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: QY6NY

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 OptAll
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 -3004391.791661
FMO2-HF: Nuclear repulsion 2908273.209149
FMO2-HF: Total energy -96118.582511
FMO2-MP2: Total energy -96394.407158


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.
-21.062-25.6111.0252.86-9.3350.003
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 : -0.009 / q_NPA : 0.002
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].
3A344GLY00.0350.0032.211-2.703-10.7325.1125.919-3.0020.017
4A345CYS0-0.084-0.0422.783-4.895-3.2790.156-0.658-1.1130.004
5A346SER00.0040.0142.713-2.647-1.4541.093-0.847-1.439-0.011
6A347CYS0-0.013-0.0182.817-2.795-3.6834.401-1.104-2.408-0.008
7A348ASP-1-0.822-0.8864.789-0.665-0.603-0.001-0.009-0.0510.000
8A349HIS0-0.054-0.0267.720-0.211-0.2110.0000.0000.0000.000
9A350ILE00.0460.02410.1490.1370.1370.0000.0000.0000.000
10A351PRO0-0.0010.01813.738-0.020-0.0200.0000.0000.0000.000
11A352GLY00.006-0.00916.7180.0120.0120.0000.0000.0000.000
12A353SER0-0.028-0.03514.265-0.013-0.0130.0000.0000.0000.000
13A354GLY00.0640.04712.1330.0010.0010.0000.0000.0000.000
14A355LEU0-0.022-0.0033.959-0.181-0.062-0.001-0.017-0.1020.000
15A356LYS10.8800.9417.9361.1861.1860.0000.0000.0000.000
16A357MET00.004-0.0124.273-1.465-1.0350.011-0.117-0.3240.000
17A358ASN00.000-0.0076.1740.6120.6120.0000.0000.0000.000
18A360ASN00.0970.0567.9460.1220.1220.0000.0000.0000.000
19A361ASN0-0.016-0.00211.4020.1220.1220.0000.0000.0000.000
20A362ARG10.8640.9437.264-1.376-1.3760.0000.0000.0000.000
21A363ASN0-0.017-0.01911.792-0.167-0.1670.0000.0000.0000.000
22A364VAL0-0.0050.0009.9190.1130.1130.0000.0000.0000.000
23A365SER00.0870.03013.157-0.082-0.0820.0000.0000.0000.000
24A366SER0-0.088-0.04814.490-0.078-0.0780.0000.0000.0000.000
25A367LEU00.0450.01812.1260.0330.0330.0000.0000.0000.000
26A368ALA0-0.033-0.01511.503-0.114-0.1140.0000.0000.0000.000
27A369ASP-1-0.911-0.94510.5800.3280.3280.0000.0000.0000.000
28A370LEU0-0.022-0.0085.9750.3390.3390.0000.0000.0000.000
29A371LYS10.9350.9502.834-4.486-3.6510.255-0.302-0.7880.001
30A372PRO0-0.029-0.0294.711-0.806-0.692-0.001-0.005-0.1080.000
31A373LYS10.8660.9356.5230.2740.2740.0000.0000.0000.000
32A374LEU00.004-0.0067.8920.1880.1880.0000.0000.0000.000
33A375SER0-0.0190.0117.825-0.074-0.0740.0000.0000.0000.000
34A376ASN00.014-0.0028.465-0.195-0.1950.0000.0000.0000.000
35A377VAL0-0.0310.0007.102-0.028-0.0280.0000.0000.0000.000
36A378GLN00.000-0.0019.7350.1880.1880.0000.0000.0000.000
37A379GLU-1-0.892-0.95510.833-0.629-0.6290.0000.0000.0000.000
38A380LEU0-0.010-0.0108.162-0.292-0.2920.0000.0000.0000.000
39A381PHE0-0.024-0.0049.9280.1860.1860.0000.0000.0000.000
40A382LEU0-0.001-0.0189.526-0.019-0.0190.0000.0000.0000.000
41A383ARG10.7850.85312.1660.2250.2250.0000.0000.0000.000
42A384ASP-1-0.849-0.91514.4540.0460.0460.0000.0000.0000.000
43A385ASN0-0.095-0.03411.0450.1250.1250.0000.0000.0000.000
44A386LYS10.9240.95315.335-0.240-0.2400.0000.0000.0000.000
45A387ILE0-0.0060.00413.4520.0150.0150.0000.0000.0000.000
46A388HIS00.0590.02817.489-0.018-0.0180.0000.0000.0000.000
47A389SER0-0.027-0.01219.938-0.014-0.0140.0000.0000.0000.000
48A390ILE0-0.0070.01617.6030.0060.0060.0000.0000.0000.000
49A391ARG10.9250.95018.6250.0070.0070.0000.0000.0000.000
50A392LYS10.9160.93918.5440.0570.0570.0000.0000.0000.000
51A393SER0-0.045-0.02317.660-0.040-0.0400.0000.0000.0000.000
52A394HIS0-0.007-0.00514.383-0.031-0.0310.0000.0000.0000.000
53A395PHE00.0750.02413.440-0.074-0.0740.0000.0000.0000.000
54A396VAL0-0.050-0.01815.356-0.033-0.0330.0000.0000.0000.000
55A397ASP-1-0.793-0.9029.405-0.870-0.8700.0000.0000.0000.000
56A398TYR00.0220.0167.415-0.176-0.1760.0000.0000.0000.000
57A399LYS10.8860.93112.8770.3530.3530.0000.0000.0000.000
58A400ASN0-0.034-0.01113.6900.0110.0110.0000.0000.0000.000
59A401LEU0-0.050-0.00611.288-0.027-0.0270.0000.0000.0000.000
60A402ILE00.0250.01714.8220.0850.0850.0000.0000.0000.000
61A403LEU0-0.025-0.00615.0430.0770.0770.0000.0000.0000.000
62A404LEU0-0.015-0.00713.918-0.098-0.0980.0000.0000.0000.000
63A405ASP-1-0.810-0.88414.467-0.170-0.1700.0000.0000.0000.000
64A406LEU00.005-0.00914.549-0.018-0.0180.0000.0000.0000.000
65A407GLY00.0540.03316.8600.0410.0410.0000.0000.0000.000
66A408ASN0-0.069-0.06018.1550.0150.0150.0000.0000.0000.000
67A409ASN0-0.031-0.01215.6920.0590.0590.0000.0000.0000.000
68A410ASN0-0.013-0.01919.7060.0150.0150.0000.0000.0000.000
69A411ILE00.0030.00718.2890.0050.0050.0000.0000.0000.000
70A412ALA00.0420.02822.277-0.009-0.0090.0000.0000.0000.000
71A413THR0-0.067-0.03924.534-0.010-0.0100.0000.0000.0000.000
72A414VAL00.0360.00722.519-0.003-0.0030.0000.0000.0000.000
73A415GLU-1-0.826-0.87422.826-0.074-0.0740.0000.0000.0000.000
74A416ASN00.0490.02124.654-0.020-0.0200.0000.0000.0000.000
75A417ASN0-0.021-0.02325.365-0.005-0.0050.0000.0000.0000.000
76A418THR0-0.022-0.02319.510-0.012-0.0120.0000.0000.0000.000
77A419PHE00.0680.02018.505-0.021-0.0210.0000.0000.0000.000
78A420LYS10.8260.91221.0760.1320.1320.0000.0000.0000.000
79A421ASN0-0.025-0.02518.8180.0000.0000.0000.0000.0000.000
80A422LEU00.0130.02416.099-0.020-0.0200.0000.0000.0000.000
81A423LEU00.0160.00719.3820.0180.0180.0000.0000.0000.000
82A424ASP-1-0.811-0.90218.247-0.423-0.4230.0000.0000.0000.000
83A425LEU0-0.062-0.01117.523-0.007-0.0070.0000.0000.0000.000
84A426ARG10.8220.88720.1170.3290.3290.0000.0000.0000.000
85A427TRP00.022-0.00219.3700.0250.0250.0000.0000.0000.000
86A428LEU00.0020.00119.226-0.041-0.0410.0000.0000.0000.000
87A429TYR00.0130.01719.0030.0250.0250.0000.0000.0000.000
88A430MET00.000-0.01419.410-0.016-0.0160.0000.0000.0000.000
89A431ASP-1-0.714-0.81121.765-0.098-0.0980.0000.0000.0000.000
90A432SER0-0.036-0.01922.5330.0050.0050.0000.0000.0000.000
91A433ASN0-0.063-0.03520.3100.0250.0250.0000.0000.0000.000
92A434TYR00.000-0.00124.3000.0080.0080.0000.0000.0000.000
93A435LEU0-0.013-0.01024.3240.0030.0030.0000.0000.0000.000
94A436ASP-1-0.797-0.87627.892-0.022-0.0220.0000.0000.0000.000
95A437THR0-0.018-0.01930.971-0.004-0.0040.0000.0000.0000.000
96A438LEU0-0.045-0.00128.433-0.007-0.0070.0000.0000.0000.000
97A439SER00.008-0.02730.8910.0050.0050.0000.0000.0000.000
98A440ARG11.0051.01630.5850.0860.0860.0000.0000.0000.000
99A441GLU-1-0.864-0.93330.171-0.089-0.0890.0000.0000.0000.000
100A442LYS10.8620.93126.6860.0490.0490.0000.0000.0000.000
101A443PHE00.0670.03125.248-0.014-0.0140.0000.0000.0000.000
102A444ALA00.0050.00826.637-0.013-0.0130.0000.0000.0000.000
103A445GLY0-0.030-0.03225.0150.0010.0010.0000.0000.0000.000
104A446LEU00.0280.05121.402-0.012-0.0120.0000.0000.0000.000
105A447GLN0-0.007-0.02525.0240.0100.0100.0000.0000.0000.000
106A448ASN0-0.049-0.02124.2580.0340.0340.0000.0000.0000.000
107A449LEU00.0040.02222.793-0.010-0.0100.0000.0000.0000.000
108A450GLU-1-0.767-0.84125.218-0.219-0.2190.0000.0000.0000.000
109A451TYR0-0.052-0.02222.8110.0230.0230.0000.0000.0000.000
110A452LEU00.0320.00924.530-0.020-0.0200.0000.0000.0000.000
111A453ASN0-0.044-0.03324.2390.0250.0250.0000.0000.0000.000
112A454VAL00.0070.00324.268-0.011-0.0110.0000.0000.0000.000
113A455GLU-1-0.776-0.85526.557-0.076-0.0760.0000.0000.0000.000
114A456TYR00.013-0.01127.0310.0040.0040.0000.0000.0000.000
115A457ASN0-0.052-0.02425.1940.0090.0090.0000.0000.0000.000
116A458ALA00.0100.00228.9180.0050.0050.0000.0000.0000.000
117A459ILE00.0050.00529.2050.0020.0020.0000.0000.0000.000
118A460GLN0-0.037-0.02332.7290.0020.0020.0000.0000.0000.000
119A461LEU0-0.027-0.01535.481-0.001-0.0010.0000.0000.0000.000
120A462ILE00.0180.00733.695-0.004-0.0040.0000.0000.0000.000
121A463LEU00.0140.00635.4990.0030.0030.0000.0000.0000.000
122A464PRO00.0730.02437.111-0.006-0.0060.0000.0000.0000.000
123A465GLY00.0420.03637.693-0.002-0.0020.0000.0000.0000.000
124A466THR0-0.060-0.05531.894-0.006-0.0060.0000.0000.0000.000
125A467PHE00.0670.01130.634-0.009-0.0090.0000.0000.0000.000
126A468ASN00.0380.02532.823-0.008-0.0080.0000.0000.0000.000
127A469ALA0-0.075-0.02629.276-0.002-0.0020.0000.0000.0000.000
128A470MET0-0.065-0.01927.241-0.016-0.0160.0000.0000.0000.000
129A471PRO00.0540.01729.9680.0000.0000.0000.0000.0000.000
130A472LYS10.8370.91328.8050.1950.1950.0000.0000.0000.000
131A473LEU0-0.0140.01128.364-0.006-0.0060.0000.0000.0000.000
132A474ARG10.8310.89628.8050.1900.1900.0000.0000.0000.000
133A475ILE00.0080.00828.8440.0090.0090.0000.0000.0000.000
134A476LEU00.0130.01229.110-0.012-0.0120.0000.0000.0000.000
135A477ILE0-0.032-0.01228.2300.0100.0100.0000.0000.0000.000
136A478LEU00.0290.00129.269-0.003-0.0030.0000.0000.0000.000
137A479ASN0-0.004-0.01830.7810.0010.0010.0000.0000.0000.000
138A480ASN0-0.0050.00631.333-0.007-0.0070.0000.0000.0000.000
139A481ASN0-0.036-0.01130.0730.0050.0050.0000.0000.0000.000
140A482LEU0-0.008-0.01133.6430.0050.0050.0000.0000.0000.000
141A483LEU0-0.0180.01234.7360.0020.0020.0000.0000.0000.000
142A484ARG10.9590.97338.0680.0170.0170.0000.0000.0000.000
143A485SER0-0.021-0.00841.1970.0000.0000.0000.0000.0000.000
144A486LEU00.0250.00937.866-0.003-0.0030.0000.0000.0000.000
145A487PRO0-0.045-0.00839.7520.0030.0030.0000.0000.0000.000
146A488VAL00.0580.01342.363-0.003-0.0030.0000.0000.0000.000
147A489ASP-1-0.882-0.92842.600-0.060-0.0600.0000.0000.0000.000
148A490VAL0-0.114-0.04537.024-0.006-0.0060.0000.0000.0000.000
149A491PHE00.007-0.01835.698-0.007-0.0070.0000.0000.0000.000
150A492ALA00.0380.03439.005-0.003-0.0030.0000.0000.0000.000
151A493GLY0-0.058-0.02237.464-0.001-0.0010.0000.0000.0000.000
152A494VAL0-0.038-0.01933.447-0.008-0.0080.0000.0000.0000.000
153A495SER0-0.022-0.01635.4480.0080.0080.0000.0000.0000.000
154A496LEU0-0.038-0.00433.366-0.007-0.0070.0000.0000.0000.000
155A497SER00.0350.02033.9270.0040.0040.0000.0000.0000.000
156A498LYS10.8670.91732.6390.1050.1050.0000.0000.0000.000
157A499LEU00.0170.01933.739-0.006-0.0060.0000.0000.0000.000
158A500SER0-0.023-0.00732.6270.0030.0030.0000.0000.0000.000
159A501LEU00.0330.00333.999-0.002-0.0020.0000.0000.0000.000
160A502HIS00.0300.02833.4880.0050.0050.0000.0000.0000.000
161A503ASN0-0.064-0.03934.7550.0010.0010.0000.0000.0000.000
162A504ASN0-0.038-0.01435.1500.0020.0020.0000.0000.0000.000
163A505TYR00.000-0.01937.5790.0050.0050.0000.0000.0000.000
164A506PHE0-0.026-0.00338.6310.0020.0020.0000.0000.0000.000
165A507MET00.0190.01343.4840.0010.0010.0000.0000.0000.000
166A508TYR0-0.003-0.01946.8110.0000.0000.0000.0000.0000.000
167A509LEU00.0220.01242.496-0.001-0.0010.0000.0000.0000.000
168A510PRO0-0.0160.00545.5640.0010.0010.0000.0000.0000.000
169A511VAL00.0590.01546.945-0.002-0.0020.0000.0000.0000.000
170A512ALA0-0.019-0.01148.066-0.003-0.0030.0000.0000.0000.000
171A513GLY00.017-0.00347.1140.0010.0010.0000.0000.0000.000
172A514VAL0-0.059-0.02442.494-0.002-0.0020.0000.0000.0000.000
173A515LEU0-0.011-0.01143.014-0.003-0.0030.0000.0000.0000.000
174A516ASP-1-0.809-0.89745.152-0.055-0.0550.0000.0000.0000.000
175A517GLN0-0.041-0.04843.340-0.004-0.0040.0000.0000.0000.000
176A518LEU0-0.0570.00339.751-0.005-0.0050.0000.0000.0000.000
177A519THR00.0320.01541.9790.0020.0020.0000.0000.0000.000
178A520SER0-0.065-0.05439.454-0.002-0.0020.0000.0000.0000.000
179A521ILE0-0.0380.00339.051-0.005-0.0050.0000.0000.0000.000
180A522ILE0-0.026-0.01437.4380.0020.0020.0000.0000.0000.000
181A523GLN00.017-0.00136.140-0.003-0.0030.0000.0000.0000.000
182A524ILE00.0230.00437.660-0.004-0.0040.0000.0000.0000.000
183A525ASP-1-0.805-0.89636.909-0.054-0.0540.0000.0000.0000.000
184A526LEU00.0460.01138.301-0.001-0.0010.0000.0000.0000.000
185A527HIS00.0420.00336.8710.0080.0080.0000.0000.0000.000
186A528GLY00.006-0.00340.180-0.001-0.0010.0000.0000.0000.000
187A529ASN0-0.0210.00139.5820.0020.0020.0000.0000.0000.000
188A530PRO00.0070.01242.7360.0010.0010.0000.0000.0000.000
189A531TRP0-0.014-0.00342.9850.0010.0010.0000.0000.0000.000
190A532GLU-1-0.822-0.86648.141-0.014-0.0140.0000.0000.0000.000
191A533CYS0-0.076-0.02648.073-0.003-0.0030.0000.0000.0000.000
192A534SER00.022-0.01954.7320.0020.0020.0000.0000.0000.000
193A535CYS0-0.096-0.06655.918-0.001-0.0010.0000.0000.0000.000
194A536THR0-0.005-0.00752.897-0.001-0.0010.0000.0000.0000.000
195A537ILE00.0050.01849.307-0.002-0.0020.0000.0000.0000.000
196A538VAL00.0060.01852.736-0.002-0.0020.0000.0000.0000.000
197A539PRO0-0.033-0.02352.492-0.002-0.0020.0000.0000.0000.000
198A540PHE00.0230.00545.120-0.002-0.0020.0000.0000.0000.000
199A541LYS10.8190.89049.8980.0280.0280.0000.0000.0000.000
200A542GLN00.0460.02152.0760.0000.0000.0000.0000.0000.000
201A543TRP0-0.062-0.03943.483-0.001-0.0010.0000.0000.0000.000
202A544ALA00.0440.00848.064-0.002-0.0020.0000.0000.0000.000
203A545GLU-1-0.848-0.91749.023-0.036-0.0360.0000.0000.0000.000
204A546ARG10.8570.93551.3540.0450.0450.0000.0000.0000.000
205A547LEU0-0.0370.00945.050-0.003-0.0030.0000.0000.0000.000
206A548GLY0-0.007-0.01146.8690.0010.0010.0000.0000.0000.000
207A549SER0-0.041-0.05347.4400.0000.0000.0000.0000.0000.000
208A550GLU-1-0.871-0.91343.389-0.061-0.0610.0000.0000.0000.000
209A551VAL0-0.063-0.00941.252-0.003-0.0030.0000.0000.0000.000
210A552LEU00.0180.00541.295-0.003-0.0030.0000.0000.0000.000
211A553MET0-0.069-0.03635.287-0.002-0.0020.0000.0000.0000.000
212A554SER0-0.008-0.00140.9510.0020.0020.0000.0000.0000.000
213A555ASP-1-0.820-0.88442.939-0.036-0.0360.0000.0000.0000.000
214A556LEU0-0.029-0.00844.1340.0000.0000.0000.0000.0000.000
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