FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: JL6Q9

Calculation Name: 3ODW-A-Xray372

Preferred Name: Rho guanine nucleotide exchange factor 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3ODW

Chain ID: A

ChEMBL ID: CHEMBL4295918

UniProt ID: Q92888

Base Structure: X-ray

Registration Date: 2023-06-21

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 343
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5271673.769544
FMO2-HF: Nuclear repulsion 5129639.316405
FMO2-HF: Total energy -142034.453139
FMO2-MP2: Total energy -142445.591995


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:411:PRO)


Summations of interaction energy for fragment #1(A:411: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.
2.038-2.4131.6156.904-4.065-0.007
Interaction energy analysis for fragmet #1(A:411:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.021
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].
3A413SER00.0580.0102.6238.5660.9950.2788.339-1.045-0.009
4A414GLN00.0630.0242.764-2.185-0.1670.883-1.020-1.8800.004
5A415VAL0-0.034-0.0042.758-2.272-1.1950.455-0.404-1.128-0.002
6A416LYS10.9830.9984.762-2.006-1.981-0.001-0.011-0.0120.000
7A417ARG10.9400.9776.763-1.415-1.4150.0000.0000.0000.000
8A418GLN00.0150.0187.487-0.622-0.6220.0000.0000.0000.000
9A419GLU-1-0.925-0.9708.4161.2331.2330.0000.0000.0000.000
10A420VAL0-0.018-0.00710.811-0.208-0.2080.0000.0000.0000.000
11A421ILE00.0240.02311.664-0.163-0.1630.0000.0000.0000.000
12A422SER0-0.021-0.02213.180-0.163-0.1630.0000.0000.0000.000
13A423GLU-1-0.967-0.97814.8880.4110.4110.0000.0000.0000.000
14A424LEU0-0.0060.02816.637-0.085-0.0850.0000.0000.0000.000
15A425LEU00.0290.01818.055-0.058-0.0580.0000.0000.0000.000
16A426VAL00.0040.00018.775-0.058-0.0580.0000.0000.0000.000
17A427THR0-0.059-0.07320.561-0.058-0.0580.0000.0000.0000.000
18A428GLU-1-0.675-0.76522.3980.2300.2300.0000.0000.0000.000
19A429ALA00.0280.01423.921-0.030-0.0300.0000.0000.0000.000
20A430ALA0-0.090-0.05225.243-0.027-0.0270.0000.0000.0000.000
21A431HIS0-0.016-0.01626.793-0.012-0.0120.0000.0000.0000.000
22A432VAL00.0600.03128.458-0.018-0.0180.0000.0000.0000.000
23A433ARG10.9040.95228.073-0.228-0.2280.0000.0000.0000.000
24A434MET0-0.0120.00431.207-0.015-0.0150.0000.0000.0000.000
25A435LEU00.0610.03431.995-0.013-0.0130.0000.0000.0000.000
26A436ARG11.0040.99633.145-0.160-0.1600.0000.0000.0000.000
27A437VAL0-0.041-0.00535.603-0.009-0.0090.0000.0000.0000.000
28A438LEU0-0.014-0.01737.052-0.008-0.0080.0000.0000.0000.000
29A439HIS10.8710.93138.732-0.112-0.1120.0000.0000.0000.000
30A440ASP-1-0.838-0.92839.6820.1110.1110.0000.0000.0000.000
31A441LEU0-0.036-0.03040.366-0.005-0.0050.0000.0000.0000.000
32A442PHE0-0.028-0.01040.737-0.004-0.0040.0000.0000.0000.000
33A443PHE00.0180.01043.211-0.004-0.0040.0000.0000.0000.000
34A444GLN00.0360.01044.6830.0000.0000.0000.0000.0000.000
35A445PRO00.0470.03145.572-0.005-0.0050.0000.0000.0000.000
36A446MET0-0.051-0.02746.375-0.004-0.0040.0000.0000.0000.000
37A447ALA0-0.021-0.00749.009-0.003-0.0030.0000.0000.0000.000
38A448GLU-1-0.913-0.95649.7470.0730.0730.0000.0000.0000.000
39A449CYS0-0.083-0.03252.577-0.003-0.0030.0000.0000.0000.000
40A450LEU0-0.007-0.00654.235-0.003-0.0030.0000.0000.0000.000
41A451PHE0-0.037-0.00652.051-0.002-0.0020.0000.0000.0000.000
42A452PHE0-0.047-0.03050.426-0.001-0.0010.0000.0000.0000.000
43A453PRO00.0250.02454.3560.0000.0000.0000.0000.0000.000
44A454LEU00.0510.01550.2060.0020.0020.0000.0000.0000.000
45A455GLU-1-0.880-0.95551.3230.0610.0610.0000.0000.0000.000
46A456GLU-1-0.919-0.96551.1200.0640.0640.0000.0000.0000.000
47A457LEU00.0000.02047.6140.0030.0030.0000.0000.0000.000
48A458GLN00.026-0.00846.8430.0060.0060.0000.0000.0000.000
49A459ASN0-0.077-0.03746.4170.0040.0040.0000.0000.0000.000
50A460ILE0-0.045-0.01444.8790.0020.0020.0000.0000.0000.000
51A461PHE0-0.005-0.00941.5130.0050.0050.0000.0000.0000.000
52A462PRO00.0040.00741.8400.0010.0010.0000.0000.0000.000
53A463SER0-0.059-0.05840.115-0.003-0.0030.0000.0000.0000.000
54A464LEU00.0300.05137.8010.0040.0040.0000.0000.0000.000
55A465ASP-1-0.832-0.93638.2690.1070.1070.0000.0000.0000.000
56A466GLU-1-0.823-0.91037.7530.1200.1200.0000.0000.0000.000
57A467LEU0-0.040-0.02633.3830.0070.0070.0000.0000.0000.000
58A468ILE0-0.021-0.02533.8280.0120.0120.0000.0000.0000.000
59A469GLU-1-0.861-0.88433.1100.1480.1480.0000.0000.0000.000
60A470VAL0-0.0200.00731.7530.0090.0090.0000.0000.0000.000
61A471HIS10.7570.84527.842-0.189-0.1890.0000.0000.0000.000
62A472SER0-0.032-0.06128.2830.0180.0180.0000.0000.0000.000
63A473LEU00.0460.04229.2420.0110.0110.0000.0000.0000.000
64A474PHE0-0.044-0.02321.8510.0110.0110.0000.0000.0000.000
65A475LEU00.013-0.01024.0170.0230.0230.0000.0000.0000.000
66A476ASP-1-0.885-0.94724.6390.2150.2150.0000.0000.0000.000
67A477ARG10.8850.94524.228-0.183-0.1830.0000.0000.0000.000
68A478LEU00.0040.00619.1750.0180.0180.0000.0000.0000.000
69A479MET0-0.0200.00120.4280.0310.0310.0000.0000.0000.000
70A480LYS10.9610.99821.715-0.176-0.1760.0000.0000.0000.000
71A481ARG10.8490.88717.942-0.329-0.3290.0000.0000.0000.000
72A482ARG10.8490.92113.579-0.645-0.6450.0000.0000.0000.000
73A483GLN0-0.026-0.02417.6850.0310.0310.0000.0000.0000.000
74A484GLU-1-0.992-0.98419.5970.2160.2160.0000.0000.0000.000
75A485SER00.0410.01714.2040.0240.0240.0000.0000.0000.000
76A486GLY0-0.027-0.00214.3250.0270.0270.0000.0000.0000.000
77A487TYR0-0.033-0.02611.7990.0040.0040.0000.0000.0000.000
78A488LEU0-0.044-0.0236.8230.1150.1150.0000.0000.0000.000
79A489ILE00.0180.01310.853-0.153-0.1530.0000.0000.0000.000
80A490GLU-1-0.853-0.92910.8450.7240.7240.0000.0000.0000.000
81A491GLU-1-0.943-0.96812.1510.1800.1800.0000.0000.0000.000
82A492ILE0-0.114-0.05414.8530.0000.0000.0000.0000.0000.000
83A493GLY00.015-0.00917.075-0.033-0.0330.0000.0000.0000.000
84A494ASP-1-0.841-0.90918.9430.2400.2400.0000.0000.0000.000
85A495VAL0-0.022-0.00420.448-0.025-0.0250.0000.0000.0000.000
86A496LEU0-0.025-0.02418.041-0.021-0.0210.0000.0000.0000.000
87A497LEU00.0390.01322.082-0.017-0.0170.0000.0000.0000.000
88A498ALA0-0.049-0.01024.617-0.020-0.0200.0000.0000.0000.000
89A499ARG10.7750.87324.734-0.236-0.2360.0000.0000.0000.000
90A500PHE0-0.0190.00823.384-0.005-0.0050.0000.0000.0000.000
91A501ASP-1-0.813-0.91427.0850.1290.1290.0000.0000.0000.000
92A502GLY0-0.0010.01928.829-0.001-0.0010.0000.0000.0000.000
93A503ALA0-0.034-0.03132.1120.0000.0000.0000.0000.0000.000
94A504GLU-1-0.881-0.95231.0280.1280.1280.0000.0000.0000.000
95A505GLY00.0180.02830.6850.0060.0060.0000.0000.0000.000
96A506SER00.007-0.01231.406-0.003-0.0030.0000.0000.0000.000
97A507TRP0-0.061-0.01534.713-0.009-0.0090.0000.0000.0000.000
98A508PHE00.0580.01329.2190.0000.0000.0000.0000.0000.000
99A509GLN00.0250.01033.0550.0040.0040.0000.0000.0000.000
100A510LYS10.9230.96934.161-0.091-0.0910.0000.0000.0000.000
101A511ILE0-0.054-0.02535.957-0.005-0.0050.0000.0000.0000.000
102A512SER00.0020.00032.891-0.005-0.0050.0000.0000.0000.000
103A513SER00.0410.02735.133-0.003-0.0030.0000.0000.0000.000
104A514ARG10.9070.97537.170-0.097-0.0970.0000.0000.0000.000
105A515PHE0-0.047-0.02136.823-0.004-0.0040.0000.0000.0000.000
106A516CYS0-0.019-0.00735.2590.0010.0010.0000.0000.0000.000
107A517SER00.006-0.02438.017-0.003-0.0030.0000.0000.0000.000
108A518ARG10.8870.95941.075-0.080-0.0800.0000.0000.0000.000
109A519GLN00.0550.03636.730-0.002-0.0020.0000.0000.0000.000
110A520SER00.029-0.00341.3070.0010.0010.0000.0000.0000.000
111A521PHE00.0200.01843.855-0.003-0.0030.0000.0000.0000.000
112A522ALA00.0410.01143.341-0.002-0.0020.0000.0000.0000.000
113A523LEU00.0030.00840.652-0.003-0.0030.0000.0000.0000.000
114A524GLU-1-0.964-0.98445.1330.0660.0660.0000.0000.0000.000
115A525GLN0-0.009-0.01248.506-0.004-0.0040.0000.0000.0000.000
116A526LEU0-0.0030.00044.886-0.003-0.0030.0000.0000.0000.000
117A527LYS10.9500.97847.489-0.075-0.0750.0000.0000.0000.000
118A528ALA0-0.031-0.01949.663-0.003-0.0030.0000.0000.0000.000
119A529LYS10.9110.96352.336-0.063-0.0630.0000.0000.0000.000
120A530GLN0-0.0140.00147.5630.0010.0010.0000.0000.0000.000
121A531ARG10.9330.95551.945-0.064-0.0640.0000.0000.0000.000
122A532LYS10.9180.96855.050-0.055-0.0550.0000.0000.0000.000
123A533ASP-1-0.851-0.93956.2920.0540.0540.0000.0000.0000.000
124A534PRO00.0400.02856.0080.0020.0020.0000.0000.0000.000
125A535ARG10.9330.96856.056-0.056-0.0560.0000.0000.0000.000
126A536PHE00.0120.00048.9230.0020.0020.0000.0000.0000.000
127A537CYS0-0.023-0.01051.5330.0040.0040.0000.0000.0000.000
128A538ALA00.0380.01851.0730.0030.0030.0000.0000.0000.000
129A539PHE00.0030.00648.0130.0020.0020.0000.0000.0000.000
130A540VAL00.0090.00645.9530.0030.0030.0000.0000.0000.000
131A541GLN0-0.033-0.02546.5460.0030.0030.0000.0000.0000.000
132A542GLU-1-0.903-0.94246.9280.0810.0810.0000.0000.0000.000
133A543ALA00.0320.02744.6260.0030.0030.0000.0000.0000.000
134A544GLU-1-0.834-0.95242.2870.1010.1010.0000.0000.0000.000
135A545SER0-0.091-0.02842.0230.0040.0040.0000.0000.0000.000
136A546ARG10.9130.96042.139-0.086-0.0860.0000.0000.0000.000
137A547PRO00.0640.02338.5810.0060.0060.0000.0000.0000.000
138A548ARG10.8260.89836.453-0.119-0.1190.0000.0000.0000.000
139A549CYS00.0170.03636.2680.0070.0070.0000.0000.0000.000
140A550ARG10.8810.93828.654-0.187-0.1870.0000.0000.0000.000
141A551ARG10.9350.95034.320-0.112-0.1120.0000.0000.0000.000
142A552LEU00.0430.04932.836-0.001-0.0010.0000.0000.0000.000
143A553GLN0-0.020-0.00336.808-0.004-0.0040.0000.0000.0000.000
144A554LEU00.0310.02139.0500.0050.0050.0000.0000.0000.000
145A555LYS10.8790.91840.263-0.098-0.0980.0000.0000.0000.000
146A556ASP-1-0.861-0.93435.7580.1240.1240.0000.0000.0000.000
147A557MET0-0.060-0.02635.4440.0070.0070.0000.0000.0000.000
148A558ILE00.0510.04535.5400.0070.0070.0000.0000.0000.000
149A559PRO0-0.028-0.00135.3940.0030.0030.0000.0000.0000.000
150A560THR0-0.045-0.04531.2010.0080.0080.0000.0000.0000.000
151A561GLU-1-0.772-0.86830.9590.1880.1880.0000.0000.0000.000
152A562MET00.0470.01131.1810.0090.0090.0000.0000.0000.000
153A563GLN0-0.010-0.01628.8070.0160.0160.0000.0000.0000.000
154A564ARG10.8110.91922.216-0.287-0.2870.0000.0000.0000.000
155A565LEU00.0520.01626.2380.0180.0180.0000.0000.0000.000
156A566THR0-0.037-0.00326.9910.0060.0060.0000.0000.0000.000
157A567LYS10.9140.94122.504-0.251-0.2510.0000.0000.0000.000
158A568TYR0-0.024-0.05121.6350.0240.0240.0000.0000.0000.000
159A569PRO00.0580.04521.0900.0300.0300.0000.0000.0000.000
160A570LEU0-0.006-0.00519.9860.0240.0240.0000.0000.0000.000
161A571LEU0-0.021-0.01217.0250.0360.0360.0000.0000.0000.000
162A572LEU00.0420.00416.1260.0670.0670.0000.0000.0000.000
163A573GLN00.0100.00216.787-0.016-0.0160.0000.0000.0000.000
164A574SER0-0.068-0.03313.0030.0180.0180.0000.0000.0000.000
165A575ILE00.0270.01811.9140.1370.1370.0000.0000.0000.000
166A576GLY00.0490.03012.2330.0570.0570.0000.0000.0000.000
167A577GLN0-0.058-0.02212.4410.0460.0460.0000.0000.0000.000
168A578ASN0-0.094-0.0637.8100.1130.1130.0000.0000.0000.000
169A579THR0-0.043-0.0178.3790.3510.3510.0000.0000.0000.000
170A580GLU-1-0.880-0.9487.3330.4930.4930.0000.0000.0000.000
171A581GLU-1-0.798-0.8989.488-0.082-0.0820.0000.0000.0000.000
172A582PRO0-0.047-0.02412.3640.0620.0620.0000.0000.0000.000
173A583THR0-0.008-0.00715.8570.0250.0250.0000.0000.0000.000
174A584GLU-1-0.673-0.84413.6260.4460.4460.0000.0000.0000.000
175A585ARG10.9040.93913.735-0.072-0.0720.0000.0000.0000.000
176A586GLU-1-0.916-0.94015.8060.0900.0900.0000.0000.0000.000
177A587LYS10.9210.97118.846-0.190-0.1900.0000.0000.0000.000
178A588VAL0-0.001-0.01015.3360.0020.0020.0000.0000.0000.000
179A589GLU-1-0.962-0.98717.7480.1680.1680.0000.0000.0000.000
180A590LEU00.0470.03619.825-0.006-0.0060.0000.0000.0000.000
181A591ALA00.0160.00820.852-0.005-0.0050.0000.0000.0000.000
182A592ALA0-0.032-0.04119.884-0.003-0.0030.0000.0000.0000.000
183A593GLU-1-0.960-0.96922.0000.1290.1290.0000.0000.0000.000
184A594CYS00.0480.03924.982-0.012-0.0120.0000.0000.0000.000
185A595CYS0-0.075-0.03424.122-0.002-0.0020.0000.0000.0000.000
186A596ARG10.8780.93621.680-0.195-0.1950.0000.0000.0000.000
187A597GLU-1-0.886-0.93927.4740.1130.1130.0000.0000.0000.000
188A598ILE0-0.027-0.01028.615-0.008-0.0080.0000.0000.0000.000
189A599LEU0-0.050-0.02527.744-0.007-0.0070.0000.0000.0000.000
190A600HIS0-0.021-0.01030.834-0.004-0.0040.0000.0000.0000.000
191A601HIS00.0120.00733.172-0.004-0.0040.0000.0000.0000.000
192A602VAL00.002-0.01433.174-0.006-0.0060.0000.0000.0000.000
193A603ASN00.002-0.01332.488-0.006-0.0060.0000.0000.0000.000
194A604GLN0-0.047-0.01236.214-0.005-0.0050.0000.0000.0000.000
195A605ALA00.0300.00538.974-0.005-0.0050.0000.0000.0000.000
196A606VAL0-0.020-0.00537.343-0.002-0.0020.0000.0000.0000.000
197A607ARG10.9670.98740.455-0.074-0.0740.0000.0000.0000.000
198A608ASP-1-0.806-0.88542.4650.0690.0690.0000.0000.0000.000
199A609MET0-0.085-0.03143.847-0.006-0.0060.0000.0000.0000.000
200A610GLU-1-0.920-0.97342.0710.0850.0850.0000.0000.0000.000
201A611ASP-1-0.862-0.92746.1250.0630.0630.0000.0000.0000.000
202A612LEU0-0.0130.00748.261-0.004-0.0040.0000.0000.0000.000
203A613LEU0-0.055-0.04447.815-0.003-0.0030.0000.0000.0000.000
204A614ARG10.9621.00348.276-0.065-0.0650.0000.0000.0000.000
205A615LEU00.013-0.00351.712-0.003-0.0030.0000.0000.0000.000
206A616LYS10.9090.94353.636-0.057-0.0570.0000.0000.0000.000
207A617ASP-1-0.889-0.91655.1170.0490.0490.0000.0000.0000.000
208A618TYR0-0.017-0.03854.741-0.002-0.0020.0000.0000.0000.000
209A619GLN00.0500.04758.273-0.002-0.0020.0000.0000.0000.000
210A620ARG10.8830.95059.351-0.047-0.0470.0000.0000.0000.000
211A621ARG10.7950.88158.209-0.047-0.0470.0000.0000.0000.000
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