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: 94YK2

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2151121.568148
FMO2-HF: Nuclear repulsion 2073934.354255
FMO2-HF: Total energy -77187.213893
FMO2-MP2: Total energy -77410.196981


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.
-4.286-0.3670.87-1.913-2.875-0.002
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 : 0.009 / q_NPA : -0.010
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].
3A46PHE00.0640.0373.452-1.8510.6040.001-1.139-1.3170.000
4A47GLN00.0010.0082.4080.0920.7780.751-0.558-0.878-0.001
5A48SER0-0.020-0.0365.0800.2860.357-0.001-0.005-0.0650.000
6A49LEU00.0810.0288.1370.0230.0230.0000.0000.0000.000
7A50GLU-1-0.750-0.8509.5410.3710.3710.0000.0000.0000.000
8A51GLN0-0.0030.0152.911-1.542-0.8810.120-0.208-0.573-0.001
9A52VAL00.0470.0247.3520.0280.0280.0000.0000.0000.000
10A53LYS10.7980.8828.797-0.257-0.2570.0000.0000.0000.000
11A54ARG10.8360.9149.665-0.506-0.5060.0000.0000.0000.000
12A55ARG10.7900.8837.185-0.299-0.2990.0000.0000.0000.000
13A56PRO00.0650.03710.293-0.013-0.0130.0000.0000.0000.000
14A57ALA00.0180.02011.1220.0010.0010.0000.0000.0000.000
15A58HIS00.028-0.0035.912-0.002-0.0020.0000.0000.0000.000
16A59LEU0-0.0200.0019.3920.0460.0460.0000.0000.0000.000
17A60MET00.0110.01511.897-0.002-0.0020.0000.0000.0000.000
18A61ALA00.0010.01411.268-0.009-0.0090.0000.0000.0000.000
19A62LEU0-0.020-0.00910.640-0.001-0.0010.0000.0000.0000.000
20A63LEU00.008-0.01513.000-0.021-0.0210.0000.0000.0000.000
21A64GLN00.0460.04016.487-0.013-0.0130.0000.0000.0000.000
22A65HIS0-0.022-0.02614.936-0.003-0.0030.0000.0000.0000.000
23A66VAL0-0.029-0.02815.171-0.014-0.0140.0000.0000.0000.000
24A67ALA0-0.022-0.01117.827-0.012-0.0120.0000.0000.0000.000
25A68LEU00.0400.03720.477-0.010-0.0100.0000.0000.0000.000
26A69GLN0-0.088-0.03618.3720.0010.0010.0000.0000.0000.000
27A70PHE0-0.053-0.02716.761-0.007-0.0070.0000.0000.0000.000
28A71GLU-1-0.774-0.87121.5380.0610.0610.0000.0000.0000.000
29A72PRO00.0250.01220.3430.0060.0060.0000.0000.0000.000
30A73GLY00.0330.02420.9540.0040.0040.0000.0000.0000.000
31A74PRO00.021-0.00319.9610.0030.0030.0000.0000.0000.000
32A75LEU00.0390.02914.5750.0040.0040.0000.0000.0000.000
33A76LEU0-0.010-0.00418.2830.0070.0070.0000.0000.0000.000
34A77CYS0-0.0160.01620.6880.0010.0010.0000.0000.0000.000
35A78CYS0-0.042-0.03217.5360.0000.0000.0000.0000.0000.000
36A79LEU0-0.016-0.00314.6050.0090.0090.0000.0000.0000.000
37A80HIS0-0.017-0.02418.520-0.002-0.0020.0000.0000.0000.000
38A81ALA00.0020.00221.126-0.003-0.0030.0000.0000.0000.000
39A82ASP-1-0.874-0.91717.0040.1960.1960.0000.0000.0000.000
40A83MET0-0.0110.00419.791-0.001-0.0010.0000.0000.0000.000
41A84LEU0-0.040-0.01821.861-0.005-0.0050.0000.0000.0000.000
42A85GLY0-0.034-0.01122.614-0.006-0.0060.0000.0000.0000.000
43A86SER0-0.101-0.05121.1110.0000.0000.0000.0000.0000.000
44A87LEU00.0130.02323.139-0.005-0.0050.0000.0000.0000.000
45A88GLY00.0380.01926.8390.0000.0000.0000.0000.0000.000
46A89PRO0-0.002-0.02230.226-0.002-0.0020.0000.0000.0000.000
47A90LYS10.9470.96632.670-0.042-0.0420.0000.0000.0000.000
48A91GLU-1-0.888-0.93329.9230.0640.0640.0000.0000.0000.000
49A92ALA00.0670.02328.984-0.001-0.0010.0000.0000.0000.000
50A93LYS10.7950.91430.335-0.049-0.0490.0000.0000.0000.000
51A94LYS10.9470.97333.549-0.045-0.0450.0000.0000.0000.000
52A95ALA00.0890.04428.511-0.001-0.0010.0000.0000.0000.000
53A96PHE00.0290.00629.1950.0020.0020.0000.0000.0000.000
54A97LEU0-0.013-0.00630.803-0.001-0.0010.0000.0000.0000.000
55A98ASP-1-0.882-0.93630.8370.0500.0500.0000.0000.0000.000
56A99PHE0-0.0020.00624.3320.0000.0000.0000.0000.0000.000
57A100TYR00.012-0.00429.0130.0000.0000.0000.0000.0000.000
58A101HIS10.8140.87431.819-0.044-0.0440.0000.0000.0000.000
59A102SER00.0010.01027.984-0.002-0.0020.0000.0000.0000.000
60A103PHE00.003-0.01124.4870.0010.0010.0000.0000.0000.000
61A104LEU0-0.010-0.00228.0710.0000.0000.0000.0000.0000.000
62A105GLU-1-0.779-0.86931.2670.0380.0380.0000.0000.0000.000
63A106LYS10.9090.94534.087-0.032-0.0320.0000.0000.0000.000
64A107THR00.017-0.00236.118-0.001-0.0010.0000.0000.0000.000
65A108ALA00.0020.02631.2300.0000.0000.0000.0000.0000.000
66A109VAL00.0580.02530.8570.0020.0020.0000.0000.0000.000
67A110LEU0-0.042-0.01625.4220.0020.0020.0000.0000.0000.000
68A111ARG10.7930.90527.036-0.042-0.0420.0000.0000.0000.000
69A112VAL00.0040.01224.1090.0010.0010.0000.0000.0000.000
70A113PRO0-0.047-0.03125.356-0.004-0.0040.0000.0000.0000.000
71A114VAL0-0.020-0.00627.5310.0020.0020.0000.0000.0000.000
72A115PRO00.0180.01427.555-0.003-0.0030.0000.0000.0000.000
73A116PRO00.0180.00230.266-0.001-0.0010.0000.0000.0000.000
74A117ASN0-0.023-0.01431.612-0.004-0.0040.0000.0000.0000.000
75A118VAL00.0670.03729.632-0.001-0.0010.0000.0000.0000.000
76A119ALA0-0.029-0.01333.025-0.001-0.0010.0000.0000.0000.000
77A120PHE0-0.005-0.00134.990-0.002-0.0020.0000.0000.0000.000
78A121GLU-1-0.853-0.93835.7330.0420.0420.0000.0000.0000.000
79A122LEU0-0.031-0.00532.494-0.001-0.0010.0000.0000.0000.000
80A123ASP-1-0.916-0.94237.0990.0340.0340.0000.0000.0000.000
81A124ARG10.7240.85540.184-0.034-0.0340.0000.0000.0000.000
82A125THR0-0.024-0.01238.689-0.001-0.0010.0000.0000.0000.000
83A126ARG10.8530.92139.856-0.030-0.0300.0000.0000.0000.000
84A127ALA00.0730.02138.6060.0010.0010.0000.0000.0000.000
85A128ASP-1-0.844-0.92338.5740.0360.0360.0000.0000.0000.000
86A129LEU0-0.022-0.00140.4090.0010.0010.0000.0000.0000.000
87A130ILE0-0.0350.00234.3460.0010.0010.0000.0000.0000.000
88A131SER00.005-0.00136.2860.0020.0020.0000.0000.0000.000
89A132GLU-1-0.854-0.95031.9390.0540.0540.0000.0000.0000.000
90A133ASP-1-0.841-0.87931.0800.0600.0600.0000.0000.0000.000
91A134VAL00.0600.02631.1670.0030.0030.0000.0000.0000.000
92A135GLN00.0190.00830.497-0.002-0.0020.0000.0000.0000.000
93A136ARG10.9440.97126.478-0.077-0.0770.0000.0000.0000.000
94A137ARG10.8280.88826.872-0.050-0.0500.0000.0000.0000.000
95A138PHE00.0450.01127.8310.0020.0020.0000.0000.0000.000
96A139VAL0-0.0060.00523.7580.0010.0010.0000.0000.0000.000
97A140GLN00.0100.00221.1910.0050.0050.0000.0000.0000.000
98A141GLU-1-0.876-0.93923.5010.0560.0560.0000.0000.0000.000
99A142VAL0-0.0120.00324.343-0.001-0.0010.0000.0000.0000.000
100A143VAL00.0450.02118.9430.0010.0010.0000.0000.0000.000
101A144GLN0-0.013-0.00120.3660.0000.0000.0000.0000.0000.000
102A145SER0-0.011-0.01421.167-0.002-0.0020.0000.0000.0000.000
103A146GLN00.0250.00220.369-0.001-0.0010.0000.0000.0000.000
104A147GLN0-0.036-0.02515.6990.0080.0080.0000.0000.0000.000
105A148VAL00.0220.01516.782-0.001-0.0010.0000.0000.0000.000
106A149ALA0-0.036-0.00118.801-0.002-0.0020.0000.0000.0000.000
107A150VAL00.0540.01213.8040.0040.0040.0000.0000.0000.000
108A151GLY00.0150.00812.9210.0100.0100.0000.0000.0000.000
109A152ARG10.9160.93512.874-0.063-0.0630.0000.0000.0000.000
110A153GLN0-0.0110.00414.8140.0150.0150.0000.0000.0000.000
111A154LEU0-0.017-0.0098.5370.0290.0290.0000.0000.0000.000
112A155GLU-1-0.885-0.91810.0490.1300.1300.0000.0000.0000.000
113A156ASP-1-0.797-0.87011.8440.1740.1740.0000.0000.0000.000
114A157PHE00.0200.0138.5180.0010.0010.0000.0000.0000.000
115A158ARG10.8070.8796.160-0.021-0.0210.0000.0000.0000.000
116A159SER0-0.022-0.0258.9420.0140.0140.0000.0000.0000.000
117A160LYS10.8120.88712.215-0.158-0.1580.0000.0000.0000.000
118A161ARG10.7760.8634.980-1.105-1.059-0.001-0.003-0.0420.000
119A162LEU0-0.063-0.0328.713-0.066-0.0660.0000.0000.0000.000
120A163MET0-0.061-0.02011.600-0.081-0.0810.0000.0000.0000.000
121A164GLY00.0000.00813.613-0.033-0.0330.0000.0000.0000.000
122A165MET0-0.082-0.03814.944-0.025-0.0250.0000.0000.0000.000
123A166THR00.0370.01311.6270.0020.0020.0000.0000.0000.000
124A167PRO0-0.0160.00414.455-0.021-0.0210.0000.0000.0000.000
125A168TRP0-0.017-0.03913.7370.0270.0270.0000.0000.0000.000
126A169GLU-1-0.760-0.8519.9010.4080.4080.0000.0000.0000.000
127A170GLN0-0.037-0.02511.964-0.043-0.0430.0000.0000.0000.000
128A171GLU-1-0.750-0.85913.726-0.027-0.0270.0000.0000.0000.000
129A172LEU0-0.033-0.0168.521-0.051-0.0510.0000.0000.0000.000
130A173ALA00.0480.0299.032-0.145-0.1450.0000.0000.0000.000
131A174GLN0-0.040-0.02710.481-0.088-0.0880.0000.0000.0000.000
132A175LEU0-0.018-0.0159.983-0.029-0.0290.0000.0000.0000.000
133A176GLU-1-0.870-0.9135.802-0.310-0.3100.0000.0000.0000.000
134A177ALA0-0.0160.0058.818-0.075-0.0750.0000.0000.0000.000
135A178TRP00.005-0.01611.8100.0620.0620.0000.0000.0000.000
136A179VAL0-0.035-0.0158.2060.0740.0740.0000.0000.0000.000
137A180GLY00.0030.00911.4270.0860.0860.0000.0000.0000.000
138A181ARG10.9320.94413.9060.1120.1120.0000.0000.0000.000
139A182ASP-1-0.753-0.84915.5590.0140.0140.0000.0000.0000.000
140A183ARG10.7940.9099.438-0.076-0.0760.0000.0000.0000.000
141A184ALA00.0180.01414.6250.0040.0040.0000.0000.0000.000
142A185SER0-0.015-0.04417.734-0.009-0.0090.0000.0000.0000.000
143A186TYR0-0.078-0.0309.144-0.011-0.0110.0000.0000.0000.000
144A187GLU-1-0.758-0.88412.4660.1880.1880.0000.0000.0000.000
145A188ALA0-0.032-0.00614.7150.0100.0100.0000.0000.0000.000
146A189ARG10.8690.93714.8350.1140.1140.0000.0000.0000.000
147A190GLU-1-0.727-0.86210.6670.0530.0530.0000.0000.0000.000
148A191ARG10.8350.91313.888-0.077-0.0770.0000.0000.0000.000
149A192HIS00.0090.01417.1560.0080.0080.0000.0000.0000.000
150A193VAL0-0.008-0.01113.9010.0030.0030.0000.0000.0000.000
151A194ALA00.0120.00215.1160.0100.0100.0000.0000.0000.000
152A195GLU-1-0.794-0.87116.7150.0370.0370.0000.0000.0000.000
153A196ARG10.8580.92018.611-0.008-0.0080.0000.0000.0000.000
154A197LEU0-0.050-0.02814.3230.0020.0020.0000.0000.0000.000
155A198LEU00.005-0.01118.7780.0060.0060.0000.0000.0000.000
156A199MET00.0000.00520.799-0.002-0.0020.0000.0000.0000.000
157A200HIS00.0390.02021.5810.0050.0050.0000.0000.0000.000
158A201LEU0-0.034-0.01919.6650.0020.0020.0000.0000.0000.000
159A202GLU-1-0.967-0.98322.7910.0430.0430.0000.0000.0000.000
160A203GLU-1-0.920-0.97226.0120.0260.0260.0000.0000.0000.000
161A204MET0-0.072-0.03924.516-0.003-0.0030.0000.0000.0000.000
162A205GLN00.0540.05026.4840.0030.0030.0000.0000.0000.000
163A206HIS00.0340.01127.4750.0030.0030.0000.0000.0000.000
164A207THR0-0.096-0.07425.5070.0020.0020.0000.0000.0000.000
165A208ILE0-0.030-0.00723.7950.0040.0040.0000.0000.0000.000
166A209SER0-0.079-0.05226.1520.0010.0010.0000.0000.0000.000
167A210THR00.0100.00329.678-0.002-0.0020.0000.0000.0000.000
168A211ASP-1-0.874-0.91832.7530.0380.0380.0000.0000.0000.000
169A212GLU-1-0.860-0.93832.2920.0340.0340.0000.0000.0000.000
170A213GLU-1-0.947-0.96432.7470.0400.0400.0000.0000.0000.000
171A214LYS10.8660.89927.009-0.055-0.0550.0000.0000.0000.000
172A215SER0-0.013-0.00828.0770.0040.0040.0000.0000.0000.000
173A216ALA00.0480.03027.8820.0040.0040.0000.0000.0000.000
174A217ALA0-0.0230.00028.9790.0020.0020.0000.0000.0000.000
175A218VAL0-0.020-0.01622.9580.0050.0050.0000.0000.0000.000
176A219VAL00.0390.02324.0920.0060.0060.0000.0000.0000.000
177A220ASN0-0.054-0.03324.8860.0010.0010.0000.0000.0000.000
178A221ALA0-0.020-0.00123.8960.0030.0030.0000.0000.0000.000
179A222ILE00.0260.00918.9300.0080.0080.0000.0000.0000.000
180A223GLY00.0340.01821.0580.0040.0040.0000.0000.0000.000
181A224LEU0-0.051-0.02423.293-0.001-0.0010.0000.0000.0000.000
182A225TYR00.002-0.01815.267-0.002-0.0020.0000.0000.0000.000
183A226MET0-0.007-0.00715.1380.0080.0080.0000.0000.0000.000
184A227ARG10.9250.95519.582-0.060-0.0600.0000.0000.0000.000
185A228HIS0-0.041-0.01419.4900.0000.0000.0000.0000.0000.000
186A229LEU0-0.0130.00414.6730.0060.0060.0000.0000.0000.000
187A230GLY0-0.035-0.01318.215-0.002-0.0020.0000.0000.0000.000
188A231VAL0-0.085-0.03317.370-0.011-0.0110.0000.0000.0000.000
189A232ARG10.8590.89620.418-0.023-0.0230.0000.0000.0000.000
190A233THR00.0690.04023.1670.0040.0040.0000.0000.0000.000