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: 94492

Calculation Name: 5DSS-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DSS

Chain ID: B

ChEMBL ID:

UniProt ID: A0A158

Base Structure: X-ray

Registration Date: 2023-06-21

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1908430.511389
FMO2-HF: Nuclear repulsion 1837410.657846
FMO2-HF: Total energy -71019.853543
FMO2-MP2: Total energy -71226.218548


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(B:1:LYS)


Summations of interaction energy for fragment #1(B:1:LYS)
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.
-146.28-144.29621.136-13.003-10.114-0.121
Interaction energy analysis for fragmet #1(B:1:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.831 / q_NPA : 0.871
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].
3B3ASP-1-0.906-0.9502.029-32.235-28.1003.532-3.784-3.883-0.006
4B4ALA0-0.027-0.0093.4630.1620.0160.0160.639-0.5080.001
5B5GLU-1-0.829-0.9155.608-19.646-19.596-0.0010.000-0.0480.000
6B6PRO0-0.063-0.0388.995-1.434-1.4340.0000.0000.0000.000
7B7VAL0-0.0080.01011.6120.3050.3050.0000.0000.0000.000
8B8ILE00.0060.01014.0051.2031.2030.0000.0000.0000.000
9B9ASP-1-0.756-0.88717.543-13.965-13.9650.0000.0000.0000.000
10B10THR0-0.073-0.04319.223-0.067-0.0670.0000.0000.0000.000
11B11ASP-1-0.871-0.93321.417-11.629-11.6290.0000.0000.0000.000
12B12GLY0-0.070-0.04022.3710.4460.4460.0000.0000.0000.000
13B13ASN0-0.105-0.06720.809-0.008-0.0080.0000.0000.0000.000
14B14PRO00.0030.00316.467-0.394-0.3940.0000.0000.0000.000
15B15LEU0-0.0130.00116.7470.8940.8940.0000.0000.0000.000
16B16LEU0-0.008-0.01317.617-0.626-0.6260.0000.0000.0000.000
17B17HIS00.0510.01614.624-0.064-0.0640.0000.0000.0000.000
18B18ARG10.8240.89719.78513.13313.1330.0000.0000.0000.000
19B19GLY0-0.052-0.03522.4710.7400.7400.0000.0000.0000.000
20B20LYS10.8490.92623.00410.10510.1050.0000.0000.0000.000
21B21TYR00.0420.02421.5550.1100.1100.0000.0000.0000.000
22B22TYR00.0210.01324.0490.3550.3550.0000.0000.0000.000
23B23ILE0-0.004-0.00419.504-0.508-0.5080.0000.0000.0000.000
24B24MET00.0290.02622.8020.4330.4330.0000.0000.0000.000
25B25PRO0-0.050-0.01023.087-0.657-0.6570.0000.0000.0000.000
26B26SER00.0250.00721.698-0.013-0.0130.0000.0000.0000.000
27B27ASN0-0.025-0.01523.7920.1660.1660.0000.0000.0000.000
28B28TRP0-0.021-0.03426.6680.0760.0760.0000.0000.0000.000
29B29GLY00.0760.03826.1350.3470.3470.0000.0000.0000.000
30B30PRO0-0.0030.03426.059-0.358-0.3580.0000.0000.0000.000
31B31PRO00.021-0.00429.2350.0270.0270.0000.0000.0000.000
32B32GLY0-0.010-0.00828.433-0.344-0.3440.0000.0000.0000.000
33B33GLY00.0320.02028.2290.4190.4190.0000.0000.0000.000
34B34GLY00.0520.04027.343-0.516-0.5160.0000.0000.0000.000
35B35LEU0-0.049-0.02822.260-0.009-0.0090.0000.0000.0000.000
36B36ARG10.8760.91827.0469.8569.8560.0000.0000.0000.000
37B37LEU00.0370.02928.201-0.103-0.1030.0000.0000.0000.000
38B38GLY00.006-0.00930.6530.2500.2500.0000.0000.0000.000
39B39LYS10.9170.96433.4087.7527.7520.0000.0000.0000.000
40B40THR00.018-0.02231.472-0.148-0.1480.0000.0000.0000.000
41B41ARG10.7770.85934.1859.1309.1300.0000.0000.0000.000
42B42ASN0-0.004-0.00836.4220.2650.2650.0000.0000.0000.000
43B43LEU00.0260.01337.651-0.219-0.2190.0000.0000.0000.000
44B44ASN0-0.004-0.00336.7080.0840.0840.0000.0000.0000.000
45B45CYS0-0.035-0.02335.384-0.161-0.1610.0000.0000.0000.000
46B46PRO0-0.016-0.01133.513-0.242-0.2420.0000.0000.0000.000
47B47VAL00.0790.07827.988-0.159-0.1590.0000.0000.0000.000
48B48THR0-0.071-0.02527.813-0.396-0.3960.0000.0000.0000.000
49B49VAL00.0220.02524.2070.3700.3700.0000.0000.0000.000
50B50LEU0-0.046-0.03426.541-0.117-0.1170.0000.0000.0000.000
51B51GLN00.0280.02124.928-0.171-0.1710.0000.0000.0000.000
52B52ASP-1-0.837-0.90827.606-9.213-9.2130.0000.0000.0000.000
53B53TYR0-0.094-0.06330.386-0.285-0.2850.0000.0000.0000.000
54B54ASN0-0.007-0.00533.1260.3010.3010.0000.0000.0000.000
55B55GLU-1-0.785-0.90132.228-9.379-9.3790.0000.0000.0000.000
56B56ALA0-0.0470.00133.279-0.089-0.0890.0000.0000.0000.000
57B57ILE0-0.018-0.00532.1260.1010.1010.0000.0000.0000.000
58B58ASN00.027-0.00228.725-0.027-0.0270.0000.0000.0000.000
59B59GLY0-0.021-0.01328.270-0.437-0.4370.0000.0000.0000.000
60B60LEU0-0.028-0.01028.7160.2690.2690.0000.0000.0000.000
61B61PRO00.012-0.00126.906-0.409-0.4090.0000.0000.0000.000
62B62VAL0-0.0060.00121.8710.1830.1830.0000.0000.0000.000
63B63LYS10.8460.92622.10111.87111.8710.0000.0000.0000.000
64B64PHE00.0910.04315.870-0.059-0.0590.0000.0000.0000.000
65B65ASN00.0150.01818.2070.1330.1330.0000.0000.0000.000
66B66ILE00.1080.05713.314-0.107-0.1070.0000.0000.0000.000
67B67ARG10.7560.85316.51414.57214.5720.0000.0000.0000.000
68B68GLU-1-0.835-0.89819.839-12.999-12.9990.0000.0000.0000.000
69B69ILE00.0100.00717.3370.3290.3290.0000.0000.0000.000
70B70LEU0-0.050-0.02621.1370.1030.1030.0000.0000.0000.000
71B71PRO00.0430.02516.6100.4070.4070.0000.0000.0000.000
72B72ARG10.9300.94518.56814.80214.8020.0000.0000.0000.000
73B73THR0-0.029-0.01713.9371.1161.1160.0000.0000.0000.000
74B74ILE00.0010.02511.978-0.656-0.6560.0000.0000.0000.000
75B75PHE00.0310.0118.8391.3211.3210.0000.0000.0000.000
76B76THR00.0170.0006.368-0.585-0.5850.0000.0000.0000.000
77B77ASP-1-0.875-0.9201.654-131.779-133.88717.590-9.858-5.624-0.116
78B78THR0-0.029-0.0135.2650.0280.081-0.0010.000-0.0510.000
79B79GLU-1-0.919-0.9438.235-23.697-23.6970.0000.0000.0000.000
80B80LEU0-0.034-0.02710.3652.1462.1460.0000.0000.0000.000
81B81ASN00.010-0.00813.847-0.026-0.0260.0000.0000.0000.000
82B82ILE00.0060.01417.0180.2610.2610.0000.0000.0000.000
83B83GLU-1-0.763-0.86419.191-12.246-12.2460.0000.0000.0000.000
84B84PHE00.0130.00723.008-0.091-0.0910.0000.0000.0000.000
85B85THR0-0.019-0.03325.9410.0230.0230.0000.0000.0000.000
86B86GLU-1-0.954-0.97428.391-8.911-8.9110.0000.0000.0000.000
87B87LYS10.8350.91830.1019.2559.2550.0000.0000.0000.000
88B88PRO00.0370.01631.8540.3050.3050.0000.0000.0000.000
89B89ASN0-0.002-0.01234.282-0.131-0.1310.0000.0000.0000.000
90B91ALA00.0680.05631.098-0.003-0.0030.0000.0000.0000.000
91B92GLU-1-0.727-0.85330.529-10.012-10.0120.0000.0000.0000.000
92B93ASN0-0.021-0.01426.340-0.049-0.0490.0000.0000.0000.000
93B94ARG10.8570.91226.57911.65611.6560.0000.0000.0000.000
94B95ALA00.0050.00122.446-0.309-0.3090.0000.0000.0000.000
95B96TRP0-0.034-0.02019.3220.1100.1100.0000.0000.0000.000
96B97SER00.0120.01720.217-0.817-0.8170.0000.0000.0000.000
97B98LEU00.002-0.00917.6260.4010.4010.0000.0000.0000.000
98B99PHE00.0190.01621.447-0.130-0.1300.0000.0000.0000.000
99B100LYS10.9170.94222.10611.96311.9630.0000.0000.0000.000
100B101GLY0-0.037-0.00323.9400.4770.4770.0000.0000.0000.000
101B102ASP-1-0.822-0.91025.314-10.998-10.9980.0000.0000.0000.000
102B103ASP-1-0.822-0.91129.030-9.252-9.2520.0000.0000.0000.000
103B104ARG10.8670.91631.9248.7518.7510.0000.0000.0000.000
104B105GLY0-0.016-0.00828.7610.1360.1360.0000.0000.0000.000
105B106HIS0-0.021-0.01927.357-0.322-0.3220.0000.0000.0000.000
106B107LYS10.8980.95721.11113.61813.6180.0000.0000.0000.000
107B108ALA00.0040.01019.9560.4130.4130.0000.0000.0000.000
108B109ARG10.7600.88421.53911.23311.2330.0000.0000.0000.000
109B110VAL0-0.0010.00321.425-0.023-0.0230.0000.0000.0000.000
110B111GLY0-0.017-0.03223.2000.6820.6820.0000.0000.0000.000
111B112ILE0-0.0300.00424.314-0.519-0.5190.0000.0000.0000.000
112B113GLY00.0350.00626.7080.4820.4820.0000.0000.0000.000
113B114GLY0-0.066-0.02626.882-0.506-0.5060.0000.0000.0000.000
114B115SER00.008-0.01628.705-0.072-0.0720.0000.0000.0000.000
115B116ASN0-0.021-0.02129.919-0.358-0.3580.0000.0000.0000.000
116B117GLY00.0040.00031.7530.3470.3470.0000.0000.0000.000
117B118HIS00.012-0.01233.667-0.301-0.3010.0000.0000.0000.000
118B119PRO00.0100.02331.7310.0010.0010.0000.0000.0000.000
119B120GLY00.0350.00629.817-0.459-0.4590.0000.0000.0000.000
120B121GLY0-0.022-0.00829.1620.3440.3440.0000.0000.0000.000
121B122GLU-1-0.822-0.88225.397-12.138-12.1380.0000.0000.0000.000
122B123MET0-0.0210.00623.227-0.332-0.3320.0000.0000.0000.000
123B124LEU0-0.037-0.02918.4120.0690.0690.0000.0000.0000.000
124B125ARG10.8230.89918.77413.60513.6050.0000.0000.0000.000
125B126GLY00.0600.00614.990-0.368-0.3680.0000.0000.0000.000
126B127GLY0-0.0160.02312.9121.3181.3180.0000.0000.0000.000
127B128PHE0-0.068-0.05612.252-0.747-0.7470.0000.0000.0000.000
128B129TYR00.0440.0275.4871.5101.5100.0000.0000.0000.000
129B130GLY0-0.037-0.0369.1642.8932.8930.0000.0000.0000.000
130B131GLU-1-0.744-0.8499.778-23.453-23.4530.0000.0000.0000.000
131B132GLN0-0.142-0.08210.769-1.114-1.1140.0000.0000.0000.000
132B133HIS0-0.0190.0066.9210.4800.4800.0000.0000.0000.000
133B134GLY00.0030.00411.4271.4221.4220.0000.0000.0000.000
134B135LEU0-0.002-0.01113.9270.0360.0360.0000.0000.0000.000
135B136ARG10.9190.95416.71013.97313.9730.0000.0000.0000.000
136B137ASN0-0.004-0.01519.3070.5740.5740.0000.0000.0000.000
137B138GLY00.0120.02619.321-0.144-0.1440.0000.0000.0000.000
138B139THR00.005-0.00415.872-0.455-0.4550.0000.0000.0000.000
139B140TYR0-0.050-0.04014.4970.8230.8230.0000.0000.0000.000
140B141LYS10.8570.93310.57026.00926.0090.0000.0000.0000.000
141B142LEU00.0440.02912.525-1.235-1.2350.0000.0000.0000.000
142B143VAL0-0.026-0.0188.5870.9040.9040.0000.0000.0000.000
143B144PHE0-0.005-0.00111.7760.5200.5200.0000.0000.0000.000
144B145CYS0-0.0110.0077.7190.1380.1380.0000.0000.0000.000
145B146ARG10.8970.94311.27720.08420.0840.0000.0000.0000.000
146B147ASP-1-0.833-0.93014.009-18.725-18.7250.0000.0000.0000.000
147B148GLY0-0.0100.00315.605-0.053-0.0530.0000.0000.0000.000
148B149SER0-0.038-0.03615.8260.6700.6700.0000.0000.0000.000
149B150SER0-0.080-0.05112.9611.3861.3860.0000.0000.0000.000
150B151THR00.0740.0578.471-2.546-2.5460.0000.0000.0000.000
151B153LEU00.0150.0129.8240.2450.2450.0000.0000.0000.000
152B154ASP-1-0.743-0.86011.597-25.549-25.5490.0000.0000.0000.000
153B155VAL0-0.038-0.01213.5141.4641.4640.0000.0000.0000.000
154B156GLY00.010-0.00416.748-0.068-0.0680.0000.0000.0000.000
155B157ARG10.7200.81219.75513.37313.3730.0000.0000.0000.000
156B158TYR00.0450.03023.5570.1170.1170.0000.0000.0000.000
157B159GLY00.0490.00826.6330.0470.0470.0000.0000.0000.000
158B160ASN0-0.046-0.02930.1630.0330.0330.0000.0000.0000.000
159B161ARG10.9410.97133.1068.6268.6260.0000.0000.0000.000
160B162GLU-1-0.798-0.83633.914-8.987-8.9870.0000.0000.0000.000
161B163GLY00.0690.02532.1370.1300.1300.0000.0000.0000.000
162B164ARG10.8430.94226.89511.03711.0370.0000.0000.0000.000
163B165ARG10.9330.98026.94710.33110.3310.0000.0000.0000.000
164B166LEU00.0560.02821.020-0.069-0.0690.0000.0000.0000.000
165B167GLY00.022-0.00321.3190.4910.4910.0000.0000.0000.000
166B168LEU0-0.0380.00215.673-0.180-0.1800.0000.0000.0000.000
167B169SER0-0.048-0.04217.0691.1041.1040.0000.0000.0000.000
168B170GLU-1-0.867-0.94016.292-15.229-15.2290.0000.0000.0000.000
169B171ALA0-0.030-0.00915.947-0.447-0.4470.0000.0000.0000.000
170B172GLY00.0450.03715.397-1.066-1.0660.0000.0000.0000.000
171B173GLU-1-0.859-0.89316.304-12.646-12.6460.0000.0000.0000.000
172B174LEU0-0.039-0.02917.439-0.818-0.8180.0000.0000.0000.000
173B175GLY00.0590.02617.821-0.951-0.9510.0000.0000.0000.000
174B176VAL0-0.059-0.03817.2110.7770.7770.0000.0000.0000.000
175B177GLY00.0380.04319.275-0.451-0.4510.0000.0000.0000.000
176B178PHE0-0.033-0.01515.8550.5030.5030.0000.0000.0000.000
177B179GLU-1-0.748-0.86121.295-10.978-10.9780.0000.0000.0000.000
178B180LYS10.9080.96724.02612.50912.5090.0000.0000.0000.000
179B181ALA00.0040.01625.6680.4970.4970.0000.0000.0000.000
180B182GLY0-0.011-0.01628.2220.3520.3520.0000.0000.0000.000
181B183GLY0-0.034-0.02629.034-0.320-0.3200.0000.0000.0000.000
182B184GLY00.0710.04330.9620.0400.0400.0000.0000.0000.000
183B185ASN0-0.0020.02027.208-0.624-0.6240.0000.0000.0000.000