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: 529MZ

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 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 276
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3405983.901945
FMO2-HF: Nuclear repulsion 3299999.024287
FMO2-HF: Total energy -105984.877659
FMO2-MP2: Total energy -106291.908634


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.
-14.869-11.11510.162-6.465-7.4520.016
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 : 0.072 / q_NPA : 0.039
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].
3B58SER00.0750.0312.863-4.629-0.9440.503-2.022-2.1660.011
4B59SER00.0240.0142.106-14.099-14.5839.648-4.267-4.8980.004
5B60LYS10.9510.9813.5501.4672.0200.011-0.176-0.3880.001
6B61GLU-1-0.908-0.9545.4130.1290.1290.0000.0000.0000.000
7B62LEU0-0.0040.0026.242-0.047-0.0470.0000.0000.0000.000
8B63LEU00.0020.0027.7190.0510.0510.0000.0000.0000.000
9B64MET0-0.008-0.0039.5180.1920.1920.0000.0000.0000.000
10B65LYS10.9680.98511.172-0.010-0.0100.0000.0000.0000.000
11B66LEU00.0330.01812.3250.0560.0560.0000.0000.0000.000
12B67ARG10.8680.93513.7300.4370.4370.0000.0000.0000.000
13B68ARG10.9160.94314.5060.3500.3500.0000.0000.0000.000
14B69LYS10.8120.90716.9800.1210.1210.0000.0000.0000.000
15B70THR00.0150.00917.6930.0140.0140.0000.0000.0000.000
16B71GLY00.0050.00019.1500.0180.0180.0000.0000.0000.000
17B72TYR0-0.003-0.01918.497-0.005-0.0050.0000.0000.0000.000
18B73SER00.0150.00417.804-0.057-0.0570.0000.0000.0000.000
19B74PHE00.1020.02912.2430.0030.0030.0000.0000.0000.000
20B75ILE00.0450.02713.254-0.085-0.0850.0000.0000.0000.000
21B76ASN00.0330.02114.664-0.026-0.0260.0000.0000.0000.000
22B77CYS0-0.021-0.00713.3130.0360.0360.0000.0000.0000.000
23B78LYS10.8840.9298.5780.8560.8560.0000.0000.0000.000
24B79LYS10.8880.93011.4390.3080.3080.0000.0000.0000.000
25B80ALA00.0280.03514.1480.0530.0530.0000.0000.0000.000
26B81LEU00.000-0.0129.0950.0440.0440.0000.0000.0000.000
27B82GLU-1-0.826-0.87810.492-0.499-0.4990.0000.0000.0000.000
28B83THR0-0.052-0.03811.5780.0930.0930.0000.0000.0000.000
29B84CYS0-0.060-0.01414.0910.0590.0590.0000.0000.0000.000
30B85GLY00.0470.02812.0290.0450.0450.0000.0000.0000.000
31B86GLY0-0.046-0.0179.1690.0530.0530.0000.0000.0000.000
32B87ASP-1-0.843-0.9169.9930.1590.1590.0000.0000.0000.000
33B88LEU0-0.010-0.02111.638-0.060-0.0600.0000.0000.0000.000
34B89LYS10.9790.99613.994-0.040-0.0400.0000.0000.0000.000
35B90GLN00.0460.02616.547-0.036-0.0360.0000.0000.0000.000
36B91ALA00.0270.00414.019-0.022-0.0220.0000.0000.0000.000
37B92GLU-1-0.791-0.88316.123-0.117-0.1170.0000.0000.0000.000
38B93SER0-0.028-0.02718.4590.0010.0010.0000.0000.0000.000
39B94TRP0-0.011-0.01218.396-0.013-0.0130.0000.0000.0000.000
40B95LEU0-0.034-0.02916.472-0.006-0.0060.0000.0000.0000.000
41B96HIS00.0060.00520.581-0.004-0.0040.0000.0000.0000.000
42B97LYS10.9460.97923.7640.0830.0830.0000.0000.0000.000
43B98GLN0-0.035-0.00321.8550.0200.0200.0000.0000.0000.000
44B99ALA0-0.0020.01324.790-0.001-0.0010.0000.0000.0000.000
45B100GLN00.0430.01925.874-0.002-0.0020.0000.0000.0000.000
46B101LYS10.9810.99227.3550.1110.1110.0000.0000.0000.000
47B102GLU-1-0.942-0.98022.759-0.208-0.2080.0000.0000.0000.000
48B103GLY00.0070.00026.824-0.002-0.0020.0000.0000.0000.000
49B104TRP00.010-0.00429.468-0.002-0.0020.0000.0000.0000.000
50B105SER0-0.0230.00128.7110.0050.0050.0000.0000.0000.000
51B106LYS10.8640.93825.3960.1900.1900.0000.0000.0000.000
52B107ALA00.014-0.00530.0590.0020.0020.0000.0000.0000.000
53B108ALA00.0030.00833.5240.0050.0050.0000.0000.0000.000
54B109ARG10.9160.96326.5310.1640.1640.0000.0000.0000.000
55B110LEU0-0.076-0.04130.4480.0000.0000.0000.0000.0000.000
56B111HIS00.0590.03934.4390.0020.0020.0000.0000.0000.000
57B112GLY00.0030.00337.7730.0010.0010.0000.0000.0000.000
58B113ARG10.8190.90832.6580.1230.1230.0000.0000.0000.000
59B114LYS10.9830.98739.2390.0760.0760.0000.0000.0000.000
60B115THR00.000-0.00538.602-0.004-0.0040.0000.0000.0000.000
61B116LYS10.8570.91641.2440.0620.0620.0000.0000.0000.000
62B117GLU-1-0.829-0.89640.287-0.069-0.0690.0000.0000.0000.000
63B118GLY00.017-0.00940.4220.0000.0000.0000.0000.0000.000
64B119LEU0-0.044-0.02939.8100.0000.0000.0000.0000.0000.000
65B120ILE0-0.0210.00643.2750.0000.0000.0000.0000.0000.000
66B121GLY0-0.004-0.01845.289-0.001-0.0010.0000.0000.0000.000
67B122LEU0-0.010-0.00146.0500.0010.0010.0000.0000.0000.000
68B123LEU00.005-0.00945.647-0.001-0.0010.0000.0000.0000.000
69B124GLN00.0170.00748.9930.0000.0000.0000.0000.0000.000
70B125GLU-1-0.891-0.94349.274-0.032-0.0320.0000.0000.0000.000
71B126GLY0-0.0030.00552.4020.0010.0010.0000.0000.0000.000
72B127ASP-1-0.916-0.94255.815-0.023-0.0230.0000.0000.0000.000
73B128THR0-0.021-0.02053.6780.0000.0000.0000.0000.0000.000
74B129THR0-0.025-0.02553.4020.0000.0000.0000.0000.0000.000
75B130VAL0-0.049-0.02348.7450.0000.0000.0000.0000.0000.000
76B131LEU0-0.0130.00350.035-0.001-0.0010.0000.0000.0000.000
77B132VAL0-0.003-0.01044.8100.0000.0000.0000.0000.0000.000
78B133GLU-1-0.694-0.81245.629-0.058-0.0580.0000.0000.0000.000
79B134VAL0-0.031-0.01639.4730.0000.0000.0000.0000.0000.000
80B135ASN0-0.062-0.04441.5030.0010.0010.0000.0000.0000.000
81B136CYS0-0.034-0.01936.328-0.002-0.0020.0000.0000.0000.000
82B137GLU-1-0.826-0.88834.706-0.111-0.1110.0000.0000.0000.000
83B138THR0-0.063-0.05434.3070.0030.0030.0000.0000.0000.000
84B139ASP-1-0.782-0.89837.054-0.090-0.0900.0000.0000.0000.000
85B140PHE00.0200.00932.9510.0000.0000.0000.0000.0000.000
86B141VAL0-0.011-0.00231.810-0.003-0.0030.0000.0000.0000.000
87B142SER0-0.0200.00134.2160.0030.0030.0000.0000.0000.000
88B143ARG10.8880.92635.9720.0890.0890.0000.0000.0000.000
89B144ASN0-0.044-0.01629.2330.0020.0020.0000.0000.0000.000
90B145LEU00.0670.02731.9280.0030.0030.0000.0000.0000.000
91B146LYS10.8600.91027.8840.1170.1170.0000.0000.0000.000
92B147PHE00.0520.02731.8740.0030.0030.0000.0000.0000.000
93B148GLN00.0350.01234.7000.0060.0060.0000.0000.0000.000
94B149GLN00.0170.01632.318-0.002-0.0020.0000.0000.0000.000
95B150LEU00.0130.01635.0260.0040.0040.0000.0000.0000.000
96B151VAL00.0230.00536.6890.0050.0050.0000.0000.0000.000
97B152GLN00.0470.02038.4130.0060.0060.0000.0000.0000.000
98B153GLN0-0.033-0.01036.6750.0050.0050.0000.0000.0000.000
99B154VAL00.0450.02339.9520.0030.0030.0000.0000.0000.000
100B155ALA00.0040.02542.3530.0030.0030.0000.0000.0000.000
101B156LEU00.0280.00141.2530.0030.0030.0000.0000.0000.000
102B157GLY00.0290.02343.6860.0030.0030.0000.0000.0000.000
103B158THR0-0.007-0.02444.7960.0020.0020.0000.0000.0000.000
104B159LEU00.0020.00147.7650.0020.0020.0000.0000.0000.000
105B160LEU0-0.028-0.01645.7300.0020.0020.0000.0000.0000.000
106B161HIS00.0290.01448.8840.0020.0020.0000.0000.0000.000
107B162CYS00.008-0.00950.4850.0010.0010.0000.0000.0000.000
108B163GLN0-0.037-0.00850.9700.0020.0020.0000.0000.0000.000
109B164ASN0-0.031-0.01552.9300.0010.0010.0000.0000.0000.000
110B165LEU0-0.041-0.00954.5860.0010.0010.0000.0000.0000.000
111B166LYS10.8930.94257.2890.0280.0280.0000.0000.0000.000
112B167ASP-1-0.800-0.90159.457-0.024-0.0240.0000.0000.0000.000
113B168GLN0-0.0440.00262.0820.0000.0000.0000.0000.0000.000
114B169LEU00.0390.00365.4090.0000.0000.0000.0000.0000.000
115B170SER0-0.019-0.00968.0680.0000.0000.0000.0000.0000.000
116B171THR00.0250.02067.5310.0000.0000.0000.0000.0000.000
117B172TYR0-0.031-0.01462.8340.0000.0000.0000.0000.0000.000
118B173SER0-0.048-0.03261.2350.0000.0000.0000.0000.0000.000
119B174LYS10.8720.91059.2070.0290.0290.0000.0000.0000.000
120B175GLY0-0.028-0.02457.6050.0010.0010.0000.0000.0000.000
121B176PHE0-0.025-0.01254.574-0.001-0.0010.0000.0000.0000.000
122B177LEU00.0090.01949.7820.0010.0010.0000.0000.0000.000
123B178ASN0-0.018-0.03050.631-0.004-0.0040.0000.0000.0000.000
124B179SER00.017-0.00645.251-0.001-0.0010.0000.0000.0000.000
125B180SER00.001-0.00446.294-0.002-0.0020.0000.0000.0000.000
126B181GLU-1-0.832-0.91547.131-0.039-0.0390.0000.0000.0000.000
127B182LEU0-0.0020.00944.8020.0000.0000.0000.0000.0000.000
128B183SER0-0.047-0.04642.902-0.003-0.0030.0000.0000.0000.000
129B184GLU-1-0.918-0.96342.916-0.054-0.0540.0000.0000.0000.000
130B185LEU0-0.0360.01145.2650.0020.0020.0000.0000.0000.000
131B186PRO00.001-0.00643.285-0.003-0.0030.0000.0000.0000.000
132B187ALA0-0.047-0.02038.686-0.001-0.0010.0000.0000.0000.000
133B188GLY00.003-0.00440.4240.0030.0030.0000.0000.0000.000
134B189PRO0-0.001-0.01239.834-0.001-0.0010.0000.0000.0000.000
135B190GLU-1-0.905-0.93036.226-0.048-0.0480.0000.0000.0000.000
136B191ARG10.7100.83933.5460.0600.0600.0000.0000.0000.000
137B192GLU-1-0.849-0.91934.469-0.043-0.0430.0000.0000.0000.000
138B193GLY0-0.029-0.00736.650-0.005-0.0050.0000.0000.0000.000
139B194SER00.0410.01738.6840.0020.0020.0000.0000.0000.000
140B195LEU00.021-0.00238.707-0.006-0.0060.0000.0000.0000.000
141B196LYS10.9480.97438.6270.0600.0600.0000.0000.0000.000
142B197ASP-1-0.810-0.89035.333-0.075-0.0750.0000.0000.0000.000
143B198GLN00.024-0.00234.174-0.011-0.0110.0000.0000.0000.000
144B199LEU0-0.0050.00034.085-0.008-0.0080.0000.0000.0000.000
145B200ALA0-0.014-0.00632.946-0.008-0.0080.0000.0000.0000.000
146B201LEU0-0.0150.00128.857-0.013-0.0130.0000.0000.0000.000
147B202ALA0-0.012-0.00429.363-0.013-0.0130.0000.0000.0000.000
148B203ILE00.0240.01830.482-0.011-0.0110.0000.0000.0000.000
149B204GLY00.001-0.01327.859-0.011-0.0110.0000.0000.0000.000
150B205LYS10.7820.90222.7840.1770.1770.0000.0000.0000.000
151B206LEU0-0.034-0.03226.284-0.014-0.0140.0000.0000.0000.000
152B207GLY0-0.115-0.04028.085-0.004-0.0040.0000.0000.0000.000
153B208GLU-1-0.728-0.83728.827-0.118-0.1180.0000.0000.0000.000
154B209ASN0-0.025-0.03032.5770.0010.0010.0000.0000.0000.000
155B210MET0-0.038-0.02732.6160.0010.0010.0000.0000.0000.000
156B211ILE00.0040.00337.5720.0010.0010.0000.0000.0000.000
157B212LEU00.0220.03240.2200.0000.0000.0000.0000.0000.000
158B213LYS10.8310.92743.0030.0590.0590.0000.0000.0000.000
159B214ARG10.7740.86046.1430.0500.0500.0000.0000.0000.000
160B215ALA00.006-0.00148.035-0.002-0.0020.0000.0000.0000.000
161B216ALA00.0010.00250.1990.0010.0010.0000.0000.0000.000
162B217TRP00.0210.01852.6960.0000.0000.0000.0000.0000.000
163B218VAL00.006-0.01254.8040.0010.0010.0000.0000.0000.000
164B219LYS10.7830.89757.0670.0250.0250.0000.0000.0000.000
165B220VAL0-0.003-0.01659.4930.0000.0000.0000.0000.0000.000
166B221PRO00.0450.06362.3530.0000.0000.0000.0000.0000.000
167B222ALA00.032-0.01265.0360.0000.0000.0000.0000.0000.000
168B223GLY00.0110.01067.2750.0000.0000.0000.0000.0000.000
169B224PHE00.0240.01165.5680.0000.0000.0000.0000.0000.000
170B225TYR0-0.028-0.03461.5080.0000.0000.0000.0000.0000.000
171B226VAL00.0020.00758.1590.0000.0000.0000.0000.0000.000
172B227GLY00.0050.01859.7060.0000.0000.0000.0000.0000.000
173B228SER0-0.018-0.01754.876-0.001-0.0010.0000.0000.0000.000
174B229TYR0-0.024-0.02853.9400.0010.0010.0000.0000.0000.000
175B230VAL00.0140.01748.044-0.001-0.0010.0000.0000.0000.000
176B231HIS00.0160.03051.3280.0010.0010.0000.0000.0000.000
177B232GLY0-0.009-0.02048.162-0.002-0.0020.0000.0000.0000.000
178B233ALA0-0.002-0.01146.185-0.003-0.0030.0000.0000.0000.000
179B234MET0-0.045-0.00740.707-0.003-0.0030.0000.0000.0000.000
180B235HIS00.0070.00840.1840.0020.0020.0000.0000.0000.000
181B236SER00.035-0.01238.610-0.005-0.0050.0000.0000.0000.000
182B237PRO00.0030.00238.9680.0010.0010.0000.0000.0000.000
183B238SER0-0.019-0.00336.7000.0010.0010.0000.0000.0000.000
184B239LEU0-0.106-0.04237.0340.0000.0000.0000.0000.0000.000
185B240HIS00.0670.02140.4550.0020.0020.0000.0000.0000.000
186B241ASN0-0.008-0.00243.8290.0000.0000.0000.0000.0000.000
187B242LEU0-0.0510.00641.7960.0000.0000.0000.0000.0000.000
188B243VAL0-0.0020.00545.228-0.001-0.0010.0000.0000.0000.000
189B244LEU00.003-0.00240.699-0.001-0.0010.0000.0000.0000.000
190B245GLY00.0560.02044.7710.0000.0000.0000.0000.0000.000
191B246LYS10.8790.94945.4720.0620.0620.0000.0000.0000.000
192B247TYR0-0.027-0.02547.5420.0000.0000.0000.0000.0000.000
193B248GLY00.0210.01550.9860.0000.0000.0000.0000.0000.000
194B249ALA0-0.023-0.00252.2540.0000.0000.0000.0000.0000.000
195B250LEU00.001-0.00354.3960.0000.0000.0000.0000.0000.000
196B251VAL00.011-0.00457.7580.0000.0000.0000.0000.0000.000
197B252ILE0-0.024-0.00760.9250.0000.0000.0000.0000.0000.000
198B253CYS0-0.050-0.03263.3710.0000.0000.0000.0000.0000.000
199B254GLU-1-0.879-0.92266.538-0.020-0.0200.0000.0000.0000.000
200B255THR0-0.028-0.06067.9120.0000.0000.0000.0000.0000.000
201B256SER00.0250.01270.0290.0000.0000.0000.0000.0000.000
202B257GLU-1-0.955-0.95970.190-0.017-0.0170.0000.0000.0000.000
203B258LEU0-0.016-0.01167.765-0.001-0.0010.0000.0000.0000.000
204B259LYS11.0711.01459.3090.0230.0230.0000.0000.0000.000
205B260ALA0-0.118-0.06263.107-0.001-0.0010.0000.0000.0000.000
206B261ASN00.0140.01864.1910.0000.0000.0000.0000.0000.000
207B262LEU00.0620.03364.5450.0000.0000.0000.0000.0000.000
208B263ALA00.0030.02159.655-0.001-0.0010.0000.0000.0000.000
209B264ASP-1-0.770-0.86860.648-0.029-0.0290.0000.0000.0000.000
210B265LEU00.0260.03462.225-0.001-0.0010.0000.0000.0000.000
211B266GLY00.0290.00261.398-0.001-0.0010.0000.0000.0000.000
212B267ARG10.7840.87356.3500.0300.0300.0000.0000.0000.000
213B268ARG10.8920.93159.2930.0260.0260.0000.0000.0000.000
214B269LEU00.0390.03261.924-0.001-0.0010.0000.0000.0000.000
215B270GLY00.0300.00958.440-0.001-0.0010.0000.0000.0000.000
216B271GLN0-0.032-0.03057.576-0.001-0.0010.0000.0000.0000.000
217B272HIS00.0610.02859.062-0.001-0.0010.0000.0000.0000.000
218B273VAL00.0130.00858.8040.0000.0000.0000.0000.0000.000
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