FMO DATABASE

FMODB ID: 3JJ8L

Calculation Name: 5J4G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5J4G

Chain ID: A

ChEMBL ID:

UniProt ID: O25562

Base Structure: X-ray

Registration Date: 2023-09-21

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-720696.615299
FMO2-HF: Nuclear repulsion	681410.953098
FMO2-HF: Total energy	-39285.662201
FMO2-MP2: Total energy	-39397.652733

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.
-0.578	1.415	-0.002	-0.833	-1.159	0.001

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 : -0.070 / q_NPA : -0.049

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	VAL	0	-0.077	-0.042	3.523	0.740	2.733	-0.002	-0.833	-1.159	0.001
4	A	4	VAL	0	0.027	0.018	6.045	-0.043	-0.043	0.000	0.000	0.000	0.000
5	A	5	HIS	0	0.053	0.028	9.081	0.324	0.324	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.005	-0.015	11.320	-0.029	-0.029	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.015	-0.007	14.889	-0.003	-0.003	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.911	-0.945	14.049	-0.413	-0.413	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.000	0.001	16.920	0.014	0.014	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.005	0.011	19.604	0.018	0.018	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.022	-0.008	21.780	-0.017	-0.017	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.012	-0.005	25.120	0.014	0.014	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.857	-0.922	28.390	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.839	0.899	28.721	0.011	0.011	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.022	-0.005	26.530	0.003	0.003	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.047	-0.011	21.429	0.002	0.002	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.017	-0.003	20.756	0.026	0.026	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.791	-0.867	17.371	0.010	0.010	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.038	-0.027	12.996	0.070	0.070	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.018	0.018	12.024	-0.077	-0.077	0.000	0.000	0.000	0.000
21	A	21	ASN	0	0.030	0.004	6.740	0.013	0.013	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.804	-0.878	8.468	0.362	0.362	0.000	0.000	0.000	0.000
23	A	23	ASN	0	0.068	0.047	7.057	-0.410	-0.410	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.011	-0.007	9.178	-0.229	-0.229	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.056	-0.027	11.609	-0.070	-0.070	0.000	0.000	0.000	0.000
26	A	26	HIS	0	0.005	-0.001	10.079	-0.196	-0.196	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.861	0.916	11.663	-0.346	-0.346	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.736	-0.802	10.003	1.257	1.257	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.005	-0.008	12.877	-0.096	-0.096	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.780	0.859	16.053	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	31	ILE	0	0.006	-0.007	17.698	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	32	CYS	0	-0.008	0.021	21.210	0.005	0.005	0.000	0.000	0.000	0.000
33	A	33	MET	0	0.003	-0.014	23.546	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.027	0.016	27.103	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.803	0.890	30.386	-0.059	-0.059	0.000	0.000	0.000	0.000
36	A	36	GLY	0	-0.008	-0.003	32.920	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.041	-0.008	30.370	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.015	-0.015	31.994	0.008	0.008	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.044	-0.012	24.505	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.772	-0.880	30.167	0.126	0.126	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.867	0.929	31.689	-0.107	-0.107	0.000	0.000	0.000	0.000
42	A	42	HIS	0	-0.002	0.010	25.668	0.001	0.001	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.904	0.955	27.936	-0.180	-0.180	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.028	0.031	23.031	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.022	-0.012	21.525	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.053	0.015	21.120	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.037	0.023	20.631	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	48	ILE	0	0.012	0.004	19.369	0.057	0.057	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.022	-0.008	18.130	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.005	0.013	19.112	0.028	0.028	0.000	0.000	0.000	0.000
51	A	51	GLN	0	-0.001	-0.011	17.628	0.050	0.050	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.002	0.016	20.268	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	53	LEU	0	0.017	0.016	15.892	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.932	-0.982	20.257	0.061	0.061	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.052	0.035	23.447	0.006	0.006	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.802	0.867	27.125	-0.116	-0.116	0.000	0.000	0.000	0.000
57	A	57	ILE	0	-0.028	0.000	25.990	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.006	0.003	29.499	0.002	0.002	0.000	0.000	0.000	0.000
59	A	59	PHE	0	0.030	0.005	25.592	0.006	0.006	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.862	-0.927	30.199	0.125	0.125	0.000	0.000	0.000	0.000
61	A	61	VAL	0	0.017	-0.007	30.832	0.011	0.011	0.000	0.000	0.000	0.000
62	A	62	GLY	0	-0.011	0.007	32.938	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.950	-0.978	36.237	0.128	0.128	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.926	-0.941	34.179	0.183	0.183	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.817	0.890	34.482	-0.126	-0.126	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.002	0.006	30.231	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.828	-0.908	31.735	0.138	0.138	0.000	0.000	0.000	0.000
68	A	68	MET	0	-0.055	-0.024	24.253	0.010	0.010	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.043	0.018	27.954	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.899	0.939	21.213	-0.165	-0.165	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.017	-0.002	22.028	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	72	ALA	0	-0.020	0.006	22.454	0.040	0.040	0.000	0.000	0.000	0.000
73	A	73	LEU	0	0.002	-0.015	19.192	0.015	0.015	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.001	0.011	22.627	-0.021	-0.021	0.000	0.000	0.000	0.000
75	A	75	SER	0	0.006	-0.017	21.036	0.037	0.037	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.021	-0.006	23.204	-0.039	-0.039	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.838	-0.927	23.479	0.406	0.406	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.035	-0.018	24.226	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.086	-0.043	25.387	-0.039	-0.039	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.066	0.037	27.711	-0.023	-0.023	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.042	-0.022	28.604	0.007	0.007	0.000	0.000	0.000	0.000
82	A	82	HIS	0	-0.038	-0.027	25.847	0.010	0.010	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.791	0.880	30.441	-0.126	-0.126	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.002	0.011	24.962	0.012	0.012	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.785	-0.887	29.732	0.111	0.111	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.020	0.002	29.535	0.008	0.008	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.017	0.005	31.004	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.822	-0.900	30.572	0.064	0.064	0.000	0.000	0.000	0.000
89	A	89	ASN	0	0.016	0.030	28.759	0.011	0.011	0.000	0.000	0.000	0.000
90	A	90	SER	0	-0.002	-0.021	25.701	0.006	0.006	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.017	-0.001	19.554	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.012	-0.008	20.699	0.023	0.023	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.844	0.907	12.152	-1.035	-1.035	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.016	0.000	17.529	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	95	SER	0	-0.039	-0.036	14.097	0.028	0.028	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.028	-0.024	15.262	-0.080	-0.080	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.037	-0.019	15.398	0.065	0.065	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.789	0.875	12.955	-0.624	-0.624	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.968	0.988	17.764	-0.357	-0.357	0.000	0.000	0.000	0.000

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