FMO DATABASE

FMODB ID: 66KMZ

Calculation Name: 3KIO-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KIO

Chain ID: C

ChEMBL ID:

UniProt ID: Q9CWY8

Base Structure: X-ray

Registration Date: 2023-06-19

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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-733525.864487
FMO2-HF: Nuclear repulsion	691332.956286
FMO2-HF: Total energy	-42192.908201
FMO2-MP2: Total energy	-42317.246037

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(C:13:ARG)

Summations of interaction energy for fragment #1(C:13:ARG)

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.
-24.623	-23.206	-0.026	-0.629	-0.763	0

Interaction energy analysis for fragmet #1(C:13:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.951 / q_NPA : 0.965

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].
3	C	15	HIS	0	0.001	-0.003	3.817	1.758	3.175	-0.026	-0.629	-0.763
4	C	16	LEU	0	0.039	0.016	6.580	0.593	0.593	0.000	0.000	0.000
5	C	17	ARG	1	0.794	0.877	10.164	19.410	19.410	0.000	0.000	0.000
6	C	18	PRO	0	0.080	0.010	12.949	0.372	0.372	0.000	0.000	0.000
7	C	19	GLY	0	-0.057	-0.031	15.888	0.765	0.765	0.000	0.000	0.000
8	C	20	SER	0	0.008	-0.015	15.151	0.618	0.618	0.000	0.000	0.000
9	C	21	LEU	0	0.002	0.020	14.255	0.547	0.547	0.000	0.000	0.000
10	C	22	ARG	1	0.920	0.939	17.850	12.932	12.932	0.000	0.000	0.000
11	C	23	GLY	0	-0.033	-0.004	21.013	-0.056	-0.056	0.000	0.000	0.000
12	C	24	ALA	0	0.007	0.012	20.300	0.314	0.314	0.000	0.000	0.000
13	C	25	ALA	0	0.016	0.013	22.439	0.324	0.324	0.000	0.000	0.000
14	C	26	PRO	0	0.025	0.012	24.652	-0.304	-0.304	0.000	0.000	0.000
15	C	27	ALA	0	0.016	0.013	24.349	0.019	0.019	0.000	0.000	0.000
16	C	28	LYS	1	0.867	0.940	26.324	8.745	8.745	0.000	0.000	0.000
17	C	29	LEU	0	-0.046	-0.033	22.611	-0.294	-0.294	0.000	0.000	0.000
18	C	30	HIS	0	0.032	0.026	26.897	0.188	0.188	0.000	0.000	0.000
19	C	31	LEU	0	-0.019	-0.006	25.044	-0.359	-0.359	0.000	0.000	0.000
20	C	32	LEU	0	0.027	0.010	28.041	0.259	0.259	0.000	0.000	0.000
21	C	33	PRO	0	0.028	0.040	29.187	-0.259	-0.259	0.000	0.000	0.000
22	C	34	CYS	0	-0.087	-0.065	30.384	0.232	0.232	0.000	0.000	0.000
23	C	35	ASP	-1	-0.869	-0.923	25.457	-10.944	-10.944	0.000	0.000	0.000
24	C	36	VAL	0	-0.066	-0.040	27.468	0.244	0.244	0.000	0.000	0.000
25	C	37	LEU	0	0.014	0.006	25.755	-0.277	-0.277	0.000	0.000	0.000
26	C	38	VAL	0	-0.036	-0.015	23.943	-0.329	-0.329	0.000	0.000	0.000
27	C	39	SER	0	0.026	0.018	20.896	0.138	0.138	0.000	0.000	0.000
28	C	40	ARG	1	0.949	0.968	22.899	9.649	9.649	0.000	0.000	0.000
29	C	41	PRO	0	0.016	0.019	24.966	0.168	0.168	0.000	0.000	0.000
30	C	42	ALA	0	0.049	0.008	27.039	0.208	0.208	0.000	0.000	0.000
31	C	43	PRO	0	-0.018	-0.004	30.122	-0.028	-0.028	0.000	0.000	0.000
32	C	44	VAL	0	0.074	0.033	29.739	0.304	0.304	0.000	0.000	0.000
33	C	45	ASP	-1	-0.803	-0.879	33.011	-8.362	-8.362	0.000	0.000	0.000
34	C	46	ARG	1	0.848	0.928	35.579	7.855	7.855	0.000	0.000	0.000
35	C	47	PHE	0	-0.049	-0.051	35.966	0.187	0.187	0.000	0.000	0.000
36	C	48	PHE	0	0.019	0.034	34.232	0.121	0.121	0.000	0.000	0.000
37	C	49	THR	0	0.062	-0.004	34.989	0.137	0.137	0.000	0.000	0.000
38	C	50	PRO	0	-0.034	-0.002	37.284	0.131	0.131	0.000	0.000	0.000
39	C	51	ALA	0	-0.037	-0.027	39.810	0.221	0.221	0.000	0.000	0.000
40	C	52	VAL	0	-0.019	0.002	36.861	0.111	0.111	0.000	0.000	0.000
41	C	53	ARG	1	0.805	0.910	40.263	6.685	6.685	0.000	0.000	0.000
42	C	54	HIS	0	0.057	0.020	39.750	-0.006	-0.006	0.000	0.000	0.000
43	C	55	ASP	-1	-0.874	-0.920	43.768	-6.345	-6.345	0.000	0.000	0.000
44	C	56	ALA	0	-0.016	-0.004	44.824	-0.063	-0.063	0.000	0.000	0.000
45	C	57	ASP	-1	-0.919	-0.937	43.307	-6.392	-6.392	0.000	0.000	0.000
46	C	58	GLY	0	0.067	0.016	39.695	0.009	0.009	0.000	0.000	0.000
47	C	59	LEU	0	-0.005	-0.002	36.576	0.005	0.005	0.000	0.000	0.000
48	C	60	GLN	0	-0.073	-0.015	40.293	-0.010	-0.010	0.000	0.000	0.000
49	C	61	ALA	0	0.047	0.009	37.994	-0.066	-0.066	0.000	0.000	0.000
50	C	62	SER	0	-0.007	0.009	39.940	0.007	0.007	0.000	0.000	0.000
51	C	63	PHE	0	0.047	0.004	32.383	-0.181	-0.181	0.000	0.000	0.000
52	C	64	ARG	1	0.896	0.947	33.833	8.294	8.294	0.000	0.000	0.000
53	C	65	GLY	0	0.015	0.012	38.601	0.084	0.084	0.000	0.000	0.000
54	C	66	ARG	1	0.800	0.877	38.031	7.514	7.514	0.000	0.000	0.000
55	C	67	GLY	0	0.003	-0.002	39.953	-0.089	-0.089	0.000	0.000	0.000
56	C	68	LEU	0	-0.015	-0.004	35.273	-0.062	-0.062	0.000	0.000	0.000
57	C	69	ARG	1	0.804	0.867	38.312	6.939	6.939	0.000	0.000	0.000
58	C	70	GLY	0	0.044	0.024	36.132	-0.145	-0.145	0.000	0.000	0.000
59	C	71	GLU	-1	-0.895	-0.923	34.976	-7.146	-7.146	0.000	0.000	0.000
60	C	72	GLU	-1	-0.921	-0.942	32.932	-8.612	-8.612	0.000	0.000	0.000
61	C	73	VAL	0	0.060	0.035	29.193	0.057	0.057	0.000	0.000	0.000
62	C	74	ALA	0	-0.053	-0.027	30.009	-0.198	-0.198	0.000	0.000	0.000
63	C	75	VAL	0	-0.039	-0.026	24.015	-0.195	-0.195	0.000	0.000	0.000
64	C	76	PRO	0	0.014	0.008	24.432	0.219	0.219	0.000	0.000	0.000
65	C	77	PRO	0	0.046	0.017	26.519	-0.135	-0.135	0.000	0.000	0.000
66	C	78	GLY	0	-0.016	-0.015	26.057	-0.144	-0.144	0.000	0.000	0.000
67	C	79	PHE	0	-0.054	-0.017	19.575	-0.523	-0.523	0.000	0.000	0.000
68	C	80	ALA	0	0.015	-0.005	21.353	0.327	0.327	0.000	0.000	0.000
69	C	81	GLY	0	-0.014	0.000	20.700	-0.465	-0.465	0.000	0.000	0.000
70	C	82	PHE	0	-0.007	-0.022	17.451	0.069	0.069	0.000	0.000	0.000
71	C	83	VAL	0	0.007	0.021	18.256	-0.170	-0.170	0.000	0.000	0.000
72	C	84	MET	0	-0.010	0.011	12.950	-0.042	-0.042	0.000	0.000	0.000
73	C	85	VAL	0	0.017	0.015	14.710	0.310	0.310	0.000	0.000	0.000
74	C	86	THR	0	-0.034	-0.028	9.899	-1.239	-1.239	0.000	0.000	0.000
75	C	87	GLU	-1	-1.010	-0.991	9.495	-21.508	-21.508	0.000	0.000	0.000
76	C	88	GLU	-1	-0.800	-0.892	9.754	-21.398	-21.398	0.000	0.000	0.000
77	C	89	LYS	1	0.790	0.868	6.058	30.425	30.425	0.000	0.000	0.000
78	C	90	GLY	0	0.063	0.028	8.971	1.409	1.409	0.000	0.000	0.000
79	C	91	GLU	-1	-0.745	-0.800	10.305	-17.069	-17.069	0.000	0.000	0.000
80	C	92	GLY	0	0.005	0.001	13.677	0.372	0.372	0.000	0.000	0.000
81	C	93	LEU	0	-0.049	-0.035	16.708	0.271	0.271	0.000	0.000	0.000
82	C	94	ILE	0	-0.015	-0.034	19.227	0.603	0.603	0.000	0.000	0.000
83	C	95	GLY	0	-0.005	0.001	20.864	-0.522	-0.522	0.000	0.000	0.000
84	C	96	LYS	1	0.891	0.962	21.510	12.036	12.036	0.000	0.000	0.000
85	C	97	LEU	0	0.050	0.020	24.678	-0.297	-0.297	0.000	0.000	0.000
86	C	98	ASN	0	0.002	-0.004	27.309	-0.119	-0.119	0.000	0.000	0.000
87	C	99	PHE	0	-0.070	-0.030	26.229	-0.300	-0.300	0.000	0.000	0.000
88	C	100	SER	0	0.034	0.007	28.958	0.138	0.138	0.000	0.000	0.000
89	C	101	GLY	0	-0.020	-0.011	30.306	-0.320	-0.320	0.000	0.000	0.000
90	C	102	ASP	-1	-0.893	-0.960	31.637	-8.077	-8.077	0.000	0.000	0.000
91	C	103	ALA	0	0.064	0.038	32.908	-0.193	-0.193	0.000	0.000	0.000
92	C	104	GLU	-1	-0.822	-0.902	35.395	-7.398	-7.398	0.000	0.000	0.000
93	C	105	ASP	-1	-0.937	-0.948	38.058	-6.447	-6.447	0.000	0.000	0.000
94	C	106	LYS	1	0.794	0.862	40.042	6.789	6.789	0.000	0.000	0.000
95	C	107	ALA	0	-0.013	-0.006	38.886	-0.129	-0.129	0.000	0.000	0.000
96	C	108	ASP	-1	-0.937	-0.982	34.213	-8.382	-8.382	0.000	0.000	0.000
97	C	109	GLU	-1	-0.841	-0.924	36.126	-7.121	-7.121	0.000	0.000	0.000
98	C	110	ALA	0	-0.050	-0.026	36.706	-0.108	-0.108	0.000	0.000	0.000
99	C	111	GLN	0	-0.059	-0.034	33.812	-0.102	-0.102	0.000	0.000	0.000
100	C	112	GLU	-1	-0.812	-0.892	32.272	-8.095	-8.095	0.000	0.000	0.000
101	C	113	PRO	0	-0.094	-0.072	27.618	-0.154	-0.154	0.000	0.000	0.000
102	C	114	LEU	0	0.001	0.018	26.368	-0.300	-0.300	0.000	0.000	0.000
103	C	115	GLU	-1	-0.937	-0.952	27.763	-8.593	-8.593	0.000	0.000	0.000
104	C	116	ARG	1	0.883	0.946	27.251	8.492	8.492	0.000	0.000	0.000
105	C	136	LEU	0	-0.008	-0.024	25.257	0.044	0.044	0.000	0.000	0.000
106	C	137	TRP	0	-0.021	-0.012	25.910	0.293	0.293	0.000	0.000	0.000
107	C	138	GLY	0	0.052	0.042	25.454	0.062	0.062	0.000	0.000	0.000
108	C	139	LEU	0	-0.053	-0.033	19.698	-0.182	-0.182	0.000	0.000	0.000
109	C	140	GLU	-1	-0.910	-0.963	18.784	-12.609	-12.609	0.000	0.000	0.000
110	C	141	THR	0	-0.047	-0.016	13.314	-0.415	-0.415	0.000	0.000	0.000
111	C	142	VAL	0	0.019	-0.008	10.154	0.088	0.088	0.000	0.000	0.000
112	C	143	PRO	0	-0.055	-0.029	9.505	-0.321	-0.321	0.000	0.000	0.000
113	C	144	GLY	0	0.030	0.043	8.163	0.885	0.885	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:13:ARG)