-0.02212.339-0.026-0.0260.0000.0000.0000.000
85A103HIS0-0.0220.00613.723-0.043-0.0430.0000.0000.0000.000
86A104THR00.0550.02311.8830.0740.0740.0000.0000.0000.000
87A105PRO00.015-0.00410.780-0.082-0.0820.0000.0000.0000.000
88A106LEU00.0440.01713.688-0.050-0.0500.0000.0000.0000.000
89A107PHE00.0080.01116.078-0.030-0.0300.0000.0000.0000.000
90A108ASN00.044-0.00914.9350.0030.0030.0000.0000.0000.000
91A109ALA0-0.0040.00317.724-0.030-0.0300.0000.0000.0000.000
92A110CYS0-0.060-0.01819.596-0.017-0.0170.0000.0000.0000.000
93A111VAL0-0.029-0.00920.297-0.014-0.0140.0000.0000.0000.000
94A112SER0-0.008-0.01520.541-0.011-0.0110.0000.0000.0000.000
95A113GLY00.0100.01023.001-0.012-0.0120.0000.0000.0000.000
96A114SER00.0440.03221.832-0.010-0.0100.0000.0000.0000.000
97A115TRP00.055-0.00222.7400.0090.0090.0000.0000.0000.000
98A116ASP-1-0.896-0.94023.9730.0000.0000.0000.0000.0000.000
99A117CYS0-0.071-0.03618.758-0.015-0.0150.0000.0000.0000.000
100A118VAL00.0050.00319.1330.0060.0060.0000.0000.0000.000
101A119ASN00.0330.02520.3400.0190.0190.0000.0000.0000.000
102A120LEU0-0.021-0.00417.928-0.002-0.0020.0000.0000.0000.000
103A121LEU00.007-0.00413.914-0.013-0.0130.0000.0000.0000.000
104A122LEU0-0.0110.00516.5540.0150.0150.0000.0000.0000.000
105A123GLN0-0.044-0.02118.997-0.005-0.0050.0000.0000.0000.000
106A124HIS0-0.107-0.05314.392-0.049-0.0490.0000.0000.0000.000
107A125GLY00.0240.01414.325-0.001-0.0010.0000.0000.0000.000
108A126ALA0-0.039-0.01613.7110.0570.0570.0000.0000.0000.000
109A127SER0-0.012-0.02513.100-0.013-0.0130.0000.0000.0000.000
110A128VAL0-0.016-0.01415.5850.0160.0160.0000.0000.0000.000
111A129GLN00.0300.03818.373-0.018-0.0180.0000.0000.0000.000
112A130PRO0-0.0010.00013.7680.0260.0260.0000.0000.0000.000
113A131GLU-1-0.935-0.96412.3201.0001.0000.0000.0000.0000.000
114A132SER00.0020.01514.725-0.064-0.0640.0000.0000.0000.000
115A133ASP-1-0.775-0.90316.4070.3010.3010.0000.0000.0000.000
116A134LEU0-0.080-0.03717.566-0.046-0.0460.0000.0000.0000.000
117A135ALA00.0110.01616.178-0.029-0.0290.0000.0000.0000.000
118A136SER00.001-0.00617.981-0.007-0.0070.0000.0000.0000.000
119A137PRO00.013-0.01018.059-0.032-0.0320.0000.0000.0000.000
120A138ILE00.0330.01020.873-0.025-0.0250.0000.0000.0000.000
121A139HIS10.7800.87823.953-0.227-0.2270.0000.0000.0000.000
122A140GLU-1-0.730-0.83722.4220.1450.1450.0000.0000.0000.000
123A141ALA0-0.006-0.00824.607-0.017-0.0170.0000.0000.0000.000
124A142ALA00.007-0.00226.190-0.014-0.0140.0000.0000.0000.000
125A143ARG10.8700.93225.482-0.167-0.1670.0000.0000.0000.000
126A144ARG10.8130.90124.601-0.120-0.1200.0000.0000.0000.000
127A145GLY00.0210.02129.891-0.009-0.0090.0000.0000.0000.000
128A146HIS0-0.070-0.01925.737-0.015-0.0150.0000.0000.0000.000
129A147VAL00.027-0.02228.6050.0070.0070.0000.0000.0000.000
130A148GLU-1-0.851-0.89829.1180.0530.0530.0000.0000.0000.000
131A149CYS0-0.0250.01424.2420.0000.0000.0000.0000.0000.000
132A150VAL0-0.011-0.00525.3890.0120.0120.0000.0000.0000.000
133A151ASN0-0.016-0.02227.4860.0110.0110.0000.0000.0000.000
134A152SER0-0.014-0.02224.4000.0020.0020.0000.0000.0000.000
135A153LEU0-0.007-0.01120.8430.0070.0070.0000.0000.0000.000
136A154ILE0-0.0010.00524.1780.0090.0090.0000.0000.0000.000
137A155ALA0-0.034-0.01326.9800.0020.0020.0000.0000.0000.000
138A156TYR0-0.031-0.01621.784-0.011-0.0110.0000.0000.0000.000
139A157GLY00.0010.00423.2630.0160.0160.0000.0000.0000.000
140A158GLY0-0.037-0.01923.9710.0160.0160.0000.0000.0000.000
141A159ASN0-0.006-0.01424.842-0.026-0.0260.0000.0000.0000.000
142A160ILE00.0430.02227.1910.0100.0100.0000.0000.0000.000
143A161ASP-1-0.837-0.91729.6690.1210.1210.0000.0000.0000.000
144A162HIS0-0.112-0.07622.809-0.018-0.0180.0000.0000.0000.000
145A163LYS10.8780.93327.868-0.143-0.1430.0000.0000.0000.000
146A164ILE0-0.0140.01422.9980.0080.0080.0000.0000.0000.000
147A165SER00.022-0.00926.508-0.021-0.0210.0000.0000.0000.000
148A166HIS0-0.011-0.01127.0660.0040.0040.0000.0000.0000.000
149A167LEU00.0030.01524.668-0.009-0.0090.0000.0000.0000.000
150A168GLY00.0550.02128.627-0.015-0.0150.0000.0000.0000.000
151A169THR00.0080.01428.8350.0140.0140.0000.0000.0000.000
152A170PRO0-0.011-0.01327.399-0.004-0.0040.0000.0000.0000.000
153A171LEU00.0560.04129.808-0.007-0.0070.0000.0000.0000.000
154A172TYR0-0.027-0.02032.785-0.005-0.0050.0000.0000.0000.000
155A173LEU0-0.0150.00327.388-0.004-0.0040.0000.0000.0000.000
156A174ALA00.0160.01331.839-0.007-0.0070.0000.0000.0000.000
157A175CYS0-0.055-0.02933.768-0.009-0.0090.0000.0000.0000.000
158A176GLU-1-0.839-0.91631.9800.1230.1230.0000.0000.0000.000
159A177ASN0-0.117-0.07331.640-0.003-0.0030.0000.0000.0000.000
160A178GLN00.001-0.00634.688-0.008-0.0080.0000.0000.0000.000
161A179GLN00.0310.03832.862-0.012-0.0120.0000.0000.0000.000
162A180ARG10.8100.85936.478-0.045-0.0450.0000.0000.0000.000
163A181ALA0-0.005-0.00837.4900.0000.0000.0000.0000.0000.000
164A182CYS00.0050.01232.6280.0020.0020.0000.0000.0000.000
165A183VAL00.0020.00735.3130.0040.0040.0000.0000.0000.000
166A184LYS10.8340.90437.272-0.047-0.0470.0000.0000.0000.000
167A185LYS10.9140.96133.772-0.063-0.0630.0000.0000.0000.000
168A186LEU0-0.022-0.00531.0860.0020.0020.0000.0000.0000.000
169A187LEU00.0150.01435.0820.0030.0030.0000.0000.0000.000
170A188GLU-1-0.825-0.90338.5230.0500.0500.0000.0000.0000.000
171A189SER0-0.107-0.06934.019-0.003-0.0030.0000.0000.0000.000
172A190GLY0-0.026-0.01035.4430.0040.0040.0000.0000.0000.000
173A191ALA0-0.027-0.00334.3750.0030.0030.0000.0000.0000.000
174A192ASP-1-0.798-0.89635.7980.0940.0940.0000.0000.0000.000
175A193VAL0-0.005-0.00737.2180.0060.0060.0000.0000.0000.000
176A194ASN0-0.018-0.01339.645-0.003-0.0030.0000.0000.0000.000
177A195GLN0-0.046-0.02634.3090.0100.0100.0000.0000.0000.000
178A196GLY00.0190.00735.0250.0010.0010.0000.0000.0000.000
179A197LYS10.8080.89931.121-0.132-0.1320.0000.0000.0000.000
180A198GLY0-0.015-0.00633.299-0.004-0.0040.0000.0000.0000.000
181A199GLN0-0.022-0.01934.8620.0020.0020.0000.0000.0000.000
182A200ASP-1-0.767-0.83837.4580.0910.0910.0000.0000.0000.000
183A201SER00.0620.00637.5560.0050.0050.0000.0000.0000.000
184A202PRO00.018-0.01636.619-0.001-0.0010.0000.0000.0000.000
185A203LEU00.0280.02038.884-0.003-0.0030.0000.0000.0000.000
186A204HIS00.0020.01841.370-0.001-0.0010.0000.0000.0000.000
187A205ALA0-0.015-0.00438.526-0.003-0.0030.0000.0000.0000.000
188A206VAL00.0160.01040.278-0.003-0.0030.0000.0000.0000.000
189A207VAL0-0.021-0.00142.264-0.004-0.0040.0000.0000.0000.000
190A208ARG10.7990.89340.518-0.091-0.0910.0000.0000.0000.000
191A209THR0-0.058-0.03540.2800.0000.0000.0000.0000.0000.000
192A210ALA0-0.002-0.00443.709-0.003-0.0030.0000.0000.0000.000
193A211SER00.0010.01343.186-0.002-0.0020.0000.0000.0000.000
194A212GLU-1-0.817-0.93845.2700.0460.0460.0000.0000.0000.000
195A213GLU-1-0.787-0.85445.2660.0440.0440.0000.0000.0000.000
196A214LEU0-0.019-0.00839.8860.0000.0000.0000.0000.0000.000
197A215ALA00.0330.01343.6400.0030.0030.0000.0000.0000.000
198A216CYS0-0.018-0.00545.8360.0000.0000.0000.0000.0000.000
199A217LEU0-0.043-0.01441.2220.0000.0000.0000.0000.0000.000
200A218LEU00.010-0.00539.7070.0020.0020.0000.0000.0000.000
201A219MET0-0.001-0.00843.7680.0010.0010.0000.0000.0000.000
202A220ASP-1-0.857-0.90947.2660.0470.0470.0000.0000.0000.000
203A221PHE0-0.058-0.03142.365-0.002-0.0020.0000.0000.0000.000
204A222GLY0-0.022-0.00544.4660.0030.0030.0000.0000.0000.000
205A223ALA0-0.064-0.03243.6540.0020.0020.0000.0000.0000.000
206A224ASP-1-0.820-0.91644.7290.0680.0680.0000.0000.0000.000
207A225THR0-0.0010.00146.2650.0010.0010.0000.0000.0000.000
208A226GLN0-0.057-0.04148.8150.0000.0000.0000.0000.0000.000
209A227ALA00.0250.02243.8820.0010.0010.0000.0000.0000.000
210A228LYS10.7920.87945.634-0.070-0.0700.0000.0000.0000.000
211A229ASN0-0.002-0.01141.6560.0020.0020.0000.0000.0000.000
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