FMO DATABASE

FMODB ID: YVJ72

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	OptHSide
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	-1054637.73498
FMO2-HF: Nuclear repulsion	1006944.304574
FMO2-HF: Total energy	-47693.430406
FMO2-MP2: Total energy	-47834.377011

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.
-24.309	-15.425	14.345	-7.01	-16.221	-0.014

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 : -0.031 / q_NPA : -0.018

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	0.862	0.899	3.399	-1.817	0.474	0.009	-1.246	-1.054	-0.002
4	A	4	GLN	0	-0.019	-0.013	6.124	0.165	0.165	0.000	0.000	0.000	0.000
5	A	5	GLN	0	0.056	0.018	2.365	-4.560	-2.628	3.555	-2.249	-3.239	-0.022
6	A	6	PHE	0	-0.032	-0.006	2.165	0.525	2.118	1.182	-0.750	-2.026	-0.006
7	A	7	ILE	0	0.030	0.015	3.417	1.077	1.299	0.025	0.074	-0.321	-0.001
8	A	8	ASP	-1	-0.848	-0.912	6.883	0.110	0.110	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.053	-0.043	4.792	0.610	0.930	0.001	-0.034	-0.287	0.000
10	A	10	ALA	0	0.004	0.000	6.839	-0.070	-0.070	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.028	0.008	8.332	-0.041	-0.041	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.815	0.908	10.499	-0.340	-0.340	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.835	0.920	8.937	-0.860	-0.860	0.000	0.000	0.000	0.000
14	A	14	TYR	0	-0.091	-0.077	7.714	0.012	0.012	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.846	-0.903	12.651	0.137	0.137	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.079	-0.024	12.117	-0.063	-0.063	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.879	0.936	12.859	0.280	0.280	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.010	0.014	11.500	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.758	-0.870	13.419	-0.236	-0.236	0.000	0.000	0.000	0.000
20	A	20	HIS	0	-0.001	-0.005	14.013	-0.069	-0.069	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.038	-0.016	17.301	0.040	0.040	0.000	0.000	0.000	0.000
22	A	22	TRP	0	-0.007	-0.005	15.969	0.018	0.018	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.811	-0.886	20.722	-0.336	-0.336	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.890	0.920	23.104	0.306	0.306	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.084	-0.041	18.314	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.075	0.030	18.275	-0.039	-0.039	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.835	-0.911	13.725	-0.969	-0.969	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.117	-0.055	13.265	-0.115	-0.115	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.041	0.025	11.346	0.095	0.095	0.000	0.000	0.000	0.000
30	A	30	VAL	0	-0.036	-0.012	11.931	-0.140	-0.140	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.035	0.004	9.166	0.014	0.014	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.797	0.876	12.702	0.264	0.264	0.000	0.000	0.000	0.000
33	A	33	HIS	1	0.799	0.906	15.059	0.122	0.122	0.000	0.000	0.000	0.000
34	A	34	SER	0	0.052	0.024	17.565	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.841	-0.905	20.507	-0.025	-0.025	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.007	-0.012	20.266	-0.021	-0.021	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.798	-0.876	20.098	-0.181	-0.181	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.890	0.945	18.565	0.097	0.097	0.000	0.000	0.000	0.000
39	A	39	TRP	0	-0.005	-0.019	15.118	-0.021	-0.021	0.000	0.000	0.000	0.000
40	A	40	TYR	0	-0.016	-0.005	9.292	0.007	0.007	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.031	0.027	8.238	-0.051	-0.051	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.023	-0.004	10.362	0.105	0.105	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.001	0.027	6.746	-0.258	-0.258	0.000	0.000	0.000	0.000
44	A	44	MET	0	-0.032	-0.011	9.776	0.358	0.358	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.726	-0.823	10.933	-1.135	-1.135	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.062	-0.033	13.520	0.187	0.187	0.000	0.000	0.000	0.000
47	A	47	PRO	0	0.017	0.001	15.150	-0.036	-0.036	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.015	-0.007	14.938	-0.025	-0.025	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.721	-0.852	15.869	-0.424	-0.424	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.774	0.871	18.275	0.432	0.432	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.053	-0.023	12.680	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.022	-0.008	16.606	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.055	-0.010	13.153	0.046	0.046	0.000	0.000	0.000	0.000
54	A	54	ASN	0	0.019	-0.010	16.442	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.024	0.008	17.368	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.930	-0.950	18.634	-0.354	-0.354	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.924	0.971	12.106	0.582	0.582	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.852	0.894	14.913	0.648	0.648	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.047	-0.035	10.560	0.040	0.040	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.753	-0.850	8.382	-1.817	-1.817	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.035	-0.022	8.190	-0.472	-0.472	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.020	0.005	4.115	-0.108	0.062	0.001	-0.022	-0.148	0.000
63	A	63	ASP	-1	-0.801	-0.878	8.205	-0.858	-0.858	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.014	-0.017	6.215	0.006	0.006	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.846	0.923	10.677	0.287	0.287	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.007	-0.010	12.732	0.039	0.039	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.033	-0.024	15.271	0.010	0.010	0.000	0.000	0.000	0.000
68	A	68	PRO	0	0.055	0.028	18.779	-0.013	-0.013	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.856	-0.919	21.118	-0.087	-0.087	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.035	-0.030	16.647	0.011	0.011	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.009	0.008	17.111	-0.029	-0.029	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.011	-0.002	17.979	-0.033	-0.033	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.010	-0.019	19.078	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.053	0.020	13.031	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.931	0.973	14.796	0.316	0.316	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.930	0.982	16.220	0.123	0.123	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.810	0.905	12.717	0.065	0.065	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.028	0.020	11.416	-0.060	-0.060	0.000	0.000	0.000	0.000
79	A	79	GLY	0	0.035	-0.004	8.839	-0.046	-0.046	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.047	-0.010	9.510	-0.319	-0.319	0.000	0.000	0.000	0.000
81	A	81	TYR	0	0.029	0.022	10.783	0.131	0.131	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.040	-0.048	14.304	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.039	0.043	15.145	-0.048	-0.048	0.000	0.000	0.000	0.000
84	A	84	TYR	0	0.043	0.019	15.203	0.143	0.143	0.000	0.000	0.000	0.000
85	A	85	HIS	1	0.869	0.928	16.363	0.495	0.495	0.000	0.000	0.000	0.000
86	A	86	MET	0	0.046	0.053	15.434	0.037	0.037	0.000	0.000	0.000	0.000
87	A	87	ASN	0	-0.015	-0.033	18.635	0.010	0.010	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.934	0.941	19.121	0.407	0.407	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.878	-0.917	19.722	-0.227	-0.227	0.000	0.000	0.000	0.000
90	A	90	HIS	0	0.034	0.018	18.947	0.020	0.020	0.000	0.000	0.000	0.000
91	A	91	TRP	0	-0.031	-0.011	12.584	0.008	0.008	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.023	0.000	10.878	0.046	0.046	0.000	0.000	0.000	0.000
93	A	93	THR	0	0.004	-0.022	11.133	-0.024	-0.024	0.000	0.000	0.000	0.000
94	A	94	VAL	0	-0.048	-0.031	6.008	0.160	0.160	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.020	-0.001	6.708	-0.295	-0.295	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.031	-0.013	3.004	-1.545	-0.629	0.115	-0.244	-0.787	-0.001
97	A	97	ASN	0	-0.026	-0.029	2.859	-0.343	0.761	0.076	-0.488	-0.693	0.001
98	A	98	GLY	0	0.036	0.018	3.402	0.564	0.835	0.002	-0.042	-0.231	0.000
99	A	99	PRO	0	-0.038	-0.031	4.292	-0.240	-0.070	-0.001	-0.018	-0.151	0.000
100	A	100	LEU	0	-0.005	0.021	5.847	0.345	0.345	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.052	0.028	4.384	-0.991	-0.847	-0.001	-0.012	-0.130	0.000
102	A	102	ALA	0	0.078	0.023	2.360	-0.755	-0.110	2.149	-0.781	-2.013	0.006
103	A	103	LYS	1	0.940	0.974	3.697	-0.590	-1.020	-0.006	0.805	-0.369	0.000
104	A	104	GLU	-1	-0.811	-0.903	7.234	0.008	0.008	0.000	0.000	0.000	0.000
105	A	105	ILE	0	0.033	0.012	2.368	-1.279	-0.832	2.700	-0.537	-2.610	-0.004
106	A	106	HIS	1	0.861	0.922	2.656	-10.732	-11.875	4.530	-1.420	-1.968	0.015
107	A	107	SER	0	0.049	0.034	5.439	-0.335	-0.335	0.000	0.000	0.000	0.000
108	A	108	LEU	0	0.023	0.025	7.256	-0.208	-0.208	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.029	-0.019	3.458	-0.447	-0.215	0.008	-0.046	-0.194	0.000
110	A	110	GLU	-1	-0.794	-0.859	7.170	0.474	0.474	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.877	-0.942	10.208	0.064	0.064	0.000	0.000	0.000	0.000
112	A	112	SER	0	-0.031	-0.042	10.334	-0.023	-0.023	0.000	0.000	0.000	0.000
113	A	113	PHE	0	-0.007	0.005	11.128	-0.010	-0.010	0.000	0.000	0.000	0.000
114	A	114	GLN	0	-0.016	-0.042	12.875	-0.049	-0.049	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.046	-0.004	15.217	-0.012	-0.012	0.000	0.000	0.000	0.000
116	A	116	THR	0	-0.063	-0.040	14.950	-0.016	-0.016	0.000	0.000	0.000	0.000
117	A	117	ARG	1	0.882	0.938	17.660	-0.055	-0.055	0.000	0.000	0.000	0.000

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