FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 1NZ7Z

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 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 837
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -21673928.238694
FMO2-HF: Nuclear repulsion 21335748.708078
FMO2-HF: Total energy -338179.530616
FMO2-MP2: Total energy -339175.980662


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.
189.968195.4050.366-2.339-3.4630.008
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 : -0.889 / q_NPA : -0.948
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].
3A300TYR00.015-0.0043.122-11.712-8.2020.065-1.720-1.8550.009
4A301ASP-1-0.932-0.9502.96936.28037.8250.301-0.542-1.304-0.001
5A302LEU00.015-0.0104.371-5.611-5.2290.000-0.077-0.3040.000
6A303GLU-1-0.976-0.9826.44523.95523.9550.0000.0000.0000.000
7A304ASP-1-0.884-0.9518.06322.82922.8290.0000.0000.0000.000
8A305LEU0-0.031-0.0077.605-2.662-2.6620.0000.0000.0000.000
9A306LYS10.9700.98110.391-20.153-20.1530.0000.0000.0000.000
10A307LYS10.8880.94712.182-21.574-21.5740.0000.0000.0000.000
11A308ASN0-0.0070.00512.632-2.109-2.1090.0000.0000.0000.000
12A309LEU0-0.075-0.02114.730-1.115-1.1150.0000.0000.0000.000
13A310MET0-0.022-0.02612.443-1.182-1.1820.0000.0000.0000.000
14A311THR00.0220.02311.1360.9500.9500.0000.0000.0000.000
15A312GLU-1-0.864-0.93812.32619.84219.8420.0000.0000.0000.000
16A313GLY00.005-0.00214.133-1.296-1.2960.0000.0000.0000.000
17A314ASP-1-0.871-0.95815.77416.41816.4180.0000.0000.0000.000
18A315MET00.0020.00415.111-1.138-1.1380.0000.0000.0000.000
19A316LYS10.9710.99217.857-13.888-13.8880.0000.0000.0000.000
20A317ILE0-0.024-0.00820.305-0.728-0.7280.0000.0000.0000.000
21A318ARG10.8070.91117.804-15.951-15.9510.0000.0000.0000.000
22A319LYS10.9020.95820.464-14.362-14.3620.0000.0000.0000.000
23A320THR0-0.040-0.01823.743-0.509-0.5090.0000.0000.0000.000
24A321ASP-1-0.786-0.90926.1359.5969.5960.0000.0000.0000.000
25A322ILE0-0.020-0.00628.795-0.333-0.3330.0000.0000.0000.000
26A323PRO00.0770.04928.9760.4290.4290.0000.0000.0000.000
27A324GLU-1-0.799-0.90224.04612.40812.4080.0000.0000.0000.000
28A325ARG10.8560.91327.452-9.320-9.3200.0000.0000.0000.000
29A326TYR0-0.010-0.02129.6780.0170.0170.0000.0000.0000.000
30A327GLN0-0.086-0.05624.8570.5160.5160.0000.0000.0000.000
31A328GLU-1-0.956-0.98324.75312.05612.0560.0000.0000.0000.000
32A329LEU0-0.018-0.00326.5600.0660.0660.0000.0000.0000.000
33A330ARG10.8530.93229.278-9.416-9.4160.0000.0000.0000.000
34A331ALA0-0.0090.00923.9090.0650.0650.0000.0000.0000.000
35A332GLY0-0.030-0.01025.4730.2920.2920.0000.0000.0000.000
36A333ILE0-0.077-0.02927.226-0.333-0.3330.0000.0000.0000.000
37A334THR0-0.0040.00029.0000.2850.2850.0000.0000.0000.000
38A335ASP-1-0.876-0.94830.0439.3529.3520.0000.0000.0000.000
39A336TYR0-0.062-0.07531.399-0.258-0.2580.0000.0000.0000.000
40A337GLY0-0.034-0.03233.169-0.258-0.2580.0000.0000.0000.000
41A338ASN0-0.056-0.01334.381-0.239-0.2390.0000.0000.0000.000
42A339MET00.0240.02737.220-0.075-0.0750.0000.0000.0000.000
43A340SER00.0520.02939.660-0.150-0.1500.0000.0000.0000.000
44A341SER00.012-0.01643.0830.0250.0250.0000.0000.0000.000
45A342GLU-1-0.912-0.95446.1816.3946.3940.0000.0000.0000.000
46A343ASP-1-0.833-0.92742.4687.2327.2320.0000.0000.0000.000
47A344GLN0-0.100-0.06042.354-0.071-0.0710.0000.0000.0000.000
48A345GLU-1-0.867-0.91044.5346.1386.1380.0000.0000.0000.000
49A346LEU0-0.037-0.01946.390-0.094-0.0940.0000.0000.0000.000
50A347GLH0-0.059-0.05840.374-0.080-0.0800.0000.0000.0000.000
51A348ARG10.9020.94345.049-6.205-6.2050.0000.0000.0000.000
52A349ASN0-0.023-0.02147.400-0.121-0.1210.0000.0000.0000.000
53A350TRP0-0.005-0.00242.001-0.059-0.0590.0000.0000.0000.000
54A351ILE0-0.003-0.01142.222-0.030-0.0300.0000.0000.0000.000
55A352ALA0-0.014-0.01146.481-0.055-0.0550.0000.0000.0000.000
56A353GLU-1-0.959-0.97349.8625.8085.8080.0000.0000.0000.000
57A354LYS10.9060.94844.663-6.838-6.8380.0000.0000.0000.000
58A355ILE0-0.0070.00345.475-0.016-0.0160.0000.0000.0000.000
59A356SER0-0.015-0.00849.361-0.105-0.1050.0000.0000.0000.000
60A357VAL0-0.030-0.01451.447-0.103-0.1030.0000.0000.0000.000
61A358ASP-1-0.953-0.97951.4995.9075.9070.0000.0000.0000.000
62A359LYS10.8310.93751.633-6.084-6.0840.0000.0000.0000.000
63A360ASN0-0.071-0.02655.590-0.080-0.0800.0000.0000.0000.000
64A361PHE00.0340.01755.408-0.052-0.0520.0000.0000.0000.000
65A362ASP-1-0.924-0.96260.3174.8564.8560.0000.0000.0000.000
66A363ALA0-0.014-0.01963.1020.0390.0390.0000.0000.0000.000
67A364ASN0-0.055-0.03764.7230.0160.0160.0000.0000.0000.000
68A365TYR0-0.0320.00358.561-0.035-0.0350.0000.0000.0000.000
69A366ASP-1-0.838-0.91862.1115.1475.1470.0000.0000.0000.000
70A367LEU00.000-0.00856.6030.0620.0620.0000.0000.0000.000
71A368THR0-0.052-0.02056.8320.1470.1470.0000.0000.0000.000
72A369GLU-1-0.799-0.90756.4705.5005.5000.0000.0000.0000.000
73A370PHE00.0000.00551.5360.1070.1070.0000.0000.0000.000
74A371LYS10.9590.96152.325-5.550-5.5500.0000.0000.0000.000
75A372GLU-1-0.943-0.96351.4395.7775.7770.0000.0000.0000.000
76A373ALA0-0.0270.01551.1750.1200.1200.0000.0000.0000.000
77A374ILE00.004-0.00447.0630.1610.1610.0000.0000.0000.000
78A375GLY0-0.007-0.01346.8220.1670.1670.0000.0000.0000.000
79A376ASN0-0.061-0.03146.4630.1970.1970.0000.0000.0000.000
80A377ALA00.0350.02344.4930.1490.1490.0000.0000.0000.000
81A378ILE00.0220.01041.8490.2030.2030.0000.0000.0000.000
82A379LYS10.8940.96041.679-6.533-6.5330.0000.0000.0000.000
83A380PHE00.0390.00541.6580.1310.1310.0000.0000.0000.000
84A381ILE00.0200.01637.5080.2080.2080.0000.0000.0000.000
85A382THR0-0.029-0.02237.2260.2950.2950.0000.0000.0000.000
86A383LYS10.8800.93837.232-7.095-7.0950.0000.0000.0000.000
87A384GLU-1-0.943-0.97138.5187.3737.3730.0000.0000.0000.000
88A385ASN0-0.0250.00634.1300.1540.1540.0000.0000.0000.000
89A386LEU00.0580.03435.6210.1860.1860.0000.0000.0000.000
90A387GLU-1-0.761-0.86533.6689.1349.1340.0000.0000.0000.000
91A388VAL00.0310.01137.717-0.183-0.1830.0000.0000.0000.000
92A389PRO00.0580.03337.853-0.185-0.1850.0000.0000.0000.000
93A390PHE00.0500.01939.877-0.178-0.1780.0000.0000.0000.000
94A391ILE0-0.044-0.01740.983-0.200-0.2000.0000.0000.0000.000
95A392TYR00.0410.00143.727-0.228-0.2280.0000.0000.0000.000
96A393ALA0-0.033-0.00244.364-0.181-0.1810.0000.0000.0000.000
97A394TYR0-0.043-0.04042.630-0.090-0.0900.0000.0000.0000.000
98A395ARG10.8240.89944.785-6.940-6.9400.0000.0000.0000.000
99A396ARG10.9721.00548.154-6.308-6.3080.0000.0000.0000.000
100A397ASN00.015-0.00250.277-0.023-0.0230.0000.0000.0000.000
101A398TYR0-0.021-0.00149.597-0.084-0.0840.0000.0000.0000.000
102A399ILE0-0.035-0.02147.2370.0700.0700.0000.0000.0000.000
103A400SER00.016-0.00250.8430.0110.0110.0000.0000.0000.000
104A401SER0-0.084-0.02754.1970.0160.0160.0000.0000.0000.000
105A402ARG10.9130.94457.796-5.367-5.3670.0000.0000.0000.000
106A403GLU-1-0.915-0.94559.9654.8884.8880.0000.0000.0000.000
107A404LYS10.9660.98661.148-4.627-4.6270.0000.0000.0000.000
108A405ASP-1-0.946-0.97160.1405.1195.1190.0000.0000.0000.000
109A406GLY00.0230.03260.303-0.052-0.0520.0000.0000.0000.000
110A407PHE0-0.019-0.02853.2290.0440.0440.0000.0000.0000.000
111A408LEU00.005-0.00251.0100.0150.0150.0000.0000.0000.000
112A409LEU0-0.070-0.02548.3580.0180.0180.0000.0000.0000.000
113A410THR00.0220.00648.6180.0960.0960.0000.0000.0000.000
114A411GLU-1-0.842-0.94543.5947.0697.0690.0000.0000.0000.000
115A412ASP-1-0.836-0.90143.5517.0447.0440.0000.0000.0000.000
116A413ASP-1-0.802-0.90044.2686.5016.5010.0000.0000.0000.000
117A414LEU0-0.040-0.02742.7240.1330.1330.0000.0000.0000.000
118A415TRP0-0.023-0.03035.6830.3280.3280.0000.0000.0000.000
119A416ASP-1-0.862-0.92839.7147.3537.3530.0000.0000.0000.000
120A417ILE0-0.002-0.01241.2970.0970.0970.0000.0000.0000.000
121A418VAL00.0080.01935.8330.1190.1190.0000.0000.0000.000
122A419SER0-0.032-0.02336.6480.2350.2350.0000.0000.0000.000
123A420LEU0-0.052-0.02637.5630.0800.0800.0000.0000.0000.000
124A421ASP-1-0.749-0.81137.0998.2798.2790.0000.0000.0000.000
125A422ILE0-0.0060.00832.5810.0790.0790.0000.0000.0000.000
126A423GLU-1-0.907-0.96235.4377.8417.8410.0000.0000.0000.000
127A424PHE00.004-0.00437.190-0.035-0.0350.0000.0000.0000.000
128A425HIS10.8980.94434.915-8.480-8.4800.0000.0000.0000.000
129A426SER0-0.0010.00433.5780.2270.2270.0000.0000.0000.000
130A427LEU0-0.055-0.00935.1190.0630.0630.0000.0000.0000.000
131A428VAL00.0690.02438.0980.0120.0120.0000.0000.0000.000
132A429ASN0-0.0110.00332.3080.2860.2860.0000.0000.0000.000
133A430LYS10.9130.95731.964-9.286-9.2860.0000.0000.0000.000
134A431LYS10.9530.96936.656-7.288-7.2880.0000.0000.0000.000
135A432ASP-1-0.871-0.93837.1147.8767.8760.0000.0000.0000.000
136A433TYR0-0.109-0.05632.5680.1460.1460.0000.0000.0000.000
137A434VAL00.0300.00736.435-0.011-0.0110.0000.0000.0000.000
138A435GLN00.0070.00439.4890.0040.0040.0000.0000.0000.000
139A436ARG10.9300.96332.834-9.156-9.1560.0000.0000.0000.000
140A437PHE00.0210.01936.9360.0140.0140.0000.0000.0000.000
141A438TYR00.012-0.02139.227-0.046-0.0460.0000.0000.0000.000
142A439ALA0-0.008-0.01642.495-0.111-0.1110.0000.0000.0000.000
143A440GLU-1-1.000-0.98936.9188.5108.5100.0000.0000.0000.000
144A441LEU00.0260.00641.420-0.058-0.0580.0000.0000.0000.000
145A442HIS0-0.091-0.02543.296-0.178-0.1780.0000.0000.0000.000
146A443ILE0-0.039-0.03346.404-0.176-0.1760.0000.0000.0000.000
147A444ASP-1-0.933-0.95548.5216.0536.0530.0000.0000.0000.000
148A445ASP-1-0.750-0.84549.9046.0846.0840.0000.0000.0000.000
149A446PRO00.013-0.00851.7090.0340.0340.0000.0000.0000.000
150A447ILE00.0240.02250.713-0.025-0.0250.0000.0000.0000.000
151A448VAL0-0.005-0.00746.3980.0310.0310.0000.0000.0000.000
152A449THR00.0000.00549.4970.1260.1260.0000.0000.0000.000
153A450GLU-1-0.955-0.96651.3805.6295.6290.0000.0000.0000.000
154A451TYR0-0.031-0.03145.8830.0350.0350.0000.0000.0000.000
155A452PHE0-0.042-0.03843.8670.0460.0460.0000.0000.0000.000
156A453LYS10.9160.98549.036-5.544-5.5440.0000.0000.0000.000
157A454ASN0-0.032-0.02552.428-0.055-0.0550.0000.0000.0000.000
158A455GLN0-0.0280.00446.815-0.052-0.0520.0000.0000.0000.000
159A464ASN00.012-0.00342.6050.1040.1040.0000.0000.0000.000
160A465SER00.0190.01044.3070.0690.0690.0000.0000.0000.000
161A466LEU00.0180.01739.904-0.011-0.0110.0000.0000.0000.000
162A467GLN0-0.012-0.00938.5090.1870.1870.0000.0000.0000.000
163A468ASP-1-0.774-0.88441.6646.7766.7760.0000.0000.0000.000
164A469ILE0-0.013-0.00544.263-0.059-0.0590.0000.0000.0000.000
165A470TYR0-0.042-0.01536.5670.0280.0280.0000.0000.0000.000
166A471ASP-1-0.810-0.91541.0127.5787.5780.0000.0000.0000.000
167A472TYR0-0.135-0.06643.039-0.088-0.0880.0000.0000.0000.000
168A473LEU0-0.019-0.01643.149-0.109-0.1090.0000.0000.0000.000
169A474GLU-1-0.946-0.96238.3558.0368.0360.0000.0000.0000.000
170A475PHE0-0.094-0.06142.342-0.032-0.0320.0000.0000.0000.000
171A476LYS10.8850.95845.304-6.103-6.1030.0000.0000.0000.000
172A477TYR0-0.027-0.06345.069-0.126-0.1260.0000.0000.0000.000
173A478ALA00.0350.03342.6080.1370.1370.0000.0000.0000.000
174A479ASN0-0.075-0.05841.9610.3000.3000.0000.0000.0000.000
175A480GLU-1-0.873-0.94942.7056.8706.8700.0000.0000.0000.000
176A481ILE00.0100.00739.1900.0960.0960.0000.0000.0000.000
177A482ASN0-0.120-0.04837.5870.3470.3470.0000.0000.0000.000
178A483GLU-1-1.031-0.99537.5987.6087.6080.0000.0000.0000.000
179A484MET0-0.0380.00435.4930.2680.2680.0000.0000.0000.000
180A501SER0-0.008-0.01244.7030.0310.0310.0000.0000.0000.000
181A502TYR00.022-0.04546.723-0.117-0.1170.0000.0000.0000.000
182A503GLU-1-0.803-0.90446.2146.5536.5530.0000.0000.0000.000
183A504LYS10.8630.92546.012-6.884-6.8840.0000.0000.0000.000
184A505PHE00.0040.00549.663-0.125-0.1250.0000.0000.0000.000
185A506LYS10.9600.97751.827-6.041-6.0410.0000.0000.0000.000
186A507ALA0-0.0200.00252.108-0.073-0.0730.0000.0000.0000.000
187A508SER0-0.032-0.00753.964-0.127-0.1270.0000.0000.0000.000
188A509PRO00.0750.03055.956-0.032-0.0320.0000.0000.0000.000
189A510LEU0-0.016-0.02457.853-0.081-0.0810.0000.0000.0000.000
190A511TYR0-0.042-0.00755.369-0.054-0.0540.0000.0000.0000.000
191A512GLN0-0.010-0.00558.5820.0380.0380.0000.0000.0000.000
192A513ALA00.015-0.00861.960-0.062-0.0620.0000.0000.0000.000
193A514VAL0-0.030-0.01957.585-0.051-0.0510.0000.0000.0000.000
194A515SER0-0.015-0.00760.9170.0140.0140.0000.0000.0000.000
195A516ASP-1-0.882-0.93762.7464.7544.7540.0000.0000.0000.000
196A517ILE0-0.073-0.02061.146-0.078-0.0780.0000.0000.0000.000
197A518GLY00.0360.02965.103-0.052-0.0520.0000.0000.0000.000
198A519ILE0-0.008-0.00562.977-0.044-0.0440.0000.0000.0000.000
199A520SER00.0470.03958.9900.0690.0690.0000.0000.0000.000
200A521ALA00.0500.00855.767-0.036-0.0360.0000.0000.0000.000
201A522GLU-1-0.918-0.97754.5415.7605.7600.0000.0000.0000.000
202A523ASP-1-0.838-0.90957.6075.0865.0860.0000.0000.0000.000
203A524VAL0-0.045-0.02959.414-0.057-0.0570.0000.0000.0000.000
204A525GLY00.0040.00057.488-0.023-0.0230.0000.0000.0000.000
205A526GLU-1-0.937-0.97658.3855.2865.2860.0000.0000.0000.000
206A527ASN00.0110.01960.706-0.102-0.1020.0000.0000.0000.000
207A528ILE0-0.015-0.01658.948-0.050-0.0500.0000.0000.0000.000
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