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: 39N8L

Calculation Name: 1IAP-A-Xray372

Preferred Name: Rho guanine nucleotide exchange factor 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1IAP

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2142653.991661
FMO2-HF: Nuclear repulsion 2065468.00998
FMO2-HF: Total energy -77185.981681
FMO2-MP2: Total energy -77408.976988


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:44:SER)


Summations of interaction energy for fragment #1(A:44:SER)
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.
-6.849-3.3962.422-2.247-3.625-0.002
Interaction energy analysis for fragmet #1(A:44:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.000
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].
3A46PHE00.0540.0293.281-2.311-0.4590.021-0.787-1.0870.000
4A47GLN0-0.0400.0002.260-0.568-0.0232.124-1.063-1.604-0.002
5A48SER00.001-0.0134.8150.1480.227-0.001-0.012-0.0660.000
6A49LEU00.0880.0407.8250.1340.1340.0000.0000.0000.000
7A50GLU-1-0.833-0.9299.4210.4040.4040.0000.0000.0000.000
8A51GLN0-0.036-0.0212.457-2.514-1.5850.279-0.377-0.8300.000
9A52VAL00.0300.0217.3920.1820.1820.0000.0000.0000.000
10A53LYS10.7990.9028.607-0.357-0.3570.0000.0000.0000.000
11A54ARG10.9210.97010.347-0.599-0.5990.0000.0000.0000.000
12A55ARG10.7430.8546.952-0.933-0.9330.0000.0000.0000.000
13A56PRO00.0740.04710.2290.0530.0530.0000.0000.0000.000
14A57ALA00.0520.02711.277-0.025-0.0250.0000.0000.0000.000
15A58HIS00.0250.0006.319-0.220-0.2200.0000.0000.0000.000
16A59LEU0-0.004-0.0049.688-0.037-0.0370.0000.0000.0000.000
17A60MET00.0310.02412.177-0.074-0.0740.0000.0000.0000.000
18A61ALA00.0090.02111.541-0.062-0.0620.0000.0000.0000.000
19A62LEU0-0.027-0.01610.375-0.059-0.0590.0000.0000.0000.000
20A63LEU00.006-0.01512.840-0.082-0.0820.0000.0000.0000.000
21A64GLN00.0470.04816.315-0.036-0.0360.0000.0000.0000.000
22A65HIS0-0.032-0.02514.560-0.019-0.0190.0000.0000.0000.000
23A66VAL0-0.002-0.02215.012-0.045-0.0450.0000.0000.0000.000
24A67ALA0-0.056-0.02417.686-0.035-0.0350.0000.0000.0000.000
25A68LEU00.0210.01620.233-0.022-0.0220.0000.0000.0000.000
26A69GLN0-0.078-0.01718.550-0.022-0.0220.0000.0000.0000.000
27A70PHE0-0.077-0.04416.586-0.021-0.0210.0000.0000.0000.000
28A71GLU-1-0.875-0.93221.3240.1460.1460.0000.0000.0000.000
29A72PRO00.006-0.01020.4470.0090.0090.0000.0000.0000.000
30A73GLY00.0400.02420.9770.0110.0110.0000.0000.0000.000
31A74PRO00.0240.00019.7650.0060.0060.0000.0000.0000.000
32A75LEU00.0280.01314.1520.0020.0020.0000.0000.0000.000
33A76LEU00.007-0.00117.9200.0160.0160.0000.0000.0000.000
34A77CYS0-0.0240.02020.365-0.005-0.0050.0000.0000.0000.000
35A78CYS0-0.021-0.02317.252-0.010-0.0100.0000.0000.0000.000
36A79LEU0-0.030-0.00514.7130.0060.0060.0000.0000.0000.000
37A80HIS00.001-0.02218.393-0.016-0.0160.0000.0000.0000.000
38A81ALA00.0090.00820.950-0.014-0.0140.0000.0000.0000.000
39A82ASP-1-0.885-0.91816.9560.2800.2800.0000.0000.0000.000
40A83MET0-0.0110.01219.689-0.005-0.0050.0000.0000.0000.000
41A84LEU0-0.028-0.02421.787-0.016-0.0160.0000.0000.0000.000
42A85GLY0-0.034-0.00522.608-0.015-0.0150.0000.0000.0000.000
43A86SER0-0.077-0.02721.356-0.003-0.0030.0000.0000.0000.000
44A87LEU00.0100.01523.445-0.006-0.0060.0000.0000.0000.000
45A88GLY00.0260.01827.079-0.006-0.0060.0000.0000.0000.000
46A89PRO00.023-0.00730.3640.0030.0030.0000.0000.0000.000
47A90LYS10.9650.98232.819-0.069-0.0690.0000.0000.0000.000
48A91GLU-1-0.932-0.97630.4670.1100.1100.0000.0000.0000.000
49A92ALA00.0690.02729.0220.0030.0030.0000.0000.0000.000
50A93LYS10.8490.95030.246-0.073-0.0730.0000.0000.0000.000
51A94LYS10.9270.94533.446-0.084-0.0840.0000.0000.0000.000
52A95ALA00.0790.04528.3500.0000.0000.0000.0000.0000.000
53A96PHE00.0090.00528.9610.0040.0040.0000.0000.0000.000
54A97LEU0-0.027-0.01030.543-0.002-0.0020.0000.0000.0000.000
55A98ASP-1-0.885-0.93130.3760.1110.1110.0000.0000.0000.000
56A99PHE0-0.014-0.01323.9130.0010.0010.0000.0000.0000.000
57A100TYR0-0.020-0.01828.8220.0010.0010.0000.0000.0000.000
58A101HIS10.8420.89631.622-0.089-0.0890.0000.0000.0000.000
59A102SER00.0120.02528.215-0.001-0.0010.0000.0000.0000.000
60A103PHE00.004-0.00624.2920.0030.0030.0000.0000.0000.000
61A104LEU0-0.017-0.00327.752-0.004-0.0040.0000.0000.0000.000
62A105GLU-1-0.834-0.91230.8990.0730.0730.0000.0000.0000.000
63A106LYS10.9180.94433.693-0.058-0.0580.0000.0000.0000.000
64A107THR00.005-0.01535.407-0.001-0.0010.0000.0000.0000.000
65A108ALA0-0.0300.01931.1910.0010.0010.0000.0000.0000.000
66A109VAL00.0800.03930.6030.0020.0020.0000.0000.0000.000
67A110LEU0-0.061-0.02225.2260.0060.0060.0000.0000.0000.000
68A111ARG10.8600.95026.884-0.080-0.0800.0000.0000.0000.000
69A112VAL0-0.0110.00323.8690.0030.0030.0000.0000.0000.000
70A113PRO0-0.060-0.04025.070-0.009-0.0090.0000.0000.0000.000
71A114VAL00.0280.01227.0430.0020.0020.0000.0000.0000.000
72A115PRO00.0020.00727.515-0.007-0.0070.0000.0000.0000.000
73A116PRO00.0340.00230.1380.0000.0000.0000.0000.0000.000
74A117ASN00.0180.00632.188-0.004-0.0040.0000.0000.0000.000
75A118VAL00.0850.04929.486-0.001-0.0010.0000.0000.0000.000
76A119ALA0-0.015-0.00832.8580.0000.0000.0000.0000.0000.000
77A120PHE0-0.0080.00334.888-0.002-0.0020.0000.0000.0000.000
78A121GLU-1-0.891-0.96134.7570.0500.0500.0000.0000.0000.000
79A122LEU0-0.0260.00032.3320.0000.0000.0000.0000.0000.000
80A123ASP-1-0.950-0.96236.8310.0600.0600.0000.0000.0000.000
81A124ARG10.8040.89939.891-0.048-0.0480.0000.0000.0000.000
82A125THR0-0.035-0.01938.220-0.003-0.0030.0000.0000.0000.000
83A126ARG10.9450.98439.996-0.046-0.0460.0000.0000.0000.000
84A127ALA00.0670.00738.6090.0010.0010.0000.0000.0000.000
85A128ASP-1-0.912-0.97038.8340.0560.0560.0000.0000.0000.000
86A129LEU0-0.046-0.00640.790-0.001-0.0010.0000.0000.0000.000
87A130ILE0-0.047-0.00734.500-0.001-0.0010.0000.0000.0000.000
88A131SER00.0680.03936.4000.0020.0020.0000.0000.0000.000
89A132GLU-1-0.904-0.97232.1800.0680.0680.0000.0000.0000.000
90A133ASP-1-0.906-0.95631.2420.0600.0600.0000.0000.0000.000
91A134VAL00.0460.01031.2290.0020.0020.0000.0000.0000.000
92A135GLN00.0230.01429.456-0.002-0.0020.0000.0000.0000.000
93A136ARG10.9430.96427.043-0.082-0.0820.0000.0000.0000.000
94A137ARG10.9050.96626.712-0.044-0.0440.0000.0000.0000.000
95A138PHE00.0700.03227.8020.0030.0030.0000.0000.0000.000
96A139VAL0-0.013-0.00123.5900.0040.0040.0000.0000.0000.000
97A140GLN00.0230.00121.6030.0150.0150.0000.0000.0000.000
98A141GLU-1-0.951-0.97523.2580.0640.0640.0000.0000.0000.000
99A142VAL0-0.0070.00224.347-0.001-0.0010.0000.0000.0000.000
100A143VAL00.0260.01219.0350.0060.0060.0000.0000.0000.000
101A144GLN0-0.021-0.01220.2310.0050.0050.0000.0000.0000.000
102A145SER0-0.047-0.03921.048-0.003-0.0030.0000.0000.0000.000
103A146GLN00.0150.00320.0480.0070.0070.0000.0000.0000.000
104A147GLN0-0.037-0.01815.2390.0100.0100.0000.0000.0000.000
105A148VAL00.0350.02816.4830.0050.0050.0000.0000.0000.000
106A149ALA0-0.038-0.02017.4420.0020.0020.0000.0000.0000.000
107A150VAL00.0580.02913.6730.0140.0140.0000.0000.0000.000
108A151GLY00.0140.00512.8900.0330.0330.0000.0000.0000.000
109A152ARG10.9610.96312.844-0.104-0.1040.0000.0000.0000.000
110A153GLN00.0060.01514.6080.0310.0310.0000.0000.0000.000
111A154LEU0-0.019-0.0098.4340.0580.0580.0000.0000.0000.000
112A155GLU-1-0.983-0.9819.7520.1500.1500.0000.0000.0000.000
113A156ASP-1-0.821-0.92511.2940.2880.2880.0000.0000.0000.000
114A157PHE00.0050.0058.5470.0030.0030.0000.0000.0000.000
115A158ARG10.8930.9275.555-0.091-0.0910.0000.0000.0000.000
116A159SER00.0050.0068.784-0.010-0.0100.0000.0000.0000.000
117A160LYS10.9010.94311.958-0.270-0.2700.0000.0000.0000.000
118A161ARG10.8380.9124.750-2.812-2.764-0.001-0.008-0.0380.000
119A162LEU0-0.065-0.0268.637-0.028-0.0280.0000.0000.0000.000
120A163MET0-0.058-0.02011.785-0.082-0.0820.0000.0000.0000.000
121A164GLY00.0060.01814.060-0.037-0.0370.0000.0000.0000.000
122A165MET0-0.087-0.05215.150-0.033-0.0330.0000.0000.0000.000
123A166THR00.0160.01511.9690.0150.0150.0000.0000.0000.000
124A167PRO0-0.015-0.00914.7600.0010.0010.0000.0000.0000.000
125A168TRP0-0.036-0.04014.0040.0910.0910.0000.0000.0000.000
126A169GLU-1-0.751-0.8509.8201.3021.3020.0000.0000.0000.000
127A170GLN0-0.030-0.00912.417-0.004-0.0040.0000.0000.0000.000
128A171GLU-1-0.793-0.91114.3070.3710.3710.0000.0000.0000.000
129A172LEU0-0.042-0.0298.5980.0270.0270.0000.0000.0000.000
130A173ALA00.0410.0309.4610.0530.0530.0000.0000.0000.000
131A174GLN0-0.008-0.01711.191-0.081-0.0810.0000.0000.0000.000
132A175LEU0-0.036-0.02210.139-0.091-0.0910.0000.0000.0000.000
133A176GLU-1-0.966-0.9697.2240.5830.5830.0000.0000.0000.000
134A177ALA0-0.043-0.0119.484-0.178-0.1780.0000.0000.0000.000
135A178TRP0-0.069-0.04712.217-0.059-0.0590.0000.0000.0000.000
136A179VAL0-0.023-0.0058.5010.0260.0260.0000.0000.0000.000
137A180GLY0-0.007-0.00511.6540.0200.0200.0000.0000.0000.000
138A181ARG10.9580.95914.0610.0860.0860.0000.0000.0000.000
139A182ASP-1-0.861-0.92416.5420.0750.0750.0000.0000.0000.000
140A183ARG10.9810.9968.470-0.384-0.3840.0000.0000.0000.000
141A184ALA00.0800.04915.1750.0480.0480.0000.0000.0000.000
142A185SER0-0.037-0.01917.6360.0200.0200.0000.0000.0000.000
143A186TYR0-0.026-0.0098.226-0.015-0.0150.0000.0000.0000.000
144A187GLU-1-0.901-0.96913.5630.3540.3540.0000.0000.0000.000
145A188ALA0-0.059-0.03014.7280.0260.0260.0000.0000.0000.000
146A189ARG10.9450.97714.928-0.150-0.1500.0000.0000.0000.000
147A190GLU-1-0.786-0.8669.8560.7880.7880.0000.0000.0000.000
148A191ARG10.9330.96013.859-0.259-0.2590.0000.0000.0000.000
149A192HIS00.0090.02617.009-0.012-0.0120.0000.0000.0000.000
150A193VAL00.009-0.00314.087-0.010-0.0100.0000.0000.0000.000
151A194ALA00.001-0.00715.1400.0010.0010.0000.0000.0000.000
152A195GLU-1-0.850-0.92416.6750.2160.2160.0000.0000.0000.000
153A196ARG10.8990.96319.546-0.289-0.2890.0000.0000.0000.000
154A197LEU0-0.042-0.02914.744-0.009-0.0090.0000.0000.0000.000
155A198LEU00.000-0.00719.168-0.009-0.0090.0000.0000.0000.000
156A199MET0-0.002-0.00221.128-0.019-0.0190.0000.0000.0000.000
157A200HIS00.0230.00821.744-0.001-0.0010.0000.0000.0000.000
158A201LEU0-0.011-0.00820.137-0.010-0.0100.0000.0000.0000.000
159A202GLU-1-0.968-0.98523.1810.1580.1580.0000.0000.0000.000
160A203GLU-1-0.946-0.97026.4120.1580.1580.0000.0000.0000.000
161A204MET0-0.080-0.03525.158-0.017-0.0170.0000.0000.0000.000
162A205GLN00.0710.05027.002-0.003-0.0030.0000.0000.0000.000
163A206HIS00.0340.00728.0320.0030.0030.0000.0000.0000.000
164A207THR0-0.090-0.06325.9310.0000.0000.0000.0000.0000.000
165A208ILE0-0.038-0.00724.0780.0050.0050.0000.0000.0000.000
166A209SER0-0.053-0.05026.015-0.003-0.0030.0000.0000.0000.000
167A210THR00.0120.01929.161-0.001-0.0010.0000.0000.0000.000
168A211ASP-1-0.890-0.94232.1040.1040.1040.0000.0000.0000.000
169A212GLU-1-0.877-0.95432.0150.1050.1050.0000.0000.0000.000
170A213GLU-1-0.932-0.95732.8270.1040.1040.0000.0000.0000.000
171A214LYS10.9230.96025.914-0.150-0.1500.0000.0000.0000.000
172A215SER0-0.024-0.02027.7620.0090.0090.0000.0000.0000.000
173A216ALA00.0400.02727.8950.0130.0130.0000.0000.0000.000
174A217ALA0-0.021-0.00628.8660.0080.0080.0000.0000.0000.000
175A218VAL0-0.014-0.01322.8380.0110.0110.0000.0000.0000.000
176A219VAL00.0490.02824.1320.0190.0190.0000.0000.0000.000
177A220ASN0-0.0090.00125.1970.0130.0130.0000.0000.0000.000
178A221ALA0-0.026-0.00723.6660.0050.0050.0000.0000.0000.000
179A222ILE00.0250.01019.4620.0160.0160.0000.0000.0000.000
180A223GLY00.0250.01221.4050.0150.0150.0000.0000.0000.000
181A224LEU0-0.077-0.04323.5450.0010.0010.0000.0000.0000.000
182A225TYR00.010-0.02315.306-0.013-0.0130.0000.0000.0000.000
183A226MET00.0140.00515.3110.0240.0240.0000.0000.0000.000
184A227ARG10.9520.99019.837-0.180-0.1800.0000.0000.0000.000
185A228HIS0-0.032-0.01519.2550.0050.0050.0000.0000.0000.000
186A229LEU0-0.031-0.00514.8450.0100.0100.0000.0000.0000.000
187A230GLY0-0.051-0.03018.2730.0110.0110.0000.0000.0000.000
188A231VAL0-0.064-0.02917.405-0.008-0.0080.0000.0000.0000.000
189A232ARG10.8920.94920.523-0.195-0.1950.0000.0000.0000.000
190A233THR00.0540.02923.6440.0030.0030.0000.0000.0000.000