FMO DATABASE

FMODB ID: R56Z8

Calculation Name: 3KIO-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KIO

Chain ID: B

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	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	145
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1288065.759506
FMO2-HF: Nuclear repulsion	1230628.818215
FMO2-HF: Total energy	-57436.941291
FMO2-MP2: Total energy	-57606.542194

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(B:10:LEU)

Summations of interaction energy for fragment #1(B:10:LEU)

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.
-2.782	-1.234	-0.024	-0.753	-0.771	0.002

Interaction energy analysis for fragmet #1(B:10:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.021

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	B	12	ALA	0	-0.043	-0.007	3.813	-0.111	1.437	-0.024	-0.753	-0.771	0.002
4	B	13	ARG	1	0.973	0.994	6.696	-1.418	-1.418	0.000	0.000	0.000	0.000
5	B	14	GLN	0	0.014	0.006	8.671	0.033	0.033	0.000	0.000	0.000	0.000
6	B	15	LEU	0	-0.091	-0.046	12.184	-0.063	-0.063	0.000	0.000	0.000	0.000
7	B	16	VAL	0	0.065	0.045	15.378	-0.007	-0.007	0.000	0.000	0.000	0.000
8	B	17	PHE	0	-0.022	-0.027	18.460	-0.010	-0.010	0.000	0.000	0.000	0.000
9	B	18	LEU	0	0.014	0.025	21.548	-0.012	-0.012	0.000	0.000	0.000	0.000
10	B	19	LEU	0	0.000	-0.024	24.377	0.006	0.006	0.000	0.000	0.000	0.000
11	B	20	PRO	0	0.013	0.004	27.391	-0.011	-0.011	0.000	0.000	0.000	0.000
12	B	21	GLU	-1	-0.905	-0.952	30.597	0.086	0.086	0.000	0.000	0.000	0.000
13	B	22	HIS	0	0.067	0.027	31.998	0.001	0.001	0.000	0.000	0.000	0.000
14	B	23	LEU	0	-0.066	-0.015	28.027	0.004	0.004	0.000	0.000	0.000	0.000
15	B	24	LYS	1	0.877	0.947	27.340	-0.120	-0.120	0.000	0.000	0.000	0.000
16	B	25	ASP	-1	-0.878	-0.935	30.003	0.098	0.098	0.000	0.000	0.000	0.000
17	B	26	ALA	0	0.003	0.012	30.966	0.004	0.004	0.000	0.000	0.000	0.000
18	B	27	SER	0	0.027	0.009	32.768	-0.003	-0.003	0.000	0.000	0.000	0.000
19	B	28	LYS	1	0.990	0.967	36.505	-0.070	-0.070	0.000	0.000	0.000	0.000
20	B	29	LYS	1	0.882	0.967	33.464	-0.128	-0.128	0.000	0.000	0.000	0.000
21	B	30	LYS	1	0.899	0.934	32.632	-0.126	-0.126	0.000	0.000	0.000	0.000
22	B	31	LYS	1	0.887	0.951	35.486	-0.116	-0.116	0.000	0.000	0.000	0.000
23	B	32	LYS	1	0.961	0.984	31.222	-0.170	-0.170	0.000	0.000	0.000	0.000
24	B	33	SER	0	0.040	0.013	26.123	-0.006	-0.006	0.000	0.000	0.000	0.000
25	B	34	SER	0	0.040	0.006	28.728	-0.009	-0.009	0.000	0.000	0.000	0.000
26	B	35	LEU	0	-0.009	-0.006	26.200	-0.007	-0.007	0.000	0.000	0.000	0.000
27	B	36	LEU	0	0.047	0.020	25.050	0.018	0.018	0.000	0.000	0.000	0.000
28	B	37	PHE	0	0.007	0.009	21.738	-0.017	-0.017	0.000	0.000	0.000	0.000
29	B	38	VAL	0	0.009	-0.003	24.181	0.015	0.015	0.000	0.000	0.000	0.000
30	B	39	LYS	1	0.926	0.970	21.057	-0.275	-0.275	0.000	0.000	0.000	0.000
31	B	40	LEU	0	0.008	0.011	25.792	-0.005	-0.005	0.000	0.000	0.000	0.000
32	B	41	ALA	0	0.103	0.045	29.041	0.002	0.002	0.000	0.000	0.000	0.000
33	B	42	ASN	0	-0.054	-0.016	29.022	-0.009	-0.009	0.000	0.000	0.000	0.000
34	B	43	PRO	0	0.046	0.019	31.381	-0.006	-0.006	0.000	0.000	0.000	0.000
35	B	44	HIS	0	-0.013	0.002	33.768	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	45	SER	0	-0.065	-0.033	34.237	-0.002	-0.002	0.000	0.000	0.000	0.000
37	B	46	GLY	0	0.014	-0.007	30.803	0.004	0.004	0.000	0.000	0.000	0.000
38	B	47	GLU	-1	-0.903	-0.937	29.414	0.143	0.143	0.000	0.000	0.000	0.000
39	B	48	GLY	0	0.048	0.028	26.064	0.005	0.005	0.000	0.000	0.000	0.000
40	B	49	ALA	0	-0.054	-0.036	25.085	-0.002	-0.002	0.000	0.000	0.000	0.000
41	B	50	THR	0	-0.038	-0.015	21.277	0.003	0.003	0.000	0.000	0.000	0.000
42	B	51	TYR	0	0.061	0.007	24.478	-0.021	-0.021	0.000	0.000	0.000	0.000
43	B	52	LEU	0	-0.003	0.014	24.930	0.016	0.016	0.000	0.000	0.000	0.000
44	B	53	ILE	0	0.008	-0.013	27.388	-0.022	-0.022	0.000	0.000	0.000	0.000
45	B	54	ASP	-1	-0.713	-0.874	29.786	0.152	0.152	0.000	0.000	0.000	0.000
46	B	55	MET	0	-0.069	-0.032	29.088	-0.013	-0.013	0.000	0.000	0.000	0.000
47	B	56	CYS	0	-0.122	-0.038	33.350	-0.005	-0.005	0.000	0.000	0.000	0.000
48	B	57	LEU	0	-0.032	-0.022	36.087	-0.009	-0.009	0.000	0.000	0.000	0.000
49	B	58	GLN	0	-0.027	-0.018	35.122	-0.007	-0.007	0.000	0.000	0.000	0.000
50	B	59	GLN	0	0.008	0.000	34.159	0.008	0.008	0.000	0.000	0.000	0.000
51	B	60	LEU	0	-0.002	0.005	31.579	0.002	0.002	0.000	0.000	0.000	0.000
52	B	61	PHE	0	0.027	0.032	29.182	-0.009	-0.009	0.000	0.000	0.000	0.000
53	B	62	GLU	-1	-0.796	-0.910	28.944	0.117	0.117	0.000	0.000	0.000	0.000
54	B	63	ILE	0	-0.044	-0.028	23.008	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	64	LYS	1	0.875	0.952	24.837	-0.087	-0.087	0.000	0.000	0.000	0.000
56	B	65	VAL	0	-0.045	-0.037	19.701	0.005	0.005	0.000	0.000	0.000	0.000
57	B	66	PHE	0	-0.003	0.003	22.563	-0.004	-0.004	0.000	0.000	0.000	0.000
58	B	67	LYS	1	0.937	0.951	19.549	-0.116	-0.116	0.000	0.000	0.000	0.000
59	B	68	GLU	-1	-0.832	-0.900	21.437	-0.008	-0.008	0.000	0.000	0.000	0.000
60	B	69	LYS	1	0.922	0.949	20.932	0.030	0.030	0.000	0.000	0.000	0.000
61	B	70	HIS	0	0.001	-0.001	19.631	-0.008	-0.008	0.000	0.000	0.000	0.000
62	B	71	HIS	0	0.033	0.027	19.050	-0.006	-0.006	0.000	0.000	0.000	0.000
63	B	72	SER	0	-0.060	-0.026	14.722	-0.017	-0.017	0.000	0.000	0.000	0.000
64	B	73	TRP	0	-0.016	-0.020	15.179	0.015	0.015	0.000	0.000	0.000	0.000
65	B	74	PHE	0	0.053	0.032	14.901	-0.045	-0.045	0.000	0.000	0.000	0.000
66	B	75	ILE	0	-0.030	-0.021	14.217	0.041	0.041	0.000	0.000	0.000	0.000
67	B	76	ASN	0	0.012	0.010	14.767	-0.018	-0.018	0.000	0.000	0.000	0.000
68	B	77	GLN	0	0.028	0.028	14.444	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	78	SER	0	-0.051	-0.043	10.692	-0.046	-0.046	0.000	0.000	0.000	0.000
70	B	79	VAL	0	0.081	0.045	10.166	0.060	0.060	0.000	0.000	0.000	0.000
71	B	80	GLN	0	-0.007	0.002	10.144	-0.020	-0.020	0.000	0.000	0.000	0.000
72	B	81	SER	0	0.015	-0.015	10.398	0.011	0.011	0.000	0.000	0.000	0.000
73	B	82	GLY	0	-0.051	-0.036	12.229	0.017	0.017	0.000	0.000	0.000	0.000
74	B	83	GLY	0	0.147	0.095	14.528	-0.025	-0.025	0.000	0.000	0.000	0.000
75	B	84	LEU	0	-0.157	-0.079	15.486	0.020	0.020	0.000	0.000	0.000	0.000
76	B	85	LEU	0	0.073	0.054	18.256	0.008	0.008	0.000	0.000	0.000	0.000
77	B	86	HIS	0	-0.001	0.007	16.628	-0.021	-0.021	0.000	0.000	0.000	0.000
78	B	87	PHE	0	0.074	0.029	21.794	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	88	ALA	0	-0.009	-0.002	25.456	0.010	0.010	0.000	0.000	0.000	0.000
80	B	89	THR	0	-0.010	0.001	27.096	-0.012	-0.012	0.000	0.000	0.000	0.000
81	B	90	PRO	0	-0.007	-0.012	30.767	0.006	0.006	0.000	0.000	0.000	0.000
82	B	91	MET	0	-0.012	0.001	32.197	-0.006	-0.006	0.000	0.000	0.000	0.000
83	B	92	ASP	-1	-0.714	-0.895	33.886	0.070	0.070	0.000	0.000	0.000	0.000
84	B	93	PRO	0	-0.119	0.046	36.721	-0.002	-0.002	0.000	0.000	0.000	0.000
85	B	94	LEU	0	0.034	0.016	38.835	0.000	0.000	0.000	0.000	0.000	0.000
86	B	95	PHE	0	-0.043	-0.037	37.459	0.000	0.000	0.000	0.000	0.000	0.000
87	B	96	LEU	0	-0.016	-0.007	32.815	0.001	0.001	0.000	0.000	0.000	0.000
88	B	97	LEU	0	0.012	0.003	35.040	0.002	0.002	0.000	0.000	0.000	0.000
89	B	98	LEU	0	0.046	0.030	37.036	-0.004	-0.004	0.000	0.000	0.000	0.000
90	B	99	HIS	0	-0.039	-0.015	32.307	0.000	0.000	0.000	0.000	0.000	0.000
91	B	100	TYR	0	-0.026	-0.004	29.361	0.001	0.001	0.000	0.000	0.000	0.000
92	B	101	LEU	0	-0.020	0.010	31.482	-0.002	-0.002	0.000	0.000	0.000	0.000
93	B	102	LEU	0	0.012	0.010	28.172	-0.006	-0.006	0.000	0.000	0.000	0.000
94	B	146	GLU	-1	-0.923	-0.961	32.677	0.151	0.151	0.000	0.000	0.000	0.000
95	B	147	VAL	0	0.050	0.027	33.556	-0.003	-0.003	0.000	0.000	0.000	0.000
96	B	148	ASN	0	-0.073	-0.062	35.365	-0.004	-0.004	0.000	0.000	0.000	0.000
97	B	149	SER	0	0.049	0.029	37.630	-0.006	-0.006	0.000	0.000	0.000	0.000
98	B	150	LYS	1	0.980	0.982	40.619	-0.090	-0.090	0.000	0.000	0.000	0.000
99	B	151	LYS	1	0.921	0.961	40.759	-0.086	-0.086	0.000	0.000	0.000	0.000
100	B	152	TYR	0	0.117	0.054	41.633	0.000	0.000	0.000	0.000	0.000	0.000
101	B	153	TYR	0	0.087	0.036	44.660	-0.002	-0.002	0.000	0.000	0.000	0.000
102	B	154	LYS	1	0.969	0.990	47.994	-0.056	-0.056	0.000	0.000	0.000	0.000
103	B	155	TYR	0	-0.084	-0.058	40.955	-0.003	-0.003	0.000	0.000	0.000	0.000
104	B	156	SER	0	-0.018	-0.006	45.226	0.002	0.002	0.000	0.000	0.000	0.000
105	B	157	SER	0	-0.042	-0.015	46.955	-0.002	-0.002	0.000	0.000	0.000	0.000
106	B	158	GLU	-1	-0.756	-0.865	47.771	0.063	0.063	0.000	0.000	0.000	0.000
107	B	159	LYS	1	0.991	0.991	42.897	-0.062	-0.062	0.000	0.000	0.000	0.000
108	B	160	THR	0	0.081	0.057	48.213	-0.002	-0.002	0.000	0.000	0.000	0.000
109	B	161	LEU	0	0.106	0.055	49.564	0.002	0.002	0.000	0.000	0.000	0.000
110	B	162	LYS	1	1.019	1.002	50.874	-0.034	-0.034	0.000	0.000	0.000	0.000
111	B	163	TRP	0	-0.009	-0.036	42.315	0.002	0.002	0.000	0.000	0.000	0.000
112	B	164	LEU	0	0.035	0.005	46.098	0.002	0.002	0.000	0.000	0.000	0.000
113	B	165	GLU	-1	-0.882	-0.941	47.285	0.034	0.034	0.000	0.000	0.000	0.000
114	B	166	LYS	1	0.960	0.978	49.431	-0.042	-0.042	0.000	0.000	0.000	0.000
115	B	167	LYS	1	0.772	0.866	40.989	-0.068	-0.068	0.000	0.000	0.000	0.000
116	B	168	VAL	0	-0.025	-0.011	44.215	0.001	0.001	0.000	0.000	0.000	0.000
117	B	169	ASN	0	0.023	0.014	45.787	-0.002	-0.002	0.000	0.000	0.000	0.000
118	B	170	GLN	0	0.021	0.000	43.414	0.002	0.002	0.000	0.000	0.000	0.000
119	B	171	THR	0	0.008	-0.040	41.305	0.000	0.000	0.000	0.000	0.000	0.000
120	B	172	VAL	0	0.024	0.039	43.557	-0.001	-0.001	0.000	0.000	0.000	0.000
121	B	173	VAL	0	-0.035	-0.037	46.271	-0.002	-0.002	0.000	0.000	0.000	0.000
122	B	174	ALA	0	-0.004	-0.002	41.807	-0.001	-0.001	0.000	0.000	0.000	0.000
123	B	175	LEU	0	-0.041	-0.010	39.741	0.000	0.000	0.000	0.000	0.000	0.000
124	B	176	LYS	1	0.939	0.983	43.223	-0.030	-0.030	0.000	0.000	0.000	0.000
125	B	177	ALA	0	-0.003	0.010	44.277	-0.002	-0.002	0.000	0.000	0.000	0.000
126	B	178	ASN	0	-0.035	-0.039	40.481	0.003	0.003	0.000	0.000	0.000	0.000
127	B	179	ASN	0	0.001	0.009	42.360	0.000	0.000	0.000	0.000	0.000	0.000
128	B	180	VAL	0	0.017	0.022	39.640	-0.001	-0.001	0.000	0.000	0.000	0.000
129	B	181	ASN	0	0.012	0.008	41.638	-0.003	-0.003	0.000	0.000	0.000	0.000
130	B	267	LEU	0	-0.049	-0.018	46.044	0.001	0.001	0.000	0.000	0.000	0.000
131	B	268	LYS	1	0.928	0.958	44.933	-0.060	-0.060	0.000	0.000	0.000	0.000
132	B	269	THR	0	0.059	0.026	40.592	0.000	0.000	0.000	0.000	0.000	0.000
133	B	270	GLY	0	0.074	0.010	37.725	-0.002	-0.002	0.000	0.000	0.000	0.000
134	B	271	LYS	1	0.848	0.963	38.485	-0.065	-0.065	0.000	0.000	0.000	0.000
135	B	272	LYS	1	0.875	0.931	36.885	-0.100	-0.100	0.000	0.000	0.000	0.000
136	B	273	ASN	0	-0.090	-0.096	37.845	0.005	0.005	0.000	0.000	0.000	0.000
137	B	274	SER	0	0.052	0.027	37.397	-0.003	-0.003	0.000	0.000	0.000	0.000
138	B	275	LYN	0	0.008	0.011	30.574	-0.003	-0.003	0.000	0.000	0.000	0.000
139	B	276	MET	0	-0.064	0.010	36.248	0.008	0.008	0.000	0.000	0.000	0.000
140	B	277	THR	0	-0.018	-0.019	38.993	-0.004	-0.004	0.000	0.000	0.000	0.000
141	B	278	ALA	0	-0.003	-0.008	37.441	-0.002	-0.002	0.000	0.000	0.000	0.000
142	B	279	ALA	0	0.060	0.035	36.277	-0.001	-0.001	0.000	0.000	0.000	0.000
143	B	280	GLN	0	-0.027	0.002	38.376	-0.003	-0.003	0.000	0.000	0.000	0.000
144	B	281	LYS	1	0.778	0.885	41.756	-0.072	-0.072	0.000	0.000	0.000	0.000
145	B	282	ALA	0	0.056	0.044	41.483	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:10:LEU)