FMO DATABASE

FMODB ID: G6QN1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-681890.282491
FMO2-HF: Nuclear repulsion	643779.580085
FMO2-HF: Total energy	-38110.702406
FMO2-MP2: Total energy	-38222.135097

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.
-8.368	-6.073	0.002	-1.265	-1.033	0.001

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 : -0.019 / 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	-0.002	0.012	3.888	-0.590	1.193	-0.017	-1.014	-0.752	-0.001
4	A	2	SER	0	0.011	0.007	6.542	-0.175	-0.175	0.000	0.000	0.000	0.000
5	A	3	ALA	0	0.056	0.016	9.841	0.188	0.188	0.000	0.000	0.000	0.000
6	A	4	ALA	0	0.009	0.005	10.590	0.129	0.129	0.000	0.000	0.000	0.000
7	A	5	ASP	-1	-0.841	-0.915	7.825	-0.141	-0.141	0.000	0.000	0.000	0.000
8	A	6	PHE	0	0.001	-0.019	10.842	0.135	0.135	0.000	0.000	0.000	0.000
9	A	7	GLU	-1	-0.885	-0.935	14.437	0.175	0.175	0.000	0.000	0.000	0.000
10	A	8	ALA	0	0.007	-0.001	11.296	0.043	0.043	0.000	0.000	0.000	0.000
11	A	9	ALA	0	-0.006	-0.013	12.883	0.063	0.063	0.000	0.000	0.000	0.000
12	A	10	VAL	0	-0.032	-0.013	14.060	0.013	0.013	0.000	0.000	0.000	0.000
13	A	11	ALA	0	0.012	0.016	16.205	0.001	0.001	0.000	0.000	0.000	0.000
14	A	12	TYR	0	-0.003	-0.008	13.678	0.047	0.047	0.000	0.000	0.000	0.000
15	A	13	VAL	0	-0.006	-0.011	16.294	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	14	ARG	1	0.902	0.953	18.980	-0.189	-0.189	0.000	0.000	0.000	0.000
17	A	15	SER	0	-0.053	-0.028	18.721	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	16	LEU	0	-0.022	0.001	18.215	0.023	0.023	0.000	0.000	0.000	0.000
19	A	17	PRO	0	0.001	0.011	21.381	-0.035	-0.035	0.000	0.000	0.000	0.000
20	A	18	LYS	1	0.842	0.897	24.512	-0.166	-0.166	0.000	0.000	0.000	0.000
21	A	19	GLU	-1	-0.865	-0.913	26.825	0.162	0.162	0.000	0.000	0.000	0.000
22	A	20	GLY	0	0.029	0.003	22.911	0.021	0.021	0.000	0.000	0.000	0.000
23	A	21	PRO	0	-0.033	-0.017	19.028	-0.027	-0.027	0.000	0.000	0.000	0.000
24	A	22	VAL	0	-0.013	0.004	17.104	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	23	GLN	0	0.013	0.017	20.025	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	24	LEU	0	0.073	0.028	21.276	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	25	ASP	-1	-0.823	-0.910	23.620	0.056	0.056	0.000	0.000	0.000	0.000
28	A	26	ASN	0	0.046	-0.014	26.652	0.009	0.009	0.000	0.000	0.000	0.000
29	A	27	ALA	0	0.034	0.031	28.265	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	28	ALA	0	0.013	0.005	22.978	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	29	LYS	1	0.846	0.923	24.106	-0.126	-0.126	0.000	0.000	0.000	0.000
32	A	30	LEU	0	0.005	0.004	25.611	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	31	GLN	0	0.065	0.055	22.820	0.006	0.006	0.000	0.000	0.000	0.000
34	A	32	PHE	0	-0.020	-0.017	17.666	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	33	TYR	0	0.014	0.004	22.515	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	34	SER	0	-0.023	-0.016	25.396	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	35	LEU	0	0.029	0.006	20.467	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	36	TYR	0	-0.004	-0.004	21.274	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	37	LYS	1	0.818	0.917	22.797	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	38	GLN	0	-0.022	-0.016	24.755	0.006	0.006	0.000	0.000	0.000	0.000
41	A	39	ALA	0	-0.035	-0.025	20.884	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	40	THR	0	-0.079	-0.044	22.459	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	41	GLU	-1	-0.858	-0.903	24.612	0.017	0.017	0.000	0.000	0.000	0.000
44	A	42	GLY	0	-0.024	0.012	27.167	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	43	ASP	-1	-0.817	-0.923	28.775	-0.075	-0.075	0.000	0.000	0.000	0.000
46	A	44	VAL	0	-0.042	-0.009	31.596	0.006	0.006	0.000	0.000	0.000	0.000
47	A	45	THR	0	0.010	0.011	33.398	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	46	GLY	0	0.010	0.004	36.494	0.005	0.005	0.000	0.000	0.000	0.000
49	A	47	SER	0	-0.013	-0.014	39.400	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	48	GLN	0	-0.027	-0.021	39.295	0.002	0.002	0.000	0.000	0.000	0.000
51	A	49	PRO	0	-0.040	-0.003	37.913	0.002	0.002	0.000	0.000	0.000	0.000
52	A	50	TRP	0	0.077	0.033	41.186	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	51	ALA	0	0.027	-0.002	42.454	0.003	0.003	0.000	0.000	0.000	0.000
54	A	52	VAL	0	0.008	0.010	42.778	0.002	0.002	0.000	0.000	0.000	0.000
55	A	53	GLN	0	0.003	0.012	40.449	0.002	0.002	0.000	0.000	0.000	0.000
56	A	54	VAL	0	0.024	0.010	37.732	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	55	GLU	-1	-0.923	-0.971	32.849	0.068	0.068	0.000	0.000	0.000	0.000
58	A	56	ALA	0	0.029	0.007	34.756	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	57	ARG	1	0.873	0.939	35.938	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	58	ALA	0	0.025	0.003	33.931	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	59	LYS	1	0.919	0.967	29.905	-0.070	-0.070	0.000	0.000	0.000	0.000
62	A	60	TRP	0	-0.007	-0.004	31.770	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	61	ASP	-1	-0.763	-0.878	33.811	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	62	ALA	0	-0.027	-0.010	29.268	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	63	TRP	0	0.007	-0.006	29.061	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	64	ASN	0	-0.005	0.001	30.419	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	65	SER	0	-0.091	-0.056	30.060	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	66	CYS	0	-0.045	-0.019	26.907	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	67	LYS	1	0.945	0.977	28.762	0.047	0.047	0.000	0.000	0.000	0.000
70	A	68	GLY	0	0.001	-0.005	30.705	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	69	MET	0	-0.079	-0.006	22.463	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	70	LYS	1	0.908	0.951	22.246	0.270	0.270	0.000	0.000	0.000	0.000
73	A	71	SER	0	0.011	-0.002	22.421	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	72	GLU	-1	-0.775	-0.912	16.460	-0.303	-0.303	0.000	0.000	0.000	0.000
75	A	73	ASP	-1	-0.830	-0.913	18.486	-0.313	-0.313	0.000	0.000	0.000	0.000
76	A	74	ALA	0	0.008	0.008	19.826	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	75	LYS	1	0.870	0.925	16.307	0.208	0.208	0.000	0.000	0.000	0.000
78	A	76	ALA	0	0.002	-0.012	14.983	0.002	0.002	0.000	0.000	0.000	0.000
79	A	77	ALA	0	-0.056	-0.029	15.590	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	78	TYR	0	0.016	0.026	16.163	0.009	0.009	0.000	0.000	0.000	0.000
81	A	79	VAL	0	0.017	0.001	10.725	0.056	0.056	0.000	0.000	0.000	0.000
82	A	80	ARG	1	0.988	1.000	13.340	0.365	0.365	0.000	0.000	0.000	0.000
83	A	81	ARG	1	0.862	0.927	14.602	0.029	0.029	0.000	0.000	0.000	0.000
84	A	82	LEU	0	0.027	0.019	12.901	0.022	0.022	0.000	0.000	0.000	0.000
85	A	83	LEU	0	0.020	0.010	9.083	0.057	0.057	0.000	0.000	0.000	0.000
86	A	84	THR	0	-0.062	-0.037	12.602	0.023	0.023	0.000	0.000	0.000	0.000
87	A	85	LEU	0	-0.043	-0.011	15.567	0.017	0.017	0.000	0.000	0.000	0.000
88	A	86	LEU	0	0.012	0.008	12.073	0.019	0.019	0.000	0.000	0.000	0.000
89	A	87	ARG	1	0.963	0.988	8.875	0.302	0.302	0.000	0.000	0.000	0.000
90	A	88	SER	0	-0.079	-0.035	13.778	0.006	0.006	0.000	0.000	0.000	0.000
91	A	89	GLN	0	0.003	-0.004	16.692	0.016	0.016	0.000	0.000	0.000	0.000
92	A	90	GLY	0	0.008	0.017	14.873	0.033	0.033	0.000	0.000	0.000	0.000
93	A	91	ILE	0	-0.021	0.005	12.608	0.098	0.098	0.000	0.000	0.000	0.000
94	A	92	GLN	0	-0.009	-0.022	5.334	-0.291	-0.291	0.000	0.000	0.000	0.000
95	A	93	TRP	0	0.020	0.010	8.798	0.108	0.108	0.000	0.000	0.000	0.000
96	A	94	LYS	1	0.934	0.951	3.648	-8.615	-8.103	0.019	-0.251	-0.281	0.002
97	A	95	PRO	0	0.011	0.021	5.488	-0.350	-0.350	0.000	0.000	0.000	0.000
98	A	96	GLY	0	0.009	0.006	6.650	0.529	0.529	0.000	0.000	0.000	0.000

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