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: 393JL

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 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 343
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5274765.623942
FMO2-HF: Nuclear repulsion 5132727.715375
FMO2-HF: Total energy -142037.908567
FMO2-MP2: Total energy -142449.003277


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.
2.526-2.1811.8667.209-4.366-0.008
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 : 0.015 / q_NPA : 0.005
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].
3A413SER00.0640.0092.6548.8000.8770.3468.598-1.020-0.009
4A414GLN00.049-0.0012.716-2.708-0.7190.901-0.982-1.9080.004
5A415VAL0-0.052-0.0122.714-2.759-1.5760.620-0.395-1.408-0.003
6A416LYS10.8570.9274.776-1.975-1.931-0.001-0.012-0.0300.000
7A417ARG10.8560.9066.736-1.510-1.5100.0000.0000.0000.000
8A418GLN00.0090.0057.401-0.703-0.7030.0000.0000.0000.000
9A419GLU-1-0.836-0.9028.4201.0241.0240.0000.0000.0000.000
10A420VAL0-0.005-0.00110.808-0.179-0.1790.0000.0000.0000.000
11A421ILE00.0310.02911.629-0.155-0.1550.0000.0000.0000.000
12A422SER0-0.057-0.04812.496-0.145-0.1450.0000.0000.0000.000
13A423GLU-1-0.954-0.97014.8890.3990.3990.0000.0000.0000.000
14A424LEU00.0020.02616.625-0.079-0.0790.0000.0000.0000.000
15A425LEU00.0410.02017.843-0.056-0.0560.0000.0000.0000.000
16A426VAL00.0010.00118.345-0.053-0.0530.0000.0000.0000.000
17A427THR0-0.057-0.06420.546-0.051-0.0510.0000.0000.0000.000
18A428GLU-1-0.677-0.78822.3870.2230.2230.0000.0000.0000.000
19A429ALA00.0310.01723.877-0.027-0.0270.0000.0000.0000.000
20A430ALA0-0.088-0.05625.105-0.025-0.0250.0000.0000.0000.000
21A431HIS0-0.003-0.00726.791-0.012-0.0120.0000.0000.0000.000
22A432VAL00.0630.03328.447-0.017-0.0170.0000.0000.0000.000
23A433ARG10.9140.96026.885-0.207-0.2070.0000.0000.0000.000
24A434MET0-0.027-0.00231.174-0.014-0.0140.0000.0000.0000.000
25A435LEU00.0550.03632.125-0.012-0.0120.0000.0000.0000.000
26A436ARG11.0060.99932.988-0.148-0.1480.0000.0000.0000.000
27A437VAL0-0.037-0.01235.140-0.009-0.0090.0000.0000.0000.000
28A438LEU0-0.022-0.01737.049-0.007-0.0070.0000.0000.0000.000
29A439HIS10.8280.88738.727-0.105-0.1050.0000.0000.0000.000
30A440ASP-1-0.784-0.87839.1010.1020.1020.0000.0000.0000.000
31A441LEU0-0.034-0.02540.242-0.005-0.0050.0000.0000.0000.000
32A442PHE0-0.025-0.01640.378-0.004-0.0040.0000.0000.0000.000
33A443PHE0-0.0040.00843.207-0.004-0.0040.0000.0000.0000.000
34A444GLN00.021-0.00444.6740.0010.0010.0000.0000.0000.000
35A445PRO00.0480.03245.637-0.004-0.0040.0000.0000.0000.000
36A446MET0-0.051-0.02346.569-0.004-0.0040.0000.0000.0000.000
37A447ALA0-0.016-0.00748.978-0.003-0.0030.0000.0000.0000.000
38A448GLU-1-0.891-0.93949.4130.0660.0660.0000.0000.0000.000
39A449CYS0-0.096-0.03452.227-0.003-0.0030.0000.0000.0000.000
40A450LEU00.0070.00054.228-0.002-0.0020.0000.0000.0000.000
41A451PHE0-0.034-0.00652.273-0.002-0.0020.0000.0000.0000.000
42A452PHE0-0.015-0.01550.233-0.001-0.0010.0000.0000.0000.000
43A453PRO00.0420.03654.3470.0000.0000.0000.0000.0000.000
44A454LEU00.0660.01950.1250.0020.0020.0000.0000.0000.000
45A455GLU-1-0.881-0.95551.3050.0580.0580.0000.0000.0000.000
46A456GLU-1-0.885-0.95351.1000.0610.0610.0000.0000.0000.000
47A457LEU00.0020.01947.7000.0030.0030.0000.0000.0000.000
48A458GLN0-0.008-0.01446.8250.0050.0050.0000.0000.0000.000
49A459ASN0-0.113-0.07046.3970.0030.0030.0000.0000.0000.000
50A460ILE0-0.025-0.00744.9390.0020.0020.0000.0000.0000.000
51A461PHE00.009-0.00441.4140.0040.0040.0000.0000.0000.000
52A462PRO00.0060.01741.6180.0000.0000.0000.0000.0000.000
53A463SER0-0.051-0.04540.155-0.003-0.0030.0000.0000.0000.000
54A464LEU00.0160.04737.7810.0040.0040.0000.0000.0000.000
55A465ASP-1-0.790-0.91138.2480.1020.1020.0000.0000.0000.000
56A466GLU-1-0.798-0.88337.6640.1180.1180.0000.0000.0000.000
57A467LEU0-0.032-0.02633.7500.0070.0070.0000.0000.0000.000
58A468ILE0-0.049-0.03533.8030.0120.0120.0000.0000.0000.000
59A469GLU-1-0.859-0.92333.0860.1420.1420.0000.0000.0000.000
60A470VAL0-0.0180.00831.9140.0090.0090.0000.0000.0000.000
61A471HIS10.7600.84327.907-0.179-0.1790.0000.0000.0000.000
62A472SER0-0.016-0.02228.2560.0180.0180.0000.0000.0000.000
63A473LEU00.0400.04129.2120.0100.0100.0000.0000.0000.000
64A474PHE0-0.022-0.02021.8700.0100.0100.0000.0000.0000.000
65A475LEU0-0.001-0.00923.9470.0220.0220.0000.0000.0000.000
66A476ASP-1-0.885-0.94724.5270.2000.2000.0000.0000.0000.000
67A477ARG10.8330.91324.421-0.182-0.1820.0000.0000.0000.000
68A478LEU00.0030.00719.2160.0200.0200.0000.0000.0000.000
69A479MET0-0.025-0.00220.1920.0280.0280.0000.0000.0000.000
70A480LYS10.8530.91921.228-0.195-0.1950.0000.0000.0000.000
71A481ARG10.7900.84617.547-0.337-0.3370.0000.0000.0000.000
72A482ARG10.8460.91912.647-0.567-0.5670.0000.0000.0000.000
73A483GLN0-0.038-0.03217.2350.0130.0130.0000.0000.0000.000
74A484GLU-1-0.848-0.88519.3080.2120.2120.0000.0000.0000.000
75A485SER00.0520.02014.0700.0280.0280.0000.0000.0000.000
76A486GLY0-0.027-0.00113.9860.0190.0190.0000.0000.0000.000
77A487TYR0-0.023-0.01911.404-0.007-0.0070.0000.0000.0000.000
78A488LEU0-0.058-0.0286.3660.0820.0820.0000.0000.0000.000
79A489ILE00.0140.00610.331-0.146-0.1460.0000.0000.0000.000
80A490GLU-1-0.778-0.85510.3671.0451.0450.0000.0000.0000.000
81A491GLU-1-0.945-0.97812.0650.1950.1950.0000.0000.0000.000
82A492ILE0-0.052-0.03314.824-0.018-0.0180.0000.0000.0000.000
83A493GLY00.022-0.00617.019-0.037-0.0370.0000.0000.0000.000
84A494ASP-1-0.787-0.86618.8890.2690.2690.0000.0000.0000.000
85A495VAL0-0.033-0.00920.404-0.027-0.0270.0000.0000.0000.000
86A496LEU0-0.034-0.02617.856-0.025-0.0250.0000.0000.0000.000
87A497LEU00.0510.02122.033-0.018-0.0180.0000.0000.0000.000
88A498ALA0-0.049-0.01124.563-0.022-0.0220.0000.0000.0000.000
89A499ARG10.7890.87925.504-0.234-0.2340.0000.0000.0000.000
90A500PHE0-0.0110.00123.135-0.010-0.0100.0000.0000.0000.000
91A501ASP-1-0.790-0.88727.0180.1480.1480.0000.0000.0000.000
92A502GLY0-0.0050.00928.777-0.003-0.0030.0000.0000.0000.000
93A503ALA0-0.034-0.03532.057-0.002-0.0020.0000.0000.0000.000
94A504GLU-1-0.826-0.92030.8730.1450.1450.0000.0000.0000.000
95A505GLY00.0190.03030.6400.0040.0040.0000.0000.0000.000
96A506SER0-0.013-0.01631.359-0.004-0.0040.0000.0000.0000.000
97A507TRP0-0.071-0.04134.654-0.010-0.0100.0000.0000.0000.000
98A508PHE00.0470.00929.304-0.001-0.0010.0000.0000.0000.000
99A509GLN00.0270.01333.0180.0030.0030.0000.0000.0000.000
100A510LYS10.9140.96434.125-0.094-0.0940.0000.0000.0000.000
101A511ILE0-0.053-0.02235.940-0.006-0.0060.0000.0000.0000.000
102A512SER00.004-0.02232.666-0.005-0.0050.0000.0000.0000.000
103A513SER00.0610.03135.107-0.002-0.0020.0000.0000.0000.000
104A514ARG10.8660.94537.144-0.097-0.0970.0000.0000.0000.000
105A515PHE0-0.026-0.01736.759-0.005-0.0050.0000.0000.0000.000
106A516CYS0-0.0050.00235.2670.0000.0000.0000.0000.0000.000
107A517SER00.003-0.01838.000-0.003-0.0030.0000.0000.0000.000
108A518ARG10.8750.95641.057-0.078-0.0780.0000.0000.0000.000
109A519GLN00.0160.02136.655-0.002-0.0020.0000.0000.0000.000
110A520SER00.007-0.04041.2990.0000.0000.0000.0000.0000.000
111A521PHE00.0250.01743.849-0.003-0.0030.0000.0000.0000.000
112A522ALA00.0380.01243.310-0.003-0.0030.0000.0000.0000.000
113A523LEU0-0.0040.00740.625-0.003-0.0030.0000.0000.0000.000
114A524GLU-1-0.955-0.97945.1330.0640.0640.0000.0000.0000.000
115A525GLN0-0.017-0.01548.522-0.004-0.0040.0000.0000.0000.000
116A526LEU0-0.022-0.00844.854-0.003-0.0030.0000.0000.0000.000
117A527LYS10.9960.99647.486-0.071-0.0710.0000.0000.0000.000
118A528ALA0-0.045-0.02549.668-0.003-0.0030.0000.0000.0000.000
119A529LYS10.8500.92952.318-0.059-0.0590.0000.0000.0000.000
120A530GLN0-0.022-0.00547.3260.0000.0000.0000.0000.0000.000
121A531ARG10.9030.94852.329-0.060-0.0600.0000.0000.0000.000
122A532LYS10.9230.96855.059-0.051-0.0510.0000.0000.0000.000
123A533ASP-1-0.816-0.90556.3280.0500.0500.0000.0000.0000.000
124A534PRO00.0530.02656.0150.0020.0020.0000.0000.0000.000
125A535ARG10.9080.95456.066-0.052-0.0520.0000.0000.0000.000
126A536PHE00.012-0.00849.0870.0020.0020.0000.0000.0000.000
127A537CYS0-0.025-0.00151.5460.0040.0040.0000.0000.0000.000
128A538ALA00.0440.02451.0850.0020.0020.0000.0000.0000.000
129A539PHE0-0.0030.00447.6420.0010.0010.0000.0000.0000.000
130A540VAL00.0250.01045.8880.0030.0030.0000.0000.0000.000
131A541GLN0-0.046-0.03946.4950.0020.0020.0000.0000.0000.000
132A542GLU-1-0.828-0.88046.7410.0720.0720.0000.0000.0000.000
133A543ALA00.0600.04044.5160.0020.0020.0000.0000.0000.000
134A544GLU-1-0.798-0.91242.1580.0920.0920.0000.0000.0000.000
135A545SER0-0.104-0.03841.7960.0030.0030.0000.0000.0000.000
136A546ARG10.8310.89941.806-0.075-0.0750.0000.0000.0000.000
137A547PRO00.0720.02537.8510.0050.0050.0000.0000.0000.000
138A548ARG10.7760.86136.100-0.106-0.1060.0000.0000.0000.000
139A549CYS0-0.0020.01735.8930.0070.0070.0000.0000.0000.000
140A550ARG10.8850.93728.598-0.158-0.1580.0000.0000.0000.000
141A551ARG10.9460.95434.119-0.096-0.0960.0000.0000.0000.000
142A552LEU00.0240.04532.703-0.001-0.0010.0000.0000.0000.000
143A553GLN0-0.039-0.03536.824-0.004-0.0040.0000.0000.0000.000
144A554LEU00.0350.02239.0590.0050.0050.0000.0000.0000.000
145A555LYS10.8160.87439.818-0.096-0.0960.0000.0000.0000.000
146A556ASP-1-0.833-0.90535.8370.1110.1110.0000.0000.0000.000
147A557MET0-0.047-0.01635.4510.0070.0070.0000.0000.0000.000
148A558ILE00.0590.04335.5390.0070.0070.0000.0000.0000.000
149A559PRO0-0.0030.00935.5100.0040.0040.0000.0000.0000.000
150A560THR0-0.041-0.03431.2630.0090.0090.0000.0000.0000.000
151A561GLU-1-0.755-0.82830.9520.1790.1790.0000.0000.0000.000
152A562MET00.0530.01631.1670.0100.0100.0000.0000.0000.000
153A563GLN0-0.040-0.03128.9180.0160.0160.0000.0000.0000.000
154A564ARG10.7920.91322.255-0.272-0.2720.0000.0000.0000.000
155A565LEU00.0560.02026.2250.0180.0180.0000.0000.0000.000
156A566THR0-0.042-0.01726.9720.0060.0060.0000.0000.0000.000
157A567LYS10.9110.94122.511-0.231-0.2310.0000.0000.0000.000
158A568TYR0-0.023-0.03821.6210.0220.0220.0000.0000.0000.000
159A569PRO00.0670.04621.0650.0310.0310.0000.0000.0000.000
160A570LEU0-0.028-0.01019.9630.0270.0270.0000.0000.0000.000
161A571LEU0-0.019-0.00917.1220.0390.0390.0000.0000.0000.000
162A572LEU00.034-0.00216.1020.0680.0680.0000.0000.0000.000
163A573GLN00.0170.00416.750-0.001-0.0010.0000.0000.0000.000
164A574SER0-0.042-0.01513.0890.0280.0280.0000.0000.0000.000
165A575ILE00.0150.01911.8890.1490.1490.0000.0000.0000.000
166A576GLY00.0560.03812.1870.0780.0780.0000.0000.0000.000
167A577GLN0-0.040-0.01512.2740.0560.0560.0000.0000.0000.000
168A578ASN0-0.108-0.0758.1010.0430.0430.0000.0000.0000.000
169A579THR0-0.043-0.0178.3250.3900.3900.0000.0000.0000.000
170A580GLU-1-0.811-0.8946.6651.6361.6360.0000.0000.0000.000
171A581GLU-1-0.785-0.8779.7880.0340.0340.0000.0000.0000.000
172A582PRO0-0.015-0.01012.6580.0410.0410.0000.0000.0000.000
173A583THR0-0.021-0.02816.1490.0100.0100.0000.0000.0000.000
174A584GLU-1-0.687-0.84614.2560.4670.4670.0000.0000.0000.000
175A585ARG10.8640.91013.703-0.208-0.2080.0000.0000.0000.000
176A586GLU-1-0.947-0.95915.9800.1340.1340.0000.0000.0000.000
177A587LYS10.8290.92518.427-0.303-0.3030.0000.0000.0000.000
178A588VAL0-0.006-0.01615.241-0.008-0.0080.0000.0000.0000.000
179A589GLU-1-0.906-0.94317.5280.2390.2390.0000.0000.0000.000
180A590LEU00.0380.02919.774-0.013-0.0130.0000.0000.0000.000
181A591ALA00.0270.01120.842-0.010-0.0100.0000.0000.0000.000
182A592ALA0-0.032-0.02919.808-0.008-0.0080.0000.0000.0000.000
183A593GLU-1-0.806-0.87321.9600.1600.1600.0000.0000.0000.000
184A594CYS00.0400.03424.940-0.011-0.0110.0000.0000.0000.000
185A595CYS0-0.100-0.04924.039-0.005-0.0050.0000.0000.0000.000
186A596ARG10.7710.85521.675-0.216-0.2160.0000.0000.0000.000
187A597GLU-1-0.874-0.93827.4430.1280.1280.0000.0000.0000.000
188A598ILE0-0.030-0.01328.530-0.010-0.0100.0000.0000.0000.000
189A599LEU0-0.039-0.02127.738-0.010-0.0100.0000.0000.0000.000
190A600HIS0-0.0050.00430.809-0.005-0.0050.0000.0000.0000.000
191A601HIS00.0030.00233.145-0.005-0.0050.0000.0000.0000.000
192A602VAL0-0.001-0.01533.048-0.007-0.0070.0000.0000.0000.000
193A603ASN0-0.049-0.04132.395-0.009-0.0090.0000.0000.0000.000
194A604GLN0-0.046-0.01336.195-0.005-0.0050.0000.0000.0000.000
195A605ALA00.0300.00638.950-0.006-0.0060.0000.0000.0000.000
196A606VAL0-0.016-0.00537.332-0.003-0.0030.0000.0000.0000.000
197A607ARG10.9240.97040.437-0.076-0.0760.0000.0000.0000.000
198A608ASP-1-0.831-0.90442.4490.0720.0720.0000.0000.0000.000
199A609MET0-0.065-0.02143.784-0.006-0.0060.0000.0000.0000.000
200A610GLU-1-0.873-0.91642.4890.0820.0820.0000.0000.0000.000
201A611ASP-1-0.849-0.92946.1120.0630.0630.0000.0000.0000.000
202A612LEU0-0.0010.01548.242-0.004-0.0040.0000.0000.0000.000
203A613LEU0-0.058-0.04547.624-0.003-0.0030.0000.0000.0000.000
204A614ARG10.9250.97148.042-0.065-0.0650.0000.0000.0000.000
205A615LEU00.011-0.00351.727-0.003-0.0030.0000.0000.0000.000
206A616LYS10.8960.93953.390-0.057-0.0570.0000.0000.0000.000
207A617ASP-1-0.812-0.88955.1040.0470.0470.0000.0000.0000.000
208A618TYR0-0.030-0.06254.566-0.002-0.0020.0000.0000.0000.000
209A619GLN00.0290.02358.258-0.002-0.0020.0000.0000.0000.000
210A620ARG10.7680.88359.342-0.046-0.0460.0000.0000.0000.000
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