Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 6YVNZ

Calculation Name: 1YPY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YPY

Chain ID: A

ChEMBL ID:

UniProt ID: P07612

Base Structure: X-ray

Registration Date: 2023-09-23

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1793974.816563
FMO2-HF: Nuclear repulsion 1724435.392787
FMO2-HF: Total energy -69539.423776
FMO2-MP2: Total energy -69737.470114


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:4:ALA)


Summations of interaction energy for fragment #1(A:4:ALA)
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.
-6.131-1.0953.07-2.683-5.4190.012
Interaction energy analysis for fragmet #1(A:4:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.080 / q_NPA : 0.031
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].
3A6SER00.0540.0353.343-0.8890.5610.003-0.651-0.8030.001
4A7ILE00.0170.0322.538-2.030-0.2610.963-0.954-1.7770.006
5A8GLN00.0180.0013.880-0.899-0.506-0.001-0.118-0.2740.000
6A9THR00.003-0.0145.7390.3410.3410.0000.0000.0000.000
7A10THR0-0.018-0.0117.7070.0490.0490.0000.0000.0000.000
8A11VAL00.005-0.0067.291-0.019-0.0190.0000.0000.0000.000
9A12ASN00.0030.0159.508-0.056-0.0560.0000.0000.0000.000
10A13THR0-0.007-0.00611.5420.0260.0260.0000.0000.0000.000
11A14LEU00.0050.01012.3640.0100.0100.0000.0000.0000.000
12A15SER0-0.024-0.01713.3180.0140.0140.0000.0000.0000.000
13A16GLU-1-0.847-0.89615.095-0.057-0.0570.0000.0000.0000.000
14A17ARG10.8520.90117.039-0.003-0.0030.0000.0000.0000.000
15A18ILE00.007-0.00916.3190.0070.0070.0000.0000.0000.000
16A19SER0-0.049-0.04618.643-0.004-0.0040.0000.0000.0000.000
17A20SER00.036-0.00321.0610.0090.0090.0000.0000.0000.000
18A21LYS10.7290.87822.413-0.020-0.0200.0000.0000.0000.000
19A22LEU00.001-0.01622.1890.0030.0030.0000.0000.0000.000
20A23GLU-1-0.923-0.95725.241-0.040-0.0400.0000.0000.0000.000
21A24GLN0-0.112-0.06225.8590.0070.0070.0000.0000.0000.000
22A25GLU-1-0.873-0.92427.2300.0200.0200.0000.0000.0000.000
23A26ALA0-0.029-0.00627.6280.0030.0030.0000.0000.0000.000
24A27ASN0-0.063-0.02429.536-0.003-0.0030.0000.0000.0000.000
25A28ALA0-0.0090.01126.989-0.002-0.0020.0000.0000.0000.000
26A29SER00.0850.02427.999-0.001-0.0010.0000.0000.0000.000
27A30ALA00.0150.00425.476-0.001-0.0010.0000.0000.0000.000
28A31GLN0-0.043-0.02827.048-0.001-0.0010.0000.0000.0000.000
29A32THR0-0.047-0.00930.2580.0040.0040.0000.0000.0000.000
30A33LYS10.9140.94430.3560.0380.0380.0000.0000.0000.000
31A34CYS0-0.0450.02124.8130.0080.0080.0000.0000.0000.000
32A35ASP-1-0.838-0.90030.500-0.025-0.0250.0000.0000.0000.000
33A36ILE0-0.078-0.03327.6110.0000.0000.0000.0000.0000.000
34A37GLU-1-0.791-0.88426.949-0.066-0.0660.0000.0000.0000.000
35A38ILE0-0.033-0.02321.0580.0030.0030.0000.0000.0000.000
36A39GLY0-0.010-0.00224.508-0.005-0.0050.0000.0000.0000.000
37A40ASN0-0.053-0.03522.431-0.012-0.0120.0000.0000.0000.000
38A41PHE00.014-0.00613.5390.0130.0130.0000.0000.0000.000
39A42TYR00.001-0.00116.404-0.017-0.0170.0000.0000.0000.000
40A43ILE0-0.0010.00411.4670.0160.0160.0000.0000.0000.000
41A44ARG10.8420.91015.4580.0700.0700.0000.0000.0000.000
42A45GLN0-0.031-0.01112.609-0.026-0.0260.0000.0000.0000.000
43A46ASN00.0140.00011.752-0.095-0.0950.0000.0000.0000.000
44A47HIS0-0.047-0.03410.5420.0750.0750.0000.0000.0000.000
45A48GLY00.0450.0198.691-0.071-0.0710.0000.0000.0000.000
46A49CYS0-0.083-0.0417.704-0.262-0.2620.0000.0000.0000.000
47A50ASN00.0190.0239.2740.1790.1790.0000.0000.0000.000
48A51LEU0-0.028-0.01911.145-0.048-0.0480.0000.0000.0000.000
49A52THR0-0.012-0.00313.7940.0170.0170.0000.0000.0000.000
50A53VAL0-0.009-0.01516.4150.0040.0040.0000.0000.0000.000
51A54LYS10.8370.93117.3500.1340.1340.0000.0000.0000.000
52A55ASN0-0.013-0.03020.6770.0040.0040.0000.0000.0000.000
53A56MET0-0.0190.01423.025-0.001-0.0010.0000.0000.0000.000
54A58SER00.0420.01527.7550.0010.0010.0000.0000.0000.000
55A59ALA0-0.012-0.01630.7690.0000.0000.0000.0000.0000.000
56A60ASP-1-0.861-0.90832.2810.0000.0000.0000.0000.0000.000
57A61ALA00.021-0.00129.7030.0000.0000.0000.0000.0000.000
58A62ASP-1-0.826-0.90029.0030.0090.0090.0000.0000.0000.000
59A63ALA00.0380.01529.3810.0040.0040.0000.0000.0000.000
60A64GLN00.0260.02126.0990.0010.0010.0000.0000.0000.000
61A65LEU0-0.044-0.01124.7190.0020.0020.0000.0000.0000.000
62A66ASP-1-0.817-0.91924.7020.0370.0370.0000.0000.0000.000
63A67ALA00.0030.01524.5870.0060.0060.0000.0000.0000.000
64A68VAL0-0.007-0.01319.3600.0050.0050.0000.0000.0000.000
65A69LEU0-0.004-0.00720.2530.0130.0130.0000.0000.0000.000
66A70SER00.0030.02421.5900.0140.0140.0000.0000.0000.000
67A71ALA00.0740.03019.1030.0110.0110.0000.0000.0000.000
68A72ALA00.0010.00516.8600.0140.0140.0000.0000.0000.000
69A73THR0-0.029-0.02117.4430.0360.0360.0000.0000.0000.000
70A74GLU-1-0.829-0.87819.8400.0570.0570.0000.0000.0000.000
71A75THR0-0.028-0.03313.5190.0070.0070.0000.0000.0000.000
72A76TYR0-0.026-0.03614.9030.0510.0510.0000.0000.0000.000
73A77SER0-0.025-0.04316.1440.0270.0270.0000.0000.0000.000
74A78GLY00.0050.01817.0330.0010.0010.0000.0000.0000.000
75A79LEU0-0.0300.01010.7330.0130.0130.0000.0000.0000.000
76A80THR00.0440.01711.892-0.024-0.0240.0000.0000.0000.000
77A81PRO00.012-0.01613.8190.0390.0390.0000.0000.0000.000
78A82GLU-1-0.924-0.95510.1610.5280.5280.0000.0000.0000.000
79A83GLN00.0250.0068.192-0.014-0.0140.0000.0000.0000.000
80A84LYS10.8110.89710.408-0.178-0.1780.0000.0000.0000.000
81A85ALA00.0120.00013.019-0.020-0.0200.0000.0000.0000.000
82A86TYR00.0000.0058.2150.0380.0380.0000.0000.0000.000
83A87VAL0-0.004-0.00511.215-0.030-0.0300.0000.0000.0000.000
84A88PRO0-0.013-0.01613.128-0.051-0.0510.0000.0000.0000.000
85A89ALA00.0150.01912.327-0.050-0.0500.0000.0000.0000.000
86A90MET00.0020.0318.587-0.079-0.0790.0000.0000.0000.000
87A91PHE00.017-0.01712.904-0.073-0.0730.0000.0000.0000.000
88A92THR0-0.049-0.01216.581-0.036-0.0360.0000.0000.0000.000
89A93ALA0-0.002-0.00813.892-0.028-0.0280.0000.0000.0000.000
90A94ALA0-0.012-0.00113.877-0.030-0.0300.0000.0000.0000.000
91A95LEU0-0.063-0.03216.028-0.027-0.0270.0000.0000.0000.000
92A96ASN0-0.0240.00919.219-0.004-0.0040.0000.0000.0000.000
93A97ILE0-0.0240.00219.639-0.007-0.0070.0000.0000.0000.000
94A98GLN00.0180.00420.1770.0330.0330.0000.0000.0000.000
95A99THR0-0.024-0.04018.990-0.004-0.0040.0000.0000.0000.000
96A100SER0-0.009-0.01220.0870.0100.0100.0000.0000.0000.000
97A101VAL00.0510.02016.468-0.006-0.0060.0000.0000.0000.000
98A102ASN0-0.0150.00118.9780.0040.0040.0000.0000.0000.000
99A103THR0-0.067-0.04521.876-0.013-0.0130.0000.0000.0000.000
100A104VAL00.0350.03816.816-0.015-0.0150.0000.0000.0000.000
101A105VAL00.0430.02420.179-0.010-0.0100.0000.0000.0000.000
102A106ARG10.9070.93421.744-0.113-0.1130.0000.0000.0000.000
103A107ASP-1-0.733-0.81022.1100.1120.1120.0000.0000.0000.000
104A108PHE00.0140.00218.301-0.006-0.0060.0000.0000.0000.000
105A109GLU-1-0.845-0.91721.5470.0500.0500.0000.0000.0000.000
106A110ASN0-0.043-0.01724.588-0.016-0.0160.0000.0000.0000.000
107A111TYR00.0420.02521.328-0.008-0.0080.0000.0000.0000.000
108A112VAL00.0100.00521.526-0.011-0.0110.0000.0000.0000.000
109A113LYS10.8180.90224.439-0.053-0.0530.0000.0000.0000.000
110A114GLN0-0.007-0.00327.839-0.002-0.0020.0000.0000.0000.000
111A115THR0-0.020-0.01124.330-0.006-0.0060.0000.0000.0000.000
112A116CYS0-0.118-0.05021.256-0.006-0.0060.0000.0000.0000.000
113A117ASN00.008-0.00427.209-0.008-0.0080.0000.0000.0000.000
114A118SER00.0080.00930.2170.0000.0000.0000.0000.0000.000
115A119SER00.004-0.02931.707-0.002-0.0020.0000.0000.0000.000
116A120ALA0-0.072-0.03031.035-0.003-0.0030.0000.0000.0000.000
117A121VAL0-0.040-0.01427.104-0.003-0.0030.0000.0000.0000.000
118A122VAL0-0.003-0.01929.759-0.004-0.0040.0000.0000.0000.000
119A123ASP-1-0.838-0.89432.371-0.004-0.0040.0000.0000.0000.000
120A124ASN0-0.046-0.02528.759-0.004-0.0040.0000.0000.0000.000
121A125LYS10.9750.97832.2320.0140.0140.0000.0000.0000.000
122A126LEU0-0.014-0.00831.043-0.002-0.0020.0000.0000.0000.000
123A127LYS10.8320.90530.5810.0250.0250.0000.0000.0000.000
124A128ILE00.0080.01928.056-0.003-0.0030.0000.0000.0000.000
125A129GLN00.0200.01625.0510.0000.0000.0000.0000.0000.000
126A130ASN0-0.003-0.00923.474-0.014-0.0140.0000.0000.0000.000
127A131VAL0-0.0100.00217.5450.0110.0110.0000.0000.0000.000
128A132ILE0-0.007-0.00118.883-0.016-0.0160.0000.0000.0000.000
129A133ILE00.0400.02512.7560.0230.0230.0000.0000.0000.000
130A134ASP-1-0.841-0.90014.941-0.053-0.0530.0000.0000.0000.000
131A135GLU-1-0.817-0.90511.951-0.078-0.0780.0000.0000.0000.000
132A137TYR00.0160.0083.816-0.0390.1780.000-0.040-0.1770.000
133A138GLY00.0460.0294.659-0.756-0.680-0.001-0.011-0.0630.000
134A139ALA00.0030.0154.7930.2870.313-0.001-0.002-0.0230.000
135A140PRO00.030-0.0026.698-0.053-0.0530.0000.0000.0000.000
136A141GLY0-0.0030.0019.5180.0210.0210.0000.0000.0000.000
137A142SER0-0.081-0.0525.0270.1490.1490.0000.0000.0000.000
138A143PRO0-0.0050.0305.426-0.305-0.3050.0000.0000.0000.000
139A144THR0-0.001-0.0234.053-0.755-0.600-0.001-0.053-0.1010.000
140A145ASN0-0.063-0.0305.9810.4920.4920.0000.0000.0000.000
141A146LEU00.004-0.0017.0360.0190.0190.0000.0000.0000.000
142A147GLU-1-0.741-0.86910.552-0.169-0.1690.0000.0000.0000.000
143A148PHE0-0.026-0.01714.1260.0340.0340.0000.0000.0000.000
144A149ILE00.0160.00416.8550.0020.0020.0000.0000.0000.000
145A150ASN0-0.019-0.01319.2410.0200.0200.0000.0000.0000.000
146A151THR00.053-0.00322.5140.0000.0000.0000.0000.0000.000
147A152GLY00.0320.00024.8460.0040.0040.0000.0000.0000.000
148A153SER0-0.020-0.03326.9370.0040.0040.0000.0000.0000.000
149A154SER00.0150.00326.509-0.002-0.0020.0000.0000.0000.000
150A155LYS10.8040.91526.087-0.006-0.0060.0000.0000.0000.000
151A156GLY00.0750.04124.5530.0060.0060.0000.0000.0000.000
152A157ASN00.029-0.00822.0630.0010.0010.0000.0000.0000.000
153A159ALA00.0680.03320.9740.0060.0060.0000.0000.0000.000
154A160ILE0-0.0130.00817.1840.0130.0130.0000.0000.0000.000
155A161LYS10.9040.94116.5820.0190.0190.0000.0000.0000.000
156A162ALA0-0.011-0.00116.7040.0010.0010.0000.0000.0000.000
157A163LEU00.0400.01614.3670.0260.0260.0000.0000.0000.000
158A164MET0-0.0040.02312.3130.0150.0150.0000.0000.0000.000
159A165GLN00.0120.02311.973-0.033-0.0330.0000.0000.0000.000
160A166LEU0-0.0250.00812.3920.0160.0160.0000.0000.0000.000
161A167THR0-0.003-0.0147.7260.1210.1210.0000.0000.0000.000
162A168THR0-0.041-0.0527.3740.0460.0460.0000.0000.0000.000
163A169LYS10.8550.9288.229-0.073-0.0730.0000.0000.0000.000
164A170ALA00.0530.0296.9160.0100.0100.0000.0000.0000.000
165A171THR0-0.063-0.0433.5800.1730.4500.004-0.062-0.2190.000
166A172THR0-0.038-0.0394.626-0.543-0.448-0.001-0.006-0.0870.000
167A173GLN0-0.042-0.0457.4240.0360.0360.0000.0000.0000.000
168A174ILE0-0.051-0.0162.661-0.949-0.5002.106-0.780-1.7740.005
169A175ALA00.0070.0214.695-0.591-0.462-0.001-0.006-0.1210.000
170A176PRO0-0.054-0.0216.3140.2210.2210.0000.0000.0000.000
171A177LYS10.9450.9558.877-0.165-0.1650.0000.0000.0000.000
172A178GLN0-0.008-0.00212.1440.0350.0350.0000.0000.0000.000
173A179VAL00.0220.00814.869-0.010-0.0100.0000.0000.0000.000
174A180ALA00.0020.00117.6580.0090.0090.0000.0000.0000.000
175A181GLY00.0070.00916.5530.0050.0050.0000.0000.0000.000
176A182THR0-0.027-0.00317.4190.0110.0110.0000.0000.0000.000
177A183GLY00.0150.00815.879-0.005-0.0050.0000.0000.0000.000
178A184VAL00.0100.01215.7660.0060.0060.0000.0000.0000.000
179A185GLN00.0010.00115.7920.0320.0320.0000.0000.0000.000