FMO DATABASE

FMODB ID: JQK99

Calculation Name: 5FD7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5FD7

Chain ID: A

ChEMBL ID:

UniProt ID: P39929

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:

Apendix: None

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	123
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-763891.77647
FMO2-HF: Nuclear repulsion	713798.087887
FMO2-HF: Total energy	-50093.688583
FMO2-MP2: Total energy	-50235.943119

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:18:SER)

Summations of interaction energy for fragment #1(A:18: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.
-9.81	-2.8	2.252	-3.725	-5.537	0.014

Interaction energy analysis for fragmet #1(A:18:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.012

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	20	THR	0	0.067	0.028	2.654	-1.164	1.985	0.380	-1.603	-1.925	-0.002
4	A	21	LYS	1	0.964	0.984	2.329	-9.580	-6.093	1.871	-2.009	-3.349	0.016
5	A	22	ALA	0	-0.018	-0.004	4.034	-0.283	0.091	0.001	-0.113	-0.263	0.000
6	A	23	ILE	0	0.060	0.031	5.731	0.705	0.705	0.000	0.000	0.000	0.000
7	A	24	VAL	0	0.026	0.014	7.775	0.215	0.215	0.000	0.000	0.000	0.000
8	A	25	ARG	1	0.944	0.974	6.789	0.323	0.323	0.000	0.000	0.000	0.000
9	A	26	LEU	0	0.023	0.016	9.725	0.097	0.097	0.000	0.000	0.000	0.000
10	A	27	ARG	1	0.906	0.931	11.746	0.496	0.496	0.000	0.000	0.000	0.000
11	A	28	GLU	-1	-0.938	-0.961	12.878	0.343	0.343	0.000	0.000	0.000	0.000
12	A	29	HIS	0	-0.030	-0.028	12.545	0.077	0.077	0.000	0.000	0.000	0.000
13	A	30	ILE	0	0.047	0.015	15.433	0.035	0.035	0.000	0.000	0.000	0.000
14	A	31	ASN	0	0.000	0.021	17.373	0.023	0.023	0.000	0.000	0.000	0.000
15	A	32	LEU	0	-0.026	-0.005	17.739	0.022	0.022	0.000	0.000	0.000	0.000
16	A	33	LEU	0	-0.046	-0.020	18.922	0.019	0.019	0.000	0.000	0.000	0.000
17	A	34	SER	0	0.043	-0.002	21.459	0.016	0.016	0.000	0.000	0.000	0.000
18	A	35	LYS	1	0.965	0.987	23.196	0.018	0.018	0.000	0.000	0.000	0.000
19	A	36	LYS	1	0.924	0.962	23.880	0.114	0.114	0.000	0.000	0.000	0.000
20	A	37	GLN	0	0.011	-0.008	25.815	0.008	0.008	0.000	0.000	0.000	0.000
21	A	38	SER	0	-0.016	-0.002	27.624	0.009	0.009	0.000	0.000	0.000	0.000
22	A	39	HIS	0	0.025	0.008	29.320	0.000	0.000	0.000	0.000	0.000	0.000
23	A	40	LEU	0	-0.017	-0.016	28.704	0.003	0.003	0.000	0.000	0.000	0.000
24	A	41	ARG	1	0.903	0.928	30.296	0.122	0.122	0.000	0.000	0.000	0.000
25	A	42	THR	0	0.015	0.017	33.718	0.005	0.005	0.000	0.000	0.000	0.000
26	A	43	GLN	0	-0.052	-0.028	33.076	0.001	0.001	0.000	0.000	0.000	0.000
27	A	44	ILE	0	-0.024	-0.008	34.173	0.003	0.003	0.000	0.000	0.000	0.000
28	A	45	THR	0	0.063	0.030	37.865	0.001	0.001	0.000	0.000	0.000	0.000
29	A	46	ASN	0	-0.009	0.005	39.816	0.002	0.002	0.000	0.000	0.000	0.000
30	A	47	GLN	0	-0.035	-0.035	40.714	0.003	0.003	0.000	0.000	0.000	0.000
31	A	48	GLU	-1	-0.945	-0.981	42.219	-0.049	-0.049	0.000	0.000	0.000	0.000
32	A	49	ASN	0	0.018	-0.007	43.734	0.004	0.004	0.000	0.000	0.000	0.000
33	A	50	GLU	-1	-0.901	-0.934	44.323	-0.032	-0.032	0.000	0.000	0.000	0.000
34	A	51	ALA	0	-0.018	-0.024	46.792	0.002	0.002	0.000	0.000	0.000	0.000
35	A	52	ARG	1	0.975	0.995	48.478	0.038	0.038	0.000	0.000	0.000	0.000
36	A	53	ILE	0	0.022	0.006	50.130	0.002	0.002	0.000	0.000	0.000	0.000
37	A	54	PHE	0	-0.003	0.006	49.017	0.002	0.002	0.000	0.000	0.000	0.000
38	A	55	LEU	0	-0.056	-0.018	52.968	0.000	0.000	0.000	0.000	0.000	0.000
39	A	56	THR	0	-0.023	-0.021	54.785	0.001	0.001	0.000	0.000	0.000	0.000
40	A	57	LYS	1	0.974	0.994	54.251	0.019	0.019	0.000	0.000	0.000	0.000
41	A	58	GLY	0	-0.044	-0.021	57.065	0.001	0.001	0.000	0.000	0.000	0.000
42	A	59	ASN	0	0.034	0.024	56.497	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	60	LYS	1	1.056	1.008	54.611	0.037	0.037	0.000	0.000	0.000	0.000
44	A	61	VAL	0	0.005	0.003	52.905	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	62	MET	0	0.022	0.025	50.264	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	63	ALA	0	0.075	0.040	49.538	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	64	LYS	1	0.904	0.954	48.477	0.049	0.049	0.000	0.000	0.000	0.000
48	A	65	ASN	0	0.004	-0.018	47.306	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	66	ALA	0	0.033	0.035	45.181	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	67	LEU	0	0.029	0.005	43.723	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	68	LYS	1	0.898	0.949	42.851	0.056	0.056	0.000	0.000	0.000	0.000
52	A	69	LYS	1	0.940	0.984	39.951	0.039	0.039	0.000	0.000	0.000	0.000
53	A	70	LYS	1	0.859	0.918	39.185	0.072	0.072	0.000	0.000	0.000	0.000
54	A	71	LYS	1	0.958	0.977	38.266	0.089	0.089	0.000	0.000	0.000	0.000
55	A	72	THR	0	-0.065	-0.032	36.781	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	73	ILE	0	-0.007	0.001	34.257	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	74	GLU	-1	-0.774	-0.876	33.516	-0.093	-0.093	0.000	0.000	0.000	0.000
58	A	75	GLN	0	-0.004	-0.006	32.974	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	76	LEU	0	-0.020	0.000	28.833	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	77	LEU	0	0.022	0.007	28.709	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	78	SER	0	0.006	0.018	28.355	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	79	LYS	1	1.000	0.989	26.573	0.154	0.154	0.000	0.000	0.000	0.000
63	A	80	VAL	0	-0.044	-0.008	24.077	-0.021	-0.021	0.000	0.000	0.000	0.000
64	A	81	GLU	-1	-0.773	-0.881	23.594	-0.172	-0.172	0.000	0.000	0.000	0.000
65	A	82	GLY	0	0.039	0.031	23.912	-0.019	-0.019	0.000	0.000	0.000	0.000
66	A	83	THR	0	-0.060	-0.037	19.025	-0.036	-0.036	0.000	0.000	0.000	0.000
67	A	84	MET	0	-0.026	-0.018	19.306	-0.037	-0.037	0.000	0.000	0.000	0.000
68	A	85	GLU	-1	-0.816	-0.881	19.460	-0.376	-0.376	0.000	0.000	0.000	0.000
69	A	86	SER	0	-0.025	-0.017	18.529	-0.037	-0.037	0.000	0.000	0.000	0.000
70	A	87	MET	0	-0.075	-0.046	15.029	-0.070	-0.070	0.000	0.000	0.000	0.000
71	A	88	GLU	-1	-0.903	-0.957	15.189	-0.417	-0.417	0.000	0.000	0.000	0.000
72	A	89	GLN	0	-0.041	-0.026	17.028	-0.076	-0.076	0.000	0.000	0.000	0.000
73	A	90	GLN	0	-0.027	-0.011	12.422	-0.192	-0.192	0.000	0.000	0.000	0.000
74	A	91	LEU	0	-0.027	-0.009	11.298	-0.195	-0.195	0.000	0.000	0.000	0.000
75	A	92	PHE	0	0.029	0.027	13.301	-0.073	-0.073	0.000	0.000	0.000	0.000
76	A	93	SER	0	0.005	-0.009	13.958	0.023	0.023	0.000	0.000	0.000	0.000
77	A	94	ILE	0	-0.050	-0.025	8.057	-0.164	-0.164	0.000	0.000	0.000	0.000
78	A	95	GLU	-1	-0.849	-0.918	11.008	-0.694	-0.694	0.000	0.000	0.000	0.000
79	A	96	SER	0	-0.008	0.011	12.608	0.088	0.088	0.000	0.000	0.000	0.000
80	A	97	ALA	0	0.013	-0.005	10.983	0.055	0.055	0.000	0.000	0.000	0.000
81	A	98	ASN	0	-0.061	-0.038	8.379	-0.253	-0.253	0.000	0.000	0.000	0.000
82	A	99	LEU	0	0.059	0.036	11.054	0.105	0.105	0.000	0.000	0.000	0.000
83	A	100	ASN	0	-0.013	0.006	14.578	0.065	0.065	0.000	0.000	0.000	0.000
84	A	101	LEU	0	0.006	0.005	9.202	0.062	0.062	0.000	0.000	0.000	0.000
85	A	102	GLU	-1	-0.946	-0.977	12.609	-0.300	-0.300	0.000	0.000	0.000	0.000
86	A	103	THR	0	-0.038	-0.021	14.785	0.082	0.082	0.000	0.000	0.000	0.000
87	A	104	MET	0	0.033	0.006	15.626	0.062	0.062	0.000	0.000	0.000	0.000
88	A	105	ARG	1	0.941	0.972	8.805	0.590	0.590	0.000	0.000	0.000	0.000
89	A	106	ALA	0	0.028	0.036	16.629	0.049	0.049	0.000	0.000	0.000	0.000
90	A	107	MET	0	0.000	-0.008	19.525	0.023	0.023	0.000	0.000	0.000	0.000
91	A	108	GLN	0	-0.016	-0.018	18.405	0.028	0.028	0.000	0.000	0.000	0.000
92	A	109	GLU	-1	-0.910	-0.955	19.812	-0.042	-0.042	0.000	0.000	0.000	0.000
93	A	110	GLY	0	0.016	0.008	21.574	0.022	0.022	0.000	0.000	0.000	0.000
94	A	111	ALA	0	0.010	0.004	24.162	0.013	0.013	0.000	0.000	0.000	0.000
95	A	112	LYS	1	0.823	0.901	18.926	0.100	0.100	0.000	0.000	0.000	0.000
96	A	113	ALA	0	0.024	0.020	25.714	0.012	0.012	0.000	0.000	0.000	0.000
97	A	114	MET	0	0.026	0.011	27.700	0.009	0.009	0.000	0.000	0.000	0.000
98	A	115	LYS	1	0.968	1.003	28.445	0.065	0.065	0.000	0.000	0.000	0.000
99	A	116	THR	0	-0.018	-0.028	29.539	0.005	0.005	0.000	0.000	0.000	0.000
100	A	117	ILE	0	-0.033	0.002	31.581	0.006	0.006	0.000	0.000	0.000	0.000
101	A	118	HIS	0	-0.019	-0.013	33.605	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	119	SER	0	-0.090	-0.045	34.546	0.004	0.004	0.000	0.000	0.000	0.000
103	A	120	GLY	0	0.053	0.021	36.152	0.001	0.001	0.000	0.000	0.000	0.000
104	A	121	LEU	0	0.001	-0.021	38.114	0.003	0.003	0.000	0.000	0.000	0.000
105	A	122	ASP	-1	-0.949	-0.963	40.798	-0.026	-0.026	0.000	0.000	0.000	0.000
106	A	123	ILE	0	-0.034	-0.021	37.076	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	124	ASP	-1	-0.978	-0.968	40.246	0.003	0.003	0.000	0.000	0.000	0.000
108	A	125	LYS	1	0.864	0.932	41.929	0.018	0.018	0.000	0.000	0.000	0.000
109	A	126	VAL	0	0.028	0.002	44.878	0.000	0.000	0.000	0.000	0.000	0.000
110	A	127	ASP	-1	-0.897	-0.929	46.688	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	128	GLU	-1	-0.828	-0.899	47.636	-0.017	-0.017	0.000	0.000	0.000	0.000
112	A	129	THR	0	0.032	0.004	43.446	0.000	0.000	0.000	0.000	0.000	0.000
113	A	130	MET	0	-0.038	-0.010	46.816	0.001	0.001	0.000	0.000	0.000	0.000
114	A	131	ASH	0	-0.054	-0.061	49.190	0.001	0.001	0.000	0.000	0.000	0.000
115	A	132	GLU	-1	-0.895	-0.933	46.871	-0.020	-0.020	0.000	0.000	0.000	0.000
116	A	133	ILE	0	-0.038	-0.034	45.030	0.000	0.000	0.000	0.000	0.000	0.000
117	A	134	ARG	1	0.886	0.942	49.275	0.001	0.001	0.000	0.000	0.000	0.000
118	A	135	GLU	-1	-0.912	-0.952	52.838	-0.012	-0.012	0.000	0.000	0.000	0.000
119	A	136	GLN	0	-0.001	0.000	49.056	0.000	0.000	0.000	0.000	0.000	0.000
120	A	137	VAL	0	-0.074	-0.033	51.119	0.001	0.001	0.000	0.000	0.000	0.000
121	A	138	GLU	-1	-0.998	-0.993	53.468	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	139	LEU	0	-0.087	-0.033	53.871	0.000	0.000	0.000	0.000	0.000	0.000
123	A	140	GLY	0	-0.083	-0.037	54.645	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:SER)