FMO DATABASE

FMODB ID: K3MK3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-748957.025075
FMO2-HF: Nuclear repulsion	707463.873344
FMO2-HF: Total energy	-41493.151731
FMO2-MP2: Total energy	-41605.195983

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.
-20.618	-15.732	20.139	-10.213	-14.811	-0.072

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 : -0.030 / 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

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	0.027	0.014	2.780	-4.286	-0.375	0.557	-2.324	-2.144	-0.006
4	A	4	ASN	0	-0.071	-0.039	2.499	-0.179	1.444	2.048	-0.900	-2.771	-0.008
5	A	5	CYS	0	-0.001	0.007	4.640	-0.195	-0.132	-0.002	-0.008	-0.053	0.000
6	A	6	ARG	1	0.935	0.982	2.374	-4.894	-3.855	2.481	-0.645	-2.875	0.001
7	A	7	GLY	0	0.068	0.021	6.186	-0.235	-0.235	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.002	0.005	8.930	0.129	0.129	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.072	0.020	12.119	-0.025	-0.025	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.022	0.015	14.549	-0.020	-0.020	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.068	-0.019	10.265	-0.056	-0.056	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.016	-0.001	14.892	-0.012	-0.012	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.001	-0.006	16.257	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.003	0.012	17.912	-0.023	-0.023	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.053	0.040	19.784	0.010	0.010	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.012	-0.001	21.676	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	17	ASN	0	0.025	0.014	17.820	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.012	-0.008	17.844	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	19	MET	0	0.033	0.039	11.509	-0.038	-0.038	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.001	-0.002	16.531	-0.032	-0.032	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.974	0.989	19.679	0.102	0.102	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.021	0.001	16.444	0.004	0.004	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.878	0.921	17.545	0.249	0.249	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.807	-0.904	19.054	-0.215	-0.215	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.047	-0.027	21.878	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.005	0.000	19.394	0.004	0.004	0.000	0.000	0.000	0.000
27	A	27	CYS	0	-0.090	-0.042	16.362	-0.022	-0.022	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.043	0.037	23.139	0.013	0.013	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.041	-0.025	24.975	0.011	0.011	0.000	0.000	0.000	0.000
30	A	30	GLN	0	0.009	0.003	22.967	-0.035	-0.035	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.008	0.019	24.644	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.042	0.003	23.189	0.012	0.012	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.001	-0.012	22.315	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	34	TRP	0	-0.004	-0.013	16.515	0.012	0.012	0.000	0.000	0.000	0.000
35	A	35	CYS	0	0.000	-0.016	16.886	-0.073	-0.073	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.022	-0.002	15.590	0.000	0.000	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.021	0.001	15.334	0.058	0.058	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.809	-0.867	16.752	-0.290	-0.290	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.811	0.891	17.152	0.160	0.160	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.807	0.863	18.972	0.340	0.340	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.007	0.026	18.945	0.018	0.018	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.921	0.946	18.685	0.151	0.151	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.001	0.009	20.027	0.012	0.012	0.000	0.000	0.000	0.000
44	A	105	CYS	0	-0.076	-0.003	21.109	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.065	0.039	23.595	0.004	0.004	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.012	-0.018	25.157	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.050	0.037	26.468	0.009	0.009	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.064	-0.030	21.099	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.017	-0.020	19.992	-0.018	-0.018	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.029	0.035	14.967	0.011	0.011	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.017	-0.023	15.709	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.026	0.015	14.085	-0.019	-0.019	0.000	0.000	0.000	0.000
53	A	53	TYR	0	-0.045	-0.024	10.489	0.083	0.083	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.064	0.046	12.574	-0.110	-0.110	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.022	0.010	8.767	0.210	0.210	0.000	0.000	0.000	0.000
56	A	56	SER	0	-0.006	-0.004	7.974	-0.174	-0.174	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.037	0.023	10.244	-0.056	-0.056	0.000	0.000	0.000	0.000
58	A	58	ASN	0	0.008	0.004	13.539	0.052	0.052	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.021	-0.006	15.823	0.125	0.125	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.019	0.005	15.016	-0.028	-0.028	0.000	0.000	0.000	0.000
61	A	62	SER	0	0.027	-0.029	18.960	0.057	0.057	0.000	0.000	0.000	0.000
62	A	63	GLY	0	0.081	0.021	19.755	-0.043	-0.043	0.000	0.000	0.000	0.000
63	A	64	THR	0	-0.003	-0.011	20.687	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.854	-0.889	16.895	-0.618	-0.618	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.020	0.014	16.009	-0.074	-0.074	0.000	0.000	0.000	0.000
66	A	68	ARG	1	0.932	0.959	13.874	0.808	0.808	0.000	0.000	0.000	0.000
67	A	69	HIS	0	-0.029	-0.009	11.261	0.086	0.086	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.001	-0.005	12.626	-0.025	-0.025	0.000	0.000	0.000	0.000
69	A	71	THR	0	-0.024	-0.029	14.696	0.072	0.072	0.000	0.000	0.000	0.000
70	A	72	ASN	0	-0.060	-0.035	11.847	0.166	0.166	0.000	0.000	0.000	0.000
71	A	73	LEU	0	0.022	0.004	8.260	0.062	0.062	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.073	-0.032	12.068	0.093	0.093	0.000	0.000	0.000	0.000
73	A	75	ASN	0	-0.023	-0.019	15.206	0.084	0.084	0.000	0.000	0.000	0.000
74	A	76	HIS	0	-0.039	-0.014	6.597	0.066	0.066	0.000	0.000	0.000	0.000
75	A	77	GLY	0	0.033	0.025	11.458	0.079	0.079	0.000	0.000	0.000	0.000
76	A	79	ARG	1	0.814	0.879	11.837	-0.050	-0.050	0.000	0.000	0.000	0.000
77	A	80	VAL	0	-0.049	-0.033	13.743	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	82	GLY	0	0.055	0.032	7.150	0.097	0.097	0.000	0.000	0.000	0.000
79	A	83	SER	0	-0.019	-0.010	4.810	0.225	0.225	0.000	0.000	0.000	0.000
80	A	84	ASP	-1	-0.740	-0.859	5.836	-1.867	-1.867	0.000	0.000	0.000	0.000
81	A	85	PRO	0	-0.009	0.000	5.175	0.187	0.187	0.000	0.000	0.000	0.000
82	A	86	LEU	0	-0.023	-0.017	7.559	0.373	0.373	0.000	0.000	0.000	0.000
83	A	87	TYR	0	0.004	0.012	10.382	0.265	0.265	0.000	0.000	0.000	0.000
84	A	88	ALA	0	0.054	0.016	9.991	-0.294	-0.294	0.000	0.000	0.000	0.000
85	A	89	GLY	0	0.004	0.002	8.763	0.041	0.041	0.000	0.000	0.000	0.000
86	A	90	ASN	0	-0.075	-0.030	6.963	0.047	0.047	0.000	0.000	0.000	0.000
87	A	91	ASP	-1	-0.763	-0.844	1.840	-16.425	-19.478	13.164	-5.603	-4.508	-0.055
88	A	92	VAL	0	0.008	-0.007	2.255	1.325	2.430	1.892	-0.718	-2.278	-0.004
89	A	93	SER	0	-0.082	-0.067	4.430	1.838	2.036	-0.001	-0.015	-0.182	0.000
90	A	94	ARG	1	0.927	0.951	6.418	2.049	2.049	0.000	0.000	0.000	0.000
91	A	95	GLY	0	-0.003	0.009	8.388	0.402	0.402	0.000	0.000	0.000	0.000
92	A	96	GLN	0	-0.022	-0.019	5.140	-0.575	-0.575	0.000	0.000	0.000	0.000
93	A	97	LEU	0	-0.003	0.016	8.929	0.320	0.320	0.000	0.000	0.000	0.000
94	A	98	THR	0	-0.011	-0.016	8.150	-0.222	-0.222	0.000	0.000	0.000	0.000
95	A	99	VAL	0	0.017	0.001	9.642	0.124	0.124	0.000	0.000	0.000	0.000
96	A	100	ASN	0	0.063	0.005	10.224	0.113	0.113	0.000	0.000	0.000	0.000
97	A	101	TYR	0	0.021	-0.009	12.059	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	102	VAL	0	-0.017	-0.007	14.819	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	103	ASN	0	0.020	0.018	17.523	0.009	0.009	0.000	0.000	0.000	0.000
100	A	104	SER	0	0.103	0.044	20.860	-0.006	-0.006	0.000	0.000	0.000	0.000

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