FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 9L8M2

Calculation Name: 3TIP-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3TIP

Chain ID: A

ChEMBL ID:

UniProt ID: Q2G2B2

Base Structure: X-ray

Registration Date: 2025-07-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 233
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -802161.842393
FMO2-HF: Nuclear repulsion 752033.107274
FMO2-HF: Total energy -50128.735119
FMO2-MP2: Total energy -50276.862159


3D Structure Molmil
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:498:GLY)


Summations of interaction energy for fragment #1(A:498:GLY)
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.
-1.6360.1590.044-0.897-0.9430.003
Interaction energy analysis for fragmet #1(A:498:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.025
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].
3A500HIS00.1830.0503.893-0.5390.588-0.004-0.597-0.5270.002
4A500HIS0-0.1280.0866.089-0.179-0.1790.0000.0000.0000.000
5A501MET00.089-0.1036.4030.5500.5500.0000.0000.0000.000
6A501MET0-0.1080.1007.1930.0480.0480.0000.0000.0000.000
7A502ILE00.051-0.1159.0460.0450.0450.0000.0000.0000.000
8A502ILE0-0.1000.10311.2260.0180.0180.0000.0000.0000.000
9A503ALA00.126-0.09312.4150.0880.0880.0000.0000.0000.000
10A503ALA0-0.0440.12414.7950.0090.0090.0000.0000.0000.000
11A504PRO0-0.094-0.13415.092-0.004-0.0040.0000.0000.0000.000
12A505GLY00.0850.04518.1970.0120.0120.0000.0000.0000.000
13A506HIS00.088-0.00121.5780.0050.0050.0000.0000.0000.000
14A506HIS10.7610.99424.4450.2130.2130.0000.0000.0000.000
15A507ARG00.086-0.06524.944-0.005-0.0050.0000.0000.0000.000
16A507ARG10.7170.96826.2060.2250.2250.0000.0000.0000.000
17A508ASP00.073-0.09028.3020.0000.0000.0000.0000.0000.000
18A508ASP-1-0.876-0.80930.623-0.174-0.1740.0000.0000.0000.000
19A509GLU00.056-0.13931.734-0.001-0.0010.0000.0000.0000.000
20A509GLU-1-0.855-0.77130.891-0.173-0.1730.0000.0000.0000.000
21A510PHE00.141-0.08334.2490.0030.0030.0000.0000.0000.000
22A510PHE0-0.0670.09638.9540.0010.0010.0000.0000.0000.000
23A511ASP00.053-0.11237.232-0.004-0.0040.0000.0000.0000.000
24A511ASP-1-0.857-0.77836.152-0.108-0.1080.0000.0000.0000.000
25A512PRO0-0.030-0.11638.3230.0050.0050.0000.0000.0000.000
26A513LYS0-0.020-0.02040.2140.0060.0060.0000.0000.0000.000
27A513LYS10.8231.02239.5780.0760.0760.0000.0000.0000.000
28A514LEU00.092-0.08238.8540.0040.0040.0000.0000.0000.000
29A514LEU0-0.0340.12135.535-0.001-0.0010.0000.0000.0000.000
30A515PRO00.008-0.09339.8070.0020.0020.0000.0000.0000.000
31A516THR00.0820.01142.037-0.005-0.0050.0000.0000.0000.000
32A516THR0-0.0750.06046.2510.0020.0020.0000.0000.0000.000
33A517GLY0-0.096-0.12242.9140.0040.0040.0000.0000.0000.000
34A518GLU00.050-0.01239.524-0.001-0.0010.0000.0000.0000.000
35A518GLU-1-0.967-0.83338.488-0.069-0.0690.0000.0000.0000.000
36A519LYS00.044-0.09335.555-0.002-0.0020.0000.0000.0000.000
37A519LYS10.7770.99432.2450.1180.1180.0000.0000.0000.000
38A520GLU00.114-0.12332.8600.0080.0080.0000.0000.0000.000
39A520GLU-1-0.997-0.83630.911-0.120-0.1200.0000.0000.0000.000
40A521GLU00.081-0.09229.179-0.006-0.0060.0000.0000.0000.000
41A521GLU-1-0.893-0.78228.424-0.135-0.1350.0000.0000.0000.000
42A522VAL00.068-0.12326.9530.0050.0050.0000.0000.0000.000
43A522VAL0-0.0690.13225.457-0.001-0.0010.0000.0000.0000.000
44A523PRO0-0.024-0.11821.877-0.020-0.0200.0000.0000.0000.000
45A524GLY00.0740.04020.6380.0000.0000.0000.0000.0000.000
46A525LYS00.066-0.01517.4880.0130.0130.0000.0000.0000.000
47A525LYS10.7991.05016.6970.3300.3300.0000.0000.0000.000
48A526PRO00.019-0.07912.503-0.001-0.0010.0000.0000.0000.000
49A527GLY00.0320.01213.5430.0650.0650.0000.0000.0000.000
50A528ILE00.048-0.0119.565-0.083-0.0830.0000.0000.0000.000
51A528ILE0-0.0840.0797.7380.0560.0560.0000.0000.0000.000
52A529LYS00.114-0.0758.8540.3370.3370.0000.0000.0000.000
53A529LYS10.7621.0308.8411.9641.9640.0000.0000.0000.000
54A530ASN00.152-0.0956.783-1.018-1.0180.0000.0000.0000.000
55A530ASN0-0.1190.0806.732-0.274-0.2740.0000.0000.0000.000
56A531PRO0-0.075-0.1352.8990.6001.1260.048-0.215-0.3590.001
57A532GLU00.028-0.0305.8590.5550.5550.0000.0000.0000.000
58A532GLU-1-0.924-0.8224.060-3.892-3.7500.000-0.085-0.0570.000
59A533THR0-0.061-0.1177.5450.3270.3270.0000.0000.0000.000
60A533THR0-0.0370.05510.255-0.103-0.1030.0000.0000.0000.000
61A534GLY00.009-0.0969.8840.1650.1650.0000.0000.0000.000
62A535ASP00.085-0.00811.608-0.032-0.0320.0000.0000.0000.000
63A535ASP-1-0.866-0.76312.039-0.805-0.8050.0000.0000.0000.000
64A536VAL00.103-0.10111.433-0.309-0.3090.0000.0000.0000.000
65A536VAL0-0.1020.10913.9640.0150.0150.0000.0000.0000.000
66A537VAL00.123-0.08011.0900.1850.1850.0000.0000.0000.000
67A537VAL0-0.1080.0829.319-0.015-0.0150.0000.0000.0000.000
68A538ARG00.084-0.10212.4850.1470.1470.0000.0000.0000.000
69A538ARG10.7541.02012.5760.6450.6450.0000.0000.0000.000
70A539PRO00.012-0.07614.010-0.116-0.1160.0000.0000.0000.000
71A540PRO00.020-0.00415.9120.0020.0020.0000.0000.0000.000
72A541VAL00.034-0.00117.1930.0280.0280.0000.0000.0000.000
73A541VAL0-0.1120.05819.4920.0070.0070.0000.0000.0000.000
74A542ASP00.083-0.12420.340-0.023-0.0230.0000.0000.0000.000
75A542ASP-1-0.899-0.80223.188-0.319-0.3190.0000.0000.0000.000
76A543SER00.069-0.05122.6020.0110.0110.0000.0000.0000.000
77A543SER0-0.0610.06722.5940.0100.0100.0000.0000.0000.000
78A544VAL0-0.004-0.13023.844-0.008-0.0080.0000.0000.0000.000
79A544VAL0-0.0890.09726.1530.0000.0000.0000.0000.0000.000
80A545THR00.031-0.07727.6340.0070.0070.0000.0000.0000.000
81A545THR0-0.0780.05429.755-0.006-0.0060.0000.0000.0000.000
82A546LYS00.032-0.10330.518-0.004-0.0040.0000.0000.0000.000
83A546LYS10.8101.02631.5240.1330.1330.0000.0000.0000.000
84A547TYR00.088-0.10133.6220.0050.0050.0000.0000.0000.000
85A547TYR0-0.1420.06532.7560.0040.0040.0000.0000.0000.000
86A548GLY00.066-0.06937.051-0.001-0.0010.0000.0000.0000.000
87A549PRO0-0.056-0.01740.204-0.001-0.0010.0000.0000.0000.000
88A550VAL00.0950.01543.6690.0030.0030.0000.0000.0000.000
89A550VAL0-0.0500.11742.5900.0000.0000.0000.0000.0000.000
90A551LYS00.119-0.09545.1230.0000.0000.0000.0000.0000.000
91A551LYS10.8821.06148.4900.0500.0500.0000.0000.0000.000
92A552GLY0-0.050-0.11648.596-0.003-0.0030.0000.0000.0000.000
93A553ASP00.047-0.02550.8800.0020.0020.0000.0000.0000.000
94A553ASP-1-0.889-0.80252.789-0.058-0.0580.0000.0000.0000.000
95A554SER00.008-0.07354.257-0.002-0.0020.0000.0000.0000.000
96A554SER0-0.0080.07356.0240.0010.0010.0000.0000.0000.000
97A555ILE00.094-0.06557.1090.0010.0010.0000.0000.0000.000
98A555ILE0-0.0940.07657.020-0.001-0.0010.0000.0000.0000.000
99A556VAL00.041-0.09759.5170.0000.0000.0000.0000.0000.000
100A556VAL0-0.1120.07460.9530.0000.0000.0000.0000.0000.000
101A557GLU00.122-0.06962.9510.0000.0000.0000.0000.0000.000
102A557GLU-1-0.989-0.87063.915-0.041-0.0410.0000.0000.0000.000
103A558LYS00.020-0.13665.8870.0010.0010.0000.0000.0000.000
104A558LYS10.7480.98168.1030.0320.0320.0000.0000.0000.000
105A559GLU00.044-0.10669.590-0.001-0.0010.0000.0000.0000.000
106A559GLU-1-0.897-0.82270.704-0.033-0.0330.0000.0000.0000.000
107A560GLU00.084-0.08972.8050.0000.0000.0000.0000.0000.000
108A560GLU-1-0.886-0.78976.677-0.027-0.0270.0000.0000.0000.000
109A561ILE00.036-0.14176.401-0.001-0.0010.0000.0000.0000.000
110A561ILE0-0.0890.13476.0610.0000.0000.0000.0000.0000.000
111A562PRO00.011-0.10578.7460.0010.0010.0000.0000.0000.000
112A563PHE00.1140.02582.2670.0000.0000.0000.0000.0000.000
113A563PHE0-0.0990.08584.6360.0000.0000.0000.0000.0000.000
114A564GLU00.030-0.11685.4160.0000.0000.0000.0000.0000.000
115A564GLU-1-0.949-0.83586.458-0.021-0.0210.0000.0000.0000.000
116A565LYS00.072-0.10188.6180.0000.0000.0000.0000.0000.000
117A565LYS10.7130.96191.2050.0190.0190.0000.0000.0000.000
118A566GLU00.118-0.10392.3960.0000.0000.0000.0000.0000.000
119A566GLU-1-0.863-0.78190.556-0.018-0.0180.0000.0000.0000.000
120A567ARG00.068-0.10794.2500.0000.0000.0000.0000.0000.000
121A567ARG10.7310.95897.7300.0160.0160.0000.0000.0000.000
122A568LYS00.066-0.08998.0720.0000.0000.0000.0000.0000.000
123A568LYS10.7421.01598.2280.0150.0150.0000.0000.0000.000
124A569PHE00.167-0.081100.0500.0000.0000.0000.0000.0000.000
125A569PHE0-0.0820.096104.0840.0000.0000.0000.0000.0000.000
126A570ASN00.068-0.101103.2510.0000.0000.0000.0000.0000.000
127A570ASN0-0.1420.051102.9020.0000.0000.0000.0000.0000.000
128A571PRO0-0.037-0.121105.3200.0000.0000.0000.0000.0000.000
129A572ASP00.1180.020107.9430.0000.0000.0000.0000.0000.000
130A572ASP-1-0.982-0.859107.409-0.012-0.0120.0000.0000.0000.000
131A573LEU0-0.013-0.133107.3010.0000.0000.0000.0000.0000.000
132A573LEU0-0.0940.110103.9010.0000.0000.0000.0000.0000.000
133A574ALA00.155-0.086108.4900.0000.0000.0000.0000.0000.000
134A574ALA0-0.0910.107111.2200.0000.0000.0000.0000.0000.000
135A575PRO0-0.018-0.107110.6500.0000.0000.0000.0000.0000.000
136A576GLY00.0040.009111.0650.0000.0000.0000.0000.0000.000
137A577THR0-0.0480.007108.6600.0000.0000.0000.0000.0000.000
138A577THR0-0.0930.024108.3850.0000.0000.0000.0000.0000.000
139A578GLU00.111-0.105104.2430.0000.0000.0000.0000.0000.000
140A578GLU-1-0.841-0.734103.121-0.015-0.0150.0000.0000.0000.000
141A579LYS00.067-0.097102.0710.0000.0000.0000.0000.0000.000
142A579LYS10.8401.047100.9980.0140.0140.0000.0000.0000.000
143A580VAL00.083-0.11597.2500.0000.0000.0000.0000.0000.000
144A580VAL0-0.0540.15395.1280.0000.0000.0000.0000.0000.000
145A581THR0-0.050-0.09997.5470.0000.0000.0000.0000.0000.000
146A581THR0-0.0540.04197.8770.0000.0000.0000.0000.0000.000
147A582ARG00.119-0.09093.2090.0000.0000.0000.0000.0000.000
148A582ARG10.6700.96790.4410.0180.0180.0000.0000.0000.000
149A583GLU00.078-0.11291.9140.0000.0000.0000.0000.0000.000
150A583GLU-1-0.963-0.84191.253-0.018-0.0180.0000.0000.0000.000
151A584GLY00.005-0.08389.0430.0000.0000.0000.0000.0000.000
152A585GLN0-0.019-0.04985.1910.0000.0000.0000.0000.0000.000
153A585GLN0-0.0250.11084.2500.0000.0000.0000.0000.0000.000
154A586LYS00.070-0.07081.5360.0000.0000.0000.0000.0000.000
155A586LYS10.7630.98480.6340.0260.0260.0000.0000.0000.000
156A587GLY00.014-0.09179.4660.0010.0010.0000.0000.0000.000
157A588GLU00.035-0.03375.4650.0000.0000.0000.0000.0000.000
158A588GLU-1-0.873-0.76172.595-0.030-0.0300.0000.0000.0000.000
159A589LYS00.004-0.09372.7120.0010.0010.0000.0000.0000.000
160A589LYS10.7541.00071.1060.0310.0310.0000.0000.0000.000
161A590THR00.044-0.08168.450-0.001-0.0010.0000.0000.0000.000
162A590THR0-0.0380.06066.3230.0000.0000.0000.0000.0000.000
163A591ILE00.061-0.10066.4290.0010.0010.0000.0000.0000.000
164A591ILE0-0.0820.11765.3600.0000.0000.0000.0000.0000.000
165A592THR00.047-0.08662.561-0.001-0.0010.0000.0000.0000.000
166A592THR0-0.0530.06360.5910.0000.0000.0000.0000.0000.000
167A593THR0-0.023-0.07659.8330.0010.0010.0000.0000.0000.000
168A593THR0-0.0770.08958.0820.0000.0000.0000.0000.0000.000
169A594PRO00.040-0.10055.030-0.001-0.0010.0000.0000.0000.000
170A595THR00.0110.01053.3140.0000.0000.0000.0000.0000.000
171A595THR0-0.0310.04752.962-0.001-0.0010.0000.0000.0000.000
172A596LEU00.089-0.08548.9920.0010.0010.0000.0000.0000.000
173A596LEU0-0.0570.10547.9050.0000.0000.0000.0000.0000.000
174A597LYS00.058-0.11447.0720.0000.0000.0000.0000.0000.000
175A597LYS10.8551.06446.6750.0660.0660.0000.0000.0000.000
176A598ASN00.149-0.07343.1200.0000.0000.0000.0000.0000.000
177A598ASN0-0.0590.11840.971-0.002-0.0020.0000.0000.0000.000
178A599PRO0-0.043-0.11339.6610.0000.0000.0000.0000.0000.000
179A600LEU00.0860.00138.9000.0010.0010.0000.0000.0000.000
180A600LEU0-0.1050.09135.7240.0000.0000.0000.0000.0000.000
181A601THR0-0.069-0.10939.841-0.004-0.0040.0000.0000.0000.000
182A601THR0-0.0490.02341.6180.0000.0000.0000.0000.0000.000
183A602GLY0-0.009-0.09543.1940.0030.0030.0000.0000.0000.000
184A603GLU00.077-0.05145.9670.0060.0060.0000.0000.0000.000
185A603GLU-1-0.899-0.75545.563-0.090-0.0900.0000.0000.0000.000
186A604ILE00.078-0.08247.430-0.002-0.0020.0000.0000.0000.000
187A604ILE0-0.0960.08251.4490.0010.0010.0000.0000.0000.000
188A605ILE00.009-0.11047.1950.0010.0010.0000.0000.0000.000
189A605ILE0-0.1130.09645.465-0.001-0.0010.0000.0000.0000.000
190A606SER0-0.006-0.11648.7260.0000.0000.0000.0000.0000.000
191A606SER00.0010.08549.3870.0010.0010.0000.0000.0000.000
192A607LYS00.011-0.10951.435-0.001-0.0010.0000.0000.0000.000
193A607LYS10.9221.07454.6670.0540.0540.0000.0000.0000.000
194A608GLY00.001-0.08154.7840.0000.0000.0000.0000.0000.000
195A609GLU00.098-0.01256.794-0.001-0.0010.0000.0000.0000.000
196A609GLU-1-0.982-0.85159.423-0.042-0.0420.0000.0000.0000.000
197A610SER00.004-0.10560.4970.0000.0000.0000.0000.0000.000
198A610SER0-0.0300.07362.3070.0000.0000.0000.0000.0000.000
199A611LYS00.103-0.07063.0010.0010.0010.0000.0000.0000.000
200A611LYS10.6850.97863.1810.0320.0320.0000.0000.0000.000
201A612GLU00.104-0.11464.781-0.001-0.0010.0000.0000.0000.000
202A612GLU-1-0.881-0.79168.575-0.032-0.0320.0000.0000.0000.000
203A613GLU00.075-0.10768.3410.0000.0000.0000.0000.0000.000
204A613GLU-1-0.953-0.82968.251-0.030-0.0300.0000.0000.0000.000
205A614ILE00.042-0.09470.220-0.001-0.0010.0000.0000.0000.000
206A614ILE0-0.0620.12373.7950.0000.0000.0000.0000.0000.000
207A615THR00.020-0.06772.4650.0010.0010.0000.0000.0000.000
208A615THR0-0.0350.04170.6130.0000.0000.0000.0000.0000.000
209A616LYS00.150-0.08773.4010.0010.0010.0000.0000.0000.000
210A616LYS10.7220.99776.9680.0230.0230.0000.0000.0000.000
211A617ASP00.065-0.08577.194-0.001-0.0010.0000.0000.0000.000
212A617ASP-1-0.915-0.82479.221-0.023-0.0230.0000.0000.0000.000
213A618PRO0-0.049-0.12879.8120.0000.0000.0000.0000.0000.000
214A619ILE00.091-0.00582.4280.0000.0000.0000.0000.0000.000
215A619ILE0-0.1300.08984.4440.0000.0000.0000.0000.0000.000
216A620ASN00.129-0.08386.0490.0000.0000.0000.0000.0000.000
217A620ASN0-0.1160.07786.9290.0000.0000.0000.0000.0000.000
218A621GLU00.202-0.05788.5230.0000.0000.0000.0000.0000.000
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