FMO DATABASE

FMODB ID: GNJ31

Calculation Name: 3KIK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KIK

Chain ID: A

ChEMBL ID:

UniProt ID: Q03067

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:

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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-622919.863649
FMO2-HF: Nuclear repulsion	584638.519495
FMO2-HF: Total energy	-38281.344154
FMO2-MP2: Total energy	-38392.346972

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:3:MET)

Summations of interaction energy for fragment #1(A:3:MET)

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.
1.625	4.989	0.429	-1.68	-2.112	0.007

Interaction energy analysis for fragmet #1(A:3:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.002

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	5	THR	0	-0.010	-0.006	2.432	-0.719	2.482	0.430	-1.667	-1.963	0.007
4	A	6	ALA	0	0.002	0.016	5.094	0.919	1.082	-0.001	-0.013	-0.149	0.000
5	A	7	GLN	0	0.022	0.003	7.926	0.412	0.412	0.000	0.000	0.000	0.000
6	A	8	LEU	0	0.018	0.012	7.225	0.252	0.252	0.000	0.000	0.000	0.000
7	A	9	LYS	1	0.811	0.886	8.777	0.897	0.897	0.000	0.000	0.000	0.000
8	A	10	SER	0	-0.010	-0.005	10.548	0.240	0.240	0.000	0.000	0.000	0.000
9	A	11	GLN	0	0.029	0.028	13.444	0.130	0.130	0.000	0.000	0.000	0.000
10	A	12	ILE	0	0.007	0.007	11.779	0.096	0.096	0.000	0.000	0.000	0.000
11	A	13	GLN	0	0.015	0.002	13.608	0.059	0.059	0.000	0.000	0.000	0.000
12	A	14	GLN	0	0.048	0.025	16.293	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	15	TYR	0	0.048	0.012	16.397	0.009	0.009	0.000	0.000	0.000	0.000
14	A	16	LEU	0	-0.046	-0.028	16.633	0.055	0.055	0.000	0.000	0.000	0.000
15	A	17	VAL	0	-0.048	-0.014	20.023	0.048	0.048	0.000	0.000	0.000	0.000
16	A	18	GLU	-1	-0.884	-0.950	21.915	-0.402	-0.402	0.000	0.000	0.000	0.000
17	A	19	SER	0	-0.099	-0.052	22.937	0.025	0.025	0.000	0.000	0.000	0.000
18	A	20	GLY	0	0.011	0.010	24.732	0.021	0.021	0.000	0.000	0.000	0.000
19	A	21	ASN	0	-0.043	-0.012	20.513	0.041	0.041	0.000	0.000	0.000	0.000
20	A	22	TYR	0	0.074	0.021	22.709	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	23	GLU	-1	-0.884	-0.944	24.317	-0.147	-0.147	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.036	0.008	16.736	0.017	0.017	0.000	0.000	0.000	0.000
23	A	25	ILE	0	0.039	0.026	19.590	0.000	0.000	0.000	0.000	0.000	0.000
24	A	26	SER	0	-0.037	-0.025	20.846	0.021	0.021	0.000	0.000	0.000	0.000
25	A	27	ASN	0	-0.033	-0.048	20.378	0.055	0.055	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.744	-0.833	13.535	-0.337	-0.337	0.000	0.000	0.000	0.000
27	A	29	LEU	0	0.023	0.015	17.148	0.029	0.029	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.905	0.958	19.508	0.052	0.052	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.009	0.003	15.671	0.040	0.040	0.000	0.000	0.000	0.000
30	A	32	ARG	1	0.851	0.908	11.820	0.450	0.450	0.000	0.000	0.000	0.000
31	A	33	LEU	0	0.019	0.012	16.227	0.053	0.053	0.000	0.000	0.000	0.000
32	A	34	LEU	0	-0.037	-0.021	18.772	0.029	0.029	0.000	0.000	0.000	0.000
33	A	35	GLN	0	-0.040	-0.011	12.594	0.077	0.077	0.000	0.000	0.000	0.000
34	A	36	GLU	-1	-0.798	-0.864	16.074	0.147	0.147	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.038	0.007	17.649	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	38	TRP	0	-0.058	-0.040	20.915	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	39	VAL	0	0.029	0.005	22.973	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.816	-0.900	24.570	0.167	0.167	0.000	0.000	0.000	0.000
39	A	41	LYS	1	0.871	0.955	20.611	-0.164	-0.164	0.000	0.000	0.000	0.000
40	A	42	VAL	0	0.044	0.024	27.021	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	43	LYS	1	0.780	0.900	27.292	-0.158	-0.158	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.836	-0.947	30.300	0.126	0.126	0.000	0.000	0.000	0.000
43	A	45	LEU	0	-0.001	0.025	31.217	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	46	THR	0	-0.020	-0.033	32.960	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	47	LYS	1	0.879	0.948	33.624	-0.115	-0.115	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.027	-0.016	34.864	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.777	-0.861	36.629	0.044	0.044	0.000	0.000	0.000	0.000
48	A	50	MET	0	-0.053	-0.031	39.105	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	51	ASN	0	-0.018	-0.018	39.478	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	52	ILE	0	-0.029	0.008	39.831	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	53	ASN	0	-0.053	-0.034	43.446	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.920	-0.932	44.881	0.052	0.052	0.000	0.000	0.000	0.000
53	A	55	SER	0	-0.064	-0.037	46.349	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	56	THR	0	0.017	0.002	43.490	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	57	ASN	0	-0.049	-0.029	44.370	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	58	PHE	0	0.070	0.030	37.152	0.001	0.001	0.000	0.000	0.000	0.000
57	A	59	THR	0	0.023	0.011	40.821	0.001	0.001	0.000	0.000	0.000	0.000
58	A	60	GLN	0	0.006	-0.007	41.785	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	61	ILE	0	0.032	0.028	38.304	0.000	0.000	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.013	0.002	35.316	0.003	0.003	0.000	0.000	0.000	0.000
61	A	63	SER	0	-0.016	-0.009	37.226	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	64	THR	0	-0.042	-0.035	38.386	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	65	VAL	0	0.013	0.006	33.105	0.003	0.003	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.905	-0.958	32.755	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	67	PRO	0	-0.007	-0.012	32.173	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	68	LYS	1	0.800	0.879	31.832	-0.042	-0.042	0.000	0.000	0.000	0.000
67	A	69	ALA	0	0.002	-0.003	28.993	0.004	0.004	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.007	0.008	27.414	0.001	0.001	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.799	-0.876	26.570	-0.042	-0.042	0.000	0.000	0.000	0.000
70	A	72	MET	0	-0.047	-0.010	25.813	0.014	0.014	0.000	0.000	0.000	0.000
71	A	73	VAL	0	-0.105	-0.034	21.327	0.020	0.020	0.000	0.000	0.000	0.000
72	A	74	SER	0	0.000	-0.021	17.987	-0.019	-0.019	0.000	0.000	0.000	0.000
73	A	75	ASP	-1	-0.838	-0.931	19.645	-0.045	-0.045	0.000	0.000	0.000	0.000
74	A	76	SER	0	0.013	0.019	14.487	-0.031	-0.031	0.000	0.000	0.000	0.000
75	A	77	THR	0	-0.045	-0.021	16.305	-0.079	-0.079	0.000	0.000	0.000	0.000
76	A	78	ARG	1	0.792	0.861	17.627	0.022	0.022	0.000	0.000	0.000	0.000
77	A	79	GLU	-1	-0.917	-0.962	18.047	-0.239	-0.239	0.000	0.000	0.000	0.000
78	A	80	THR	0	-0.081	-0.069	13.601	-0.041	-0.041	0.000	0.000	0.000	0.000
79	A	81	VAL	0	0.012	0.002	16.825	-0.036	-0.036	0.000	0.000	0.000	0.000
80	A	82	LEU	0	0.014	0.014	19.312	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	83	LYS	1	0.791	0.879	16.399	0.564	0.564	0.000	0.000	0.000	0.000
82	A	84	GLN	0	-0.062	-0.032	16.189	0.022	0.022	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.003	-0.001	20.043	0.010	0.010	0.000	0.000	0.000	0.000
84	A	86	ARG	1	0.798	0.897	21.860	0.332	0.332	0.000	0.000	0.000	0.000
85	A	87	GLU	-1	-0.720	-0.849	20.076	-0.496	-0.496	0.000	0.000	0.000	0.000
86	A	88	PHE	0	-0.021	0.006	23.544	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	89	LEU	0	-0.004	-0.017	24.881	0.014	0.014	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.874	-0.945	25.588	-0.299	-0.299	0.000	0.000	0.000	0.000
89	A	91	GLU	-1	-0.926	-0.942	25.891	-0.306	-0.306	0.000	0.000	0.000	0.000
90	A	92	ILE	0	-0.111	-0.052	28.807	0.015	0.015	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.083	-0.036	31.714	0.018	0.018	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.913	-0.947	32.900	-0.172	-0.172	0.000	0.000	0.000	0.000
93	A	95	THR	0	0.026	0.006	30.478	0.001	0.001	0.000	0.000	0.000	0.000
94	A	96	GLN	0	-0.091	-0.038	31.128	0.017	0.017	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:MET)