FMO DATABASE

FMODB ID: 5J8QZ

Calculation Name: 3H9X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H9X

Chain ID: A

ChEMBL ID:

UniProt ID: Q880Y4

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:

Apendix: None

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	117
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1052961.147239
FMO2-HF: Nuclear repulsion	1005268.826507
FMO2-HF: Total energy	-47692.320732
FMO2-MP2: Total energy	-47833.312002

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.
-23.833	-14.347	13.494	-6.791	-16.188	-0.02

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 : -0.019 / q_NPA : -0.013

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	ARG	1	0.941	0.942	3.434	-1.586	0.580	0.005	-1.182	-0.989	-0.001
4	A	4	GLN	0	0.012	-0.002	6.146	0.129	0.129	0.000	0.000	0.000	0.000
5	A	5	GLN	0	0.035	0.004	2.319	-4.976	-3.581	5.057	-2.601	-3.851	-0.028
6	A	6	PHE	0	-0.042	-0.010	2.356	0.198	2.086	1.059	-0.823	-2.124	-0.005
7	A	7	ILE	0	0.044	0.017	3.255	1.284	1.338	0.039	0.241	-0.334	-0.001
8	A	8	ASP	-1	-0.885	-0.928	6.709	0.056	0.056	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.047	-0.040	4.542	0.539	0.852	0.001	-0.034	-0.279	0.000
10	A	10	ALA	0	0.008	0.000	6.631	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.048	0.033	8.151	0.006	0.006	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.889	0.948	10.235	-0.356	-0.356	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.853	0.931	8.569	-0.828	-0.828	0.000	0.000	0.000	0.000
14	A	14	TYR	0	-0.081	-0.063	7.808	0.025	0.025	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.934	-0.954	12.466	0.015	0.015	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.057	-0.015	12.025	-0.059	-0.059	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.944	0.983	12.710	0.259	0.259	0.000	0.000	0.000	0.000
18	A	18	PRO	0	-0.020	-0.009	11.403	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.812	-0.927	13.368	-0.270	-0.270	0.000	0.000	0.000	0.000
20	A	20	HIS	0	-0.015	-0.013	13.798	-0.061	-0.061	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.039	-0.019	17.370	0.040	0.040	0.000	0.000	0.000	0.000
22	A	22	TRP	0	-0.003	0.003	16.418	0.017	0.017	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.840	-0.916	20.826	-0.332	-0.332	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.897	0.935	23.206	0.299	0.299	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.080	-0.037	18.419	0.011	0.011	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.061	0.026	18.395	-0.037	-0.037	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.865	-0.920	14.123	-0.844	-0.844	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.128	-0.071	13.373	-0.117	-0.117	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.043	0.022	11.363	0.091	0.091	0.000	0.000	0.000	0.000
30	A	30	VAL	0	-0.039	-0.007	12.045	-0.136	-0.136	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.026	0.005	8.846	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.887	0.948	12.750	0.300	0.300	0.000	0.000	0.000	0.000
33	A	33	HIS	1	0.814	0.923	15.543	0.152	0.152	0.000	0.000	0.000	0.000
34	A	34	SER	0	0.039	0.014	17.549	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.869	-0.931	20.493	-0.042	-0.042	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.008	-0.009	20.410	-0.024	-0.024	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.854	-0.921	20.196	-0.184	-0.184	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.886	0.937	18.795	0.118	0.118	0.000	0.000	0.000	0.000
39	A	39	TRP	0	0.005	-0.013	15.241	-0.024	-0.024	0.000	0.000	0.000	0.000
40	A	40	TYR	0	-0.002	0.001	9.172	0.009	0.009	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.034	0.046	8.438	-0.049	-0.049	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.004	0.003	10.526	0.098	0.098	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.003	0.027	6.890	-0.229	-0.229	0.000	0.000	0.000	0.000
44	A	44	MET	0	-0.053	-0.019	9.957	0.346	0.346	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.737	-0.851	11.322	-1.141	-1.141	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.074	-0.052	13.738	0.188	0.188	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.004	-0.012	15.021	-0.025	-0.025	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.013	0.000	14.727	-0.023	-0.023	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.883	-0.950	15.741	-0.348	-0.348	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.912	0.956	18.002	0.416	0.416	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.053	-0.015	12.509	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.028	-0.012	16.429	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.070	-0.007	13.318	0.046	0.046	0.000	0.000	0.000	0.000
54	A	54	ASN	0	0.029	-0.006	16.313	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.021	0.001	17.281	-0.025	-0.025	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.928	-0.946	18.554	-0.320	-0.320	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.945	0.977	11.682	0.441	0.441	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.888	0.936	14.673	0.605	0.605	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.063	-0.032	10.447	0.047	0.047	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.722	-0.835	8.534	-1.811	-1.811	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.043	-0.025	8.047	-0.431	-0.431	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.025	0.003	4.418	-0.067	0.043	-0.001	-0.009	-0.100	0.000
63	A	63	ASP	-1	-0.829	-0.902	8.334	-0.839	-0.839	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.011	-0.023	6.824	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.914	0.958	10.932	0.313	0.313	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.013	-0.008	13.029	0.030	0.030	0.000	0.000	0.000	0.000
67	A	67	GLN	0	0.011	0.006	15.493	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	68	PRO	0	0.056	0.030	18.988	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.895	-0.949	21.367	-0.078	-0.078	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.016	-0.020	16.806	0.011	0.011	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.007	0.005	17.279	-0.023	-0.023	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.010	-0.002	18.177	-0.028	-0.028	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.009	-0.017	18.192	0.000	0.000	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.017	0.007	13.077	0.005	0.005	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.942	0.979	15.014	0.289	0.289	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.942	0.985	16.447	0.098	0.098	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.898	0.957	12.531	0.040	0.040	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.018	0.015	11.325	-0.058	-0.058	0.000	0.000	0.000	0.000
79	A	79	GLY	0	0.051	0.001	8.680	-0.030	-0.030	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.048	-0.006	9.309	-0.295	-0.295	0.000	0.000	0.000	0.000
81	A	81	TYR	0	0.020	0.017	10.595	0.128	0.128	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.071	-0.060	14.530	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.030	0.027	15.330	-0.044	-0.044	0.000	0.000	0.000	0.000
84	A	84	TYR	0	0.031	0.023	15.392	0.123	0.123	0.000	0.000	0.000	0.000
85	A	85	HIS	1	0.887	0.930	16.518	0.476	0.476	0.000	0.000	0.000	0.000
86	A	86	MET	0	0.043	0.052	15.683	0.036	0.036	0.000	0.000	0.000	0.000
87	A	87	ASN	0	0.021	-0.003	18.801	0.021	0.021	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.998	0.970	19.335	0.309	0.309	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.933	-0.949	19.897	-0.197	-0.197	0.000	0.000	0.000	0.000
90	A	90	HIS	0	-0.022	-0.013	19.218	0.014	0.014	0.000	0.000	0.000	0.000
91	A	91	TRP	0	-0.032	-0.010	12.844	0.008	0.008	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.005	0.002	11.043	0.046	0.046	0.000	0.000	0.000	0.000
93	A	93	THR	0	0.004	-0.006	11.313	-0.022	-0.022	0.000	0.000	0.000	0.000
94	A	94	VAL	0	-0.043	-0.028	6.150	0.172	0.172	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.016	0.004	6.344	-0.279	-0.279	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.044	-0.018	3.296	-1.484	-0.603	0.049	-0.238	-0.691	-0.001
97	A	97	ASN	0	-0.033	-0.035	2.750	-0.463	0.808	0.110	-0.565	-0.816	0.001
98	A	98	GLY	0	0.033	0.014	3.284	0.297	0.591	0.004	-0.047	-0.251	0.000
99	A	99	PRO	0	-0.037	-0.027	4.257	-0.107	0.087	-0.001	-0.020	-0.174	0.000
100	A	100	LEU	0	-0.005	0.020	5.702	0.293	0.293	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.046	0.024	4.291	-0.990	-0.819	-0.001	-0.017	-0.153	0.000
102	A	102	ALA	0	0.082	0.025	2.424	-0.748	-0.285	2.348	-0.776	-2.034	0.007
103	A	103	LYS	1	0.936	0.969	3.684	-0.741	-1.196	-0.007	0.816	-0.354	0.000
104	A	104	GLU	-1	-0.911	-0.963	7.228	0.087	0.087	0.000	0.000	0.000	0.000
105	A	105	ILE	0	0.039	0.016	2.370	-1.492	-0.657	1.818	-0.448	-2.205	-0.002
106	A	106	HIS	1	0.858	0.921	2.786	-9.410	-9.675	3.014	-1.059	-1.691	0.010
107	A	107	SER	0	0.057	0.035	5.375	-0.305	-0.301	-0.001	-0.002	-0.001	0.000
108	A	108	LEU	0	0.030	0.034	7.334	-0.198	-0.198	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.036	-0.024	3.913	-0.370	-0.203	0.001	-0.027	-0.141	0.000
110	A	110	GLU	-1	-0.834	-0.902	7.253	0.331	0.331	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.885	-0.949	10.201	0.052	0.052	0.000	0.000	0.000	0.000
112	A	112	SER	0	-0.033	-0.057	10.453	-0.021	-0.021	0.000	0.000	0.000	0.000
113	A	113	PHE	0	-0.030	0.008	11.137	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	114	GLN	0	-0.033	-0.039	12.910	-0.034	-0.034	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.054	-0.008	15.306	-0.007	-0.007	0.000	0.000	0.000	0.000
116	A	116	THR	0	-0.072	-0.067	15.026	-0.015	-0.015	0.000	0.000	0.000	0.000
117	A	117	ARG	1	0.908	0.971	17.644	-0.032	-0.032	0.000	0.000	0.000	0.000

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