FMO DATABASE

FMODB ID: NN6GQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-764255.277917
FMO2-HF: Nuclear repulsion	714163.093606
FMO2-HF: Total energy	-50092.18431
FMO2-MP2: Total energy	-50234.529059

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.
-13.56	-7.654	4.812	-4.544	-6.172	0.027

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 : 0.067 / q_NPA : 0.028

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	0.057	0.025	2.884	-2.151	1.191	0.172	-1.641	-1.873	0.000
4	A	21	LYS	1	0.964	0.980	2.232	-9.872	-7.812	4.625	-2.722	-3.962	0.026
5	A	22	ALA	0	-0.018	-0.003	3.973	-1.015	-0.511	0.015	-0.181	-0.337	0.001
6	A	23	ILE	0	0.059	0.032	6.069	0.267	0.267	0.000	0.000	0.000	0.000
7	A	24	VAL	0	0.026	0.015	7.442	0.113	0.113	0.000	0.000	0.000	0.000
8	A	25	ARG	1	0.951	0.974	7.261	-0.548	-0.548	0.000	0.000	0.000	0.000
9	A	26	LEU	0	0.024	0.018	10.005	0.031	0.031	0.000	0.000	0.000	0.000
10	A	27	ARG	1	0.926	0.961	11.949	0.572	0.572	0.000	0.000	0.000	0.000
11	A	28	GLU	-1	-0.935	-0.959	12.548	-0.021	-0.021	0.000	0.000	0.000	0.000
12	A	29	HIS	0	-0.038	-0.032	13.349	0.018	0.018	0.000	0.000	0.000	0.000
13	A	30	ILE	0	0.050	0.015	15.675	0.021	0.021	0.000	0.000	0.000	0.000
14	A	31	ASN	0	0.063	0.061	17.538	0.012	0.012	0.000	0.000	0.000	0.000
15	A	32	LEU	0	-0.015	0.056	17.637	0.013	0.013	0.000	0.000	0.000	0.000
16	A	33	LEU	0	-0.051	-0.025	19.557	0.012	0.012	0.000	0.000	0.000	0.000
17	A	34	SER	0	-0.075	-0.090	21.709	0.007	0.007	0.000	0.000	0.000	0.000
18	A	35	LYS	1	1.009	0.981	23.229	0.034	0.034	0.000	0.000	0.000	0.000
19	A	36	LYS	1	0.919	0.960	24.151	0.014	0.014	0.000	0.000	0.000	0.000
20	A	37	GLN	0	0.012	-0.004	26.077	0.001	0.001	0.000	0.000	0.000	0.000
21	A	38	SER	0	-0.028	-0.009	27.910	0.004	0.004	0.000	0.000	0.000	0.000
22	A	39	HIS	0	0.022	0.003	28.774	0.002	0.002	0.000	0.000	0.000	0.000
23	A	40	LEU	0	-0.015	-0.015	28.883	0.004	0.004	0.000	0.000	0.000	0.000
24	A	41	ARG	1	0.970	0.984	29.868	0.073	0.073	0.000	0.000	0.000	0.000
25	A	42	THR	0	0.030	0.031	34.007	0.002	0.002	0.000	0.000	0.000	0.000
26	A	43	GLN	0	-0.049	-0.028	33.711	0.003	0.003	0.000	0.000	0.000	0.000
27	A	44	ILE	0	-0.019	-0.007	34.662	0.003	0.003	0.000	0.000	0.000	0.000
28	A	45	THR	0	0.041	0.016	38.170	0.000	0.000	0.000	0.000	0.000	0.000
29	A	46	ASN	0	-0.005	0.004	40.086	0.000	0.000	0.000	0.000	0.000	0.000
30	A	47	GLN	0	-0.003	-0.017	40.967	0.004	0.004	0.000	0.000	0.000	0.000
31	A	48	GLU	-1	-0.946	-0.977	42.533	-0.025	-0.025	0.000	0.000	0.000	0.000
32	A	49	ASN	0	0.067	0.021	44.410	0.001	0.001	0.000	0.000	0.000	0.000
33	A	50	GLU	-1	-0.995	-0.985	45.612	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	51	ALA	0	0.003	-0.017	47.089	0.001	0.001	0.000	0.000	0.000	0.000
35	A	52	ARG	1	0.977	0.997	48.776	0.024	0.024	0.000	0.000	0.000	0.000
36	A	53	ILE	0	0.022	0.007	50.311	0.001	0.001	0.000	0.000	0.000	0.000
37	A	54	PHE	0	0.031	0.051	50.550	0.001	0.001	0.000	0.000	0.000	0.000
38	A	55	LEU	0	-0.047	-0.014	53.205	0.001	0.001	0.000	0.000	0.000	0.000
39	A	56	THR	0	-0.072	-0.071	55.099	0.000	0.000	0.000	0.000	0.000	0.000
40	A	57	LYS	1	0.967	0.973	54.145	0.012	0.012	0.000	0.000	0.000	0.000
41	A	58	GLY	0	-0.043	-0.017	57.350	0.001	0.001	0.000	0.000	0.000	0.000
42	A	59	ASN	0	0.055	0.035	56.730	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	60	LYS	1	1.054	1.003	54.967	0.010	0.010	0.000	0.000	0.000	0.000
44	A	61	VAL	0	-0.010	0.000	53.230	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	62	MET	0	0.013	0.033	50.544	0.000	0.000	0.000	0.000	0.000	0.000
46	A	63	ALA	0	0.088	0.043	49.853	0.000	0.000	0.000	0.000	0.000	0.000
47	A	64	LYS	1	0.889	0.945	48.813	0.008	0.008	0.000	0.000	0.000	0.000
48	A	65	ASN	0	0.007	-0.017	47.657	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	66	ALA	0	0.045	0.042	45.505	0.000	0.000	0.000	0.000	0.000	0.000
50	A	67	LEU	0	0.023	0.002	44.050	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	68	LYS	1	0.900	0.948	43.199	0.006	0.006	0.000	0.000	0.000	0.000
52	A	69	LYS	1	0.966	1.003	40.176	0.006	0.006	0.000	0.000	0.000	0.000
53	A	70	LYS	1	0.959	0.990	39.521	0.029	0.029	0.000	0.000	0.000	0.000
54	A	71	LYS	1	1.011	1.008	38.619	0.014	0.014	0.000	0.000	0.000	0.000
55	A	72	THR	0	-0.100	-0.050	37.052	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	73	ILE	0	0.019	0.007	34.610	0.001	0.001	0.000	0.000	0.000	0.000
57	A	74	GLU	-1	-0.878	-0.943	33.864	-0.034	-0.034	0.000	0.000	0.000	0.000
58	A	75	GLN	0	-0.061	-0.042	33.255	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	76	LEU	0	-0.029	-0.003	29.312	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	77	LEU	0	0.027	0.007	29.031	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	78	SER	0	0.033	0.024	28.674	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	79	LYS	1	0.986	0.985	26.746	0.009	0.009	0.000	0.000	0.000	0.000
63	A	80	VAL	0	-0.059	-0.015	24.462	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	81	GLU	-1	-0.839	-0.936	23.916	-0.080	-0.080	0.000	0.000	0.000	0.000
65	A	82	GLY	0	0.041	0.033	24.122	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	83	THR	0	-0.057	-0.031	19.370	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	84	MET	0	-0.031	-0.025	19.478	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	85	GLU	-1	-0.848	-0.910	19.682	-0.164	-0.164	0.000	0.000	0.000	0.000
69	A	86	SER	0	-0.028	-0.024	18.120	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	87	MET	0	-0.084	-0.045	15.343	-0.027	-0.027	0.000	0.000	0.000	0.000
71	A	88	GLU	-1	-0.901	-0.956	15.315	-0.248	-0.248	0.000	0.000	0.000	0.000
72	A	89	GLN	0	0.004	0.008	17.078	-0.042	-0.042	0.000	0.000	0.000	0.000
73	A	90	GLN	0	-0.030	-0.019	12.256	-0.089	-0.089	0.000	0.000	0.000	0.000
74	A	91	LEU	0	-0.010	-0.004	11.562	-0.111	-0.111	0.000	0.000	0.000	0.000
75	A	92	PHE	0	0.040	0.033	13.301	-0.077	-0.077	0.000	0.000	0.000	0.000
76	A	93	SER	0	0.013	-0.002	13.972	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	94	ILE	0	-0.051	-0.019	8.103	-0.087	-0.087	0.000	0.000	0.000	0.000
78	A	95	GLU	-1	-0.901	-0.962	11.004	-0.647	-0.647	0.000	0.000	0.000	0.000
79	A	96	SER	0	-0.016	0.011	12.732	0.017	0.017	0.000	0.000	0.000	0.000
80	A	97	ALA	0	0.028	-0.004	10.975	0.024	0.024	0.000	0.000	0.000	0.000
81	A	98	ASN	0	-0.044	-0.034	7.908	-0.076	-0.076	0.000	0.000	0.000	0.000
82	A	99	LEU	0	0.032	0.026	11.050	0.038	0.038	0.000	0.000	0.000	0.000
83	A	100	ASN	0	-0.007	0.005	14.503	0.055	0.055	0.000	0.000	0.000	0.000
84	A	101	LEU	0	-0.002	0.002	9.128	0.048	0.048	0.000	0.000	0.000	0.000
85	A	102	GLU	-1	-0.940	-0.980	12.745	-0.493	-0.493	0.000	0.000	0.000	0.000
86	A	103	THR	0	-0.025	-0.002	14.570	0.058	0.058	0.000	0.000	0.000	0.000
87	A	104	MET	0	0.016	0.001	15.645	0.043	0.043	0.000	0.000	0.000	0.000
88	A	105	ARG	1	0.938	0.969	8.913	0.633	0.633	0.000	0.000	0.000	0.000
89	A	106	ALA	0	0.052	0.048	16.625	0.032	0.032	0.000	0.000	0.000	0.000
90	A	107	MET	0	-0.011	-0.016	19.235	0.027	0.027	0.000	0.000	0.000	0.000
91	A	108	GLN	0	-0.033	-0.026	18.471	0.017	0.017	0.000	0.000	0.000	0.000
92	A	109	GLU	-1	-1.012	-1.021	19.388	-0.194	-0.194	0.000	0.000	0.000	0.000
93	A	110	GLY	0	0.032	0.022	21.349	0.015	0.015	0.000	0.000	0.000	0.000
94	A	111	ALA	0	0.009	0.005	24.161	0.014	0.014	0.000	0.000	0.000	0.000
95	A	112	LYS	1	0.903	0.947	19.541	0.138	0.138	0.000	0.000	0.000	0.000
96	A	113	ALA	0	0.055	0.032	25.583	0.011	0.011	0.000	0.000	0.000	0.000
97	A	114	MET	0	0.018	0.004	27.368	0.010	0.010	0.000	0.000	0.000	0.000
98	A	115	LYS	1	0.960	0.998	28.474	0.057	0.057	0.000	0.000	0.000	0.000
99	A	116	THR	0	0.004	-0.018	29.242	0.007	0.007	0.000	0.000	0.000	0.000
100	A	117	ILE	0	-0.015	0.052	31.107	0.004	0.004	0.000	0.000	0.000	0.000
101	A	118	HIS	0	-0.012	-0.010	33.520	0.000	0.000	0.000	0.000	0.000	0.000
102	A	119	SER	0	-0.128	-0.091	34.288	0.004	0.004	0.000	0.000	0.000	0.000
103	A	120	GLY	0	0.062	0.018	35.995	0.003	0.003	0.000	0.000	0.000	0.000
104	A	121	LEU	0	-0.017	-0.035	37.930	0.002	0.002	0.000	0.000	0.000	0.000
105	A	122	ASP	-1	-0.939	-0.954	40.719	-0.042	-0.042	0.000	0.000	0.000	0.000
106	A	123	ILE	0	-0.042	-0.019	37.024	0.003	0.003	0.000	0.000	0.000	0.000
107	A	124	ASP	-1	-0.993	-0.977	40.333	-0.032	-0.032	0.000	0.000	0.000	0.000
108	A	125	LYS	1	0.971	1.003	41.933	0.031	0.031	0.000	0.000	0.000	0.000
109	A	126	VAL	0	0.011	0.011	45.093	0.002	0.002	0.000	0.000	0.000	0.000
110	A	127	ASP	-1	-0.891	-0.925	46.799	-0.016	-0.016	0.000	0.000	0.000	0.000
111	A	128	GLU	-1	-0.879	-0.935	47.559	-0.024	-0.024	0.000	0.000	0.000	0.000
112	A	129	THR	0	0.042	-0.010	43.579	0.002	0.002	0.000	0.000	0.000	0.000
113	A	130	MET	0	-0.066	-0.024	46.843	0.003	0.003	0.000	0.000	0.000	0.000
114	A	131	ASH	0	-0.056	-0.068	49.323	0.002	0.002	0.000	0.000	0.000	0.000
115	A	132	GLU	-1	-0.888	-0.930	47.529	-0.013	-0.013	0.000	0.000	0.000	0.000
116	A	133	ILE	0	-0.065	-0.044	45.342	0.002	0.002	0.000	0.000	0.000	0.000
117	A	134	ARG	1	0.895	0.940	49.281	0.011	0.011	0.000	0.000	0.000	0.000
118	A	135	GLU	-1	-0.915	-0.955	52.892	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	136	GLN	0	0.009	0.005	49.042	0.002	0.002	0.000	0.000	0.000	0.000
120	A	137	VAL	0	-0.089	-0.035	51.290	0.002	0.002	0.000	0.000	0.000	0.000
121	A	138	GLU	-1	-1.000	-0.999	53.469	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	139	LEU	0	-0.094	-0.033	53.815	0.001	0.001	0.000	0.000	0.000	0.000
123	A	140	GLY	0	-0.064	-0.028	54.167	0.002	0.002	0.000	0.000	0.000	0.000

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