FMO DATABASE

FMODB ID: YVQV2

Calculation Name: 3H8K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H8K

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UKV5

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	164
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1636343.230619
FMO2-HF: Nuclear repulsion	1570137.122891
FMO2-HF: Total energy	-66206.107728
FMO2-MP2: Total energy	-66393.73635

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-1.547	1.326	4.474	-2.625	-4.722	-0.002

Interaction energy analysis for fragmet #1(A:2:ALA)

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 : 0.015

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

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	4	THR	0	0.012	-0.014	3.452	-2.472	-0.704	0.016	-1.019	-0.765	0.003
4	A	5	ALA	0	0.067	0.057	6.064	-0.036	-0.036	0.000	0.000	0.000	0.000
5	A	6	LEU	0	0.023	0.011	2.236	-0.466	-0.863	3.166	-0.749	-2.020	-0.005
6	A	7	LYS	1	0.892	0.942	2.373	1.785	3.075	1.292	-0.816	-1.766	0.000
7	A	8	ARG	1	0.820	0.899	4.429	0.519	0.602	0.000	-0.017	-0.066	0.000
8	A	9	LEU	0	0.036	0.023	7.117	0.103	0.103	0.000	0.000	0.000	0.000
9	A	10	MET	0	-0.010	0.001	5.050	-0.137	-0.008	0.000	-0.024	-0.105	0.000
10	A	11	ALA	0	-0.082	-0.035	7.960	0.100	0.100	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.749	-0.859	10.001	-0.272	-0.272	0.000	0.000	0.000	0.000
12	A	13	TYR	0	0.042	0.031	11.291	0.046	0.046	0.000	0.000	0.000	0.000
13	A	14	LYS	1	0.954	0.979	11.889	0.438	0.438	0.000	0.000	0.000	0.000
14	A	15	GLN	0	-0.025	-0.018	13.690	0.044	0.044	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.042	0.022	15.559	0.024	0.024	0.000	0.000	0.000	0.000
16	A	17	THR	0	-0.036	-0.018	15.660	0.019	0.019	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.106	-0.043	17.816	0.017	0.017	0.000	0.000	0.000	0.000
18	A	19	ASN	0	-0.062	-0.035	19.619	0.025	0.025	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.007	0.010	21.780	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	21	PRO	0	-0.017	0.004	21.371	0.009	0.009	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.876	-0.951	24.367	-0.085	-0.085	0.000	0.000	0.000	0.000
22	A	23	GLY	0	-0.017	0.005	27.851	0.001	0.001	0.000	0.000	0.000	0.000
23	A	24	ILE	0	-0.040	-0.027	22.220	0.001	0.001	0.000	0.000	0.000	0.000
24	A	25	VAL	0	0.007	0.010	21.825	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	26	ALA	0	-0.006	-0.013	18.338	0.006	0.006	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.023	0.004	15.260	-0.017	-0.017	0.000	0.000	0.000	0.000
27	A	28	PRO	0	-0.043	-0.011	11.635	0.022	0.022	0.000	0.000	0.000	0.000
28	A	29	MET	0	-0.011	0.012	14.251	0.015	0.015	0.000	0.000	0.000	0.000
29	A	30	ASN	0	0.002	-0.020	14.914	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.894	-0.947	10.566	-0.352	-0.352	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.975	-0.971	9.452	-0.132	-0.132	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.023	-0.033	10.024	0.017	0.017	0.000	0.000	0.000	0.000
33	A	34	PHE	0	0.036	0.006	7.289	-0.032	-0.032	0.000	0.000	0.000	0.000
34	A	35	PHE	0	-0.054	-0.022	6.989	-0.050	-0.050	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.833	-0.889	11.189	-0.072	-0.072	0.000	0.000	0.000	0.000
36	A	37	TRP	0	-0.055	-0.030	11.178	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.899	-0.942	16.092	-0.077	-0.077	0.000	0.000	0.000	0.000
38	A	39	ALA	0	-0.031	-0.030	19.400	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.002	-0.004	21.502	0.013	0.013	0.000	0.000	0.000	0.000
40	A	41	ILE	0	0.006	0.005	24.837	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	42	MET	0	-0.012	0.003	27.127	0.006	0.006	0.000	0.000	0.000	0.000
42	A	43	GLY	0	-0.024	-0.003	30.730	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	44	PRO	0	0.013	-0.001	32.384	0.001	0.001	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.902	-0.949	34.552	-0.052	-0.052	0.000	0.000	0.000	0.000
45	A	46	ASP	-1	-0.909	-0.943	37.905	-0.048	-0.048	0.000	0.000	0.000	0.000
46	A	47	THR	0	-0.052	-0.032	36.801	0.001	0.001	0.000	0.000	0.000	0.000
47	A	48	CYS	0	-0.047	-0.033	39.191	0.001	0.001	0.000	0.000	0.000	0.000
48	A	49	PHE	0	-0.023	-0.025	35.470	0.002	0.002	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.891	-0.920	36.146	-0.047	-0.047	0.000	0.000	0.000	0.000
50	A	51	PHE	0	-0.007	-0.031	35.485	0.003	0.003	0.000	0.000	0.000	0.000
51	A	52	GLY	0	-0.002	0.011	34.892	0.001	0.001	0.000	0.000	0.000	0.000
52	A	53	VAL	0	-0.011	-0.009	29.628	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	54	PHE	0	0.021	-0.011	29.271	0.004	0.004	0.000	0.000	0.000	0.000
54	A	55	PRO	0	0.009	0.002	25.856	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	56	ALA	0	0.018	0.002	23.460	0.007	0.007	0.000	0.000	0.000	0.000
56	A	57	ILE	0	-0.015	0.004	19.457	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.011	-0.021	17.093	0.004	0.004	0.000	0.000	0.000	0.000
58	A	59	SER	0	-0.038	-0.034	15.850	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	60	PHE	0	-0.029	-0.024	11.894	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	61	PRO	0	-0.009	0.012	13.216	0.017	0.017	0.000	0.000	0.000	0.000
61	A	62	LEU	0	0.006	-0.018	8.320	-0.046	-0.046	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.849	-0.914	9.760	-0.196	-0.196	0.000	0.000	0.000	0.000
63	A	64	TYR	0	-0.040	0.005	9.861	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	65	PRO	0	-0.052	-0.049	9.748	-0.106	-0.106	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.016	-0.032	12.929	0.034	0.034	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.033	-0.027	14.855	0.034	0.034	0.000	0.000	0.000	0.000
67	A	68	PRO	0	-0.010	0.007	15.465	-0.034	-0.034	0.000	0.000	0.000	0.000
68	A	69	PRO	0	-0.001	-0.007	15.630	0.006	0.006	0.000	0.000	0.000	0.000
69	A	70	LYS	1	0.930	0.968	17.123	0.070	0.070	0.000	0.000	0.000	0.000
70	A	71	MET	0	0.043	0.026	19.503	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	72	ARG	1	0.887	0.949	21.942	0.062	0.062	0.000	0.000	0.000	0.000
72	A	73	PHE	0	0.059	0.026	24.658	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	74	THR	0	-0.067	-0.043	25.413	0.006	0.006	0.000	0.000	0.000	0.000
74	A	75	CYS	0	-0.022	0.018	28.206	0.003	0.003	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.818	-0.897	31.418	-0.033	-0.033	0.000	0.000	0.000	0.000
76	A	77	MET	0	0.009	0.003	30.747	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	78	PHE	0	-0.010	-0.016	34.658	0.003	0.003	0.000	0.000	0.000	0.000
78	A	79	HIS	0	0.046	0.006	34.054	0.001	0.001	0.000	0.000	0.000	0.000
79	A	80	PRO	0	-0.013	0.002	35.634	0.001	0.001	0.000	0.000	0.000	0.000
80	A	81	ASN	0	0.062	0.017	31.455	0.005	0.005	0.000	0.000	0.000	0.000
81	A	82	ILE	0	-0.047	-0.017	29.942	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	83	TYR	0	0.040	0.008	30.240	0.006	0.006	0.000	0.000	0.000	0.000
83	A	84	PRO	0	0.013	-0.004	32.496	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.837	-0.898	30.004	-0.038	-0.038	0.000	0.000	0.000	0.000
85	A	86	GLY	0	0.042	0.016	29.211	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.746	0.869	25.848	0.034	0.034	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.036	0.021	25.307	0.004	0.004	0.000	0.000	0.000	0.000
88	A	89	CYS	0	-0.111	-0.052	26.173	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	90	ILE	0	0.103	0.058	25.356	0.003	0.003	0.000	0.000	0.000	0.000
90	A	91	SER	0	0.027	0.004	26.558	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	92	ILE	0	0.002	0.014	22.518	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.044	-0.040	20.857	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	94	HIS	0	-0.031	-0.004	22.763	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	95	ALA	0	0.019	-0.002	21.436	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	96	PRO	0	-0.013	-0.016	22.092	0.009	0.009	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.015	0.005	24.919	0.003	0.003	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.974	-0.973	27.548	-0.025	-0.025	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.867	-0.957	30.387	-0.019	-0.019	0.000	0.000	0.000	0.000
99	A	100	PRO	0	-0.079	-0.050	30.878	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	101	MET	0	-0.038	-0.009	29.104	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	102	GLY	0	-0.057	-0.015	32.742	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	103	TYR	0	0.029	0.023	27.854	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.839	-0.946	33.479	-0.049	-0.049	0.000	0.000	0.000	0.000
104	A	105	SER	0	-0.081	-0.037	35.177	0.003	0.003	0.000	0.000	0.000	0.000
105	A	106	SER	0	-0.068	-0.038	33.203	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.010	0.028	30.818	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.871	-0.939	25.442	-0.098	-0.098	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.886	0.971	24.980	0.052	0.052	0.000	0.000	0.000	0.000
109	A	110	TRP	0	0.020	0.013	15.488	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	111	SER	0	0.011	-0.012	20.147	0.004	0.004	0.000	0.000	0.000	0.000
111	A	112	PRO	0	0.011	0.004	15.286	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	113	VAL	0	-0.019	0.006	16.503	-0.029	-0.029	0.000	0.000	0.000	0.000
113	A	114	GLN	0	-0.019	-0.004	19.172	-0.012	-0.012	0.000	0.000	0.000	0.000
114	A	115	SER	0	0.005	-0.009	16.148	-0.020	-0.020	0.000	0.000	0.000	0.000
115	A	116	VAL	0	0.061	0.019	14.523	0.025	0.025	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.930	-0.964	17.305	-0.158	-0.158	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.881	0.943	19.796	0.184	0.184	0.000	0.000	0.000	0.000
118	A	119	ILE	0	-0.006	0.007	18.047	0.013	0.013	0.000	0.000	0.000	0.000
119	A	120	LEU	0	0.007	-0.006	19.955	0.013	0.013	0.000	0.000	0.000	0.000
120	A	121	LEU	0	0.022	0.016	23.195	0.010	0.010	0.000	0.000	0.000	0.000
121	A	122	SER	0	-0.002	0.008	25.045	0.012	0.012	0.000	0.000	0.000	0.000
122	A	123	VAL	0	0.007	-0.007	25.002	0.008	0.008	0.000	0.000	0.000	0.000
123	A	124	VAL	0	0.004	-0.004	27.195	0.007	0.007	0.000	0.000	0.000	0.000
124	A	125	SER	0	0.010	-0.015	29.348	0.005	0.005	0.000	0.000	0.000	0.000
125	A	126	MET	0	-0.029	0.006	30.035	0.005	0.005	0.000	0.000	0.000	0.000
126	A	127	LEU	0	-0.061	-0.027	30.628	0.006	0.006	0.000	0.000	0.000	0.000
127	A	128	ALA	0	0.013	0.007	33.535	0.004	0.004	0.000	0.000	0.000	0.000
128	A	129	GLU	-1	-0.966	-0.974	34.480	-0.058	-0.058	0.000	0.000	0.000	0.000
129	A	130	PRO	0	-0.021	-0.031	35.978	0.000	0.000	0.000	0.000	0.000	0.000
130	A	131	ASN	0	-0.041	0.011	33.618	0.006	0.006	0.000	0.000	0.000	0.000
131	A	132	ASP	-1	-0.880	-0.945	35.266	-0.038	-0.038	0.000	0.000	0.000	0.000
132	A	133	GLU	-1	-0.841	-0.923	30.672	-0.061	-0.061	0.000	0.000	0.000	0.000
133	A	134	SER	0	-0.010	-0.033	31.838	0.002	0.002	0.000	0.000	0.000	0.000
134	A	135	GLY	0	-0.018	0.014	34.331	0.002	0.002	0.000	0.000	0.000	0.000
135	A	136	ALA	0	-0.029	-0.003	32.749	0.003	0.003	0.000	0.000	0.000	0.000
136	A	137	ASN	0	-0.026	0.000	34.697	0.005	0.005	0.000	0.000	0.000	0.000
137	A	138	VAL	0	0.086	0.022	37.202	0.000	0.000	0.000	0.000	0.000	0.000
138	A	139	ASP	-1	-0.878	-0.933	40.520	-0.022	-0.022	0.000	0.000	0.000	0.000
139	A	140	ALA	0	0.001	0.005	38.587	0.000	0.000	0.000	0.000	0.000	0.000
140	A	141	SER	0	-0.018	-0.032	38.866	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	142	LYS	1	0.789	0.882	41.002	0.024	0.024	0.000	0.000	0.000	0.000
142	A	143	MET	0	0.011	0.027	43.870	0.000	0.000	0.000	0.000	0.000	0.000
143	A	144	TRP	0	0.028	0.029	40.955	0.001	0.001	0.000	0.000	0.000	0.000
144	A	145	ARG	1	0.785	0.865	43.604	0.025	0.025	0.000	0.000	0.000	0.000
145	A	146	ASP	-1	-0.834	-0.888	45.950	-0.022	-0.022	0.000	0.000	0.000	0.000
146	A	147	ASP	-1	-0.887	-0.941	47.760	-0.024	-0.024	0.000	0.000	0.000	0.000
147	A	148	ARG	1	0.899	0.962	44.255	0.034	0.034	0.000	0.000	0.000	0.000
148	A	149	GLU	-1	-0.790	-0.910	46.201	-0.031	-0.031	0.000	0.000	0.000	0.000
149	A	150	GLN	0	-0.073	-0.034	47.386	0.000	0.000	0.000	0.000	0.000	0.000
150	A	151	PHE	0	0.025	0.002	38.466	0.000	0.000	0.000	0.000	0.000	0.000
151	A	152	TYR	0	0.008	-0.007	42.953	-0.002	-0.002	0.000	0.000	0.000	0.000
152	A	153	LYS	1	0.774	0.884	43.932	0.028	0.028	0.000	0.000	0.000	0.000
153	A	154	ILE	0	0.019	0.008	41.208	0.000	0.000	0.000	0.000	0.000	0.000
154	A	155	ALA	0	0.029	0.026	39.661	-0.001	-0.001	0.000	0.000	0.000	0.000
155	A	156	LYS	1	0.919	0.955	39.745	0.038	0.038	0.000	0.000	0.000	0.000
156	A	157	GLN	0	-0.017	-0.011	41.514	0.000	0.000	0.000	0.000	0.000	0.000
157	A	158	ILE	0	-0.036	-0.006	36.013	0.000	0.000	0.000	0.000	0.000	0.000
158	A	159	VAL	0	0.034	0.023	36.912	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	160	GLN	0	-0.017	-0.008	37.654	0.000	0.000	0.000	0.000	0.000	0.000
160	A	161	LYS	1	0.788	0.875	37.836	0.033	0.033	0.000	0.000	0.000	0.000
161	A	162	SER	0	-0.085	-0.032	33.373	-0.001	-0.001	0.000	0.000	0.000	0.000
162	A	163	LEU	0	0.002	0.006	34.270	-0.002	-0.002	0.000	0.000	0.000	0.000
163	A	164	GLY	0	-0.040	-0.009	36.683	0.001	0.001	0.000	0.000	0.000	0.000
164	A	165	LEU	0	-0.083	-0.036	38.381	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)