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: 229NR

Calculation Name: 2Z9O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Z9O

Chain ID: A

ChEMBL ID:

UniProt ID: P03856

Base Structure: X-ray

Registration Date: 2023-06-19

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2772924.899179
FMO2-HF: Nuclear repulsion 2681535.175523
FMO2-HF: Total energy -91389.723656
FMO2-MP2: Total energy -91656.608685


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:21:SER)


Summations of interaction energy for fragment #1(A:21: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.
-30.317-35.93724.861-10.024-9.215-0.085
Interaction energy analysis for fragmet #1(A:21:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.070 / q_NPA : -0.035
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].
3A23ASP-1-0.775-0.8813.855-5.913-3.493-0.014-1.157-1.2490.004
4A24LEU00.0080.0155.3831.0701.154-0.001-0.004-0.0780.000
5A25THR0-0.008-0.0355.1310.7860.7860.0000.0000.0000.000
6A26GLU-1-0.745-0.8561.771-23.186-33.94222.731-6.889-5.086-0.101
7A27ALA00.0250.0166.1240.4850.4850.0000.0000.0000.000
8A28ALA00.007-0.0089.3230.2530.2530.0000.0000.0000.000
9A29TYR0-0.065-0.0727.3250.0170.0170.0000.0000.0000.000
10A30SER00.0020.01110.7320.0760.0760.0000.0000.0000.000
11A31LEU0-0.0560.00712.7690.0200.0200.0000.0000.0000.000
12A32SER00.017-0.00315.4280.0680.0680.0000.0000.0000.000
13A33ARG10.8740.92218.171-0.078-0.0780.0000.0000.0000.000
14A34ASP-1-0.761-0.88019.2870.0310.0310.0000.0000.0000.000
15A35GLN0-0.037-0.00218.437-0.014-0.0140.0000.0000.0000.000
16A36LYS10.7900.89913.804-0.094-0.0940.0000.0000.0000.000
17A37ARG10.8540.95317.035-0.047-0.0470.0000.0000.0000.000
18A38MET0-0.045-0.02320.274-0.010-0.0100.0000.0000.0000.000
19A39LEU0-0.003-0.01214.809-0.004-0.0040.0000.0000.0000.000
20A40TYR0-0.032-0.01017.7490.0030.0030.0000.0000.0000.000
21A41LEU00.0220.00619.193-0.002-0.0020.0000.0000.0000.000
22A42PHE0-0.033-0.02319.735-0.007-0.0070.0000.0000.0000.000
23A43VAL0-0.0020.00115.926-0.016-0.0160.0000.0000.0000.000
24A44ASP-1-0.911-0.94419.1510.0540.0540.0000.0000.0000.000
25A45GLN0-0.030-0.03422.2190.0000.0000.0000.0000.0000.000
26A46ILE0-0.0440.00219.687-0.013-0.0130.0000.0000.0000.000
27A47ARG10.8950.95219.349-0.070-0.0700.0000.0000.0000.000
28A57ASP-1-0.810-0.89924.325-0.160-0.1600.0000.0000.0000.000
29A58GLY0-0.082-0.07024.250-0.031-0.0310.0000.0000.0000.000
30A59ILE0-0.045-0.00725.122-0.004-0.0040.0000.0000.0000.000
31A60CYS0-0.001-0.00325.3380.0140.0140.0000.0000.0000.000
32A61GLU-1-0.741-0.84027.473-0.113-0.1130.0000.0000.0000.000
33A62ILE0-0.046-0.03825.5570.0060.0060.0000.0000.0000.000
34A63HIS00.0380.02128.3090.0120.0120.0000.0000.0000.000
35A64VAL0-0.031-0.01929.8280.0100.0100.0000.0000.0000.000
36A65ALA00.0340.01431.1520.0080.0080.0000.0000.0000.000
37A66LYS10.8840.94227.157-0.027-0.0270.0000.0000.0000.000
38A67TYR0-0.038-0.02623.8260.0100.0100.0000.0000.0000.000
39A68ALA0-0.034-0.03427.9620.0110.0110.0000.0000.0000.000
40A69GLU-1-0.810-0.88629.7550.0460.0460.0000.0000.0000.000
41A70ILE0-0.0060.00524.2950.0080.0080.0000.0000.0000.000
42A71PHE0-0.064-0.04821.7550.0170.0170.0000.0000.0000.000
43A72GLY0-0.0030.02127.2270.0040.0040.0000.0000.0000.000
44A73LEU0-0.040-0.01728.593-0.001-0.0010.0000.0000.0000.000
45A74THR00.024-0.02632.307-0.007-0.0070.0000.0000.0000.000
46A75SER00.042-0.01433.514-0.004-0.0040.0000.0000.0000.000
47A76ALA0-0.0160.00134.387-0.007-0.0070.0000.0000.0000.000
48A77GLU-1-0.804-0.87331.9540.0220.0220.0000.0000.0000.000
49A78ALA00.0460.03529.632-0.005-0.0050.0000.0000.0000.000
50A79SER00.0090.00929.651-0.013-0.0130.0000.0000.0000.000
51A80LYS10.8090.90629.597-0.010-0.0100.0000.0000.0000.000
52A81ASP-1-0.790-0.90326.4040.0050.0050.0000.0000.0000.000
53A82ILE00.0290.02225.208-0.014-0.0140.0000.0000.0000.000
54A83ARG10.9320.97426.7940.0300.0300.0000.0000.0000.000
55A84GLN00.0240.00226.296-0.021-0.0210.0000.0000.0000.000
56A85ALA00.0290.02922.605-0.015-0.0150.0000.0000.0000.000
57A86LEU00.0450.02623.102-0.026-0.0260.0000.0000.0000.000
58A87LYS10.9380.97725.0930.0770.0770.0000.0000.0000.000
59A88SER0-0.022-0.03222.636-0.011-0.0110.0000.0000.0000.000
60A89PHE00.005-0.00417.290-0.011-0.0110.0000.0000.0000.000
61A90ALA0-0.060-0.01521.733-0.028-0.0280.0000.0000.0000.000
62A91GLY00.0270.02121.7210.0020.0020.0000.0000.0000.000
63A92LYS10.8470.91817.1670.2910.2910.0000.0000.0000.000
64A93GLU-1-0.863-0.90614.916-0.615-0.6150.0000.0000.0000.000
65A94VAL0-0.046-0.0179.8840.0000.0000.0000.0000.0000.000
66A95VAL00.0350.0279.9050.0450.0450.0000.0000.0000.000
67A96PHE0-0.034-0.0307.756-0.384-0.3840.0000.0000.0000.000
68A97TYR0-0.007-0.0276.3880.6730.6730.0000.0000.0000.000
69A98ARG10.8210.8868.4280.9210.9210.0000.0000.0000.000
70A99PRO0-0.055-0.0089.1570.0900.0900.0000.0000.0000.000
71A100GLU-1-0.858-0.94311.609-0.887-0.8870.0000.0000.0000.000
72A101GLU-1-0.982-0.98414.545-0.550-0.5500.0000.0000.0000.000
73A102ASP-1-0.904-0.96013.666-0.603-0.6030.0000.0000.0000.000
74A103ALA00.0130.00416.8210.0310.0310.0000.0000.0000.000
75A104GLY0-0.0020.00418.0030.0430.0430.0000.0000.0000.000
76A105ASP-1-0.997-0.99117.455-0.225-0.2250.0000.0000.0000.000
77A106GLU-1-1.013-1.00817.414-0.356-0.3560.0000.0000.0000.000
78A107LYS10.8810.9659.5030.9640.9640.0000.0000.0000.000
79A108GLY00.0840.04213.4160.0050.0050.0000.0000.0000.000
80A109TYR0-0.123-0.07511.597-0.216-0.2160.0000.0000.0000.000
81A110GLU-1-0.789-0.85512.154-0.760-0.7600.0000.0000.0000.000
82A111SER0-0.051-0.06912.559-0.223-0.2230.0000.0000.0000.000
83A112PHE00.0350.02713.9230.1380.1380.0000.0000.0000.000
84A113PRO00.0180.01415.966-0.033-0.0330.0000.0000.0000.000
85A114TRP00.037-0.00411.9000.0220.0220.0000.0000.0000.000
86A115PHE0-0.064-0.03617.9480.0260.0260.0000.0000.0000.000
87A116ILE00.0330.03521.692-0.004-0.0040.0000.0000.0000.000
88A117LYS10.9520.97624.1820.1810.1810.0000.0000.0000.000
89A118ARG10.8860.93023.7110.2010.2010.0000.0000.0000.000
90A119ALA00.0010.00527.2020.0030.0030.0000.0000.0000.000
91A120HIS10.8370.91130.4650.0780.0780.0000.0000.0000.000
92A121SER00.0450.03532.780-0.004-0.0040.0000.0000.0000.000
93A122PRO0-0.007-0.01036.5420.0040.0040.0000.0000.0000.000
94A123SER00.0370.01638.3060.0040.0040.0000.0000.0000.000
95A124ARG10.8770.93834.0300.0890.0890.0000.0000.0000.000
96A125GLY00.0310.02637.5480.0000.0000.0000.0000.0000.000
97A126LEU00.002-0.01633.573-0.001-0.0010.0000.0000.0000.000
98A127TYR0-0.036-0.03229.336-0.004-0.0040.0000.0000.0000.000
99A128SER0-0.010-0.01929.7300.0060.0060.0000.0000.0000.000
100A129VAL0-0.056-0.03023.945-0.008-0.0080.0000.0000.0000.000
101A130HIS00.0190.01625.5890.0180.0180.0000.0000.0000.000
102A131ILE00.0430.01319.595-0.023-0.0230.0000.0000.0000.000
103A132ASN00.0260.00718.6430.0140.0140.0000.0000.0000.000
104A133PRO00.0550.01819.123-0.038-0.0380.0000.0000.0000.000
105A134TYR00.0200.01216.6480.0120.0120.0000.0000.0000.000
106A135LEU0-0.015-0.01113.703-0.089-0.0890.0000.0000.0000.000
107A136ILE0-0.0090.00815.108-0.004-0.0040.0000.0000.0000.000
108A137PRO00.0090.00915.4190.0530.0530.0000.0000.0000.000
109A138PHE00.0370.0179.801-0.021-0.0210.0000.0000.0000.000
110A139PHE0-0.030-0.01912.2830.1240.1240.0000.0000.0000.000
111A140ILE00.0400.01414.1410.1000.1000.0000.0000.0000.000
112A141GLY00.0150.00810.6730.0850.0850.0000.0000.0000.000
113A142LEU00.003-0.0039.7680.2630.2630.0000.0000.0000.000
114A143GLN00.0250.03211.9090.0770.0770.0000.0000.0000.000
115A144ASN0-0.0080.01211.5610.0050.0050.0000.0000.0000.000
116A145ARG10.8350.8953.760-4.481-4.1950.000-0.135-0.1510.001
117A146PHE0-0.011-0.03111.2240.0030.0030.0000.0000.0000.000
118A147THR0-0.019-0.00614.596-0.028-0.0280.0000.0000.0000.000
119A148GLN0-0.030-0.02012.6480.0080.0080.0000.0000.0000.000
120A149PHE00.016-0.0118.4990.0390.0390.0000.0000.0000.000
121A150ARG10.7910.85613.300-0.352-0.3520.0000.0000.0000.000
122A151LEU00.0420.02710.846-0.058-0.0580.0000.0000.0000.000
123A152SER00.033-0.00314.178-0.059-0.0590.0000.0000.0000.000
124A153GLU-1-0.862-0.89217.6670.2290.2290.0000.0000.0000.000
125A154THR0-0.049-0.01513.3040.0270.0270.0000.0000.0000.000
126A155LYS10.8630.92516.476-0.146-0.1460.0000.0000.0000.000
127A156GLU-1-0.785-0.89715.3510.0560.0560.0000.0000.0000.000
128A157ILE0-0.026-0.02011.2100.0450.0450.0000.0000.0000.000
129A158THR00.0560.02011.695-0.043-0.0430.0000.0000.0000.000
130A159ASN00.0280.01510.944-0.034-0.0340.0000.0000.0000.000
131A160PRO00.0950.0295.9490.1850.1850.0000.0000.0000.000
132A161TYR0-0.026-0.0216.7870.4530.4530.0000.0000.0000.000
133A162ALA0-0.003-0.0139.1370.2080.2080.0000.0000.0000.000
134A163MET0-0.0380.0236.390-0.005-0.0050.0000.0000.0000.000
135A164ARG10.8560.9212.063-1.3100.7922.146-1.828-2.4190.011
136A165LEU0-0.0220.0136.874-0.122-0.1220.0000.0000.0000.000
137A166TYR00.024-0.01910.596-0.114-0.1140.0000.0000.0000.000
138A167GLU-1-0.724-0.8045.9483.4513.4510.0000.0000.0000.000
139A168SER0-0.019-0.0188.930-0.171-0.1710.0000.0000.0000.000
140A169LEU0-0.056-0.03410.812-0.216-0.2160.0000.0000.0000.000
141A170CYS0-0.075-0.02712.547-0.172-0.1720.0000.0000.0000.000
142A171GLN00.0270.03111.835-0.032-0.0320.0000.0000.0000.000
143A172TYR0-0.035-0.02013.572-0.120-0.1200.0000.0000.0000.000
144A173ARG10.8530.93415.752-0.686-0.6860.0000.0000.0000.000
145A174LYS10.8330.90019.056-0.309-0.3090.0000.0000.0000.000
146A175PRO00.014-0.00822.6370.0070.0070.0000.0000.0000.000
147A176ASP-1-0.780-0.85724.1730.2740.2740.0000.0000.0000.000
148A177GLY00.0170.01422.6040.0000.0000.0000.0000.0000.000
149A178SER0-0.045-0.03822.4830.0060.0060.0000.0000.0000.000
150A179GLY00.0600.02320.9630.0270.0270.0000.0000.0000.000
151A180ILE0-0.033-0.01121.977-0.009-0.0090.0000.0000.0000.000
152A181VAL00.0100.01916.9000.0000.0000.0000.0000.0000.000
153A182SER0-0.026-0.01519.982-0.019-0.0190.0000.0000.0000.000
154A183LEU00.0170.01713.6510.0060.0060.0000.0000.0000.000
155A184LYS10.8440.91117.245-0.445-0.4450.0000.0000.0000.000
156A185ILE00.0230.01315.9710.0790.0790.0000.0000.0000.000
157A186ASP-1-0.793-0.90715.5550.4740.4740.0000.0000.0000.000
158A187TRP00.0220.01711.266-0.004-0.0040.0000.0000.0000.000
159A188ILE0-0.037-0.02111.5520.1460.1460.0000.0000.0000.000
160A189ILE0-0.021-0.01910.7900.1890.1890.0000.0000.0000.000
161A190GLU-1-0.810-0.8759.8731.0471.0470.0000.0000.0000.000
162A191ARG10.8850.9227.516-0.815-0.8150.0000.0000.0000.000
163A192TYR0-0.082-0.0625.9620.5530.5530.0000.0000.0000.000
164A193GLN00.0300.0115.0721.1721.416-0.001-0.011-0.2320.000
165A194LEU0-0.038-0.0108.564-0.256-0.2560.0000.0000.0000.000
166A195PRO00.0280.02811.784-0.048-0.0480.0000.0000.0000.000
167A196GLN00.0900.02814.2990.0290.0290.0000.0000.0000.000
168A197SER00.0040.00317.2310.0140.0140.0000.0000.0000.000
169A198TYR0-0.033-0.03214.821-0.035-0.0350.0000.0000.0000.000
170A199GLN00.0890.03418.0760.0500.0500.0000.0000.0000.000
171A200ARG10.8670.93719.771-0.169-0.1690.0000.0000.0000.000
172A201MET00.0220.00721.6450.0060.0060.0000.0000.0000.000
173A202PRO0-0.043-0.04022.9150.0130.0130.0000.0000.0000.000
174A203ASP-1-0.768-0.85621.2130.1650.1650.0000.0000.0000.000
175A204PHE00.0550.03015.5600.0030.0030.0000.0000.0000.000
176A205ARG10.8430.90318.856-0.211-0.2110.0000.0000.0000.000
177A206ARG10.9250.95420.740-0.132-0.1320.0000.0000.0000.000
178A207ARG10.8310.91717.936-0.198-0.1980.0000.0000.0000.000
179A208PHE00.0750.03911.840-0.005-0.0050.0000.0000.0000.000
180A209LEU0-0.0120.00016.4150.0060.0060.0000.0000.0000.000
181A210GLN00.021-0.00818.1660.0080.0080.0000.0000.0000.000
182A211VAL00.0010.01316.555-0.011-0.0110.0000.0000.0000.000
183A212CYS0-0.0170.00213.185-0.027-0.0270.0000.0000.0000.000
184A213VAL00.0270.01415.4800.0170.0170.0000.0000.0000.000
185A214ASN0-0.017-0.01318.1420.0010.0010.0000.0000.0000.000
186A215GLU-1-0.801-0.87614.6140.1630.1630.0000.0000.0000.000
187A216ILE0-0.033-0.02313.101-0.010-0.0100.0000.0000.0000.000
188A217ASN0-0.037-0.02516.708-0.031-0.0310.0000.0000.0000.000
189A218SER0-0.0250.01119.395-0.037-0.0370.0000.0000.0000.000
190A219ARG10.7760.86916.001-0.163-0.1630.0000.0000.0000.000
191A220THR0-0.0030.00514.5990.0020.0020.0000.0000.0000.000
192A221PRO00.0580.03717.036-0.033-0.0330.0000.0000.0000.000
193A222MET0-0.0250.00415.591-0.012-0.0120.0000.0000.0000.000
194A223ARG10.8970.94819.490-0.302-0.3020.0000.0000.0000.000
195A224LEU0-0.052-0.02016.8390.0130.0130.0000.0000.0000.000
196A225SER00.0060.00920.966-0.043-0.0430.0000.0000.0000.000
197A226TYR00.025-0.00721.0390.0400.0400.0000.0000.0000.000
198A227ILE00.0440.03423.119-0.033-0.0330.0000.0000.0000.000
199A228GLU-1-0.760-0.84023.6960.2950.2950.0000.0000.0000.000
200A229LYS10.9891.00424.282-0.315-0.3150.0000.0000.0000.000
201A230LYS10.8790.93125.089-0.225-0.2250.0000.0000.0000.000
202A231LYS10.9830.99527.699-0.218-0.2180.0000.0000.0000.000
203A232GLY00.0590.04129.756-0.005-0.0050.0000.0000.0000.000
204A233ARG10.9020.93431.462-0.160-0.1600.0000.0000.0000.000
205A234GLN00.0930.05423.923-0.004-0.0040.0000.0000.0000.000
206A235THR0-0.020-0.03722.871-0.007-0.0070.0000.0000.0000.000
207A236THR0-0.0130.00422.9160.0100.0100.0000.0000.0000.000
208A237HIS0-0.004-0.01920.2290.0320.0320.0000.0000.0000.000
209A238ILE0-0.0040.01418.539-0.050-0.0500.0000.0000.0000.000
210A239VAL0-0.020-0.01019.6760.0420.0420.0000.0000.0000.000
211A240PHE00.0700.02516.248-0.030-0.0300.0000.0000.0000.000
212A241SER0-0.017-0.02320.492-0.025-0.0250.0000.0000.0000.000
213A242PHE00.016-0.00218.287-0.013-0.0130.0000.0000.0000.000
214A243ARG10.9120.95121.614-0.326-0.3260.0000.0000.0000.000
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