FMO DATABASE

FMODB ID: ZYR2N

Calculation Name: 3KIO-C-Xray317

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	117
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-744819.676915
FMO2-HF: Nuclear repulsion	702285.813272
FMO2-HF: Total energy	-42533.863643
FMO2-MP2: Total energy	-42659.41947

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:12:ACE )

Summations of interaction energy for fragment #1(C:12:ACE )

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.
0.967	2.191	0.028	-0.54	-0.713	-0.001

Interaction energy analysis for fragmet #1(C:12:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.076 / q_NPA : 0.032

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	14	ILE	0	0.037	0.028	3.464	0.262	1.486	0.028	-0.540	-0.713	-0.001
4	C	15	HIS	0	-0.005	-0.001	5.827	0.034	0.034	0.000	0.000	0.000	0.000
5	C	16	LEU	0	0.063	0.028	9.196	0.082	0.082	0.000	0.000	0.000	0.000
6	C	17	ARG	1	0.830	0.922	12.073	0.113	0.113	0.000	0.000	0.000	0.000
7	C	18	PRO	0	0.081	0.002	15.401	0.023	0.023	0.000	0.000	0.000	0.000
8	C	19	GLY	0	-0.013	-0.021	17.827	0.015	0.015	0.000	0.000	0.000	0.000
9	C	20	SER	0	-0.005	0.000	16.509	0.015	0.015	0.000	0.000	0.000	0.000
10	C	21	LEU	0	0.007	0.044	15.423	0.011	0.011	0.000	0.000	0.000	0.000
11	C	22	ARG	1	0.883	0.914	18.756	0.045	0.045	0.000	0.000	0.000	0.000
12	C	23	GLY	0	-0.030	0.004	22.270	-0.005	-0.005	0.000	0.000	0.000	0.000
13	C	24	ALA	0	0.006	0.014	21.034	0.004	0.004	0.000	0.000	0.000	0.000
14	C	25	ALA	0	0.019	0.012	23.147	0.002	0.002	0.000	0.000	0.000	0.000
15	C	26	PRO	0	0.022	0.012	24.647	0.006	0.006	0.000	0.000	0.000	0.000
16	C	27	ALA	0	0.012	0.013	23.862	0.000	0.000	0.000	0.000	0.000	0.000
17	C	28	LYS	1	0.940	0.977	25.950	-0.042	-0.042	0.000	0.000	0.000	0.000
18	C	29	LEU	0	-0.035	-0.034	21.713	0.005	0.005	0.000	0.000	0.000	0.000
19	C	30	HIS	0	0.046	0.024	25.984	-0.006	-0.006	0.000	0.000	0.000	0.000
20	C	31	LEU	0	-0.007	0.008	23.667	0.008	0.008	0.000	0.000	0.000	0.000
21	C	32	LEU	0	0.020	0.007	26.648	-0.005	-0.005	0.000	0.000	0.000	0.000
22	C	33	PRO	0	0.028	0.043	27.658	0.008	0.008	0.000	0.000	0.000	0.000
23	C	34	CYS	0	-0.080	-0.069	28.909	-0.004	-0.004	0.000	0.000	0.000	0.000
24	C	35	ASP	-1	-0.867	-0.914	24.131	0.142	0.142	0.000	0.000	0.000	0.000
25	C	36	VAL	0	-0.061	-0.039	26.365	-0.007	-0.007	0.000	0.000	0.000	0.000
26	C	37	LEU	0	0.013	0.005	24.637	0.005	0.005	0.000	0.000	0.000	0.000
27	C	38	VAL	0	-0.036	-0.014	23.134	0.008	0.008	0.000	0.000	0.000	0.000
28	C	39	SER	0	0.024	0.016	19.465	-0.011	-0.011	0.000	0.000	0.000	0.000
29	C	40	ARG	1	0.938	0.964	22.396	-0.071	-0.071	0.000	0.000	0.000	0.000
30	C	41	PRO	0	0.019	0.025	24.840	-0.002	-0.002	0.000	0.000	0.000	0.000
31	C	42	ALA	0	0.044	-0.001	27.060	0.001	0.001	0.000	0.000	0.000	0.000
32	C	43	PRO	0	-0.010	0.004	30.013	-0.002	-0.002	0.000	0.000	0.000	0.000
33	C	44	VAL	0	0.080	0.035	29.339	-0.003	-0.003	0.000	0.000	0.000	0.000
34	C	45	ASP	-1	-0.807	-0.906	32.670	0.035	0.035	0.000	0.000	0.000	0.000
35	C	46	ARG	1	0.824	0.915	35.345	-0.033	-0.033	0.000	0.000	0.000	0.000
36	C	47	PHE	0	-0.047	-0.049	35.820	-0.002	-0.002	0.000	0.000	0.000	0.000
37	C	48	PHE	0	0.006	0.032	32.437	-0.001	-0.001	0.000	0.000	0.000	0.000
38	C	49	THR	0	0.048	0.019	34.763	-0.001	-0.001	0.000	0.000	0.000	0.000
39	C	50	PRO	0	-0.050	-0.020	36.680	-0.001	-0.001	0.000	0.000	0.000	0.000
40	C	51	ALA	0	-0.036	-0.032	38.942	-0.002	-0.002	0.000	0.000	0.000	0.000
41	C	52	VAL	0	-0.014	0.006	35.956	0.000	0.000	0.000	0.000	0.000	0.000
42	C	53	ARG	1	0.807	0.922	39.319	-0.031	-0.031	0.000	0.000	0.000	0.000
43	C	54	HIS	0	0.066	0.025	38.814	0.001	0.001	0.000	0.000	0.000	0.000
44	C	55	ASP	-1	-0.873	-0.918	42.568	0.030	0.030	0.000	0.000	0.000	0.000
45	C	56	ALA	0	-0.015	-0.006	43.366	0.000	0.000	0.000	0.000	0.000	0.000
46	C	57	ASP	-1	-0.928	-0.943	41.660	0.031	0.031	0.000	0.000	0.000	0.000
47	C	58	GLY	0	0.043	0.010	38.112	-0.001	-0.001	0.000	0.000	0.000	0.000
48	C	59	LEU	0	0.024	0.002	35.707	-0.002	-0.002	0.000	0.000	0.000	0.000
49	C	60	GLN	0	-0.044	0.010	38.863	0.003	0.003	0.000	0.000	0.000	0.000
50	C	61	ALA	0	0.031	0.000	36.872	-0.001	-0.001	0.000	0.000	0.000	0.000
51	C	62	SER	0	0.013	0.020	38.728	0.002	0.002	0.000	0.000	0.000	0.000
52	C	63	PHE	0	0.028	-0.007	31.670	0.001	0.001	0.000	0.000	0.000	0.000
53	C	64	ARG	1	0.891	0.944	32.994	-0.062	-0.062	0.000	0.000	0.000	0.000
54	C	65	GLY	0	-0.003	0.003	37.693	-0.001	-0.001	0.000	0.000	0.000	0.000
55	C	66	ARG	1	0.870	0.934	36.838	-0.058	-0.058	0.000	0.000	0.000	0.000
56	C	67	GLY	0	0.019	0.005	38.721	0.000	0.000	0.000	0.000	0.000	0.000
57	C	68	LEU	0	-0.028	-0.011	33.876	0.002	0.002	0.000	0.000	0.000	0.000
58	C	69	ARG	1	0.787	0.852	36.731	-0.041	-0.041	0.000	0.000	0.000	0.000
59	C	70	GLY	0	0.051	0.030	34.559	0.003	0.003	0.000	0.000	0.000	0.000
60	C	71	GLU	-1	-0.910	-0.931	33.240	0.037	0.037	0.000	0.000	0.000	0.000
61	C	72	GLU	-1	-0.927	-0.947	31.801	0.046	0.046	0.000	0.000	0.000	0.000
62	C	73	VAL	0	0.079	0.046	27.201	-0.001	-0.001	0.000	0.000	0.000	0.000
63	C	74	ALA	0	-0.076	-0.040	28.620	0.000	0.000	0.000	0.000	0.000	0.000
64	C	75	VAL	0	-0.039	-0.023	22.687	0.005	0.005	0.000	0.000	0.000	0.000
65	C	76	PRO	0	0.017	0.012	22.528	-0.006	-0.006	0.000	0.000	0.000	0.000
66	C	77	PRO	0	0.054	0.020	25.337	-0.004	-0.004	0.000	0.000	0.000	0.000
67	C	78	GLY	0	-0.013	-0.013	25.387	0.001	0.001	0.000	0.000	0.000	0.000
68	C	79	PHE	0	-0.061	-0.020	18.421	-0.001	-0.001	0.000	0.000	0.000	0.000
69	C	80	ALA	0	0.013	-0.006	20.992	-0.005	-0.005	0.000	0.000	0.000	0.000
70	C	81	GLY	0	0.030	0.001	19.863	0.009	0.009	0.000	0.000	0.000	0.000
71	C	82	PHE	0	-0.047	-0.034	16.759	-0.014	-0.014	0.000	0.000	0.000	0.000
72	C	83	VAL	0	0.015	0.026	17.427	0.020	0.020	0.000	0.000	0.000	0.000
73	C	84	MET	0	-0.021	0.005	12.553	-0.032	-0.032	0.000	0.000	0.000	0.000
74	C	85	VAL	0	0.017	0.015	14.704	0.033	0.033	0.000	0.000	0.000	0.000
75	C	86	THR	0	-0.055	-0.031	9.785	-0.005	-0.005	0.000	0.000	0.000	0.000
76	C	87	GLU	-1	-0.991	-0.984	10.188	0.161	0.161	0.000	0.000	0.000	0.000
77	C	88	GLU	-1	-0.786	-0.884	11.419	-0.078	-0.078	0.000	0.000	0.000	0.000
78	C	89	LYS	1	0.760	0.854	8.325	0.227	0.227	0.000	0.000	0.000	0.000
79	C	90	GLY	0	0.063	0.032	9.995	-0.013	-0.013	0.000	0.000	0.000	0.000
80	C	91	GLU	-1	-0.789	-0.871	10.880	-0.045	-0.045	0.000	0.000	0.000	0.000
81	C	92	GLY	0	0.009	-0.008	14.621	0.029	0.029	0.000	0.000	0.000	0.000
82	C	93	LEU	0	-0.049	-0.031	17.049	-0.011	-0.011	0.000	0.000	0.000	0.000
83	C	94	ILE	0	-0.008	-0.034	19.534	-0.002	-0.002	0.000	0.000	0.000	0.000
84	C	95	GLY	0	-0.008	0.000	20.636	0.003	0.003	0.000	0.000	0.000	0.000
85	C	96	LYS	1	0.862	0.962	20.063	-0.077	-0.077	0.000	0.000	0.000	0.000
86	C	97	LEU	0	0.048	0.016	23.852	0.001	0.001	0.000	0.000	0.000	0.000
87	C	98	ASN	0	-0.007	-0.013	26.409	0.003	0.003	0.000	0.000	0.000	0.000
88	C	99	PHE	0	-0.037	-0.018	24.049	0.002	0.002	0.000	0.000	0.000	0.000
89	C	100	SER	0	0.009	-0.002	27.695	-0.002	-0.002	0.000	0.000	0.000	0.000
90	C	101	GLY	0	-0.012	-0.010	28.912	0.007	0.007	0.000	0.000	0.000	0.000
91	C	102	ASP	-1	-0.909	-0.964	30.035	0.052	0.052	0.000	0.000	0.000	0.000
92	C	103	ALA	0	0.044	0.039	31.248	0.006	0.006	0.000	0.000	0.000	0.000
93	C	104	GLU	-1	-0.866	-0.950	33.687	0.055	0.055	0.000	0.000	0.000	0.000
94	C	105	ASP	-1	-0.937	-0.948	36.364	0.042	0.042	0.000	0.000	0.000	0.000
95	C	106	LYS	1	0.757	0.844	38.255	-0.045	-0.045	0.000	0.000	0.000	0.000
96	C	107	ALA	0	-0.005	-0.003	37.069	0.002	0.002	0.000	0.000	0.000	0.000
97	C	108	ASP	-1	-0.908	-0.972	32.186	0.068	0.068	0.000	0.000	0.000	0.000
98	C	109	GLU	-1	-0.823	-0.910	34.046	0.046	0.046	0.000	0.000	0.000	0.000
99	C	110	ALA	0	-0.063	-0.029	34.577	0.003	0.003	0.000	0.000	0.000	0.000
100	C	111	GLN	0	-0.061	-0.042	31.442	0.000	0.000	0.000	0.000	0.000	0.000
101	C	112	GLU	-1	-0.797	-0.880	29.767	0.071	0.071	0.000	0.000	0.000	0.000
102	C	113	PRO	0	-0.113	-0.081	25.229	0.001	0.001	0.000	0.000	0.000	0.000
103	C	114	LEU	0	0.003	0.019	24.134	0.006	0.006	0.000	0.000	0.000	0.000
104	C	115	GLU	-1	-0.911	-0.945	25.684	0.061	0.061	0.000	0.000	0.000	0.000
105	C	116	ARG	1	0.877	0.944	26.856	-0.076	-0.076	0.000	0.000	0.000	0.000
106	C	117	NME	0	0.002	0.003	23.950	0.006	0.006	0.000	0.000	0.000	0.000
107	C	135	ACE	0	-0.008	-0.017	28.542	-0.002	-0.002	0.000	0.000	0.000	0.000
108	C	136	LEU	0	0.020	-0.015	22.787	0.006	0.006	0.000	0.000	0.000	0.000
109	C	137	TRP	0	-0.066	-0.019	23.366	-0.006	-0.006	0.000	0.000	0.000	0.000
110	C	138	GLY	0	0.058	0.048	22.977	-0.002	-0.002	0.000	0.000	0.000	0.000
111	C	139	LEU	0	-0.044	-0.026	17.515	0.003	0.003	0.000	0.000	0.000	0.000
112	C	140	GLU	-1	-0.907	-0.964	16.225	0.219	0.219	0.000	0.000	0.000	0.000
113	C	141	THR	0	-0.063	-0.023	10.849	0.009	0.009	0.000	0.000	0.000	0.000
114	C	142	VAL	0	0.029	0.000	7.985	0.004	0.004	0.000	0.000	0.000	0.000
115	C	143	PRO	0	-0.068	-0.046	7.139	0.079	0.079	0.000	0.000	0.000	0.000
116	C	144	GLY	0	0.018	0.034	6.177	-0.120	-0.120	0.000	0.000	0.000	0.000
117	C	145	NME	0	0.019	0.015	5.790	-0.311	-0.311	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:12:ACE )