FMO DATABASE

FMODB ID: 3JR9L

Calculation Name: 3GHJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GHJ

Chain ID: A

ChEMBL ID:

UniProt ID: B0BGV9

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	OptH
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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-944994.703167
FMO2-HF: Nuclear repulsion	899177.088748
FMO2-HF: Total energy	-45817.614419
FMO2-MP2: Total energy	-45953.517038

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:5:ILE)

Summations of interaction energy for fragment #1(A:5:ILE)

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.
-5.338	-0.305	0.395	-2.454	-2.975	-0.002

Interaction energy analysis for fragmet #1(A:5:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.015

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	7	GLY	0	0.036	0.030	2.490	-4.575	-0.038	0.376	-2.296	-2.618	-0.001
4	A	8	LEU	0	-0.017	0.002	3.717	-0.483	0.013	0.019	-0.158	-0.357	-0.001
5	A	9	PHE	0	-0.027	0.001	6.153	0.198	0.198	0.000	0.000	0.000	0.000
6	A	10	GLU	-1	-0.892	-0.960	8.040	-0.028	-0.028	0.000	0.000	0.000	0.000
7	A	11	VAL	0	-0.024	0.004	10.301	-0.110	-0.110	0.000	0.000	0.000	0.000
8	A	12	ALA	0	0.000	0.006	13.056	0.058	0.058	0.000	0.000	0.000	0.000
9	A	13	VAL	0	-0.009	0.003	16.211	-0.028	-0.028	0.000	0.000	0.000	0.000
10	A	14	LYS	1	0.896	0.958	19.244	0.186	0.186	0.000	0.000	0.000	0.000
11	A	15	VAL	0	-0.024	-0.004	22.489	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	16	LYS	1	0.937	0.962	25.441	0.106	0.106	0.000	0.000	0.000	0.000
13	A	17	ASN	0	-0.038	-0.022	28.827	0.009	0.009	0.000	0.000	0.000	0.000
14	A	18	LEU	0	0.042	0.025	24.934	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	19	GLU	-1	-0.806	-0.888	27.793	-0.035	-0.035	0.000	0.000	0.000	0.000
16	A	20	LYS	1	0.966	0.973	29.997	0.053	0.053	0.000	0.000	0.000	0.000
17	A	21	SER	0	0.036	0.020	25.085	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	22	SER	0	0.002	-0.012	25.263	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	23	GLN	0	0.012	0.021	26.342	0.000	0.000	0.000	0.000	0.000	0.000
20	A	24	PHE	0	0.036	0.029	23.834	0.003	0.003	0.000	0.000	0.000	0.000
21	A	25	TYR	0	-0.021	-0.059	19.984	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	26	THR	0	-0.045	-0.023	23.432	0.005	0.005	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.945	-0.959	25.468	-0.018	-0.018	0.000	0.000	0.000	0.000
24	A	28	ILE	0	-0.060	-0.038	26.602	0.002	0.002	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.058	-0.038	20.835	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	30	GLY	0	-0.015	0.017	22.824	0.002	0.002	0.000	0.000	0.000	0.000
27	A	31	PHE	0	-0.044	-0.027	18.440	0.008	0.008	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.923	-0.970	20.898	0.076	0.076	0.000	0.000	0.000	0.000
29	A	33	ALA	0	0.011	0.002	21.575	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	34	GLY	0	0.039	0.006	20.697	0.015	0.015	0.000	0.000	0.000	0.000
31	A	35	LEU	0	-0.068	-0.019	21.260	0.010	0.010	0.000	0.000	0.000	0.000
32	A	36	LEU	0	0.009	0.016	22.767	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.823	-0.923	24.450	0.000	0.000	0.000	0.000	0.000	0.000
34	A	38	SER	0	-0.001	-0.031	26.219	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	39	ALA	0	-0.036	-0.001	28.765	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	40	ARG	1	0.897	0.952	20.711	0.024	0.024	0.000	0.000	0.000	0.000
37	A	41	ARG	1	0.748	0.863	26.461	0.031	0.031	0.000	0.000	0.000	0.000
38	A	42	TRP	0	0.012	-0.011	19.293	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	43	ASN	0	0.002	-0.020	22.332	0.022	0.022	0.000	0.000	0.000	0.000
40	A	44	PHE	0	-0.037	-0.007	16.868	-0.019	-0.019	0.000	0.000	0.000	0.000
41	A	45	LEU	0	0.011	0.001	18.602	0.020	0.020	0.000	0.000	0.000	0.000
42	A	46	TRP	0	0.022	0.009	14.053	0.004	0.004	0.000	0.000	0.000	0.000
43	A	47	VAL	0	0.012	0.010	14.778	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	48	SER	0	0.015	-0.006	15.676	0.017	0.017	0.000	0.000	0.000	0.000
45	A	49	GLY	0	0.059	0.035	16.850	0.035	0.035	0.000	0.000	0.000	0.000
46	A	50	ARG	1	0.908	0.935	14.581	-0.335	-0.335	0.000	0.000	0.000	0.000
47	A	51	ALA	0	-0.028	-0.011	12.258	0.063	0.063	0.000	0.000	0.000	0.000
48	A	52	GLY	0	0.033	0.018	10.825	-0.028	-0.028	0.000	0.000	0.000	0.000
49	A	53	MET	0	-0.042	-0.005	12.272	0.049	0.049	0.000	0.000	0.000	0.000
50	A	54	VAL	0	0.008	0.019	13.548	-0.059	-0.059	0.000	0.000	0.000	0.000
51	A	55	VAL	0	-0.001	-0.001	15.208	0.036	0.036	0.000	0.000	0.000	0.000
52	A	56	LEU	0	-0.017	0.003	17.817	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	57	GLN	0	0.039	0.006	18.614	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	58	GLU	-1	-0.805	-0.885	22.747	-0.066	-0.066	0.000	0.000	0.000	0.000
55	A	59	GLU	-1	-0.905	-0.956	24.661	-0.134	-0.134	0.000	0.000	0.000	0.000
56	A	60	LYS	1	0.954	0.966	27.505	0.054	0.054	0.000	0.000	0.000	0.000
57	A	61	GLU	-1	-0.996	-0.995	30.017	-0.077	-0.077	0.000	0.000	0.000	0.000
58	A	62	ASN	0	-0.005	-0.002	27.772	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	63	TRP	0	-0.055	-0.024	26.393	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	64	GLN	0	0.016	-0.005	22.888	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	65	GLN	0	-0.055	-0.011	22.761	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	66	GLN	0	-0.034	-0.024	17.283	0.004	0.004	0.000	0.000	0.000	0.000
63	A	67	HIS	0	-0.031	-0.018	16.514	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	68	PHE	0	-0.018	-0.008	14.422	-0.040	-0.040	0.000	0.000	0.000	0.000
65	A	69	SER	0	-0.030	-0.002	14.057	0.023	0.023	0.000	0.000	0.000	0.000
66	A	70	PHE	0	0.020	0.009	13.612	-0.031	-0.031	0.000	0.000	0.000	0.000
67	A	71	ARG	1	0.937	0.973	11.540	0.246	0.246	0.000	0.000	0.000	0.000
68	A	72	VAL	0	0.027	0.015	14.767	0.037	0.037	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.908	-0.958	18.026	-0.030	-0.030	0.000	0.000	0.000	0.000
70	A	74	LYS	1	0.907	0.928	19.968	0.148	0.148	0.000	0.000	0.000	0.000
71	A	75	SER	0	-0.015	-0.008	22.287	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	76	GLU	-1	-0.864	-0.934	22.873	-0.023	-0.023	0.000	0.000	0.000	0.000
73	A	77	ILE	0	-0.043	-0.013	21.450	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	78	GLU	-1	-0.894	-0.964	24.961	-0.077	-0.077	0.000	0.000	0.000	0.000
75	A	79	PRO	0	-0.004	0.002	27.379	0.001	0.001	0.000	0.000	0.000	0.000
76	A	80	LEU	0	0.021	0.012	22.209	0.002	0.002	0.000	0.000	0.000	0.000
77	A	81	LYS	1	0.886	0.945	26.361	0.085	0.085	0.000	0.000	0.000	0.000
78	A	82	LYS	1	0.978	0.994	28.154	0.048	0.048	0.000	0.000	0.000	0.000
79	A	83	ALA	0	-0.011	-0.005	28.205	0.003	0.003	0.000	0.000	0.000	0.000
80	A	84	LEU	0	0.000	0.010	24.613	0.004	0.004	0.000	0.000	0.000	0.000
81	A	85	GLU	-1	-0.883	-0.947	29.108	-0.067	-0.067	0.000	0.000	0.000	0.000
82	A	86	SER	0	-0.146	-0.077	32.367	0.005	0.005	0.000	0.000	0.000	0.000
83	A	87	LYS	1	0.871	0.940	28.302	0.040	0.040	0.000	0.000	0.000	0.000
84	A	88	GLY	0	-0.013	0.001	33.057	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	89	VAL	0	-0.041	-0.012	27.427	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	90	SER	0	-0.023	-0.019	30.900	0.002	0.002	0.000	0.000	0.000	0.000
87	A	91	VAL	0	-0.008	-0.001	26.536	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	92	HIS	0	-0.004	0.008	26.599	0.011	0.011	0.000	0.000	0.000	0.000
89	A	93	GLY	0	0.023	0.026	26.472	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	94	PRO	0	0.021	-0.006	25.843	0.010	0.010	0.000	0.000	0.000	0.000
91	A	95	VAL	0	-0.006	-0.001	24.115	0.007	0.007	0.000	0.000	0.000	0.000
92	A	96	ASN	0	-0.008	-0.008	23.607	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	97	GLN	0	0.003	0.001	19.556	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	98	GLU	-1	-0.925	-0.976	21.021	-0.164	-0.164	0.000	0.000	0.000	0.000
95	A	99	TRP	0	-0.005	-0.005	15.870	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	100	MET	0	-0.025	-0.004	14.637	-0.020	-0.020	0.000	0.000	0.000	0.000
97	A	101	GLN	0	-0.028	-0.011	17.517	-0.016	-0.016	0.000	0.000	0.000	0.000
98	A	102	ALA	0	-0.022	-0.009	17.386	0.007	0.007	0.000	0.000	0.000	0.000
99	A	103	VAL	0	-0.013	-0.001	19.397	0.016	0.016	0.000	0.000	0.000	0.000
100	A	104	SER	0	-0.005	-0.015	19.035	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	105	LEU	0	-0.045	-0.004	21.352	0.018	0.018	0.000	0.000	0.000	0.000
102	A	106	TYR	0	0.016	-0.001	20.208	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	107	PHE	0	0.025	0.006	21.695	0.017	0.017	0.000	0.000	0.000	0.000
104	A	108	ALA	0	0.027	0.025	23.992	-0.014	-0.014	0.000	0.000	0.000	0.000
105	A	109	ASP	-1	-0.707	-0.828	23.536	-0.129	-0.129	0.000	0.000	0.000	0.000
106	A	110	PRO	0	-0.024	-0.030	25.649	0.000	0.000	0.000	0.000	0.000	0.000
107	A	111	ASN	0	-0.079	-0.036	24.768	0.015	0.015	0.000	0.000	0.000	0.000
108	A	112	GLY	0	0.024	0.016	27.192	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	113	HIS	0	-0.024	-0.010	21.396	-0.020	-0.020	0.000	0.000	0.000	0.000
110	A	114	ALA	0	0.000	-0.002	21.376	0.014	0.014	0.000	0.000	0.000	0.000
111	A	115	LEU	0	-0.009	-0.002	19.636	-0.026	-0.026	0.000	0.000	0.000	0.000
112	A	116	GLU	-1	-0.765	-0.884	17.947	-0.303	-0.303	0.000	0.000	0.000	0.000
113	A	117	PHE	0	-0.022	0.001	18.181	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	118	THR	0	0.028	-0.008	15.227	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	119	ALA	0	0.000	0.013	16.540	0.003	0.003	0.000	0.000	0.000	0.000
116	A	120	LEU	0	-0.018	-0.018	12.870	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ILE)