FMO DATABASE

FMODB ID: 85J2Y

Calculation Name: 5IJM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IJM

Chain ID: A

ChEMBL ID:

UniProt ID: Q4QED2

Base Structure: X-ray

Registration Date: 2023-06-21

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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-681586.042581
FMO2-HF: Nuclear repulsion	643474.867609
FMO2-HF: Total energy	-38111.174973
FMO2-MP2: Total energy	-38222.60397

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:SER)

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

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.
-10.851	-7.941	0.126	-1.622	-1.415	0.006

Interaction energy analysis for fragmet #1(A:-1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.026

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	1	MET	0	-0.020	0.005	3.888	-0.231	1.489	-0.016	-0.981	-0.723	-0.001
4	A	2	SER	0	-0.009	-0.004	6.585	-0.273	-0.273	0.000	0.000	0.000	0.000
5	A	3	ALA	0	0.054	0.016	9.873	0.199	0.199	0.000	0.000	0.000	0.000
6	A	4	ALA	0	0.016	0.011	10.606	0.124	0.124	0.000	0.000	0.000	0.000
7	A	5	ASP	-1	-0.821	-0.911	7.791	0.176	0.176	0.000	0.000	0.000	0.000
8	A	6	PHE	0	0.019	-0.008	10.893	0.128	0.128	0.000	0.000	0.000	0.000
9	A	7	GLU	-1	-0.892	-0.942	14.491	0.232	0.232	0.000	0.000	0.000	0.000
10	A	8	ALA	0	0.003	-0.001	11.379	0.036	0.036	0.000	0.000	0.000	0.000
11	A	9	ALA	0	0.002	-0.011	12.906	0.055	0.055	0.000	0.000	0.000	0.000
12	A	10	VAL	0	-0.022	-0.009	14.127	0.000	0.000	0.000	0.000	0.000	0.000
13	A	11	ALA	0	0.010	0.016	16.264	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	12	TYR	0	0.021	0.001	14.034	-0.018	-0.018	0.000	0.000	0.000	0.000
15	A	13	VAL	0	-0.008	-0.009	16.364	-0.027	-0.027	0.000	0.000	0.000	0.000
16	A	14	ARG	1	0.904	0.953	19.051	-0.229	-0.229	0.000	0.000	0.000	0.000
17	A	15	SER	0	-0.053	-0.029	18.830	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	16	LEU	0	-0.018	-0.003	18.197	0.019	0.019	0.000	0.000	0.000	0.000
19	A	17	PRO	0	-0.007	0.010	21.381	-0.035	-0.035	0.000	0.000	0.000	0.000
20	A	18	LYS	1	0.853	0.894	24.512	-0.174	-0.174	0.000	0.000	0.000	0.000
21	A	19	GLU	-1	-0.857	-0.905	26.843	0.165	0.165	0.000	0.000	0.000	0.000
22	A	20	GLY	0	0.015	-0.001	22.939	0.023	0.023	0.000	0.000	0.000	0.000
23	A	21	PRO	0	-0.038	-0.016	18.893	-0.028	-0.028	0.000	0.000	0.000	0.000
24	A	22	VAL	0	-0.002	0.005	17.110	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	23	GLN	0	0.009	0.012	20.057	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	24	LEU	0	0.060	0.024	21.343	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	25	ASP	-1	-0.795	-0.891	23.656	0.065	0.065	0.000	0.000	0.000	0.000
28	A	26	ASN	0	0.045	-0.007	26.689	0.012	0.012	0.000	0.000	0.000	0.000
29	A	27	ALA	0	0.033	0.030	28.388	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	28	ALA	0	0.000	-0.004	22.984	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	29	LYS	1	0.843	0.913	24.172	-0.137	-0.137	0.000	0.000	0.000	0.000
32	A	30	LEU	0	-0.016	-0.009	25.678	0.001	0.001	0.000	0.000	0.000	0.000
33	A	31	GLN	0	0.046	0.044	22.985	0.004	0.004	0.000	0.000	0.000	0.000
34	A	32	PHE	0	-0.015	-0.012	17.716	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	33	TYR	0	0.010	0.001	22.579	0.000	0.000	0.000	0.000	0.000	0.000
36	A	34	SER	0	0.024	0.005	25.460	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	35	LEU	0	0.019	0.002	20.538	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	36	TYR	0	0.004	-0.004	21.238	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	37	LYS	1	0.775	0.895	22.856	-0.039	-0.039	0.000	0.000	0.000	0.000
40	A	38	GLN	0	-0.019	-0.016	24.846	0.005	0.005	0.000	0.000	0.000	0.000
41	A	39	ALA	0	-0.032	-0.021	20.917	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	40	THR	0	-0.077	-0.043	22.474	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	41	GLU	-1	-0.821	-0.881	24.661	0.040	0.040	0.000	0.000	0.000	0.000
44	A	42	GLY	0	-0.025	0.011	27.205	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	43	ASP	-1	-0.754	-0.876	28.819	-0.058	-0.058	0.000	0.000	0.000	0.000
46	A	44	VAL	0	-0.042	-0.009	31.642	0.007	0.007	0.000	0.000	0.000	0.000
47	A	45	THR	0	0.017	0.013	33.449	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	46	GLY	0	0.011	0.010	36.546	0.005	0.005	0.000	0.000	0.000	0.000
49	A	47	SER	0	-0.010	-0.013	39.454	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	48	GLN	0	-0.032	-0.028	39.284	0.003	0.003	0.000	0.000	0.000	0.000
51	A	49	PRO	0	-0.029	-0.001	37.972	0.001	0.001	0.000	0.000	0.000	0.000
52	A	50	TRP	0	0.066	0.025	41.248	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	51	ALA	0	0.031	0.005	42.514	0.003	0.003	0.000	0.000	0.000	0.000
54	A	52	VAL	0	0.015	0.010	42.844	0.002	0.002	0.000	0.000	0.000	0.000
55	A	53	GLN	0	0.004	0.013	40.474	0.002	0.002	0.000	0.000	0.000	0.000
56	A	54	VAL	0	0.021	0.008	38.057	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	55	GLU	-1	-0.852	-0.915	32.885	0.084	0.084	0.000	0.000	0.000	0.000
58	A	56	ALA	0	0.045	0.014	34.822	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	57	ARG	1	0.850	0.918	36.002	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	58	ALA	0	0.018	0.001	33.991	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	59	LYS	1	0.851	0.918	29.816	-0.091	-0.091	0.000	0.000	0.000	0.000
62	A	60	TRP	0	-0.018	-0.012	31.831	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	61	ASP	-1	-0.760	-0.859	33.869	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	62	ALA	0	-0.014	-0.002	29.341	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	63	TRP	0	0.010	-0.003	29.189	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	64	ASN	0	-0.002	0.000	30.475	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	65	SER	0	-0.086	-0.058	30.251	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	66	CYS	0	-0.067	-0.030	27.060	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	67	LYS	1	0.863	0.924	28.807	0.039	0.039	0.000	0.000	0.000	0.000
70	A	68	GLY	0	-0.002	-0.006	30.743	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	69	MET	0	-0.081	-0.009	22.271	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	70	LYS	1	0.874	0.919	22.421	0.254	0.254	0.000	0.000	0.000	0.000
73	A	71	SER	0	0.017	-0.001	22.481	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	72	GLU	-1	-0.762	-0.889	16.646	-0.225	-0.225	0.000	0.000	0.000	0.000
75	A	73	ASP	-1	-0.807	-0.894	18.520	-0.282	-0.282	0.000	0.000	0.000	0.000
76	A	74	ALA	0	0.021	0.012	19.866	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	75	LYS	1	0.873	0.920	16.310	0.162	0.162	0.000	0.000	0.000	0.000
78	A	76	ALA	0	-0.014	-0.021	15.021	0.007	0.007	0.000	0.000	0.000	0.000
79	A	77	ALA	0	-0.063	-0.034	15.636	-0.022	-0.022	0.000	0.000	0.000	0.000
80	A	78	TYR	0	0.030	0.031	16.227	0.003	0.003	0.000	0.000	0.000	0.000
81	A	79	VAL	0	0.005	-0.002	10.816	0.051	0.051	0.000	0.000	0.000	0.000
82	A	80	ARG	1	0.982	0.998	13.399	0.358	0.358	0.000	0.000	0.000	0.000
83	A	81	ARG	1	0.889	0.951	14.653	0.004	0.004	0.000	0.000	0.000	0.000
84	A	82	LEU	0	0.021	0.013	13.093	0.017	0.017	0.000	0.000	0.000	0.000
85	A	83	LEU	0	0.009	0.008	9.089	0.049	0.049	0.000	0.000	0.000	0.000
86	A	84	THR	0	-0.063	-0.045	12.641	0.005	0.005	0.000	0.000	0.000	0.000
87	A	85	LEU	0	-0.024	-0.009	15.607	0.009	0.009	0.000	0.000	0.000	0.000
88	A	86	LEU	0	0.016	0.015	12.417	0.014	0.014	0.000	0.000	0.000	0.000
89	A	87	ARG	1	0.962	0.988	8.724	0.399	0.399	0.000	0.000	0.000	0.000
90	A	88	SER	0	-0.078	-0.036	13.816	0.000	0.000	0.000	0.000	0.000	0.000
91	A	89	GLN	0	-0.017	-0.017	16.728	0.020	0.020	0.000	0.000	0.000	0.000
92	A	90	GLY	0	0.012	0.021	14.905	0.035	0.035	0.000	0.000	0.000	0.000
93	A	91	ILE	0	-0.029	-0.001	12.747	0.099	0.099	0.000	0.000	0.000	0.000
94	A	92	GLN	0	-0.007	-0.019	5.446	-0.226	-0.226	0.000	0.000	0.000	0.000
95	A	93	TRP	0	0.000	0.007	8.873	0.176	0.176	0.000	0.000	0.000	0.000
96	A	94	LYS	1	0.934	0.947	3.238	-11.907	-10.717	0.142	-0.641	-0.692	0.007
97	A	95	PRO	0	-0.002	0.023	5.801	-0.355	-0.355	0.000	0.000	0.000	0.000
98	A	96	GLY	0	0.012	0.007	6.704	0.647	0.647	0.000	0.000	0.000	0.000

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