FMO DATABASE

FMODB ID: 8JZLY

Calculation Name: 2IKB-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IKB

Chain ID: A

ChEMBL ID:

UniProt ID: Q7DDI9

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	164
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1614982.939382
FMO2-HF: Nuclear repulsion	1550832.934425
FMO2-HF: Total energy	-64150.004957
FMO2-MP2: Total energy	-64336.867351

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:1:MET )

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

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.
-15.178	-7.989	8.477	-5.034	-10.633	-0.01

Interaction energy analysis for fragmet #1(A:1:MET )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.024

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	3	ASP	-1	-0.796	-0.899	2.263	-8.272	-3.693	2.403	-2.725	-4.258	-0.023
4	A	4	LYS	1	0.902	0.947	1.891	-7.770	-6.523	6.050	-1.992	-5.305	0.013
5	A	5	PHE	0	0.019	0.021	3.858	-1.366	-0.789	0.011	-0.153	-0.436	0.000
6	A	6	ASN	0	0.033	0.003	5.812	0.214	0.214	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.016	-0.008	6.415	0.138	0.138	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.003	-0.010	7.860	-0.109	-0.109	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.018	0.003	9.793	-0.103	-0.103	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.025	-0.031	10.862	-0.048	-0.048	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.929	0.979	11.792	-0.748	-0.748	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.039	0.002	13.441	-0.018	-0.018	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.048	-0.008	15.800	-0.034	-0.034	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.035	0.029	17.335	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	15	HIS	0	0.048	0.010	16.687	-0.039	-0.039	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.937	-0.963	21.175	-0.025	-0.025	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.017	-0.001	23.514	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.037	0.021	24.591	0.003	0.003	0.000	0.000	0.000	0.000
19	A	19	TYR	0	-0.125	-0.090	27.021	0.002	0.002	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.016	0.004	28.583	0.006	0.006	0.000	0.000	0.000	0.000
21	A	21	ASN	0	0.015	-0.005	30.260	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	22	HIS	0	0.051	0.042	32.921	0.000	0.000	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.019	-0.005	35.703	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.906	0.940	38.229	0.006	0.006	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.817	-0.900	31.975	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.056	0.033	32.675	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.032	-0.020	29.884	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.008	-0.004	28.160	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.840	-0.876	28.876	-0.040	-0.040	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.035	-0.050	24.248	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.001	-0.012	24.499	0.010	0.010	0.000	0.000	0.000	0.000
32	A	32	TRP	0	0.007	0.005	19.846	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.029	0.031	19.874	0.004	0.004	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.032	0.000	17.579	0.005	0.005	0.000	0.000	0.000	0.000
35	A	35	THR	0	0.038	0.019	21.459	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.997	0.985	23.611	0.048	0.048	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.880	0.937	25.373	0.002	0.002	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.018	0.000	19.219	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	39	ALA	0	0.034	0.016	20.928	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.015	0.000	21.917	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.041	0.005	21.471	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.123	-0.083	17.054	-0.029	-0.029	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.048	0.032	19.092	-0.021	-0.021	0.000	0.000	0.000	0.000
44	A	44	TYR	0	-0.034	-0.014	21.128	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.019	-0.019	22.875	0.018	0.018	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.017	0.025	26.020	0.007	0.007	0.000	0.000	0.000	0.000
47	A	47	SER	0	0.002	-0.002	27.812	0.008	0.008	0.000	0.000	0.000	0.000
48	A	48	MET	0	0.031	0.041	23.746	-0.012	-0.012	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.948	0.974	26.412	0.040	0.040	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.010	-0.006	27.909	0.000	0.000	0.000	0.000	0.000	0.000
51	A	51	MET	0	-0.029	0.022	21.480	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	52	THR	0	0.060	0.039	20.853	0.010	0.010	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.890	0.937	15.452	0.062	0.062	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.867	-0.942	16.447	-0.203	-0.203	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.002	-0.006	16.157	-0.022	-0.022	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.039	0.012	17.267	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	57	ILE	0	-0.014	-0.005	11.781	0.003	0.003	0.000	0.000	0.000	0.000
58	A	58	SER	0	-0.009	-0.009	12.425	-0.063	-0.063	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.016	0.002	13.222	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	60	TYR	0	-0.030	-0.051	12.437	0.014	0.014	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.921	0.971	4.218	1.596	1.758	0.000	-0.029	-0.132	0.000
62	A	62	LYS	1	0.981	1.001	9.529	0.152	0.152	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.053	-0.038	12.101	0.035	0.035	0.000	0.000	0.000	0.000
64	A	64	PHE	0	-0.032	-0.027	10.606	0.033	0.033	0.000	0.000	0.000	0.000
65	A	65	TRP	0	0.016	0.012	3.186	0.201	0.513	0.006	-0.075	-0.243	0.000
66	A	66	GLU	-1	-0.891	-0.962	7.440	-0.733	-0.733	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.876	0.959	8.869	0.112	0.112	0.000	0.000	0.000	0.000
68	A	68	TYR	0	-0.028	-0.029	11.461	0.018	0.018	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.982	1.000	7.777	0.302	0.302	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.028	0.014	8.518	0.146	0.146	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.944	-0.973	3.652	-0.177	0.135	0.007	-0.060	-0.259	0.000
72	A	72	GLN	0	-0.016	-0.018	5.512	0.518	0.518	0.000	0.000	0.000	0.000
73	A	73	MET	0	-0.048	0.007	8.388	-0.119	-0.119	0.000	0.000	0.000	0.000
74	A	74	PRO	0	0.066	0.042	10.098	0.243	0.243	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.917	-0.959	9.811	1.340	1.340	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.022	0.011	12.138	-0.114	-0.114	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.016	0.008	14.288	-0.086	-0.086	0.000	0.000	0.000	0.000
78	A	78	ALA	0	0.029	0.016	10.586	-0.089	-0.089	0.000	0.000	0.000	0.000
79	A	79	PHE	0	-0.023	-0.020	12.619	-0.106	-0.106	0.000	0.000	0.000	0.000
80	A	80	GLN	0	0.040	0.017	14.835	-0.098	-0.098	0.000	0.000	0.000	0.000
81	A	81	PHE	0	0.017	0.004	13.549	-0.057	-0.057	0.000	0.000	0.000	0.000
82	A	82	PHE	0	0.028	0.002	13.469	-0.044	-0.044	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.764	-0.865	15.742	0.100	0.100	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.013	-0.012	19.241	-0.028	-0.028	0.000	0.000	0.000	0.000
85	A	85	CYS	0	-0.072	-0.019	17.124	-0.029	-0.029	0.000	0.000	0.000	0.000
86	A	86	VAL	0	-0.042	-0.015	17.962	-0.023	-0.023	0.000	0.000	0.000	0.000
87	A	87	ASN	0	-0.029	-0.001	20.555	-0.027	-0.027	0.000	0.000	0.000	0.000
88	A	88	HIS	0	-0.009	0.002	23.199	0.002	0.002	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.053	0.044	22.879	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	90	TYR	0	0.022	0.000	15.765	0.010	0.010	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.009	0.003	20.023	0.012	0.012	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.001	-0.013	22.065	0.007	0.007	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.027	0.006	19.709	0.010	0.010	0.000	0.000	0.000	0.000
94	A	94	ALA	0	-0.001	-0.013	18.329	0.019	0.019	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.935	0.970	19.499	-0.031	-0.031	0.000	0.000	0.000	0.000
96	A	96	MET	0	-0.056	-0.004	22.522	0.009	0.009	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.032	0.006	15.794	0.008	0.008	0.000	0.000	0.000	0.000
98	A	98	GLN	0	-0.029	-0.011	19.803	0.007	0.007	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.853	0.916	21.514	-0.088	-0.088	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.082	-0.037	22.139	0.001	0.001	0.000	0.000	0.000	0.000
101	A	101	ALA	0	0.027	-0.006	20.101	0.010	0.010	0.000	0.000	0.000	0.000
102	A	102	GLY	0	-0.040	-0.005	22.115	0.001	0.001	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.055	-0.025	20.486	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	104	PRO	0	0.018	-0.009	23.918	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.828	-0.903	23.647	0.075	0.075	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.838	-0.916	22.005	0.048	0.048	0.000	0.000	0.000	0.000
107	A	107	GLY	0	-0.098	-0.058	21.110	-0.013	-0.013	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.058	-0.032	18.072	-0.012	-0.012	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.004	-0.008	13.876	0.014	0.014	0.000	0.000	0.000	0.000
110	A	110	GLY	0	0.051	0.028	14.311	-0.020	-0.020	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.006	-0.004	15.168	0.033	0.033	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.047	0.012	16.165	0.033	0.033	0.000	0.000	0.000	0.000
113	A	113	SER	0	0.027	0.023	16.905	0.018	0.018	0.000	0.000	0.000	0.000
114	A	114	LEU	0	0.005	0.000	11.110	0.027	0.027	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.940	0.976	14.861	-0.257	-0.257	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.025	0.015	17.057	0.023	0.023	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.027	-0.025	14.545	0.012	0.012	0.000	0.000	0.000	0.000
118	A	118	ASN	0	-0.049	-0.045	12.219	0.101	0.101	0.000	0.000	0.000	0.000
119	A	119	SER	0	-0.105	-0.031	16.225	0.004	0.004	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.014	0.009	19.672	-0.016	-0.016	0.000	0.000	0.000	0.000
121	A	121	PRO	0	0.050	0.029	20.338	0.040	0.040	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.836	-0.940	16.733	0.548	0.548	0.000	0.000	0.000	0.000
123	A	123	ASN	0	0.015	0.004	20.121	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.817	-0.913	23.345	0.198	0.198	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.043	-0.007	17.890	-0.020	-0.020	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.025	-0.026	18.543	-0.026	-0.026	0.000	0.000	0.000	0.000
127	A	127	LEU	0	0.013	0.018	22.183	-0.024	-0.024	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.948	0.980	24.950	-0.168	-0.168	0.000	0.000	0.000	0.000
129	A	129	PHE	0	-0.018	-0.003	19.812	-0.016	-0.016	0.000	0.000	0.000	0.000
130	A	130	ASN	0	0.002	-0.034	22.843	-0.029	-0.029	0.000	0.000	0.000	0.000
131	A	131	ALA	0	0.029	0.020	25.484	-0.016	-0.016	0.000	0.000	0.000	0.000
132	A	132	GLU	-1	-0.844	-0.916	25.295	0.094	0.094	0.000	0.000	0.000	0.000
133	A	133	ARG	1	0.812	0.882	22.081	-0.167	-0.167	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.002	0.005	26.831	-0.012	-0.012	0.000	0.000	0.000	0.000
135	A	135	VAL	0	0.016	0.014	30.136	-0.011	-0.011	0.000	0.000	0.000	0.000
136	A	136	PHE	0	-0.004	-0.005	28.305	-0.009	-0.009	0.000	0.000	0.000	0.000
137	A	137	TYR	0	0.008	-0.007	30.321	-0.007	-0.007	0.000	0.000	0.000	0.000
138	A	138	THR	0	-0.077	-0.040	32.091	-0.007	-0.007	0.000	0.000	0.000	0.000
139	A	139	LYS	1	0.911	0.973	32.372	-0.068	-0.068	0.000	0.000	0.000	0.000
140	A	140	LEU	0	0.007	-0.005	31.447	-0.005	-0.005	0.000	0.000	0.000	0.000
141	A	141	GLY	0	-0.036	0.004	32.788	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	142	THR	0	0.017	0.017	33.660	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	143	PHE	0	0.032	-0.001	35.313	0.005	0.005	0.000	0.000	0.000	0.000
144	A	144	THR	0	0.039	0.007	34.596	0.000	0.000	0.000	0.000	0.000	0.000
145	A	145	SER	0	0.017	-0.005	34.508	0.005	0.005	0.000	0.000	0.000	0.000
146	A	146	PHE	0	0.028	0.017	26.760	0.007	0.007	0.000	0.000	0.000	0.000
147	A	147	GLY	0	0.006	0.013	30.426	0.008	0.008	0.000	0.000	0.000	0.000
148	A	148	LYS	1	0.964	0.968	31.819	-0.047	-0.047	0.000	0.000	0.000	0.000
149	A	149	GLY	0	-0.006	0.000	30.389	0.007	0.007	0.000	0.000	0.000	0.000
150	A	150	TRP	0	-0.011	-0.002	26.400	0.014	0.014	0.000	0.000	0.000	0.000
151	A	151	VAL	0	0.034	0.028	27.805	0.013	0.013	0.000	0.000	0.000	0.000
152	A	152	ARG	1	0.948	0.976	30.299	-0.078	-0.078	0.000	0.000	0.000	0.000
153	A	153	ARG	1	0.892	0.935	23.120	-0.139	-0.139	0.000	0.000	0.000	0.000
154	A	154	VAL	0	-0.007	0.003	25.253	0.014	0.014	0.000	0.000	0.000	0.000
155	A	155	ALA	0	0.026	0.013	26.999	0.008	0.008	0.000	0.000	0.000	0.000
156	A	156	GLN	0	-0.019	-0.018	27.489	0.010	0.010	0.000	0.000	0.000	0.000
157	A	157	ASN	0	-0.025	-0.026	22.962	0.018	0.018	0.000	0.000	0.000	0.000
158	A	158	LEU	0	-0.027	-0.005	25.648	0.013	0.013	0.000	0.000	0.000	0.000
159	A	159	ILE	0	-0.026	-0.006	28.130	0.001	0.001	0.000	0.000	0.000	0.000
160	A	160	HIS	0	-0.017	-0.013	24.619	0.016	0.016	0.000	0.000	0.000	0.000
161	A	161	ALA	0	-0.045	-0.010	24.524	0.010	0.010	0.000	0.000	0.000	0.000
162	A	162	SER	0	-0.052	-0.019	25.803	-0.002	-0.002	0.000	0.000	0.000	0.000
163	A	163	ALA	0	-0.023	-0.003	27.363	-0.012	-0.012	0.000	0.000	0.000	0.000
164	A	164	NME	0	-0.004	0.002	28.980	0.008	0.008	0.000	0.000	0.000	0.000

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