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: 7GQZK

Calculation Name: 3H4R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H4R

Chain ID: A

ChEMBL ID:

UniProt ID: P15032

Base Structure: X-ray

Registration Date: 2023-06-19

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 OptHSide
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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2602215.647077
FMO2-HF: Nuclear repulsion 2512662.648106
FMO2-HF: Total energy -89552.998972
FMO2-MP2: Total energy -89811.909792


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:612:PRO)


Summations of interaction energy for fragment #1(A:612:PRO)
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.
-4.014-0.00499999999999981.314-2.231-3.0920.001
Interaction energy analysis for fragmet #1(A:612:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.008
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].
3A614ILE0-0.031-0.0083.629-1.7751.034-0.008-1.593-1.2090.005
4A615SER0-0.010-0.0245.706-0.085-0.0850.0000.0000.0000.000
5A616LYS10.8540.9047.134-0.110-0.1100.0000.0000.0000.000
6A617SER0-0.021-0.0279.170-0.011-0.0110.0000.0000.0000.000
7A618GLN00.0060.0404.185-0.1000.001-0.001-0.010-0.0900.000
8A619LEU00.0420.0279.406-0.013-0.0130.0000.0000.0000.000
9A620ASP-1-0.761-0.87112.4220.0970.0970.0000.0000.0000.000
10A621ASP-1-0.855-0.90810.7490.1980.1980.0000.0000.0000.000
11A622ILE0-0.025-0.02310.683-0.012-0.0120.0000.0000.0000.000
12A623ALA0-0.037-0.00614.626-0.016-0.0160.0000.0000.0000.000
13A624ASP-1-0.887-0.91117.0460.0740.0740.0000.0000.0000.000
14A625THR0-0.036-0.03117.308-0.015-0.0150.0000.0000.0000.000
15A626PRO00.0660.03115.4100.0130.0130.0000.0000.0000.000
16A627ALA00.0500.04614.4370.0260.0260.0000.0000.0000.000
17A628LEU0-0.048-0.02714.5150.0160.0160.0000.0000.0000.000
18A629TYR00.0360.0057.2900.1020.1020.0000.0000.0000.000
19A630LEU0-0.018-0.02110.1220.0490.0490.0000.0000.0000.000
20A631TRP0-0.0410.00311.326-0.016-0.0160.0000.0000.0000.000
21A632ARG10.9130.9279.225-0.170-0.1700.0000.0000.0000.000
22A633LYS10.8340.9485.752-0.666-0.6660.0000.0000.0000.000
23A634ASN0-0.015-0.0249.489-0.022-0.0220.0000.0000.0000.000
24A635ALA0-0.050-0.00112.746-0.022-0.0220.0000.0000.0000.000
25A636PRO0-0.0010.01014.3840.0000.0000.0000.0000.0000.000
26A637VAL00.0070.00213.9710.0030.0030.0000.0000.0000.000
27A638ASP-1-0.884-0.94216.6980.0280.0280.0000.0000.0000.000
28A639THR0-0.049-0.03617.2470.0010.0010.0000.0000.0000.000
29A640THR0-0.016-0.01119.233-0.004-0.0040.0000.0000.0000.000
30A641LYS10.8730.93117.107-0.027-0.0270.0000.0000.0000.000
31A642THR00.0050.01021.922-0.003-0.0030.0000.0000.0000.000
32A643LYS10.9340.96021.183-0.030-0.0300.0000.0000.0000.000
33A644THR0-0.047-0.01824.558-0.001-0.0010.0000.0000.0000.000
34A645LEU00.0760.02324.5740.0000.0000.0000.0000.0000.000
35A646ASP-1-0.852-0.88618.9640.0350.0350.0000.0000.0000.000
36A647LEU00.0750.01522.201-0.001-0.0010.0000.0000.0000.000
37A648GLY00.0400.03722.753-0.002-0.0020.0000.0000.0000.000
38A649THR00.006-0.00917.3770.0010.0010.0000.0000.0000.000
39A650ALA0-0.0090.00320.103-0.002-0.0020.0000.0000.0000.000
40A651PHE0-0.003-0.02222.908-0.002-0.0020.0000.0000.0000.000
41A652HIS0-0.086-0.05315.926-0.007-0.0070.0000.0000.0000.000
42A653CYS0-0.0130.00020.180-0.002-0.0020.0000.0000.0000.000
43A654ARG10.7940.89721.172-0.005-0.0050.0000.0000.0000.000
44A655VAL0-0.035-0.04823.344-0.002-0.0020.0000.0000.0000.000
45A656LEU0-0.058-0.00518.067-0.001-0.0010.0000.0000.0000.000
46A657GLU-1-0.893-0.93517.898-0.008-0.0080.0000.0000.0000.000
47A658LEU00.016-0.00621.6210.0000.0000.0000.0000.0000.000
48A659GLU-1-0.918-0.96324.524-0.010-0.0100.0000.0000.0000.000
49A660GLU-1-0.791-0.88619.252-0.012-0.0120.0000.0000.0000.000
50A661PHE00.0090.01122.7580.0010.0010.0000.0000.0000.000
51A662SER0-0.079-0.03324.3020.0010.0010.0000.0000.0000.000
52A663ASN0-0.088-0.02322.6080.0000.0000.0000.0000.0000.000
53A664ARG10.7930.85818.6940.0080.0080.0000.0000.0000.000
54A699ALA00.010-0.00431.3520.0000.0000.0000.0000.0000.000
55A700GLU-1-0.913-0.95333.0710.0060.0060.0000.0000.0000.000
56A701GLU-1-0.766-0.89231.1650.0130.0130.0000.0000.0000.000
57A702GLY0-0.015-0.00230.9110.0010.0010.0000.0000.0000.000
58A703ARG10.9720.98531.949-0.006-0.0060.0000.0000.0000.000
59A704LYS10.8040.89431.257-0.013-0.0130.0000.0000.0000.000
60A705ILE00.0340.01826.8610.0000.0000.0000.0000.0000.000
61A706GLU-1-0.800-0.86930.2170.0030.0030.0000.0000.0000.000
62A707LEU0-0.039-0.03032.5630.0000.0000.0000.0000.0000.000
63A708MET0-0.079-0.04827.8370.0000.0000.0000.0000.0000.000
64A709TYR00.0550.03927.6890.0000.0000.0000.0000.0000.000
65A710GLN00.0070.00030.389-0.001-0.0010.0000.0000.0000.000
66A711SER0-0.092-0.06032.932-0.001-0.0010.0000.0000.0000.000
67A712VAL0-0.015-0.02028.2420.0000.0000.0000.0000.0000.000
68A713MET0-0.0220.00531.2270.0000.0000.0000.0000.0000.000
69A714ALA0-0.0270.00633.269-0.001-0.0010.0000.0000.0000.000
70A715LEU0-0.044-0.01331.8950.0000.0000.0000.0000.0000.000
71A716PRO00.0920.02633.8120.0000.0000.0000.0000.0000.000
72A717LEU0-0.031-0.01029.6440.0000.0000.0000.0000.0000.000
73A718GLY00.0650.02329.3070.0000.0000.0000.0000.0000.000
74A719GLN0-0.037-0.02029.3520.0000.0000.0000.0000.0000.000
75A720TRP0-0.033-0.01728.8780.0000.0000.0000.0000.0000.000
76A721LEU0-0.0190.00525.472-0.001-0.0010.0000.0000.0000.000
77A722VAL0-0.001-0.00325.898-0.001-0.0010.0000.0000.0000.000
78A723GLU-1-0.911-0.93226.776-0.001-0.0010.0000.0000.0000.000
79A724SER0-0.047-0.03927.2720.0000.0000.0000.0000.0000.000
80A725ALA00.0110.00526.865-0.001-0.0010.0000.0000.0000.000
81A726GLY0-0.011-0.03522.9740.0010.0010.0000.0000.0000.000
82A727HIS0-0.0130.01618.143-0.001-0.0010.0000.0000.0000.000
83A728ALA00.0880.02717.6640.0030.0030.0000.0000.0000.000
84A729GLU-1-0.762-0.85212.7330.0360.0360.0000.0000.0000.000
85A730SER0-0.066-0.02011.9190.0060.0060.0000.0000.0000.000
86A731SER0-0.055-0.0497.9500.0370.0370.0000.0000.0000.000
87A732ILE00.0430.0319.360-0.023-0.0230.0000.0000.0000.000
88A733TYR0-0.041-0.0473.775-0.1390.2200.003-0.055-0.3060.000
89A734TRP00.0600.0399.2730.0050.0050.0000.0000.0000.000
90A735GLU-1-0.897-0.94110.714-0.081-0.0810.0000.0000.0000.000
91A736ASP-1-0.815-0.90112.4690.0490.0490.0000.0000.0000.000
92A737PRO0-0.024-0.01414.8090.0050.0050.0000.0000.0000.000
93A738GLU-1-0.868-0.91018.1260.0460.0460.0000.0000.0000.000
94A739THR0-0.038-0.05214.9590.0050.0050.0000.0000.0000.000
95A740GLY00.0040.01314.8860.0100.0100.0000.0000.0000.000
96A741ILE0-0.015-0.0039.773-0.002-0.0020.0000.0000.0000.000
97A742LEU0-0.0130.0175.026-0.070-0.0700.0000.0000.0000.000
98A743CYS0-0.063-0.0297.6740.0240.0240.0000.0000.0000.000
99A744ARG10.8970.9292.730-1.717-0.9771.320-0.573-1.487-0.004
100A745CYS0-0.049-0.0206.9940.0640.0640.0000.0000.0000.000
101A746ARG10.7730.8778.184-0.084-0.0840.0000.0000.0000.000
102A747PRO00.0290.00910.6710.0040.0040.0000.0000.0000.000
103A748ASP-1-0.776-0.85714.4430.0430.0430.0000.0000.0000.000
104A749LYS10.8770.92916.446-0.010-0.0100.0000.0000.0000.000
105A750ILE0-0.0290.00116.9420.0030.0030.0000.0000.0000.000
106A751ILE0-0.007-0.01519.790-0.004-0.0040.0000.0000.0000.000
107A752PRO00.000-0.00421.7270.0010.0010.0000.0000.0000.000
108A753GLU-1-0.922-0.95523.776-0.007-0.0070.0000.0000.0000.000
109A754PHE0-0.016-0.00526.9730.0000.0000.0000.0000.0000.000
110A755HIS0-0.064-0.02723.4510.0010.0010.0000.0000.0000.000
111A756TRP00.0420.00923.8230.0030.0030.0000.0000.0000.000
112A757ILE0-0.0090.00816.931-0.001-0.0010.0000.0000.0000.000
113A758MET0-0.0250.00020.3490.0000.0000.0000.0000.0000.000
114A759ASP-1-0.831-0.89916.9100.0560.0560.0000.0000.0000.000
115A760VAL0-0.002-0.00119.397-0.002-0.0020.0000.0000.0000.000
116A761LYS10.8350.87816.634-0.055-0.0550.0000.0000.0000.000
117A762THR0-0.0120.00421.821-0.004-0.0040.0000.0000.0000.000
118A763THR0-0.027-0.02624.1780.0030.0030.0000.0000.0000.000
119A764ALA00.0130.02126.897-0.002-0.0020.0000.0000.0000.000
120A765ASP-1-0.804-0.91030.1090.0240.0240.0000.0000.0000.000
121A766ILE00.0270.02529.6850.0020.0020.0000.0000.0000.000
122A767GLN00.020-0.01031.3300.0010.0010.0000.0000.0000.000
123A768ARG10.8890.94026.800-0.032-0.0320.0000.0000.0000.000
124A769PHE00.1110.03223.4700.0020.0020.0000.0000.0000.000
125A770LYS10.8700.92628.112-0.018-0.0180.0000.0000.0000.000
126A771THR0-0.064-0.02129.769-0.001-0.0010.0000.0000.0000.000
127A772ALA0-0.053-0.00526.7910.0020.0020.0000.0000.0000.000
128A773TYR0-0.006-0.00223.5650.0040.0040.0000.0000.0000.000
129A774TYR00.0190.02122.6950.0060.0060.0000.0000.0000.000
130A775ASP-1-0.889-0.95523.1610.0480.0480.0000.0000.0000.000
131A776TYR0-0.086-0.03019.8270.0020.0020.0000.0000.0000.000
132A777ARG10.7860.86215.998-0.087-0.0870.0000.0000.0000.000
133A778TYR00.008-0.01117.7020.0050.0050.0000.0000.0000.000
134A779HIS00.0620.03719.832-0.001-0.0010.0000.0000.0000.000
135A780VAL0-0.005-0.00616.118-0.003-0.0030.0000.0000.0000.000
136A781GLN0-0.016-0.00613.421-0.004-0.0040.0000.0000.0000.000
137A782ASP-1-0.797-0.87516.3620.0290.0290.0000.0000.0000.000
138A783ALA00.0240.00718.189-0.003-0.0030.0000.0000.0000.000
139A784PHE0-0.004-0.0099.543-0.002-0.0020.0000.0000.0000.000
140A785TYR00.007-0.00912.1150.0080.0080.0000.0000.0000.000
141A786SER00.001-0.01015.036-0.010-0.0100.0000.0000.0000.000
142A787ASP-1-0.740-0.83616.7400.0220.0220.0000.0000.0000.000
143A788GLY00.0200.00413.639-0.007-0.0070.0000.0000.0000.000
144A789TYR0-0.032-0.02514.616-0.010-0.0100.0000.0000.0000.000
145A790GLU-1-0.791-0.88516.7880.0000.0000.0000.0000.0000.000
146A791ALA0-0.0440.00716.691-0.005-0.0050.0000.0000.0000.000
147A792GLN0-0.078-0.06214.083-0.008-0.0080.0000.0000.0000.000
148A793PHE0-0.064-0.04316.457-0.006-0.0060.0000.0000.0000.000
149A794GLY0-0.043-0.00420.1540.0010.0010.0000.0000.0000.000
150A795VAL0-0.022-0.01622.9070.0020.0020.0000.0000.0000.000
151A796GLN0-0.031-0.02821.0890.0040.0040.0000.0000.0000.000
152A797PRO0-0.0180.01219.575-0.001-0.0010.0000.0000.0000.000
153A798THR0-0.0150.00022.9050.0020.0020.0000.0000.0000.000
154A799PHE0-0.018-0.00716.9710.0000.0000.0000.0000.0000.000
155A800VAL0-0.029-0.02422.3410.0000.0000.0000.0000.0000.000
156A801PHE0-0.026-0.01419.1660.0000.0000.0000.0000.0000.000
157A802LEU00.0120.01723.171-0.003-0.0030.0000.0000.0000.000
158A803VAL0-0.030-0.02524.2960.0020.0020.0000.0000.0000.000
159A804ALA00.0530.02226.291-0.003-0.0030.0000.0000.0000.000
160A805SER0-0.018-0.00327.7020.0020.0020.0000.0000.0000.000
161A806THR0-0.026-0.02027.269-0.001-0.0010.0000.0000.0000.000
162A807THR0-0.041-0.05330.5650.0000.0000.0000.0000.0000.000
163A808ILE0-0.070-0.01333.9940.0000.0000.0000.0000.0000.000
164A809GLU-1-0.907-0.95336.7870.0120.0120.0000.0000.0000.000
165A810CYS0-0.013-0.01839.074-0.001-0.0010.0000.0000.0000.000
166A811GLY0-0.013-0.00341.712-0.001-0.0010.0000.0000.0000.000
167A812ARG10.9530.98138.247-0.008-0.0080.0000.0000.0000.000
168A813TYR00.0460.01733.0940.0000.0000.0000.0000.0000.000
169A814PRO00.0120.02834.0090.0000.0000.0000.0000.0000.000
170A815VAL00.000-0.01129.3080.0010.0010.0000.0000.0000.000
171A816GLU-1-0.876-0.93829.7410.0160.0160.0000.0000.0000.000
172A817ILE00.0080.01927.7720.0020.0020.0000.0000.0000.000
173A818PHE0-0.023-0.02426.312-0.001-0.0010.0000.0000.0000.000
174A819MET00.0370.02125.8130.0000.0000.0000.0000.0000.000
175A820MET0-0.0140.01122.5050.0000.0000.0000.0000.0000.000
176A821GLY00.0200.01326.089-0.002-0.0020.0000.0000.0000.000
177A822GLU-1-0.913-0.96028.0240.0180.0180.0000.0000.0000.000
178A823GLU-1-0.931-0.95928.2050.0250.0250.0000.0000.0000.000
179A824ALA00.001-0.01325.9940.0020.0020.0000.0000.0000.000
180A825LYS10.8040.89821.850-0.021-0.0210.0000.0000.0000.000
181A826LEU00.0400.03022.9760.0030.0030.0000.0000.0000.000
182A827ALA00.0280.00723.9490.0030.0030.0000.0000.0000.000
183A828GLY00.004-0.01221.1500.0050.0050.0000.0000.0000.000
184A829GLN0-0.021-0.03919.6360.0070.0070.0000.0000.0000.000
185A830GLN0-0.037-0.02320.2070.0030.0030.0000.0000.0000.000
186A831GLU-1-0.819-0.87318.9810.0750.0750.0000.0000.0000.000
187A832TYR0-0.003-0.03514.8230.0100.0100.0000.0000.0000.000
188A833HIS10.8630.96116.127-0.032-0.0320.0000.0000.0000.000
189A834ARG10.8540.91918.315-0.055-0.0550.0000.0000.0000.000
190A835ASN0-0.016-0.02215.2480.0050.0050.0000.0000.0000.000
191A836LEU00.022-0.00511.7050.0150.0150.0000.0000.0000.000
192A837ARG10.8320.89815.104-0.039-0.0390.0000.0000.0000.000
193A838THR00.0000.01716.8660.0060.0060.0000.0000.0000.000
194A839LEU0-0.014-0.01810.1180.0120.0120.0000.0000.0000.000
195A840SER00.012-0.00914.1580.0260.0260.0000.0000.0000.000
196A841ASP-1-0.917-0.94115.6190.0870.0870.0000.0000.0000.000
197A842CYS0-0.037-0.02114.636-0.006-0.0060.0000.0000.0000.000
198A843LEU0-0.0330.00210.6440.0190.0190.0000.0000.0000.000
199A844ASN0-0.061-0.03314.770-0.017-0.0170.0000.0000.0000.000
200A845THR0-0.088-0.05817.786-0.017-0.0170.0000.0000.0000.000
201A846ASP-1-0.911-0.96115.7720.1510.1510.0000.0000.0000.000
202A847GLU-1-0.913-0.93517.8480.0950.0950.0000.0000.0000.000
203A848TRP0-0.082-0.05611.5690.0340.0340.0000.0000.0000.000
204A849PRO00.0530.02717.994-0.005-0.0050.0000.0000.0000.000
205A850ALA00.030-0.02419.5550.0080.0080.0000.0000.0000.000
206A851ILE0-0.058-0.02921.070-0.003-0.0030.0000.0000.0000.000
207A852LYS10.8710.94921.513-0.077-0.0770.0000.0000.0000.000
208A853THR0-0.035-0.02925.155-0.003-0.0030.0000.0000.0000.000
209A854LEU0-0.0060.00228.6870.0000.0000.0000.0000.0000.000
210A855SER00.016-0.00430.996-0.002-0.0020.0000.0000.0000.000
211A856LEU0-0.018-0.00133.7910.0000.0000.0000.0000.0000.000
212A857PRO00.0350.03335.8480.0010.0010.0000.0000.0000.000
213A858ARG11.0000.97436.189-0.027-0.0270.0000.0000.0000.000
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215A860ALA0-0.0060.01140.071-0.001-0.0010.0000.0000.0000.000
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