FMO DATABASE

FMODB ID: R82Q8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-641939.024987
FMO2-HF: Nuclear repulsion	605571.816012
FMO2-HF: Total energy	-36367.208975
FMO2-MP2: Total energy	-36472.588065

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.
-14.521	-7.134	8.452	-5.004	-10.835	-0.028

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 : -0.016 / q_NPA : 0.009

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	-0.027	-0.028	2.483	-5.763	-2.184	1.256	-2.304	-2.532	-0.014
4	A	4	LEU	0	-0.031	-0.024	5.273	0.750	0.834	-0.001	-0.004	-0.078	0.000
5	A	5	MET	0	0.007	0.015	8.034	-0.147	-0.147	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.029	-0.020	11.627	0.109	0.109	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.039	0.013	14.249	-0.055	-0.055	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.731	-0.840	17.613	0.053	0.053	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.052	0.018	19.952	-0.017	-0.017	0.000	0.000	0.000	0.000
10	A	10	ALA	0	-0.022	-0.007	23.603	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	24	GLN	0	0.003	-0.017	22.796	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	25	ALA	0	0.030	0.009	21.029	0.001	0.001	0.000	0.000	0.000	0.000
13	A	26	LEU	0	0.032	0.014	19.483	0.021	0.021	0.000	0.000	0.000	0.000
14	A	27	VAL	0	0.002	0.006	19.516	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	28	ASP	-1	-0.842	-0.905	18.626	0.123	0.123	0.000	0.000	0.000	0.000
16	A	29	PHE	0	0.050	0.017	12.568	0.015	0.015	0.000	0.000	0.000	0.000
17	A	30	SER	0	0.002	-0.003	14.722	0.013	0.013	0.000	0.000	0.000	0.000
18	A	31	THR	0	-0.041	-0.027	15.182	-0.034	-0.034	0.000	0.000	0.000	0.000
19	A	32	ASP	-1	-0.824	-0.908	12.012	0.289	0.289	0.000	0.000	0.000	0.000
20	A	33	VAL	0	-0.001	-0.003	10.554	0.044	0.044	0.000	0.000	0.000	0.000
21	A	34	GLN	0	-0.002	-0.003	10.237	-0.088	-0.088	0.000	0.000	0.000	0.000
22	A	35	TRP	0	0.038	0.018	8.199	-0.016	-0.016	0.000	0.000	0.000	0.000
23	A	36	LEU	0	0.000	0.004	5.851	-0.068	-0.068	0.000	0.000	0.000	0.000
24	A	37	LYS	1	0.894	0.949	6.138	0.090	0.090	0.000	0.000	0.000	0.000
25	A	38	GLN	0	-0.045	-0.025	8.168	-0.132	-0.132	0.000	0.000	0.000	0.000
26	A	39	SER	0	-0.056	-0.026	5.019	0.055	0.055	0.000	0.000	0.000	0.000
27	A	40	GLY	0	-0.019	-0.003	4.792	-0.506	-0.393	-0.001	-0.010	-0.103	0.000
28	A	41	VAL	0	-0.039	-0.020	2.397	-2.651	-1.412	2.042	-0.708	-2.573	0.000
29	A	42	GLN	0	0.006	0.004	3.523	0.436	0.542	0.010	0.126	-0.241	0.000
30	A	43	ILE	0	-0.012	-0.013	5.575	0.309	0.309	0.000	0.000	0.000	0.000
31	A	44	GLU	-1	-0.942	-0.962	8.197	-0.670	-0.670	0.000	0.000	0.000	0.000
32	A	45	ARG	1	0.807	0.867	11.704	0.094	0.094	0.000	0.000	0.000	0.000
33	A	46	PHE	0	0.017	0.026	14.022	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	47	ASN	0	0.026	-0.013	18.303	0.032	0.032	0.000	0.000	0.000	0.000
35	A	48	LEU	0	0.044	0.009	21.749	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	49	ALA	0	-0.016	0.002	25.158	0.000	0.000	0.000	0.000	0.000	0.000
37	A	50	GLN	0	-0.033	-0.005	22.966	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	51	GLN	0	0.027	0.020	19.981	0.000	0.000	0.000	0.000	0.000	0.000
39	A	52	PRO	0	0.038	0.024	22.552	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	53	MET	0	0.013	0.005	24.754	0.003	0.003	0.000	0.000	0.000	0.000
41	A	54	SER	0	0.042	0.016	19.233	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	55	PHE	0	-0.041	-0.026	20.594	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	56	VAL	0	-0.023	-0.013	22.537	0.012	0.012	0.000	0.000	0.000	0.000
44	A	57	GLN	0	-0.034	-0.013	21.818	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	58	ASN	0	0.014	0.011	16.532	0.001	0.001	0.000	0.000	0.000	0.000
46	A	59	GLU	-1	-0.832	-0.936	20.601	-0.081	-0.081	0.000	0.000	0.000	0.000
47	A	60	LYS	1	0.794	0.890	16.534	0.125	0.125	0.000	0.000	0.000	0.000
48	A	61	VAL	0	-0.043	-0.007	18.585	0.025	0.025	0.000	0.000	0.000	0.000
49	A	62	LYS	1	0.881	0.947	21.159	0.075	0.075	0.000	0.000	0.000	0.000
50	A	63	ALA	0	0.013	0.000	24.169	0.011	0.011	0.000	0.000	0.000	0.000
51	A	64	PHE	0	-0.012	-0.005	22.332	0.014	0.014	0.000	0.000	0.000	0.000
52	A	65	ILE	0	-0.017	-0.014	24.121	0.007	0.007	0.000	0.000	0.000	0.000
53	A	66	GLU	-1	-0.909	-0.950	26.468	-0.038	-0.038	0.000	0.000	0.000	0.000
54	A	67	ALA	0	-0.031	-0.007	27.512	0.003	0.003	0.000	0.000	0.000	0.000
55	A	68	SER	0	-0.071	-0.038	26.391	0.011	0.011	0.000	0.000	0.000	0.000
56	A	69	GLY	0	0.045	0.044	28.530	0.005	0.005	0.000	0.000	0.000	0.000
57	A	70	ALA	0	-0.018	-0.031	26.488	0.001	0.001	0.000	0.000	0.000	0.000
58	A	71	GLU	-1	-0.922	-0.975	26.376	0.011	0.011	0.000	0.000	0.000	0.000
59	A	72	GLY	0	0.010	0.024	25.899	0.009	0.009	0.000	0.000	0.000	0.000
60	A	73	LEU	0	-0.075	-0.027	21.267	0.013	0.013	0.000	0.000	0.000	0.000
61	A	74	PRO	0	-0.049	-0.025	18.227	0.001	0.001	0.000	0.000	0.000	0.000
62	A	75	LEU	0	-0.004	0.001	17.631	0.016	0.016	0.000	0.000	0.000	0.000
63	A	76	LEU	0	-0.048	-0.026	12.426	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	77	LEU	0	0.019	0.011	12.948	0.031	0.031	0.000	0.000	0.000	0.000
65	A	78	LEU	0	-0.017	-0.011	6.332	0.010	0.010	0.000	0.000	0.000	0.000
66	A	79	ASP	-1	-0.808	-0.900	6.856	-1.207	-1.207	0.000	0.000	0.000	0.000
67	A	80	GLY	0	0.025	0.022	9.375	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	81	GLU	-1	-0.840	-0.913	12.487	-0.037	-0.037	0.000	0.000	0.000	0.000
69	A	82	THR	0	-0.011	-0.012	13.485	0.057	0.057	0.000	0.000	0.000	0.000
70	A	83	VAL	0	-0.028	-0.003	11.350	0.029	0.029	0.000	0.000	0.000	0.000
71	A	84	MET	0	-0.102	-0.046	14.545	0.040	0.040	0.000	0.000	0.000	0.000
72	A	85	ALA	0	0.041	0.023	16.793	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	86	GLY	0	0.048	0.047	20.076	0.017	0.017	0.000	0.000	0.000	0.000
74	A	87	ARG	1	0.767	0.858	17.437	-0.286	-0.286	0.000	0.000	0.000	0.000
75	A	88	TYR	0	0.003	-0.020	16.541	0.013	0.013	0.000	0.000	0.000	0.000
76	A	89	PRO	0	-0.014	0.004	12.678	-0.015	-0.015	0.000	0.000	0.000	0.000
77	A	90	LYS	1	0.987	0.983	15.125	-0.240	-0.240	0.000	0.000	0.000	0.000
78	A	91	ARG	1	0.908	0.944	11.358	-0.129	-0.129	0.000	0.000	0.000	0.000
79	A	92	ALA	0	0.018	0.009	10.484	0.107	0.107	0.000	0.000	0.000	0.000
80	A	93	GLU	-1	-0.812	-0.886	11.107	0.453	0.453	0.000	0.000	0.000	0.000
81	A	94	LEU	0	0.030	0.021	8.581	0.123	0.123	0.000	0.000	0.000	0.000
82	A	95	ALA	0	0.023	0.012	6.440	0.572	0.572	0.000	0.000	0.000	0.000
83	A	96	ARG	1	0.872	0.930	6.481	-0.497	-0.497	0.000	0.000	0.000	0.000
84	A	97	TRP	0	-0.010	-0.011	7.561	-0.030	-0.030	0.000	0.000	0.000	0.000
85	A	98	PHE	0	0.043	0.001	2.656	-1.491	-1.396	4.404	-1.061	-3.438	0.002
86	A	99	GLY	0	0.003	0.020	2.644	-3.621	-1.848	0.732	-0.987	-1.519	-0.016
87	A	100	ILE	0	-0.025	-0.009	3.593	-0.795	-0.431	0.011	-0.055	-0.319	0.000
88	A	101	PRO	0	-0.026	-0.018	5.116	0.135	0.169	-0.001	-0.001	-0.032	0.000
89	A	102	LEU	0	0.017	0.014	8.534	-0.038	-0.038	0.000	0.000	0.000	0.000
90	A	103	ASP	-1	-0.872	-0.925	11.722	0.142	0.142	0.000	0.000	0.000	0.000
91	A	104	LYS	1	0.830	0.896	12.870	-0.223	-0.223	0.000	0.000	0.000	0.000
92	A	105	VAL	0	0.026	0.027	17.228	-0.008	-0.008	0.000	0.000	0.000	0.000

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