FMO DATABASE

FMODB ID: 1724Z

Calculation Name: 3K8U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K8U

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DW05

Base Structure: X-ray

Registration Date: 2023-06-21

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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1283079.660415
FMO2-HF: Nuclear repulsion	1229469.644309
FMO2-HF: Total energy	-53610.016105
FMO2-MP2: Total energy	-53768.492806

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:HIS)

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

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.
-3.062	-1.49	-0.022	-0.699	-0.851	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / 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	7	LYS	1	0.890	0.952	3.800	-1.685	-0.113	-0.022	-0.699	-0.851	0.001
4	A	8	LEU	0	0.017	0.029	5.974	-0.295	-0.295	0.000	0.000	0.000	0.000
5	A	9	VAL	0	-0.076	-0.027	9.158	0.048	0.048	0.000	0.000	0.000	0.000
6	A	10	PRO	0	-0.025	-0.011	11.742	-0.065	-0.065	0.000	0.000	0.000	0.000
7	A	11	GLN	0	-0.019	-0.026	14.415	-0.036	-0.036	0.000	0.000	0.000	0.000
8	A	12	ILE	0	0.008	-0.003	18.181	0.017	0.017	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.879	-0.928	20.817	0.275	0.275	0.000	0.000	0.000	0.000
10	A	14	THR	0	-0.012	-0.033	22.874	0.020	0.020	0.000	0.000	0.000	0.000
11	A	15	ARG	1	0.927	0.970	24.571	-0.231	-0.231	0.000	0.000	0.000	0.000
12	A	16	ASP	-1	-0.753	-0.867	21.013	0.339	0.339	0.000	0.000	0.000	0.000
13	A	17	CYS	0	0.009	0.043	19.153	0.035	0.035	0.000	0.000	0.000	0.000
14	A	18	GLY	0	0.066	0.030	18.968	0.034	0.034	0.000	0.000	0.000	0.000
15	A	19	PRO	0	-0.020	-0.011	19.616	0.027	0.027	0.000	0.000	0.000	0.000
16	A	20	ALA	0	0.009	0.016	15.876	0.024	0.024	0.000	0.000	0.000	0.000
17	A	21	VAL	0	0.044	0.029	14.784	0.086	0.086	0.000	0.000	0.000	0.000
18	A	22	LEU	0	0.007	0.013	14.801	0.034	0.034	0.000	0.000	0.000	0.000
19	A	23	ALA	0	0.014	-0.003	15.176	0.015	0.015	0.000	0.000	0.000	0.000
20	A	24	SER	0	-0.060	-0.031	10.931	0.104	0.104	0.000	0.000	0.000	0.000
21	A	25	VAL	0	0.025	0.017	10.815	0.069	0.069	0.000	0.000	0.000	0.000
22	A	26	ALA	0	0.015	0.009	12.283	0.007	0.007	0.000	0.000	0.000	0.000
23	A	27	LYS	1	0.955	0.984	8.807	-1.100	-1.100	0.000	0.000	0.000	0.000
24	A	28	HIS	0	-0.099	-0.049	6.783	0.169	0.169	0.000	0.000	0.000	0.000
25	A	29	TYR	0	0.017	0.000	9.233	0.058	0.058	0.000	0.000	0.000	0.000
26	A	30	GLY	0	0.023	0.019	11.184	-0.060	-0.060	0.000	0.000	0.000	0.000
27	A	31	SER	0	-0.005	0.011	12.645	-0.061	-0.061	0.000	0.000	0.000	0.000
28	A	32	ASN	0	-0.057	-0.040	12.212	0.100	0.100	0.000	0.000	0.000	0.000
29	A	33	TYR	0	0.074	0.038	15.466	-0.052	-0.052	0.000	0.000	0.000	0.000
30	A	34	SER	0	0.022	0.008	17.151	0.038	0.038	0.000	0.000	0.000	0.000
31	A	35	ILE	0	0.072	0.026	17.086	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	36	ALA	0	-0.012	-0.015	20.098	-0.024	-0.024	0.000	0.000	0.000	0.000
33	A	37	TYR	0	0.031	0.021	21.972	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	38	LEU	0	0.052	0.020	18.263	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	39	ARG	1	0.816	0.899	22.601	-0.326	-0.326	0.000	0.000	0.000	0.000
36	A	40	GLU	-1	-0.925	-0.952	24.734	0.195	0.195	0.000	0.000	0.000	0.000
37	A	41	LEU	0	-0.018	-0.012	24.194	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	42	SER	0	-0.066	-0.038	24.304	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	43	LYS	1	0.935	0.967	26.424	-0.199	-0.199	0.000	0.000	0.000	0.000
40	A	44	THR	0	-0.010	0.031	25.371	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	45	ASN	0	0.070	0.029	27.969	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	46	LYS	1	0.938	0.947	29.229	-0.164	-0.164	0.000	0.000	0.000	0.000
43	A	47	GLN	0	-0.049	-0.029	30.052	0.002	0.002	0.000	0.000	0.000	0.000
44	A	48	GLY	0	0.035	0.039	26.843	0.007	0.007	0.000	0.000	0.000	0.000
45	A	49	THR	0	-0.005	-0.026	24.230	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	50	THR	0	0.021	0.018	26.152	0.005	0.005	0.000	0.000	0.000	0.000
47	A	51	ALA	0	0.107	0.034	24.914	0.013	0.013	0.000	0.000	0.000	0.000
48	A	52	LEU	0	0.015	0.001	25.578	0.009	0.009	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.065	0.047	27.185	0.002	0.002	0.000	0.000	0.000	0.000
50	A	54	ILE	0	-0.021	-0.014	20.654	0.010	0.010	0.000	0.000	0.000	0.000
51	A	55	VAL	0	-0.015	0.001	23.023	0.012	0.012	0.000	0.000	0.000	0.000
52	A	56	GLU	-1	-0.937	-0.980	24.657	0.191	0.191	0.000	0.000	0.000	0.000
53	A	57	ALA	0	-0.014	-0.009	23.437	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	58	ALA	0	0.031	0.004	20.878	0.006	0.006	0.000	0.000	0.000	0.000
55	A	59	LYS	1	0.962	0.978	22.206	-0.200	-0.200	0.000	0.000	0.000	0.000
56	A	60	LYS	1	0.867	0.947	25.132	-0.223	-0.223	0.000	0.000	0.000	0.000
57	A	61	LEU	0	-0.089	-0.035	19.519	0.000	0.000	0.000	0.000	0.000	0.000
58	A	62	GLY	0	0.037	0.039	21.834	0.013	0.013	0.000	0.000	0.000	0.000
59	A	63	PHE	0	-0.064	-0.030	16.223	0.016	0.016	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.938	-0.970	21.442	0.175	0.175	0.000	0.000	0.000	0.000
61	A	65	THR	0	-0.059	-0.053	21.134	0.013	0.013	0.000	0.000	0.000	0.000
62	A	66	ARG	1	1.002	0.997	19.133	-0.228	-0.228	0.000	0.000	0.000	0.000
63	A	67	SER	0	-0.014	-0.009	22.324	0.025	0.025	0.000	0.000	0.000	0.000
64	A	68	ILE	0	0.009	0.012	21.697	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	69	LYS	1	0.872	0.929	24.481	-0.145	-0.145	0.000	0.000	0.000	0.000
66	A	70	ALA	0	-0.001	-0.007	22.514	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	71	ASP	-1	-0.764	-0.866	24.082	0.084	0.084	0.000	0.000	0.000	0.000
68	A	72	MET	0	-0.035	-0.036	18.951	0.020	0.020	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.014	-0.003	21.201	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.016	-0.001	18.459	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	75	PHE	0	-0.079	-0.074	15.276	0.014	0.014	0.000	0.000	0.000	0.000
72	A	76	ASP	-1	-0.921	-0.939	17.265	-0.026	-0.026	0.000	0.000	0.000	0.000
73	A	77	TYR	0	-0.047	-0.011	19.054	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	78	ASN	0	-0.002	-0.033	16.823	0.019	0.019	0.000	0.000	0.000	0.000
75	A	79	ASP	-1	-0.900	-0.921	16.109	0.022	0.022	0.000	0.000	0.000	0.000
76	A	80	LEU	0	-0.102	-0.045	14.894	0.039	0.039	0.000	0.000	0.000	0.000
77	A	81	THR	0	-0.035	-0.012	13.438	0.006	0.006	0.000	0.000	0.000	0.000
78	A	82	TYR	0	-0.006	0.019	9.486	0.017	0.017	0.000	0.000	0.000	0.000
79	A	83	PRO	0	-0.014	-0.020	8.961	0.024	0.024	0.000	0.000	0.000	0.000
80	A	84	PHE	0	-0.014	-0.015	10.807	-0.031	-0.031	0.000	0.000	0.000	0.000
81	A	85	ILE	0	0.002	0.003	14.109	0.054	0.054	0.000	0.000	0.000	0.000
82	A	86	VAL	0	0.008	0.018	16.605	-0.050	-0.050	0.000	0.000	0.000	0.000
83	A	87	HIS	0	-0.062	-0.034	18.922	0.020	0.020	0.000	0.000	0.000	0.000
84	A	88	VAL	0	-0.001	-0.005	19.236	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	89	ILE	0	0.008	0.002	22.244	0.009	0.009	0.000	0.000	0.000	0.000
86	A	90	LYS	1	0.899	0.958	20.327	-0.316	-0.316	0.000	0.000	0.000	0.000
87	A	91	GLY	0	0.020	0.008	24.975	0.003	0.003	0.000	0.000	0.000	0.000
88	A	92	LYS	1	0.968	0.964	28.427	-0.143	-0.143	0.000	0.000	0.000	0.000
89	A	93	ARG	1	0.902	0.963	22.013	-0.310	-0.310	0.000	0.000	0.000	0.000
90	A	94	LEU	0	0.065	0.020	26.629	0.006	0.006	0.000	0.000	0.000	0.000
91	A	95	GLN	0	-0.018	0.009	25.875	0.004	0.004	0.000	0.000	0.000	0.000
92	A	96	HIS	0	-0.048	-0.030	18.718	-0.019	-0.019	0.000	0.000	0.000	0.000
93	A	97	TYR	0	-0.006	-0.029	18.890	-0.028	-0.028	0.000	0.000	0.000	0.000
94	A	98	TYR	0	-0.033	-0.034	14.553	0.042	0.042	0.000	0.000	0.000	0.000
95	A	99	VAL	0	0.005	0.007	10.620	-0.055	-0.055	0.000	0.000	0.000	0.000
96	A	100	VAL	0	-0.008	-0.005	11.694	0.059	0.059	0.000	0.000	0.000	0.000
97	A	101	TYR	0	0.002	-0.051	6.443	0.075	0.075	0.000	0.000	0.000	0.000
98	A	102	GLY	0	0.056	0.027	7.958	-0.049	-0.049	0.000	0.000	0.000	0.000
99	A	103	SER	0	-0.034	-0.002	9.694	0.021	0.021	0.000	0.000	0.000	0.000
100	A	104	GLN	0	0.035	0.023	8.683	-0.131	-0.131	0.000	0.000	0.000	0.000
101	A	105	ASN	0	0.014	0.004	12.339	-0.008	-0.008	0.000	0.000	0.000	0.000
102	A	106	ASN	0	0.048	0.021	15.739	0.042	0.042	0.000	0.000	0.000	0.000
103	A	107	GLN	0	-0.026	-0.028	13.775	-0.012	-0.012	0.000	0.000	0.000	0.000
104	A	108	LEU	0	0.046	0.031	12.600	-0.053	-0.053	0.000	0.000	0.000	0.000
105	A	109	ILE	0	-0.033	-0.007	6.139	0.018	0.018	0.000	0.000	0.000	0.000
106	A	110	ILE	0	0.005	-0.007	9.595	0.013	0.013	0.000	0.000	0.000	0.000
107	A	111	GLY	0	0.016	-0.009	10.214	0.221	0.221	0.000	0.000	0.000	0.000
108	A	112	ASP	-1	-0.788	-0.892	11.160	0.389	0.389	0.000	0.000	0.000	0.000
109	A	113	PRO	0	-0.011	-0.021	14.456	0.068	0.068	0.000	0.000	0.000	0.000
110	A	114	ASP	-1	-0.796	-0.862	15.569	0.437	0.437	0.000	0.000	0.000	0.000
111	A	115	PRO	0	-0.015	-0.023	15.536	0.077	0.077	0.000	0.000	0.000	0.000
112	A	116	SER	0	-0.096	-0.057	16.024	0.031	0.031	0.000	0.000	0.000	0.000
113	A	117	VAL	0	-0.050	-0.011	14.480	-0.030	-0.030	0.000	0.000	0.000	0.000
114	A	118	LYS	1	0.929	0.958	10.757	-0.926	-0.926	0.000	0.000	0.000	0.000
115	A	119	VAL	0	-0.007	-0.006	6.036	-0.118	-0.118	0.000	0.000	0.000	0.000
116	A	120	THR	0	0.015	0.015	9.454	-0.062	-0.062	0.000	0.000	0.000	0.000
117	A	121	ARG	1	0.912	0.965	8.012	0.371	0.371	0.000	0.000	0.000	0.000
118	A	122	MET	0	-0.024	0.000	11.922	-0.027	-0.027	0.000	0.000	0.000	0.000
119	A	123	SER	0	-0.006	-0.006	15.278	-0.024	-0.024	0.000	0.000	0.000	0.000
120	A	124	LYS	1	1.026	0.994	16.508	0.045	0.045	0.000	0.000	0.000	0.000
121	A	125	GLU	-1	-0.867	-0.926	19.166	0.050	0.050	0.000	0.000	0.000	0.000
122	A	126	ARG	1	0.912	0.955	19.758	-0.148	-0.148	0.000	0.000	0.000	0.000
123	A	127	PHE	0	0.037	0.000	17.021	0.016	0.016	0.000	0.000	0.000	0.000
124	A	128	GLN	0	0.010	-0.002	19.809	0.007	0.007	0.000	0.000	0.000	0.000
125	A	129	SER	0	-0.065	-0.021	22.796	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	130	GLU	-1	-0.851	-0.911	20.506	0.279	0.279	0.000	0.000	0.000	0.000
127	A	131	TRP	0	-0.020	-0.002	20.979	0.007	0.007	0.000	0.000	0.000	0.000
128	A	132	THR	0	0.024	0.011	22.828	-0.020	-0.020	0.000	0.000	0.000	0.000
129	A	133	GLY	0	0.065	0.026	23.747	-0.017	-0.017	0.000	0.000	0.000	0.000
130	A	134	LEU	0	-0.091	-0.029	23.471	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	135	ALA	0	0.031	0.023	19.310	0.023	0.023	0.000	0.000	0.000	0.000
132	A	136	ILE	0	-0.016	-0.017	19.375	-0.021	-0.021	0.000	0.000	0.000	0.000
133	A	137	PHE	0	-0.004	-0.001	16.318	0.039	0.039	0.000	0.000	0.000	0.000
134	A	138	LEU	0	-0.019	-0.031	16.750	-0.020	-0.020	0.000	0.000	0.000	0.000
135	A	139	ALA	0	0.024	0.018	16.522	0.028	0.028	0.000	0.000	0.000	0.000
136	A	140	PRO	0	0.001	0.014	16.102	-0.019	-0.019	0.000	0.000	0.000	0.000
137	A	141	GLN	0	0.005	0.022	19.171	-0.016	-0.016	0.000	0.000	0.000	0.000

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