FMO DATABASE

FMODB ID: 5J9NZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1635940.584939
FMO2-HF: Nuclear repulsion	1569735.447542
FMO2-HF: Total energy	-66205.137397
FMO2-MP2: Total energy	-66392.78419

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.
0.41	1.209	6.684	-2.806	-4.677	-0.007

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 : 0.027 / q_NPA : 0.005

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	0.007	-0.015	3.340	-2.509	-0.759	0.032	-1.018	-0.765	0.002
4	A	5	ALA	0	0.062	0.053	5.953	0.003	0.003	0.000	0.000	0.000	0.000
5	A	6	LEU	0	0.030	0.016	2.030	0.811	-1.695	6.257	-1.210	-2.541	-0.007
6	A	7	LYS	1	0.911	0.951	2.843	2.203	3.515	0.393	-0.526	-1.178	-0.002
7	A	8	ARG	1	0.835	0.918	4.398	0.646	0.730	0.000	-0.017	-0.067	0.000
8	A	9	LEU	0	0.038	0.019	7.059	0.119	0.119	0.000	0.000	0.000	0.000
9	A	10	MET	0	-0.011	0.004	4.901	-0.156	0.003	0.002	-0.035	-0.126	0.000
10	A	11	ALA	0	-0.080	-0.035	7.974	0.102	0.102	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.744	-0.850	10.009	-0.293	-0.293	0.000	0.000	0.000	0.000
12	A	13	TYR	0	0.039	0.032	11.390	0.047	0.047	0.000	0.000	0.000	0.000
13	A	14	LYS	1	0.967	0.988	11.998	0.439	0.439	0.000	0.000	0.000	0.000
14	A	15	GLN	0	-0.036	-0.022	13.725	0.054	0.054	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.048	0.023	15.624	0.024	0.024	0.000	0.000	0.000	0.000
16	A	17	THR	0	-0.071	-0.029	15.691	0.021	0.021	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.085	-0.044	17.868	0.015	0.015	0.000	0.000	0.000	0.000
18	A	19	ASN	0	-0.071	-0.039	19.659	0.026	0.026	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.015	0.018	21.799	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	21	PRO	0	-0.013	0.010	21.424	0.008	0.008	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.883	-0.956	24.361	-0.080	-0.080	0.000	0.000	0.000	0.000
22	A	23	GLY	0	-0.027	-0.002	27.834	0.000	0.000	0.000	0.000	0.000	0.000
23	A	24	ILE	0	-0.031	-0.021	22.169	0.002	0.002	0.000	0.000	0.000	0.000
24	A	25	VAL	0	0.008	0.011	21.746	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	26	ALA	0	0.001	-0.012	18.263	0.007	0.007	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.035	0.005	15.249	-0.019	-0.019	0.000	0.000	0.000	0.000
27	A	28	PRO	0	-0.037	-0.004	11.626	0.020	0.020	0.000	0.000	0.000	0.000
28	A	29	MET	0	0.003	0.017	14.244	0.014	0.014	0.000	0.000	0.000	0.000
29	A	30	ASN	0	0.036	0.013	13.990	0.000	0.000	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.907	-0.959	10.375	-0.271	-0.271	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-1.015	-0.995	9.299	0.030	0.030	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.034	-0.034	9.941	0.048	0.048	0.000	0.000	0.000	0.000
33	A	34	PHE	0	0.038	0.002	7.281	-0.054	-0.054	0.000	0.000	0.000	0.000
34	A	35	PHE	0	-0.050	-0.020	6.759	-0.073	-0.073	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.844	-0.903	11.125	-0.043	-0.043	0.000	0.000	0.000	0.000
36	A	37	TRP	0	-0.050	-0.030	11.174	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.919	-0.961	16.055	-0.050	-0.050	0.000	0.000	0.000	0.000
38	A	39	ALA	0	-0.023	-0.026	19.377	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.006	-0.001	21.471	0.013	0.013	0.000	0.000	0.000	0.000
40	A	41	ILE	0	-0.009	0.003	24.760	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	42	MET	0	-0.018	0.003	27.096	0.007	0.007	0.000	0.000	0.000	0.000
42	A	43	GLY	0	-0.041	-0.009	30.702	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	44	PRO	0	0.015	-0.002	32.529	0.001	0.001	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.907	-0.952	34.517	-0.050	-0.050	0.000	0.000	0.000	0.000
45	A	46	ASP	-1	-0.908	-0.946	37.877	-0.050	-0.050	0.000	0.000	0.000	0.000
46	A	47	THR	0	-0.069	-0.046	36.796	0.001	0.001	0.000	0.000	0.000	0.000
47	A	48	CYS	0	-0.048	-0.032	39.205	0.001	0.001	0.000	0.000	0.000	0.000
48	A	49	PHE	0	-0.048	-0.035	35.380	0.002	0.002	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.924	-0.933	36.107	-0.046	-0.046	0.000	0.000	0.000	0.000
50	A	51	PHE	0	0.003	-0.026	35.491	0.003	0.003	0.000	0.000	0.000	0.000
51	A	52	GLY	0	-0.016	0.004	34.860	0.002	0.002	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.002	-0.005	29.527	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	54	PHE	0	0.015	-0.017	29.184	0.005	0.005	0.000	0.000	0.000	0.000
54	A	55	PRO	0	0.024	0.006	25.778	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	56	ALA	0	0.016	-0.002	23.347	0.006	0.006	0.000	0.000	0.000	0.000
56	A	57	ILE	0	-0.024	0.002	19.247	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.012	-0.022	16.993	0.000	0.000	0.000	0.000	0.000	0.000
58	A	59	SER	0	-0.032	-0.018	15.773	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	60	PHE	0	-0.033	-0.024	11.779	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	61	PRO	0	0.012	0.021	13.118	0.029	0.029	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.009	-0.025	8.417	-0.049	-0.049	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.878	-0.935	9.635	-0.258	-0.258	0.000	0.000	0.000	0.000
63	A	64	TYR	0	-0.043	-0.008	9.838	-0.018	-0.018	0.000	0.000	0.000	0.000
64	A	65	PRO	0	-0.037	-0.055	9.632	-0.132	-0.132	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.023	-0.028	12.823	0.039	0.039	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.030	-0.013	14.736	0.040	0.040	0.000	0.000	0.000	0.000
67	A	68	PRO	0	0.012	0.013	15.354	-0.037	-0.037	0.000	0.000	0.000	0.000
68	A	69	PRO	0	0.007	-0.003	15.739	0.007	0.007	0.000	0.000	0.000	0.000
69	A	70	LYS	1	0.922	0.966	17.027	0.056	0.056	0.000	0.000	0.000	0.000
70	A	71	MET	0	0.047	0.028	19.421	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	72	ARG	1	0.896	0.953	21.864	0.046	0.046	0.000	0.000	0.000	0.000
72	A	73	PHE	0	0.046	0.020	24.596	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	74	THR	0	-0.063	-0.043	25.382	0.005	0.005	0.000	0.000	0.000	0.000
74	A	75	CYS	0	-0.028	0.017	28.154	0.003	0.003	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.870	-0.936	31.370	-0.027	-0.027	0.000	0.000	0.000	0.000
76	A	77	MET	0	-0.001	-0.004	30.473	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	78	PHE	0	-0.013	-0.017	34.596	0.003	0.003	0.000	0.000	0.000	0.000
78	A	79	HIS	0	0.031	-0.003	33.940	0.001	0.001	0.000	0.000	0.000	0.000
79	A	80	PRO	0	-0.012	-0.003	35.554	0.001	0.001	0.000	0.000	0.000	0.000
80	A	81	ASN	0	0.043	-0.007	31.477	0.005	0.005	0.000	0.000	0.000	0.000
81	A	82	ILE	0	-0.041	-0.006	30.086	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	83	TYR	0	-0.026	0.006	29.742	0.003	0.003	0.000	0.000	0.000	0.000
83	A	84	PRO	0	0.005	-0.010	32.416	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.841	-0.901	29.915	-0.031	-0.031	0.000	0.000	0.000	0.000
85	A	86	GLY	0	0.043	0.019	29.139	0.000	0.000	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.779	0.877	25.744	0.031	0.031	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.038	0.019	25.199	0.004	0.004	0.000	0.000	0.000	0.000
88	A	89	CYS	0	-0.085	-0.064	26.082	0.000	0.000	0.000	0.000	0.000	0.000
89	A	90	ILE	0	0.077	0.043	25.156	0.002	0.002	0.000	0.000	0.000	0.000
90	A	91	SER	0	0.039	0.015	26.459	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.016	0.002	22.079	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.036	-0.039	20.679	-0.017	-0.017	0.000	0.000	0.000	0.000
93	A	94	HIS	0	-0.019	0.003	22.658	0.000	0.000	0.000	0.000	0.000	0.000
94	A	95	ALA	0	0.015	-0.007	21.301	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	96	PRO	0	-0.014	-0.015	21.926	0.011	0.011	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.012	0.002	24.797	0.001	0.001	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.969	-0.967	27.425	-0.041	-0.041	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.896	-0.975	30.218	-0.025	-0.025	0.000	0.000	0.000	0.000
99	A	100	PRO	0	-0.077	-0.053	30.759	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	101	MET	0	-0.035	-0.009	28.768	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	102	GLY	0	-0.054	-0.014	32.627	0.000	0.000	0.000	0.000	0.000	0.000
102	A	103	TYR	0	0.035	0.029	27.803	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.846	-0.949	33.372	-0.059	-0.059	0.000	0.000	0.000	0.000
104	A	105	SER	0	-0.078	-0.041	35.067	0.002	0.002	0.000	0.000	0.000	0.000
105	A	106	SER	0	-0.061	-0.030	33.070	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	107	ALA	0	-0.007	0.012	30.719	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.924	-0.962	25.853	-0.118	-0.118	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.901	0.974	24.928	0.068	0.068	0.000	0.000	0.000	0.000
109	A	110	TRP	0	0.012	0.008	15.493	-0.005	-0.005	0.000	0.000	0.000	0.000
110	A	111	SER	0	0.010	-0.010	20.042	0.000	0.000	0.000	0.000	0.000	0.000
111	A	112	PRO	0	0.001	-0.003	15.264	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	113	VAL	0	-0.006	0.007	16.421	-0.032	-0.032	0.000	0.000	0.000	0.000
113	A	114	GLN	0	-0.003	-0.004	18.968	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	115	SER	0	-0.003	-0.011	16.083	-0.025	-0.025	0.000	0.000	0.000	0.000
115	A	116	VAL	0	0.057	0.018	14.511	0.028	0.028	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.919	-0.962	17.248	-0.162	-0.162	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.901	0.958	19.742	0.206	0.206	0.000	0.000	0.000	0.000
118	A	119	ILE	0	0.000	0.010	17.916	0.014	0.014	0.000	0.000	0.000	0.000
119	A	120	LEU	0	0.000	-0.005	19.931	0.015	0.015	0.000	0.000	0.000	0.000
120	A	121	LEU	0	0.029	0.018	23.142	0.012	0.012	0.000	0.000	0.000	0.000
121	A	122	SER	0	-0.012	0.004	24.984	0.013	0.013	0.000	0.000	0.000	0.000
122	A	123	VAL	0	0.029	0.001	24.728	0.009	0.009	0.000	0.000	0.000	0.000
123	A	124	VAL	0	0.014	0.002	27.130	0.008	0.008	0.000	0.000	0.000	0.000
124	A	125	SER	0	0.010	-0.003	29.291	0.007	0.007	0.000	0.000	0.000	0.000
125	A	126	MET	0	0.006	0.022	29.660	0.005	0.005	0.000	0.000	0.000	0.000
126	A	127	LEU	0	-0.070	-0.028	30.642	0.006	0.006	0.000	0.000	0.000	0.000
127	A	128	ALA	0	0.026	0.015	33.474	0.005	0.005	0.000	0.000	0.000	0.000
128	A	129	GLU	-1	-1.020	-1.010	34.873	-0.061	-0.061	0.000	0.000	0.000	0.000
129	A	130	PRO	0	-0.037	-0.040	35.905	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	131	ASN	0	0.010	0.030	34.411	0.003	0.003	0.000	0.000	0.000	0.000
131	A	132	ASP	-1	-0.939	-0.971	35.181	-0.041	-0.041	0.000	0.000	0.000	0.000
132	A	133	GLU	-1	-0.850	-0.909	30.561	-0.069	-0.069	0.000	0.000	0.000	0.000
133	A	134	SER	0	-0.002	-0.017	32.129	0.001	0.001	0.000	0.000	0.000	0.000
134	A	135	GLY	0	0.005	0.025	34.232	0.003	0.003	0.000	0.000	0.000	0.000
135	A	136	ALA	0	-0.032	-0.007	32.648	0.003	0.003	0.000	0.000	0.000	0.000
136	A	137	ASN	0	-0.022	0.005	34.603	0.006	0.006	0.000	0.000	0.000	0.000
137	A	138	VAL	0	0.044	-0.003	37.114	0.000	0.000	0.000	0.000	0.000	0.000
138	A	139	ASP	-1	-0.898	-0.950	40.428	-0.021	-0.021	0.000	0.000	0.000	0.000
139	A	140	ALA	0	-0.012	-0.004	38.508	0.000	0.000	0.000	0.000	0.000	0.000
140	A	141	SER	0	0.016	0.000	38.794	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	142	LYS	1	0.876	0.930	40.915	0.022	0.022	0.000	0.000	0.000	0.000
142	A	143	MET	0	0.023	0.035	43.854	0.000	0.000	0.000	0.000	0.000	0.000
143	A	144	TRP	0	0.035	0.032	41.199	0.001	0.001	0.000	0.000	0.000	0.000
144	A	145	ARG	1	0.831	0.928	43.526	0.026	0.026	0.000	0.000	0.000	0.000
145	A	146	ASP	-1	-0.889	-0.957	45.867	-0.024	-0.024	0.000	0.000	0.000	0.000
146	A	147	ASP	-1	-0.903	-0.946	47.682	-0.023	-0.023	0.000	0.000	0.000	0.000
147	A	148	ARG	1	0.920	0.970	43.996	0.036	0.036	0.000	0.000	0.000	0.000
148	A	149	GLU	-1	-0.856	-0.949	46.136	-0.031	-0.031	0.000	0.000	0.000	0.000
149	A	150	GLN	0	-0.125	-0.069	47.130	0.000	0.000	0.000	0.000	0.000	0.000
150	A	151	PHE	0	0.029	0.001	38.389	0.000	0.000	0.000	0.000	0.000	0.000
151	A	152	TYR	0	0.042	0.006	42.539	-0.002	-0.002	0.000	0.000	0.000	0.000
152	A	153	LYS	1	0.865	0.943	43.879	0.025	0.025	0.000	0.000	0.000	0.000
153	A	154	ILE	0	0.021	0.011	41.105	0.000	0.000	0.000	0.000	0.000	0.000
154	A	155	ALA	0	0.038	0.030	39.578	0.000	0.000	0.000	0.000	0.000	0.000
155	A	156	LYS	1	1.018	1.009	39.697	0.031	0.031	0.000	0.000	0.000	0.000
156	A	157	GLN	0	-0.037	-0.025	41.475	0.000	0.000	0.000	0.000	0.000	0.000
157	A	158	ILE	0	-0.031	-0.001	35.981	0.000	0.000	0.000	0.000	0.000	0.000
158	A	159	VAL	0	0.046	0.027	36.878	-0.001	-0.001	0.000	0.000	0.000	0.000
159	A	160	GLN	0	-0.027	-0.020	37.623	0.001	0.001	0.000	0.000	0.000	0.000
160	A	161	LYS	1	0.852	0.922	37.834	0.027	0.027	0.000	0.000	0.000	0.000
161	A	162	SER	0	-0.076	-0.017	33.292	0.000	0.000	0.000	0.000	0.000	0.000
162	A	163	LEU	0	-0.003	0.002	34.247	-0.001	-0.001	0.000	0.000	0.000	0.000
163	A	164	GLY	0	-0.036	-0.007	36.664	0.001	0.001	0.000	0.000	0.000	0.000
164	A	165	LEU	0	-0.084	-0.037	38.362	0.003	0.003	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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