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: R92Y8

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 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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2997031.821151
FMO2-HF: Nuclear repulsion 2900914.186297
FMO2-HF: Total energy -96117.634853
FMO2-MP2: Total energy -96393.336159


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.
-5.113-20.7298.16316.116-8.664-0.011
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 : -0.043 / q_NPA : 0.006
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].
3A344GLY0-0.0030.0022.51112.982-5.0590.04119.585-1.586-0.001
4A345CYS0-0.086-0.0423.000-6.383-4.6210.228-0.764-1.2260.009
5A346SER0-0.0090.0102.587-1.468-0.5131.749-0.933-1.771-0.012
6A347CYS0-0.001-0.0152.708-2.449-4.4625.879-1.304-2.562-0.008
7A348ASP-1-0.827-0.8984.395-0.553-0.484-0.001-0.013-0.0560.000
8A349HIS0-0.025-0.0037.790-0.148-0.1480.0000.0000.0000.000
9A350ILE00.0330.02010.1920.1550.1550.0000.0000.0000.000
10A351PRO0-0.0120.01813.761-0.024-0.0240.0000.0000.0000.000
11A352GLY00.020-0.00216.5150.0100.0100.0000.0000.0000.000
12A353SER0-0.022-0.04213.681-0.028-0.0280.0000.0000.0000.000
13A354GLY00.0530.03311.7020.0020.0020.0000.0000.0000.000
14A355LEU0-0.026-0.0043.744-0.189-0.0370.001-0.025-0.1280.000
15A356LYS10.8650.9317.9571.1281.1280.0000.0000.0000.000
16A357MET0-0.008-0.0254.154-1.495-1.1020.017-0.109-0.3010.000
17A358ASN0-0.006-0.0085.8960.5720.5720.0000.0000.0000.000
18A360ASN00.1400.0768.329-0.053-0.0530.0000.0000.0000.000
19A361ASN0-0.0090.00411.9420.1280.1280.0000.0000.0000.000
20A362ARG10.8630.9487.530-1.772-1.7720.0000.0000.0000.000
21A363ASN0-0.006-0.02412.312-0.164-0.1640.0000.0000.0000.000
22A364VAL00.0130.00910.5780.1130.1130.0000.0000.0000.000
23A365SER00.0390.02313.704-0.075-0.0750.0000.0000.0000.000
24A366SER0-0.027-0.02214.791-0.090-0.0900.0000.0000.0000.000
25A367LEU00.0510.01912.5730.0420.0420.0000.0000.0000.000
26A368ALA0-0.098-0.04211.728-0.098-0.0980.0000.0000.0000.000
27A369ASP-1-0.893-0.94210.8680.3680.3680.0000.0000.0000.000
28A370LEU0-0.0010.0116.2690.2880.2880.0000.0000.0000.000
29A371LYS10.9380.9492.752-3.810-2.9060.250-0.297-0.8560.001
30A372PRO0-0.062-0.0524.322-0.973-0.770-0.001-0.024-0.1780.000
31A373LYS10.8870.9456.2920.3200.3200.0000.0000.0000.000
32A374LEU00.009-0.0138.1730.1990.1990.0000.0000.0000.000
33A375SER0-0.0290.0278.330-0.093-0.0930.0000.0000.0000.000
34A376ASN00.014-0.0038.330-0.209-0.2090.0000.0000.0000.000
35A377VAL0-0.0100.0096.760-0.074-0.0740.0000.0000.0000.000
36A378GLN00.0230.0189.4290.1960.1960.0000.0000.0000.000
37A379GLU-1-0.903-0.94110.993-0.553-0.5530.0000.0000.0000.000
38A380LEU0-0.012-0.0028.075-0.268-0.2680.0000.0000.0000.000
39A381PHE0-0.029-0.0179.6080.1530.1530.0000.0000.0000.000
40A382LEU0-0.031-0.0269.5870.0570.0570.0000.0000.0000.000
41A383ARG10.7370.82012.4380.1090.1090.0000.0000.0000.000
42A384ASP-1-0.854-0.92614.7380.1470.1470.0000.0000.0000.000
43A385ASN0-0.081-0.03912.0300.1440.1440.0000.0000.0000.000
44A386LYS10.9350.96915.988-0.309-0.3090.0000.0000.0000.000
45A387ILE00.0170.01313.6410.0090.0090.0000.0000.0000.000
46A388HIS00.0580.02917.983-0.020-0.0200.0000.0000.0000.000
47A389SER0-0.060-0.03020.098-0.019-0.0190.0000.0000.0000.000
48A390ILE00.0100.02117.7180.0030.0030.0000.0000.0000.000
49A391ARG10.9710.97118.981-0.008-0.0080.0000.0000.0000.000
50A392LYS10.9530.97619.1040.0740.0740.0000.0000.0000.000
51A393SER0-0.038-0.02317.505-0.037-0.0370.0000.0000.0000.000
52A394HIS0-0.0090.00314.658-0.040-0.0400.0000.0000.0000.000
53A395PHE00.0660.02213.746-0.074-0.0740.0000.0000.0000.000
54A396VAL0-0.036-0.00315.744-0.017-0.0170.0000.0000.0000.000
55A397ASP-1-0.835-0.9209.659-0.958-0.9580.0000.0000.0000.000
56A398TYR00.0330.0158.087-0.162-0.1620.0000.0000.0000.000
57A399LYS10.9030.94413.2780.4510.4510.0000.0000.0000.000
58A400ASN0-0.025-0.00313.014-0.005-0.0050.0000.0000.0000.000
59A401LEU0-0.0120.00811.366-0.027-0.0270.0000.0000.0000.000
60A402ILE00.007-0.01214.6470.0800.0800.0000.0000.0000.000
61A403LEU0-0.023-0.01514.8310.0790.0790.0000.0000.0000.000
62A404LEU0-0.006-0.00213.793-0.089-0.0890.0000.0000.0000.000
63A405ASP-1-0.815-0.89414.331-0.115-0.1150.0000.0000.0000.000
64A406LEU0-0.023-0.01514.7240.0070.0070.0000.0000.0000.000
65A407GLY00.0820.03916.9550.0150.0150.0000.0000.0000.000
66A408ASN0-0.069-0.05218.1370.0260.0260.0000.0000.0000.000
67A409ASN0-0.037-0.00616.0580.0730.0730.0000.0000.0000.000
68A410ASN0-0.001-0.02319.6910.0120.0120.0000.0000.0000.000
69A411ILE0-0.018-0.00518.4280.0010.0010.0000.0000.0000.000
70A412ALA00.0340.02522.425-0.007-0.0070.0000.0000.0000.000
71A413THR0-0.049-0.03524.799-0.013-0.0130.0000.0000.0000.000
72A414VAL00.020-0.00122.933-0.002-0.0020.0000.0000.0000.000
73A415GLU-1-0.873-0.92123.315-0.076-0.0760.0000.0000.0000.000
74A416ASN00.0490.02225.224-0.016-0.0160.0000.0000.0000.000
75A417ASN0-0.033-0.02825.939-0.011-0.0110.0000.0000.0000.000
76A418THR00.021-0.00520.225-0.010-0.0100.0000.0000.0000.000
77A419PHE00.0560.01818.647-0.025-0.0250.0000.0000.0000.000
78A420LYS10.9330.95921.6520.1430.1430.0000.0000.0000.000
79A421ASN0-0.052-0.04119.552-0.006-0.0060.0000.0000.0000.000
80A422LEU00.0250.03316.714-0.022-0.0220.0000.0000.0000.000
81A423LEU00.0200.00719.9620.0320.0320.0000.0000.0000.000
82A424ASP-1-0.855-0.93518.030-0.434-0.4340.0000.0000.0000.000
83A425LEU0-0.061-0.00817.360-0.010-0.0100.0000.0000.0000.000
84A426ARG10.8330.90619.9700.3140.3140.0000.0000.0000.000
85A427TRP00.0140.00119.3950.0260.0260.0000.0000.0000.000
86A428LEU00.002-0.00119.143-0.038-0.0380.0000.0000.0000.000
87A429TYR00.0100.00818.8260.0200.0200.0000.0000.0000.000
88A430MET0-0.006-0.01119.409-0.009-0.0090.0000.0000.0000.000
89A431ASP-1-0.746-0.83121.736-0.063-0.0630.0000.0000.0000.000
90A432SER00.0010.00222.3680.0120.0120.0000.0000.0000.000
91A433ASN0-0.056-0.01220.8760.0310.0310.0000.0000.0000.000
92A434TYR0-0.009-0.00924.2690.0010.0010.0000.0000.0000.000
93A435LEU00.003-0.01024.556-0.001-0.0010.0000.0000.0000.000
94A436ASP-1-0.821-0.90628.219-0.010-0.0100.0000.0000.0000.000
95A437THR00.0050.00531.300-0.005-0.0050.0000.0000.0000.000
96A438LEU0-0.0260.00028.640-0.006-0.0060.0000.0000.0000.000
97A439SER00.015-0.02130.8430.0030.0030.0000.0000.0000.000
98A440ARG10.9991.01730.9410.0850.0850.0000.0000.0000.000
99A441GLU-1-0.888-0.94630.819-0.084-0.0840.0000.0000.0000.000
100A442LYS10.8590.93227.0280.0420.0420.0000.0000.0000.000
101A443PHE00.0490.02424.964-0.013-0.0130.0000.0000.0000.000
102A444ALA0-0.022-0.00427.192-0.011-0.0110.0000.0000.0000.000
103A445GLY0-0.065-0.04325.118-0.007-0.0070.0000.0000.0000.000
104A446LEU00.0150.03921.722-0.019-0.0190.0000.0000.0000.000
105A447GLN00.012-0.00625.3460.0170.0170.0000.0000.0000.000
106A448ASN0-0.039-0.02024.0950.0360.0360.0000.0000.0000.000
107A449LEU00.0330.03022.581-0.012-0.0120.0000.0000.0000.000
108A450GLU-1-0.808-0.86825.101-0.204-0.2040.0000.0000.0000.000
109A451TYR0-0.0220.00222.6600.0230.0230.0000.0000.0000.000
110A452LEU00.0370.01824.192-0.018-0.0180.0000.0000.0000.000
111A453ASN0-0.050-0.03923.9850.0210.0210.0000.0000.0000.000
112A454VAL0-0.039-0.02224.354-0.005-0.0050.0000.0000.0000.000
113A455GLU-1-0.782-0.86526.538-0.050-0.0500.0000.0000.0000.000
114A456TYR00.004-0.01726.9500.0070.0070.0000.0000.0000.000
115A457ASN0-0.0370.01125.8630.0130.0130.0000.0000.0000.000
116A458ALA0-0.006-0.01629.0530.0030.0030.0000.0000.0000.000
117A459ILE00.0020.00129.0210.0000.0000.0000.0000.0000.000
118A460GLN0-0.023-0.02032.8460.0020.0020.0000.0000.0000.000
119A461LEU0-0.039-0.02135.438-0.001-0.0010.0000.0000.0000.000
120A462ILE00.0040.00734.044-0.004-0.0040.0000.0000.0000.000
121A463LEU00.0130.00035.3500.0020.0020.0000.0000.0000.000
122A464PRO00.0610.02236.751-0.006-0.0060.0000.0000.0000.000
123A465GLY00.0630.04437.531-0.002-0.0020.0000.0000.0000.000
124A466THR0-0.044-0.05731.688-0.007-0.0070.0000.0000.0000.000
125A467PHE00.035-0.00130.609-0.009-0.0090.0000.0000.0000.000
126A468ASN00.0210.00833.236-0.004-0.0040.0000.0000.0000.000
127A469ALA0-0.075-0.02729.707-0.004-0.0040.0000.0000.0000.000
128A470MET0-0.0240.00426.992-0.014-0.0140.0000.0000.0000.000
129A471PRO00.0370.01229.8860.0030.0030.0000.0000.0000.000
130A472LYS10.8350.91728.7420.1930.1930.0000.0000.0000.000
131A473LEU00.0030.01528.287-0.008-0.0080.0000.0000.0000.000
132A474ARG10.8420.90228.9630.1790.1790.0000.0000.0000.000
133A475ILE0-0.008-0.01028.6750.0090.0090.0000.0000.0000.000
134A476LEU00.0160.01729.077-0.009-0.0090.0000.0000.0000.000
135A477ILE0-0.030-0.01027.9130.0080.0080.0000.0000.0000.000
136A478LEU00.0470.01229.332-0.001-0.0010.0000.0000.0000.000
137A479ASN0-0.039-0.01730.6220.0000.0000.0000.0000.0000.000
138A480ASN00.001-0.00131.562-0.005-0.0050.0000.0000.0000.000
139A481ASN0-0.022-0.01030.3670.0070.0070.0000.0000.0000.000
140A482LEU0-0.024-0.01733.7990.0050.0050.0000.0000.0000.000
141A483LEU00.0020.01634.7560.0000.0000.0000.0000.0000.000
142A484ARG10.9760.97538.1490.0070.0070.0000.0000.0000.000
143A485SER0-0.020-0.01740.9710.0000.0000.0000.0000.0000.000
144A486LEU00.0050.00737.654-0.002-0.0020.0000.0000.0000.000
145A487PRO0-0.043-0.00639.1420.0020.0020.0000.0000.0000.000
146A488VAL00.0380.00042.144-0.002-0.0020.0000.0000.0000.000
147A489ASP-1-0.883-0.92642.689-0.055-0.0550.0000.0000.0000.000
148A490VAL0-0.097-0.04036.914-0.005-0.0050.0000.0000.0000.000
149A491PHE00.001-0.03035.525-0.006-0.0060.0000.0000.0000.000
150A492ALA00.0430.04938.972-0.003-0.0030.0000.0000.0000.000
151A493GLY0-0.078-0.03537.273-0.002-0.0020.0000.0000.0000.000
152A494VAL0-0.035-0.01233.100-0.008-0.0080.0000.0000.0000.000
153A495SER0-0.0060.00135.7850.0070.0070.0000.0000.0000.000
154A496LEU0-0.023-0.00633.133-0.007-0.0070.0000.0000.0000.000
155A497SER00.0110.00833.9120.0040.0040.0000.0000.0000.000
156A498LYS10.8880.93632.3260.0900.0900.0000.0000.0000.000
157A499LEU0-0.0030.00633.661-0.006-0.0060.0000.0000.0000.000
158A500SER00.0030.00632.5040.0030.0030.0000.0000.0000.000
159A501LEU00.021-0.00233.9640.0000.0000.0000.0000.0000.000
160A502HIS00.0280.02533.3900.0030.0030.0000.0000.0000.000
161A503ASN0-0.052-0.02435.1470.0020.0020.0000.0000.0000.000
162A504ASN0-0.053-0.02635.2740.0040.0040.0000.0000.0000.000
163A505TYR00.004-0.01837.7970.0050.0050.0000.0000.0000.000
164A506PHE0-0.037-0.00638.7860.0010.0010.0000.0000.0000.000
165A507MET00.0300.01943.6620.0010.0010.0000.0000.0000.000
166A508TYR0-0.006-0.02746.713-0.001-0.0010.0000.0000.0000.000
167A509LEU00.0290.00942.499-0.001-0.0010.0000.0000.0000.000
168A510PRO0-0.0190.00945.3350.0010.0010.0000.0000.0000.000
169A511VAL00.0670.01646.710-0.002-0.0020.0000.0000.0000.000
170A512ALA0-0.021-0.00747.910-0.003-0.0030.0000.0000.0000.000
171A513GLY00.0180.00446.8670.0020.0020.0000.0000.0000.000
172A514VAL0-0.053-0.02142.004-0.003-0.0030.0000.0000.0000.000
173A515LEU00.002-0.00942.695-0.003-0.0030.0000.0000.0000.000
174A516ASP-1-0.854-0.92544.765-0.050-0.0500.0000.0000.0000.000
175A517GLN0-0.045-0.03743.246-0.004-0.0040.0000.0000.0000.000
176A518LEU0-0.050-0.00839.246-0.005-0.0050.0000.0000.0000.000
177A519THR00.0260.01341.9860.0030.0030.0000.0000.0000.000
178A520SER0-0.058-0.04839.527-0.002-0.0020.0000.0000.0000.000
179A521ILE0-0.0010.02439.216-0.005-0.0050.0000.0000.0000.000
180A522ILE0-0.054-0.04037.6520.0020.0020.0000.0000.0000.000
181A523GLN00.0370.00935.753-0.002-0.0020.0000.0000.0000.000
182A524ILE00.0130.00637.641-0.004-0.0040.0000.0000.0000.000
183A525ASP-1-0.829-0.90636.715-0.041-0.0410.0000.0000.0000.000
184A526LEU00.0140.00138.4830.0000.0000.0000.0000.0000.000
185A527HIS00.011-0.01637.3660.0060.0060.0000.0000.0000.000
186A528GLY00.0710.02839.862-0.001-0.0010.0000.0000.0000.000
187A529ASN0-0.043-0.01139.9450.0030.0030.0000.0000.0000.000
188A530PRO00.0090.01742.8590.0000.0000.0000.0000.0000.000
189A531TRP00.0110.00343.3500.0000.0000.0000.0000.0000.000
190A532GLU-1-0.821-0.89048.274-0.007-0.0070.0000.0000.0000.000
191A533CYS0-0.099-0.06647.992-0.003-0.0030.0000.0000.0000.000
192A534SER00.0370.00354.6750.0020.0020.0000.0000.0000.000
193A535CYS0-0.086-0.07656.4480.0000.0000.0000.0000.0000.000
194A536THR00.001-0.00353.076-0.001-0.0010.0000.0000.0000.000
195A537ILE0-0.0060.01549.180-0.002-0.0020.0000.0000.0000.000
196A538VAL00.0200.01752.690-0.002-0.0020.0000.0000.0000.000
197A539PRO0-0.023-0.01752.676-0.002-0.0020.0000.0000.0000.000
198A540PHE00.009-0.00645.317-0.002-0.0020.0000.0000.0000.000
199A541LYS10.8330.90049.9120.0220.0220.0000.0000.0000.000
200A542GLN00.0160.00652.1390.0000.0000.0000.0000.0000.000
201A543TRP0-0.033-0.02643.224-0.001-0.0010.0000.0000.0000.000
202A544ALA00.0400.00847.989-0.002-0.0020.0000.0000.0000.000
203A545GLU-1-0.843-0.90448.943-0.029-0.0290.0000.0000.0000.000
204A546ARG10.8420.92351.6590.0390.0390.0000.0000.0000.000
205A547LEU0-0.0370.00544.840-0.003-0.0030.0000.0000.0000.000
206A548GLY0-0.003-0.00546.6400.0010.0010.0000.0000.0000.000
207A549SER00.019-0.00347.4600.0010.0010.0000.0000.0000.000
208A550GLU-1-0.931-0.96943.491-0.052-0.0520.0000.0000.0000.000
209A551VAL0-0.075-0.01041.745-0.003-0.0030.0000.0000.0000.000
210A552LEU00.0010.00041.397-0.003-0.0030.0000.0000.0000.000
211A553MET0-0.063-0.02335.094-0.002-0.0020.0000.0000.0000.000
212A554SER00.0050.00540.7850.0030.0030.0000.0000.0000.000
213A555ASP-1-0.908-0.94042.556-0.030-0.0300.0000.0000.0000.000
214A556LEU0-0.029-0.01444.5460.0020.0020.0000.0000.0000.000
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