FMO DATABASE

FMODB ID: ZV87N

Calculation Name: 3KGK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KGK

Chain ID: A

ChEMBL ID:

UniProt ID: P46003

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	92
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-641210.826151
FMO2-HF: Nuclear repulsion	604843.714244
FMO2-HF: Total energy	-36367.111908
FMO2-MP2: Total energy	-36472.541737

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:MET)

Summations of interaction energy for fragment #1(A:1: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.
-14.386	-7.005	8.163	-4.888	-10.653	-0.025

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : 0.000

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	3	THR	0	-0.038	-0.022	2.462	-4.991	-1.313	1.289	-2.407	-2.560	-0.013
4	A	4	LEU	0	-0.022	-0.023	5.011	0.753	0.840	-0.001	-0.006	-0.079	0.000
5	A	5	MET	0	0.006	0.013	7.616	-0.112	-0.112	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.030	-0.025	11.244	0.131	0.131	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.029	0.013	13.878	-0.047	-0.047	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.737	-0.840	17.369	0.039	0.039	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.053	0.020	19.674	-0.019	-0.019	0.000	0.000	0.000	0.000
10	A	10	ALA	0	-0.019	-0.007	23.138	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	24	GLN	0	-0.005	-0.022	23.081	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	25	ALA	0	0.034	0.014	21.157	0.011	0.011	0.000	0.000	0.000	0.000
13	A	26	LEU	0	0.036	0.013	19.395	0.024	0.024	0.000	0.000	0.000	0.000
14	A	27	VAL	0	-0.012	0.004	19.475	0.000	0.000	0.000	0.000	0.000	0.000
15	A	28	ASP	-1	-0.836	-0.916	18.694	0.166	0.166	0.000	0.000	0.000	0.000
16	A	29	PHE	0	0.026	0.008	12.366	0.026	0.026	0.000	0.000	0.000	0.000
17	A	30	SER	0	0.014	0.003	14.807	0.016	0.016	0.000	0.000	0.000	0.000
18	A	31	THR	0	-0.038	-0.020	15.165	-0.025	-0.025	0.000	0.000	0.000	0.000
19	A	32	ASP	-1	-0.808	-0.897	12.227	0.406	0.406	0.000	0.000	0.000	0.000
20	A	33	VAL	0	-0.028	-0.010	10.675	0.086	0.086	0.000	0.000	0.000	0.000
21	A	34	GLN	0	-0.007	-0.006	10.251	-0.060	-0.060	0.000	0.000	0.000	0.000
22	A	35	TRP	0	0.038	0.018	8.407	0.011	0.011	0.000	0.000	0.000	0.000
23	A	36	LEU	0	0.016	0.007	5.865	-0.056	-0.056	0.000	0.000	0.000	0.000
24	A	37	LYS	1	0.885	0.934	6.335	0.133	0.133	0.000	0.000	0.000	0.000
25	A	38	GLN	0	-0.047	-0.020	8.238	-0.144	-0.144	0.000	0.000	0.000	0.000
26	A	39	SER	0	-0.050	-0.023	4.990	0.038	0.038	0.000	0.000	0.000	0.000
27	A	40	GLY	0	-0.022	0.000	4.905	-0.355	-0.259	-0.001	-0.008	-0.087	0.000
28	A	41	VAL	0	-0.043	-0.017	2.457	-2.630	-1.386	1.966	-0.653	-2.556	0.000
29	A	42	GLN	0	0.004	0.007	3.519	0.396	0.524	0.008	0.110	-0.245	0.000
30	A	43	ILE	0	-0.017	-0.020	5.766	0.139	0.139	0.000	0.000	0.000	0.000
31	A	44	GLU	-1	-0.919	-0.942	8.303	-0.740	-0.740	0.000	0.000	0.000	0.000
32	A	45	ARG	1	0.804	0.863	11.673	0.083	0.083	0.000	0.000	0.000	0.000
33	A	46	PHE	0	0.031	0.026	13.778	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	47	ASN	0	0.022	-0.011	18.055	0.036	0.036	0.000	0.000	0.000	0.000
35	A	48	LEU	0	0.054	0.013	21.432	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	49	ALA	0	-0.016	0.003	24.868	0.000	0.000	0.000	0.000	0.000	0.000
37	A	50	GLN	0	-0.026	-0.005	22.668	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	51	GLN	0	0.020	0.016	19.891	0.000	0.000	0.000	0.000	0.000	0.000
39	A	52	PRO	0	0.061	0.030	22.331	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	53	MET	0	0.007	-0.003	24.732	0.003	0.003	0.000	0.000	0.000	0.000
41	A	54	SER	0	0.049	0.020	19.062	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	55	PHE	0	-0.056	-0.038	20.598	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	56	VAL	0	-0.021	-0.007	22.456	0.013	0.013	0.000	0.000	0.000	0.000
44	A	57	GLN	0	-0.020	0.000	21.740	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	58	ASN	0	0.002	0.016	15.989	0.010	0.010	0.000	0.000	0.000	0.000
46	A	59	GLU	-1	-0.833	-0.942	20.002	-0.132	-0.132	0.000	0.000	0.000	0.000
47	A	60	LYS	1	0.787	0.888	15.977	0.247	0.247	0.000	0.000	0.000	0.000
48	A	61	VAL	0	-0.035	-0.010	18.183	0.032	0.032	0.000	0.000	0.000	0.000
49	A	62	LYS	1	0.902	0.969	20.725	0.118	0.118	0.000	0.000	0.000	0.000
50	A	63	ALA	0	0.003	0.000	23.662	0.016	0.016	0.000	0.000	0.000	0.000
51	A	64	PHE	0	-0.008	-0.008	21.780	0.017	0.017	0.000	0.000	0.000	0.000
52	A	65	ILE	0	-0.020	-0.012	23.641	0.014	0.014	0.000	0.000	0.000	0.000
53	A	66	GLU	-1	-0.913	-0.954	25.892	-0.062	-0.062	0.000	0.000	0.000	0.000
54	A	67	ALA	0	-0.046	-0.015	26.733	0.007	0.007	0.000	0.000	0.000	0.000
55	A	68	SER	0	-0.050	-0.029	25.800	0.013	0.013	0.000	0.000	0.000	0.000
56	A	69	GLY	0	0.062	0.054	27.764	0.007	0.007	0.000	0.000	0.000	0.000
57	A	70	ALA	0	-0.015	-0.031	25.972	0.003	0.003	0.000	0.000	0.000	0.000
58	A	71	GLU	-1	-0.939	-0.979	25.865	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	72	GLY	0	-0.016	0.002	25.318	0.011	0.011	0.000	0.000	0.000	0.000
60	A	73	LEU	0	-0.087	-0.025	20.716	0.012	0.012	0.000	0.000	0.000	0.000
61	A	74	PRO	0	-0.021	-0.012	17.617	0.007	0.007	0.000	0.000	0.000	0.000
62	A	75	LEU	0	-0.011	0.003	16.905	0.024	0.024	0.000	0.000	0.000	0.000
63	A	76	LEU	0	-0.041	-0.025	12.124	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	77	LEU	0	0.006	0.002	12.282	0.032	0.032	0.000	0.000	0.000	0.000
65	A	78	LEU	0	-0.028	-0.020	6.200	0.029	0.029	0.000	0.000	0.000	0.000
66	A	79	ASP	-1	-0.787	-0.893	6.202	-2.726	-2.726	0.000	0.000	0.000	0.000
67	A	80	GLY	0	0.003	0.007	9.031	0.098	0.098	0.000	0.000	0.000	0.000
68	A	81	GLU	-1	-0.826	-0.901	11.877	-0.113	-0.113	0.000	0.000	0.000	0.000
69	A	82	THR	0	-0.006	-0.008	12.953	0.048	0.048	0.000	0.000	0.000	0.000
70	A	83	VAL	0	-0.032	-0.004	11.244	0.043	0.043	0.000	0.000	0.000	0.000
71	A	84	MET	0	-0.096	-0.043	14.478	0.061	0.061	0.000	0.000	0.000	0.000
72	A	85	ALA	0	0.003	-0.003	16.696	-0.037	-0.037	0.000	0.000	0.000	0.000
73	A	86	GLY	0	0.068	0.057	19.595	0.010	0.010	0.000	0.000	0.000	0.000
74	A	87	ARG	1	0.734	0.830	17.342	-0.311	-0.311	0.000	0.000	0.000	0.000
75	A	88	TYR	0	-0.005	-0.032	16.091	0.012	0.012	0.000	0.000	0.000	0.000
76	A	89	PRO	0	-0.042	-0.009	12.515	-0.014	-0.014	0.000	0.000	0.000	0.000
77	A	90	LYS	1	0.989	0.978	14.943	-0.275	-0.275	0.000	0.000	0.000	0.000
78	A	91	ARG	1	0.936	0.961	11.487	-0.260	-0.260	0.000	0.000	0.000	0.000
79	A	92	ALA	0	0.002	-0.005	10.975	0.144	0.144	0.000	0.000	0.000	0.000
80	A	93	GLU	-1	-0.815	-0.877	11.642	0.513	0.513	0.000	0.000	0.000	0.000
81	A	94	LEU	0	0.042	0.020	8.611	0.158	0.158	0.000	0.000	0.000	0.000
82	A	95	ALA	0	0.029	0.014	6.957	0.674	0.674	0.000	0.000	0.000	0.000
83	A	96	ARG	1	0.935	0.974	6.946	-0.502	-0.502	0.000	0.000	0.000	0.000
84	A	97	TRP	0	-0.024	-0.021	7.372	0.051	0.051	0.000	0.000	0.000	0.000
85	A	98	PHE	0	0.033	0.000	2.839	-1.708	-1.511	4.334	-1.148	-3.383	0.003
86	A	99	GLY	0	-0.001	0.021	2.801	-3.007	-1.323	0.566	-0.742	-1.508	-0.015
87	A	100	ILE	0	-0.031	-0.013	3.841	-0.810	-0.543	0.002	-0.034	-0.235	0.000
88	A	101	PRO	0	-0.019	-0.015	5.412	0.074	0.074	0.000	0.000	0.000	0.000
89	A	102	LEU	0	0.018	0.009	8.659	-0.042	-0.042	0.000	0.000	0.000	0.000
90	A	103	ASP	-1	-0.878	-0.924	12.011	0.271	0.271	0.000	0.000	0.000	0.000
91	A	104	LYS	1	0.834	0.898	12.546	-0.362	-0.362	0.000	0.000	0.000	0.000
92	A	105	VAL	0	0.027	0.026	16.994	-0.010	-0.010	0.000	0.000	0.000	0.000

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