FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: G5961

Calculation Name: 3PSF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PSF

Chain ID: A

ChEMBL ID:

UniProt ID: P23615

Base Structure: X-ray

Registration Date: 2023-09-24

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 837
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -21679624.798358
FMO2-HF: Nuclear repulsion 21341440.038246
FMO2-HF: Total energy -338184.760113
FMO2-MP2: Total energy -339181.244188


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:298:ASP)


Summations of interaction energy for fragment #1(A:298:ASP)
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.
182.786188.30.383-2.432-3.4660.01
Interaction energy analysis for fragmet #1(A:298:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.900 / q_NPA : -0.951
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].
3A300TYR0-0.006-0.0093.123-12.577-8.8390.066-1.872-1.9330.011
4A301ASP-1-0.941-0.9542.91834.15735.5700.317-0.493-1.238-0.001
5A302LEU00.027-0.0064.429-5.969-5.6060.000-0.067-0.2950.000
6A303GLU-1-0.885-0.9346.47022.50622.5060.0000.0000.0000.000
7A304ASP-1-0.819-0.9108.16122.31422.3140.0000.0000.0000.000
8A305LEU0-0.0120.0147.543-2.730-2.7300.0000.0000.0000.000
9A306LYS10.9630.98010.411-19.893-19.8930.0000.0000.0000.000
10A307LYS10.7590.86510.634-24.827-24.8270.0000.0000.0000.000
11A308ASN0-0.044-0.02312.607-2.281-2.2810.0000.0000.0000.000
12A309LEU0-0.054-0.00914.777-1.056-1.0560.0000.0000.0000.000
13A310MET0-0.017-0.02512.561-1.228-1.2280.0000.0000.0000.000
14A311THR0-0.010-0.01611.0600.9730.9730.0000.0000.0000.000
15A312GLU-1-0.867-0.93812.35219.44919.4490.0000.0000.0000.000
16A313GLY00.0230.00414.159-1.286-1.2860.0000.0000.0000.000
17A314ASP-1-0.809-0.89015.31716.38716.3870.0000.0000.0000.000
18A315MET00.0040.00315.338-1.128-1.1280.0000.0000.0000.000
19A316LYS10.9090.95117.879-13.552-13.5520.0000.0000.0000.000
20A317ILE0-0.0260.00120.331-0.778-0.7780.0000.0000.0000.000
21A318ARG10.8030.89217.709-15.949-15.9490.0000.0000.0000.000
22A319LYS10.8200.90820.787-14.058-14.0580.0000.0000.0000.000
23A320THR0-0.025-0.00923.764-0.484-0.4840.0000.0000.0000.000
24A321ASP-1-0.768-0.87726.1589.5059.5050.0000.0000.0000.000
25A322ILE0-0.0040.00028.816-0.323-0.3230.0000.0000.0000.000
26A323PRO00.0780.04429.0010.4170.4170.0000.0000.0000.000
27A324GLU-1-0.772-0.87523.86012.54412.5440.0000.0000.0000.000
28A325ARG10.8170.86927.479-9.313-9.3130.0000.0000.0000.000
29A326TYR0-0.022-0.03029.7050.0330.0330.0000.0000.0000.000
30A327GLN0-0.047-0.02525.1670.4420.4420.0000.0000.0000.000
31A328GLU-1-0.819-0.89423.91612.53612.5360.0000.0000.0000.000
32A329LEU0-0.0090.00426.6540.0720.0720.0000.0000.0000.000
33A330ARG10.8360.91629.349-9.320-9.3200.0000.0000.0000.000
34A331ALA0-0.0100.01024.0240.0520.0520.0000.0000.0000.000
35A332GLY0-0.026-0.00725.5610.2800.2800.0000.0000.0000.000
36A333ILE0-0.079-0.03127.329-0.327-0.3270.0000.0000.0000.000
37A334THR0-0.006-0.00828.8810.2970.2970.0000.0000.0000.000
38A335ASP-1-0.835-0.91130.1089.2989.2980.0000.0000.0000.000
39A336TYR0-0.030-0.04831.450-0.262-0.2620.0000.0000.0000.000
40A337GLY0-0.028-0.02833.223-0.256-0.2560.0000.0000.0000.000
41A338ASN0-0.090-0.04433.857-0.259-0.2590.0000.0000.0000.000
42A339MET00.0120.02237.253-0.066-0.0660.0000.0000.0000.000
43A340SER00.023-0.02239.710-0.151-0.1510.0000.0000.0000.000
44A341SER00.013-0.01543.1280.0220.0220.0000.0000.0000.000
45A342GLU-1-0.912-0.95346.2266.3426.3420.0000.0000.0000.000
46A343ASP-1-0.807-0.87742.7597.1757.1750.0000.0000.0000.000
47A344GLN0-0.034-0.02242.433-0.045-0.0450.0000.0000.0000.000
48A345GLU-1-0.796-0.86144.5966.1216.1210.0000.0000.0000.000
49A346LEU00.0000.00246.546-0.093-0.0930.0000.0000.0000.000
50A347GLH0-0.067-0.04740.240-0.032-0.0320.0000.0000.0000.000
51A348ARG10.8740.90945.135-6.133-6.1330.0000.0000.0000.000
52A349ASN0-0.033-0.02447.482-0.177-0.1770.0000.0000.0000.000
53A350TRP00.0110.00641.989-0.037-0.0370.0000.0000.0000.000
54A351ILE0-0.016-0.02042.196-0.025-0.0250.0000.0000.0000.000
55A352ALA0-0.003-0.00246.584-0.048-0.0480.0000.0000.0000.000
56A353GLU-1-0.943-0.96549.9615.7665.7660.0000.0000.0000.000
57A354LYS10.8910.94344.821-6.798-6.7980.0000.0000.0000.000
58A355ILE0-0.012-0.00345.471-0.013-0.0130.0000.0000.0000.000
59A356SER00.0150.00449.477-0.095-0.0950.0000.0000.0000.000
60A357VAL0-0.035-0.01551.642-0.099-0.0990.0000.0000.0000.000
61A358ASP-1-0.972-0.98751.6545.9205.9200.0000.0000.0000.000
62A359LYS10.8380.91050.508-6.177-6.1770.0000.0000.0000.000
63A360ASN0-0.111-0.04455.711-0.143-0.1430.0000.0000.0000.000
64A361PHE00.0490.03055.385-0.057-0.0570.0000.0000.0000.000
65A362ASP-1-0.921-0.96160.4334.8414.8410.0000.0000.0000.000
66A363ALA0-0.016-0.02063.2150.0370.0370.0000.0000.0000.000
67A364ASN0-0.060-0.03864.839-0.001-0.0010.0000.0000.0000.000
68A365TYR0-0.0140.00658.6360.0080.0080.0000.0000.0000.000
69A366ASP-1-0.808-0.87461.8145.1685.1680.0000.0000.0000.000
70A367LEU00.002-0.00756.5540.0560.0560.0000.0000.0000.000
71A368THR0-0.067-0.05856.9180.1450.1450.0000.0000.0000.000
72A369GLU-1-0.812-0.91656.5445.4935.4930.0000.0000.0000.000
73A370PHE00.0240.01852.0190.1170.1170.0000.0000.0000.000
74A371LYS10.9150.93552.411-5.629-5.6290.0000.0000.0000.000
75A372GLU-1-0.974-0.97551.5135.7655.7650.0000.0000.0000.000
76A373ALA0-0.0170.01851.2370.1210.1210.0000.0000.0000.000
77A374ILE0-0.001-0.00747.0680.1680.1680.0000.0000.0000.000
78A375GLY0-0.013-0.01446.8960.1690.1690.0000.0000.0000.000
79A376ASN0-0.038-0.02146.5220.1960.1960.0000.0000.0000.000
80A377ALA00.0270.01844.6280.1550.1550.0000.0000.0000.000
81A378ILE00.0090.00141.9590.2080.2080.0000.0000.0000.000
82A379LYS10.7900.89841.737-6.726-6.7260.0000.0000.0000.000
83A380PHE00.026-0.00241.6850.1440.1440.0000.0000.0000.000
84A381ILE00.0090.01537.5210.2120.2120.0000.0000.0000.000
85A382THR0-0.043-0.03537.2680.3150.3150.0000.0000.0000.000
86A383LYS10.8510.92437.272-7.130-7.1300.0000.0000.0000.000
87A384GLU-1-0.825-0.89938.5447.2677.2670.0000.0000.0000.000
88A385ASN0-0.0360.00834.1280.2340.2340.0000.0000.0000.000
89A386LEU00.0620.03735.6460.1780.1780.0000.0000.0000.000
90A387GLU-1-0.746-0.84033.8629.1049.1040.0000.0000.0000.000
91A388VAL00.0360.01437.743-0.181-0.1810.0000.0000.0000.000
92A389PRO00.0500.02937.990-0.180-0.1800.0000.0000.0000.000
93A390PHE00.0450.02039.820-0.178-0.1780.0000.0000.0000.000
94A391ILE0-0.048-0.02140.945-0.196-0.1960.0000.0000.0000.000
95A392TYR00.0190.00143.750-0.237-0.2370.0000.0000.0000.000
96A393ALA0-0.0360.00144.350-0.174-0.1740.0000.0000.0000.000
97A394TYR0-0.034-0.04242.636-0.088-0.0880.0000.0000.0000.000
98A395ARG10.7840.84644.528-6.907-6.9070.0000.0000.0000.000
99A396ARG10.9590.99148.179-6.333-6.3330.0000.0000.0000.000
100A397ASN00.0360.01550.302-0.028-0.0280.0000.0000.0000.000
101A398TYR0-0.0160.00349.671-0.087-0.0870.0000.0000.0000.000
102A399ILE0-0.039-0.02447.1150.0740.0740.0000.0000.0000.000
103A400SER00.0270.01150.8700.0220.0220.0000.0000.0000.000
104A401SER0-0.054-0.00754.2230.0200.0200.0000.0000.0000.000
105A402ARG10.8400.89257.823-5.341-5.3410.0000.0000.0000.000
106A403GLU-1-0.937-0.95859.9924.8444.8440.0000.0000.0000.000
107A404LYS10.9530.97461.175-4.629-4.6290.0000.0000.0000.000
108A405ASP-1-0.951-0.97860.1595.0905.0900.0000.0000.0000.000
109A406GLY00.0170.03060.327-0.053-0.0530.0000.0000.0000.000
110A407PHE0-0.023-0.03353.3690.0450.0450.0000.0000.0000.000
111A408LEU00.009-0.00251.3430.0100.0100.0000.0000.0000.000
112A409LEU0-0.070-0.02048.3920.0350.0350.0000.0000.0000.000
113A410THR00.018-0.02248.8160.0910.0910.0000.0000.0000.000
114A411GLU-1-0.818-0.93843.6786.9646.9640.0000.0000.0000.000
115A412ASP-1-0.841-0.89543.5797.0527.0520.0000.0000.0000.000
116A413ASP-1-0.791-0.84744.2976.4776.4770.0000.0000.0000.000
117A414LEU0-0.015-0.01642.7930.1350.1350.0000.0000.0000.000
118A415TRP0-0.018-0.03935.8080.3220.3220.0000.0000.0000.000
119A416ASP-1-0.803-0.87339.8187.3477.3470.0000.0000.0000.000
120A417ILE0-0.005-0.01041.4110.0970.0970.0000.0000.0000.000
121A418VAL00.0140.01735.9690.1200.1200.0000.0000.0000.000
122A419SER0-0.045-0.02836.7640.2610.2610.0000.0000.0000.000
123A420LEU0-0.043-0.02737.6800.0860.0860.0000.0000.0000.000
124A421ASP-1-0.737-0.82537.0478.2528.2520.0000.0000.0000.000
125A422ILE00.0130.01132.6040.0660.0660.0000.0000.0000.000
126A423GLU-1-0.835-0.91035.5427.9067.9060.0000.0000.0000.000
127A424PHE00.021-0.00237.307-0.042-0.0420.0000.0000.0000.000
128A425HIS10.8750.93334.989-8.459-8.4590.0000.0000.0000.000
129A426SER0-0.029-0.01634.0540.2240.2240.0000.0000.0000.000
130A427LEU0-0.042-0.00735.2260.0640.0640.0000.0000.0000.000
131A428VAL00.0720.02638.2550.0080.0080.0000.0000.0000.000
132A429ASN0-0.0240.00232.2220.2960.2960.0000.0000.0000.000
133A430LYS10.9210.95931.886-9.281-9.2810.0000.0000.0000.000
134A431LYS10.8700.92636.762-7.376-7.3760.0000.0000.0000.000
135A432ASP-1-0.834-0.91837.3187.7277.7270.0000.0000.0000.000
136A433TYR0-0.099-0.04532.5540.1320.1320.0000.0000.0000.000
137A434VAL00.0280.00436.521-0.015-0.0150.0000.0000.0000.000
138A435GLN00.0220.01839.583-0.003-0.0030.0000.0000.0000.000
139A436ARG10.9340.96332.859-9.044-9.0440.0000.0000.0000.000
140A437PHE00.0290.01637.4770.0180.0180.0000.0000.0000.000
141A438TYR00.016-0.01039.304-0.033-0.0330.0000.0000.0000.000
142A439ALA0-0.006-0.01542.583-0.108-0.1080.0000.0000.0000.000
143A440GLU-1-0.992-0.98837.0398.4238.4230.0000.0000.0000.000
144A441LEU00.0340.01341.448-0.063-0.0630.0000.0000.0000.000
145A442HIS0-0.106-0.03843.362-0.156-0.1560.0000.0000.0000.000
146A443ILE0-0.033-0.02246.250-0.180-0.1800.0000.0000.0000.000
147A444ASP-1-0.891-0.92548.5916.0216.0210.0000.0000.0000.000
148A445ASP-1-0.725-0.83050.0115.9955.9950.0000.0000.0000.000
149A446PRO00.012-0.01351.7980.0350.0350.0000.0000.0000.000
150A447ILE00.0230.02451.170-0.021-0.0210.0000.0000.0000.000
151A448VAL00.000-0.00346.4590.0290.0290.0000.0000.0000.000
152A449THR0-0.014-0.02049.5890.1200.1200.0000.0000.0000.000
153A450GLU-1-0.907-0.92551.4655.5875.5870.0000.0000.0000.000
154A451TYR0-0.023-0.01745.7590.0350.0350.0000.0000.0000.000
155A452PHE0-0.024-0.02943.6430.0440.0440.0000.0000.0000.000
156A453LYS10.9200.98549.124-5.500-5.5000.0000.0000.0000.000
157A454ASN0-0.041-0.02952.511-0.060-0.0600.0000.0000.0000.000
158A455GLN0-0.0220.00747.5440.0270.0270.0000.0000.0000.000
159A464ASN00.002-0.00542.4920.1350.1350.0000.0000.0000.000
160A465SER00.0260.00744.4480.0710.0710.0000.0000.0000.000
161A466LEU00.0100.01339.795-0.006-0.0060.0000.0000.0000.000
162A467GLN0-0.002-0.00838.6270.1630.1630.0000.0000.0000.000
163A468ASP-1-0.767-0.84941.7986.6966.6960.0000.0000.0000.000
164A469ILE00.0100.00244.410-0.051-0.0510.0000.0000.0000.000
165A470TYR0-0.065-0.04237.1360.0160.0160.0000.0000.0000.000
166A471ASP-1-0.768-0.87541.4057.4697.4690.0000.0000.0000.000
167A472TYR0-0.104-0.07343.170-0.074-0.0740.0000.0000.0000.000
168A473LEU0-0.007-0.00643.291-0.107-0.1070.0000.0000.0000.000
169A474GLU-1-0.917-0.93138.3278.0358.0350.0000.0000.0000.000
170A475PHE0-0.081-0.05542.461-0.023-0.0230.0000.0000.0000.000
171A476LYS10.7810.89445.431-6.072-6.0720.0000.0000.0000.000
172A477TYR0-0.025-0.04545.324-0.117-0.1170.0000.0000.0000.000
173A478ALA00.0150.02542.7180.1380.1380.0000.0000.0000.000
174A479ASN0-0.005-0.02542.0620.2900.2900.0000.0000.0000.000
175A480GLU-1-0.878-0.95542.7926.8086.8080.0000.0000.0000.000
176A481ILE00.0080.00739.1520.0940.0940.0000.0000.0000.000
177A482ASN0-0.119-0.04837.9390.3100.3100.0000.0000.0000.000
178A483GLU-1-1.030-0.99637.6817.5407.5400.0000.0000.0000.000
179A484MET0-0.0510.00235.6310.2250.2250.0000.0000.0000.000
180A501SER0-0.012-0.01844.8130.0220.0220.0000.0000.0000.000
181A502TYR00.025-0.03546.860-0.108-0.1080.0000.0000.0000.000
182A503GLU-1-0.807-0.90646.0296.5366.5360.0000.0000.0000.000
183A504LYS10.8400.91645.795-6.887-6.8870.0000.0000.0000.000
184A505PHE0-0.003-0.00149.784-0.129-0.1290.0000.0000.0000.000
185A506LYS10.9130.96151.848-5.983-5.9830.0000.0000.0000.000
186A507ALA0-0.0120.00652.183-0.076-0.0760.0000.0000.0000.000
187A508SER0-0.034-0.00754.075-0.121-0.1210.0000.0000.0000.000
188A509PRO00.0690.02456.076-0.034-0.0340.0000.0000.0000.000
189A510LEU0-0.026-0.02257.822-0.079-0.0790.0000.0000.0000.000
190A511TYR0-0.030-0.03055.418-0.053-0.0530.0000.0000.0000.000
191A512GLN0-0.017-0.01258.7090.0340.0340.0000.0000.0000.000
192A513ALA00.0260.00062.102-0.059-0.0590.0000.0000.0000.000
193A514VAL0-0.039-0.02657.707-0.049-0.0490.0000.0000.0000.000
194A515SER0-0.012-0.00161.0510.0150.0150.0000.0000.0000.000
195A516ASP-1-0.890-0.94462.8704.7404.7400.0000.0000.0000.000
196A517ILE0-0.072-0.01561.200-0.078-0.0780.0000.0000.0000.000
197A518GLY00.0320.02365.241-0.052-0.0520.0000.0000.0000.000
198A519ILE0-0.021-0.00963.134-0.045-0.0450.0000.0000.0000.000
199A520SER0-0.006-0.00959.0830.0940.0940.0000.0000.0000.000
200A521ALA00.0510.00055.893-0.032-0.0320.0000.0000.0000.000
201A522GLU-1-0.859-0.94254.5315.7645.7640.0000.0000.0000.000
202A523ASP-1-0.818-0.87057.7315.0875.0870.0000.0000.0000.000
203A524VAL00.008-0.00959.606-0.055-0.0550.0000.0000.0000.000
204A525GLY00.000-0.00357.607-0.020-0.0200.0000.0000.0000.000
205A526GLU-1-0.855-0.92958.5185.3005.3000.0000.0000.0000.000
206A527ASN0-0.0270.00560.832-0.094-0.0940.0000.0000.0000.000
207A528ILE0-0.022-0.01858.994-0.049-0.0490.0000.0000.0000.000
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