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: 4JQ9N

Calculation Name: 5D1H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D1H

Chain ID: A

ChEMBL ID:

UniProt ID: C7Q5P8

Base Structure: X-ray

Registration Date: 2023-09-22

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 OptHSide
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 -2140161.242699
FMO2-HF: Nuclear repulsion 2065100.923421
FMO2-HF: Total energy -75060.319277
FMO2-MP2: Total energy -75283.323169


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:5:THR)


Summations of interaction energy for fragment #1(A:5: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.
-0.0132.139-0.002-0.847-1.3050.003
Interaction energy analysis for fragmet #1(A:5:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.023
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].
3A7LEU00.0180.0223.7871.9253.6450.001-0.795-0.9260.003
4A8LYS10.8620.9116.322-0.070-0.0700.0000.0000.0000.000
5A9VAL00.0260.0068.1490.0740.0740.0000.0000.0000.000
6A10LEU0-0.024-0.02111.417-0.038-0.0380.0000.0000.0000.000
7A11ALA00.0120.01614.926-0.028-0.0280.0000.0000.0000.000
8A12GLY0-0.003-0.00416.9530.0030.0030.0000.0000.0000.000
9A13LYS10.8980.92619.6590.0420.0420.0000.0000.0000.000
10A14LYS10.9380.97415.4090.2530.2530.0000.0000.0000.000
11A15LEU00.0280.01710.930-0.004-0.0040.0000.0000.0000.000
12A16THR0-0.045-0.03311.393-0.031-0.0310.0000.0000.0000.000
13A17ASP-1-0.841-0.8806.314-0.617-0.6170.0000.0000.0000.000
14A18LEU0-0.028-0.0187.950-0.007-0.0070.0000.0000.0000.000
15A19ASP-1-0.812-0.9307.298-1.610-1.6100.0000.0000.0000.000
16A20PRO0-0.013-0.0183.945-0.0830.0720.000-0.026-0.1300.000
17A21ASP-1-0.883-0.9326.120-0.631-0.6310.0000.0000.0000.000
18A22GLU-1-0.836-0.9079.386-0.261-0.2610.0000.0000.0000.000
19A23TRP0-0.057-0.0357.1570.1630.1630.0000.0000.0000.000
20A24ALA00.0150.0199.3950.1410.1410.0000.0000.0000.000
21A25LYS10.8070.88310.9870.4740.4740.0000.0000.0000.000
22A26ALA0-0.0010.00013.6340.0630.0630.0000.0000.0000.000
23A27GLN0-0.006-0.02310.0380.1310.1310.0000.0000.0000.000
24A28ALA0-0.035-0.00615.1370.0410.0410.0000.0000.0000.000
25A29SER0-0.103-0.04817.1210.0230.0230.0000.0000.0000.000
26A30ALA0-0.031-0.00318.6530.0180.0180.0000.0000.0000.000
27A31GLU-1-0.917-0.95620.296-0.066-0.0660.0000.0000.0000.000
28A32ARG10.8060.90021.9090.0210.0210.0000.0000.0000.000
29A33ILE00.0050.00515.499-0.013-0.0130.0000.0000.0000.000
30A34LEU0-0.0230.00119.1020.0200.0200.0000.0000.0000.000
31A35VAL00.007-0.00115.047-0.010-0.0100.0000.0000.0000.000
32A36ASP-1-0.836-0.92017.8140.0360.0360.0000.0000.0000.000
33A37VAL00.005-0.01416.4980.0160.0160.0000.0000.0000.000
34A38GLY0-0.0050.00218.683-0.009-0.0090.0000.0000.0000.000
35A39THR0-0.047-0.02019.266-0.028-0.0280.0000.0000.0000.000
36A40GLY00.0430.03021.898-0.016-0.0160.0000.0000.0000.000
37A41ASP-1-0.875-0.95022.5100.0160.0160.0000.0000.0000.000
38A42ALA0-0.006-0.00821.013-0.014-0.0140.0000.0000.0000.000
39A43ARG10.8450.88823.0110.0000.0000.0000.0000.0000.000
40A44THR00.010-0.01126.004-0.009-0.0090.0000.0000.0000.000
41A45ALA00.1010.06221.406-0.005-0.0050.0000.0000.0000.000
42A46TYR0-0.062-0.05323.545-0.008-0.0080.0000.0000.0000.000
43A47ARG10.8970.94925.066-0.009-0.0090.0000.0000.0000.000
44A48GLN0-0.032-0.01623.6430.0000.0000.0000.0000.0000.000
45A49ALA00.0040.00722.931-0.005-0.0050.0000.0000.0000.000
46A50ILE0-0.047-0.02624.764-0.007-0.0070.0000.0000.0000.000
47A51ALA0-0.066-0.02928.166-0.001-0.0010.0000.0000.0000.000
48A52HIS10.8100.90126.3660.0380.0380.0000.0000.0000.000
49A53PRO0-0.0050.00725.337-0.005-0.0050.0000.0000.0000.000
50A54GLU-1-0.760-0.86724.376-0.069-0.0690.0000.0000.0000.000
51A55TRP0-0.047-0.02622.5110.0010.0010.0000.0000.0000.000
52A56LEU00.0200.01614.587-0.009-0.0090.0000.0000.0000.000
53A57VAL0-0.037-0.01118.6610.0150.0150.0000.0000.0000.000
54A58VAL00.012-0.00813.108-0.016-0.0160.0000.0000.0000.000
55A59GLY00.0280.01216.4180.0280.0280.0000.0000.0000.000
56A60VAL0-0.008-0.00313.0010.0080.0080.0000.0000.0000.000
57A61ASP-1-0.765-0.90815.0980.1260.1260.0000.0000.0000.000
58A62PRO00.0200.02714.7970.0130.0130.0000.0000.0000.000
59A63ALA0-0.012-0.00115.863-0.016-0.0160.0000.0000.0000.000
60A64TRP00.0820.02514.846-0.055-0.0550.0000.0000.0000.000
61A65GLN00.009-0.00117.368-0.028-0.0280.0000.0000.0000.000
62A66ARG10.8800.93620.231-0.076-0.0760.0000.0000.0000.000
63A67MET00.0740.07415.944-0.015-0.0150.0000.0000.0000.000
64A68THR0-0.056-0.02919.421-0.019-0.0190.0000.0000.0000.000
65A69GLU-1-0.797-0.85121.505-0.037-0.0370.0000.0000.0000.000
66A70THR00.007-0.01323.054-0.012-0.0120.0000.0000.0000.000
67A71ALA00.0430.02119.354-0.011-0.0110.0000.0000.0000.000
68A72VAL0-0.065-0.03221.317-0.020-0.0200.0000.0000.0000.000
69A73ARG10.8080.89423.8940.0310.0310.0000.0000.0000.000
70A74ALA00.0560.03322.043-0.003-0.0030.0000.0000.0000.000
71A75ALA00.0320.02921.386-0.011-0.0110.0000.0000.0000.000
72A76ARG10.8580.94422.9900.0880.0880.0000.0000.0000.000
73A77LYS11.0260.99726.3220.1050.1050.0000.0000.0000.000
74A78PRO00.0900.03027.3390.0080.0080.0000.0000.0000.000
75A79ALA0-0.0080.00929.5080.0060.0060.0000.0000.0000.000
76A80LYS10.8790.92831.3680.0670.0670.0000.0000.0000.000
77A81GLY00.0320.02630.2510.0020.0020.0000.0000.0000.000
78A82GLY0-0.0210.03126.3840.0020.0020.0000.0000.0000.000
79A83ALA00.014-0.00823.9920.0060.0060.0000.0000.0000.000
80A84PRO0-0.020-0.01621.266-0.001-0.0010.0000.0000.0000.000
81A85ASN00.0010.00419.644-0.027-0.0270.0000.0000.0000.000
82A86LEU0-0.030-0.00519.5590.0090.0090.0000.0000.0000.000
83A87VAL0-0.010-0.00612.930-0.026-0.0260.0000.0000.0000.000
84A88LEU0-0.021-0.00815.7260.0370.0370.0000.0000.0000.000
85A89VAL00.027-0.0029.806-0.025-0.0250.0000.0000.0000.000
86A90SER0-0.025-0.01911.287-0.019-0.0190.0000.0000.0000.000
87A91SER0-0.038-0.0359.9760.2490.2490.0000.0000.0000.000
88A92ALA0-0.0180.00411.781-0.108-0.1080.0000.0000.0000.000
89A93ILE00.0270.01112.9560.0770.0770.0000.0000.0000.000
90A94GLU-1-0.836-0.92914.5970.3220.3220.0000.0000.0000.000
91A95THR0-0.072-0.03710.709-0.024-0.0240.0000.0000.0000.000
92A96VAL00.0020.0259.9910.1710.1710.0000.0000.0000.000
93A97PRO00.0280.0004.6360.0650.149-0.001-0.003-0.0800.000
94A98ALA00.0610.0214.253-0.580-0.456-0.001-0.010-0.1130.000
95A99ALA0-0.018-0.0034.466-0.350-0.281-0.001-0.013-0.0560.000
96A100LEU0-0.006-0.0055.953-0.064-0.0640.0000.0000.0000.000
97A101HIS0-0.055-0.0318.5610.0380.0380.0000.0000.0000.000
98A102GLY0-0.016-0.00410.512-0.074-0.0740.0000.0000.0000.000
99A103VAL0-0.012-0.00210.877-0.042-0.0420.0000.0000.0000.000
100A104ALA0-0.021-0.00713.966-0.024-0.0240.0000.0000.0000.000
101A105ASP-1-0.819-0.91117.033-0.032-0.0320.0000.0000.0000.000
102A106GLU-1-0.884-0.94620.1130.0180.0180.0000.0000.0000.000
103A107VAL00.0190.01418.093-0.002-0.0020.0000.0000.0000.000
104A108MET0-0.0150.00520.637-0.003-0.0030.0000.0000.0000.000
105A109VAL00.001-0.01121.4520.0120.0120.0000.0000.0000.000
106A110LEU0-0.001-0.00723.700-0.006-0.0060.0000.0000.0000.000
107A111MET0-0.053-0.01826.2740.0020.0020.0000.0000.0000.000
108A112PRO00.0030.02324.6580.0010.0010.0000.0000.0000.000
109A113TRP00.0380.00225.326-0.007-0.0070.0000.0000.0000.000
110A114GLY0-0.005-0.01124.9850.0140.0140.0000.0000.0000.000
111A115LYS10.8100.87620.112-0.221-0.2210.0000.0000.0000.000
112A116LEU00.0210.03220.2380.0040.0040.0000.0000.0000.000
113A117LEU00.0000.00923.032-0.002-0.0020.0000.0000.0000.000
114A118ARG10.8050.84826.732-0.105-0.1050.0000.0000.0000.000
115A119GLY00.0350.01223.961-0.002-0.0020.0000.0000.0000.000
116A120VAL0-0.030-0.01623.9190.0000.0000.0000.0000.0000.000
117A121VAL0-0.032-0.01526.151-0.006-0.0060.0000.0000.0000.000
118A122LEU0-0.0130.00228.322-0.005-0.0050.0000.0000.0000.000
119A123GLY00.0340.01426.507-0.004-0.0040.0000.0000.0000.000
120A124GLU-1-0.929-0.95723.7190.1690.1690.0000.0000.0000.000
121A125ALA00.0720.01722.2760.0070.0070.0000.0000.0000.000
122A126ASP-1-0.810-0.88718.2250.2560.2560.0000.0000.0000.000
123A127VAL00.0060.00517.7320.0320.0320.0000.0000.0000.000
124A128LEU00.0040.00818.9730.0060.0060.0000.0000.0000.000
125A129SER00.012-0.01917.635-0.011-0.0110.0000.0000.0000.000
126A130GLY00.0180.01714.7420.0190.0190.0000.0000.0000.000
127A131LEU0-0.037-0.03615.0640.0010.0010.0000.0000.0000.000
128A132ARG10.8190.91617.414-0.166-0.1660.0000.0000.0000.000
129A133ALA00.0080.01312.658-0.018-0.0180.0000.0000.0000.000
130A134VAL0-0.0010.00811.843-0.009-0.0090.0000.0000.0000.000
131A135ALA0-0.0220.00513.912-0.054-0.0540.0000.0000.0000.000
132A136LYS10.8130.91716.8760.0570.0570.0000.0000.0000.000
133A137PRO00.017-0.01918.3890.0070.0070.0000.0000.0000.000
134A138GLY0-0.017-0.00321.457-0.013-0.0130.0000.0000.0000.000
135A139ALA0-0.0200.00420.860-0.008-0.0080.0000.0000.0000.000
136A140PRO0-0.008-0.01322.8240.0110.0110.0000.0000.0000.000
137A141LEU0-0.0220.00021.7410.0030.0030.0000.0000.0000.000
138A142GLU-1-0.798-0.89224.2410.0380.0380.0000.0000.0000.000
139A143ILE00.0030.00625.2110.0060.0060.0000.0000.0000.000
140A144SER0-0.025-0.01327.373-0.007-0.0070.0000.0000.0000.000
141A145ILE00.0430.00728.8270.0040.0040.0000.0000.0000.000
142A146GLY00.0290.02231.745-0.004-0.0040.0000.0000.0000.000
143A147THR0-0.011-0.04234.8720.0020.0020.0000.0000.0000.000
144A148SER0-0.044-0.04337.4360.0010.0010.0000.0000.0000.000
145A149ILE0-0.0070.00432.811-0.001-0.0010.0000.0000.0000.000
146A150TRP00.0320.01333.3400.0020.0020.0000.0000.0000.000
147A151ARG10.7900.88839.015-0.039-0.0390.0000.0000.0000.000
148A152GLU-1-0.876-0.91940.5610.0430.0430.0000.0000.0000.000
149A153PRO0-0.106-0.06039.777-0.003-0.0030.0000.0000.0000.000
150A154ILE00.0370.01636.8240.0010.0010.0000.0000.0000.000
151A155PRO0-0.015-0.00133.0150.0010.0010.0000.0000.0000.000
152A156LEU00.007-0.01332.2970.0010.0010.0000.0000.0000.000
153A157GLU-1-0.847-0.92928.9110.0850.0850.0000.0000.0000.000
154A158ILE00.0270.01030.9350.0070.0070.0000.0000.0000.000
155A159ARG10.9350.98533.309-0.057-0.0570.0000.0000.0000.000
156A160ASP-1-0.846-0.88034.3310.0800.0800.0000.0000.0000.000
157A161LEU0-0.034-0.01131.6430.0010.0010.0000.0000.0000.000
158A162PRO00.0010.00436.320-0.003-0.0030.0000.0000.0000.000
159A163GLU-1-0.860-0.92737.0290.0460.0460.0000.0000.0000.000
160A164LEU0-0.0010.01032.0260.0000.0000.0000.0000.0000.000
161A165THR00.0210.00236.278-0.003-0.0030.0000.0000.0000.000
162A166PRO00.055-0.00237.3080.0030.0030.0000.0000.0000.000
163A167GLU-1-0.931-0.95438.2170.0450.0450.0000.0000.0000.000
164A168THR0-0.0120.00637.5660.0020.0020.0000.0000.0000.000
165A169VAL0-0.0060.01432.8580.0040.0040.0000.0000.0000.000
166A170VAL00.001-0.00234.5660.0050.0050.0000.0000.0000.000
167A171SER00.0040.00637.0390.0040.0040.0000.0000.0000.000
168A172THR0-0.026-0.03334.7230.0030.0030.0000.0000.0000.000
169A173GLY00.0640.03834.4170.0050.0050.0000.0000.0000.000
170A174LEU0-0.057-0.01028.2810.0060.0060.0000.0000.0000.000
171A175THR00.020-0.01229.8530.0070.0070.0000.0000.0000.000
172A176ASP-1-0.877-0.93930.7790.0820.0820.0000.0000.0000.000
173A177ARG10.7940.88827.500-0.100-0.1000.0000.0000.0000.000
174A178LEU0-0.015-0.00725.1700.0120.0120.0000.0000.0000.000
175A179ALA0-0.0130.00725.9560.0050.0050.0000.0000.0000.000
176A180ALA00.0100.00527.0990.0020.0020.0000.0000.0000.000
177A181LEU0-0.043-0.01721.8460.0130.0130.0000.0000.0000.000
178A182GLY00.0020.01221.8390.0120.0120.0000.0000.0000.000
179A183TRP0-0.021-0.00919.831-0.013-0.0130.0000.0000.0000.000
180A184GLN0-0.035-0.01925.2790.0000.0000.0000.0000.0000.000
181A185VAL00.005-0.00228.747-0.004-0.0040.0000.0000.0000.000
182A186ALA0-0.059-0.03930.811-0.004-0.0040.0000.0000.0000.000
183A187ASP-1-0.830-0.91032.3960.0320.0320.0000.0000.0000.000
184A188VAL00.0100.01333.0230.0040.0040.0000.0000.0000.000
185A189ARG10.8220.90535.299-0.033-0.0330.0000.0000.0000.000
186A190LEU00.0120.00436.7650.0010.0010.0000.0000.0000.000
187A191VAL0-0.032-0.02437.339-0.003-0.0030.0000.0000.0000.000
188A192PRO00.0100.02639.1110.0000.0000.0000.0000.0000.000
189A212THR0-0.017-0.01340.6960.0000.0000.0000.0000.0000.000
190A213GLU-1-0.872-0.92837.0920.0340.0340.0000.0000.0000.000
191A214THR0-0.019-0.00539.396-0.001-0.0010.0000.0000.0000.000
192A215VAL00.0170.02233.7390.0030.0030.0000.0000.0000.000
193A216LEU00.0040.00033.145-0.003-0.0030.0000.0000.0000.000
194A217HIS00.0070.00332.1370.0050.0050.0000.0000.0000.000
195A218LEU00.0010.00028.202-0.001-0.0010.0000.0000.0000.000
196A219ARG10.8870.93328.475-0.034-0.0340.0000.0000.0000.000
197A220ALA00.0140.01726.1530.0000.0000.0000.0000.0000.000
198A221VAL0-0.0090.00025.756-0.004-0.0040.0000.0000.0000.000
199A222ALA0-0.0040.01321.2070.0070.0070.0000.0000.0000.000
200A223VAL0-0.042-0.03223.242-0.011-0.0110.0000.0000.0000.000
201A224ASP-1-0.871-0.93123.2440.1220.1220.0000.0000.0000.000
202A225PRO0-0.057-0.03822.175-0.007-0.0070.0000.0000.0000.000
203A226ARG10.9250.96725.070-0.091-0.0910.0000.0000.0000.000
204A227ASP-1-0.947-0.96228.7700.1060.1060.0000.0000.0000.000