FMO DATABASE

FMODB ID: R5VQ8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-746760.547759
FMO2-HF: Nuclear repulsion	705267.68022
FMO2-HF: Total energy	-41492.867539
FMO2-MP2: Total energy	-41604.951681

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.
-22.843	-15.792	16.711	-9.716	-14.045	-0.066

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 : -0.023 / q_NPA : -0.003

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	0.008	0.006	2.870	-3.892	0.276	0.352	-2.407	-2.112	-0.002
4	A	4	ASN	0	-0.075	-0.037	2.467	-0.252	1.418	1.501	-0.811	-2.360	-0.007
5	A	5	CYS	0	-0.032	-0.014	4.752	-0.262	-0.210	-0.002	-0.005	-0.045	0.000
6	A	6	ARG	1	0.939	0.980	2.597	-5.464	-3.691	1.326	-0.574	-2.525	-0.001
7	A	7	GLY	0	0.055	0.015	6.383	-0.251	-0.251	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.007	0.004	9.077	0.118	0.118	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.078	0.021	12.163	0.001	0.001	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.016	0.015	14.597	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.078	-0.036	10.605	-0.067	-0.067	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.016	-0.010	15.195	-0.016	-0.016	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.003	0.008	16.662	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.015	0.011	18.678	-0.022	-0.022	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.053	0.035	20.273	0.013	0.013	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.026	0.002	22.363	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	17	ASN	0	0.035	0.017	18.460	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.013	-0.007	18.178	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	19	MET	0	0.040	0.039	12.044	-0.040	-0.040	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.011	0.003	17.101	-0.035	-0.035	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.969	0.990	20.079	0.095	0.095	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.001	-0.002	16.882	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.930	0.968	18.059	0.221	0.221	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.875	-0.950	19.435	-0.194	-0.194	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.063	-0.037	22.340	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.012	-0.007	19.744	0.000	0.000	0.000	0.000	0.000	0.000
27	A	27	CYS	0	-0.088	-0.035	16.569	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.042	0.041	23.257	0.011	0.011	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.035	-0.019	25.200	0.015	0.015	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.025	-0.035	23.439	-0.032	-0.032	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.027	0.030	25.115	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.032	-0.003	23.403	0.008	0.008	0.000	0.000	0.000	0.000
33	A	33	THR	0	0.003	-0.010	22.256	-0.023	-0.023	0.000	0.000	0.000	0.000
34	A	34	TRP	0	-0.047	-0.034	16.975	0.015	0.015	0.000	0.000	0.000	0.000
35	A	35	CYS	0	0.011	0.013	17.471	-0.076	-0.076	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.002	-0.014	15.954	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.013	-0.003	15.890	0.059	0.059	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.849	-0.911	17.351	-0.310	-0.310	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.858	0.919	17.655	0.197	0.197	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.853	0.922	19.577	0.364	0.364	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.028	0.042	19.195	0.020	0.020	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.909	0.940	19.186	0.169	0.169	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.000	0.015	20.508	0.014	0.014	0.000	0.000	0.000	0.000
44	A	105	CYS	0	-0.093	-0.039	21.549	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.074	0.051	24.027	0.007	0.007	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.025	-0.026	25.328	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.027	0.013	26.471	0.008	0.008	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.047	-0.011	21.127	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.004	-0.012	20.324	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.050	0.054	15.387	0.005	0.005	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.034	-0.038	16.184	0.000	0.000	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.038	0.028	14.485	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	53	TYR	0	-0.035	-0.025	11.786	0.077	0.077	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.064	0.052	12.947	-0.101	-0.101	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.003	-0.006	9.034	0.150	0.150	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.021	0.010	8.422	-0.210	-0.210	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.039	0.023	10.690	-0.073	-0.073	0.000	0.000	0.000	0.000
58	A	58	ASN	0	0.015	0.012	13.786	0.076	0.076	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.046	-0.021	16.046	0.139	0.139	0.000	0.000	0.000	0.000
60	A	61	ILE	0	0.000	0.007	15.206	-0.025	-0.025	0.000	0.000	0.000	0.000
61	A	62	SER	0	0.026	0.009	19.043	0.065	0.065	0.000	0.000	0.000	0.000
62	A	63	GLY	0	0.081	0.023	20.055	-0.040	-0.040	0.000	0.000	0.000	0.000
63	A	64	THR	0	0.003	0.002	21.086	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.870	-0.937	17.240	-0.633	-0.633	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.023	0.013	16.235	-0.066	-0.066	0.000	0.000	0.000	0.000
66	A	68	ARG	1	0.985	0.997	13.986	0.838	0.838	0.000	0.000	0.000	0.000
67	A	69	HIS	0	-0.052	-0.036	11.719	0.057	0.057	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.014	-0.002	12.963	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	71	THR	0	-0.031	-0.020	14.984	0.080	0.080	0.000	0.000	0.000	0.000
70	A	72	ASN	0	-0.058	-0.025	11.916	0.197	0.197	0.000	0.000	0.000	0.000
71	A	73	LEU	0	0.009	0.001	8.652	0.070	0.070	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.061	-0.022	12.259	0.098	0.098	0.000	0.000	0.000	0.000
73	A	75	ASN	0	-0.030	-0.033	15.168	0.085	0.085	0.000	0.000	0.000	0.000
74	A	76	HIS	0	0.001	0.010	7.239	-0.078	-0.078	0.000	0.000	0.000	0.000
75	A	77	GLY	0	0.017	0.018	11.904	0.096	0.096	0.000	0.000	0.000	0.000
76	A	79	ARG	1	0.875	0.925	12.188	-0.091	-0.091	0.000	0.000	0.000	0.000
77	A	80	VAL	0	-0.056	-0.037	14.012	-0.024	-0.024	0.000	0.000	0.000	0.000
78	A	82	GLY	0	0.050	0.030	7.672	0.119	0.119	0.000	0.000	0.000	0.000
79	A	83	SER	0	-0.025	-0.017	5.350	0.151	0.151	0.000	0.000	0.000	0.000
80	A	84	ASP	-1	-0.757	-0.885	6.207	-1.657	-1.657	0.000	0.000	0.000	0.000
81	A	85	PRO	0	-0.012	0.004	5.297	0.090	0.090	0.000	0.000	0.000	0.000
82	A	86	LEU	0	-0.013	-0.007	7.646	0.414	0.414	0.000	0.000	0.000	0.000
83	A	87	TYR	0	-0.011	0.002	10.482	0.282	0.282	0.000	0.000	0.000	0.000
84	A	88	ALA	0	0.050	0.011	9.588	-0.340	-0.340	0.000	0.000	0.000	0.000
85	A	89	GLY	0	0.006	0.011	8.317	-0.022	-0.022	0.000	0.000	0.000	0.000
86	A	90	ASN	0	-0.063	-0.035	6.676	0.083	0.083	0.000	0.000	0.000	0.000
87	A	91	ASP	-1	-0.772	-0.869	1.878	-19.378	-21.633	11.851	-5.098	-4.498	-0.053
88	A	92	VAL	0	-0.009	-0.023	2.255	1.551	2.985	1.684	-0.803	-2.315	-0.003
89	A	93	SER	0	-0.070	-0.030	4.375	2.086	2.295	-0.001	-0.018	-0.190	0.000
90	A	94	ARG	1	0.903	0.936	6.137	2.636	2.636	0.000	0.000	0.000	0.000
91	A	95	GLY	0	0.009	0.014	8.324	0.445	0.445	0.000	0.000	0.000	0.000
92	A	96	GLN	0	-0.013	-0.024	5.588	-0.561	-0.561	0.000	0.000	0.000	0.000
93	A	97	LEU	0	-0.010	0.013	8.922	0.326	0.326	0.000	0.000	0.000	0.000
94	A	98	THR	0	-0.014	-0.017	8.478	-0.201	-0.201	0.000	0.000	0.000	0.000
95	A	99	VAL	0	0.038	0.021	10.225	0.109	0.109	0.000	0.000	0.000	0.000
96	A	100	ASN	0	0.065	0.008	10.574	0.119	0.119	0.000	0.000	0.000	0.000
97	A	101	TYR	0	0.017	-0.008	12.403	-0.014	-0.014	0.000	0.000	0.000	0.000
98	A	102	VAL	0	-0.028	-0.008	14.944	-0.018	-0.018	0.000	0.000	0.000	0.000
99	A	103	ASN	0	-0.004	-0.012	17.642	0.030	0.030	0.000	0.000	0.000	0.000
100	A	104	SER	0	0.083	0.045	20.827	0.000	0.000	0.000	0.000	0.000	0.000

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