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: R5R58

Calculation Name: 3KDG-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KDG

Chain ID: B

ChEMBL ID:

UniProt ID: P49850

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2060385.841543
FMO2-HF: Nuclear repulsion 1981451.991019
FMO2-HF: Total energy -78933.850524
FMO2-MP2: Total energy -79160.824546


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:435:ARG)


Summations of interaction energy for fragment #1(B:435:ARG)
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.
-106.858-104.2610.084-1.05-1.6320.005
Interaction energy analysis for fragmet #1(B:435:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.980 / q_NPA : 0.976
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].
3B437PRO00.0280.0093.806-0.1841.198-0.015-0.565-0.8030.001
4B438ILE00.0490.0206.5031.6441.6440.0000.0000.0000.000
5B439MET0-0.0100.0227.9800.1060.1060.0000.0000.0000.000
6B440TYR0-0.025-0.01811.0820.6850.6850.0000.0000.0000.000
7B441PRO0-0.001-0.00414.8380.0380.0380.0000.0000.0000.000
8B442ILE0-0.068-0.02517.1800.3180.3180.0000.0000.0000.000
9B443GLY00.004-0.01119.6560.6570.6570.0000.0000.0000.000
10B444GLN00.0340.02520.017-0.567-0.5670.0000.0000.0000.000
11B445MET0-0.035-0.01021.9670.3040.3040.0000.0000.0000.000
12B446HIS00.029-0.00523.738-0.218-0.2180.0000.0000.0000.000
13B447GLY00.0380.04025.0780.1500.1500.0000.0000.0000.000
14B448THR0-0.083-0.03921.6640.0090.0090.0000.0000.0000.000
15B449TYR0-0.001-0.00118.492-0.255-0.2550.0000.0000.0000.000
16B450ILE00.0080.00615.8980.4770.4770.0000.0000.0000.000
17B451LEU0-0.020-0.00116.483-0.522-0.5220.0000.0000.0000.000
18B452ALA00.0390.00413.3550.2940.2940.0000.0000.0000.000
19B453GLN00.0300.01413.907-0.633-0.6330.0000.0000.0000.000
20B454ASN00.0280.0098.397-0.312-0.3120.0000.0000.0000.000
21B455GLU-1-0.919-0.94611.438-21.195-21.1950.0000.0000.0000.000
22B456ASN0-0.039-0.0186.6911.2591.2590.0000.0000.0000.000
23B457GLY00.0210.01810.5950.2270.2270.0000.0000.0000.000
24B458LEU0-0.023-0.01613.3430.1240.1240.0000.0000.0000.000
25B459TYR0-0.026-0.0387.736-1.490-1.4900.0000.0000.0000.000
26B460ILE0-0.014-0.00712.7890.9150.9150.0000.0000.0000.000
27B461ILE00.0150.00411.367-0.509-0.5090.0000.0000.0000.000
28B462ASP-1-0.820-0.90514.554-12.251-12.2510.0000.0000.0000.000
29B463GLN0-0.010-0.02415.998-0.447-0.4470.0000.0000.0000.000
30B464HIS0-0.045-0.02117.535-0.144-0.1440.0000.0000.0000.000
31B465ALA00.0370.01215.282-0.117-0.1170.0000.0000.0000.000
32B466ALA00.027-0.00313.004-0.574-0.5740.0000.0000.0000.000
33B467GLN0-0.019-0.01913.945-0.213-0.2130.0000.0000.0000.000
34B468GLU-1-0.828-0.90016.673-12.496-12.4960.0000.0000.0000.000
35B469ARG10.8390.9169.57221.33921.3390.0000.0000.0000.000
36B470ILE0-0.004-0.00512.422-0.470-0.4700.0000.0000.0000.000
37B471LYS10.8130.91113.91912.42612.4260.0000.0000.0000.000
38B472TYR0-0.035-0.04012.6440.0310.0310.0000.0000.0000.000
39B473GLU-1-0.766-0.85810.280-22.479-22.4790.0000.0000.0000.000
40B474TYR0-0.0100.00913.9670.1240.1240.0000.0000.0000.000
41B475PHE00.031-0.00317.3280.2790.2790.0000.0000.0000.000
42B476ARG10.8030.88815.42615.91415.9140.0000.0000.0000.000
43B477GLU-1-0.895-0.93617.116-14.686-14.6860.0000.0000.0000.000
44B478LYS10.8070.89118.66913.35313.3530.0000.0000.0000.000
45B479VAL0-0.004-0.00320.8780.4320.4320.0000.0000.0000.000
46B480GLY0-0.061-0.02921.6300.2770.2770.0000.0000.0000.000
47B481GLU-1-0.868-0.92722.590-11.900-11.9000.0000.0000.0000.000
48B482VAL0-0.047-0.03625.3060.2280.2280.0000.0000.0000.000
49B483GLU-1-0.962-0.98128.618-9.078-9.0780.0000.0000.0000.000
50B484PRO0-0.0220.01427.444-0.030-0.0300.0000.0000.0000.000
51B485GLU-1-0.921-0.96229.251-9.115-9.1150.0000.0000.0000.000
52B486VAL0-0.029-0.02131.007-0.113-0.1130.0000.0000.0000.000
53B487GLN0-0.056-0.03833.719-0.047-0.0470.0000.0000.0000.000
54B488GLU-1-0.944-0.97135.685-7.042-7.0420.0000.0000.0000.000
55B489MET0-0.053-0.01336.678-0.102-0.1020.0000.0000.0000.000
56B490ILE00.010-0.00339.3330.1570.1570.0000.0000.0000.000
57B491VAL0-0.025-0.02340.8270.1860.1860.0000.0000.0000.000
58B492PRO0-0.0030.00540.849-0.136-0.1360.0000.0000.0000.000
59B493LEU00.0030.02536.9430.0790.0790.0000.0000.0000.000
60B494THR0-0.020-0.02141.4100.0920.0920.0000.0000.0000.000
61B495PHE00.0070.00937.044-0.042-0.0420.0000.0000.0000.000
62B496HIS0-0.054-0.04042.3270.1210.1210.0000.0000.0000.000
63B497TYR00.0620.03137.671-0.077-0.0770.0000.0000.0000.000
64B498SER0-0.049-0.06843.4940.1960.1960.0000.0000.0000.000
65B499THR00.023-0.02044.686-0.085-0.0850.0000.0000.0000.000
66B500ASN0-0.008-0.01443.593-0.001-0.0010.0000.0000.0000.000
67B501GLU-1-0.781-0.84939.995-7.378-7.3780.0000.0000.0000.000
68B502ALA00.0420.02140.336-0.168-0.1680.0000.0000.0000.000
69B503LEU0-0.043-0.01041.946-0.068-0.0680.0000.0000.0000.000
70B504ILE00.0040.00736.484-0.099-0.0990.0000.0000.0000.000
71B505ILE00.0180.01637.243-0.214-0.2140.0000.0000.0000.000
72B506GLU-1-0.827-0.90337.807-7.489-7.4890.0000.0000.0000.000
73B507GLN0-0.069-0.02635.8150.0710.0710.0000.0000.0000.000
74B508HIS0-0.018-0.00832.460-0.361-0.3610.0000.0000.0000.000
75B509LYS10.8590.94434.2407.4557.4550.0000.0000.0000.000
76B510GLN0-0.010-0.00133.413-0.170-0.1700.0000.0000.0000.000
77B511GLU-1-0.867-0.94629.926-9.800-9.8000.0000.0000.0000.000
78B512LEU00.0030.01029.775-0.320-0.3200.0000.0000.0000.000
79B513GLU-1-0.887-0.94531.176-8.578-8.5780.0000.0000.0000.000
80B514SER0-0.100-0.05727.992-0.316-0.3160.0000.0000.0000.000
81B515VAL0-0.040-0.02425.373-0.472-0.4720.0000.0000.0000.000
82B516GLY0-0.016-0.01127.560-0.052-0.0520.0000.0000.0000.000
83B517VAL0-0.025-0.01730.1710.2540.2540.0000.0000.0000.000
84B518PHE00.012-0.00232.0520.0550.0550.0000.0000.0000.000
85B519LEU0-0.0050.00636.1690.2140.2140.0000.0000.0000.000
86B520GLU-1-0.799-0.86038.840-7.085-7.0850.0000.0000.0000.000
87B521SER0-0.021-0.01342.4280.1320.1320.0000.0000.0000.000
88B522PHE0-0.026-0.01745.0780.1140.1140.0000.0000.0000.000
89B523GLY00.0240.01848.3180.0720.0720.0000.0000.0000.000
90B524SER0-0.008-0.03048.381-0.092-0.0920.0000.0000.0000.000
91B525ASN0-0.035-0.00645.8050.0370.0370.0000.0000.0000.000
92B526SER00.0170.03145.219-0.074-0.0740.0000.0000.0000.000
93B527TYR0-0.052-0.05141.5100.0240.0240.0000.0000.0000.000
94B528ILE00.0120.00442.5620.0460.0460.0000.0000.0000.000
95B529VAL00.0200.01636.330-0.087-0.0870.0000.0000.0000.000
96B530ARG10.8470.87339.7637.0037.0030.0000.0000.0000.000
97B531CYS0-0.036-0.00937.0830.0090.0090.0000.0000.0000.000
98B532HIS10.8710.91432.1308.7498.7490.0000.0000.0000.000
99B533PRO00.0540.03928.6360.1440.1440.0000.0000.0000.000
100B534ALA0-0.0030.01730.2350.0560.0560.0000.0000.0000.000
101B535TRP0-0.025-0.02125.1750.0220.0220.0000.0000.0000.000
102B536PHE0-0.004-0.00525.971-0.323-0.3230.0000.0000.0000.000
103B537PRO00.0130.00725.0560.1250.1250.0000.0000.0000.000
104B538LYS10.9710.97127.5938.6908.6900.0000.0000.0000.000
105B539GLY0-0.065-0.03030.919-0.022-0.0220.0000.0000.0000.000
106B540GLU-1-0.805-0.89128.520-9.687-9.6870.0000.0000.0000.000
107B541GLU-1-0.844-0.91931.145-8.674-8.6740.0000.0000.0000.000
108B542ALA00.003-0.00632.438-0.043-0.0430.0000.0000.0000.000
109B543GLU-1-0.845-0.93531.902-8.449-8.4490.0000.0000.0000.000
110B544LEU0-0.0110.00426.345-0.153-0.1530.0000.0000.0000.000
111B545ILE0-0.017-0.01130.172-0.136-0.1360.0000.0000.0000.000
112B546GLU-1-0.947-0.96532.419-7.880-7.8800.0000.0000.0000.000
113B547GLU-1-0.819-0.90227.348-10.193-10.1930.0000.0000.0000.000
114B548ILE0-0.007-0.01927.158-0.166-0.1660.0000.0000.0000.000
115B549ILE0-0.015-0.01029.837-0.057-0.0570.0000.0000.0000.000
116B550GLN0-0.026-0.01432.5050.2030.2030.0000.0000.0000.000
117B551GLN00.0300.02126.888-0.042-0.0420.0000.0000.0000.000
118B552VAL0-0.0100.00230.266-0.080-0.0800.0000.0000.0000.000
119B553LEU0-0.048-0.00832.1160.1270.1270.0000.0000.0000.000
120B554ASP-1-0.888-0.94331.793-8.534-8.5340.0000.0000.0000.000
121B555SER0-0.072-0.04229.648-0.140-0.1400.0000.0000.0000.000
122B556LYS10.8110.92631.8028.2858.2850.0000.0000.0000.000
123B557ASN0-0.076-0.07333.1380.0840.0840.0000.0000.0000.000
124B558ILE0-0.041-0.00126.208-0.268-0.2680.0000.0000.0000.000
125B559ASP-1-0.781-0.89325.650-11.882-11.8820.0000.0000.0000.000
126B560ILE00.0600.02125.344-0.307-0.3070.0000.0000.0000.000
127B561LYS10.8620.94817.39215.75415.7540.0000.0000.0000.000
128B562LYS10.7960.86321.91311.22211.2220.0000.0000.0000.000
129B563LEU00.0520.02923.125-0.147-0.1470.0000.0000.0000.000
130B564ARG10.9140.95721.76312.03512.0350.0000.0000.0000.000
131B565GLU-1-0.830-0.87816.703-16.689-16.6890.0000.0000.0000.000
132B566GLU-1-0.767-0.87820.079-12.050-12.0500.0000.0000.0000.000
133B567ALA00.0400.01922.4810.1130.1130.0000.0000.0000.000
134B568ALA00.0180.01018.9040.1200.1200.0000.0000.0000.000
135B569ILE0-0.013-0.01217.687-0.157-0.1570.0000.0000.0000.000
136B570MET0-0.0160.02719.9110.1650.1650.0000.0000.0000.000
137B571MET0-0.0160.00322.1080.1410.1410.0000.0000.0000.000
138B572SER0-0.065-0.03218.116-0.050-0.0500.0000.0000.0000.000
139B573CYS0-0.063-0.01620.235-0.216-0.2160.0000.0000.0000.000
140B574LYS10.7920.91122.24110.66910.6690.0000.0000.0000.000
141B575GLY00.0230.00523.893-0.466-0.4660.0000.0000.0000.000
142B576SER0-0.032-0.02826.1890.1960.1960.0000.0000.0000.000
143B577ILE00.0030.00321.8170.2050.2050.0000.0000.0000.000
144B578LYS10.9090.95525.0359.7349.7340.0000.0000.0000.000
145B579ALA00.0430.01524.9960.2640.2640.0000.0000.0000.000
146B580ASN0-0.037-0.02627.1520.0340.0340.0000.0000.0000.000
147B581ARG10.7830.86625.75210.24610.2460.0000.0000.0000.000
148B582HIS00.0330.01626.066-0.467-0.4670.0000.0000.0000.000
149B583LEU0-0.0010.01020.1350.1900.1900.0000.0000.0000.000
150B584ARG10.8290.88823.89610.52210.5220.0000.0000.0000.000
151B585ASN00.041-0.00222.039-0.512-0.5120.0000.0000.0000.000
152B586ASP-1-0.844-0.91720.521-11.493-11.4930.0000.0000.0000.000
153B587GLU-1-0.697-0.79719.730-11.104-11.1040.0000.0000.0000.000
154B588ILE00.0050.00417.490-0.533-0.5330.0000.0000.0000.000
155B589LYS10.9060.94815.94613.32113.3210.0000.0000.0000.000
156B590ALA00.0330.02714.760-0.799-0.7990.0000.0000.0000.000
157B591LEU00.0400.03713.452-0.607-0.6070.0000.0000.0000.000
158B592LEU0-0.046-0.03111.760-0.831-0.8310.0000.0000.0000.000
159B593ASP-1-0.923-0.97010.031-22.026-22.0260.0000.0000.0000.000
160B594ASP-1-0.853-0.9209.901-17.393-17.3930.0000.0000.0000.000
161B595LEU0-0.048-0.0158.734-0.961-0.9610.0000.0000.0000.000
162B596ARG10.8400.9265.12326.12426.1240.0000.0000.0000.000
163B597SER0-0.099-0.0455.307-2.683-2.6830.0000.0000.0000.000
164B598THR0-0.039-0.0197.2910.3720.3720.0000.0000.0000.000
165B599SER0-0.063-0.0675.915-2.846-2.8460.0000.0000.0000.000
166B600ASP-1-0.855-0.9324.921-30.276-30.2760.0000.0000.0000.000
167B601PRO0-0.026-0.0093.6502.0812.4770.015-0.134-0.2770.001
168B602PHE00.001-0.0143.1700.3071.1260.084-0.351-0.5520.003
169B603THR00.0140.0127.8042.0782.0780.0000.0000.0000.000
170B604CYS0-0.0600.00510.347-0.252-0.2520.0000.0000.0000.000
171B605PRO00.0650.03413.063-0.299-0.2990.0000.0000.0000.000
172B606HIS00.015-0.02814.8220.3470.3470.0000.0000.0000.000
173B607GLY0-0.008-0.00114.2120.4460.4460.0000.0000.0000.000
174B608ARG10.8810.93215.12712.90212.9020.0000.0000.0000.000
175B609PRO00.0250.00812.518-0.669-0.6690.0000.0000.0000.000
176B610ILE0-0.0420.0039.8811.0521.0520.0000.0000.0000.000
177B611ILE0-0.044-0.0347.6620.6870.6870.0000.0000.0000.000
178B612ILE0-0.026-0.00211.518-0.230-0.2300.0000.0000.0000.000
179B613HIS0-0.047-0.0468.554-1.239-1.2390.0000.0000.0000.000
180B614HIS00.0150.02011.646-0.167-0.1670.0000.0000.0000.000
181B615SER00.018-0.03011.3400.2380.2380.0000.0000.0000.000
182B616THR00.0500.00312.8961.1571.1570.0000.0000.0000.000
183B617TYR00.0660.04314.2631.4251.4250.0000.0000.0000.000
184B618GLU-1-0.835-0.89213.504-17.823-17.8230.0000.0000.0000.000
185B619MET0-0.020-0.01416.8420.9470.9470.0000.0000.0000.000
186B620GLU-1-0.923-0.96318.791-14.061-14.0610.0000.0000.0000.000
187B621LYS10.8920.94919.47014.56714.5670.0000.0000.0000.000
188B622MET0-0.042-0.00618.1070.7990.7990.0000.0000.0000.000
189B623PHE0-0.049-0.02421.8430.6830.6830.0000.0000.0000.000
190B624LYS10.8710.93524.72411.02711.0270.0000.0000.0000.000
191B625ARG10.9420.98923.78810.99510.9950.0000.0000.0000.000