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: ZY3YN

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 OptH
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 -2058805.145387
FMO2-HF: Nuclear repulsion 1979872.302203
FMO2-HF: Total energy -78932.843184
FMO2-MP2: Total energy -79159.755469


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.
-108.484-106.1640.026-0.91-1.4360.004
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 : 0.989 / q_NPA : 0.985
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].
3B437PRO00.0480.0313.806-0.3051.050-0.015-0.554-0.7860.002
4B438ILE00.0510.0176.4951.6811.6810.0000.0000.0000.000
5B439MET0-0.0060.0158.0470.0590.0590.0000.0000.0000.000
6B440TYR0-0.035-0.02011.0920.7170.7170.0000.0000.0000.000
7B441PRO00.0040.00014.8480.0410.0410.0000.0000.0000.000
8B442ILE0-0.067-0.02717.1960.3150.3150.0000.0000.0000.000
9B443GLY00.002-0.01119.6770.6600.6600.0000.0000.0000.000
10B444GLN00.0450.03820.017-0.559-0.5590.0000.0000.0000.000
11B445MET0-0.035-0.01822.0560.3250.3250.0000.0000.0000.000
12B446HIS00.019-0.00923.738-0.220-0.2200.0000.0000.0000.000
13B447GLY00.0250.03725.0820.1570.1570.0000.0000.0000.000
14B448THR0-0.075-0.03621.6260.0340.0340.0000.0000.0000.000
15B449TYR00.0040.00018.661-0.251-0.2510.0000.0000.0000.000
16B450ILE00.0140.00515.9850.4880.4880.0000.0000.0000.000
17B451LEU0-0.0220.00016.483-0.514-0.5140.0000.0000.0000.000
18B452ALA00.0410.00713.3020.3010.3010.0000.0000.0000.000
19B453GLN00.0320.01613.935-0.635-0.6350.0000.0000.0000.000
20B454ASN00.0320.0038.524-0.196-0.1960.0000.0000.0000.000
21B455GLU-1-0.917-0.95111.322-21.970-21.9700.0000.0000.0000.000
22B456ASN0-0.049-0.0166.5241.2461.2460.0000.0000.0000.000
23B457GLY00.0200.01510.5120.2550.2550.0000.0000.0000.000
24B458LEU0-0.013-0.01513.2530.1070.1070.0000.0000.0000.000
25B459TYR0-0.024-0.0207.598-1.615-1.6150.0000.0000.0000.000
26B460ILE0-0.014-0.00812.8310.9190.9190.0000.0000.0000.000
27B461ILE00.0220.00711.611-0.489-0.4890.0000.0000.0000.000
28B462ASP-1-0.832-0.90714.554-12.267-12.2670.0000.0000.0000.000
29B463GLN0-0.014-0.03115.998-0.379-0.3790.0000.0000.0000.000
30B464HIS00.0010.01017.535-0.398-0.3980.0000.0000.0000.000
31B465ALA00.0480.01815.260-0.137-0.1370.0000.0000.0000.000
32B466ALA00.015-0.00812.966-0.576-0.5760.0000.0000.0000.000
33B467GLN0-0.026-0.02313.901-0.252-0.2520.0000.0000.0000.000
34B468GLU-1-0.893-0.94816.630-12.665-12.6650.0000.0000.0000.000
35B469ARG10.8510.9269.53620.60820.6080.0000.0000.0000.000
36B470ILE0-0.006-0.00512.468-0.456-0.4560.0000.0000.0000.000
37B471LYS10.8620.94713.87612.34712.3470.0000.0000.0000.000
38B472TYR0-0.061-0.06713.136-0.020-0.0200.0000.0000.0000.000
39B473GLU-1-0.826-0.92610.567-22.157-22.1570.0000.0000.0000.000
40B474TYR0-0.0020.01513.9320.2980.2980.0000.0000.0000.000
41B475PHE00.012-0.01317.2910.2980.2980.0000.0000.0000.000
42B476ARG10.9110.95515.61915.62415.6240.0000.0000.0000.000
43B477GLU-1-0.948-0.96617.130-15.110-15.1100.0000.0000.0000.000
44B478LYS10.8450.91518.64212.68612.6860.0000.0000.0000.000
45B479VAL0-0.019-0.01420.8360.4200.4200.0000.0000.0000.000
46B480GLY0-0.087-0.04421.6100.2390.2390.0000.0000.0000.000
47B481GLU-1-0.869-0.91622.569-11.924-11.9240.0000.0000.0000.000
48B482VAL0-0.047-0.03225.2830.2360.2360.0000.0000.0000.000
49B483GLU-1-0.969-0.98628.598-8.997-8.9970.0000.0000.0000.000
50B484PRO0-0.0020.02427.493-0.050-0.0500.0000.0000.0000.000
51B485GLU-1-0.928-0.96529.222-9.010-9.0100.0000.0000.0000.000
52B486VAL0-0.029-0.02130.974-0.118-0.1180.0000.0000.0000.000
53B487GLN0-0.019-0.01133.633-0.055-0.0550.0000.0000.0000.000
54B488GLU-1-0.972-0.98935.650-7.009-7.0090.0000.0000.0000.000
55B489MET0-0.081-0.03436.973-0.114-0.1140.0000.0000.0000.000
56B490ILE00.0340.01639.2960.1460.1460.0000.0000.0000.000
57B491VAL0-0.030-0.02940.7920.1890.1890.0000.0000.0000.000
58B492PRO0-0.0030.00740.813-0.147-0.1470.0000.0000.0000.000
59B493LEU00.0060.01936.9400.0820.0820.0000.0000.0000.000
60B494THR0-0.018-0.01741.3770.0910.0910.0000.0000.0000.000
61B495PHE00.0050.00637.046-0.042-0.0420.0000.0000.0000.000
62B496HIS0-0.045-0.03842.2980.1110.1110.0000.0000.0000.000
63B497TYR00.0480.03038.209-0.105-0.1050.0000.0000.0000.000
64B498SER0-0.020-0.02143.5280.2100.2100.0000.0000.0000.000
65B499THR00.045-0.00544.666-0.077-0.0770.0000.0000.0000.000
66B500ASN0-0.009-0.01943.485-0.028-0.0280.0000.0000.0000.000
67B501GLU-1-0.837-0.90839.975-7.366-7.3660.0000.0000.0000.000
68B502ALA00.0490.02340.318-0.167-0.1670.0000.0000.0000.000
69B503LEU0-0.050-0.01241.929-0.066-0.0660.0000.0000.0000.000
70B504ILE00.0100.00936.460-0.096-0.0960.0000.0000.0000.000
71B505ILE00.0150.01737.226-0.214-0.2140.0000.0000.0000.000
72B506GLU-1-0.870-0.94037.789-7.432-7.4320.0000.0000.0000.000
73B507GLN0-0.090-0.04436.0380.0830.0830.0000.0000.0000.000
74B508HIS0-0.023-0.00632.425-0.346-0.3460.0000.0000.0000.000
75B509LYS10.8910.96634.2237.4677.4670.0000.0000.0000.000
76B510GLN00.0200.01033.363-0.220-0.2200.0000.0000.0000.000
77B511GLU-1-0.873-0.94929.953-9.685-9.6850.0000.0000.0000.000
78B512LEU00.0000.01329.755-0.314-0.3140.0000.0000.0000.000
79B513GLU-1-0.930-0.95431.152-8.541-8.5410.0000.0000.0000.000
80B514SER0-0.126-0.07527.941-0.324-0.3240.0000.0000.0000.000
81B515VAL0-0.033-0.01825.400-0.453-0.4530.0000.0000.0000.000
82B516GLY0-0.019-0.01327.535-0.049-0.0490.0000.0000.0000.000
83B517VAL0-0.018-0.01230.1440.2510.2510.0000.0000.0000.000
84B518PHE00.0240.00532.1390.0490.0490.0000.0000.0000.000
85B519LEU0-0.025-0.00536.1430.2150.2150.0000.0000.0000.000
86B520GLU-1-0.848-0.92038.814-7.066-7.0660.0000.0000.0000.000
87B521SER0-0.004-0.00842.4020.1240.1240.0000.0000.0000.000
88B522PHE0-0.043-0.01945.0540.1130.1130.0000.0000.0000.000
89B523GLY00.0170.01348.2920.0770.0770.0000.0000.0000.000
90B524SER0-0.005-0.03648.358-0.133-0.1330.0000.0000.0000.000
91B525ASN0-0.0280.00445.7850.0190.0190.0000.0000.0000.000
92B526SER00.0190.02945.195-0.076-0.0760.0000.0000.0000.000
93B527TYR0-0.034-0.04341.480-0.006-0.0060.0000.0000.0000.000
94B528ILE00.0140.00642.5360.0420.0420.0000.0000.0000.000
95B529VAL00.0160.01936.337-0.086-0.0860.0000.0000.0000.000
96B530ARG10.9030.93339.7326.9236.9230.0000.0000.0000.000
97B531CYS0-0.027-0.00836.9630.0170.0170.0000.0000.0000.000
98B532HIS10.9240.95931.8478.7228.7220.0000.0000.0000.000
99B533PRO00.0640.04728.6420.1400.1400.0000.0000.0000.000
100B534ALA00.0140.01630.3090.0370.0370.0000.0000.0000.000
101B535TRP0-0.010-0.01524.996-0.046-0.0460.0000.0000.0000.000
102B536PHE0-0.007-0.00825.934-0.312-0.3120.0000.0000.0000.000
103B537PRO00.0040.00025.0200.1340.1340.0000.0000.0000.000
104B538LYS10.9760.98027.5548.6558.6550.0000.0000.0000.000
105B539GLY0-0.098-0.04830.878-0.023-0.0230.0000.0000.0000.000
106B540GLU-1-0.825-0.90328.702-9.513-9.5130.0000.0000.0000.000
107B541GLU-1-0.867-0.94631.109-8.788-8.7880.0000.0000.0000.000
108B542ALA0-0.001-0.01032.402-0.038-0.0380.0000.0000.0000.000
109B543GLU-1-0.838-0.93031.870-8.391-8.3910.0000.0000.0000.000
110B544LEU0-0.0080.00726.443-0.156-0.1560.0000.0000.0000.000
111B545ILE0-0.014-0.01430.139-0.129-0.1290.0000.0000.0000.000
112B546GLU-1-0.955-0.96932.389-7.905-7.9050.0000.0000.0000.000
113B547GLU-1-0.850-0.93027.486-10.057-10.0570.0000.0000.0000.000
114B548ILE0-0.015-0.02127.382-0.161-0.1610.0000.0000.0000.000
115B549ILE0-0.027-0.01629.811-0.042-0.0420.0000.0000.0000.000
116B550GLN0-0.014-0.00332.4560.1970.1970.0000.0000.0000.000
117B551GLN00.0170.01826.981-0.059-0.0590.0000.0000.0000.000
118B552VAL0-0.022-0.01730.246-0.075-0.0750.0000.0000.0000.000
119B553LEU0-0.069-0.02832.0990.1290.1290.0000.0000.0000.000
120B554ASP-1-0.907-0.95531.741-8.534-8.5340.0000.0000.0000.000
121B555SER0-0.076-0.03729.432-0.171-0.1710.0000.0000.0000.000
122B556LYS10.8780.96431.7918.1108.1100.0000.0000.0000.000
123B557ASN0-0.039-0.05033.1270.0530.0530.0000.0000.0000.000
124B558ILE0-0.045-0.00226.235-0.283-0.2830.0000.0000.0000.000
125B559ASP-1-0.813-0.91126.040-11.651-11.6510.0000.0000.0000.000
126B560ILE00.0650.02025.248-0.308-0.3080.0000.0000.0000.000
127B561LYS10.8860.95117.75115.43215.4320.0000.0000.0000.000
128B562LYS10.9210.96321.90011.09411.0940.0000.0000.0000.000
129B563LEU00.0570.03823.110-0.125-0.1250.0000.0000.0000.000
130B564ARG10.9310.95921.64012.07212.0720.0000.0000.0000.000
131B565GLU-1-0.884-0.90316.778-16.318-16.3180.0000.0000.0000.000
132B566GLU-1-0.849-0.95220.056-12.753-12.7530.0000.0000.0000.000
133B567ALA00.0260.01622.4600.1280.1280.0000.0000.0000.000
134B568ALA00.0130.00618.8740.1260.1260.0000.0000.0000.000
135B569ILE0-0.013-0.00417.783-0.097-0.0970.0000.0000.0000.000
136B570MET0-0.0090.01519.8820.2060.2060.0000.0000.0000.000
137B571MET0-0.024-0.00322.0980.1490.1490.0000.0000.0000.000
138B572SER0-0.082-0.03318.072-0.019-0.0190.0000.0000.0000.000
139B573CYS0-0.033-0.00720.198-0.179-0.1790.0000.0000.0000.000
140B574LYS10.8130.93622.20510.65010.6500.0000.0000.0000.000
141B575GLY00.0130.00023.852-0.472-0.4720.0000.0000.0000.000
142B576SER0-0.038-0.03026.1470.1990.1990.0000.0000.0000.000
143B577ILE00.0150.01521.7960.1950.1950.0000.0000.0000.000
144B578LYS10.9080.94724.9819.5539.5530.0000.0000.0000.000
145B579ALA00.0530.02624.7260.2340.2340.0000.0000.0000.000
146B580ASN0-0.027-0.02626.8910.0210.0210.0000.0000.0000.000
147B581ARG10.8110.90025.70010.30010.3000.0000.0000.0000.000
148B582HIS00.0380.01726.065-0.427-0.4270.0000.0000.0000.000
149B583LEU0-0.0100.00619.9950.2100.2100.0000.0000.0000.000
150B584ARG10.9280.96623.92210.32810.3280.0000.0000.0000.000
151B585ASN00.040-0.00622.041-0.538-0.5380.0000.0000.0000.000
152B586ASP-1-0.875-0.93820.538-11.609-11.6090.0000.0000.0000.000
153B587GLU-1-0.787-0.88219.747-11.229-11.2290.0000.0000.0000.000
154B588ILE0-0.0090.00017.322-0.527-0.5270.0000.0000.0000.000
155B589LYS10.9020.94215.94913.18213.1820.0000.0000.0000.000
156B590ALA00.0440.03514.775-0.785-0.7850.0000.0000.0000.000
157B591LEU00.0300.03413.469-0.588-0.5880.0000.0000.0000.000
158B592LEU0-0.049-0.03611.770-0.838-0.8380.0000.0000.0000.000
159B593ASP-1-0.989-0.99710.051-20.950-20.9500.0000.0000.0000.000
160B594ASP-1-0.812-0.9089.915-17.443-17.4430.0000.0000.0000.000
161B595LEU0-0.066-0.0138.695-0.975-0.9750.0000.0000.0000.000
162B596ARG10.8310.9045.23428.41428.4140.0000.0000.0000.000
163B597SER0-0.088-0.0495.323-2.558-2.5580.0000.0000.0000.000
164B598THR0-0.033-0.0097.3120.3600.3600.0000.0000.0000.000
165B599SER0-0.061-0.0385.877-3.027-3.0270.0000.0000.0000.000
166B600ASP-1-0.874-0.9584.902-30.736-30.7360.0000.0000.0000.000
167B601PRO0-0.034-0.0123.6272.0942.5320.020-0.155-0.3030.001
168B602PHE00.005-0.0153.4690.7231.2500.021-0.201-0.3470.001
169B603THR00.0340.0407.7932.1722.1720.0000.0000.0000.000
170B604CYS0-0.0580.02610.325-0.303-0.3030.0000.0000.0000.000
171B605PRO00.0670.02713.035-0.357-0.3570.0000.0000.0000.000
172B606HIS00.009-0.04114.7960.2040.2040.0000.0000.0000.000
173B607GLY0-0.011-0.00514.2020.4270.4270.0000.0000.0000.000
174B608ARG10.9130.94515.11412.84312.8430.0000.0000.0000.000
175B609PRO00.0240.01012.529-0.655-0.6550.0000.0000.0000.000
176B610ILE0-0.0270.01210.0471.0161.0160.0000.0000.0000.000
177B611ILE0-0.035-0.0257.5950.6720.6720.0000.0000.0000.000
178B612ILE0-0.024-0.00311.548-0.217-0.2170.0000.0000.0000.000
179B613HIS0-0.060-0.0528.849-1.087-1.0870.0000.0000.0000.000
180B614HIS00.0200.02911.683-0.078-0.0780.0000.0000.0000.000
181B615SER00.0370.01811.4180.1950.1950.0000.0000.0000.000
182B616THR00.0600.00812.8070.9950.9950.0000.0000.0000.000
183B617TYR00.0210.01714.1801.2891.2890.0000.0000.0000.000
184B618GLU-1-0.877-0.95113.988-17.407-17.4070.0000.0000.0000.000
185B619MET0-0.027-0.01616.6020.9530.9530.0000.0000.0000.000
186B620GLU-1-0.913-0.96018.707-14.081-14.0810.0000.0000.0000.000
187B621LYS10.9320.96419.64114.05014.0500.0000.0000.0000.000
188B622MET0-0.055-0.01018.2400.7820.7820.0000.0000.0000.000
189B623PHE0-0.059-0.02421.9070.6650.6650.0000.0000.0000.000
190B624LYS10.8910.94424.66510.63810.6380.0000.0000.0000.000
191B625ARG10.9510.99123.68211.00511.0050.0000.0000.0000.000