FMO DATABASE

FMODB ID: 7GQ9K

Calculation Name: 3KJL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KJL

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-531978.093819
FMO2-HF: Nuclear repulsion	497025.832108
FMO2-HF: Total energy	-34952.261711
FMO2-MP2: Total energy	-35054.505067

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:7:GLN)

Summations of interaction energy for fragment #1(A:7:GLN)

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.
-0.625	1.706	-0.018	-1.228	-1.085	0

Interaction energy analysis for fragmet #1(A:7:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.020

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].
3	A	9	LYS	1	0.968	0.977	3.595	-2.207	0.124	-0.018	-1.228	-1.085
4	A	10	SER	0	-0.002	0.000	5.522	-0.290	-0.290	0.000	0.000	0.000
5	A	11	GLN	0	0.053	0.030	7.322	0.459	0.459	0.000	0.000	0.000
6	A	12	ILE	0	-0.003	-0.010	6.705	-0.116	-0.116	0.000	0.000	0.000
7	A	13	GLN	0	-0.028	-0.017	10.080	-0.190	-0.190	0.000	0.000	0.000
8	A	14	GLN	0	0.000	0.010	11.858	-0.048	-0.048	0.000	0.000	0.000
9	A	15	TYR	0	0.081	0.037	12.076	0.017	0.017	0.000	0.000	0.000
10	A	16	LEU	0	-0.054	-0.020	14.676	-0.081	-0.081	0.000	0.000	0.000
11	A	17	VAL	0	-0.022	-0.004	16.928	-0.075	-0.075	0.000	0.000	0.000
12	A	18	GLU	-1	-0.867	-0.942	15.386	0.838	0.838	0.000	0.000	0.000
13	A	19	SER	0	-0.063	-0.041	18.822	-0.033	-0.033	0.000	0.000	0.000
14	A	20	GLY	0	0.036	0.019	20.657	-0.049	-0.049	0.000	0.000	0.000
15	A	21	ASN	0	-0.038	-0.043	22.586	-0.065	-0.065	0.000	0.000	0.000
16	A	22	TYR	0	-0.022	0.002	23.179	-0.041	-0.041	0.000	0.000	0.000
17	A	23	GLU	-1	-0.908	-0.953	23.338	0.429	0.429	0.000	0.000	0.000
18	A	24	LEU	0	0.001	0.008	26.649	-0.033	-0.033	0.000	0.000	0.000
19	A	25	ILE	0	0.004	0.005	26.584	-0.027	-0.027	0.000	0.000	0.000
20	A	26	SER	0	-0.010	-0.003	28.923	-0.031	-0.031	0.000	0.000	0.000
21	A	27	ASN	0	-0.076	-0.029	30.534	-0.012	-0.012	0.000	0.000	0.000
22	A	28	GLU	-1	-0.763	-0.852	32.750	0.184	0.184	0.000	0.000	0.000
23	A	29	LEU	0	0.033	0.016	33.871	-0.016	-0.016	0.000	0.000	0.000
24	A	30	LYS	1	0.871	0.918	32.154	-0.278	-0.278	0.000	0.000	0.000
25	A	31	ALA	0	-0.005	0.005	37.170	-0.012	-0.012	0.000	0.000	0.000
26	A	32	ARG	1	0.858	0.913	37.159	-0.184	-0.184	0.000	0.000	0.000
27	A	33	LEU	0	0.033	0.022	38.386	-0.009	-0.009	0.000	0.000	0.000
28	A	34	LEU	0	-0.017	-0.019	41.466	-0.008	-0.008	0.000	0.000	0.000
29	A	35	GLN	0	-0.024	-0.012	41.615	-0.007	-0.007	0.000	0.000	0.000
30	A	36	GLU	-1	-0.807	-0.848	43.435	0.140	0.140	0.000	0.000	0.000
31	A	37	GLY	0	0.025	0.014	46.485	-0.005	-0.005	0.000	0.000	0.000
32	A	38	TRP	0	-0.059	-0.028	40.704	-0.001	-0.001	0.000	0.000	0.000
33	A	39	VAL	0	0.046	0.016	42.015	-0.001	-0.001	0.000	0.000	0.000
34	A	40	ASP	-1	-0.819	-0.908	44.729	0.125	0.125	0.000	0.000	0.000
35	A	41	LYS	1	0.911	0.955	48.409	-0.126	-0.126	0.000	0.000	0.000
36	A	42	VAL	0	0.042	0.033	43.637	-0.003	-0.003	0.000	0.000	0.000
37	A	43	LYS	1	0.777	0.893	46.512	-0.131	-0.131	0.000	0.000	0.000
38	A	44	ASP	-1	-0.817	-0.904	48.460	0.106	0.106	0.000	0.000	0.000
39	A	45	LEU	0	-0.023	0.002	47.409	-0.004	-0.004	0.000	0.000	0.000
40	A	46	THR	0	-0.008	-0.026	47.113	0.000	0.000	0.000	0.000	0.000
41	A	47	LYS	1	0.830	0.899	49.409	-0.112	-0.112	0.000	0.000	0.000
42	A	48	SER	0	0.014	0.020	52.838	-0.005	-0.005	0.000	0.000	0.000
43	A	49	GLU	-1	-0.813	-0.903	50.021	0.110	0.110	0.000	0.000	0.000
44	A	50	MET	0	-0.087	-0.052	48.525	-0.002	-0.002	0.000	0.000	0.000
45	A	51	ASN	0	-0.076	-0.038	53.448	-0.005	-0.005	0.000	0.000	0.000
46	A	52	ILE	0	-0.043	-0.008	55.175	-0.004	-0.004	0.000	0.000	0.000
47	A	53	ASN	0	-0.039	-0.025	52.072	-0.005	-0.005	0.000	0.000	0.000
48	A	54	GLU	-1	-0.926	-0.951	55.559	0.087	0.087	0.000	0.000	0.000
49	A	55	SER	0	-0.045	-0.022	51.419	0.000	0.000	0.000	0.000	0.000
50	A	56	THR	0	0.030	0.000	51.197	0.003	0.003	0.000	0.000	0.000
51	A	57	ASN	0	-0.009	-0.013	45.824	0.008	0.008	0.000	0.000	0.000
52	A	58	PHE	0	0.058	0.023	39.183	-0.001	-0.001	0.000	0.000	0.000
53	A	59	THR	0	0.030	0.010	41.369	0.001	0.001	0.000	0.000	0.000
54	A	60	GLN	0	0.031	0.031	43.584	-0.003	-0.003	0.000	0.000	0.000
55	A	61	ILE	0	0.042	0.043	47.014	-0.001	-0.001	0.000	0.000	0.000
56	A	62	LEU	0	-0.020	-0.005	39.524	-0.002	-0.002	0.000	0.000	0.000
57	A	63	SER	0	-0.072	-0.047	44.032	0.000	0.000	0.000	0.000	0.000
58	A	64	THR	0	-0.029	-0.021	44.982	-0.001	-0.001	0.000	0.000	0.000
59	A	65	VAL	0	-0.021	-0.019	44.880	-0.001	-0.001	0.000	0.000	0.000
60	A	66	GLU	-1	-0.912	-0.961	38.944	0.202	0.202	0.000	0.000	0.000
61	A	67	PRO	0	-0.006	-0.012	42.821	0.002	0.002	0.000	0.000	0.000
62	A	68	LYS	1	0.885	0.947	43.803	-0.116	-0.116	0.000	0.000	0.000
63	A	69	ALA	0	0.039	0.003	43.311	-0.002	-0.002	0.000	0.000	0.000
64	A	70	LEU	0	-0.018	-0.011	38.175	0.002	0.002	0.000	0.000	0.000
65	A	71	GLU	-1	-0.878	-0.923	41.801	0.156	0.156	0.000	0.000	0.000
66	A	72	MET	0	-0.081	-0.022	44.531	-0.007	-0.007	0.000	0.000	0.000
67	A	73	VAL	0	-0.084	-0.024	39.740	-0.003	-0.003	0.000	0.000	0.000
68	A	74	SER	0	0.010	-0.018	43.128	-0.001	-0.001	0.000	0.000	0.000
69	A	75	ASP	-1	-0.837	-0.928	42.362	0.137	0.137	0.000	0.000	0.000
70	A	76	SER	0	-0.031	-0.016	41.776	0.003	0.003	0.000	0.000	0.000
71	A	77	THR	0	-0.051	-0.044	38.735	0.007	0.007	0.000	0.000	0.000
72	A	78	ARG	1	0.852	0.910	37.987	-0.155	-0.155	0.000	0.000	0.000
73	A	79	GLU	-1	-0.872	-0.937	36.878	0.179	0.179	0.000	0.000	0.000
74	A	80	THR	0	-0.079	-0.050	36.586	0.004	0.004	0.000	0.000	0.000
75	A	81	VAL	0	0.013	-0.001	32.931	0.009	0.009	0.000	0.000	0.000
76	A	82	LEU	0	-0.001	0.003	32.443	0.019	0.019	0.000	0.000	0.000
77	A	83	LYS	1	0.783	0.877	31.870	-0.193	-0.193	0.000	0.000	0.000
78	A	84	GLN	0	-0.042	-0.030	29.804	0.010	0.010	0.000	0.000	0.000
79	A	85	ILE	0	0.007	-0.005	27.710	0.020	0.020	0.000	0.000	0.000
80	A	86	ARG	1	0.935	0.975	27.044	-0.187	-0.187	0.000	0.000	0.000
81	A	87	GLU	-1	-0.813	-0.886	26.745	0.231	0.231	0.000	0.000	0.000
82	A	88	PHE	0	-0.006	0.002	20.928	0.010	0.010	0.000	0.000	0.000
83	A	89	LEU	0	-0.010	-0.003	22.564	0.036	0.036	0.000	0.000	0.000
84	A	90	GLU	-1	-0.963	-0.989	22.254	0.260	0.260	0.000	0.000	0.000
85	A	91	GLU	-1	-0.914	-0.932	19.869	0.430	0.430	0.000	0.000	0.000
86	A	92	ILE	0	-0.132	-0.068	17.596	0.040	0.040	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:GLN)