FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: YZQ32

Calculation Name: 1XB2-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XB2

Chain ID: B

ChEMBL ID:

UniProt ID: P43896

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 276
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3411870.47269
FMO2-HF: Nuclear repulsion 3305884.971021
FMO2-HF: Total energy -105985.501669
FMO2-MP2: Total energy -106292.519587


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(B:56:SER)


Summations of interaction energy for fragment #1(B:56: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.
-16.181-16.77318.081-8.704-8.786-0.001
Interaction energy analysis for fragmet #1(B:56:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.066 / q_NPA : 0.033
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].
3B58SER00.0700.0372.758-4.663-1.2070.746-1.986-2.2150.011
4B59SER00.0330.0191.940-16.400-21.23017.318-6.540-5.949-0.013
5B60LYS10.9750.9943.3792.2522.8760.018-0.168-0.4750.001
6B61GLU-1-0.826-0.9145.1750.1360.294-0.001-0.010-0.1470.000
7B62LEU0-0.0110.0025.8270.0370.0370.0000.0000.0000.000
8B63LEU00.002-0.0027.4260.0800.0800.0000.0000.0000.000
9B64MET0-0.032-0.0119.0480.2370.2370.0000.0000.0000.000
10B65LYS10.8910.93910.8710.0300.0300.0000.0000.0000.000
11B66LEU00.0380.02112.0860.0500.0500.0000.0000.0000.000
12B67ARG10.8770.94313.2810.4790.4790.0000.0000.0000.000
13B68ARG10.9150.94013.6110.3970.3970.0000.0000.0000.000
14B69LYS10.8240.91216.6390.1130.1130.0000.0000.0000.000
15B70THR0-0.004-0.00217.4320.0180.0180.0000.0000.0000.000
16B71GLY00.0520.03218.7830.0160.0160.0000.0000.0000.000
17B72TYR0-0.009-0.01618.2520.0030.0030.0000.0000.0000.000
18B73SER00.010-0.01617.585-0.063-0.0630.0000.0000.0000.000
19B74PHE00.0920.02511.6990.0080.0080.0000.0000.0000.000
20B75ILE00.0550.03112.761-0.088-0.0880.0000.0000.0000.000
21B76ASN00.0210.03314.419-0.010-0.0100.0000.0000.0000.000
22B77CYS0-0.005-0.00213.0290.0440.0440.0000.0000.0000.000
23B78LYS10.8760.9228.6830.7440.7440.0000.0000.0000.000
24B79LYS10.8640.92611.1260.3020.3020.0000.0000.0000.000
25B80ALA00.0360.03514.0800.0620.0620.0000.0000.0000.000
26B81LEU0-0.005-0.0108.9580.0430.0430.0000.0000.0000.000
27B82GLU-1-0.811-0.86910.440-0.397-0.3970.0000.0000.0000.000
28B83THR0-0.068-0.04911.6330.0920.0920.0000.0000.0000.000
29B84CYS0-0.055-0.01413.7260.0500.0500.0000.0000.0000.000
30B85GLY00.0350.02511.6040.0500.0500.0000.0000.0000.000
31B86GLY0-0.035-0.0138.9620.0880.0880.0000.0000.0000.000
32B87ASP-1-0.824-0.9059.7010.1620.1620.0000.0000.0000.000
33B88LEU00.016-0.01510.898-0.084-0.0840.0000.0000.0000.000
34B89LYS10.9580.98613.772-0.067-0.0670.0000.0000.0000.000
35B90GLN00.0300.02416.348-0.042-0.0420.0000.0000.0000.000
36B91ALA00.0430.01413.865-0.026-0.0260.0000.0000.0000.000
37B92GLU-1-0.794-0.88515.931-0.112-0.1120.0000.0000.0000.000
38B93SER0-0.016-0.02618.361-0.003-0.0030.0000.0000.0000.000
39B94TRP0-0.021-0.01318.214-0.016-0.0160.0000.0000.0000.000
40B95LEU0-0.031-0.02616.197-0.009-0.0090.0000.0000.0000.000
41B96HIS00.0140.00420.347-0.007-0.0070.0000.0000.0000.000
42B97LYS10.9450.98323.4860.0590.0590.0000.0000.0000.000
43B98GLN0-0.024-0.00321.5190.0200.0200.0000.0000.0000.000
44B99ALA0-0.0020.00424.1990.0000.0000.0000.0000.0000.000
45B100GLN00.0400.02425.322-0.001-0.0010.0000.0000.0000.000
46B101LYS10.9760.99226.8490.1010.1010.0000.0000.0000.000
47B102GLU-1-0.933-0.97722.322-0.206-0.2060.0000.0000.0000.000
48B103GLY00.0190.00026.287-0.003-0.0030.0000.0000.0000.000
49B104TRP0-0.020-0.02729.095-0.002-0.0020.0000.0000.0000.000
50B105SER0-0.037-0.00527.9770.0040.0040.0000.0000.0000.000
51B106LYS10.8040.90725.6900.1890.1890.0000.0000.0000.000
52B107ALA00.0430.01629.5200.0010.0010.0000.0000.0000.000
53B108ALA0-0.005-0.00133.0620.0040.0040.0000.0000.0000.000
54B109ARG10.9030.95626.0150.1750.1750.0000.0000.0000.000
55B110LEU0-0.066-0.03230.044-0.002-0.0020.0000.0000.0000.000
56B111HIS00.0870.03734.1900.0010.0010.0000.0000.0000.000
57B112GLY0-0.0140.00437.6860.0000.0000.0000.0000.0000.000
58B113ARG10.8360.90832.4480.1310.1310.0000.0000.0000.000
59B114LYS10.9950.99539.0020.0840.0840.0000.0000.0000.000
60B115THR0-0.028-0.01538.197-0.002-0.0020.0000.0000.0000.000
61B116LYS10.8500.91840.7710.0660.0660.0000.0000.0000.000
62B117GLU-1-0.806-0.85340.114-0.074-0.0740.0000.0000.0000.000
63B118GLY00.008-0.01639.9150.0000.0000.0000.0000.0000.000
64B119LEU0-0.033-0.02739.330-0.001-0.0010.0000.0000.0000.000
65B120ILE0-0.0320.00242.8440.0010.0010.0000.0000.0000.000
66B121GLY0-0.002-0.01444.885-0.002-0.0020.0000.0000.0000.000
67B122LEU0-0.014-0.00245.6860.0020.0020.0000.0000.0000.000
68B123LEU00.0040.00045.355-0.002-0.0020.0000.0000.0000.000
69B124GLN00.0220.00548.6200.0000.0000.0000.0000.0000.000
70B125GLU-1-0.869-0.92749.192-0.031-0.0310.0000.0000.0000.000
71B126GLY00.0140.01352.1850.0010.0010.0000.0000.0000.000
72B127ASP-1-0.948-0.95955.448-0.023-0.0230.0000.0000.0000.000
73B128THR0-0.019-0.01753.2710.0000.0000.0000.0000.0000.000
74B129THR0-0.030-0.02352.9800.0000.0000.0000.0000.0000.000
75B130VAL0-0.034-0.01648.4680.0000.0000.0000.0000.0000.000
76B131LEU0-0.0090.00349.638-0.001-0.0010.0000.0000.0000.000
77B132VAL00.011-0.00744.4780.0010.0010.0000.0000.0000.000
78B133GLU-1-0.699-0.82445.140-0.061-0.0610.0000.0000.0000.000
79B134VAL0-0.025-0.00839.0940.0000.0000.0000.0000.0000.000
80B135ASN0-0.076-0.05341.0920.0000.0000.0000.0000.0000.000
81B136CYS0-0.039-0.02536.051-0.001-0.0010.0000.0000.0000.000
82B137GLU-1-0.820-0.88934.747-0.116-0.1160.0000.0000.0000.000
83B138THR0-0.082-0.07134.3980.0030.0030.0000.0000.0000.000
84B139ASP-1-0.734-0.86336.910-0.101-0.1010.0000.0000.0000.000
85B140PHE00.0080.01632.8790.0000.0000.0000.0000.0000.000
86B141VAL0-0.0170.00031.704-0.004-0.0040.0000.0000.0000.000
87B142SER00.002-0.01234.0150.0040.0040.0000.0000.0000.000
88B143ARG10.8840.91835.5930.0980.0980.0000.0000.0000.000
89B144ASN0-0.030-0.00428.8500.0030.0030.0000.0000.0000.000
90B145LEU00.0660.02831.9890.0030.0030.0000.0000.0000.000
91B146LYS10.8610.91027.7880.1180.1180.0000.0000.0000.000
92B147PHE00.0430.02431.8260.0030.0030.0000.0000.0000.000
93B148GLN00.010-0.00334.6200.0080.0080.0000.0000.0000.000
94B149GLN00.0450.02832.196-0.001-0.0010.0000.0000.0000.000
95B150LEU00.0170.01934.8400.0050.0050.0000.0000.0000.000
96B151VAL00.0250.00836.4470.0050.0050.0000.0000.0000.000
97B152GLN00.0480.02138.7230.0030.0030.0000.0000.0000.000
98B153GLN0-0.027-0.00936.2420.0070.0070.0000.0000.0000.000
99B154VAL00.0320.01839.5820.0040.0040.0000.0000.0000.000
100B155ALA00.0100.02342.0470.0040.0040.0000.0000.0000.000
101B156LEU00.0220.00240.7980.0030.0030.0000.0000.0000.000
102B157GLY00.0310.02143.2460.0030.0030.0000.0000.0000.000
103B158THR0-0.025-0.03944.5560.0030.0030.0000.0000.0000.000
104B159LEU00.0260.01247.3520.0020.0020.0000.0000.0000.000
105B160LEU0-0.020-0.00445.4040.0020.0020.0000.0000.0000.000
106B161HIS00.0370.01548.5580.0020.0020.0000.0000.0000.000
107B162CYS0-0.027-0.02950.3380.0010.0010.0000.0000.0000.000
108B163GLN0-0.031-0.01650.5820.0020.0020.0000.0000.0000.000
109B164ASN0-0.063-0.01852.5280.0010.0010.0000.0000.0000.000
110B165LEU0-0.031-0.00754.2690.0010.0010.0000.0000.0000.000
111B166LYS10.8950.94356.6880.0270.0270.0000.0000.0000.000
112B167ASP-1-0.775-0.86959.231-0.024-0.0240.0000.0000.0000.000
113B168GLN0-0.046-0.01161.9130.0000.0000.0000.0000.0000.000
114B169LEU00.0340.00565.2670.0000.0000.0000.0000.0000.000
115B170SER0-0.023-0.00767.8570.0000.0000.0000.0000.0000.000
116B171THR0-0.003-0.00566.9870.0000.0000.0000.0000.0000.000
117B172TYR0-0.041-0.01862.4730.0000.0000.0000.0000.0000.000
118B173SER0-0.028-0.02260.9800.0010.0010.0000.0000.0000.000
119B174LYS10.8360.90158.7100.0300.0300.0000.0000.0000.000
120B175GLY0-0.017-0.02057.3650.0010.0010.0000.0000.0000.000
121B176PHE0-0.023-0.01254.052-0.001-0.0010.0000.0000.0000.000
122B177LEU0-0.0030.01549.0770.0010.0010.0000.0000.0000.000
123B178ASN0-0.010-0.03150.134-0.004-0.0040.0000.0000.0000.000
124B179SER0-0.004-0.01544.925-0.001-0.0010.0000.0000.0000.000
125B180SER0-0.073-0.03045.502-0.001-0.0010.0000.0000.0000.000
126B181GLU-1-0.786-0.88846.489-0.039-0.0390.0000.0000.0000.000
127B182LEU0-0.006-0.00544.4720.0000.0000.0000.0000.0000.000
128B183SER0-0.063-0.05242.339-0.004-0.0040.0000.0000.0000.000
129B184GLU-1-0.747-0.87042.435-0.055-0.0550.0000.0000.0000.000
130B185LEU0-0.0050.01944.7940.0030.0030.0000.0000.0000.000
131B186PRO0-0.007-0.00642.844-0.003-0.0030.0000.0000.0000.000
132B187ALA0-0.021-0.00738.325-0.001-0.0010.0000.0000.0000.000
133B188GLY00.0240.01340.0840.0030.0030.0000.0000.0000.000
134B189PRO00.017-0.00839.182-0.002-0.0020.0000.0000.0000.000
135B190GLU-1-0.874-0.91235.821-0.043-0.0430.0000.0000.0000.000
136B191ARG10.6630.81033.9200.0520.0520.0000.0000.0000.000
137B192GLU-1-0.868-0.93934.146-0.037-0.0370.0000.0000.0000.000
138B193GLY0-0.040-0.00136.239-0.005-0.0050.0000.0000.0000.000
139B194SER0-0.011-0.01938.4060.0020.0020.0000.0000.0000.000
140B195LEU00.0340.00338.366-0.006-0.0060.0000.0000.0000.000
141B196LYS10.8310.89838.3490.0540.0540.0000.0000.0000.000
142B197ASP-1-0.794-0.85734.907-0.072-0.0720.0000.0000.0000.000
143B198GLN00.0290.00533.710-0.012-0.0120.0000.0000.0000.000
144B199LEU00.0030.00433.844-0.008-0.0080.0000.0000.0000.000
145B200ALA0-0.008-0.00332.702-0.009-0.0090.0000.0000.0000.000
146B201LEU0-0.0200.00328.577-0.014-0.0140.0000.0000.0000.000
147B202ALA0-0.0070.00529.124-0.014-0.0140.0000.0000.0000.000
148B203ILE00.0330.02330.126-0.013-0.0130.0000.0000.0000.000
149B204GLY00.033-0.00127.413-0.015-0.0150.0000.0000.0000.000
150B205LYS10.7300.86722.1680.1850.1850.0000.0000.0000.000
151B206LEU0-0.030-0.01725.869-0.016-0.0160.0000.0000.0000.000
152B207GLY0-0.101-0.05927.924-0.007-0.0070.0000.0000.0000.000
153B208GLU-1-0.741-0.82828.664-0.125-0.1250.0000.0000.0000.000
154B209ASN0-0.001-0.02332.3940.0000.0000.0000.0000.0000.000
155B210MET0-0.055-0.03132.2750.0010.0010.0000.0000.0000.000
156B211ILE00.0130.01337.2590.0020.0020.0000.0000.0000.000
157B212LEU00.0290.02739.8160.0000.0000.0000.0000.0000.000
158B213LYS10.8260.93242.6310.0620.0620.0000.0000.0000.000
159B214ARG10.7700.85445.8030.0530.0530.0000.0000.0000.000
160B215ALA00.0180.00847.713-0.002-0.0020.0000.0000.0000.000
161B216ALA0-0.007-0.00449.8080.0020.0020.0000.0000.0000.000
162B217TRP00.0220.01452.333-0.001-0.0010.0000.0000.0000.000
163B218VAL00.008-0.00854.5490.0010.0010.0000.0000.0000.000
164B219LYS10.7840.88756.5100.0240.0240.0000.0000.0000.000
165B220VAL00.0110.00059.1520.0000.0000.0000.0000.0000.000
166B221PRO00.0260.04862.2110.0000.0000.0000.0000.0000.000
167B222ALA00.023-0.01764.9970.0000.0000.0000.0000.0000.000
168B223GLY00.0150.01967.1390.0010.0010.0000.0000.0000.000
169B224PHE00.0240.01565.4060.0000.0000.0000.0000.0000.000
170B225TYR0-0.045-0.04361.2350.0000.0000.0000.0000.0000.000
171B226VAL0-0.003-0.00657.7760.0000.0000.0000.0000.0000.000
172B227GLY00.0240.02859.5710.0000.0000.0000.0000.0000.000
173B228SER0-0.045-0.01954.622-0.001-0.0010.0000.0000.0000.000
174B229TYR0-0.021-0.02053.4350.0010.0010.0000.0000.0000.000
175B230VAL00.0140.00547.549-0.001-0.0010.0000.0000.0000.000
176B231HIS00.0200.03050.5030.0000.0000.0000.0000.0000.000
177B232GLY00.007-0.00847.690-0.002-0.0020.0000.0000.0000.000
178B233ALA0-0.006-0.00545.808-0.003-0.0030.0000.0000.0000.000
179B234MET0-0.047-0.01640.055-0.004-0.0040.0000.0000.0000.000
180B235HIS00.0170.01340.2200.0030.0030.0000.0000.0000.000
181B236SER00.0340.00838.468-0.005-0.0050.0000.0000.0000.000
182B237PRO00.0160.00138.4560.0020.0020.0000.0000.0000.000
183B238SER0-0.015-0.01236.2550.0010.0010.0000.0000.0000.000
184B239LEU0-0.119-0.04536.6010.0000.0000.0000.0000.0000.000
185B240HIS00.0600.01940.1980.0020.0020.0000.0000.0000.000
186B241ASN0-0.023-0.02043.545-0.001-0.0010.0000.0000.0000.000
187B242LEU0-0.051-0.00241.3670.0000.0000.0000.0000.0000.000
188B243VAL0-0.0010.00245.125-0.001-0.0010.0000.0000.0000.000
189B244LEU00.0020.00240.321-0.001-0.0010.0000.0000.0000.000
190B245GLY00.0560.01744.3130.0000.0000.0000.0000.0000.000
191B246LYS10.8160.90944.9980.0690.0690.0000.0000.0000.000
192B247TYR0-0.026-0.03046.8130.0000.0000.0000.0000.0000.000
193B248GLY00.0230.00350.037-0.001-0.0010.0000.0000.0000.000
194B249ALA0-0.031-0.00351.8310.0000.0000.0000.0000.0000.000
195B250LEU0-0.007-0.01154.0750.0000.0000.0000.0000.0000.000
196B251VAL00.003-0.00757.4730.0000.0000.0000.0000.0000.000
197B252ILE0-0.0100.01460.5360.0000.0000.0000.0000.0000.000
198B253CYS0-0.051-0.03163.0500.0000.0000.0000.0000.0000.000
199B254GLU-1-0.871-0.93366.302-0.020-0.0200.0000.0000.0000.000
200B255THR0-0.032-0.05767.6920.0000.0000.0000.0000.0000.000
201B256SER00.0280.01470.1900.0000.0000.0000.0000.0000.000
202B257GLU-1-0.874-0.92469.555-0.017-0.0170.0000.0000.0000.000
203B258LEU0-0.026-0.00867.6100.0000.0000.0000.0000.0000.000
204B259LYS11.0320.99858.5260.0230.0230.0000.0000.0000.000
205B260ALA0-0.085-0.04462.717-0.001-0.0010.0000.0000.0000.000
206B261ASN0-0.013-0.00863.717-0.001-0.0010.0000.0000.0000.000
207B262LEU00.0360.02864.462-0.001-0.0010.0000.0000.0000.000
208B263ALA00.0090.02359.325-0.001-0.0010.0000.0000.0000.000
209B264ASP-1-0.776-0.87260.299-0.031-0.0310.0000.0000.0000.000
210B265LEU00.0080.01861.674-0.001-0.0010.0000.0000.0000.000
211B266GLY00.0330.00460.975-0.001-0.0010.0000.0000.0000.000
212B267ARG10.8250.90155.8440.0320.0320.0000.0000.0000.000
213B268ARG10.8610.91958.7480.0280.0280.0000.0000.0000.000
214B269LEU00.0300.02261.395-0.001-0.0010.0000.0000.0000.000
215B270GLY00.0390.01657.872-0.001-0.0010.0000.0000.0000.000
216B271GLN0-0.023-0.03057.013-0.001-0.0010.0000.0000.0000.000
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