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: 8935Y

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 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 837
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -21717423.158579
FMO2-HF: Nuclear repulsion 21379236.109443
FMO2-HF: Total energy -338187.049136
FMO2-MP2: Total energy -339183.741869


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.
182.491186.8660.354-1.835-2.8950.006
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 : -0.907 / q_NPA : -0.953
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].
3A300TYR00.010-0.0093.439-10.079-7.4570.033-1.267-1.3880.007
4A301ASP-1-0.922-0.9372.80833.09334.4090.321-0.451-1.187-0.001
5A302LEU00.0470.0104.214-6.334-5.8970.000-0.117-0.3200.000
6A303GLU-1-0.899-0.9376.26022.37722.3770.0000.0000.0000.000
7A304ASP-1-0.819-0.9097.57722.09522.0950.0000.0000.0000.000
8A305LEU0-0.0190.0017.153-3.130-3.1300.0000.0000.0000.000
9A306LYS10.9520.97510.120-20.182-20.1820.0000.0000.0000.000
10A307LYS10.7360.84910.166-25.506-25.5060.0000.0000.0000.000
11A308ASN0-0.056-0.04012.102-2.330-2.3300.0000.0000.0000.000
12A309LEU0-0.030-0.00114.934-0.936-0.9360.0000.0000.0000.000
13A310MET0-0.012-0.01812.932-1.384-1.3840.0000.0000.0000.000
14A311THR0-0.002-0.01310.6240.8970.8970.0000.0000.0000.000
15A312GLU-1-0.901-0.95212.17519.26119.2610.0000.0000.0000.000
16A313GLY00.0340.01514.106-1.262-1.2620.0000.0000.0000.000
17A314ASP-1-0.801-0.87614.87716.68816.6880.0000.0000.0000.000
18A315MET00.009-0.00215.204-1.253-1.2530.0000.0000.0000.000
19A316LYS10.9110.95317.804-13.546-13.5460.0000.0000.0000.000
20A317ILE0-0.0250.00220.087-0.799-0.7990.0000.0000.0000.000
21A318ARG10.7730.87117.723-15.848-15.8480.0000.0000.0000.000
22A319LYS10.8370.89820.722-13.963-13.9630.0000.0000.0000.000
23A320THR0-0.024-0.00623.695-0.418-0.4180.0000.0000.0000.000
24A321ASP-1-0.768-0.86425.9159.4289.4280.0000.0000.0000.000
25A322ILE00.0110.00028.665-0.303-0.3030.0000.0000.0000.000
26A323PRO00.0730.04328.5760.4440.4440.0000.0000.0000.000
27A324GLU-1-0.784-0.85923.45412.62212.6220.0000.0000.0000.000
28A325ARG10.8100.85927.082-9.366-9.3660.0000.0000.0000.000
29A326TYR0-0.017-0.03729.3850.0310.0310.0000.0000.0000.000
30A327GLN0-0.054-0.02424.8330.4180.4180.0000.0000.0000.000
31A328GLU-1-0.803-0.89723.38812.61712.6170.0000.0000.0000.000
32A329LEU0-0.020-0.00326.2000.0640.0640.0000.0000.0000.000
33A330ARG10.8450.92328.991-9.394-9.3940.0000.0000.0000.000
34A331ALA0-0.033-0.00723.8250.0150.0150.0000.0000.0000.000
35A332GLY0-0.0120.00725.1320.3600.3600.0000.0000.0000.000
36A333ILE0-0.087-0.03327.328-0.327-0.3270.0000.0000.0000.000
37A334THR00.008-0.00729.0080.2880.2880.0000.0000.0000.000
38A335ASP-1-0.832-0.91130.2639.2379.2370.0000.0000.0000.000
39A336TYR0-0.028-0.03931.811-0.262-0.2620.0000.0000.0000.000
40A337GLY0-0.020-0.01233.565-0.238-0.2380.0000.0000.0000.000
41A338ASN0-0.081-0.05433.874-0.278-0.2780.0000.0000.0000.000
42A339MET00.0130.03037.475-0.091-0.0910.0000.0000.0000.000
43A340SER00.018-0.01239.756-0.152-0.1520.0000.0000.0000.000
44A341SER00.009-0.02943.3510.0610.0610.0000.0000.0000.000
45A342GLU-1-0.928-0.94646.3236.3176.3170.0000.0000.0000.000
46A343ASP-1-0.791-0.87342.4947.2257.2250.0000.0000.0000.000
47A344GLN0-0.017-0.01442.136-0.041-0.0410.0000.0000.0000.000
48A345GLU-1-0.765-0.83644.5976.1406.1400.0000.0000.0000.000
49A346LEU0-0.014-0.00246.359-0.084-0.0840.0000.0000.0000.000
50A347GLH0-0.069-0.04940.262-0.022-0.0220.0000.0000.0000.000
51A348ARG10.8300.87044.926-6.142-6.1420.0000.0000.0000.000
52A349ASN0-0.036-0.02747.454-0.179-0.1790.0000.0000.0000.000
53A350TRP00.0210.00441.751-0.043-0.0430.0000.0000.0000.000
54A351ILE0-0.027-0.02142.0450.0070.0070.0000.0000.0000.000
55A352ALA00.0160.00646.368-0.043-0.0430.0000.0000.0000.000
56A353GLU-1-0.922-0.96149.7775.7465.7460.0000.0000.0000.000
57A354LYS10.8320.92144.625-6.826-6.8260.0000.0000.0000.000
58A355ILE00.0060.00945.673-0.006-0.0060.0000.0000.0000.000
59A356SER00.0020.00249.764-0.105-0.1050.0000.0000.0000.000
60A357VAL0-0.039-0.02052.012-0.093-0.0930.0000.0000.0000.000
61A358ASP-1-0.892-0.93251.1646.0086.0080.0000.0000.0000.000
62A359LYS10.7960.88450.063-6.238-6.2380.0000.0000.0000.000
63A360ASN0-0.118-0.05455.502-0.157-0.1570.0000.0000.0000.000
64A361PHE00.0460.02755.318-0.083-0.0830.0000.0000.0000.000
65A362ASP-1-0.913-0.95060.3244.8454.8450.0000.0000.0000.000
66A363ALA0-0.025-0.02463.2110.0400.0400.0000.0000.0000.000
67A364ASN0-0.053-0.03164.773-0.033-0.0330.0000.0000.0000.000
68A365TYR0-0.020-0.00158.172-0.010-0.0100.0000.0000.0000.000
69A366ASP-1-0.809-0.87761.6135.2065.2060.0000.0000.0000.000
70A367LEU0-0.008-0.00856.3080.0580.0580.0000.0000.0000.000
71A368THR0-0.048-0.04356.7240.1440.1440.0000.0000.0000.000
72A369GLU-1-0.745-0.87256.2135.5475.5470.0000.0000.0000.000
73A370PHE00.0240.01852.0460.1240.1240.0000.0000.0000.000
74A371LYS10.9210.93452.335-5.658-5.6580.0000.0000.0000.000
75A372GLU-1-0.975-0.97051.6575.7565.7560.0000.0000.0000.000
76A373ALA0-0.0080.01650.7850.1420.1420.0000.0000.0000.000
77A374ILE00.0120.00046.7050.1690.1690.0000.0000.0000.000
78A375GLY0-0.002-0.00546.6700.1700.1700.0000.0000.0000.000
79A376ASN0-0.048-0.02446.4340.2080.2080.0000.0000.0000.000
80A377ALA00.0190.01944.6080.1560.1560.0000.0000.0000.000
81A378ILE00.0200.00641.8010.2030.2030.0000.0000.0000.000
82A379LYS10.7800.89141.493-6.731-6.7310.0000.0000.0000.000
83A380PHE00.035-0.01141.4990.1430.1430.0000.0000.0000.000
84A381ILE00.0030.01637.3370.2100.2100.0000.0000.0000.000
85A382THR0-0.057-0.05937.0400.3230.3230.0000.0000.0000.000
86A383LYS10.8420.91337.462-7.168-7.1680.0000.0000.0000.000
87A384GLU-1-0.807-0.88038.8077.2157.2150.0000.0000.0000.000
88A385ASN0-0.0300.00233.9640.2210.2210.0000.0000.0000.000
89A386LEU00.0320.02335.4550.1840.1840.0000.0000.0000.000
90A387GLU-1-0.726-0.82933.4699.1269.1260.0000.0000.0000.000
91A388VAL00.0160.01337.333-0.177-0.1770.0000.0000.0000.000
92A389PRO00.0290.01438.133-0.186-0.1860.0000.0000.0000.000
93A390PHE00.0240.02039.568-0.172-0.1720.0000.0000.0000.000
94A391ILE0-0.023-0.01540.795-0.198-0.1980.0000.0000.0000.000
95A392TYR00.003-0.00343.603-0.238-0.2380.0000.0000.0000.000
96A393ALA0-0.0160.00844.328-0.165-0.1650.0000.0000.0000.000
97A394TYR0-0.034-0.03742.450-0.082-0.0820.0000.0000.0000.000
98A395ARG10.7950.85744.005-6.941-6.9410.0000.0000.0000.000
99A396ARG10.9300.97647.779-6.375-6.3750.0000.0000.0000.000
100A397ASN00.0480.01949.979-0.015-0.0150.0000.0000.0000.000
101A398TYR0-0.0030.01549.533-0.085-0.0850.0000.0000.0000.000
102A399ILE0-0.049-0.02546.8000.0540.0540.0000.0000.0000.000
103A400SER0-0.033-0.04250.4570.0070.0070.0000.0000.0000.000
104A401SER0-0.026-0.01753.9410.0230.0230.0000.0000.0000.000
105A402ARG10.8290.89257.574-5.337-5.3370.0000.0000.0000.000
106A403GLU-1-0.930-0.95459.7614.8314.8310.0000.0000.0000.000
107A404LYS10.8990.94660.728-4.733-4.7330.0000.0000.0000.000
108A405ASP-1-0.904-0.95560.3514.9854.9850.0000.0000.0000.000
109A406GLY00.0050.03160.392-0.021-0.0210.0000.0000.0000.000
110A407PHE00.006-0.01353.0340.0540.0540.0000.0000.0000.000
111A408LEU00.0030.00950.612-0.005-0.0050.0000.0000.0000.000
112A409LEU0-0.067-0.01347.7720.0250.0250.0000.0000.0000.000
113A410THR00.029-0.02248.2510.0840.0840.0000.0000.0000.000
114A411GLU-1-0.781-0.91642.9426.8496.8490.0000.0000.0000.000
115A412ASP-1-0.836-0.89043.0977.1287.1280.0000.0000.0000.000
116A413ASP-1-0.783-0.85243.9356.5006.5000.0000.0000.0000.000
117A414LEU0-0.012-0.00642.6020.1130.1130.0000.0000.0000.000
118A415TRP0-0.008-0.03935.5060.3110.3110.0000.0000.0000.000
119A416ASP-1-0.816-0.87639.5037.3977.3970.0000.0000.0000.000
120A417ILE0-0.017-0.01441.2530.1090.1090.0000.0000.0000.000
121A418VAL0-0.0020.00435.9220.1240.1240.0000.0000.0000.000
122A419SER0-0.039-0.03436.6790.2670.2670.0000.0000.0000.000
123A420LEU0-0.044-0.03037.5080.1070.1070.0000.0000.0000.000
124A421ASP-1-0.715-0.79836.8878.2648.2640.0000.0000.0000.000
125A422ILE00.0150.02032.5210.0710.0710.0000.0000.0000.000
126A423GLU-1-0.821-0.88735.4347.9067.9060.0000.0000.0000.000
127A424PHE00.018-0.00137.402-0.003-0.0030.0000.0000.0000.000
128A425HIS10.8640.91734.857-8.482-8.4820.0000.0000.0000.000
129A426SER0-0.044-0.03034.0190.2150.2150.0000.0000.0000.000
130A427LEU0-0.037-0.01335.2260.0510.0510.0000.0000.0000.000
131A428VAL00.0510.02038.250-0.030-0.0300.0000.0000.0000.000
132A429ASN0-0.021-0.01032.1310.3050.3050.0000.0000.0000.000
133A430LYS10.8770.94632.095-9.156-9.1560.0000.0000.0000.000
134A431LYS10.8790.93236.979-7.374-7.3740.0000.0000.0000.000
135A432ASP-1-0.811-0.90737.4647.7437.7430.0000.0000.0000.000
136A433TYR0-0.073-0.02432.4710.1190.1190.0000.0000.0000.000
137A434VAL00.0250.00836.674-0.014-0.0140.0000.0000.0000.000
138A435GLN00.0260.01839.776-0.024-0.0240.0000.0000.0000.000
139A436ARG10.8200.90033.526-8.921-8.9210.0000.0000.0000.000
140A437PHE00.0200.00637.612-0.081-0.0810.0000.0000.0000.000
141A438TYR00.029-0.01739.315-0.051-0.0510.0000.0000.0000.000
142A439ALA0-0.006-0.00442.664-0.106-0.1060.0000.0000.0000.000
143A440GLU-1-0.903-0.94936.4478.5378.5370.0000.0000.0000.000
144A441LEU00.0350.01740.952-0.029-0.0290.0000.0000.0000.000
145A442HIS0-0.118-0.05243.115-0.155-0.1550.0000.0000.0000.000
146A443ILE0-0.017-0.00745.910-0.183-0.1830.0000.0000.0000.000
147A444ASP-1-0.876-0.90048.3946.0146.0140.0000.0000.0000.000
148A445ASP-1-0.696-0.81249.9615.9965.9960.0000.0000.0000.000
149A446PRO00.000-0.01251.6850.0350.0350.0000.0000.0000.000
150A447ILE00.0410.03051.491-0.016-0.0160.0000.0000.0000.000
151A448VAL0-0.019-0.00846.4820.0540.0540.0000.0000.0000.000
152A449THR0-0.001-0.01949.4850.1290.1290.0000.0000.0000.000
153A450GLU-1-0.915-0.93351.4235.5935.5930.0000.0000.0000.000
154A451TYR0-0.028-0.02345.6540.0420.0420.0000.0000.0000.000
155A452PHE0-0.003-0.02743.5420.0330.0330.0000.0000.0000.000
156A453LYS10.9080.98948.997-5.491-5.4910.0000.0000.0000.000
157A454ASN0-0.006-0.01152.429-0.076-0.0760.0000.0000.0000.000
158A455GLN0-0.062-0.01347.2720.0920.0920.0000.0000.0000.000
159A464ASN0-0.023-0.02642.3920.1530.1530.0000.0000.0000.000
160A465SER00.009-0.00444.5770.1090.1090.0000.0000.0000.000
161A466LEU00.0240.01539.972-0.013-0.0130.0000.0000.0000.000
162A467GLN0-0.027-0.01538.7380.1950.1950.0000.0000.0000.000
163A468ASP-1-0.776-0.85642.0996.6536.6530.0000.0000.0000.000
164A469ILE00.0180.00444.406-0.058-0.0580.0000.0000.0000.000
165A470TYR0-0.063-0.03737.3780.0260.0260.0000.0000.0000.000
166A471ASP-1-0.781-0.87541.5597.4477.4470.0000.0000.0000.000
167A472TYR0-0.066-0.06143.206-0.073-0.0730.0000.0000.0000.000
168A473LEU0-0.021-0.01043.242-0.083-0.0830.0000.0000.0000.000
169A474GLU-1-0.905-0.93638.6527.9047.9040.0000.0000.0000.000
170A475PHE0-0.063-0.04442.512-0.028-0.0280.0000.0000.0000.000
171A476LYS10.7590.87445.536-6.094-6.0940.0000.0000.0000.000
172A477TYR0-0.022-0.03445.491-0.176-0.1760.0000.0000.0000.000
173A478ALA00.0510.03542.7360.1600.1600.0000.0000.0000.000
174A479ASN0-0.076-0.06142.0440.2480.2480.0000.0000.0000.000
175A480GLU-1-0.831-0.91942.4946.8776.8770.0000.0000.0000.000
176A481ILE00.0160.00839.0980.1090.1090.0000.0000.0000.000
177A482ASN0-0.092-0.02637.8970.3400.3400.0000.0000.0000.000
178A483GLU-1-1.009-0.99637.6387.5157.5150.0000.0000.0000.000
179A484MET0-0.099-0.02435.3050.1710.1710.0000.0000.0000.000
180A501SER00.011-0.00744.8050.0400.0400.0000.0000.0000.000
181A502TYR00.012-0.02846.728-0.117-0.1170.0000.0000.0000.000
182A503GLU-1-0.800-0.89045.2196.5266.5260.0000.0000.0000.000
183A504LYS10.8090.88946.174-6.695-6.6950.0000.0000.0000.000
184A505PHE00.0120.00049.817-0.128-0.1280.0000.0000.0000.000
185A506LYS10.8990.95051.644-5.989-5.9890.0000.0000.0000.000
186A507ALA0-0.0100.01252.404-0.065-0.0650.0000.0000.0000.000
187A508SER0-0.0140.00654.171-0.101-0.1010.0000.0000.0000.000
188A509PRO00.0330.00556.225-0.033-0.0330.0000.0000.0000.000
189A510LEU0-0.023-0.01957.340-0.076-0.0760.0000.0000.0000.000
190A511TYR0-0.002-0.02255.300-0.053-0.0530.0000.0000.0000.000
191A512GLN0-0.016-0.00358.5230.0300.0300.0000.0000.0000.000
192A513ALA00.019-0.00761.939-0.066-0.0660.0000.0000.0000.000
193A514VAL0-0.042-0.02057.576-0.040-0.0400.0000.0000.0000.000
194A515SER0-0.017-0.00960.9890.0020.0020.0000.0000.0000.000
195A516ASP-1-0.882-0.94163.0814.7254.7250.0000.0000.0000.000
196A517ILE0-0.042-0.00861.246-0.076-0.0760.0000.0000.0000.000
197A518GLY00.0190.01665.312-0.056-0.0560.0000.0000.0000.000
198A519ILE0-0.022-0.01662.974-0.049-0.0490.0000.0000.0000.000
199A520SER0-0.010-0.01358.7730.0880.0880.0000.0000.0000.000
200A521ALA00.0630.00255.683-0.034-0.0340.0000.0000.0000.000
201A522GLU-1-0.834-0.91554.3825.7845.7840.0000.0000.0000.000
202A523ASP-1-0.808-0.86757.4825.0965.0960.0000.0000.0000.000
203A524VAL00.0260.00759.412-0.059-0.0590.0000.0000.0000.000
204A525GLY00.005-0.00557.413-0.016-0.0160.0000.0000.0000.000
205A526GLU-1-0.882-0.92558.3695.3055.3050.0000.0000.0000.000
206A527ASN0-0.029-0.00460.842-0.080-0.0800.0000.0000.0000.000
207A528ILE0-0.013-0.02258.628-0.041-0.0410.0000.0000.0000.000
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