Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: V56R1

Calculation Name: 4KXR-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KXR

Chain ID: B

ChEMBL ID:

UniProt ID: O53943

Base Structure: X-ray

Registration Date: 2023-06-26

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 174
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1515794.724229
FMO2-HF: Nuclear repulsion 1444879.258324
FMO2-HF: Total energy -70915.465905
FMO2-MP2: Total energy -71119.027896


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:1:MET)


Summations of interaction energy for fragment #1(B:1:MET)
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.
-5.745-2.3819.83-4.337-8.857-0.011
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.008
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].
3B3PHE00.0450.0072.721-2.8690.6403.091-2.334-4.265-0.015
4B4GLU-1-0.700-0.8355.389-2.717-2.709-0.001-0.005-0.0020.000
5B5ALA0-0.088-0.0296.7360.3250.3250.0000.0000.0000.000
6B6TYR0-0.095-0.0494.9540.2590.2590.0000.0000.0000.000
7B7PRO00.0440.0339.891-0.041-0.0410.0000.0000.0000.000
8B8PRO00.0680.03412.4060.0390.0390.0000.0000.0000.000
9B9GLU-1-0.820-0.90114.182-0.081-0.0810.0000.0000.0000.000
10B10VAL0-0.083-0.04210.0110.0730.0730.0000.0000.0000.000
11B11ASN0-0.019-0.0188.3720.2240.2240.0000.0000.0000.000
12B12SER00.0470.00410.9250.1230.1230.0000.0000.0000.000
13B13ALA0-0.030-0.01614.4610.0550.0550.0000.0000.0000.000
14B14ASN0-0.082-0.0459.6650.0410.0410.0000.0000.0000.000
15B15ILE0-0.033-0.00111.1340.1060.1060.0000.0000.0000.000
16B16TYR0-0.035-0.01013.583-0.012-0.0120.0000.0000.0000.000
17B17ALA0-0.0450.00116.029-0.018-0.0180.0000.0000.0000.000
18B18GLY0-0.011-0.00916.0950.0540.0540.0000.0000.0000.000
19B19PRO0-0.054-0.04016.228-0.030-0.0300.0000.0000.0000.000
20B20GLY00.0840.05617.424-0.035-0.0350.0000.0000.0000.000
21B21PRO00.0250.00516.8890.0270.0270.0000.0000.0000.000
22B22ASP-1-0.869-0.93817.9080.1890.1890.0000.0000.0000.000
23B23SER0-0.050-0.03017.693-0.008-0.0080.0000.0000.0000.000
24B24MET00.0320.01211.626-0.019-0.0190.0000.0000.0000.000
25B25LEU00.0410.01917.633-0.021-0.0210.0000.0000.0000.000
26B26ALA0-0.071-0.04120.851-0.020-0.0200.0000.0000.0000.000
27B27ALA00.0150.00618.653-0.015-0.0150.0000.0000.0000.000
28B28ALA00.0350.02519.748-0.013-0.0130.0000.0000.0000.000
29B29ARG10.9360.96921.184-0.190-0.1900.0000.0000.0000.000
30B30ALA0-0.0060.00323.186-0.013-0.0130.0000.0000.0000.000
31B31TRP00.042-0.00218.567-0.017-0.0170.0000.0000.0000.000
32B32ARG10.8840.93823.317-0.149-0.1490.0000.0000.0000.000
33B33SER0-0.012-0.01025.975-0.010-0.0100.0000.0000.0000.000
34B34LEU00.0090.01824.029-0.009-0.0090.0000.0000.0000.000
35B35ASP-1-0.850-0.92225.8210.1200.1200.0000.0000.0000.000
36B36VAL0-0.024-0.01627.659-0.010-0.0100.0000.0000.0000.000
37B37GLU-1-0.925-0.97230.9050.0890.0890.0000.0000.0000.000
38B38MET0-0.020-0.02428.478-0.007-0.0070.0000.0000.0000.000
39B39THR00.0150.00930.686-0.007-0.0070.0000.0000.0000.000
40B40ALA00.0100.00532.857-0.007-0.0070.0000.0000.0000.000
41B41VAL00.0100.01733.747-0.006-0.0060.0000.0000.0000.000
42B42GLN00.0430.02833.463-0.004-0.0040.0000.0000.0000.000
43B43ARG10.8710.92234.093-0.080-0.0800.0000.0000.0000.000
44B44SER0-0.026-0.02638.458-0.005-0.0050.0000.0000.0000.000
45B45PHE0-0.0230.00237.985-0.004-0.0040.0000.0000.0000.000
46B46ASN00.0160.00439.492-0.003-0.0030.0000.0000.0000.000
47B47ARG10.9910.99941.163-0.053-0.0530.0000.0000.0000.000
48B48THR0-0.031-0.01243.076-0.003-0.0030.0000.0000.0000.000
49B49LEU0-0.018-0.00640.868-0.002-0.0020.0000.0000.0000.000
50B50LEU00.023-0.00644.478-0.002-0.0020.0000.0000.0000.000
51B51SER0-0.045-0.02847.065-0.002-0.0020.0000.0000.0000.000
52B52LEU0-0.0070.00447.641-0.002-0.0020.0000.0000.0000.000
53B53MET0-0.040-0.03548.901-0.001-0.0010.0000.0000.0000.000
54B54ASP-1-0.982-0.98450.7920.0340.0340.0000.0000.0000.000
55B55ALA0-0.027-0.00352.981-0.001-0.0010.0000.0000.0000.000
56B56TRP0-0.066-0.03753.688-0.001-0.0010.0000.0000.0000.000
57B57ALA00.0550.04154.2920.0010.0010.0000.0000.0000.000
58B58GLY00.0310.00154.452-0.001-0.0010.0000.0000.0000.000
59B59PRO0-0.010-0.03153.8350.0010.0010.0000.0000.0000.000
60B60VAL00.0330.03152.2550.0010.0010.0000.0000.0000.000
61B61VAL00.0720.04049.4800.0020.0020.0000.0000.0000.000
62B62MET0-0.046-0.01348.6420.0010.0010.0000.0000.0000.000
63B63GLN00.0490.02347.5740.0010.0010.0000.0000.0000.000
64B64LEU0-0.0080.00645.8020.0020.0020.0000.0000.0000.000
65B65MET0-0.029-0.01644.2640.0030.0030.0000.0000.0000.000
66B66GLU-1-0.981-0.99742.8710.0420.0420.0000.0000.0000.000
67B67ALA0-0.023-0.01141.8310.0020.0020.0000.0000.0000.000
68B68ALA00.0430.02439.8680.0030.0030.0000.0000.0000.000
69B69LYS10.9390.98238.359-0.045-0.0450.0000.0000.0000.000
70B70PRO0-0.012-0.02035.1630.0030.0030.0000.0000.0000.000
71B71PHE00.0740.04233.3200.0040.0040.0000.0000.0000.000
72B72VAL00.0410.01533.8960.0040.0040.0000.0000.0000.000
73B73ARG10.8980.95232.966-0.061-0.0610.0000.0000.0000.000
74B74TRP00.0230.01327.0650.0000.0000.0000.0000.0000.000
75B75LEU00.0180.00629.3370.0060.0060.0000.0000.0000.000
76B76THR0-0.043-0.04330.3220.0020.0020.0000.0000.0000.000
77B77ASP-1-0.858-0.91326.6210.1070.1070.0000.0000.0000.000
78B78LEU0-0.024-0.00424.8960.0090.0090.0000.0000.0000.000
79B79CYS0-0.016-0.01225.5840.0090.0090.0000.0000.0000.000
80B80VAL00.0040.01524.7480.0040.0040.0000.0000.0000.000
81B81GLN0-0.018-0.01020.129-0.008-0.0080.0000.0000.0000.000
82B82LEU0-0.017-0.01121.6840.0150.0150.0000.0000.0000.000
83B83SER0-0.040-0.00223.0690.0080.0080.0000.0000.0000.000
84B84GLU-1-0.817-0.87518.7680.1650.1650.0000.0000.0000.000
85B85VAL00.002-0.00617.4260.0190.0190.0000.0000.0000.000
86B86GLU-1-0.841-0.92118.3090.1840.1840.0000.0000.0000.000
87B87ARG10.8470.90719.744-0.135-0.1350.0000.0000.0000.000
88B88GLN00.0650.01514.7680.0290.0290.0000.0000.0000.000
89B89ILE00.0040.01614.8630.0440.0440.0000.0000.0000.000
90B90HIS0-0.061-0.03215.8910.0230.0230.0000.0000.0000.000
91B91GLU-1-0.933-0.95015.3630.2050.2050.0000.0000.0000.000
92B92ILE0-0.0040.00310.7920.0230.0230.0000.0000.0000.000
93B93VAL0-0.025-0.01813.2470.0460.0460.0000.0000.0000.000
94B94ARG10.9120.95915.783-0.198-0.1980.0000.0000.0000.000
95B95ALA0-0.014-0.00212.036-0.013-0.0130.0000.0000.0000.000
96B96TYR0-0.012-0.01212.666-0.021-0.0210.0000.0000.0000.000
97B97GLU-1-0.931-0.98213.6680.1950.1950.0000.0000.0000.000
98B98TRP0-0.048-0.03115.632-0.032-0.0320.0000.0000.0000.000
99B99ALA00.0640.04211.750-0.039-0.0390.0000.0000.0000.000
100B100HIS0-0.031-0.02113.645-0.053-0.0530.0000.0000.0000.000
101B101HIS0-0.186-0.11016.263-0.039-0.0390.0000.0000.0000.000
102B102ASP-1-0.862-0.92715.3270.0170.0170.0000.0000.0000.000
103B103MET0-0.0850.00110.721-0.067-0.0670.0000.0000.0000.000
104B104VAL00.0200.02215.5580.0120.0120.0000.0000.0000.000
105B105PRO00.0090.00617.7730.0200.0200.0000.0000.0000.000
106B106LEU00.0330.00017.433-0.021-0.0210.0000.0000.0000.000
107B107ALA0-0.039-0.01620.595-0.017-0.0170.0000.0000.0000.000
108B108GLN00.0130.00222.1870.0060.0060.0000.0000.0000.000
109B109ILE00.0670.05517.369-0.011-0.0110.0000.0000.0000.000
110B110TYR0-0.032-0.03620.3910.0010.0010.0000.0000.0000.000
111B111ASN0-0.027-0.00624.1440.0030.0030.0000.0000.0000.000
112B112ASN00.0470.04123.620-0.004-0.0040.0000.0000.0000.000
113B113ARG10.8050.87421.9510.1520.1520.0000.0000.0000.000
114B114ALA0-0.039-0.02525.6500.0030.0030.0000.0000.0000.000
115B115GLU-1-0.942-0.98528.981-0.065-0.0650.0000.0000.0000.000
116B116ARG10.8570.90526.2150.1390.1390.0000.0000.0000.000
117B117GLN0-0.077-0.05529.671-0.006-0.0060.0000.0000.0000.000
118B118ILE00.0220.02131.1930.0040.0040.0000.0000.0000.000
119B119LEU00.0130.01532.0950.0030.0030.0000.0000.0000.000
120B120ILE0-0.036-0.02430.1460.0010.0010.0000.0000.0000.000
121B121ASP-1-0.908-0.93634.478-0.049-0.0490.0000.0000.0000.000
122B122ASN0-0.110-0.05536.9270.0070.0070.0000.0000.0000.000
123B123ASN00.005-0.00536.0220.0020.0020.0000.0000.0000.000
124B124ALA0-0.0150.00438.730-0.002-0.0020.0000.0000.0000.000
125B125LEU0-0.018-0.02241.743-0.001-0.0010.0000.0000.0000.000
126B126GLY00.0050.00838.924-0.001-0.0010.0000.0000.0000.000
127B127GLN0-0.079-0.03838.771-0.006-0.0060.0000.0000.0000.000
128B128PHE00.0400.02435.8430.0000.0000.0000.0000.0000.000
129B129THR0-0.016-0.01933.845-0.005-0.0050.0000.0000.0000.000
130B130ALA00.0000.00332.752-0.008-0.0080.0000.0000.0000.000
131B131GLN00.0390.02531.954-0.004-0.0040.0000.0000.0000.000
132B132ILE0-0.028-0.02429.710-0.004-0.0040.0000.0000.0000.000
133B133ALA0-0.022-0.01228.139-0.008-0.0080.0000.0000.0000.000
134B134ASP-1-0.887-0.94127.124-0.146-0.1460.0000.0000.0000.000
135B135LEU00.0050.00526.570-0.010-0.0100.0000.0000.0000.000
136B136ASP-1-0.793-0.86723.819-0.170-0.1700.0000.0000.0000.000
137B137GLN0-0.062-0.02121.447-0.016-0.0160.0000.0000.0000.000
138B138GLU-1-0.853-0.91121.987-0.144-0.1440.0000.0000.0000.000
139B139TYR0-0.135-0.09317.721-0.018-0.0180.0000.0000.0000.000
140B140ASP-1-0.892-0.96617.927-0.363-0.3630.0000.0000.0000.000
141B141ASP-1-0.857-0.91717.228-0.333-0.3330.0000.0000.0000.000
142B142PHE0-0.028-0.02617.235-0.012-0.0120.0000.0000.0000.000
143B143TRP0-0.087-0.04911.4740.0850.0850.0000.0000.0000.000
144B144ASP-1-0.965-0.98312.670-0.757-0.7570.0000.0000.0000.000
145B145GLU-1-0.905-0.94312.883-0.311-0.3110.0000.0000.0000.000
146B146ASP-1-0.734-0.88911.475-0.125-0.1250.0000.0000.0000.000
147B147GLY0-0.047-0.0168.7560.0080.0080.0000.0000.0000.000
148B148GLU-1-0.838-0.9168.247-0.764-0.7640.0000.0000.0000.000
149B149VAL00.0470.03410.3290.1070.1070.0000.0000.0000.000
150B150MET0-0.030-0.0305.9960.3360.3360.0000.0000.0000.000
151B151ARG10.7060.8505.7171.1651.1650.0000.0000.0000.000
152B152ASP-1-0.805-0.9036.7520.0910.0910.0000.0000.0000.000
153B153TYR0-0.026-0.0068.1890.1750.1750.0000.0000.0000.000
154B154ARG10.9010.9442.3120.6070.4546.740-1.998-4.5900.004
155B155LEU0-0.024-0.0166.274-0.110-0.1100.0000.0000.0000.000
156B156ARG10.9580.9778.755-0.146-0.1460.0000.0000.0000.000
157B157VAL0-0.013-0.0036.880-0.097-0.0970.0000.0000.0000.000
158B158SER0-0.025-0.0186.082-0.116-0.1160.0000.0000.0000.000
159B159ASP-1-0.920-0.9497.7940.0940.0940.0000.0000.0000.000
160B160ALA0-0.045-0.01911.369-0.061-0.0610.0000.0000.0000.000
161B161LEU00.007-0.0086.957-0.059-0.0590.0000.0000.0000.000
162B162SER0-0.086-0.03510.984-0.067-0.0670.0000.0000.0000.000
163B163LYS10.8710.93112.371-0.283-0.2830.0000.0000.0000.000
164B164LEU0-0.081-0.02813.771-0.029-0.0290.0000.0000.0000.000
165B165THR0-0.0040.00214.8560.0110.0110.0000.0000.0000.000
166B166PRO00.003-0.00316.477-0.001-0.0010.0000.0000.0000.000
167B167TRP00.0270.00818.141-0.023-0.0230.0000.0000.0000.000
168B168LYS10.8680.92821.326-0.131-0.1310.0000.0000.0000.000
169B169ALA00.0110.00724.230-0.002-0.0020.0000.0000.0000.000
170B170PRO0-0.0030.00927.030-0.004-0.0040.0000.0000.0000.000
171B171PRO0-0.024-0.00230.312-0.002-0.0020.0000.0000.0000.000
172B172PRO00.005-0.00833.1810.0000.0000.0000.0000.0000.000
173B173ILE00.003-0.00136.491-0.001-0.0010.0000.0000.0000.000
174B174ALA0-0.0150.00039.692-0.003-0.0030.0000.0000.0000.000