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: KGK93

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 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 -2138138.151878
FMO2-HF: Nuclear repulsion 2063078.779377
FMO2-HF: Total energy -75059.372501
FMO2-MP2: Total energy -75282.358315


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.
-0.831.3640.02-0.939-1.276-0.002
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 : -0.001 / 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].
3A7LEU00.0060.0143.255-1.1120.6830.024-0.898-0.921-0.002
4A8LYS10.9630.9865.5041.1481.1480.0000.0000.0000.000
5A9VAL00.0180.0097.5110.1150.1150.0000.0000.0000.000
6A10LEU0-0.045-0.02910.7680.1480.1480.0000.0000.0000.000
7A11ALA00.0200.02114.360-0.014-0.0140.0000.0000.0000.000
8A12GLY0-0.008-0.00616.6460.0570.0570.0000.0000.0000.000
9A13LYS10.9450.95819.1700.1900.1900.0000.0000.0000.000
10A14LYS10.9470.97815.6280.1430.1430.0000.0000.0000.000
11A15LEU00.0220.00710.641-0.031-0.0310.0000.0000.0000.000
12A16THR0-0.065-0.04311.3740.1610.1610.0000.0000.0000.000
13A17ASP-1-0.883-0.9236.797-0.309-0.3090.0000.0000.0000.000
14A18LEU0-0.054-0.0357.7480.2050.2050.0000.0000.0000.000
15A19ASP-1-0.832-0.9387.274-1.296-1.2960.0000.0000.0000.000
16A20PRO0-0.012-0.0184.278-0.275-0.157-0.001-0.015-0.1020.000
17A21ASP-1-0.888-0.9346.384-0.508-0.5080.0000.0000.0000.000
18A22GLU-1-0.970-0.9949.633-0.443-0.4430.0000.0000.0000.000
19A23TRP0-0.061-0.0387.3050.1070.1070.0000.0000.0000.000
20A24ALA00.0220.0149.5470.1010.1010.0000.0000.0000.000
21A25LYS10.9410.97211.0960.4910.4910.0000.0000.0000.000
22A26ALA00.0090.00113.8140.0770.0770.0000.0000.0000.000
23A27GLN0-0.001-0.00910.1500.2110.2110.0000.0000.0000.000
24A28ALA0-0.034-0.00715.1910.0620.0620.0000.0000.0000.000
25A29SER0-0.121-0.05717.1860.0500.0500.0000.0000.0000.000
26A30ALA0-0.0090.00918.7310.0320.0320.0000.0000.0000.000
27A31GLU-1-0.900-0.95320.360-0.231-0.2310.0000.0000.0000.000
28A32ARG10.8350.92821.8580.2970.2970.0000.0000.0000.000
29A33ILE00.0120.02115.370-0.020-0.0200.0000.0000.0000.000
30A34LEU0-0.027-0.00119.1090.0130.0130.0000.0000.0000.000
31A35VAL0-0.005-0.00315.109-0.050-0.0500.0000.0000.0000.000
32A36ASP-1-0.830-0.92117.835-0.332-0.3320.0000.0000.0000.000
33A37VAL0-0.008-0.02116.330-0.050-0.0500.0000.0000.0000.000
34A38GLY0-0.0030.00517.8180.0490.0490.0000.0000.0000.000
35A39THR0-0.022-0.00718.3680.0300.0300.0000.0000.0000.000
36A40GLY00.0450.03220.9040.0300.0300.0000.0000.0000.000
37A41ASP-1-0.883-0.95021.497-0.247-0.2470.0000.0000.0000.000
38A42ALA0-0.016-0.00820.020-0.008-0.0080.0000.0000.0000.000
39A43ARG10.9600.96722.0250.1890.1890.0000.0000.0000.000
40A44THR0-0.004-0.00224.9800.0190.0190.0000.0000.0000.000
41A45ALA00.0960.05520.7450.0070.0070.0000.0000.0000.000
42A46TYR0-0.076-0.09322.8410.0070.0070.0000.0000.0000.000
43A47ARG10.9330.96224.2380.2150.2150.0000.0000.0000.000
44A48GLN0-0.026-0.00723.2890.0370.0370.0000.0000.0000.000
45A49ALA00.0170.01122.4900.0040.0040.0000.0000.0000.000
46A50ILE0-0.046-0.02424.3790.0090.0090.0000.0000.0000.000
47A51ALA0-0.064-0.03027.7010.0130.0130.0000.0000.0000.000
48A52HIS10.8700.94826.2540.2520.2520.0000.0000.0000.000
49A53PRO00.0020.01025.408-0.026-0.0260.0000.0000.0000.000
50A54GLU-1-0.836-0.91324.489-0.262-0.2620.0000.0000.0000.000
51A55TRP0-0.053-0.03122.549-0.017-0.0170.0000.0000.0000.000
52A56LEU00.0180.00914.659-0.003-0.0030.0000.0000.0000.000
53A57VAL0-0.033-0.01118.674-0.018-0.0180.0000.0000.0000.000
54A58VAL00.018-0.00612.977-0.037-0.0370.0000.0000.0000.000
55A59GLY00.0090.00516.0160.0460.0460.0000.0000.0000.000
56A60VAL0-0.009-0.00312.172-0.089-0.0890.0000.0000.0000.000
57A61ASP-1-0.787-0.92014.093-0.289-0.2890.0000.0000.0000.000
58A62PRO00.0170.02713.815-0.048-0.0480.0000.0000.0000.000
59A63ALA0-0.014-0.00514.8860.0270.0270.0000.0000.0000.000
60A64TRP00.0700.01814.3280.0260.0260.0000.0000.0000.000
61A65GLN0-0.031-0.03316.4540.0070.0070.0000.0000.0000.000
62A66ARG10.9120.95919.4830.2350.2350.0000.0000.0000.000
63A67MET00.0930.08415.1000.0150.0150.0000.0000.0000.000
64A68THR0-0.090-0.05419.0960.0130.0130.0000.0000.0000.000
65A69GLU-1-0.907-0.94520.811-0.182-0.1820.0000.0000.0000.000
66A70THR0-0.040-0.04922.0780.0210.0210.0000.0000.0000.000
67A71ALA00.0360.01918.684-0.002-0.0020.0000.0000.0000.000
68A72VAL0-0.058-0.02420.6280.0030.0030.0000.0000.0000.000
69A73ARG10.8640.92923.3740.1970.1970.0000.0000.0000.000
70A74ALA00.0550.03321.3480.0120.0120.0000.0000.0000.000
71A75ALA00.0440.03420.999-0.004-0.0040.0000.0000.0000.000
72A76ARG10.8530.94222.5660.1950.1950.0000.0000.0000.000
73A77LYS11.0220.99625.9160.1560.1560.0000.0000.0000.000
74A78PRO00.0860.02927.4490.0060.0060.0000.0000.0000.000
75A79ALA00.0030.01329.2990.0030.0030.0000.0000.0000.000
76A80LYS10.8810.93030.7920.1590.1590.0000.0000.0000.000
77A81GLY00.0410.03129.6050.0000.0000.0000.0000.0000.000
78A82GLY0-0.0290.05925.810-0.011-0.0110.0000.0000.0000.000
79A83ALA00.010-0.01023.2630.0120.0120.0000.0000.0000.000
80A84PRO0-0.024-0.01321.030-0.024-0.0240.0000.0000.0000.000
81A85ASN00.0220.01519.779-0.032-0.0320.0000.0000.0000.000
82A86LEU0-0.038-0.01118.725-0.021-0.0210.0000.0000.0000.000
83A87VAL00.000-0.00112.481-0.016-0.0160.0000.0000.0000.000
84A88LEU0-0.025-0.01514.880-0.008-0.0080.0000.0000.0000.000
85A89VAL00.027-0.0018.843-0.043-0.0430.0000.0000.0000.000
86A90SER0-0.057-0.02810.4570.1340.1340.0000.0000.0000.000
87A91SER00.000-0.0238.855-0.231-0.2310.0000.0000.0000.000
88A92ALA0-0.0120.01010.8020.0900.0900.0000.0000.0000.000
89A93ILE00.0200.00612.149-0.103-0.1030.0000.0000.0000.000
90A94GLU-1-0.841-0.93214.363-0.355-0.3550.0000.0000.0000.000
91A95THR0-0.078-0.03810.4840.0840.0840.0000.0000.0000.000
92A96VAL0-0.0200.0189.460-0.173-0.1730.0000.0000.0000.000
93A97PRO00.0410.0034.346-0.115-0.032-0.001-0.005-0.0770.000
94A98ALA00.0620.0204.3080.0440.171-0.001-0.010-0.1170.000
95A99ALA0-0.0120.0004.5180.1640.235-0.001-0.011-0.0590.000
96A100LEU0-0.005-0.0115.9560.3230.3230.0000.0000.0000.000
97A101HIS0-0.060-0.0268.5770.4150.4150.0000.0000.0000.000
98A102GLY0-0.020-0.00810.519-0.017-0.0170.0000.0000.0000.000
99A103VAL0-0.023-0.00810.8040.0190.0190.0000.0000.0000.000
100A104ALA0-0.028-0.01213.9680.0440.0440.0000.0000.0000.000
101A105ASP-1-0.856-0.95117.042-0.335-0.3350.0000.0000.0000.000
102A106GLU-1-0.927-0.98820.124-0.232-0.2320.0000.0000.0000.000
103A107VAL00.0160.01718.262-0.048-0.0480.0000.0000.0000.000
104A108MET0-0.0100.01320.6590.0400.0400.0000.0000.0000.000
105A109VAL00.000-0.01021.209-0.030-0.0300.0000.0000.0000.000
106A110LEU0-0.008-0.01523.3580.0300.0300.0000.0000.0000.000
107A111MET0-0.051-0.02025.513-0.002-0.0020.0000.0000.0000.000
108A112PRO0-0.0020.02523.962-0.005-0.0050.0000.0000.0000.000
109A113TRP00.0500.00724.3720.0240.0240.0000.0000.0000.000
110A114GLY0-0.010-0.01224.058-0.018-0.0180.0000.0000.0000.000
111A115LYS10.9250.95219.6870.1830.1830.0000.0000.0000.000
112A116LEU00.0400.04119.4490.0040.0040.0000.0000.0000.000
113A117LEU00.0050.01122.2280.0050.0050.0000.0000.0000.000
114A118ARG10.8300.89525.9670.1110.1110.0000.0000.0000.000
115A119GLY00.0350.01023.4510.0110.0110.0000.0000.0000.000
116A120VAL0-0.019-0.00823.6350.0060.0060.0000.0000.0000.000
117A121VAL0-0.042-0.02025.8460.0100.0100.0000.0000.0000.000
118A122LEU0-0.020-0.00927.9300.0100.0100.0000.0000.0000.000
119A123GLY00.0190.01126.4920.0110.0110.0000.0000.0000.000
120A124GLU-1-0.961-0.97523.334-0.139-0.1390.0000.0000.0000.000
121A125ALA00.0570.00722.244-0.017-0.0170.0000.0000.0000.000
122A126ASP-1-0.848-0.92418.059-0.201-0.2010.0000.0000.0000.000
123A127VAL00.0110.00117.654-0.049-0.0490.0000.0000.0000.000
124A128LEU0-0.009-0.00218.990-0.038-0.0380.0000.0000.0000.000
125A129SER00.012-0.01017.619-0.009-0.0090.0000.0000.0000.000
126A130GLY00.0250.02214.769-0.027-0.0270.0000.0000.0000.000
127A131LEU0-0.045-0.03515.091-0.072-0.0720.0000.0000.0000.000
128A132ARG10.8300.92417.4360.2290.2290.0000.0000.0000.000
129A133ALA00.0070.01612.668-0.001-0.0010.0000.0000.0000.000
130A134VAL00.0070.01412.180-0.064-0.0640.0000.0000.0000.000
131A135ALA0-0.0220.00313.928-0.022-0.0220.0000.0000.0000.000
132A136LYS10.8760.95816.8810.4220.4220.0000.0000.0000.000
133A137PRO00.012-0.02118.4190.0190.0190.0000.0000.0000.000
134A138GLY0-0.0120.00221.532-0.001-0.0010.0000.0000.0000.000
135A139ALA0-0.0210.00220.8710.0080.0080.0000.0000.0000.000
136A140PRO0-0.029-0.02722.8320.0130.0130.0000.0000.0000.000
137A141LEU0-0.0080.00821.748-0.029-0.0290.0000.0000.0000.000
138A142GLU-1-0.851-0.93424.262-0.177-0.1770.0000.0000.0000.000
139A143ILE00.0090.00625.108-0.019-0.0190.0000.0000.0000.000
140A144SER0-0.036-0.01627.2550.0140.0140.0000.0000.0000.000
141A145ILE00.0490.01228.642-0.009-0.0090.0000.0000.0000.000
142A146GLY00.0350.02731.2100.0090.0090.0000.0000.0000.000
143A147THR00.003-0.03834.1910.0030.0030.0000.0000.0000.000
144A148SER0-0.019-0.01036.7800.0050.0050.0000.0000.0000.000
145A149ILE00.0000.00832.1400.0050.0050.0000.0000.0000.000
146A150TRP00.0430.02733.027-0.001-0.0010.0000.0000.0000.000
147A151ARG10.8820.94538.1430.0840.0840.0000.0000.0000.000
148A152GLU-1-0.879-0.92939.625-0.071-0.0710.0000.0000.0000.000
149A153PRO0-0.100-0.05438.8290.0010.0010.0000.0000.0000.000
150A154ILE00.0380.01835.855-0.005-0.0050.0000.0000.0000.000
151A155PRO0-0.025-0.00532.0640.0030.0030.0000.0000.0000.000
152A156LEU00.014-0.01031.2940.0030.0030.0000.0000.0000.000
153A157GLU-1-0.858-0.93628.087-0.132-0.1320.0000.0000.0000.000
154A158ILE00.0300.00830.194-0.003-0.0030.0000.0000.0000.000
155A159ARG10.9320.98632.5400.0720.0720.0000.0000.0000.000
156A160ASP-1-0.870-0.92733.848-0.077-0.0770.0000.0000.0000.000
157A161LEU0-0.040-0.01531.0570.0020.0020.0000.0000.0000.000
158A162PRO0-0.006-0.00135.6920.0000.0000.0000.0000.0000.000
159A163GLU-1-0.916-0.96936.522-0.093-0.0930.0000.0000.0000.000
160A164LEU0-0.0170.00031.8060.0020.0020.0000.0000.0000.000
161A165THR00.0210.00135.937-0.003-0.0030.0000.0000.0000.000
162A166PRO00.044-0.00237.355-0.001-0.0010.0000.0000.0000.000
163A167GLU-1-0.925-0.94838.245-0.066-0.0660.0000.0000.0000.000
164A168THR0-0.0040.00237.5630.0010.0010.0000.0000.0000.000
165A169VAL00.0050.03133.0080.0000.0000.0000.0000.0000.000
166A170VAL00.002-0.00134.594-0.001-0.0010.0000.0000.0000.000
167A171SER0-0.0060.00037.0660.0010.0010.0000.0000.0000.000
168A172THR0-0.021-0.04534.7970.0020.0020.0000.0000.0000.000
169A173GLY00.0570.03834.4440.0010.0010.0000.0000.0000.000
170A174LEU0-0.053-0.01028.388-0.002-0.0020.0000.0000.0000.000
171A175THR00.024-0.01029.880-0.010-0.0100.0000.0000.0000.000
172A176ASP-1-0.893-0.94330.800-0.081-0.0810.0000.0000.0000.000
173A177ARG10.8160.89627.4960.0950.0950.0000.0000.0000.000
174A178LEU0-0.016-0.01025.206-0.010-0.0100.0000.0000.0000.000
175A179ALA0-0.0130.01225.975-0.009-0.0090.0000.0000.0000.000
176A180ALA00.0120.00327.115-0.001-0.0010.0000.0000.0000.000
177A181LEU0-0.044-0.01721.7160.0050.0050.0000.0000.0000.000
178A182GLY00.0010.01021.855-0.023-0.0230.0000.0000.0000.000
179A183TRP0-0.029-0.00919.878-0.014-0.0140.0000.0000.0000.000
180A184GLN0-0.030-0.01825.2950.0110.0110.0000.0000.0000.000
181A185VAL00.0110.00228.762-0.010-0.0100.0000.0000.0000.000
182A186ALA0-0.071-0.04930.8300.0080.0080.0000.0000.0000.000
183A187ASP-1-0.862-0.94632.418-0.110-0.1100.0000.0000.0000.000
184A188VAL00.0040.01233.046-0.009-0.0090.0000.0000.0000.000
185A189ARG10.8710.94835.3240.1260.1260.0000.0000.0000.000
186A190LEU00.0180.00736.723-0.006-0.0060.0000.0000.0000.000
187A191VAL0-0.024-0.01837.1810.0040.0040.0000.0000.0000.000
188A192PRO0-0.0090.01538.755-0.005-0.0050.0000.0000.0000.000
189A212THR0-0.021-0.01539.985-0.001-0.0010.0000.0000.0000.000
190A213GLU-1-0.934-0.97836.253-0.121-0.1210.0000.0000.0000.000
191A214THR0-0.017-0.00438.932-0.002-0.0020.0000.0000.0000.000
192A215VAL00.0250.03133.301-0.003-0.0030.0000.0000.0000.000
193A216LEU0-0.002-0.00733.0470.0030.0030.0000.0000.0000.000
194A217HIS0-0.008-0.00532.038-0.015-0.0150.0000.0000.0000.000
195A218LEU00.0040.00328.1400.0110.0110.0000.0000.0000.000
196A219ARG10.9530.99128.8560.1700.1700.0000.0000.0000.000
197A220ALA00.0110.01326.1010.0160.0160.0000.0000.0000.000
198A221VAL0-0.020-0.00725.771-0.014-0.0140.0000.0000.0000.000
199A222ALA0-0.0010.01221.2520.0130.0130.0000.0000.0000.000
200A223VAL0-0.046-0.03023.2520.0070.0070.0000.0000.0000.000
201A224ASP-1-0.879-0.94623.250-0.129-0.1290.0000.0000.0000.000
202A225PRO0-0.061-0.03922.1550.0010.0010.0000.0000.0000.000
203A226ARG10.9230.97325.0780.1150.1150.0000.0000.0000.000
204A227ASP-1-0.952-0.97028.778-0.054-0.0540.0000.0000.0000.000