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

tag_button

FMODB ID: Q1Q1Y

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2064707.60957
FMO2-HF: Nuclear repulsion 1985773.476799
FMO2-HF: Total energy -78934.13277
FMO2-MP2: Total energy -79161.13218


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.
-107.103-104.3660.104-1.075-1.7650.005
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 : 0.984 / q_NPA : 0.977
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].
3B437PRO00.0230.0033.865-0.0171.143-0.009-0.486-0.6650.001
4B438ILE00.0400.0176.7441.3611.3610.0000.0000.0000.000
5B439MET0-0.0150.0258.2110.1900.1900.0000.0000.0000.000
6B440TYR00.007-0.00311.0100.8570.8570.0000.0000.0000.000
7B441PRO0-0.013-0.01314.7020.0470.0470.0000.0000.0000.000
8B442ILE0-0.063-0.02517.1250.3050.3050.0000.0000.0000.000
9B443GLY00.001-0.00719.5800.6630.6630.0000.0000.0000.000
10B444GLN00.0140.00519.774-0.549-0.5490.0000.0000.0000.000
11B445MET0-0.031-0.01121.8170.3920.3920.0000.0000.0000.000
12B446HIS00.027-0.00923.556-0.225-0.2250.0000.0000.0000.000
13B447GLY00.0410.04225.0410.1040.1040.0000.0000.0000.000
14B448THR0-0.053-0.01621.5490.0130.0130.0000.0000.0000.000
15B449TYR00.0000.00118.396-0.256-0.2560.0000.0000.0000.000
16B450ILE00.0310.01515.6630.5150.5150.0000.0000.0000.000
17B451LEU0-0.021-0.00316.787-0.387-0.3870.0000.0000.0000.000
18B452ALA00.0320.00213.3970.3080.3080.0000.0000.0000.000
19B453GLN00.0190.00613.772-0.564-0.5640.0000.0000.0000.000
20B454ASN00.0180.0028.668-0.794-0.7940.0000.0000.0000.000
21B455GLU-1-0.911-0.94411.694-20.757-20.7570.0000.0000.0000.000
22B456ASN0-0.0010.0066.3971.2111.2110.0000.0000.0000.000
23B457GLY00.0100.01410.5650.3310.3310.0000.0000.0000.000
24B458LEU0-0.021-0.00613.203-0.028-0.0280.0000.0000.0000.000
25B459TYR0-0.025-0.0318.113-1.577-1.5770.0000.0000.0000.000
26B460ILE0-0.011-0.01012.9880.9860.9860.0000.0000.0000.000
27B461ILE00.000-0.00311.167-0.509-0.5090.0000.0000.0000.000
28B462ASP-1-0.834-0.91214.480-12.521-12.5210.0000.0000.0000.000
29B463GLN0-0.004-0.02215.604-0.515-0.5150.0000.0000.0000.000
30B464HIS0-0.040-0.01317.451-0.040-0.0400.0000.0000.0000.000
31B465ALA00.025-0.00315.198-0.218-0.2180.0000.0000.0000.000
32B466ALA00.0420.00812.784-0.669-0.6690.0000.0000.0000.000
33B467GLN0-0.009-0.00813.741-0.170-0.1700.0000.0000.0000.000
34B468GLU-1-0.799-0.88316.183-12.595-12.5950.0000.0000.0000.000
35B469ARG10.8400.9119.27722.28622.2860.0000.0000.0000.000
36B470ILE0-0.008-0.00912.361-0.354-0.3540.0000.0000.0000.000
37B471LYS10.7750.88913.61612.59012.5900.0000.0000.0000.000
38B472TYR0-0.022-0.02412.2920.0410.0410.0000.0000.0000.000
39B473GLU-1-0.754-0.8549.776-22.803-22.8030.0000.0000.0000.000
40B474TYR00.0060.01313.5430.2180.2180.0000.0000.0000.000
41B475PHE00.0390.00016.8460.3390.3390.0000.0000.0000.000
42B476ARG10.7910.87514.90616.10416.1040.0000.0000.0000.000
43B477GLU-1-0.903-0.93716.421-14.754-14.7540.0000.0000.0000.000
44B478LYS10.7950.88817.98813.39713.3970.0000.0000.0000.000
45B479VAL0-0.012-0.01220.3940.4360.4360.0000.0000.0000.000
46B480GLY0-0.017-0.01220.9440.0890.0890.0000.0000.0000.000
47B481GLU-1-0.830-0.90221.859-11.706-11.7060.0000.0000.0000.000
48B482VAL0-0.022-0.01324.6860.1570.1570.0000.0000.0000.000
49B483GLU-1-0.954-0.97928.053-9.229-9.2290.0000.0000.0000.000
50B484PRO0-0.0210.00926.878-0.046-0.0460.0000.0000.0000.000
51B485GLU-1-0.902-0.95228.588-9.179-9.1790.0000.0000.0000.000
52B486VAL0-0.042-0.02030.268-0.134-0.1340.0000.0000.0000.000
53B487GLN0-0.060-0.03433.045-0.022-0.0220.0000.0000.0000.000
54B488GLU-1-0.931-0.96635.105-7.099-7.0990.0000.0000.0000.000
55B489MET0-0.046-0.00535.976-0.118-0.1180.0000.0000.0000.000
56B490ILE00.000-0.01538.8110.1650.1650.0000.0000.0000.000
57B491VAL0-0.025-0.01440.4900.2000.2000.0000.0000.0000.000
58B492PRO0-0.009-0.00140.314-0.156-0.1560.0000.0000.0000.000
59B493LEU00.0200.03536.1520.0960.0960.0000.0000.0000.000
60B494THR0-0.051-0.04640.6870.1500.1500.0000.0000.0000.000
61B495PHE00.0080.01936.642-0.032-0.0320.0000.0000.0000.000
62B496HIS0-0.045-0.04042.0510.1200.1200.0000.0000.0000.000
63B497TYR00.0480.03937.618-0.057-0.0570.0000.0000.0000.000
64B498SER0-0.052-0.07643.3250.2030.2030.0000.0000.0000.000
65B499THR00.021-0.01744.317-0.094-0.0940.0000.0000.0000.000
66B500ASN0-0.015-0.00743.2240.0130.0130.0000.0000.0000.000
67B501GLU-1-0.756-0.83839.654-7.423-7.4230.0000.0000.0000.000
68B502ALA00.0380.02639.935-0.158-0.1580.0000.0000.0000.000
69B503LEU0-0.049-0.02341.437-0.075-0.0750.0000.0000.0000.000
70B504ILE00.0040.00736.308-0.102-0.1020.0000.0000.0000.000
71B505ILE00.0170.01836.779-0.230-0.2300.0000.0000.0000.000
72B506GLU-1-0.804-0.89237.317-7.613-7.6130.0000.0000.0000.000
73B507GLN0-0.074-0.02635.7050.0700.0700.0000.0000.0000.000
74B508HIS0-0.010-0.00732.394-0.374-0.3740.0000.0000.0000.000
75B509LYS10.8110.92433.7217.4877.4870.0000.0000.0000.000
76B510GLN0-0.0100.00233.012-0.177-0.1770.0000.0000.0000.000
77B511GLU-1-0.873-0.94329.619-9.898-9.8980.0000.0000.0000.000
78B512LEU00.0320.02129.285-0.329-0.3290.0000.0000.0000.000
79B513GLU-1-0.863-0.94230.771-8.624-8.6240.0000.0000.0000.000
80B514SER0-0.084-0.04627.695-0.315-0.3150.0000.0000.0000.000
81B515VAL0-0.017-0.00724.979-0.532-0.5320.0000.0000.0000.000
82B516GLY0-0.014-0.01827.256-0.052-0.0520.0000.0000.0000.000
83B517VAL0-0.017-0.01030.0640.2740.2740.0000.0000.0000.000
84B518PHE00.011-0.00331.8420.1070.1070.0000.0000.0000.000
85B519LEU00.0040.00535.7860.2350.2350.0000.0000.0000.000
86B520GLU-1-0.787-0.86638.368-7.113-7.1130.0000.0000.0000.000
87B521SER0-0.008-0.00841.8110.1250.1250.0000.0000.0000.000
88B522PHE0-0.040-0.02244.4350.0960.0960.0000.0000.0000.000
89B523GLY00.0210.01147.7900.1710.1710.0000.0000.0000.000
90B524SER0-0.018-0.02247.830-0.130-0.1300.0000.0000.0000.000
91B525ASN0-0.0290.00345.3500.0200.0200.0000.0000.0000.000
92B526SER00.0100.00944.721-0.080-0.0800.0000.0000.0000.000
93B527TYR0-0.052-0.05641.1860.0580.0580.0000.0000.0000.000
94B528ILE00.000-0.00242.2240.0690.0690.0000.0000.0000.000
95B529VAL00.0220.01335.852-0.117-0.1170.0000.0000.0000.000
96B530ARG10.8660.90739.3047.0077.0070.0000.0000.0000.000
97B531CYS0-0.047-0.01136.513-0.008-0.0080.0000.0000.0000.000
98B532HIS10.8750.90631.3548.8638.8630.0000.0000.0000.000
99B533PRO00.0490.03728.1010.1390.1390.0000.0000.0000.000
100B534ALA0-0.0220.00229.8030.0390.0390.0000.0000.0000.000
101B535TRP0-0.046-0.03424.4280.0670.0670.0000.0000.0000.000
102B536PHE00.010-0.00625.342-0.323-0.3230.0000.0000.0000.000
103B537PRO0-0.009-0.01224.5990.1500.1500.0000.0000.0000.000
104B538LYS10.9520.98627.1968.7558.7550.0000.0000.0000.000
105B539GLY0-0.060-0.03630.545-0.027-0.0270.0000.0000.0000.000
106B540GLU-1-0.808-0.89727.838-9.852-9.8520.0000.0000.0000.000
107B541GLU-1-0.831-0.90330.815-8.690-8.6900.0000.0000.0000.000
108B542ALA00.0180.00731.867-0.048-0.0480.0000.0000.0000.000
109B543GLU-1-0.843-0.93531.609-8.534-8.5340.0000.0000.0000.000
110B544LEU0-0.0160.00225.930-0.151-0.1510.0000.0000.0000.000
111B545ILE0-0.013-0.00829.663-0.164-0.1640.0000.0000.0000.000
112B546GLU-1-0.938-0.96932.067-7.944-7.9440.0000.0000.0000.000
113B547GLU-1-0.851-0.91227.052-10.369-10.3690.0000.0000.0000.000
114B548ILE00.011-0.00926.384-0.170-0.1700.0000.0000.0000.000
115B549ILE0-0.017-0.00629.301-0.050-0.0500.0000.0000.0000.000
116B550GLN0-0.027-0.02631.9980.1560.1560.0000.0000.0000.000
117B551GLN0-0.015-0.01126.3970.1800.1800.0000.0000.0000.000
118B552VAL0-0.014-0.00229.815-0.124-0.1240.0000.0000.0000.000
119B553LEU0-0.031-0.00131.8390.1280.1280.0000.0000.0000.000
120B554ASP-1-0.845-0.90832.189-8.320-8.3200.0000.0000.0000.000
121B555SER0-0.039-0.02228.994-0.189-0.1890.0000.0000.0000.000
122B556LYS10.7330.87331.2478.4168.4160.0000.0000.0000.000
123B557ASN0-0.082-0.07533.0390.1470.1470.0000.0000.0000.000
124B558ILE0-0.062-0.01426.282-0.293-0.2930.0000.0000.0000.000
125B559ASP-1-0.770-0.87825.363-12.054-12.0540.0000.0000.0000.000
126B560ILE00.0640.03025.211-0.250-0.2500.0000.0000.0000.000
127B561LYS10.8430.91917.16216.05216.0520.0000.0000.0000.000
128B562LYS10.7930.87621.90211.17411.1740.0000.0000.0000.000
129B563LEU00.0490.02523.022-0.175-0.1750.0000.0000.0000.000
130B564ARG10.8120.89421.58712.02612.0260.0000.0000.0000.000
131B565GLU-1-0.827-0.86916.573-16.983-16.9830.0000.0000.0000.000
132B566GLU-1-0.756-0.87419.709-11.912-11.9120.0000.0000.0000.000
133B567ALA00.0680.03422.1800.1020.1020.0000.0000.0000.000
134B568ALA00.0140.01718.1570.0860.0860.0000.0000.0000.000
135B569ILE0-0.021-0.01217.438-0.156-0.1560.0000.0000.0000.000
136B570MET0-0.0270.01919.5350.1560.1560.0000.0000.0000.000
137B571MET00.0000.01021.6720.2060.2060.0000.0000.0000.000
138B572SER0-0.080-0.04517.498-0.068-0.0680.0000.0000.0000.000
139B573CYS0-0.064-0.02419.586-0.156-0.1560.0000.0000.0000.000
140B574LYS10.7790.89121.92010.84610.8460.0000.0000.0000.000
141B575GLY00.0450.01323.211-0.457-0.4570.0000.0000.0000.000
142B576SER0-0.020-0.01525.4990.0340.0340.0000.0000.0000.000
143B577ILE0-0.020-0.01321.4170.2000.2000.0000.0000.0000.000
144B578LYS10.8930.94724.5659.9779.9770.0000.0000.0000.000
145B579ALA00.0380.01224.7540.2800.2800.0000.0000.0000.000
146B580ASN0-0.044-0.02826.8370.0280.0280.0000.0000.0000.000
147B581ARG10.7900.87125.55310.30410.3040.0000.0000.0000.000
148B582HIS00.0520.02725.848-0.509-0.5090.0000.0000.0000.000
149B583LEU0-0.0060.01620.0460.1730.1730.0000.0000.0000.000
150B584ARG10.8050.87623.91510.66110.6610.0000.0000.0000.000
151B585ASN00.028-0.00521.958-0.491-0.4910.0000.0000.0000.000
152B586ASP-1-0.830-0.90820.332-11.535-11.5350.0000.0000.0000.000
153B587GLU-1-0.686-0.79019.386-11.143-11.1430.0000.0000.0000.000
154B588ILE0-0.008-0.00417.543-0.554-0.5540.0000.0000.0000.000
155B589LYS10.9050.94015.97213.59413.5940.0000.0000.0000.000
156B590ALA00.0110.02314.751-0.736-0.7360.0000.0000.0000.000
157B591LEU00.0350.02813.388-0.761-0.7610.0000.0000.0000.000
158B592LEU0-0.029-0.02611.879-0.815-0.8150.0000.0000.0000.000
159B593ASP-1-0.870-0.9279.666-22.779-22.7790.0000.0000.0000.000
160B594ASP-1-0.864-0.9299.412-17.450-17.4500.0000.0000.0000.000
161B595LEU0-0.024-0.0038.506-0.909-0.9090.0000.0000.0000.000
162B596ARG10.7720.8834.87526.45426.4540.0000.0000.0000.000
163B597SER0-0.085-0.0474.959-2.783-2.692-0.001-0.001-0.0880.000
164B598THR0-0.052-0.0217.314-0.521-0.5210.0000.0000.0000.000
165B599SER0-0.054-0.0665.275-2.801-2.8010.0000.0000.0000.000
166B600ASP-1-0.851-0.9234.551-30.982-30.895-0.001-0.005-0.0810.000
167B601PRO0-0.024-0.0013.4811.8812.5900.070-0.294-0.4840.002
168B602PHE0-0.013-0.0163.2180.3461.0360.045-0.289-0.4470.002
169B603THR00.013-0.0157.7822.0092.0090.0000.0000.0000.000
170B604CYS0-0.0420.01110.277-0.311-0.3110.0000.0000.0000.000
171B605PRO00.0470.01712.983-0.275-0.2750.0000.0000.0000.000
172B606HIS00.0280.00614.8120.5620.5620.0000.0000.0000.000
173B607GLY00.0050.00614.2980.4700.4700.0000.0000.0000.000
174B608ARG10.8660.92415.30412.97612.9760.0000.0000.0000.000
175B609PRO00.012-0.00512.479-0.614-0.6140.0000.0000.0000.000
176B610ILE0-0.0370.0099.8891.0341.0340.0000.0000.0000.000
177B611ILE0-0.046-0.0227.4410.9040.9040.0000.0000.0000.000
178B612ILE0-0.0090.00611.028-0.527-0.5270.0000.0000.0000.000
179B613HIS0-0.046-0.0509.229-1.361-1.3610.0000.0000.0000.000
180B614HIS00.0160.01912.019-0.044-0.0440.0000.0000.0000.000
181B615SER00.024-0.03211.4860.2810.2810.0000.0000.0000.000
182B616THR00.011-0.02112.9941.3771.3770.0000.0000.0000.000
183B617TYR00.0930.05714.8331.3911.3910.0000.0000.0000.000
184B618GLU-1-0.846-0.88813.746-17.965-17.9650.0000.0000.0000.000
185B619MET0-0.010-0.00516.9200.8930.8930.0000.0000.0000.000
186B620GLU-1-0.921-0.96318.947-13.964-13.9640.0000.0000.0000.000
187B621LYS10.8830.94419.61314.76214.7620.0000.0000.0000.000
188B622MET0-0.049-0.01418.4620.7830.7830.0000.0000.0000.000
189B623PHE0-0.029-0.01521.9110.7230.7230.0000.0000.0000.000
190B624LYS10.8550.93424.81111.21711.2170.0000.0000.0000.000
191B625ARG10.9340.97423.86211.10211.1020.0000.0000.0000.000