FMO DATABASE

FMODB ID: Q1JKY

Calculation Name: 1KPT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KPT

Chain ID: A

ChEMBL ID:

UniProt ID: Q90121

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-747062.418471
FMO2-HF: Nuclear repulsion	705569.311116
FMO2-HF: Total energy	-41493.107355
FMO2-MP2: Total energy	-41605.143339

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:1:LEU)

Summations of interaction energy for fragment #1(A:1: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.
-20.956	-9.823	9.727	-7.731	-13.128	-0.053

Interaction energy analysis for fragmet #1(A:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / 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 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	3	ILE	0	0.014	0.008	2.845	-3.986	0.097	0.364	-2.320	-2.127	-0.002
4	A	4	ASN	0	-0.082	-0.046	2.655	-0.304	1.526	1.039	-0.731	-2.138	-0.006
5	A	5	CYS	0	-0.030	-0.014	4.698	-0.227	-0.172	-0.002	-0.007	-0.045	0.000
6	A	6	ARG	1	0.936	0.983	2.515	-5.173	-4.000	2.379	-0.612	-2.941	0.000
7	A	7	GLY	0	0.058	0.017	6.406	-0.243	-0.243	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.001	0.006	9.072	0.120	0.120	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.075	0.023	12.167	-0.016	-0.016	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.017	0.015	14.630	-0.021	-0.021	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.088	-0.036	10.564	-0.061	-0.061	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.010	-0.005	15.192	-0.018	-0.018	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.003	0.006	16.688	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.006	0.020	18.662	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.055	0.043	20.250	0.011	0.011	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.026	0.002	22.345	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	17	ASN	0	0.026	0.017	18.456	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.021	-0.007	18.202	-0.019	-0.019	0.000	0.000	0.000	0.000
19	A	19	MET	0	0.033	0.036	12.084	-0.040	-0.040	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.016	0.002	17.017	-0.033	-0.033	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.962	0.992	20.001	0.096	0.096	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.009	-0.006	16.775	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.869	0.923	17.963	0.229	0.229	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.810	-0.906	19.456	-0.200	-0.200	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.046	-0.023	22.338	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.009	-0.007	19.776	0.001	0.001	0.000	0.000	0.000	0.000
27	A	27	CYS	0	-0.093	-0.038	16.566	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.045	0.039	23.260	0.011	0.011	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.039	-0.025	25.205	0.015	0.015	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.015	-0.018	23.209	-0.032	-0.032	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.025	0.030	25.107	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.022	0.009	23.398	0.009	0.009	0.000	0.000	0.000	0.000
33	A	33	THR	0	0.002	-0.008	22.548	-0.025	-0.025	0.000	0.000	0.000	0.000
34	A	34	TRP	0	-0.027	-0.029	16.783	0.013	0.013	0.000	0.000	0.000	0.000
35	A	35	CYS	0	0.012	0.001	17.331	-0.071	-0.071	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.008	-0.014	15.727	0.005	0.005	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.020	-0.003	15.779	0.057	0.057	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.824	-0.870	17.246	-0.291	-0.291	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.813	0.897	17.513	0.170	0.170	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.820	0.880	19.459	0.346	0.346	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.017	0.031	19.150	0.018	0.018	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.917	0.946	19.084	0.156	0.156	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.004	0.008	20.428	0.013	0.013	0.000	0.000	0.000	0.000
44	A	105	CYS	0	-0.079	-0.025	21.485	-0.015	-0.015	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.071	0.052	23.962	0.005	0.005	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.017	-0.023	25.281	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.033	0.018	26.419	0.008	0.008	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.047	-0.018	21.103	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.014	-0.023	20.348	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.040	0.046	15.306	0.007	0.007	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.026	-0.029	16.107	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.040	0.026	14.378	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	53	TYR	0	-0.038	-0.023	10.989	0.084	0.084	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.068	0.051	12.837	-0.099	-0.099	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.031	0.011	9.070	0.185	0.185	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.003	-0.002	8.225	-0.187	-0.187	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.045	0.018	10.567	-0.067	-0.067	0.000	0.000	0.000	0.000
58	A	58	ASN	0	0.008	0.007	13.726	0.060	0.060	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.031	-0.011	16.087	0.130	0.130	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.010	0.005	15.087	-0.025	-0.025	0.000	0.000	0.000	0.000
61	A	62	SER	0	0.018	-0.023	19.016	0.061	0.061	0.000	0.000	0.000	0.000
62	A	63	GLY	0	0.072	0.017	20.036	-0.040	-0.040	0.000	0.000	0.000	0.000
63	A	64	THR	0	0.002	-0.008	21.075	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.847	-0.891	17.090	-0.622	-0.622	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.005	0.004	16.225	-0.069	-0.069	0.000	0.000	0.000	0.000
66	A	68	ARG	1	0.943	0.959	13.957	0.811	0.811	0.000	0.000	0.000	0.000
67	A	69	HIS	0	-0.039	-0.007	11.461	0.078	0.078	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.001	-0.006	12.961	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	71	THR	0	-0.019	-0.021	14.992	0.074	0.074	0.000	0.000	0.000	0.000
70	A	72	ASN	0	-0.062	-0.034	11.975	0.172	0.172	0.000	0.000	0.000	0.000
71	A	73	LEU	0	0.015	0.004	8.690	0.058	0.058	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.059	-0.026	12.246	0.094	0.094	0.000	0.000	0.000	0.000
73	A	75	ASN	0	-0.036	-0.032	15.210	0.082	0.082	0.000	0.000	0.000	0.000
74	A	76	HIS	0	-0.006	0.007	6.897	-0.027	-0.027	0.000	0.000	0.000	0.000
75	A	77	GLY	0	0.022	0.021	11.890	0.090	0.090	0.000	0.000	0.000	0.000
76	A	79	ARG	1	0.867	0.917	12.136	-0.072	-0.072	0.000	0.000	0.000	0.000
77	A	80	VAL	0	-0.057	-0.044	13.950	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	82	GLY	0	0.055	0.032	7.630	0.107	0.107	0.000	0.000	0.000	0.000
79	A	83	SER	0	-0.024	-0.019	5.367	0.155	0.155	0.000	0.000	0.000	0.000
80	A	84	ASP	-1	-0.751	-0.867	6.222	-1.684	-1.684	0.000	0.000	0.000	0.000
81	A	85	PRO	0	-0.003	0.009	5.350	0.094	0.094	0.000	0.000	0.000	0.000
82	A	86	LEU	0	-0.013	-0.013	7.599	0.404	0.404	0.000	0.000	0.000	0.000
83	A	87	TYR	0	-0.007	0.007	10.430	0.263	0.263	0.000	0.000	0.000	0.000
84	A	88	ALA	0	0.055	0.013	9.675	-0.334	-0.334	0.000	0.000	0.000	0.000
85	A	89	GLY	0	0.003	0.004	8.355	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	90	ASN	0	-0.054	-0.027	6.728	0.069	0.069	0.000	0.000	0.000	0.000
87	A	91	ASP	-1	-0.755	-0.835	2.141	-16.899	-14.500	4.261	-3.321	-3.339	-0.042
88	A	92	VAL	0	-0.007	-0.022	2.387	1.222	2.605	1.687	-0.723	-2.346	-0.003
89	A	93	SER	0	-0.090	-0.072	4.402	1.962	2.172	-0.001	-0.017	-0.192	0.000
90	A	94	ARG	1	0.893	0.934	6.180	2.413	2.413	0.000	0.000	0.000	0.000
91	A	95	GLY	0	0.008	0.014	8.415	0.414	0.414	0.000	0.000	0.000	0.000
92	A	96	GLN	0	-0.021	-0.025	5.150	-0.552	-0.552	0.000	0.000	0.000	0.000
93	A	97	LEU	0	-0.020	0.010	8.905	0.320	0.320	0.000	0.000	0.000	0.000
94	A	98	THR	0	-0.017	-0.023	8.540	-0.215	-0.215	0.000	0.000	0.000	0.000
95	A	99	VAL	0	0.035	0.021	10.106	0.108	0.108	0.000	0.000	0.000	0.000
96	A	100	ASN	0	0.050	-0.005	10.387	0.116	0.116	0.000	0.000	0.000	0.000
97	A	101	TYR	0	0.021	-0.012	12.336	-0.013	-0.013	0.000	0.000	0.000	0.000
98	A	102	VAL	0	-0.029	-0.007	14.886	-0.012	-0.012	0.000	0.000	0.000	0.000
99	A	103	ASN	0	0.004	0.004	17.577	0.020	0.020	0.000	0.000	0.000	0.000
100	A	104	SER	0	0.112	0.059	20.773	-0.002	-0.002	0.000	0.000	0.000	0.000

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