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: YV632

Calculation Name: 2RAE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RAE

Chain ID: A

ChEMBL ID:

UniProt ID: Q0S3N9

Base Structure: X-ray

Registration Date: 2023-09-20

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2009928.934889
FMO2-HF: Nuclear repulsion 1935499.667507
FMO2-HF: Total energy -74429.267382
FMO2-MP2: Total energy -74647.317642


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:11:ILE)


Summations of interaction energy for fragment #1(A:11:ILE)
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.
-24.552-12.57810.266-8.145-14.1-0.045
Interaction energy analysis for fragmet #1(A:11:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / 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].
3A13ARG10.9500.9802.055-5.193-2.7943.026-2.302-3.1230.006
4A14ARG10.7960.8833.506-2.960-2.7060.0270.115-0.3960.000
5A15PRO00.020-0.0036.5850.0590.0590.0000.0000.0000.000
6A16SER00.0020.0139.6130.1200.1200.0000.0000.0000.000
7A17THR00.022-0.0099.813-0.400-0.4000.0000.0000.0000.000
8A18THR0-0.025-0.03312.227-0.008-0.0080.0000.0000.0000.000
9A19GLN00.0000.00812.427-0.191-0.1910.0000.0000.0000.000
10A20ASP-1-0.737-0.8638.6802.2472.2470.0000.0000.0000.000
11A21ARG10.8550.93710.674-0.631-0.6310.0000.0000.0000.000
12A22ILE0-0.024-0.00913.035-0.101-0.1010.0000.0000.0000.000
13A23SER0-0.050-0.02910.4730.0050.0050.0000.0000.0000.000
14A24THR00.000-0.0119.572-0.034-0.0340.0000.0000.0000.000
15A25VAL00.002-0.00311.359-0.130-0.1300.0000.0000.0000.000
16A26GLY00.0060.00014.837-0.079-0.0790.0000.0000.0000.000
17A27ILE0-0.025-0.0079.378-0.065-0.0650.0000.0000.0000.000
18A28GLU-1-0.807-0.86713.5530.0810.0810.0000.0000.0000.000
19A29LEU0-0.014-0.00915.445-0.050-0.0500.0000.0000.0000.000
20A30PHE0-0.047-0.04215.250-0.024-0.0240.0000.0000.0000.000
21A31THR0-0.030-0.01815.052-0.052-0.0520.0000.0000.0000.000
22A32GLU-1-0.954-0.97817.5850.0300.0300.0000.0000.0000.000
23A33GLN0-0.100-0.05820.606-0.016-0.0160.0000.0000.0000.000
24A34GLY00.0300.03120.927-0.011-0.0110.0000.0000.0000.000
25A35PHE00.011-0.01017.8020.0220.0220.0000.0000.0000.000
26A36ASP-1-0.926-0.97020.2770.0850.0850.0000.0000.0000.000
27A37ALA0-0.028-0.01623.8060.0070.0070.0000.0000.0000.000
28A38THR00.0300.05220.3860.0060.0060.0000.0000.0000.000
29A39SER0-0.072-0.07223.0650.0140.0140.0000.0000.0000.000
30A40VAL00.017-0.02621.3410.0170.0170.0000.0000.0000.000
31A41ASP-1-0.825-0.90422.5550.2200.2200.0000.0000.0000.000
32A42GLU-1-0.695-0.79423.3730.1650.1650.0000.0000.0000.000
33A43VAL00.0270.02817.5780.0160.0160.0000.0000.0000.000
34A44ALA0-0.064-0.01920.0250.0420.0420.0000.0000.0000.000
35A45GLU-1-0.911-0.96522.2450.1990.1990.0000.0000.0000.000
36A46ALA00.0150.01620.1920.0040.0040.0000.0000.0000.000
37A47SER0-0.037-0.02918.3260.0570.0570.0000.0000.0000.000
38A48GLY0-0.0220.00319.7850.0300.0300.0000.0000.0000.000
39A49ILE0-0.114-0.05820.0180.0020.0020.0000.0000.0000.000
40A50ALA00.0550.02823.988-0.018-0.0180.0000.0000.0000.000
41A51ARG10.9460.93824.510-0.166-0.1660.0000.0000.0000.000
42A52ARG10.9290.96524.511-0.200-0.2000.0000.0000.0000.000
43A53THR0-0.014-0.01621.702-0.003-0.0030.0000.0000.0000.000
44A54LEU00.0530.04019.2140.0390.0390.0000.0000.0000.000
45A55PHE0-0.002-0.00920.0380.0290.0290.0000.0000.0000.000
46A56ARG10.8280.93420.057-0.431-0.4310.0000.0000.0000.000
47A57TYR0-0.036-0.01816.3760.0090.0090.0000.0000.0000.000
48A58PHE00.0520.03412.8120.0060.0060.0000.0000.0000.000
49A59PRO00.0090.00618.145-0.043-0.0430.0000.0000.0000.000
50A60SER0-0.019-0.02319.854-0.034-0.0340.0000.0000.0000.000
51A61LYS10.8520.91419.102-0.111-0.1110.0000.0000.0000.000
52A62ASN0-0.017-0.01817.9570.0330.0330.0000.0000.0000.000
53A63ALA00.0170.01515.5170.0010.0010.0000.0000.0000.000
54A64ILE00.0080.02113.9140.0820.0820.0000.0000.0000.000
55A65PRO00.0230.01611.8830.1570.1570.0000.0000.0000.000
56A66TRP00.0250.0139.1890.0910.0910.0000.0000.0000.000
57A67GLY0-0.0060.0098.7630.2850.2850.0000.0000.0000.000
58A68ASP-1-0.875-0.9438.9870.8560.8560.0000.0000.0000.000
59A69PHE00.007-0.0117.3730.2330.2330.0000.0000.0000.000
60A70ASP-1-0.886-0.9378.9370.3620.3620.0000.0000.0000.000
61A71ALA0-0.011-0.0088.014-0.127-0.1270.0000.0000.0000.000
62A72HIS0-0.040-0.0162.552-0.7760.6760.718-0.439-1.732-0.002
63A73LEU00.0140.0075.394-0.536-0.5360.0000.0000.0000.000
64A74ALA0-0.028-0.0118.042-0.164-0.1640.0000.0000.0000.000
65A75GLU-1-0.857-0.9113.3511.0071.8230.039-0.404-0.451-0.003
66A76MET0-0.0160.0065.406-0.252-0.2520.0000.0000.0000.000
67A77ARG10.8240.8676.470-0.119-0.1190.0000.0000.0000.000
68A78ALA0-0.042-0.0219.207-0.025-0.0250.0000.0000.0000.000
69A79GLN0-0.029-0.0356.259-0.099-0.0990.0000.0000.0000.000
70A80LEU0-0.028-0.0229.414-0.013-0.0130.0000.0000.0000.000
71A81ALA0-0.040-0.01911.5280.0130.0130.0000.0000.0000.000
72A82ALA0-0.041-0.01312.2940.0300.0300.0000.0000.0000.000
73A83GLN0-0.068-0.02910.982-0.003-0.0030.0000.0000.0000.000
74A84PRO0-0.020-0.00714.6280.0170.0170.0000.0000.0000.000
75A85ASP-1-0.918-0.95318.443-0.128-0.1280.0000.0000.0000.000
76A86ASP-1-0.904-0.95520.740-0.158-0.1580.0000.0000.0000.000
77A87ILE0-0.0020.01316.310-0.010-0.0100.0000.0000.0000.000
78A88PRO00.0160.01919.6120.0090.0090.0000.0000.0000.000
79A89ILE00.001-0.00118.041-0.034-0.0340.0000.0000.0000.000
80A90VAL00.0570.01816.580-0.034-0.0340.0000.0000.0000.000
81A91ASP-1-0.807-0.90016.042-0.399-0.3990.0000.0000.0000.000
82A92GLY00.0120.01013.694-0.076-0.0760.0000.0000.0000.000
83A93LEU0-0.030-0.02211.923-0.069-0.0690.0000.0000.0000.000
84A94THR00.008-0.00611.383-0.121-0.1210.0000.0000.0000.000
85A95ALA0-0.008-0.00110.735-0.164-0.1640.0000.0000.0000.000
86A96ALA00.0040.0037.263-0.254-0.2540.0000.0000.0000.000
87A97LEU0-0.006-0.0076.622-0.416-0.4160.0000.0000.0000.000
88A98LEU00.0410.0218.063-0.244-0.2440.0000.0000.0000.000
89A99GLN0-0.0100.0034.545-0.542-0.416-0.001-0.008-0.1180.000
90A100PHE0-0.051-0.0232.253-4.575-3.1063.814-1.771-3.512-0.011
91A101ASN0-0.0170.0013.286-0.874-0.3100.0710.112-0.747-0.003
92A102ALA00.0300.0413.7470.3840.6890.000-0.086-0.2200.000
93A103PHE00.016-0.0072.356-8.215-4.3112.559-3.143-3.321-0.031
94A104PRO0-0.042-0.0203.7460.6751.0110.010-0.076-0.2700.000
95A105ALA00.0480.0166.881-0.070-0.0700.0000.0000.0000.000
96A106SER0-0.085-0.0569.0590.0580.0580.0000.0000.0000.000
97A107GLU-1-0.855-0.9065.2220.5240.5240.0000.0000.0000.000
98A108GLU-1-0.840-0.8936.643-0.796-0.7960.0000.0000.0000.000
99A109ILE00.0830.0328.5010.0550.0550.0000.0000.0000.000
100A110ASN0-0.059-0.0457.2780.0250.0250.0000.0000.0000.000
101A111HIS0-0.029-0.0304.042-0.1020.2470.003-0.143-0.210-0.001
102A112ARG10.8310.9116.4670.6150.6150.0000.0000.0000.000
103A113LYS10.8630.91110.0930.0170.0170.0000.0000.0000.000
104A114ARG10.8380.9195.902-1.215-1.2150.0000.0000.0000.000
105A115MET00.002-0.0086.4200.1510.1510.0000.0000.0000.000
106A116GLY00.0560.03210.4350.0210.0210.0000.0000.0000.000
107A117LEU0-0.061-0.03313.0500.0350.0350.0000.0000.0000.000
108A118ILE0-0.029-0.03110.0110.0120.0120.0000.0000.0000.000
109A119LEU0-0.001-0.00112.7940.0080.0080.0000.0000.0000.000
110A120ARG10.8090.88815.8060.2130.2130.0000.0000.0000.000
111A121VAL00.0260.03717.9300.0160.0160.0000.0000.0000.000
112A122PRO00.0440.01619.4900.0120.0120.0000.0000.0000.000
113A123ALA0-0.003-0.00421.6380.0020.0020.0000.0000.0000.000
114A124LEU0-0.0230.00115.1420.0300.0300.0000.0000.0000.000
115A125GLN00.0320.03317.3470.0160.0160.0000.0000.0000.000
116A126ALA0-0.018-0.00218.697-0.008-0.0080.0000.0000.0000.000
117A127TYR0-0.020-0.02216.5750.0130.0130.0000.0000.0000.000
118A128SER00.003-0.01414.6280.0020.0020.0000.0000.0000.000
119A129VAL00.0220.02215.970-0.021-0.0210.0000.0000.0000.000
120A130VAL0-0.002-0.00517.890-0.016-0.0160.0000.0000.0000.000
121A131MET0-0.0080.01312.4710.0400.0400.0000.0000.0000.000
122A132TYR00.0590.00312.578-0.048-0.0480.0000.0000.0000.000
123A133GLU-1-0.823-0.87214.897-0.085-0.0850.0000.0000.0000.000
124A134GLY00.0050.00914.265-0.016-0.0160.0000.0000.0000.000
125A135TRP00.0410.0057.7810.0500.0500.0000.0000.0000.000
126A136ARG10.8050.87311.9860.0760.0760.0000.0000.0000.000
127A137ASN0-0.083-0.04914.954-0.016-0.0160.0000.0000.0000.000
128A138VAL00.0170.02510.1470.0050.0050.0000.0000.0000.000
129A139ILE00.0020.01110.431-0.016-0.0160.0000.0000.0000.000
130A140ALA0-0.006-0.00213.8220.0060.0060.0000.0000.0000.000
131A141GLU-1-0.808-0.87915.1090.0190.0190.0000.0000.0000.000
132A142TYR00.0130.03113.9860.0160.0160.0000.0000.0000.000
133A143VAL00.008-0.00616.0660.0080.0080.0000.0000.0000.000
134A144ALA0-0.014-0.01218.5370.0090.0090.0000.0000.0000.000
135A145SER0-0.031-0.02718.8020.0170.0170.0000.0000.0000.000
136A146ARG10.7810.87617.7410.2060.2060.0000.0000.0000.000
137A147LEU0-0.039-0.01321.070-0.002-0.0020.0000.0000.0000.000
138A148GLY0-0.0370.00123.9470.0080.0080.0000.0000.0000.000
139A149THR0-0.071-0.05024.3240.0110.0110.0000.0000.0000.000
140A150SER0-0.034-0.05224.2070.0050.0050.0000.0000.0000.000
141A151PRO00.0680.01619.870-0.011-0.0110.0000.0000.0000.000
142A152THR0-0.024-0.02721.634-0.007-0.0070.0000.0000.0000.000
143A153ASP-1-0.772-0.81124.329-0.062-0.0620.0000.0000.0000.000
144A154HIS00.011-0.00724.379-0.005-0.0050.0000.0000.0000.000
145A155VAL00.0360.03023.525-0.009-0.0090.0000.0000.0000.000
146A156PRO00.0300.01620.473-0.018-0.0180.0000.0000.0000.000
147A157ARG10.9060.95419.7470.0480.0480.0000.0000.0000.000
148A158THR0-0.037-0.03220.635-0.010-0.0100.0000.0000.0000.000
149A159VAL00.0100.00017.395-0.018-0.0180.0000.0000.0000.000
150A160GLY00.0400.02516.097-0.040-0.0400.0000.0000.0000.000
151A161TYR0-0.024-0.03416.327-0.029-0.0290.0000.0000.0000.000
152A162LEU0-0.022-0.00318.581-0.018-0.0180.0000.0000.0000.000
153A163LEU00.0250.01211.899-0.023-0.0230.0000.0000.0000.000
154A164LEU00.001-0.00313.897-0.065-0.0650.0000.0000.0000.000
155A165GLY0-0.019-0.00415.186-0.026-0.0260.0000.0000.0000.000
156A166VAL0-0.004-0.00214.662-0.007-0.0070.0000.0000.0000.000
157A167ALA00.0100.00511.474-0.051-0.0510.0000.0000.0000.000
158A168MET0-0.022-0.01113.029-0.055-0.0550.0000.0000.0000.000
159A169SER0-0.0100.00814.8420.0020.0020.0000.0000.0000.000
160A170ALA00.0220.01513.4000.0170.0170.0000.0000.0000.000
161A171TYR0-0.010-0.0356.535-0.128-0.1280.0000.0000.0000.000
162A172GLU-1-0.883-0.92612.980-0.222-0.2220.0000.0000.0000.000
163A173GLN0-0.030-0.01016.3510.0410.0410.0000.0000.0000.000
164A174TRP00.007-0.0088.300-0.070-0.0700.0000.0000.0000.000
165A175LEU0-0.069-0.03312.0730.0220.0220.0000.0000.0000.000
166A176ASP-1-0.987-0.97715.348-0.205-0.2050.0000.0000.0000.000
167A177ASP-1-0.824-0.89217.906-0.286-0.2860.0000.0000.0000.000
168A178ASP-1-0.893-0.94916.564-0.357-0.3570.0000.0000.0000.000
169A179SER0-0.168-0.09917.242-0.018-0.0180.0000.0000.0000.000
170A180LEU0-0.0070.01017.274-0.007-0.0070.0000.0000.0000.000
171A181GLU-1-0.864-0.94511.977-0.988-0.9880.0000.0000.0000.000
172A182LEU0-0.0080.0067.7760.0170.0170.0000.0000.0000.000
173A183ASN00.002-0.0209.8930.0310.0310.0000.0000.0000.000
174A184GLU-1-0.918-0.94911.286-0.445-0.4450.0000.0000.0000.000
175A185LEU00.0320.03314.4460.0660.0660.0000.0000.0000.000
176A186LEU0-0.038-0.0219.0140.0530.0530.0000.0000.0000.000
177A187ALA0-0.017-0.00613.2210.0740.0740.0000.0000.0000.000
178A188SER0-0.025-0.01915.1130.0910.0910.0000.0000.0000.000
179A189GLY00.002-0.00217.0050.0540.0540.0000.0000.0000.000
180A190MET0-0.045-0.02814.9420.0520.0520.0000.0000.0000.000
181A191GLN0-0.038-0.02917.0970.0160.0160.0000.0000.0000.000
182A192SER00.0050.00120.1200.0440.0440.0000.0000.0000.000
183A193LEU0-0.080-0.04317.6620.0330.0330.0000.0000.0000.000
184A194TYR0-0.101-0.04119.5460.0320.0320.0000.0000.0000.000
185A195ASP-1-0.849-0.91421.737-0.258-0.2580.0000.0000.0000.000
186A196GLY0-0.0290.00124.3810.0240.0240.0000.0000.0000.000
187A197LEU0-0.020-0.03124.6270.0050.0050.0000.0000.0000.000
188A198SER0-0.048-0.02028.0130.0090.0090.0000.0000.0000.000
189A199SER00.0460.02329.4640.0100.0100.0000.0000.0000.000
190A200LEU0-0.0120.00027.481-0.001-0.0010.0000.0000.0000.000
191A201GLY0-0.011-0.00930.5700.0080.0080.0000.0000.0000.000
192A202GLU-1-0.945-0.96433.322-0.114-0.1140.0000.0000.0000.000
193A203PRO0-0.095-0.04135.134-0.006-0.0060.0000.0000.0000.000