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: V5KL1

Calculation Name: 4KGO-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KGO

Chain ID: B

ChEMBL ID:

UniProt ID: Q9NP55

Base Structure: X-ray

Registration Date: 2023-06-22

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2046998.401615
FMO2-HF: Nuclear repulsion 1970446.788797
FMO2-HF: Total energy -76551.612818
FMO2-MP2: Total energy -76777.22695


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:34:LEU)


Summations of interaction energy for fragment #1(B:34:LEU)
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.
0.2862.433-0.034-1.094-1.020
Interaction energy analysis for fragmet #1(B:34:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.022
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].
3B36VAL00.0060.0133.8050.2492.396-0.034-1.094-1.0200.000
4B37ASN00.023-0.0026.775-0.367-0.3670.0000.0000.0000.000
5B38PRO0-0.0140.01110.0380.1000.1000.0000.0000.0000.000
6B39ALA00.0250.00213.028-0.093-0.0930.0000.0000.0000.000
7B40LEU00.0430.00513.8680.1000.1000.0000.0000.0000.000
8B41PRO00.6050.68314.275-0.007-0.0070.0000.0000.0000.000
9B42LEU0-0.375-0.38716.071-0.030-0.0300.0000.0000.0000.000
10B43SER0-0.306-0.29519.402-0.039-0.0390.0000.0000.0000.000
11B44PRO0-0.022-0.01021.5370.0020.0020.0000.0000.0000.000
12B45THR00.016-0.01115.9590.0290.0290.0000.0000.0000.000
13B46GLY00.0160.01816.661-0.034-0.0340.0000.0000.0000.000
14B47LEU00.0560.03017.649-0.003-0.0030.0000.0000.0000.000
15B48ALA00.0300.00815.758-0.004-0.0040.0000.0000.0000.000
16B49GLY00.0220.01016.778-0.004-0.0040.0000.0000.0000.000
17B50SER00.003-0.01117.677-0.003-0.0030.0000.0000.0000.000
18B51LEU0-0.0100.00420.718-0.016-0.0160.0000.0000.0000.000
19B52THR00.0480.02118.306-0.015-0.0150.0000.0000.0000.000
20B53ASN00.0330.01319.540-0.010-0.0100.0000.0000.0000.000
21B54ALA00.0210.02522.540-0.012-0.0120.0000.0000.0000.000
22B55LEU00.018-0.00324.015-0.013-0.0130.0000.0000.0000.000
23B56SER0-0.049-0.02222.998-0.015-0.0150.0000.0000.0000.000
24B57ASN0-0.020-0.03225.041-0.012-0.0120.0000.0000.0000.000
25B58GLY00.0140.03327.735-0.010-0.0100.0000.0000.0000.000
26B59LEU00.0160.00626.969-0.010-0.0100.0000.0000.0000.000
27B60LEU00.0150.01826.792-0.010-0.0100.0000.0000.0000.000
28B61SER0-0.089-0.04930.840-0.008-0.0080.0000.0000.0000.000
29B62GLY0-0.0080.01033.103-0.005-0.0050.0000.0000.0000.000
30B63GLY0-0.004-0.00434.618-0.005-0.0050.0000.0000.0000.000
31B64LEU00.033-0.02129.944-0.005-0.0050.0000.0000.0000.000
32B65LEU0-0.019-0.01929.935-0.004-0.0040.0000.0000.0000.000
33B66GLY00.0190.02533.556-0.003-0.0030.0000.0000.0000.000
34B67ILE00.0020.00036.125-0.005-0.0050.0000.0000.0000.000
35B68MET0-0.038-0.02132.307-0.005-0.0050.0000.0000.0000.000
36B69GLU-1-0.893-0.95635.7780.0700.0700.0000.0000.0000.000
37B70ASN0-0.078-0.04238.130-0.006-0.0060.0000.0000.0000.000
38B71LEU0-0.0070.01136.192-0.003-0.0030.0000.0000.0000.000
39B72PRO00.0240.02340.770-0.001-0.0010.0000.0000.0000.000
40B73LEU00.030-0.00839.145-0.003-0.0030.0000.0000.0000.000
41B74LEU00.0220.00743.573-0.003-0.0030.0000.0000.0000.000
42B75ASP-1-0.832-0.91646.7760.0270.0270.0000.0000.0000.000
43B76ILE0-0.033-0.00243.763-0.002-0.0020.0000.0000.0000.000
44B77LEU0-0.062-0.00447.262-0.002-0.0020.0000.0000.0000.000
45B78LYS10.7930.88649.964-0.029-0.0290.0000.0000.0000.000
46B92LEU00.0480.01564.3750.0000.0000.0000.0000.0000.000
47B93GLY00.0410.02063.4390.0010.0010.0000.0000.0000.000
48B94LYS10.9350.94861.729-0.006-0.0060.0000.0000.0000.000
49B95VAL0-0.0050.00160.3390.0000.0000.0000.0000.0000.000
50B96THR0-0.021-0.00159.0470.0010.0010.0000.0000.0000.000
51B97SER0-0.047-0.02256.9490.0010.0010.0000.0000.0000.000
52B98VAL00.0280.01551.9960.0000.0000.0000.0000.0000.000
53B99ILE0-0.018-0.01251.3090.0000.0000.0000.0000.0000.000
54B100PRO00.0000.02347.726-0.001-0.0010.0000.0000.0000.000
55B101GLY00.0240.00450.4120.0010.0010.0000.0000.0000.000
56B102LEU00.0300.00845.9730.0000.0000.0000.0000.0000.000
57B103ASN00.020-0.01049.2870.0020.0020.0000.0000.0000.000
58B104ASN0-0.034-0.01550.9120.0000.0000.0000.0000.0000.000
59B105VAL0-0.041-0.01246.3590.0010.0010.0000.0000.0000.000
60B106ILE0-0.034-0.01049.4120.0000.0000.0000.0000.0000.000
61B107ASP-1-0.860-0.96547.7450.0350.0350.0000.0000.0000.000
62B108ILE0-0.029-0.00942.2510.0000.0000.0000.0000.0000.000
63B109LYS10.8610.94042.820-0.036-0.0360.0000.0000.0000.000
64B110VAL00.006-0.00137.2500.0000.0000.0000.0000.0000.000
65B111THR00.0030.00136.5790.0000.0000.0000.0000.0000.000
66B112ASP-1-0.896-0.93431.7460.0950.0950.0000.0000.0000.000
67B113PRO00.0260.03932.1590.0030.0030.0000.0000.0000.000
68B114GLN0-0.019-0.03026.2700.0050.0050.0000.0000.0000.000
69B115LEU0-0.002-0.00324.704-0.009-0.0090.0000.0000.0000.000
70B116LEU0-0.083-0.03221.4530.0140.0140.0000.0000.0000.000
71B117GLU-1-0.886-0.95417.6300.3340.3340.0000.0000.0000.000
72B118LEU0-0.0090.00919.468-0.016-0.0160.0000.0000.0000.000
73B119GLY00.0170.02117.1670.0380.0380.0000.0000.0000.000
74B120LEU0-0.019-0.02216.614-0.024-0.0240.0000.0000.0000.000
75B121VAL0-0.008-0.00215.7270.0010.0010.0000.0000.0000.000
76B122GLN00.0410.02616.5760.0110.0110.0000.0000.0000.000
77B123SER0-0.064-0.04417.722-0.023-0.0230.0000.0000.0000.000
78B124PRO00.0250.01017.4660.0040.0040.0000.0000.0000.000
79B125ASP-1-0.766-0.84918.362-0.026-0.0260.0000.0000.0000.000
80B126GLY00.0340.01719.8890.0040.0040.0000.0000.0000.000
81B127HIS10.8390.90020.5410.0150.0150.0000.0000.0000.000
82B128ARG10.9080.96322.9270.0200.0200.0000.0000.0000.000
83B129LEU00.0230.01619.852-0.001-0.0010.0000.0000.0000.000
84B130TYR0-0.020-0.01621.231-0.005-0.0050.0000.0000.0000.000
85B131VAL0-0.0060.00320.8420.0130.0130.0000.0000.0000.000
86B132THR0-0.002-0.00120.418-0.015-0.0150.0000.0000.0000.000
87B133ILE00.005-0.01222.0100.0220.0220.0000.0000.0000.000
88B134PRO00.0140.02921.075-0.016-0.0160.0000.0000.0000.000
89B135LEU00.0270.00224.2300.0110.0110.0000.0000.0000.000
90B136GLY0-0.018-0.02427.291-0.002-0.0020.0000.0000.0000.000
91B137ILE00.0210.01129.1510.0010.0010.0000.0000.0000.000
92B138LYS10.8320.92430.347-0.090-0.0900.0000.0000.0000.000
93B139LEU00.0250.00334.722-0.002-0.0020.0000.0000.0000.000
94B140GLN00.0250.02738.156-0.003-0.0030.0000.0000.0000.000
95B141VAL00.0040.00541.304-0.001-0.0010.0000.0000.0000.000
96B142ASN0-0.013-0.01144.0990.0010.0010.0000.0000.0000.000
97B143THR00.0330.01547.668-0.002-0.0020.0000.0000.0000.000
98B144PRO00.0120.00850.1650.0010.0010.0000.0000.0000.000
99B145LEU0-0.002-0.00251.747-0.001-0.0010.0000.0000.0000.000
100B146VAL0-0.0190.03551.8710.0010.0010.0000.0000.0000.000
101B147GLY00.046-0.01551.435-0.001-0.0010.0000.0000.0000.000
102B148ALA00.021-0.00647.5380.0000.0000.0000.0000.0000.000
103B149SER0-0.0100.01547.2370.0010.0010.0000.0000.0000.000
104B150LEU0-0.034-0.03443.4980.0010.0010.0000.0000.0000.000
105B151LEU0-0.0100.00841.961-0.001-0.0010.0000.0000.0000.000
106B152ARG10.8720.90736.670-0.046-0.0460.0000.0000.0000.000
107B153LEU00.0010.00036.126-0.002-0.0020.0000.0000.0000.000
108B154ALA0-0.012-0.01030.8790.0050.0050.0000.0000.0000.000
109B155VAL0-0.009-0.00631.858-0.004-0.0040.0000.0000.0000.000
110B156LYS10.8940.95224.108-0.098-0.0980.0000.0000.0000.000
111B157MET0-0.0110.00528.014-0.011-0.0110.0000.0000.0000.000
112B158ASP-1-0.833-0.92322.7140.0970.0970.0000.0000.0000.000
113B159ILE0-0.018-0.00726.230-0.011-0.0110.0000.0000.0000.000
114B160THR0-0.027-0.00623.5780.0090.0090.0000.0000.0000.000
115B161ALA00.0170.01125.786-0.009-0.0090.0000.0000.0000.000
116B162GLU-1-0.853-0.91725.8560.0240.0240.0000.0000.0000.000
117B163ILE0-0.023-0.02123.8360.0020.0020.0000.0000.0000.000
118B164LEU0-0.0090.00226.505-0.003-0.0030.0000.0000.0000.000
119B165ALA00.0240.00528.2820.0060.0060.0000.0000.0000.000
120B166VAL0-0.0160.01030.184-0.005-0.0050.0000.0000.0000.000
121B167ARG10.9120.93733.916-0.017-0.0170.0000.0000.0000.000
122B168ASP-1-0.732-0.83636.8000.0320.0320.0000.0000.0000.000
123B169LYS10.9460.95740.240-0.023-0.0230.0000.0000.0000.000
124B170GLN0-0.082-0.04842.315-0.001-0.0010.0000.0000.0000.000
125B171GLU-1-0.878-0.91639.7810.0210.0210.0000.0000.0000.000
126B172ARG10.8610.93137.864-0.037-0.0370.0000.0000.0000.000
127B173ILE0-0.015-0.03131.841-0.002-0.0020.0000.0000.0000.000
128B174HIS0-0.058-0.03033.5660.0060.0060.0000.0000.0000.000
129B175LEU00.0180.00526.718-0.002-0.0020.0000.0000.0000.000
130B176VAL0-0.058-0.03230.7520.0010.0010.0000.0000.0000.000
131B177LEU00.0220.00529.349-0.001-0.0010.0000.0000.0000.000
132B178GLY0-0.0080.00230.412-0.004-0.0040.0000.0000.0000.000
133B179ASP-1-0.891-0.94530.3710.0150.0150.0000.0000.0000.000
134B180CYS0-0.131-0.07429.9910.0080.0080.0000.0000.0000.000
135B181THR00.0190.01430.062-0.004-0.0040.0000.0000.0000.000
136B182HIS00.0470.01829.5590.0100.0100.0000.0000.0000.000
137B183SER0-0.027-0.00424.587-0.012-0.0120.0000.0000.0000.000
138B184PRO00.0750.03527.4710.0010.0010.0000.0000.0000.000
139B185GLY0-0.026-0.00827.2930.0010.0010.0000.0000.0000.000
140B186SER0-0.053-0.03825.7580.0020.0020.0000.0000.0000.000
141B187LEU0-0.023-0.00426.7180.0080.0080.0000.0000.0000.000
142B188GLN0-0.021-0.01024.552-0.001-0.0010.0000.0000.0000.000
143B189ILE0-0.0010.00029.8040.0070.0070.0000.0000.0000.000
144B190SER0-0.015-0.00730.158-0.004-0.0040.0000.0000.0000.000
145B191LEU0-0.022-0.01132.6100.0020.0020.0000.0000.0000.000
146B192LEU0-0.007-0.01631.8570.0020.0020.0000.0000.0000.000
147B193ASP-1-0.786-0.84934.6950.0420.0420.0000.0000.0000.000
148B194GLY00.022-0.01037.855-0.002-0.0020.0000.0000.0000.000
149B195LEU0-0.060-0.04238.813-0.001-0.0010.0000.0000.0000.000
150B196GLY00.0760.04041.218-0.003-0.0030.0000.0000.0000.000
151B197PRO0-0.036-0.02642.612-0.002-0.0020.0000.0000.0000.000
152B198LEU00.0250.03045.755-0.001-0.0010.0000.0000.0000.000
153B199PRO00.0110.01347.181-0.002-0.0020.0000.0000.0000.000
154B200ILE00.0160.01143.3330.0000.0000.0000.0000.0000.000
155B201GLN00.0150.00542.3660.0020.0020.0000.0000.0000.000
156B202GLY00.0260.02844.155-0.001-0.0010.0000.0000.0000.000
157B203LEU0-0.0020.00045.6040.0000.0000.0000.0000.0000.000
158B204LEU00.007-0.00938.5020.0010.0010.0000.0000.0000.000
159B205ASP-1-0.938-0.96341.3070.0050.0050.0000.0000.0000.000
160B206SER00.0040.01242.639-0.001-0.0010.0000.0000.0000.000
161B207LEU0-0.040-0.03841.5060.0010.0010.0000.0000.0000.000
162B208THR0-0.016-0.02137.3940.0010.0010.0000.0000.0000.000
163B209GLY00.0440.03638.6200.0000.0000.0000.0000.0000.000
164B210ILE0-0.028-0.02540.6480.0000.0000.0000.0000.0000.000
165B211LEU00.0110.00137.2840.0010.0010.0000.0000.0000.000
166B212ASN0-0.007-0.01334.8420.0040.0040.0000.0000.0000.000
167B213LYS10.9170.96036.842-0.009-0.0090.0000.0000.0000.000
168B214VAL0-0.0180.00639.5150.0000.0000.0000.0000.0000.000
169B215LEU00.0230.00735.2220.0020.0020.0000.0000.0000.000
170B216PRO00.0110.02033.7770.0040.0040.0000.0000.0000.000
171B217GLU-1-0.829-0.92835.0270.0250.0250.0000.0000.0000.000
172B218LEU0-0.050-0.01637.8990.0010.0010.0000.0000.0000.000
173B219VAL00.010-0.00832.2480.0030.0030.0000.0000.0000.000
174B220GLN00.0190.00833.5500.0040.0040.0000.0000.0000.000
175B221GLY0-0.005-0.00734.5150.0010.0010.0000.0000.0000.000
176B222ASN0-0.030-0.02336.848-0.002-0.0020.0000.0000.0000.000
177B223VAL0-0.029-0.01630.5370.0040.0040.0000.0000.0000.000
178B225PRO00.0250.00733.9310.0020.0020.0000.0000.0000.000
179B226LEU00.0340.03333.1700.0020.0020.0000.0000.0000.000
180B227VAL00.0300.00528.3080.0030.0030.0000.0000.0000.000
181B228ASN0-0.033-0.02431.3970.0010.0010.0000.0000.0000.000
182B229GLU-1-0.887-0.92533.5140.0520.0520.0000.0000.0000.000
183B230VAL0-0.020-0.00529.5320.0020.0020.0000.0000.0000.000
184B231LEU0-0.032-0.01627.2110.0040.0040.0000.0000.0000.000
185B232ARG10.8690.92730.795-0.050-0.0500.0000.0000.0000.000
186B233GLY0-0.024-0.00533.274-0.004-0.0040.0000.0000.0000.000
187B234LEU0-0.052-0.01027.3110.0070.0070.0000.0000.0000.000
188B235ASP-1-0.868-0.93928.8130.0970.0970.0000.0000.0000.000
189B236ILE00.0410.00829.936-0.001-0.0010.0000.0000.0000.000
190B237THR0-0.008-0.00827.683-0.006-0.0060.0000.0000.0000.000
191B238LEU0-0.0160.00223.7570.0020.0020.0000.0000.0000.000
192B239VAL00.0180.00425.8920.0000.0000.0000.0000.0000.000
193B240HIS0-0.026-0.00927.583-0.007-0.0070.0000.0000.0000.000
194B241ASP-1-0.855-0.94124.0260.0910.0910.0000.0000.0000.000
195B242ILE0-0.030-0.01122.095-0.003-0.0030.0000.0000.0000.000
196B243VAL00.0240.00724.053-0.009-0.0090.0000.0000.0000.000
197B244ASN00.0130.00225.851-0.014-0.0140.0000.0000.0000.000
198B245MET0-0.0020.01820.370-0.013-0.0130.0000.0000.0000.000
199B246LEU0-0.0040.01521.829-0.011-0.0110.0000.0000.0000.000
200B247ILE0-0.047-0.02624.011-0.011-0.0110.0000.0000.0000.000
201B248HIS10.8110.88524.017-0.036-0.0360.0000.0000.0000.000
202B249GLY0-0.0510.00122.119-0.007-0.0070.0000.0000.0000.000
203B250LEU0-0.005-0.00918.828-0.010-0.0100.0000.0000.0000.000
204B251GLN0-0.027-0.03114.2410.0180.0180.0000.0000.0000.000
205B252PHE00.0270.00315.1960.0130.0130.0000.0000.0000.000
206B253VAL0-0.031-0.00614.0460.0450.0450.0000.0000.0000.000
207B254ILE0-0.009-0.0048.007-0.050-0.0500.0000.0000.0000.000
208B255LYS10.8920.9507.6660.0020.0020.0000.0000.0000.000