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: Z68NN

Calculation Name: 4RCW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RCW

Chain ID: A

ChEMBL ID:

UniProt ID: Q96PX8

Base Structure: X-ray

Registration Date: 2023-09-19

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2995724.741699
FMO2-HF: Nuclear repulsion 2899608.844649
FMO2-HF: Total energy -96115.89705
FMO2-MP2: Total energy -96391.65995


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:342:PRO)


Summations of interaction energy for fragment #1(A:342: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.
5.586-11.087.90216.316-7.552-0.02
Interaction energy analysis for fragmet #1(A:342:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.067 / q_NPA : -0.013
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].
3A344GLY0-0.024-0.0132.14916.411-2.4200.42219.856-1.447-0.008
4A345CYS0-0.079-0.0412.797-4.018-2.6260.214-0.606-1.0000.006
5A346SER0-0.0190.0043.0890.6031.8590.441-0.620-1.077-0.004
6A347CYS0-0.017-0.0192.292-1.899-3.7406.200-1.772-2.587-0.017
7A348ASP-1-0.876-0.9334.603-0.659-0.559-0.001-0.018-0.0810.000
8A349HIS0-0.033-0.0127.867-0.018-0.0180.0000.0000.0000.000
9A350ILE00.0640.03210.5630.0890.0890.0000.0000.0000.000
10A351PRO0-0.0270.01314.153-0.020-0.0200.0000.0000.0000.000
11A352GLY00.011-0.00517.1060.0170.0170.0000.0000.0000.000
12A353SER0-0.022-0.04414.109-0.032-0.0320.0000.0000.0000.000
13A354GLY00.0420.03412.7210.0050.0050.0000.0000.0000.000
14A355LEU0-0.0250.0034.884-0.030-0.0300.0000.0000.0000.000
15A356LYS10.9570.9838.3490.5110.5110.0000.0000.0000.000
16A357MET0-0.011-0.0245.473-0.471-0.344-0.001-0.022-0.1040.000
17A358ASN0-0.023-0.0186.6390.1360.1360.0000.0000.0000.000
18A360ASN00.1410.0709.384-0.083-0.0830.0000.0000.0000.000
19A361ASN00.0100.01212.5290.0670.0670.0000.0000.0000.000
20A362ARG10.9000.9698.148-1.018-1.0180.0000.0000.0000.000
21A363ASN0-0.002-0.01912.236-0.087-0.0870.0000.0000.0000.000
22A364VAL00.0170.01411.0530.0650.0650.0000.0000.0000.000
23A365SER00.0390.01913.822-0.054-0.0540.0000.0000.0000.000
24A366SER0-0.023-0.02114.781-0.067-0.0670.0000.0000.0000.000
25A367LEU00.0520.01712.8640.0480.0480.0000.0000.0000.000
26A368ALA0-0.095-0.04011.907-0.037-0.0370.0000.0000.0000.000
27A369ASP-1-0.900-0.94010.8680.3390.3390.0000.0000.0000.000
28A370LEU0-0.0050.0116.4330.2080.2080.0000.0000.0000.000
29A371LYS10.9330.9432.497-3.320-2.3470.628-0.496-1.1050.003
30A372PRO0-0.047-0.0394.666-0.654-0.496-0.001-0.006-0.1510.000
31A373LYS10.8790.9406.9260.1810.1810.0000.0000.0000.000
32A374LEU00.010-0.0118.4020.1210.1210.0000.0000.0000.000
33A375SER0-0.0180.0338.528-0.123-0.1230.0000.0000.0000.000
34A376ASN00.012-0.0068.901-0.158-0.1580.0000.0000.0000.000
35A377VAL0-0.0150.0057.433-0.044-0.0440.0000.0000.0000.000
36A378GLN00.0440.02010.1040.1110.1110.0000.0000.0000.000
37A379GLU-1-0.921-0.94411.827-0.189-0.1890.0000.0000.0000.000
38A380LEU0-0.010-0.0019.121-0.085-0.0850.0000.0000.0000.000
39A381PHE0-0.044-0.02010.7880.0290.0290.0000.0000.0000.000
40A382LEU0-0.028-0.02910.6960.1140.1140.0000.0000.0000.000
41A383ARG10.8240.91513.845-0.097-0.0970.0000.0000.0000.000
42A384ASP-1-0.860-0.92715.7280.2220.2220.0000.0000.0000.000
43A385ASN0-0.071-0.02512.8340.0720.0720.0000.0000.0000.000
44A386LYS10.9310.95716.681-0.280-0.2800.0000.0000.0000.000
45A387ILE00.0140.01014.7590.0000.0000.0000.0000.0000.000
46A388HIS00.0580.03018.496-0.018-0.0180.0000.0000.0000.000
47A389SER0-0.064-0.02720.431-0.021-0.0210.0000.0000.0000.000
48A390ILE00.0280.02618.3320.0120.0120.0000.0000.0000.000
49A391ARG10.9780.97119.062-0.085-0.0850.0000.0000.0000.000
50A392LYS10.9510.98219.2030.0200.0200.0000.0000.0000.000
51A393SER0-0.026-0.01617.939-0.018-0.0180.0000.0000.0000.000
52A394HIS0-0.0020.00814.875-0.021-0.0210.0000.0000.0000.000
53A395PHE00.0340.01313.838-0.030-0.0300.0000.0000.0000.000
54A396VAL0-0.0140.01115.773-0.019-0.0190.0000.0000.0000.000
55A397ASP-1-0.857-0.9369.855-0.530-0.5300.0000.0000.0000.000
56A398TYR00.0110.0118.329-0.096-0.0960.0000.0000.0000.000
57A399LYS10.9350.95713.2600.2450.2450.0000.0000.0000.000
58A400ASN0-0.016-0.00613.477-0.020-0.0200.0000.0000.0000.000
59A401LEU0-0.0010.01311.834-0.015-0.0150.0000.0000.0000.000
60A402ILE00.007-0.00715.1460.0350.0350.0000.0000.0000.000
61A403LEU0-0.015-0.01115.6550.0370.0370.0000.0000.0000.000
62A404LEU0-0.015-0.00514.527-0.027-0.0270.0000.0000.0000.000
63A405ASP-1-0.824-0.91915.6330.0680.0680.0000.0000.0000.000
64A406LEU0-0.055-0.03215.7290.0320.0320.0000.0000.0000.000
65A407GLY00.1000.05518.363-0.010-0.0100.0000.0000.0000.000
66A408ASN0-0.062-0.05919.3540.0220.0220.0000.0000.0000.000
67A409ASN0-0.0310.00017.1950.0530.0530.0000.0000.0000.000
68A410ASN00.014-0.01320.700-0.010-0.0100.0000.0000.0000.000
69A411ILE0-0.037-0.01919.628-0.005-0.0050.0000.0000.0000.000
70A412ALA00.0510.02923.257-0.009-0.0090.0000.0000.0000.000
71A413THR0-0.063-0.03525.398-0.012-0.0120.0000.0000.0000.000
72A414VAL00.025-0.00623.3530.0050.0050.0000.0000.0000.000
73A415GLU-1-0.871-0.92623.8430.0020.0020.0000.0000.0000.000
74A416ASN00.0550.06325.282-0.005-0.0050.0000.0000.0000.000
75A417ASN0-0.055-0.04025.947-0.005-0.0050.0000.0000.0000.000
76A418THR0-0.034-0.07120.297-0.005-0.0050.0000.0000.0000.000
77A419PHE00.0810.02319.417-0.011-0.0110.0000.0000.0000.000
78A420LYS10.9800.99321.6270.0590.0590.0000.0000.0000.000
79A421ASN0-0.094-0.06919.324-0.003-0.0030.0000.0000.0000.000
80A422LEU00.0270.03017.098-0.016-0.0160.0000.0000.0000.000
81A423LEU00.0110.00420.1300.0170.0170.0000.0000.0000.000
82A424ASP-1-0.878-0.94018.596-0.221-0.2210.0000.0000.0000.000
83A425LEU0-0.071-0.01917.795-0.003-0.0030.0000.0000.0000.000
84A426ARG10.8550.92120.4580.1350.1350.0000.0000.0000.000
85A427TRP00.0070.00220.4210.0100.0100.0000.0000.0000.000
86A428LEU0-0.008-0.00420.051-0.012-0.0120.0000.0000.0000.000
87A429TYR0-0.0020.00020.0630.0070.0070.0000.0000.0000.000
88A430MET0-0.044-0.03420.7380.0070.0070.0000.0000.0000.000
89A431ASP-1-0.743-0.86223.0010.0430.0430.0000.0000.0000.000
90A432SER0-0.038-0.01023.7260.0160.0160.0000.0000.0000.000
91A433ASN0-0.0280.00722.0910.0260.0260.0000.0000.0000.000
92A434TYR0-0.016-0.01025.476-0.003-0.0030.0000.0000.0000.000
93A435LEU0-0.011-0.01325.713-0.002-0.0020.0000.0000.0000.000
94A436ASP-1-0.843-0.92329.2460.0290.0290.0000.0000.0000.000
95A437THR0-0.0010.00232.084-0.004-0.0040.0000.0000.0000.000
96A438LEU0-0.023-0.00629.4200.0000.0000.0000.0000.0000.000
97A439SER00.0620.02631.3780.0000.0000.0000.0000.0000.000
98A440ARG10.9871.00731.3660.0290.0290.0000.0000.0000.000
99A441GLU-1-0.934-0.98731.013-0.018-0.0180.0000.0000.0000.000
100A442LYS10.8770.94927.457-0.019-0.0190.0000.0000.0000.000
101A443PHE00.0490.02825.637-0.003-0.0030.0000.0000.0000.000
102A444ALA0-0.0060.00227.453-0.008-0.0080.0000.0000.0000.000
103A445GLY0-0.096-0.06125.139-0.002-0.0020.0000.0000.0000.000
104A446LEU00.0220.03922.131-0.011-0.0110.0000.0000.0000.000
105A447GLN00.017-0.00725.5640.0070.0070.0000.0000.0000.000
106A448ASN0-0.026-0.02224.8300.0140.0140.0000.0000.0000.000
107A449LEU00.0120.02123.231-0.006-0.0060.0000.0000.0000.000
108A450GLU-1-0.915-0.93725.853-0.084-0.0840.0000.0000.0000.000
109A451TYR0-0.0130.00824.0480.0080.0080.0000.0000.0000.000
110A452LEU00.0370.01825.284-0.004-0.0040.0000.0000.0000.000
111A453ASN0-0.015-0.02025.1190.0090.0090.0000.0000.0000.000
112A454VAL0-0.037-0.02425.7050.0030.0030.0000.0000.0000.000
113A455GLU-1-0.843-0.90627.8200.0240.0240.0000.0000.0000.000
114A456TYR0-0.004-0.01528.3640.0080.0080.0000.0000.0000.000
115A457ASN00.0050.01826.8130.0120.0120.0000.0000.0000.000
116A458ALA0-0.022-0.02630.378-0.001-0.0010.0000.0000.0000.000
117A459ILE00.0030.00030.277-0.002-0.0020.0000.0000.0000.000
118A460GLN0-0.002-0.00933.989-0.003-0.0030.0000.0000.0000.000
119A461LEU0-0.038-0.01836.410-0.002-0.0020.0000.0000.0000.000
120A462ILE00.0110.00634.8150.0000.0000.0000.0000.0000.000
121A463LEU00.0270.00935.734-0.001-0.0010.0000.0000.0000.000
122A464PRO00.0650.05137.343-0.002-0.0020.0000.0000.0000.000
123A465GLY00.0580.04637.975-0.001-0.0010.0000.0000.0000.000
124A466THR0-0.065-0.09932.322-0.002-0.0020.0000.0000.0000.000
125A467PHE00.034-0.00631.683-0.003-0.0030.0000.0000.0000.000
126A468ASN00.0310.01333.826-0.003-0.0030.0000.0000.0000.000
127A469ALA0-0.093-0.03629.881-0.004-0.0040.0000.0000.0000.000
128A470MET0-0.0280.00927.525-0.005-0.0050.0000.0000.0000.000
129A471PRO00.0330.01530.3050.0020.0020.0000.0000.0000.000
130A472LYS10.8930.95429.3820.0810.0810.0000.0000.0000.000
131A473LEU00.0280.02428.953-0.004-0.0040.0000.0000.0000.000
132A474ARG10.9250.95630.7180.0700.0700.0000.0000.0000.000
133A475ILE00.001-0.00729.4640.0040.0040.0000.0000.0000.000
134A476LEU00.0180.01830.237-0.002-0.0020.0000.0000.0000.000
135A477ILE0-0.031-0.00529.1850.0020.0020.0000.0000.0000.000
136A478LEU00.022-0.00330.6860.0020.0020.0000.0000.0000.000
137A479ASN0-0.038-0.02631.830-0.003-0.0030.0000.0000.0000.000
138A480ASN0-0.0180.01032.8080.0000.0000.0000.0000.0000.000
139A481ASN0-0.017-0.00632.2180.0080.0080.0000.0000.0000.000
140A482LEU0-0.037-0.02635.2180.0010.0010.0000.0000.0000.000
141A483LEU0-0.0080.00836.092-0.001-0.0010.0000.0000.0000.000
142A484ARG10.9910.97939.401-0.020-0.0200.0000.0000.0000.000
143A485SER0-0.019-0.01242.090-0.001-0.0010.0000.0000.0000.000
144A486LEU00.0080.00538.9880.0000.0000.0000.0000.0000.000
145A487PRO0-0.047-0.00339.7980.0000.0000.0000.0000.0000.000
146A488VAL00.0390.00342.953-0.001-0.0010.0000.0000.0000.000
147A489ASP-1-0.873-0.91943.111-0.015-0.0150.0000.0000.0000.000
148A490VAL0-0.096-0.04537.873-0.002-0.0020.0000.0000.0000.000
149A491PHE00.003-0.02836.841-0.002-0.0020.0000.0000.0000.000
150A492ALA00.0320.03639.773-0.002-0.0020.0000.0000.0000.000
151A493GLY0-0.073-0.02737.741-0.002-0.0020.0000.0000.0000.000
152A494VAL0-0.049-0.02033.791-0.004-0.0040.0000.0000.0000.000
153A495SER0-0.0020.00236.4840.0030.0030.0000.0000.0000.000
154A496LEU0-0.027-0.00934.223-0.003-0.0030.0000.0000.0000.000
155A497SER0-0.0110.00634.6040.0010.0010.0000.0000.0000.000
156A498LYS10.9570.97432.4890.0190.0190.0000.0000.0000.000
157A499LEU00.0040.00734.778-0.001-0.0010.0000.0000.0000.000
158A500SER0-0.014-0.00633.7450.0000.0000.0000.0000.0000.000
159A501LEU00.008-0.00535.2510.0020.0020.0000.0000.0000.000
160A502HIS00.0310.01834.6450.0000.0000.0000.0000.0000.000
161A503ASN0-0.046-0.02237.0290.0030.0030.0000.0000.0000.000
162A504ASN0-0.0030.01937.1840.0050.0050.0000.0000.0000.000
163A505TYR0-0.014-0.02939.2970.0010.0010.0000.0000.0000.000
164A506PHE0-0.045-0.00940.2590.0000.0000.0000.0000.0000.000
165A507MET00.0280.01545.0740.0000.0000.0000.0000.0000.000
166A508TYR00.023-0.00348.052-0.001-0.0010.0000.0000.0000.000
167A509LEU00.006-0.00343.8210.0000.0000.0000.0000.0000.000
168A510PRO0-0.0080.01446.3640.0000.0000.0000.0000.0000.000
169A511VAL00.0700.01647.777-0.001-0.0010.0000.0000.0000.000
170A512ALA0-0.016-0.00748.901-0.001-0.0010.0000.0000.0000.000
171A513GLY00.0190.00047.6280.0010.0010.0000.0000.0000.000
172A514VAL0-0.047-0.01643.060-0.001-0.0010.0000.0000.0000.000
173A515LEU00.000-0.00943.707-0.001-0.0010.0000.0000.0000.000
174A516ASP-1-0.851-0.91645.830-0.014-0.0140.0000.0000.0000.000
175A517GLN0-0.065-0.04844.085-0.002-0.0020.0000.0000.0000.000
176A518LEU0-0.047-0.00540.263-0.002-0.0020.0000.0000.0000.000
177A519THR0-0.002-0.00442.8120.0000.0000.0000.0000.0000.000
178A520SER0-0.037-0.03440.472-0.002-0.0020.0000.0000.0000.000
179A521ILE0-0.0070.01640.183-0.002-0.0020.0000.0000.0000.000
180A522ILE0-0.053-0.03738.3020.0000.0000.0000.0000.0000.000
181A523GLN00.003-0.01536.4930.0000.0000.0000.0000.0000.000
182A524ILE00.0030.00638.692-0.001-0.0010.0000.0000.0000.000
183A525ASP-1-0.835-0.91137.8540.0030.0030.0000.0000.0000.000
184A526LEU00.0220.00439.6970.0010.0010.0000.0000.0000.000
185A527HIS00.012-0.01538.6560.0030.0030.0000.0000.0000.000
186A528GLY00.0510.01741.1080.0010.0010.0000.0000.0000.000
187A529ASN0-0.050-0.01341.1450.0030.0030.0000.0000.0000.000
188A530PRO00.0150.02244.197-0.001-0.0010.0000.0000.0000.000
189A531TRP00.0220.00244.752-0.001-0.0010.0000.0000.0000.000
190A532GLU-1-0.927-0.96849.6240.0100.0100.0000.0000.0000.000
191A533CYS0-0.137-0.07549.230-0.001-0.0010.0000.0000.0000.000
192A534SER00.0650.02156.0080.0000.0000.0000.0000.0000.000
193A535CYS-1-0.764-0.90457.8120.0020.0020.0000.0000.0000.000
194A536THR0-0.129-0.07054.511-0.001-0.0010.0000.0000.0000.000
195A537ILE0-0.037-0.00450.601-0.001-0.0010.0000.0000.0000.000
196A538VAL00.0650.03754.005-0.001-0.0010.0000.0000.0000.000
197A539PRO0-0.038-0.02753.882-0.001-0.0010.0000.0000.0000.000
198A540PHE0-0.004-0.01246.619-0.001-0.0010.0000.0000.0000.000
199A541LYS10.8340.90651.1570.0010.0010.0000.0000.0000.000
200A542GLN00.0050.00153.3740.0000.0000.0000.0000.0000.000
201A543TRP0-0.030-0.02444.5720.0000.0000.0000.0000.0000.000
202A544ALA00.0400.00949.130-0.001-0.0010.0000.0000.0000.000
203A545GLU-1-0.861-0.91550.094-0.005-0.0050.0000.0000.0000.000
204A546ARG10.8300.92152.5830.0100.0100.0000.0000.0000.000
205A547LEU0-0.0270.00345.834-0.002-0.0020.0000.0000.0000.000
206A548GLY0-0.012-0.00847.6190.0000.0000.0000.0000.0000.000
207A549SER00.017-0.00848.3990.0010.0010.0000.0000.0000.000
208A550GLU-1-0.937-0.97044.201-0.014-0.0140.0000.0000.0000.000
209A551VAL0-0.070-0.00442.630-0.001-0.0010.0000.0000.0000.000
210A552LEU00.0030.00242.3940.0000.0000.0000.0000.0000.000
211A553MET0-0.078-0.03235.928-0.001-0.0010.0000.0000.0000.000
212A554SER0-0.017-0.01041.7340.0010.0010.0000.0000.0000.000
213A555ASP-1-0.868-0.91843.567-0.001-0.0010.0000.0000.0000.000
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