FMO DATABASE

FMODB ID: 85GLY

Calculation Name: 1KFM-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 1KFM

Chain ID: A

ChEMBL ID:
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UniProt ID: P69776

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	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	50
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-172921.189332
FMO2-HF: Nuclear repulsion	153869.834772
FMO2-HF: Total energy	-19051.354561
FMO2-MP2: Total energy	-19106.50882

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)

Summations of interaction energy for fragment #1(A:2: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.
1.465	4.3	0.3	-1.155	-1.981	0

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.010

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

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

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].
3	A	4	ALA	0	0.070	0.032	3.534	-2.079	-0.341	-0.012	-0.756	-0.971	0.001
4	A	5	LYS	1	0.922	0.959	2.767	2.231	2.865	0.302	-0.272	-0.664	-0.001
5	A	6	ILE	0	0.071	0.025	3.411	0.474	0.937	0.010	-0.127	-0.346	0.000
6	A	7	ASP	-1	-0.838	-0.912	6.223	-0.015	-0.015	0.000	0.000	0.000	0.000
7	A	8	GLN	0	-0.032	-0.003	7.768	0.308	0.308	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.031	-0.020	7.692	0.186	0.186	0.000	0.000	0.000	0.000
9	A	10	SER	0	0.008	0.005	10.109	0.225	0.225	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.020	-0.011	12.194	0.146	0.146	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.934	-0.962	13.195	-0.436	-0.436	0.000	0.000	0.000	0.000
12	A	13	VAL	0	0.032	0.002	13.958	0.074	0.074	0.000	0.000	0.000	0.000
13	A	14	GLN	0	-0.004	0.003	16.179	0.064	0.064	0.000	0.000	0.000	0.000
14	A	15	THR	0	-0.025	-0.014	17.828	0.048	0.048	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.038	-0.026	17.368	0.044	0.044	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.003	-0.002	19.583	0.046	0.046	0.000	0.000	0.000	0.000
17	A	18	ALA	0	0.055	0.043	22.257	0.020	0.020	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.904	0.934	22.970	0.213	0.213	0.000	0.000	0.000	0.000
19	A	20	VAL	0	-0.012	-0.011	23.760	0.012	0.012	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.888	-0.934	26.357	-0.108	-0.108	0.000	0.000	0.000	0.000
21	A	22	GLN	0	-0.060	-0.045	28.305	0.021	0.021	0.000	0.000	0.000	0.000
22	A	23	LEU	0	0.015	0.020	27.538	0.005	0.005	0.000	0.000	0.000	0.000
23	A	24	SER	0	-0.025	0.005	30.615	0.009	0.009	0.000	0.000	0.000	0.000
24	A	25	ASN	0	-0.012	-0.012	32.375	0.013	0.013	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.886	-0.943	33.385	-0.099	-0.099	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.059	-0.030	33.185	0.005	0.005	0.000	0.000	0.000	0.000
27	A	28	ASN	0	-0.045	-0.023	36.238	0.007	0.007	0.000	0.000	0.000	0.000
28	A	29	ALA	0	0.021	0.003	38.360	0.005	0.005	0.000	0.000	0.000	0.000
29	A	30	ALA	0	0.058	0.035	39.097	0.003	0.003	0.000	0.000	0.000	0.000
30	A	31	ARG	1	0.881	0.944	38.750	0.068	0.068	0.000	0.000	0.000	0.000
31	A	32	SER	0	0.014	-0.004	41.987	0.004	0.004	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.907	-0.940	43.875	-0.057	-0.057	0.000	0.000	0.000	0.000
33	A	34	ALA	0	-0.051	-0.028	44.521	0.002	0.002	0.000	0.000	0.000	0.000
34	A	35	GLN	0	-0.106	-0.063	46.260	0.001	0.001	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.060	0.029	48.147	0.003	0.003	0.000	0.000	0.000	0.000
36	A	37	ALA	0	0.006	0.007	49.439	0.002	0.002	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.901	0.953	49.329	0.048	0.048	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.839	-0.918	51.991	-0.037	-0.037	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.884	-0.945	54.006	-0.035	-0.035	0.000	0.000	0.000	0.000
40	A	41	ALA	0	-0.013	-0.011	54.840	0.001	0.001	0.000	0.000	0.000	0.000
41	A	42	ALA	0	-0.013	-0.004	56.270	0.001	0.001	0.000	0.000	0.000	0.000
42	A	43	ARG	1	0.908	0.962	58.042	0.034	0.034	0.000	0.000	0.000	0.000
43	A	44	ALA	0	-0.051	-0.033	59.676	0.001	0.001	0.000	0.000	0.000	0.000
44	A	45	ASN	0	0.009	-0.024	58.837	0.001	0.001	0.000	0.000	0.000	0.000
45	A	46	GLN	0	0.031	0.049	60.943	0.001	0.001	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.853	0.922	63.188	0.030	0.030	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.012	-0.010	63.433	0.001	0.001	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.869	-0.927	65.160	-0.028	-0.028	0.000	0.000	0.000	0.000
49	A	50	ASN	0	-0.116	-0.050	68.138	0.001	0.001	0.000	0.000	0.000	0.000
50	A	51	MET	0	-0.080	-0.023	69.754	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)