FMO DATABASE

FMODB ID: ZYKJN

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	OptAll
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	-733121.209794
FMO2-HF: Nuclear repulsion	690927.372091
FMO2-HF: Total energy	-42193.837703
FMO2-MP2: Total energy	-42318.118075

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.
-31.946	-30.903	-0.014	-0.428	-0.602	0.001

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 : 0.945 / q_NPA : 0.958

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	C	15	HIS	0	-0.001	-0.005	3.871	2.067	3.110	-0.014	-0.428	-0.602	0.001
4	C	16	LEU	0	0.051	0.029	6.430	0.127	0.127	0.000	0.000	0.000	0.000
5	C	17	ARG	1	0.805	0.879	10.254	19.376	19.376	0.000	0.000	0.000	0.000
6	C	18	PRO	0	0.077	0.013	13.104	0.499	0.499	0.000	0.000	0.000	0.000
7	C	19	GLY	0	-0.037	-0.028	15.850	0.724	0.724	0.000	0.000	0.000	0.000
8	C	20	SER	0	-0.029	-0.029	15.137	0.549	0.549	0.000	0.000	0.000	0.000
9	C	21	LEU	0	0.036	0.022	14.651	0.539	0.539	0.000	0.000	0.000	0.000
10	C	22	ARG	1	0.867	0.914	18.043	13.015	13.015	0.000	0.000	0.000	0.000
11	C	23	GLY	0	0.014	0.011	21.145	0.029	0.029	0.000	0.000	0.000	0.000
12	C	24	ALA	0	-0.003	0.023	20.336	0.297	0.297	0.000	0.000	0.000	0.000
13	C	25	ALA	0	0.019	0.015	22.485	0.320	0.320	0.000	0.000	0.000	0.000
14	C	26	PRO	0	0.026	-0.003	25.000	-0.286	-0.286	0.000	0.000	0.000	0.000
15	C	27	ALA	0	-0.019	-0.001	24.279	-0.005	-0.005	0.000	0.000	0.000	0.000
16	C	28	LYS	1	0.871	0.933	26.387	8.788	8.788	0.000	0.000	0.000	0.000
17	C	29	LEU	0	-0.055	-0.033	23.137	-0.260	-0.260	0.000	0.000	0.000	0.000
18	C	30	HIS	0	-0.014	-0.015	27.453	0.230	0.230	0.000	0.000	0.000	0.000
19	C	31	LEU	0	-0.014	-0.003	25.506	-0.411	-0.411	0.000	0.000	0.000	0.000
20	C	32	LEU	0	0.019	0.018	28.480	0.262	0.262	0.000	0.000	0.000	0.000
21	C	33	PRO	0	0.038	0.035	29.648	-0.243	-0.243	0.000	0.000	0.000	0.000
22	C	34	CYS	0	-0.089	-0.055	30.913	0.163	0.163	0.000	0.000	0.000	0.000
23	C	35	ASP	-1	-0.827	-0.905	25.505	-11.045	-11.045	0.000	0.000	0.000	0.000
24	C	36	VAL	0	-0.087	-0.055	26.748	0.395	0.395	0.000	0.000	0.000	0.000
25	C	37	LEU	0	0.009	0.007	25.546	-0.277	-0.277	0.000	0.000	0.000	0.000
26	C	38	VAL	0	-0.051	-0.026	24.098	-0.277	-0.277	0.000	0.000	0.000	0.000
27	C	39	SER	0	0.027	0.017	20.846	0.157	0.157	0.000	0.000	0.000	0.000
28	C	40	ARG	1	0.952	0.980	22.871	9.616	9.616	0.000	0.000	0.000	0.000
29	C	41	PRO	0	0.021	0.013	24.759	0.211	0.211	0.000	0.000	0.000	0.000
30	C	42	ALA	0	0.035	0.009	27.410	0.263	0.263	0.000	0.000	0.000	0.000
31	C	43	PRO	0	-0.017	-0.008	30.528	-0.032	-0.032	0.000	0.000	0.000	0.000
32	C	44	VAL	0	0.081	0.039	30.058	0.292	0.292	0.000	0.000	0.000	0.000
33	C	45	ASP	-1	-0.781	-0.858	33.158	-8.408	-8.408	0.000	0.000	0.000	0.000
34	C	46	ARG	1	0.885	0.949	35.797	7.896	7.896	0.000	0.000	0.000	0.000
35	C	47	PHE	0	-0.044	-0.047	36.100	0.193	0.193	0.000	0.000	0.000	0.000
36	C	48	PHE	0	0.013	0.031	34.711	0.105	0.105	0.000	0.000	0.000	0.000
37	C	49	THR	0	0.022	-0.033	35.329	0.103	0.103	0.000	0.000	0.000	0.000
38	C	50	PRO	0	-0.026	-0.007	37.662	0.136	0.136	0.000	0.000	0.000	0.000
39	C	51	ALA	0	-0.029	-0.015	40.307	0.217	0.217	0.000	0.000	0.000	0.000
40	C	52	VAL	0	0.005	0.021	36.872	0.068	0.068	0.000	0.000	0.000	0.000
41	C	53	ARG	1	0.797	0.898	40.290	6.726	6.726	0.000	0.000	0.000	0.000
42	C	54	HIS	0	0.066	0.032	39.605	-0.014	-0.014	0.000	0.000	0.000	0.000
43	C	55	ASP	-1	-0.847	-0.904	43.760	-6.342	-6.342	0.000	0.000	0.000	0.000
44	C	56	ALA	0	-0.039	-0.015	45.623	-0.037	-0.037	0.000	0.000	0.000	0.000
45	C	57	ASP	-1	-0.890	-0.933	43.154	-6.430	-6.430	0.000	0.000	0.000	0.000
46	C	58	GLY	0	0.044	0.027	39.589	0.008	0.008	0.000	0.000	0.000	0.000
47	C	59	LEU	0	-0.058	-0.035	36.256	0.023	0.023	0.000	0.000	0.000	0.000
48	C	60	GLN	0	-0.081	-0.022	40.332	0.047	0.047	0.000	0.000	0.000	0.000
49	C	61	ALA	0	0.034	0.011	38.054	-0.051	-0.051	0.000	0.000	0.000	0.000
50	C	62	SER	0	-0.014	-0.009	39.361	0.078	0.078	0.000	0.000	0.000	0.000
51	C	63	PHE	0	0.042	0.015	32.206	-0.165	-0.165	0.000	0.000	0.000	0.000
52	C	64	ARG	1	0.895	0.940	33.481	8.428	8.428	0.000	0.000	0.000	0.000
53	C	65	GLY	0	0.012	0.011	38.691	0.097	0.097	0.000	0.000	0.000	0.000
54	C	66	ARG	1	0.768	0.857	37.887	7.573	7.573	0.000	0.000	0.000	0.000
55	C	67	GLY	0	0.028	0.012	40.017	-0.117	-0.117	0.000	0.000	0.000	0.000
56	C	68	LEU	0	-0.035	-0.025	35.640	-0.085	-0.085	0.000	0.000	0.000	0.000
57	C	69	ARG	1	0.814	0.881	38.959	6.904	6.904	0.000	0.000	0.000	0.000
58	C	70	GLY	0	0.057	0.027	36.483	-0.166	-0.166	0.000	0.000	0.000	0.000
59	C	71	GLU	-1	-0.845	-0.931	35.435	-7.122	-7.122	0.000	0.000	0.000	0.000
60	C	72	GLU	-1	-0.862	-0.899	33.504	-8.772	-8.772	0.000	0.000	0.000	0.000
61	C	73	VAL	0	0.023	0.018	29.317	0.074	0.074	0.000	0.000	0.000	0.000
62	C	74	ALA	0	-0.024	-0.017	30.061	-0.198	-0.198	0.000	0.000	0.000	0.000
63	C	75	VAL	0	-0.040	-0.028	24.011	-0.229	-0.229	0.000	0.000	0.000	0.000
64	C	76	PRO	0	0.025	0.012	24.581	0.239	0.239	0.000	0.000	0.000	0.000
65	C	77	PRO	0	0.033	0.011	26.590	-0.175	-0.175	0.000	0.000	0.000	0.000
66	C	78	GLY	0	-0.012	-0.011	26.169	-0.070	-0.070	0.000	0.000	0.000	0.000
67	C	79	PHE	0	-0.063	-0.022	20.072	-0.487	-0.487	0.000	0.000	0.000	0.000
68	C	80	ALA	0	0.021	0.008	21.958	0.376	0.376	0.000	0.000	0.000	0.000
69	C	81	GLY	0	0.023	0.017	20.762	-0.455	-0.455	0.000	0.000	0.000	0.000
70	C	82	PHE	0	-0.028	-0.030	17.664	0.150	0.150	0.000	0.000	0.000	0.000
71	C	83	VAL	0	0.005	0.001	18.317	0.124	0.124	0.000	0.000	0.000	0.000
72	C	84	MET	0	-0.027	-0.004	12.937	-0.001	-0.001	0.000	0.000	0.000	0.000
73	C	85	VAL	0	0.011	0.012	14.644	0.061	0.061	0.000	0.000	0.000	0.000
74	C	86	THR	0	-0.004	-0.019	9.794	-1.462	-1.462	0.000	0.000	0.000	0.000
75	C	87	GLU	-1	-0.957	-0.965	9.749	-21.459	-21.459	0.000	0.000	0.000	0.000
76	C	88	GLU	-1	-0.840	-0.917	10.233	-24.002	-24.002	0.000	0.000	0.000	0.000
77	C	89	LYS	1	0.763	0.866	7.262	26.603	26.603	0.000	0.000	0.000	0.000
78	C	90	GLY	0	0.035	0.036	9.601	1.161	1.161	0.000	0.000	0.000	0.000
79	C	91	GLU	-1	-0.769	-0.841	10.504	-16.832	-16.832	0.000	0.000	0.000	0.000
80	C	92	GLY	0	0.051	0.022	13.939	0.411	0.411	0.000	0.000	0.000	0.000
81	C	93	LEU	0	-0.043	-0.008	16.943	0.494	0.494	0.000	0.000	0.000	0.000
82	C	94	ILE	0	-0.009	-0.010	19.339	0.566	0.566	0.000	0.000	0.000	0.000
83	C	95	GLY	0	-0.019	-0.020	20.845	-0.604	-0.604	0.000	0.000	0.000	0.000
84	C	96	LYS	1	0.874	0.960	21.722	12.152	12.152	0.000	0.000	0.000	0.000
85	C	97	LEU	0	0.036	0.007	24.922	-0.310	-0.310	0.000	0.000	0.000	0.000
86	C	98	ASN	0	-0.069	-0.036	27.607	-0.067	-0.067	0.000	0.000	0.000	0.000
87	C	99	PHE	0	-0.053	-0.030	26.773	-0.382	-0.382	0.000	0.000	0.000	0.000
88	C	100	SER	0	0.029	0.014	29.150	0.157	0.157	0.000	0.000	0.000	0.000
89	C	101	GLY	0	-0.010	0.004	30.472	-0.312	-0.312	0.000	0.000	0.000	0.000
90	C	102	ASP	-1	-0.852	-0.942	31.811	-8.111	-8.111	0.000	0.000	0.000	0.000
91	C	103	ALA	0	0.053	0.028	33.107	-0.182	-0.182	0.000	0.000	0.000	0.000
92	C	104	GLU	-1	-0.783	-0.872	35.655	-7.390	-7.390	0.000	0.000	0.000	0.000
93	C	105	ASP	-1	-0.877	-0.924	38.309	-6.454	-6.454	0.000	0.000	0.000	0.000
94	C	106	LYS	1	0.767	0.862	40.526	6.764	6.764	0.000	0.000	0.000	0.000
95	C	107	ALA	0	-0.028	-0.011	38.451	-0.129	-0.129	0.000	0.000	0.000	0.000
96	C	108	ASP	-1	-0.940	-0.983	33.636	-8.416	-8.416	0.000	0.000	0.000	0.000
97	C	109	GLU	-1	-0.815	-0.901	36.063	-7.138	-7.138	0.000	0.000	0.000	0.000
98	C	110	ALA	0	-0.031	-0.005	38.052	0.000	0.000	0.000	0.000	0.000	0.000
99	C	111	GLN	0	-0.044	-0.047	33.427	-0.154	-0.154	0.000	0.000	0.000	0.000
100	C	112	GLU	-1	-0.804	-0.867	32.040	-8.165	-8.165	0.000	0.000	0.000	0.000
101	C	113	PRO	0	-0.093	-0.079	28.040	-0.155	-0.155	0.000	0.000	0.000	0.000
102	C	114	LEU	0	-0.004	0.007	26.149	-0.328	-0.328	0.000	0.000	0.000	0.000
103	C	115	GLU	-1	-0.955	-0.962	28.171	-8.449	-8.449	0.000	0.000	0.000	0.000
104	C	116	ARG	1	0.811	0.904	26.801	8.474	8.474	0.000	0.000	0.000	0.000
105	C	136	LEU	0	-0.016	-0.028	25.323	0.022	0.022	0.000	0.000	0.000	0.000
106	C	137	TRP	0	-0.012	-0.011	26.244	0.316	0.316	0.000	0.000	0.000	0.000
107	C	138	GLY	0	0.057	0.050	25.625	0.105	0.105	0.000	0.000	0.000	0.000
108	C	139	LEU	0	-0.046	-0.034	19.515	-0.188	-0.188	0.000	0.000	0.000	0.000
109	C	140	GLU	-1	-0.843	-0.898	18.912	-13.228	-13.228	0.000	0.000	0.000	0.000
110	C	141	THR	0	-0.097	-0.068	13.789	-0.509	-0.509	0.000	0.000	0.000	0.000
111	C	142	VAL	0	0.009	-0.006	10.416	-0.055	-0.055	0.000	0.000	0.000	0.000
112	C	143	PRO	0	-0.075	-0.039	9.691	-0.499	-0.499	0.000	0.000	0.000	0.000
113	C	144	GLY	0	0.031	0.037	8.362	0.424	0.424	0.000	0.000	0.000	0.000

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