FMO DATABASE

FMODB ID: N931Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-681828.817691
FMO2-HF: Nuclear repulsion	643717.375875
FMO2-HF: Total energy	-38111.441816
FMO2-MP2: Total energy	-38222.789491

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.
-20.131	-17.967	3.034	-2.295	-2.903	0.021

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 : -0.020 / q_NPA : -0.023

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	-0.021	0.008	3.854	-0.096	1.253	-0.010	-0.696	-0.643	0.000
4	A	2	SER	0	-0.046	-0.042	6.437	-0.170	-0.170	0.000	0.000	0.000	0.000
5	A	3	ALA	0	0.043	0.005	9.896	0.209	0.209	0.000	0.000	0.000	0.000
6	A	4	ALA	0	0.034	0.017	10.921	0.129	0.129	0.000	0.000	0.000	0.000
7	A	5	ASP	-1	-0.811	-0.889	7.424	-0.191	-0.191	0.000	0.000	0.000	0.000
8	A	6	PHE	0	0.026	0.001	10.712	0.155	0.155	0.000	0.000	0.000	0.000
9	A	7	GLU	-1	-0.889	-0.943	14.315	0.171	0.171	0.000	0.000	0.000	0.000
10	A	8	ALA	0	0.011	0.012	11.129	0.056	0.056	0.000	0.000	0.000	0.000
11	A	9	ALA	0	0.005	-0.012	12.561	0.079	0.079	0.000	0.000	0.000	0.000
12	A	10	VAL	0	-0.015	-0.005	13.829	0.008	0.008	0.000	0.000	0.000	0.000
13	A	11	ALA	0	0.000	0.000	15.845	0.001	0.001	0.000	0.000	0.000	0.000
14	A	12	TYR	0	0.031	0.020	13.747	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	13	VAL	0	0.000	-0.009	15.950	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	14	ARG	1	0.890	0.950	18.548	-0.222	-0.222	0.000	0.000	0.000	0.000
17	A	15	SER	0	-0.037	-0.036	18.341	0.008	0.008	0.000	0.000	0.000	0.000
18	A	16	LEU	0	-0.013	0.008	17.630	0.027	0.027	0.000	0.000	0.000	0.000
19	A	17	PRO	0	-0.024	0.002	20.751	-0.040	-0.040	0.000	0.000	0.000	0.000
20	A	18	LYS	1	0.825	0.885	24.067	-0.184	-0.184	0.000	0.000	0.000	0.000
21	A	19	GLU	-1	-0.840	-0.907	26.516	0.173	0.173	0.000	0.000	0.000	0.000
22	A	20	GLY	0	0.024	0.009	22.973	0.024	0.024	0.000	0.000	0.000	0.000
23	A	21	PRO	0	-0.030	-0.012	18.859	-0.033	-0.033	0.000	0.000	0.000	0.000
24	A	22	VAL	0	0.004	0.006	17.335	0.008	0.008	0.000	0.000	0.000	0.000
25	A	23	GLN	0	-0.008	0.005	20.256	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	24	LEU	0	0.039	0.025	21.225	-0.025	-0.025	0.000	0.000	0.000	0.000
27	A	25	ASP	-1	-0.743	-0.877	23.621	0.053	0.053	0.000	0.000	0.000	0.000
28	A	26	ASN	0	0.032	-0.003	26.349	0.018	0.018	0.000	0.000	0.000	0.000
29	A	27	ALA	0	0.025	0.025	28.223	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	28	ALA	0	0.003	-0.003	22.765	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	29	LYS	1	0.827	0.906	23.867	-0.135	-0.135	0.000	0.000	0.000	0.000
32	A	30	LEU	0	-0.014	-0.002	25.488	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	31	GLN	0	0.042	0.036	22.917	0.002	0.002	0.000	0.000	0.000	0.000
34	A	32	PHE	0	-0.013	-0.017	17.598	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	33	TYR	0	0.000	-0.002	22.352	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	34	SER	0	0.022	-0.002	25.275	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	35	LEU	0	0.008	0.003	20.399	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	36	TYR	0	0.007	-0.002	21.041	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	37	LYS	1	0.772	0.892	22.694	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	38	GLN	0	-0.007	-0.013	25.009	0.009	0.009	0.000	0.000	0.000	0.000
41	A	39	ALA	0	-0.037	-0.020	20.727	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	40	THR	0	-0.078	-0.039	22.105	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	41	GLU	-1	-0.825	-0.890	24.446	0.022	0.022	0.000	0.000	0.000	0.000
44	A	42	GLY	0	-0.017	0.016	27.165	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	43	ASP	-1	-0.744	-0.866	28.554	-0.079	-0.079	0.000	0.000	0.000	0.000
46	A	44	VAL	0	-0.026	0.003	31.426	0.008	0.008	0.000	0.000	0.000	0.000
47	A	45	THR	0	0.010	0.000	33.406	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	46	GLY	0	0.021	0.015	36.479	0.006	0.006	0.000	0.000	0.000	0.000
49	A	47	SER	0	-0.018	-0.011	39.311	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	48	GLN	0	-0.011	-0.020	39.209	0.005	0.005	0.000	0.000	0.000	0.000
51	A	49	PRO	0	-0.023	0.001	37.807	0.001	0.001	0.000	0.000	0.000	0.000
52	A	50	TRP	0	0.058	0.022	41.056	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	51	ALA	0	0.022	0.002	42.336	0.003	0.003	0.000	0.000	0.000	0.000
54	A	52	VAL	0	0.033	0.018	42.445	0.002	0.002	0.000	0.000	0.000	0.000
55	A	53	GLN	0	-0.006	0.005	40.149	0.002	0.002	0.000	0.000	0.000	0.000
56	A	54	VAL	0	0.026	0.006	37.550	0.000	0.000	0.000	0.000	0.000	0.000
57	A	55	GLU	-1	-0.854	-0.907	32.860	0.076	0.076	0.000	0.000	0.000	0.000
58	A	56	ALA	0	0.045	0.012	34.242	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	57	ARG	1	0.801	0.899	35.535	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	58	ALA	0	0.022	0.014	33.700	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	59	LYS	1	0.867	0.914	29.353	-0.083	-0.083	0.000	0.000	0.000	0.000
62	A	60	TRP	0	-0.009	-0.007	31.576	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	61	ASP	-1	-0.760	-0.876	33.767	-0.023	-0.023	0.000	0.000	0.000	0.000
64	A	62	ALA	0	-0.017	0.000	29.284	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	63	TRP	0	0.003	-0.005	29.223	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	64	ASN	0	0.003	-0.004	30.435	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	65	SER	0	-0.083	-0.052	30.062	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	66	CYS	0	-0.063	-0.023	26.956	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	67	LYS	1	0.861	0.930	28.726	0.053	0.053	0.000	0.000	0.000	0.000
70	A	68	GLY	0	-0.010	-0.003	31.013	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	69	MET	0	-0.070	-0.014	22.350	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	70	LYS	1	0.865	0.912	22.288	0.314	0.314	0.000	0.000	0.000	0.000
73	A	71	SER	0	0.026	-0.004	22.429	-0.025	-0.025	0.000	0.000	0.000	0.000
74	A	72	GLU	-1	-0.781	-0.892	16.832	-0.313	-0.313	0.000	0.000	0.000	0.000
75	A	73	ASP	-1	-0.802	-0.881	18.468	-0.359	-0.359	0.000	0.000	0.000	0.000
76	A	74	ALA	0	0.032	0.012	19.742	-0.013	-0.013	0.000	0.000	0.000	0.000
77	A	75	LYS	1	0.859	0.911	16.389	0.243	0.243	0.000	0.000	0.000	0.000
78	A	76	ALA	0	-0.002	-0.011	14.946	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	77	ALA	0	-0.078	-0.044	15.575	-0.039	-0.039	0.000	0.000	0.000	0.000
80	A	78	TYR	0	0.027	0.017	15.919	0.001	0.001	0.000	0.000	0.000	0.000
81	A	79	VAL	0	0.024	0.011	10.525	0.063	0.063	0.000	0.000	0.000	0.000
82	A	80	ARG	1	0.963	0.996	13.101	0.448	0.448	0.000	0.000	0.000	0.000
83	A	81	ARG	1	0.898	0.970	14.460	0.036	0.036	0.000	0.000	0.000	0.000
84	A	82	LEU	0	0.020	0.013	12.726	0.028	0.028	0.000	0.000	0.000	0.000
85	A	83	LEU	0	-0.007	-0.008	8.741	0.058	0.058	0.000	0.000	0.000	0.000
86	A	84	THR	0	-0.061	-0.044	12.580	0.005	0.005	0.000	0.000	0.000	0.000
87	A	85	LEU	0	-0.034	-0.012	15.768	0.016	0.016	0.000	0.000	0.000	0.000
88	A	86	LEU	0	0.031	0.028	12.585	0.010	0.010	0.000	0.000	0.000	0.000
89	A	87	ARG	1	0.986	0.998	8.466	0.381	0.381	0.000	0.000	0.000	0.000
90	A	88	SER	0	-0.105	-0.063	13.999	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	89	GLN	0	0.001	-0.007	16.837	0.032	0.032	0.000	0.000	0.000	0.000
92	A	90	GLY	0	0.013	0.020	15.309	0.036	0.036	0.000	0.000	0.000	0.000
93	A	91	ILE	0	-0.048	-0.016	12.846	0.110	0.110	0.000	0.000	0.000	0.000
94	A	92	GLN	0	0.014	0.002	4.839	-0.503	-0.503	0.000	0.000	0.000	0.000
95	A	93	TRP	0	-0.009	-0.007	8.501	0.204	0.204	0.000	0.000	0.000	0.000
96	A	94	LYS	1	0.900	0.931	2.611	-21.172	-20.357	3.044	-1.599	-2.260	0.021
97	A	95	PRO	0	0.013	0.035	5.447	-0.385	-0.385	0.000	0.000	0.000	0.000
98	A	96	GLY	0	0.004	0.002	6.386	0.909	0.909	0.000	0.000	0.000	0.000

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