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

tag_button

FMODB ID: LZL99

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2144283.95348
FMO2-HF: Nuclear repulsion 2067097.066033
FMO2-HF: Total energy -77186.887447
FMO2-MP2: Total energy -77409.892544


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.
-3.763-0.6972.096-2.021-3.143-0.001
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].
3A46PHE00.0520.0283.273-1.7160.2100.023-0.816-1.1340.000
4A47GLN0-0.0150.0082.2410.1030.4931.991-0.993-1.3880.000
5A48SER0-0.005-0.0334.8380.3670.444-0.001-0.011-0.0650.000
6A49LEU00.0890.0397.818-0.022-0.0220.0000.0000.0000.000
7A50GLU-1-0.757-0.8529.3980.2390.2390.0000.0000.0000.000
8A51GLN0-0.0180.0012.933-1.535-0.9000.084-0.198-0.522-0.001
9A52VAL00.0260.0187.3200.0440.0440.0000.0000.0000.000
10A53LYS10.7770.8828.607-0.122-0.1220.0000.0000.0000.000
11A54ARG10.8600.91610.346-0.334-0.3340.0000.0000.0000.000
12A55ARG10.7450.8496.811-0.189-0.1890.0000.0000.0000.000
13A56PRO00.0710.03710.1190.0230.0230.0000.0000.0000.000
14A57ALA00.0330.02211.1420.0030.0030.0000.0000.0000.000
15A58HIS00.0340.0016.192-0.110-0.1100.0000.0000.0000.000
16A59LEU0-0.015-0.0029.5330.0190.0190.0000.0000.0000.000
17A60MET00.0260.02012.034-0.013-0.0130.0000.0000.0000.000
18A61ALA00.0040.01711.545-0.017-0.0170.0000.0000.0000.000
19A62LEU0-0.026-0.01210.292-0.018-0.0180.0000.0000.0000.000
20A63LEU00.011-0.01412.836-0.030-0.0300.0000.0000.0000.000
21A64GLN00.0370.04316.312-0.014-0.0140.0000.0000.0000.000
22A65HIS0-0.015-0.02014.685-0.001-0.0010.0000.0000.0000.000
23A66VAL0-0.016-0.02815.005-0.019-0.0190.0000.0000.0000.000
24A67ALA0-0.053-0.02117.685-0.013-0.0130.0000.0000.0000.000
25A68LEU00.0310.02520.229-0.008-0.0080.0000.0000.0000.000
26A69GLN0-0.091-0.02218.502-0.007-0.0070.0000.0000.0000.000
27A70PHE0-0.081-0.05016.553-0.009-0.0090.0000.0000.0000.000
28A71GLU-1-0.782-0.87521.3250.0520.0520.0000.0000.0000.000
29A72PRO00.018-0.00320.4540.0020.0020.0000.0000.0000.000
30A73GLY00.0350.02620.9850.0020.0020.0000.0000.0000.000
31A74PRO00.029-0.00319.7360.0020.0020.0000.0000.0000.000
32A75LEU00.0340.02114.3050.0000.0000.0000.0000.0000.000
33A76LEU00.0070.00117.9310.0040.0040.0000.0000.0000.000
34A77CYS0-0.0350.01220.3750.0000.0000.0000.0000.0000.000
35A78CYS0-0.031-0.03117.272-0.001-0.0010.0000.0000.0000.000
36A79LEU0-0.022-0.00214.5590.0050.0050.0000.0000.0000.000
37A80HIS0-0.003-0.02218.393-0.001-0.0010.0000.0000.0000.000
38A81ALA00.0030.00620.885-0.002-0.0020.0000.0000.0000.000
39A82ASP-1-0.870-0.91616.9790.1310.1310.0000.0000.0000.000
40A83MET0-0.0170.00219.6260.0020.0020.0000.0000.0000.000
41A84LEU0-0.026-0.01521.754-0.004-0.0040.0000.0000.0000.000
42A85GLY0-0.034-0.00822.538-0.004-0.0040.0000.0000.0000.000
43A86SER0-0.086-0.03421.5630.0020.0020.0000.0000.0000.000
44A87LEU00.0060.01623.610-0.004-0.0040.0000.0000.0000.000
45A88GLY00.0300.01927.2450.0000.0000.0000.0000.0000.000
46A89PRO00.010-0.01830.535-0.001-0.0010.0000.0000.0000.000
47A90LYS10.9490.97432.800-0.033-0.0330.0000.0000.0000.000
48A91GLU-1-0.890-0.95130.4560.0490.0490.0000.0000.0000.000
49A92ALA00.0720.02628.9440.0000.0000.0000.0000.0000.000
50A93LYS10.8220.93830.177-0.036-0.0360.0000.0000.0000.000
51A94LYS10.9380.95433.381-0.036-0.0360.0000.0000.0000.000
52A95ALA00.0730.04028.354-0.001-0.0010.0000.0000.0000.000
53A96PHE00.0120.00528.8690.0010.0010.0000.0000.0000.000
54A97LEU0-0.020-0.00530.488-0.001-0.0010.0000.0000.0000.000
55A98ASP-1-0.874-0.92730.4980.0410.0410.0000.0000.0000.000
56A99PHE0-0.010-0.00223.9940.0000.0000.0000.0000.0000.000
57A100TYR0-0.014-0.01428.8220.0000.0000.0000.0000.0000.000
58A101HIS10.8070.86131.622-0.035-0.0350.0000.0000.0000.000
59A102SER0-0.0020.01128.314-0.001-0.0010.0000.0000.0000.000
60A103PHE00.009-0.00924.2740.0000.0000.0000.0000.0000.000
61A104LEU00.0040.01027.971-0.001-0.0010.0000.0000.0000.000
62A105GLU-1-0.789-0.86930.9150.0300.0300.0000.0000.0000.000
63A106LYS10.9240.94733.705-0.024-0.0240.0000.0000.0000.000
64A107THR00.022-0.00535.4190.0000.0000.0000.0000.0000.000
65A108ALA0-0.0340.01631.2650.0000.0000.0000.0000.0000.000
66A109VAL00.0930.04030.4990.0010.0010.0000.0000.0000.000
67A110LEU0-0.067-0.02425.2620.0020.0020.0000.0000.0000.000
68A111ARG10.8150.92026.894-0.033-0.0330.0000.0000.0000.000
69A112VAL0-0.0130.00223.8440.0010.0010.0000.0000.0000.000
70A113PRO0-0.059-0.03425.049-0.002-0.0020.0000.0000.0000.000
71A114VAL00.0220.00927.0610.0010.0010.0000.0000.0000.000
72A115PRO00.0190.01327.388-0.002-0.0020.0000.0000.0000.000
73A116PRO00.0270.00130.1340.0000.0000.0000.0000.0000.000
74A117ASN00.0150.00631.859-0.002-0.0020.0000.0000.0000.000
75A118VAL00.0680.03829.4420.0000.0000.0000.0000.0000.000
76A119ALA0-0.013-0.00432.8390.0000.0000.0000.0000.0000.000
77A120PHE0-0.008-0.00134.872-0.001-0.0010.0000.0000.0000.000
78A121GLU-1-0.872-0.94535.1080.0300.0300.0000.0000.0000.000
79A122LEU0-0.031-0.00232.2490.0000.0000.0000.0000.0000.000
80A123ASP-1-0.967-0.97136.8020.0270.0270.0000.0000.0000.000
81A124ARG10.7970.89139.866-0.025-0.0250.0000.0000.0000.000
82A125THR0-0.039-0.01938.215-0.001-0.0010.0000.0000.0000.000
83A126ARG10.8490.92439.957-0.024-0.0240.0000.0000.0000.000
84A127ALA00.0740.01238.5560.0010.0010.0000.0000.0000.000
85A128ASP-1-0.836-0.92238.7800.0270.0270.0000.0000.0000.000
86A129LEU0-0.033-0.00440.7330.0000.0000.0000.0000.0000.000
87A130ILE0-0.045-0.00534.4550.0010.0010.0000.0000.0000.000
88A131SER00.0620.04136.4130.0010.0010.0000.0000.0000.000
89A132GLU-1-0.876-0.96432.0440.0400.0400.0000.0000.0000.000
90A133ASP-1-0.876-0.91531.1850.0440.0440.0000.0000.0000.000
91A134VAL00.0530.01531.1810.0020.0020.0000.0000.0000.000
92A135GLN00.0250.01129.900-0.002-0.0020.0000.0000.0000.000
93A136ARG10.9370.96326.764-0.055-0.0550.0000.0000.0000.000
94A137ARG10.8610.92426.668-0.036-0.0360.0000.0000.0000.000
95A138PHE00.0510.01827.7700.0010.0010.0000.0000.0000.000
96A139VAL0-0.0050.00423.5760.0000.0000.0000.0000.0000.000
97A140GLN00.017-0.00321.1160.0020.0020.0000.0000.0000.000
98A141GLU-1-0.926-0.96323.2330.0380.0380.0000.0000.0000.000
99A142VAL0-0.021-0.00724.376-0.002-0.0020.0000.0000.0000.000
100A143VAL00.0310.01418.945-0.001-0.0010.0000.0000.0000.000
101A144GLN0-0.0050.00120.217-0.002-0.0020.0000.0000.0000.000
102A145SER0-0.039-0.03021.048-0.003-0.0030.0000.0000.0000.000
103A146GLN00.0150.00520.125-0.001-0.0010.0000.0000.0000.000
104A147GLN0-0.056-0.03415.552-0.001-0.0010.0000.0000.0000.000
105A148VAL00.0230.01816.503-0.004-0.0040.0000.0000.0000.000
106A149ALA0-0.026-0.01317.458-0.002-0.0020.0000.0000.0000.000
107A150VAL00.0690.03013.6790.0040.0040.0000.0000.0000.000
108A151GLY00.0100.00812.9080.0020.0020.0000.0000.0000.000
109A152ARG10.9590.96212.858-0.039-0.0390.0000.0000.0000.000
110A153GLN0-0.0070.01014.6150.0120.0120.0000.0000.0000.000
111A154LEU0-0.025-0.0118.5280.0270.0270.0000.0000.0000.000
112A155GLU-1-0.976-0.9849.7560.0610.0610.0000.0000.0000.000
113A156ASP-1-0.786-0.88411.3000.1440.1440.0000.0000.0000.000
114A157PHE00.0160.0088.5080.0030.0030.0000.0000.0000.000
115A158ARG10.8840.9295.6640.1200.1200.0000.0000.0000.000
116A159SER0-0.018-0.0108.7770.0130.0130.0000.0000.0000.000
117A160LYS10.8630.91011.950-0.123-0.1230.0000.0000.0000.000
118A161ARG10.8230.9004.956-1.653-1.615-0.001-0.003-0.0340.000
119A162LEU0-0.062-0.0268.765-0.027-0.0270.0000.0000.0000.000
120A163MET0-0.069-0.02611.764-0.060-0.0600.0000.0000.0000.000
121A164GLY00.0010.01514.037-0.026-0.0260.0000.0000.0000.000
122A165MET0-0.079-0.04915.122-0.023-0.0230.0000.0000.0000.000
123A166THR00.0290.02311.8670.0070.0070.0000.0000.0000.000
124A167PRO0-0.013-0.00714.742-0.002-0.0020.0000.0000.0000.000
125A168TRP0-0.027-0.03614.0040.0460.0460.0000.0000.0000.000
126A169GLU-1-0.746-0.8409.8570.6620.6620.0000.0000.0000.000
127A170GLN0-0.020-0.00712.373-0.019-0.0190.0000.0000.0000.000
128A171GLU-1-0.783-0.88514.1670.0740.0740.0000.0000.0000.000
129A172LEU0-0.031-0.0238.754-0.030-0.0300.0000.0000.0000.000
130A173ALA00.0390.0299.341-0.053-0.0530.0000.0000.0000.000
131A174GLN0-0.018-0.01711.083-0.091-0.0910.0000.0000.0000.000
132A175LEU0-0.040-0.02210.075-0.053-0.0530.0000.0000.0000.000
133A176GLU-1-0.942-0.9686.7280.0750.0750.0000.0000.0000.000
134A177ALA0-0.036-0.0069.421-0.099-0.0990.0000.0000.0000.000
135A178TRP0-0.037-0.03812.1590.0220.0220.0000.0000.0000.000
136A179VAL0-0.016-0.0038.4820.0440.0440.0000.0000.0000.000
137A180GLY0-0.006-0.00211.6320.0600.0600.0000.0000.0000.000
138A181ARG10.9620.96113.8840.0900.0900.0000.0000.0000.000
139A182ASP-1-0.819-0.90516.4200.0120.0120.0000.0000.0000.000
140A183ARG10.8440.9379.525-0.028-0.0280.0000.0000.0000.000
141A184ALA00.0440.02415.1110.0060.0060.0000.0000.0000.000
142A185SER0-0.0040.00017.807-0.003-0.0030.0000.0000.0000.000
143A186TYR0-0.040-0.0098.760-0.010-0.0100.0000.0000.0000.000
144A187GLU-1-0.788-0.90912.9400.1350.1350.0000.0000.0000.000
145A188ALA0-0.049-0.02114.6560.0120.0120.0000.0000.0000.000
146A189ARG10.9100.95914.7800.0580.0580.0000.0000.0000.000
147A190GLU-1-0.753-0.85210.1190.0870.0870.0000.0000.0000.000
148A191ARG10.8910.93113.744-0.058-0.0580.0000.0000.0000.000
149A192HIS00.0000.02016.8890.0030.0030.0000.0000.0000.000
150A193VAL00.009-0.00513.9720.0030.0030.0000.0000.0000.000
151A194ALA00.004-0.00114.9920.0090.0090.0000.0000.0000.000
152A195GLU-1-0.805-0.87516.5290.0500.0500.0000.0000.0000.000
153A196ARG10.8650.92218.793-0.068-0.0680.0000.0000.0000.000
154A197LEU0-0.040-0.02414.5280.0010.0010.0000.0000.0000.000
155A198LEU00.004-0.01119.0100.0000.0000.0000.0000.0000.000
156A199MET0-0.011-0.00420.973-0.005-0.0050.0000.0000.0000.000
157A200HIS00.0230.01121.6520.0050.0050.0000.0000.0000.000
158A201LEU0-0.018-0.01420.009-0.001-0.0010.0000.0000.0000.000
159A202GLU-1-0.971-0.98623.0490.0480.0480.0000.0000.0000.000
160A203GLU-1-0.920-0.96226.2540.0440.0440.0000.0000.0000.000
161A204MET0-0.089-0.04125.125-0.005-0.0050.0000.0000.0000.000
162A205GLN00.0780.05027.0020.0010.0010.0000.0000.0000.000
163A206HIS00.0260.00628.0030.0010.0010.0000.0000.0000.000
164A207THR0-0.090-0.06225.9160.0010.0010.0000.0000.0000.000
165A208ILE0-0.038-0.01123.9170.0030.0030.0000.0000.0000.000
166A209SER0-0.034-0.02726.010-0.001-0.0010.0000.0000.0000.000
167A210THR00.0150.00929.157-0.001-0.0010.0000.0000.0000.000
168A211ASP-1-0.905-0.95332.2060.0350.0350.0000.0000.0000.000
169A212GLU-1-0.886-0.95132.0130.0340.0340.0000.0000.0000.000
170A213GLU-1-0.940-0.96432.8250.0360.0360.0000.0000.0000.000
171A214LYS10.8670.91826.572-0.049-0.0490.0000.0000.0000.000
172A215SER0-0.011-0.01127.7600.0030.0030.0000.0000.0000.000
173A216ALA00.0380.02627.8930.0040.0040.0000.0000.0000.000
174A217ALA0-0.037-0.01428.9270.0020.0020.0000.0000.0000.000
175A218VAL0-0.016-0.01422.8030.0040.0040.0000.0000.0000.000
176A219VAL00.0500.02824.1320.0060.0060.0000.0000.0000.000
177A220ASN0-0.015-0.00325.0550.0020.0020.0000.0000.0000.000
178A221ALA0-0.020-0.00123.7520.0020.0020.0000.0000.0000.000
179A222ILE00.0200.00719.2110.0050.0050.0000.0000.0000.000
180A223GLY00.0200.01021.2720.0030.0030.0000.0000.0000.000
181A224LEU0-0.076-0.04223.4160.0000.0000.0000.0000.0000.000
182A225TYR00.015-0.01715.382-0.002-0.0020.0000.0000.0000.000
183A226MET00.0040.00115.2520.0050.0050.0000.0000.0000.000
184A227ARG10.9260.96319.712-0.057-0.0570.0000.0000.0000.000
185A228HIS0-0.031-0.01219.9020.0000.0000.0000.0000.0000.000
186A229LEU0-0.0250.00214.6130.0050.0050.0000.0000.0000.000
187A230GLY0-0.045-0.02618.174-0.001-0.0010.0000.0000.0000.000
188A231VAL0-0.082-0.03717.277-0.006-0.0060.0000.0000.0000.000
189A232ARG10.8630.91120.400-0.040-0.0400.0000.0000.0000.000
190A233THR00.0720.04723.5080.0000.0000.0000.0000.0000.000