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: 7GN3K

Calculation Name: 1TII-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TII

Chain ID: A

ChEMBL ID:

UniProt ID: P43528

Base Structure: X-ray

Registration Date: 2023-03-13

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2030278.065343
FMO2-HF: Nuclear repulsion 1957294.070902
FMO2-HF: Total energy -72983.994441
FMO2-MP2: Total energy -73199.773397


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:1:ASN)


Summations of interaction energy for fragment #1(A:1:ASN)
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.
-14.044-9.3433.775-2.947-5.531-0.026
Interaction energy analysis for fragmet #1(A:1:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.049 / q_NPA : -0.036
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].
3A3TYR0-0.018-0.0162.272-8.541-4.5932.891-2.469-4.370-0.025
4A4PHE0-0.025-0.0225.5871.0301.0300.0000.0000.0000.000
5A5ARG10.8400.8959.2411.0961.0960.0000.0000.0000.000
6A6ALA0-0.0270.01912.5280.1530.1530.0000.0000.0000.000
7A7ASP-1-0.729-0.83415.976-0.858-0.8580.0000.0000.0000.000
8A8SER00.040-0.00318.4420.0430.0430.0000.0000.0000.000
9A9ARG10.7810.89718.7980.7780.7780.0000.0000.0000.000
10A10THR00.0140.02320.891-0.028-0.0280.0000.0000.0000.000
11A11PRO00.0390.00720.046-0.018-0.0180.0000.0000.0000.000
12A12ASP-1-0.902-0.95521.514-0.253-0.2530.0000.0000.0000.000
13A13GLU-1-0.894-0.94823.576-0.393-0.3930.0000.0000.0000.000
14A14VAL00.0240.02017.840-0.015-0.0150.0000.0000.0000.000
15A15ARG10.9110.94820.9050.2650.2650.0000.0000.0000.000
16A16ARG10.9050.95722.2480.3010.3010.0000.0000.0000.000
17A17SER00.0020.01622.1390.0130.0130.0000.0000.0000.000
18A18GLY00.0040.01821.188-0.021-0.0210.0000.0000.0000.000
19A19GLY00.009-0.00817.791-0.058-0.0580.0000.0000.0000.000
20A20LEU0-0.076-0.02313.9950.0720.0720.0000.0000.0000.000
21A21ILE00.0550.03717.006-0.131-0.1310.0000.0000.0000.000
22A22PRO00.022-0.00418.6810.0070.0070.0000.0000.0000.000
23A23ARG10.9420.96120.5630.5740.5740.0000.0000.0000.000
24A24GLY0-0.027-0.00723.7480.0440.0440.0000.0000.0000.000
25A25GLN0-0.034-0.00222.537-0.022-0.0220.0000.0000.0000.000
26A26ASP-1-0.887-0.94925.492-0.410-0.4100.0000.0000.0000.000
27A27GLU-1-0.978-0.98027.108-0.353-0.3530.0000.0000.0000.000
28A28ALA00.018-0.01824.182-0.040-0.0400.0000.0000.0000.000
29A29TYR0-0.002-0.01816.700-0.028-0.0280.0000.0000.0000.000
30A30GLU-1-0.941-0.99419.874-0.588-0.5880.0000.0000.0000.000
31A31ARG10.7930.93222.7970.3970.3970.0000.0000.0000.000
32A32GLY00.1110.06725.5530.0240.0240.0000.0000.0000.000
33A33THR0-0.009-0.00823.717-0.029-0.0290.0000.0000.0000.000
34A34PRO0-0.043-0.01421.2570.0260.0260.0000.0000.0000.000
35A35ILE00.0080.00424.3800.0120.0120.0000.0000.0000.000
36A36ASN0-0.020-0.01226.0310.0420.0420.0000.0000.0000.000
37A37ILE0-0.031-0.01220.369-0.041-0.0410.0000.0000.0000.000
38A38ASN00.0390.02521.876-0.011-0.0110.0000.0000.0000.000
39A39LEU00.0230.01815.002-0.019-0.0190.0000.0000.0000.000
40A40TYR00.0280.01419.030-0.015-0.0150.0000.0000.0000.000
41A41ASP-1-0.863-0.93821.086-0.566-0.5660.0000.0000.0000.000
42A42HIS10.7290.84815.7571.1731.1730.0000.0000.0000.000
43A43ALA0-0.033-0.01817.412-0.005-0.0050.0000.0000.0000.000
44A44ARG10.8760.93018.8380.5890.5890.0000.0000.0000.000
45A45GLY0-0.0040.01822.2110.0550.0550.0000.0000.0000.000
46A46THR0-0.0050.00622.137-0.049-0.0490.0000.0000.0000.000
47A47ALA0-0.072-0.02721.8160.0160.0160.0000.0000.0000.000
48A48THR00.0260.00623.7400.0210.0210.0000.0000.0000.000
49A49GLY00.0160.01825.9980.0010.0010.0000.0000.0000.000
50A50ASN00.0480.00020.371-0.031-0.0310.0000.0000.0000.000
51A51THR00.0270.00317.2740.0030.0030.0000.0000.0000.000
52A52ARG10.8220.88017.6090.8580.8580.0000.0000.0000.000
53A53TYR0-0.019-0.02117.363-0.110-0.1100.0000.0000.0000.000
54A54ASN00.0470.02619.2390.0560.0560.0000.0000.0000.000
55A55ASP-1-0.831-0.90920.793-0.730-0.7300.0000.0000.0000.000
56A56GLY00.0630.01720.943-0.039-0.0390.0000.0000.0000.000
57A57TYR00.0140.02014.972-0.027-0.0270.0000.0000.0000.000
58A58VAL0-0.044-0.01913.9040.1300.1300.0000.0000.0000.000
59A59SER0-0.0080.01113.334-0.228-0.2280.0000.0000.0000.000
60A60THR0-0.050-0.0138.560-0.135-0.1350.0000.0000.0000.000
61A61THR00.0540.0209.2040.0130.0130.0000.0000.0000.000
62A62THR00.0670.0164.986-0.210-0.2100.0000.0000.0000.000
63A63THR0-0.0010.0146.6260.6330.6330.0000.0000.0000.000
64A64LEU00.0500.0319.175-0.142-0.1420.0000.0000.0000.000
65A65ARG11.0040.99311.6960.1700.1700.0000.0000.0000.000
66A66GLN00.002-0.00611.732-0.058-0.0580.0000.0000.0000.000
67A67ALA00.0600.02311.6890.0020.0020.0000.0000.0000.000
68A68HIS0-0.032-0.01913.5530.0660.0660.0000.0000.0000.000
69A69LEU0-0.073-0.03216.4100.0430.0430.0000.0000.0000.000
70A70LEU00.026-0.00114.0150.0400.0400.0000.0000.0000.000
71A71GLY00.0170.01117.6350.0230.0230.0000.0000.0000.000
72A72GLN0-0.010-0.00319.2720.0250.0250.0000.0000.0000.000
73A73ASN0-0.051-0.01020.9980.0600.0600.0000.0000.0000.000
74A74MET0-0.013-0.01019.808-0.016-0.0160.0000.0000.0000.000
75A75LEU0-0.036-0.00619.7700.0100.0100.0000.0000.0000.000
76A76GLY00.0500.04723.4100.0360.0360.0000.0000.0000.000
77A77GLY0-0.027-0.02225.804-0.007-0.0070.0000.0000.0000.000
78A78TYR0-0.055-0.01125.3370.0190.0190.0000.0000.0000.000
79A79ASN0-0.051-0.03727.0620.0150.0150.0000.0000.0000.000
80A80GLU-1-0.874-0.94424.636-0.193-0.1930.0000.0000.0000.000
81A81TYR0-0.0110.00018.463-0.046-0.0460.0000.0000.0000.000
82A82TYR0-0.002-0.01218.2290.0640.0640.0000.0000.0000.000
83A83ILE0-0.0010.00912.938-0.083-0.0830.0000.0000.0000.000
84A84TYR0-0.033-0.05913.2180.1270.1270.0000.0000.0000.000
85A85VAL0-0.0100.0017.927-0.194-0.1940.0000.0000.0000.000
86A86VAL0-0.030-0.0207.5390.4070.4070.0000.0000.0000.000
87A87ALA00.0580.0334.804-1.141-1.1410.0000.0000.0000.000
88A88ALA00.0060.0022.4290.1150.5960.886-0.429-0.939-0.001
89A89ALA00.005-0.0014.5471.2881.455-0.001-0.023-0.1440.000
90A90PRO00.0460.0167.650-0.434-0.4340.0000.0000.0000.000
91A91ASN00.0370.03610.093-0.129-0.1290.0000.0000.0000.000
92A92LEU0-0.064-0.0155.9970.0790.0790.0000.0000.0000.000
93A93PHE00.0570.0199.125-0.193-0.1930.0000.0000.0000.000
94A94ASP-1-0.839-0.9207.987-2.745-2.7450.0000.0000.0000.000
95A95VAL00.0240.0009.4190.4230.4230.0000.0000.0000.000
96A96ASN0-0.020-0.00611.6570.3290.3290.0000.0000.0000.000
97A97GLY0-0.0210.00811.6890.2230.2230.0000.0000.0000.000
98A98VAL0-0.029-0.00412.7400.1980.1980.0000.0000.0000.000
99A99LEU00.005-0.00814.9800.1660.1660.0000.0000.0000.000
100A100GLY00.0590.04416.4120.1230.1230.0000.0000.0000.000
101A101ARG10.9320.94917.9640.3960.3960.0000.0000.0000.000
102A102TYR0-0.062-0.03720.3480.0520.0520.0000.0000.0000.000
103A103SER0-0.041-0.02615.247-0.005-0.0050.0000.0000.0000.000
104A104PRO00.0150.00718.3280.0520.0520.0000.0000.0000.000
105A105TYR0-0.020-0.00817.3480.1040.1040.0000.0000.0000.000
106A106PRO00.0340.02915.231-0.111-0.1110.0000.0000.0000.000
107A107SER0-0.018-0.01414.253-0.120-0.1200.0000.0000.0000.000
108A108GLU-1-0.842-0.91814.061-0.995-0.9950.0000.0000.0000.000
109A109ASN0-0.085-0.0258.983-0.210-0.2100.0000.0000.0000.000
110A110GLU-1-0.800-0.9029.205-1.969-1.9690.0000.0000.0000.000
111A111TYR00.0130.0125.277-1.153-1.1530.0000.0000.0000.000
112A112ALA0-0.0090.0019.0310.0950.0950.0000.0000.0000.000
113A113ALA00.0110.00411.322-0.140-0.1400.0000.0000.0000.000
114A114LEU00.011-0.00912.5430.2490.2490.0000.0000.0000.000
115A115GLY00.0180.00515.6360.0130.0130.0000.0000.0000.000
116A116GLY0-0.037-0.01815.8580.1100.1100.0000.0000.0000.000
117A117ILE0-0.060-0.03111.308-0.148-0.1480.0000.0000.0000.000
118A118PRO00.0650.05013.3340.1710.1710.0000.0000.0000.000
119A119LEU00.046-0.00314.156-0.100-0.1000.0000.0000.0000.000
120A120SER0-0.027-0.01314.286-0.043-0.0430.0000.0000.0000.000
121A121GLN00.0170.0068.2270.5500.5500.0000.0000.0000.000
122A122ILE0-0.046-0.0169.606-0.292-0.2920.0000.0000.0000.000
123A123ILE00.0470.0336.2370.3330.3330.0000.0000.0000.000
124A124GLY00.005-0.01610.8290.2800.2800.0000.0000.0000.000
125A125TRP00.0080.01213.302-0.189-0.1890.0000.0000.0000.000
126A126TYR00.0070.01411.9310.1720.1720.0000.0000.0000.000
127A127ARG10.9290.96117.0460.0600.0600.0000.0000.0000.000
128A128VAL0-0.0110.00119.1000.0440.0440.0000.0000.0000.000
129A129SER00.0250.00621.807-0.024-0.0240.0000.0000.0000.000
130A130PHE00.005-0.01525.5540.0200.0200.0000.0000.0000.000
131A131GLY0-0.0110.01223.7990.0110.0110.0000.0000.0000.000
132A132ALA00.0010.01122.961-0.002-0.0020.0000.0000.0000.000
133A133ILE0-0.013-0.01616.468-0.026-0.0260.0000.0000.0000.000
134A134GLU-1-0.938-0.97020.5940.0000.0000.0000.0000.0000.000
135A135GLY0-0.025-0.00321.640-0.007-0.0070.0000.0000.0000.000
136A136GLY0-0.009-0.01417.8690.0160.0160.0000.0000.0000.000
137A137MET0-0.052-0.01312.086-0.054-0.0540.0000.0000.0000.000
138A138HIS0-0.020-0.00916.0030.0920.0920.0000.0000.0000.000
139A139ARG10.9280.95113.152-0.611-0.6110.0000.0000.0000.000
140A140ASN00.000-0.00914.2230.0990.0990.0000.0000.0000.000
141A141ARG10.9230.94515.5560.0480.0480.0000.0000.0000.000
142A142ASP-1-0.899-0.95017.458-0.226-0.2260.0000.0000.0000.000
143A143TYR0-0.0170.0127.2560.2470.2470.0000.0000.0000.000
144A144ARG10.8740.93812.7170.3430.3430.0000.0000.0000.000
145A145ARG10.9800.97510.018-0.482-0.4820.0000.0000.0000.000
146A146ASP-1-0.936-0.98110.303-0.016-0.0160.0000.0000.0000.000
147A147LEU00.0090.01212.2000.0090.0090.0000.0000.0000.000
148A148PHE00.0280.0057.015-0.117-0.1170.0000.0000.0000.000
149A149ARG10.8850.9476.455-1.500-1.5000.0000.0000.0000.000
150A150GLY0-0.010-0.0125.645-0.006-0.0060.0000.0000.0000.000
151A151LEU00.0120.0495.8640.0450.0450.0000.0000.0000.000
152A152SER0-0.027-0.0284.257-0.597-0.492-0.001-0.026-0.0780.000
153A153ALA0-0.001-0.0114.8610.2690.2690.0000.0000.0000.000
154A154ALA0-0.0120.0036.6420.5740.5740.0000.0000.0000.000
155A155PRO0-0.0220.0139.867-0.278-0.2780.0000.0000.0000.000
156A156ASN00.049-0.00611.245-0.162-0.1620.0000.0000.0000.000
157A157GLU-1-0.905-0.95113.287-0.846-0.8460.0000.0000.0000.000
158A158ASP-1-0.907-0.96014.788-0.919-0.9190.0000.0000.0000.000
159A159GLY0-0.019-0.01815.1670.0130.0130.0000.0000.0000.000
160A160TYR0-0.056-0.03316.0300.0850.0850.0000.0000.0000.000
161A161ARG10.9640.99218.8960.5620.5620.0000.0000.0000.000
162A162ILE0-0.059-0.02716.8240.0620.0620.0000.0000.0000.000
163A163ALA00.0120.01219.007-0.032-0.0320.0000.0000.0000.000
164A164GLY0-0.015-0.01720.012-0.012-0.0120.0000.0000.0000.000
165A165PHE00.0240.01820.7650.0110.0110.0000.0000.0000.000
166A166PRO0-0.0180.00124.8810.0150.0150.0000.0000.0000.000
167A167ASP-1-0.864-0.95828.527-0.337-0.3370.0000.0000.0000.000
168A168GLY00.0340.02431.2050.0110.0110.0000.0000.0000.000
169A169PHE0-0.068-0.02024.8690.0110.0110.0000.0000.0000.000
170A170PRO00.0470.00428.073-0.001-0.0010.0000.0000.0000.000
171A171ALA00.0280.01723.9460.0090.0090.0000.0000.0000.000
172A172TRP0-0.047-0.02523.528-0.024-0.0240.0000.0000.0000.000
173A173GLU-1-0.952-0.97727.747-0.259-0.2590.0000.0000.0000.000
174A174GLU-1-0.906-0.94525.934-0.388-0.3880.0000.0000.0000.000
175A175VAL0-0.0150.02823.699-0.027-0.0270.0000.0000.0000.000
176A176PRO0-0.016-0.03419.5090.0120.0120.0000.0000.0000.000
177A177TRP0-0.001-0.02619.0550.0350.0350.0000.0000.0000.000
178A178ARG10.9650.98423.2940.3000.3000.0000.0000.0000.000
179A179GLU-1-0.960-0.98224.406-0.305-0.3050.0000.0000.0000.000
180A180PHE0-0.063-0.03620.907-0.007-0.0070.0000.0000.0000.000
181A181ALA00.0020.01324.208-0.025-0.0250.0000.0000.0000.000
182A182PRO0-0.035-0.00725.1760.0300.0300.0000.0000.0000.000
183A183ASN00.061-0.00427.8420.0030.0030.0000.0000.0000.000
184A184SER0-0.057-0.03331.2860.0080.0080.0000.0000.0000.000
185A185CYS0-0.0300.01028.453-0.010-0.0100.0000.0000.0000.000
186A186LEU0-0.037-0.00129.448-0.001-0.0010.0000.0000.0000.000
187A187PRO0-0.0220.00331.7900.0180.0180.0000.0000.0000.000