FMO DATABASE

FMODB ID: V5VY1

Calculation Name: 5N9J-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5N9J

Chain ID: C

ChEMBL ID:

UniProt ID: P87310

Base Structure: X-ray

Registration Date: 2023-06-22

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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-609403.022542
FMO2-HF: Nuclear repulsion	564955.226196
FMO2-HF: Total energy	-44447.796347
FMO2-MP2: Total energy	-44580.259681

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(C:5:PRO)

Summations of interaction energy for fragment #1(C:5:PRO)

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.
0.715	2.314	-0.023	-0.684	-0.891	-0.001

Interaction energy analysis for fragmet #1(C:5:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / 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	C	7	TYR	0	-0.040	-0.017	3.478	1.256	2.855	-0.023	-0.684	-0.891	-0.001
4	C	8	HIS	0	0.072	0.024	6.580	-0.276	-0.276	0.000	0.000	0.000	0.000
5	C	9	TYR	0	-0.037	-0.035	8.781	-0.014	-0.014	0.000	0.000	0.000	0.000
6	C	10	VAL	0	-0.012	0.011	8.711	0.099	0.099	0.000	0.000	0.000	0.000
7	C	11	GLY	0	0.013	0.003	10.941	-0.130	-0.130	0.000	0.000	0.000	0.000
8	C	12	SER	0	-0.008	-0.001	13.091	0.001	0.001	0.000	0.000	0.000	0.000
9	C	13	VAL	0	-0.061	-0.024	13.854	0.043	0.043	0.000	0.000	0.000	0.000
10	C	14	ASP	-1	-0.857	-0.919	17.015	-0.506	-0.506	0.000	0.000	0.000	0.000
11	C	15	TYR	0	-0.079	-0.040	19.159	0.056	0.056	0.000	0.000	0.000	0.000
12	C	16	GLN	0	-0.001	-0.002	22.705	-0.031	-0.031	0.000	0.000	0.000	0.000
13	C	17	PRO	0	-0.010	-0.016	25.098	0.013	0.013	0.000	0.000	0.000	0.000
14	C	18	THR	0	0.029	0.018	27.642	0.005	0.005	0.000	0.000	0.000	0.000
15	C	19	ARG	1	0.942	0.978	30.814	0.141	0.141	0.000	0.000	0.000	0.000
16	C	20	PRO	0	-0.006	-0.005	33.441	-0.001	-0.001	0.000	0.000	0.000	0.000
17	C	21	SER	0	0.037	0.026	33.289	-0.002	-0.002	0.000	0.000	0.000	0.000
18	C	22	ALA	0	0.039	-0.001	35.057	0.006	0.006	0.000	0.000	0.000	0.000
19	C	23	HIS	0	-0.005	-0.004	31.528	0.010	0.010	0.000	0.000	0.000	0.000
20	C	24	GLN	0	-0.013	-0.001	36.280	-0.002	-0.002	0.000	0.000	0.000	0.000
21	C	25	ASN	0	0.099	0.052	38.743	0.004	0.004	0.000	0.000	0.000	0.000
22	C	26	LEU	0	0.029	0.005	39.692	0.002	0.002	0.000	0.000	0.000	0.000
23	C	27	ILE	0	-0.019	-0.010	43.330	0.002	0.002	0.000	0.000	0.000	0.000
24	C	28	GLU	-1	-0.922	-0.974	45.489	-0.075	-0.075	0.000	0.000	0.000	0.000
25	C	29	LEU	0	-0.071	-0.007	39.900	0.001	0.001	0.000	0.000	0.000	0.000
26	C	30	TYR	0	-0.011	-0.020	40.294	-0.001	-0.001	0.000	0.000	0.000	0.000
27	C	31	GLY	0	0.016	0.019	46.573	0.003	0.003	0.000	0.000	0.000	0.000
28	C	32	LEU	0	-0.023	-0.020	48.246	0.003	0.003	0.000	0.000	0.000	0.000
29	C	33	THR	0	0.033	0.014	49.901	0.002	0.002	0.000	0.000	0.000	0.000
30	C	34	GLU	-1	-0.848	-0.926	52.437	-0.050	-0.050	0.000	0.000	0.000	0.000
31	C	35	LEU	0	0.004	0.007	53.579	0.003	0.003	0.000	0.000	0.000	0.000
32	C	36	ALA	0	-0.006	-0.017	53.132	0.002	0.002	0.000	0.000	0.000	0.000
33	C	37	LYS	1	0.989	0.993	55.264	0.053	0.053	0.000	0.000	0.000	0.000
34	C	38	LYS	1	1.001	1.004	57.901	0.044	0.044	0.000	0.000	0.000	0.000
35	C	39	VAL	0	-0.091	-0.026	57.987	0.002	0.002	0.000	0.000	0.000	0.000
36	C	40	GLY	0	-0.007	0.016	57.277	0.001	0.001	0.000	0.000	0.000	0.000
37	C	41	ARG	1	0.933	0.949	57.039	0.041	0.041	0.000	0.000	0.000	0.000
38	C	42	VAL	0	-0.047	-0.028	57.524	0.002	0.002	0.000	0.000	0.000	0.000
39	C	43	ASP	-1	-0.901	-0.950	59.302	-0.041	-0.041	0.000	0.000	0.000	0.000
40	C	44	GLU	-1	-0.925	-0.965	59.013	-0.047	-0.047	0.000	0.000	0.000	0.000
41	C	45	PHE	0	-0.008	-0.002	60.002	0.000	0.000	0.000	0.000	0.000	0.000
42	C	46	GLY	0	0.010	0.014	60.930	0.000	0.000	0.000	0.000	0.000	0.000
43	C	47	ASN	0	-0.030	-0.007	61.953	0.001	0.001	0.000	0.000	0.000	0.000
44	C	48	LYS	1	0.963	0.972	63.063	0.033	0.033	0.000	0.000	0.000	0.000
45	C	49	ARG	1	0.882	0.939	60.521	0.042	0.042	0.000	0.000	0.000	0.000
46	C	50	LYS	1	0.896	0.946	64.423	0.028	0.028	0.000	0.000	0.000	0.000
47	C	51	MET	0	0.078	0.026	61.647	0.000	0.000	0.000	0.000	0.000	0.000
48	C	52	ARG	1	0.893	0.959	66.433	0.026	0.026	0.000	0.000	0.000	0.000
49	C	53	ARG	1	1.020	1.007	63.898	0.027	0.027	0.000	0.000	0.000	0.000
50	C	54	SER	0	-0.006	0.014	66.854	0.000	0.000	0.000	0.000	0.000	0.000
51	C	55	TYR	0	0.103	0.039	68.426	-0.001	-0.001	0.000	0.000	0.000	0.000
52	C	56	LYS	1	0.976	0.968	69.889	0.022	0.022	0.000	0.000	0.000	0.000
53	C	57	ALA	0	-0.025	-0.017	70.419	0.000	0.000	0.000	0.000	0.000	0.000
54	C	58	TYR	0	0.034	0.005	66.246	0.000	0.000	0.000	0.000	0.000	0.000
55	C	59	ILE	0	0.000	0.008	73.155	0.000	0.000	0.000	0.000	0.000	0.000
56	C	60	GLN	0	-0.090	-0.046	75.309	0.001	0.001	0.000	0.000	0.000	0.000
57	C	61	ASP	-1	-0.955	-0.977	76.505	-0.024	-0.024	0.000	0.000	0.000	0.000
58	C	62	LEU	0	-0.013	0.025	76.513	0.000	0.000	0.000	0.000	0.000	0.000
59	C	63	PRO	0	0.019	0.008	80.188	0.000	0.000	0.000	0.000	0.000	0.000
60	C	64	GLY	0	0.064	0.041	82.737	0.000	0.000	0.000	0.000	0.000	0.000
61	C	65	TYR	0	-0.102	-0.046	82.630	-0.001	-0.001	0.000	0.000	0.000	0.000
62	C	66	ASN	0	-0.025	-0.018	78.991	0.000	0.000	0.000	0.000	0.000	0.000
63	C	67	GLU	-1	-0.940	-0.974	78.908	-0.018	-0.018	0.000	0.000	0.000	0.000
64	C	68	ILE	0	-0.065	-0.032	72.230	-0.001	-0.001	0.000	0.000	0.000	0.000
65	C	69	LEU	0	0.045	0.029	74.712	0.000	0.000	0.000	0.000	0.000	0.000
66	C	70	ARG	1	0.899	0.925	69.126	0.021	0.021	0.000	0.000	0.000	0.000
67	C	71	ASP	-1	-0.679	-0.748	70.913	-0.020	-0.020	0.000	0.000	0.000	0.000
68	C	72	ASN	0	-0.088	-0.053	66.747	-0.002	-0.002	0.000	0.000	0.000	0.000
69	C	73	THR	0	-0.048	-0.107	68.109	-0.001	-0.001	0.000	0.000	0.000	0.000
70	C	74	ILE	0	0.061	0.036	66.322	0.000	0.000	0.000	0.000	0.000	0.000
71	C	75	LYS	1	0.966	0.974	62.968	0.025	0.025	0.000	0.000	0.000	0.000
72	C	76	GLN	0	0.027	0.021	65.309	0.000	0.000	0.000	0.000	0.000	0.000
73	C	77	TRP	0	0.011	-0.006	67.518	0.000	0.000	0.000	0.000	0.000	0.000
74	C	78	LEU	0	-0.016	-0.005	62.978	0.000	0.000	0.000	0.000	0.000	0.000
75	C	79	THR	0	-0.120	-0.053	62.437	0.000	0.000	0.000	0.000	0.000	0.000
76	C	80	ASN	0	-0.049	-0.025	64.360	0.000	0.000	0.000	0.000	0.000	0.000
77	C	81	PRO	0	-0.010	0.009	64.822	0.001	0.001	0.000	0.000	0.000	0.000
78	C	82	ILE	0	-0.021	0.002	68.059	0.001	0.001	0.000	0.000	0.000	0.000
79	C	83	ARG	1	0.937	0.949	70.218	0.017	0.017	0.000	0.000	0.000	0.000
80	C	84	GLU	-1	-0.915	-0.961	70.214	-0.023	-0.023	0.000	0.000	0.000	0.000
81	C	85	GLU	-1	-0.909	-0.951	72.795	-0.021	-0.021	0.000	0.000	0.000	0.000
82	C	86	VAL	0	-0.114	-0.054	76.397	0.001	0.001	0.000	0.000	0.000	0.000
83	C	87	PRO	0	-0.010	0.001	79.432	0.000	0.000	0.000	0.000	0.000	0.000
84	C	88	ILE	0	0.007	-0.003	83.032	0.000	0.000	0.000	0.000	0.000	0.000
85	C	89	ASP	-1	-0.865	-0.928	85.486	-0.014	-0.014	0.000	0.000	0.000	0.000
86	C	90	ILE	0	0.033	-0.006	88.612	0.000	0.000	0.000	0.000	0.000	0.000
87	C	91	GLU	-1	-0.898	-0.940	90.649	-0.013	-0.013	0.000	0.000	0.000	0.000
88	C	92	PHE	0	-0.002	0.002	91.034	0.000	0.000	0.000	0.000	0.000	0.000
89	C	93	LEU	0	-0.019	-0.018	87.326	0.000	0.000	0.000	0.000	0.000	0.000
90	C	94	HIS	0	0.000	-0.007	91.864	0.000	0.000	0.000	0.000	0.000	0.000
91	C	95	HIS	0	-0.013	-0.001	94.574	0.000	0.000	0.000	0.000	0.000	0.000
92	C	96	VAL	0	-0.091	-0.047	92.195	0.000	0.000	0.000	0.000	0.000	0.000
93	C	97	PHE	0	-0.033	-0.021	88.441	0.000	0.000	0.000	0.000	0.000	0.000
94	C	98	SER	0	-0.052	-0.004	94.511	0.000	0.000	0.000	0.000	0.000	0.000
95	C	99	VAL	0	0.000	-0.005	95.572	0.000	0.000	0.000	0.000	0.000	0.000
96	C	100	GLU	-1	-0.951	-0.976	98.854	-0.011	-0.011	0.000	0.000	0.000	0.000
97	C	101	PRO	0	-0.046	-0.035	100.815	0.000	0.000	0.000	0.000	0.000	0.000
98	C	102	GLY	0	-0.020	0.017	101.882	0.000	0.000	0.000	0.000	0.000	0.000
99	C	103	ILE	0	-0.012	-0.008	100.121	0.000	0.000	0.000	0.000	0.000	0.000
100	C	104	ILE	0	0.069	0.025	95.139	0.000	0.000	0.000	0.000	0.000	0.000
101	C	105	PRO	0	-0.036	-0.019	97.277	0.000	0.000	0.000	0.000	0.000	0.000
102	C	106	GLY	0	-0.015	-0.015	94.601	0.000	0.000	0.000	0.000	0.000	0.000
103	C	107	PHE	0	0.020	0.024	89.285	0.000	0.000	0.000	0.000	0.000	0.000
104	C	108	ASN	0	-0.009	0.000	89.832	0.000	0.000	0.000	0.000	0.000	0.000
105	C	109	PRO	0	0.067	0.014	90.762	0.000	0.000	0.000	0.000	0.000	0.000
106	C	110	LYS	1	0.947	0.979	86.444	0.016	0.016	0.000	0.000	0.000	0.000
107	C	111	VAL	0	0.028	0.005	84.585	0.000	0.000	0.000	0.000	0.000	0.000
108	C	112	PHE	0	0.044	0.011	85.939	0.000	0.000	0.000	0.000	0.000	0.000
109	C	113	GLY	0	-0.071	-0.027	87.275	0.000	0.000	0.000	0.000	0.000	0.000
110	C	114	LEU	0	-0.037	-0.001	88.329	0.000	0.000	0.000	0.000	0.000	0.000
111	C	115	GLU	-1	-0.957	-0.973	90.442	-0.016	-0.016	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:5:PRO)