FMO DATABASE

FMODB ID: 3JGKL

Calculation Name: 4IT7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IT7

Chain ID: A

ChEMBL ID:

UniProt ID: E9N3T6

Base Structure: X-ray

Registration Date: 2023-09-23

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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-742002.762266
FMO2-HF: Nuclear repulsion	701342.215181
FMO2-HF: Total energy	-40660.547085
FMO2-MP2: Total energy	-40777.98923

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:6:GLY)

Summations of interaction energy for fragment #1(A:6:GLY)

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.
-0.143	1.58	2.629	-2.04	-2.315	-0.001

Interaction energy analysis for fragmet #1(A:6:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.002

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	8	PHE	0	-0.072	-0.044	3.810	1.607	3.097	-0.019	-0.897	-0.574	0.002
4	A	9	SER	0	-0.001	0.013	7.212	-0.219	-0.219	0.000	0.000	0.000	0.000
5	A	10	THR	0	0.023	-0.001	9.540	-0.047	-0.047	0.000	0.000	0.000	0.000
6	A	11	LYS	1	0.917	0.972	12.932	-0.412	-0.412	0.000	0.000	0.000	0.000
7	A	12	ASP	-1	-0.832	-0.933	15.138	0.149	0.149	0.000	0.000	0.000	0.000
8	A	13	VAL	0	-0.016	0.000	18.908	0.007	0.007	0.000	0.000	0.000	0.000
9	A	14	ASN	0	0.004	0.011	20.964	-0.024	-0.024	0.000	0.000	0.000	0.000
10	A	15	ASP	-1	-0.851	-0.907	18.398	0.280	0.280	0.000	0.000	0.000	0.000
11	A	16	PRO	0	0.043	0.012	21.353	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	17	LYS	1	0.864	0.930	16.712	-0.259	-0.259	0.000	0.000	0.000	0.000
13	A	18	ILE	0	-0.023	-0.014	15.693	0.001	0.001	0.000	0.000	0.000	0.000
14	A	19	GLN	0	0.005	-0.020	19.547	-0.029	-0.029	0.000	0.000	0.000	0.000
15	A	20	ALA	0	-0.010	0.005	22.273	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	21	LEU	0	-0.034	-0.027	16.319	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	22	ALA	0	0.037	0.018	20.792	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	23	GLY	0	0.033	0.029	22.463	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	24	LYS	1	0.841	0.906	20.941	-0.125	-0.125	0.000	0.000	0.000	0.000
20	A	25	ALA	0	0.025	-0.003	21.009	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	26	LEU	0	0.002	0.008	23.041	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	27	GLN	0	-0.003	-0.002	26.565	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	28	ARG	1	0.906	0.958	23.427	-0.044	-0.044	0.000	0.000	0.000	0.000
24	A	29	ILE	0	-0.015	-0.001	24.210	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	30	ASN	0	0.025	0.003	27.235	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	31	ALA	0	-0.027	-0.016	29.254	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	32	ALA	0	0.003	0.005	27.972	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	33	SER	0	-0.048	-0.004	29.914	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	34	ASN	0	0.022	-0.014	31.523	0.002	0.002	0.000	0.000	0.000	0.000
30	A	35	ASP	-1	-0.897	-0.935	34.338	0.000	0.000	0.000	0.000	0.000	0.000
31	A	36	LEU	0	0.030	0.013	36.195	0.001	0.001	0.000	0.000	0.000	0.000
32	A	37	PHE	0	-0.033	0.006	38.028	0.002	0.002	0.000	0.000	0.000	0.000
33	A	38	GLN	0	0.008	0.013	34.729	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	39	GLN	0	-0.065	-0.046	30.996	0.000	0.000	0.000	0.000	0.000	0.000
35	A	40	THR	0	0.066	0.034	31.483	0.005	0.005	0.000	0.000	0.000	0.000
36	A	41	ILE	0	-0.017	-0.012	25.899	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	42	VAL	0	-0.018	-0.006	29.097	0.001	0.001	0.000	0.000	0.000	0.000
38	A	43	LYS	1	0.948	0.955	26.417	-0.053	-0.053	0.000	0.000	0.000	0.000
39	A	44	VAL	0	0.024	0.015	20.810	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	45	ILE	0	-0.046	-0.010	21.780	0.007	0.007	0.000	0.000	0.000	0.000
41	A	46	SER	0	-0.045	-0.048	17.747	0.014	0.014	0.000	0.000	0.000	0.000
42	A	47	ALA	0	0.053	0.014	16.092	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	48	LYS	1	0.910	0.979	11.000	0.061	0.061	0.000	0.000	0.000	0.000
44	A	49	THR	0	-0.018	-0.007	9.837	-0.035	-0.035	0.000	0.000	0.000	0.000
45	A	50	GLN	0	0.019	0.003	4.317	-0.086	0.099	-0.001	-0.033	-0.151	0.000
46	A	51	VAL	0	0.027	0.006	4.462	-0.888	-0.775	-0.001	-0.020	-0.093	0.000
47	A	52	VAL	0	-0.004	0.008	1.884	-0.334	-0.594	2.643	-1.005	-1.379	-0.002
48	A	53	ALA	0	0.029	0.013	3.786	-0.282	-0.087	0.007	-0.085	-0.118	-0.001
49	A	54	GLY	0	0.071	0.045	7.538	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	55	THR	0	-0.039	-0.017	7.986	0.203	0.203	0.000	0.000	0.000	0.000
51	A	56	ASN	0	-0.001	0.006	8.293	-0.145	-0.145	0.000	0.000	0.000	0.000
52	A	57	THR	0	0.020	-0.001	9.530	0.185	0.185	0.000	0.000	0.000	0.000
53	A	58	VAL	0	-0.060	-0.029	11.617	-0.082	-0.082	0.000	0.000	0.000	0.000
54	A	59	LEU	0	0.001	-0.012	13.919	0.040	0.040	0.000	0.000	0.000	0.000
55	A	60	GLU	-1	-0.880	-0.900	17.428	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	61	LEU	0	-0.014	-0.010	20.220	0.015	0.015	0.000	0.000	0.000	0.000
57	A	62	LEU	0	0.005	0.006	23.520	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	63	ILE	0	0.000	-0.011	26.718	0.006	0.006	0.000	0.000	0.000	0.000
59	A	64	ALA	0	-0.009	-0.016	29.376	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	65	PRO	0	0.037	0.043	33.185	0.002	0.002	0.000	0.000	0.000	0.000
61	A	66	THR	0	0.034	0.013	35.513	0.002	0.002	0.000	0.000	0.000	0.000
62	A	67	SER	0	-0.073	-0.054	38.112	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	68	CYS	-1	-0.792	-0.897	38.516	0.020	0.020	0.000	0.000	0.000	0.000
64	A	69	ARG	1	0.816	0.933	39.175	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	70	LYS	1	0.889	0.918	33.602	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	71	ASN	0	-0.098	-0.043	38.894	0.000	0.000	0.000	0.000	0.000	0.000
67	A	72	GLU	-1	-0.924	-0.981	41.372	0.011	0.011	0.000	0.000	0.000	0.000
68	A	73	THR	0	-0.055	-0.037	41.425	0.001	0.001	0.000	0.000	0.000	0.000
69	A	74	SER	0	0.098	0.053	39.604	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	75	ALA	0	-0.052	-0.029	42.083	0.001	0.001	0.000	0.000	0.000	0.000
71	A	76	GLY	0	-0.050	-0.027	41.126	0.001	0.001	0.000	0.000	0.000	0.000
72	A	77	ASN	0	-0.024	0.010	36.122	0.001	0.001	0.000	0.000	0.000	0.000
73	A	78	CYS	-1	-0.739	-0.854	36.369	0.023	0.023	0.000	0.000	0.000	0.000
74	A	79	GLU	-1	-1.033	-1.020	36.438	0.037	0.037	0.000	0.000	0.000	0.000
75	A	80	ALA	0	-0.023	-0.018	35.098	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	81	VAL	0	-0.011	0.003	37.080	0.000	0.000	0.000	0.000	0.000	0.000
77	A	82	SER	0	-0.001	-0.023	38.997	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	83	ASN	0	-0.094	0.020	39.683	0.000	0.000	0.000	0.000	0.000	0.000
79	A	84	GLY	0	0.103	0.026	37.386	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	85	THR	0	-0.017	-0.043	34.679	0.002	0.002	0.000	0.000	0.000	0.000
81	A	86	LYS	1	0.901	0.952	31.405	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	87	GLN	0	0.007	-0.001	28.480	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	88	ILE	0	0.007	0.007	23.205	0.008	0.008	0.000	0.000	0.000	0.000
84	A	89	CYS	0	-0.075	-0.015	22.820	0.001	0.001	0.000	0.000	0.000	0.000
85	A	90	THR	0	0.051	0.028	17.309	0.019	0.019	0.000	0.000	0.000	0.000
86	A	91	VAL	0	-0.016	-0.008	18.515	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	92	ALA	0	-0.031	-0.012	13.656	0.018	0.018	0.000	0.000	0.000	0.000
88	A	93	ILE	0	0.016	0.011	14.477	-0.018	-0.018	0.000	0.000	0.000	0.000
89	A	94	TRP	0	-0.042	-0.022	10.105	0.023	0.023	0.000	0.000	0.000	0.000
90	A	95	GLU	-1	-0.840	-0.935	12.734	0.253	0.253	0.000	0.000	0.000	0.000
91	A	96	LYS	1	0.882	0.956	12.594	0.087	0.087	0.000	0.000	0.000	0.000
92	A	97	PRO	0	0.018	0.005	14.260	-0.026	-0.026	0.000	0.000	0.000	0.000
93	A	98	TRP	0	0.022	0.007	11.205	0.015	0.015	0.000	0.000	0.000	0.000
94	A	99	GLU	-1	-0.951	-0.975	17.205	-0.041	-0.041	0.000	0.000	0.000	0.000
95	A	100	ASN	0	-0.071	-0.031	19.363	0.003	0.003	0.000	0.000	0.000	0.000
96	A	101	PHE	0	-0.003	0.011	15.491	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	102	GLU	-1	-0.831	-0.922	17.259	0.135	0.135	0.000	0.000	0.000	0.000
98	A	103	GLU	-1	-0.917	-0.948	16.643	-0.069	-0.069	0.000	0.000	0.000	0.000
99	A	104	ILE	0	-0.034	-0.030	16.941	0.009	0.009	0.000	0.000	0.000	0.000
100	A	105	THR	0	0.031	0.010	17.155	-0.020	-0.020	0.000	0.000	0.000	0.000
101	A	106	ILE	0	-0.016	-0.017	18.794	0.008	0.008	0.000	0.000	0.000	0.000
102	A	107	LYS	1	0.900	0.944	15.720	0.123	0.123	0.000	0.000	0.000	0.000
103	A	108	GLU	-1	-0.846	-0.920	19.914	-0.083	-0.083	0.000	0.000	0.000	0.000
104	A	110	LYS	1	0.927	0.973	23.024	0.039	0.039	0.000	0.000	0.000	0.000
105	A	111	SER	0	0.021	-0.002	27.905	0.006	0.006	0.000	0.000	0.000	0.000
106	A	112	ALA	0	-0.010	0.007	28.713	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:GLY)