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: 3Q67L

Calculation Name: 4KRD-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KRD

Chain ID: B

ChEMBL ID:

UniProt ID: P53124

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2232249.822714
FMO2-HF: Nuclear repulsion 2155697.300139
FMO2-HF: Total energy -76552.522575
FMO2-MP2: Total energy -76774.070106


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:243:SER)


Summations of interaction energy for fragment #1(B:243: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.
-21.419-17.3345.907-4.974-5.019-0.03
Interaction energy analysis for fragmet #1(B:243:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.005
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].
3B245ASN0-0.002-0.0191.943-12.850-11.9225.573-3.671-2.830-0.042
4B246PRO00.0430.0124.0060.1700.384-0.001-0.017-0.1960.000
5B247LEU00.0390.0275.1480.4190.462-0.001-0.001-0.0410.000
6B248LEU0-0.039-0.0176.4910.1300.1300.0000.0000.0000.000
7B249HIS10.8240.8962.934-4.391-3.2340.094-0.453-0.7980.005
8B250GLY00.0620.0387.814-0.046-0.0460.0000.0000.0000.000
9B251ILE0-0.0430.00010.470-0.049-0.0490.0000.0000.0000.000
10B252PRO00.0590.03211.078-0.010-0.0100.0000.0000.0000.000
11B253VAL0-0.021-0.0259.971-0.079-0.0790.0000.0000.0000.000
12B254ASP-1-0.875-0.95011.999-0.200-0.2000.0000.0000.0000.000
13B255VAL0-0.066-0.01114.5300.0160.0160.0000.0000.0000.000
14B256GLU-1-0.737-0.86116.873-0.184-0.1840.0000.0000.0000.000
15B257VAL0-0.052-0.03619.227-0.014-0.0140.0000.0000.0000.000
16B258PRO0-0.049-0.03418.8970.0200.0200.0000.0000.0000.000
17B259HIS0-0.018-0.00821.8840.0050.0050.0000.0000.0000.000
18B260ILE0-0.058-0.01822.3890.0100.0100.0000.0000.0000.000
19B261SER00.002-0.01526.371-0.005-0.0050.0000.0000.0000.000
20B262VAL00.0540.00527.984-0.005-0.0050.0000.0000.0000.000
21B263ASP-1-0.822-0.89428.965-0.062-0.0620.0000.0000.0000.000
22B264GLU-1-0.760-0.85525.549-0.070-0.0700.0000.0000.0000.000
23B265ALA00.0040.01024.584-0.002-0.0020.0000.0000.0000.000
24B266LEU0-0.035-0.01524.947-0.004-0.0040.0000.0000.0000.000
25B267ALA0-0.024-0.00927.3000.0030.0030.0000.0000.0000.000
26B268ASN00.021-0.01722.4630.0120.0120.0000.0000.0000.000
27B269PHE00.0110.02521.9320.0030.0030.0000.0000.0000.000
28B270LYS10.8300.90623.7300.0380.0380.0000.0000.0000.000
29B271GLU-1-0.862-0.93725.234-0.024-0.0240.0000.0000.0000.000
30B272THR00.0450.00619.2190.0080.0080.0000.0000.0000.000
31B273ILE0-0.025-0.01122.4230.0080.0080.0000.0000.0000.000
32B274GLU-1-0.855-0.92724.222-0.018-0.0180.0000.0000.0000.000
33B275LEU0-0.0110.00522.7770.0090.0090.0000.0000.0000.000
34B276LEU00.0480.02418.3380.0110.0110.0000.0000.0000.000
35B277LEU0-0.051-0.01122.4180.0100.0100.0000.0000.0000.000
36B278LYS10.9200.96425.9780.0140.0140.0000.0000.0000.000
37B279LEU00.0440.02119.7270.0080.0080.0000.0000.0000.000
38B280SER0-0.061-0.03923.3500.0080.0080.0000.0000.0000.000
39B281GLY0-0.0140.00024.6990.0020.0020.0000.0000.0000.000
40B282ASN0-0.038-0.01825.6360.0050.0050.0000.0000.0000.000
41B283ARG10.9200.96617.920-0.091-0.0910.0000.0000.0000.000
42B284LYS10.8580.92224.569-0.046-0.0460.0000.0000.0000.000
43B285CYS0-0.029-0.00219.9080.0110.0110.0000.0000.0000.000
44B286THR00.0530.02617.972-0.002-0.0020.0000.0000.0000.000
45B287GLY0-0.042-0.00119.933-0.002-0.0020.0000.0000.0000.000
46B288PHE0-0.009-0.01717.7430.0080.0080.0000.0000.0000.000
47B289ASN00.0010.00014.2040.0350.0350.0000.0000.0000.000
48B290THR00.001-0.01717.659-0.001-0.0010.0000.0000.0000.000
49B291ARG10.8410.88520.641-0.062-0.0620.0000.0000.0000.000
50B292VAL00.0780.04722.049-0.006-0.0060.0000.0000.0000.000
51B293GLU-1-0.689-0.80316.6610.0250.0250.0000.0000.0000.000
52B294LYS10.9790.99621.368-0.028-0.0280.0000.0000.0000.000
53B295LYS10.8480.93024.0210.0100.0100.0000.0000.0000.000
54B296GLU-1-0.773-0.86123.257-0.035-0.0350.0000.0000.0000.000
55B297TYR00.040-0.01221.863-0.007-0.0070.0000.0000.0000.000
56B298SER0-0.087-0.05624.543-0.001-0.0010.0000.0000.0000.000
57B299ASN0-0.076-0.04627.4320.0060.0060.0000.0000.0000.000
58B300PHE00.0460.01722.812-0.002-0.0020.0000.0000.0000.000
59B301TYR0-0.028-0.00428.272-0.001-0.0010.0000.0000.0000.000
60B302MET0-0.060-0.02631.048-0.001-0.0010.0000.0000.0000.000
61B303LYS10.9860.98334.0520.0060.0060.0000.0000.0000.000
62B304SER00.0380.03337.1410.0020.0020.0000.0000.0000.000
63B305LYS10.8930.93334.4470.0170.0170.0000.0000.0000.000
64B306PRO0-0.017-0.02534.4490.0000.0000.0000.0000.0000.000
65B307THR00.0120.00837.5890.0010.0010.0000.0000.0000.000
66B308LEU00.0090.01837.2150.0000.0000.0000.0000.0000.000
67B309SER00.013-0.02335.602-0.001-0.0010.0000.0000.0000.000
68B310SER00.035-0.00730.085-0.002-0.0020.0000.0000.0000.000
69B311ALA00.0700.04031.695-0.005-0.0050.0000.0000.0000.000
70B312ASP-1-0.798-0.85933.028-0.033-0.0330.0000.0000.0000.000
71B313PHE0-0.046-0.02130.856-0.001-0.0010.0000.0000.0000.000
72B314LEU00.011-0.00227.754-0.003-0.0030.0000.0000.0000.000
73B315LYS10.9040.95931.7990.0320.0320.0000.0000.0000.000
74B316ARG10.8950.94234.9270.0390.0390.0000.0000.0000.000
75B317ILE0-0.025-0.02429.9500.0000.0000.0000.0000.0000.000
76B318GLN00.0890.06031.220-0.005-0.0050.0000.0000.0000.000
77B319ASP-1-0.877-0.94033.479-0.047-0.0470.0000.0000.0000.000
78B320LYS10.7980.88835.9750.0490.0490.0000.0000.0000.000
79B321CYS0-0.058-0.01932.3940.0020.0020.0000.0000.0000.000
80B322GLU-1-0.917-0.94233.275-0.064-0.0640.0000.0000.0000.000
81B323TYR0-0.045-0.03828.126-0.003-0.0030.0000.0000.0000.000
82B324GLN00.1320.06326.8220.0080.0080.0000.0000.0000.000
83B325PRO00.0240.00425.440-0.004-0.0040.0000.0000.0000.000
84B326THR00.0340.01121.115-0.001-0.0010.0000.0000.0000.000
85B327VAL00.0340.03721.548-0.018-0.0180.0000.0000.0000.000
86B328TYR00.016-0.00522.543-0.008-0.0080.0000.0000.0000.000
87B329LEU00.0240.03719.457-0.002-0.0020.0000.0000.0000.000
88B330VAL00.0240.00617.193-0.024-0.0240.0000.0000.0000.000
89B331ALA0-0.013-0.00417.967-0.014-0.0140.0000.0000.0000.000
90B332THR0-0.033-0.04118.3410.0140.0140.0000.0000.0000.000
91B333PHE00.0790.0319.544-0.032-0.0320.0000.0000.0000.000
92B334LEU0-0.067-0.02714.451-0.031-0.0310.0000.0000.0000.000
93B335ILE0-0.025-0.01816.5880.0160.0160.0000.0000.0000.000
94B336ASP-1-0.807-0.91513.897-0.165-0.1650.0000.0000.0000.000
95B337THR00.004-0.01410.803-0.042-0.0420.0000.0000.0000.000
96B338LEU0-0.046-0.01012.5930.0290.0290.0000.0000.0000.000
97B339PHE00.008-0.01715.6340.0310.0310.0000.0000.0000.000
98B340LEU00.0030.01613.5170.0460.0460.0000.0000.0000.000
99B341THR0-0.013-0.0179.198-0.099-0.0990.0000.0000.0000.000
100B342ARG10.7490.8488.351-0.117-0.1170.0000.0000.0000.000
101B343ASP-1-0.810-0.8839.2530.4480.4480.0000.0000.0000.000
102B344GLY00.009-0.0059.7140.1140.1140.0000.0000.0000.000
103B345ASN0-0.039-0.02010.7690.0880.0880.0000.0000.0000.000
104B346ASN0-0.048-0.0338.8980.1640.1640.0000.0000.0000.000
105B347ILE00.0490.03811.139-0.099-0.0990.0000.0000.0000.000
106B348LEU00.0170.01312.5970.0160.0160.0000.0000.0000.000
107B349GLN0-0.026-0.01513.456-0.036-0.0360.0000.0000.0000.000
108B350LEU0-0.024-0.01214.455-0.032-0.0320.0000.0000.0000.000
109B351LYS10.8500.91912.2910.1460.1460.0000.0000.0000.000
110B352LEU0-0.044-0.02316.5050.0120.0120.0000.0000.0000.000
111B353ASN0-0.028-0.03119.9860.0090.0090.0000.0000.0000.000
112B354LEU00.0140.02222.918-0.003-0.0030.0000.0000.0000.000
113B355GLN0-0.001-0.02124.5740.0080.0080.0000.0000.0000.000
114B356GLU-1-0.761-0.88528.382-0.030-0.0300.0000.0000.0000.000
115B357LYS10.8160.88830.4650.0080.0080.0000.0000.0000.000
116B358GLU-1-0.805-0.86526.174-0.018-0.0180.0000.0000.0000.000
117B359VAL00.0560.03826.719-0.007-0.0070.0000.0000.0000.000
118B360HIS10.8990.96327.8720.0350.0350.0000.0000.0000.000
119B361ARG10.8580.91628.8900.0270.0270.0000.0000.0000.000
120B362MET00.0180.02522.334-0.010-0.0100.0000.0000.0000.000
121B363ILE00.0270.01724.482-0.011-0.0110.0000.0000.0000.000
122B364ILE0-0.041-0.01926.241-0.007-0.0070.0000.0000.0000.000
123B365ALA0-0.003-0.00524.037-0.005-0.0050.0000.0000.0000.000
124B366ALA00.0330.01621.410-0.010-0.0100.0000.0000.0000.000
125B367VAL00.0290.01322.324-0.015-0.0150.0000.0000.0000.000
126B368ARG10.7900.89024.9220.0790.0790.0000.0000.0000.000
127B369LEU0-0.007-0.00918.885-0.002-0.0020.0000.0000.0000.000
128B370SER0-0.004-0.02520.579-0.020-0.0200.0000.0000.0000.000
129B371THR0-0.019-0.01721.609-0.005-0.0050.0000.0000.0000.000
130B372LYS10.8360.89123.8390.0950.0950.0000.0000.0000.000
131B373LEU0-0.064-0.02217.281-0.007-0.0070.0000.0000.0000.000
132B374LEU0-0.063-0.03220.067-0.029-0.0290.0000.0000.0000.000
133B375GLU-1-0.909-0.94622.591-0.135-0.1350.0000.0000.0000.000
134B376ASP-1-0.918-0.94926.274-0.139-0.1390.0000.0000.0000.000
135B377PHE0-0.050-0.02527.6740.0100.0100.0000.0000.0000.000
136B378VAL00.0010.00627.419-0.001-0.0010.0000.0000.0000.000
137B379HIS00.0850.06530.7880.0030.0030.0000.0000.0000.000
138B380SER00.0640.02732.742-0.002-0.0020.0000.0000.0000.000
139B381HIS00.0450.00430.210-0.002-0.0020.0000.0000.0000.000
140B382GLU-1-0.820-0.87834.425-0.038-0.0380.0000.0000.0000.000
141B383TYR0-0.036-0.03135.8220.0040.0040.0000.0000.0000.000
142B384PHE00.1000.03428.5980.0040.0040.0000.0000.0000.000
143B385SER0-0.040-0.03934.2240.0010.0010.0000.0000.0000.000
144B386LYS10.9020.94935.5180.0410.0410.0000.0000.0000.000
145B387VAL00.0150.02634.4160.0030.0030.0000.0000.0000.000
146B388CYS0-0.022-0.00732.1220.0010.0010.0000.0000.0000.000
147B389GLY0-0.0130.00834.5510.0020.0020.0000.0000.0000.000
148B390ILE0-0.060-0.02832.3410.0030.0030.0000.0000.0000.000
149B391SER00.0330.00936.807-0.001-0.0010.0000.0000.0000.000
150B392LYS10.9500.94935.1710.0390.0390.0000.0000.0000.000
151B393ARG10.9690.99033.9380.0260.0260.0000.0000.0000.000
152B394LEU0-0.019-0.00731.8250.0010.0010.0000.0000.0000.000
153B395LEU00.0600.02829.743-0.002-0.0020.0000.0000.0000.000
154B396THR00.0070.00329.241-0.006-0.0060.0000.0000.0000.000
155B397LYS10.9290.98428.3650.0260.0260.0000.0000.0000.000
156B398LEU0-0.002-0.00626.9250.0000.0000.0000.0000.0000.000
157B399GLU-1-0.787-0.87024.718-0.092-0.0920.0000.0000.0000.000
158B400VAL00.0110.01223.268-0.009-0.0090.0000.0000.0000.000
159B401SER0-0.015-0.03622.741-0.001-0.0010.0000.0000.0000.000
160B402LEU0-0.0080.01519.1010.0060.0060.0000.0000.0000.000
161B403LEU00.0550.02917.826-0.009-0.0090.0000.0000.0000.000
162B404ILE0-0.002-0.01517.898-0.004-0.0040.0000.0000.0000.000
163B405CYS0-0.090-0.04417.8010.0140.0140.0000.0000.0000.000
164B406VAL00.0270.02114.4550.0040.0040.0000.0000.0000.000
165B407CYS0-0.0330.00113.319-0.046-0.0460.0000.0000.0000.000
166B408ASN0-0.052-0.02512.121-0.026-0.0260.0000.0000.0000.000
167B409THR0-0.045-0.0119.014-0.012-0.0120.0000.0000.0000.000
168B410LYS10.9030.9332.922-5.870-4.1270.242-0.832-1.1540.007
169B411LEU00.041-0.0018.275-0.225-0.2250.0000.0000.0000.000
170B412MET0-0.0120.0109.9450.0290.0290.0000.0000.0000.000
171B413VAL00.0850.05111.934-0.122-0.1220.0000.0000.0000.000
172B414SER00.013-0.00311.985-0.054-0.0540.0000.0000.0000.000
173B415ASN00.0510.02114.425-0.014-0.0140.0000.0000.0000.000
174B416ARG10.8000.8797.1310.4480.4480.0000.0000.0000.000
175B417LYS10.7900.9069.1391.0191.0190.0000.0000.0000.000
176B418LEU00.0020.01213.0870.0550.0550.0000.0000.0000.000
177B419ALA00.0480.02214.9360.0360.0360.0000.0000.0000.000
178B420ALA0-0.014-0.01612.0530.0370.0370.0000.0000.0000.000
179B421SER0-0.033-0.00614.0990.0510.0510.0000.0000.0000.000
180B422LYS10.8690.91617.0150.0970.0970.0000.0000.0000.000
181B423LEU0-0.026-0.01015.0060.0250.0250.0000.0000.0000.000
182B424LEU00.0210.00712.0930.0270.0270.0000.0000.0000.000
183B425LEU0-0.0350.00616.1860.0250.0250.0000.0000.0000.000
184B426ASN00.0250.00419.7710.0180.0180.0000.0000.0000.000
185B427GLU-1-0.771-0.83614.5310.0990.0990.0000.0000.0000.000
186B428LEU0-0.005-0.00118.2070.0140.0140.0000.0000.0000.000
187B429ARG10.8380.89420.4250.0350.0350.0000.0000.0000.000
188B430SER0-0.080-0.03920.9890.0080.0080.0000.0000.0000.000
189B431PHE00.0000.00817.7020.0070.0070.0000.0000.0000.000
190B432CYS0-0.110-0.05223.556-0.007-0.0070.0000.0000.0000.000