FMO DATABASE

FMODB ID: 3JVKL

Calculation Name: 2F9H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2F9H

Chain ID: A

ChEMBL ID:

UniProt ID: Q831B0

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	OptAll
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	121
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1002459.318634
FMO2-HF: Nuclear repulsion	956071.67855
FMO2-HF: Total energy	-46387.640084
FMO2-MP2: Total energy	-46524.603998

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:3:TRP)

Summations of interaction energy for fragment #1(A:3:TRP)

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.
-36.156	-33.579	18.444	-7.92	-13.102	-0.065

Interaction energy analysis for fragmet #1(A:3:TRP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.004

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

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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	5	MET	0	-0.015	0.014	2.004	-3.034	-0.603	6.802	-2.894	-6.340	0.006
4	A	6	GLN	0	-0.109	-0.077	3.198	3.458	3.412	0.070	0.319	-0.343	0.000
5	A	7	ALA	0	0.001	0.018	6.805	-0.097	-0.097	0.000	0.000	0.000	0.000
6	A	8	THR	0	-0.026	-0.024	10.054	0.252	0.252	0.000	0.000	0.000	0.000
7	A	9	VAL	0	-0.022	-0.005	13.387	0.037	0.037	0.000	0.000	0.000	0.000
8	A	10	THR	0	-0.026	-0.031	16.653	0.091	0.091	0.000	0.000	0.000	0.000
9	A	11	GLU	-1	-0.845	-0.921	19.051	-0.526	-0.526	0.000	0.000	0.000	0.000
10	A	12	ILE	0	-0.009	-0.003	21.234	-0.064	-0.064	0.000	0.000	0.000	0.000
11	A	13	GLY	0	0.012	0.023	23.649	0.052	0.052	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.860	0.909	26.364	0.355	0.355	0.000	0.000	0.000	0.000
13	A	15	HIS	0	-0.005	-0.008	28.799	0.030	0.030	0.000	0.000	0.000	0.000
14	A	16	ALA	0	-0.037	0.006	23.675	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	17	ILE	0	-0.015	-0.014	22.272	-0.046	-0.046	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.824	-0.879	25.816	-0.325	-0.325	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.836	-0.920	27.570	-0.409	-0.409	0.000	0.000	0.000	0.000
18	A	20	SER	0	-0.096	-0.060	28.867	0.014	0.014	0.000	0.000	0.000	0.000
19	A	21	GLU	-1	-0.903	-0.955	27.330	-0.436	-0.436	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.778	0.883	25.254	0.370	0.370	0.000	0.000	0.000	0.000
21	A	23	MET	0	-0.057	-0.027	23.043	-0.041	-0.041	0.000	0.000	0.000	0.000
22	A	24	ILE	0	0.017	0.009	19.925	0.009	0.009	0.000	0.000	0.000	0.000
23	A	25	ILE	0	-0.002	0.014	19.912	-0.072	-0.072	0.000	0.000	0.000	0.000
24	A	26	LEU	0	0.000	0.009	14.273	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	27	PHE	0	0.019	-0.012	17.914	0.076	0.076	0.000	0.000	0.000	0.000
26	A	28	GLY	0	0.087	0.069	16.597	-0.098	-0.098	0.000	0.000	0.000	0.000
27	A	29	GLU	-1	-0.774	-0.893	16.214	-1.076	-1.076	0.000	0.000	0.000	0.000
28	A	30	THR	0	-0.059	-0.020	19.317	0.059	0.059	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.000	0.016	21.383	0.063	0.063	0.000	0.000	0.000	0.000
30	A	32	THR	0	0.040	0.012	23.349	0.016	0.016	0.000	0.000	0.000	0.000
31	A	33	ASP	-1	-0.809	-0.915	27.047	-0.467	-0.467	0.000	0.000	0.000	0.000
32	A	34	THR	0	-0.058	-0.035	28.727	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.001	0.003	25.371	0.015	0.015	0.000	0.000	0.000	0.000
34	A	36	LYS	1	0.835	0.908	23.955	0.546	0.546	0.000	0.000	0.000	0.000
35	A	37	GLN	0	-0.088	-0.037	25.461	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	38	HIS	0	0.009	-0.002	26.603	0.014	0.014	0.000	0.000	0.000	0.000
37	A	39	ALA	0	0.026	0.017	21.282	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	40	VAL	0	0.008	0.004	17.960	0.038	0.038	0.000	0.000	0.000	0.000
39	A	41	ILE	0	-0.060	-0.025	18.644	-0.066	-0.066	0.000	0.000	0.000	0.000
40	A	42	GLN	0	0.034	0.007	12.468	-0.186	-0.186	0.000	0.000	0.000	0.000
41	A	43	SER	0	0.001	-0.009	13.708	-0.082	-0.082	0.000	0.000	0.000	0.000
42	A	44	PHE	0	0.003	-0.022	6.063	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	45	PRO	0	-0.028	-0.024	7.580	0.068	0.068	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.786	-0.887	1.864	-29.419	-29.706	7.176	-3.536	-3.354	-0.056
45	A	47	LYS	1	0.850	0.923	6.389	1.542	1.542	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.907	-0.949	9.080	-1.649	-1.649	0.000	0.000	0.000	0.000
47	A	49	GLN	0	-0.048	-0.038	5.733	1.063	1.063	0.000	0.000	0.000	0.000
48	A	50	VAL	0	-0.037	-0.006	5.799	0.097	0.097	0.000	0.000	0.000	0.000
49	A	51	THR	0	-0.053	-0.035	6.680	0.745	0.745	0.000	0.000	0.000	0.000
50	A	52	LEU	0	-0.016	0.005	7.778	-0.079	-0.079	0.000	0.000	0.000	0.000
51	A	53	ALA	0	0.003	-0.001	8.954	0.381	0.381	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.862	-0.941	10.763	-0.656	-0.656	0.000	0.000	0.000	0.000
53	A	55	GLY	0	-0.027	-0.012	11.896	0.114	0.114	0.000	0.000	0.000	0.000
54	A	56	ASP	-1	-0.810	-0.903	7.264	-2.091	-2.091	0.000	0.000	0.000	0.000
55	A	57	HIS	0	-0.019	-0.017	7.903	0.380	0.380	0.000	0.000	0.000	0.000
56	A	58	LEU	0	-0.004	0.010	8.742	-0.546	-0.546	0.000	0.000	0.000	0.000
57	A	59	LYS	1	0.803	0.888	10.549	1.199	1.199	0.000	0.000	0.000	0.000
58	A	60	ILE	0	0.015	0.005	11.930	-0.204	-0.204	0.000	0.000	0.000	0.000
59	A	61	GLY	0	0.070	0.041	14.697	0.160	0.160	0.000	0.000	0.000	0.000
60	A	62	ASP	-1	-0.851	-0.909	16.138	-0.549	-0.549	0.000	0.000	0.000	0.000
61	A	63	THR	0	-0.022	-0.001	18.129	0.074	0.074	0.000	0.000	0.000	0.000
62	A	64	ASN	0	-0.043	-0.033	12.125	-0.225	-0.225	0.000	0.000	0.000	0.000
63	A	65	TYR	0	-0.016	-0.011	13.998	0.118	0.118	0.000	0.000	0.000	0.000
64	A	66	THR	0	-0.020	-0.007	12.634	-0.130	-0.130	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.003	-0.006	10.489	0.093	0.093	0.000	0.000	0.000	0.000
66	A	68	THR	0	-0.024	-0.025	13.906	0.055	0.055	0.000	0.000	0.000	0.000
67	A	69	LYS	1	0.839	0.914	16.930	0.486	0.486	0.000	0.000	0.000	0.000
68	A	70	VAL	0	-0.039	-0.005	12.943	-0.099	-0.099	0.000	0.000	0.000	0.000
69	A	71	GLY	0	0.035	0.034	16.355	0.099	0.099	0.000	0.000	0.000	0.000
70	A	72	SER	0	-0.009	-0.026	17.531	-0.075	-0.075	0.000	0.000	0.000	0.000
71	A	73	PHE	0	-0.044	-0.025	18.559	0.039	0.039	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.012	0.030	15.541	-0.042	-0.042	0.000	0.000	0.000	0.000
73	A	75	ASN	0	0.022	0.012	11.251	-0.319	-0.319	0.000	0.000	0.000	0.000
74	A	76	SER	0	0.036	0.023	13.200	-0.113	-0.113	0.000	0.000	0.000	0.000
75	A	77	ASN	0	-0.058	-0.044	15.730	0.033	0.033	0.000	0.000	0.000	0.000
76	A	78	LEU	0	0.020	0.025	10.726	-0.034	-0.034	0.000	0.000	0.000	0.000
77	A	79	GLN	0	-0.003	-0.010	10.753	0.119	0.119	0.000	0.000	0.000	0.000
78	A	80	SER	0	-0.048	-0.015	12.646	0.025	0.025	0.000	0.000	0.000	0.000
79	A	81	ILE	0	-0.048	-0.025	16.157	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.024	0.013	13.343	0.024	0.024	0.000	0.000	0.000	0.000
81	A	83	HIS	0	-0.072	-0.024	14.256	0.065	0.065	0.000	0.000	0.000	0.000
82	A	84	SER	0	-0.005	-0.023	15.175	-0.071	-0.071	0.000	0.000	0.000	0.000
83	A	85	THR	0	-0.012	-0.018	17.243	0.041	0.041	0.000	0.000	0.000	0.000
84	A	86	LEU	0	0.004	0.019	14.584	-0.012	-0.012	0.000	0.000	0.000	0.000
85	A	87	ILE	0	0.023	0.008	18.552	0.077	0.077	0.000	0.000	0.000	0.000
86	A	88	PHE	0	-0.018	-0.005	18.261	-0.028	-0.028	0.000	0.000	0.000	0.000
87	A	89	ALA	0	0.028	-0.013	21.984	0.058	0.058	0.000	0.000	0.000	0.000
88	A	90	ASP	-1	-0.860	-0.922	22.235	-0.432	-0.432	0.000	0.000	0.000	0.000
89	A	91	ALA	0	-0.008	-0.007	21.700	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	92	PRO	0	-0.011	0.012	23.693	0.028	0.028	0.000	0.000	0.000	0.000
91	A	93	THR	0	-0.040	-0.036	26.123	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.918	-0.965	28.074	-0.201	-0.201	0.000	0.000	0.000	0.000
93	A	95	GLU	-1	-0.821	-0.906	23.066	-0.369	-0.369	0.000	0.000	0.000	0.000
94	A	96	ASP	-1	-0.968	-0.978	26.133	-0.264	-0.264	0.000	0.000	0.000	0.000
95	A	97	ASP	-1	-0.971	-0.982	28.571	-0.309	-0.309	0.000	0.000	0.000	0.000
96	A	98	VAL	0	-0.059	-0.011	21.718	-0.034	-0.034	0.000	0.000	0.000	0.000
97	A	99	ILE	0	0.001	-0.011	22.235	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.998	0.989	21.559	0.323	0.323	0.000	0.000	0.000	0.000
99	A	101	ASN	0	-0.018	0.003	19.212	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	102	GLY	0	0.053	0.022	18.170	-0.099	-0.099	0.000	0.000	0.000	0.000
101	A	103	VAL	0	-0.018	-0.011	13.738	-0.024	-0.024	0.000	0.000	0.000	0.000
102	A	104	TYR	0	0.054	0.041	16.853	0.011	0.011	0.000	0.000	0.000	0.000
103	A	105	LEU	0	-0.008	-0.001	14.537	-0.090	-0.090	0.000	0.000	0.000	0.000
104	A	106	THR	0	0.037	0.025	17.381	0.092	0.092	0.000	0.000	0.000	0.000
105	A	107	PRO	0	0.015	-0.006	17.519	-0.057	-0.057	0.000	0.000	0.000	0.000
106	A	108	HIS	0	-0.061	-0.037	20.939	-0.034	-0.034	0.000	0.000	0.000	0.000
107	A	109	GLN	0	-0.048	-0.015	22.577	0.036	0.036	0.000	0.000	0.000	0.000
108	A	110	LEU	0	0.053	0.039	22.151	-0.058	-0.058	0.000	0.000	0.000	0.000
109	A	111	PRO	0	-0.017	0.013	18.214	0.043	0.043	0.000	0.000	0.000	0.000
110	A	112	LYS	1	0.823	0.887	20.860	0.494	0.494	0.000	0.000	0.000	0.000
111	A	113	ILE	0	0.014	0.007	18.201	-0.062	-0.062	0.000	0.000	0.000	0.000
112	A	114	THR	0	-0.025	-0.019	20.287	0.068	0.068	0.000	0.000	0.000	0.000
113	A	115	ILE	0	0.016	0.002	19.967	-0.072	-0.072	0.000	0.000	0.000	0.000
114	A	116	GLY	0	-0.007	0.000	17.656	0.067	0.067	0.000	0.000	0.000	0.000
115	A	117	THR	0	-0.061	-0.021	16.204	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	118	THR	0	-0.027	-0.016	11.377	0.030	0.030	0.000	0.000	0.000	0.000
117	A	119	ILE	0	0.008	0.001	10.657	0.216	0.216	0.000	0.000	0.000	0.000
118	A	120	ASP	-1	-0.812	-0.885	7.728	-2.808	-2.808	0.000	0.000	0.000	0.000
119	A	121	TYR	0	0.033	-0.017	5.344	0.603	0.603	0.000	0.000	0.000	0.000
120	A	122	LEU	0	-0.064	-0.030	4.691	-1.956	-1.836	-0.001	-0.035	-0.084	0.000
121	A	123	VAL	0	-0.017	-0.001	2.240	-0.526	-0.167	4.397	-1.774	-2.981	-0.015

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:TRP)