FMO DATABASE

FMODB ID: ZVK9N

Calculation Name: 6B9X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 6B9X

Chain ID: B

ChEMBL ID:

UniProt ID: Q6IAA8

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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-995816.276146
FMO2-HF: Nuclear repulsion	947252.74409
FMO2-HF: Total energy	-48563.532056
FMO2-MP2: Total energy	-48701.664416

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(B:0:ALA)

Summations of interaction energy for fragment #1(B:0:ALA)

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.
-5.715	-2.168	0.904	-1.879	-2.574	-0.005

Interaction energy analysis for fragmet #1(B:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.009

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	B	2	LEU	0	0.062	0.042	3.880	-0.318	1.223	-0.017	-0.845	-0.680	0.003
4	B	3	ARG	1	0.976	0.977	6.972	-0.226	-0.226	0.000	0.000	0.000	0.000
5	B	4	PRO	0	0.089	0.032	9.822	-0.029	-0.029	0.000	0.000	0.000	0.000
6	B	5	LYS	1	0.976	0.991	12.938	-0.140	-0.140	0.000	0.000	0.000	0.000
7	B	6	ALA	0	-0.012	0.005	11.764	0.003	0.003	0.000	0.000	0.000	0.000
8	B	7	LEU	0	0.062	0.043	11.786	-0.004	-0.004	0.000	0.000	0.000	0.000
9	B	8	THR	0	-0.010	-0.022	13.744	-0.001	-0.001	0.000	0.000	0.000	0.000
10	B	9	GLN	0	0.020	0.019	17.006	0.000	0.000	0.000	0.000	0.000	0.000
11	B	10	VAL	0	0.036	0.036	14.091	0.000	0.000	0.000	0.000	0.000	0.000
12	B	11	LEU	0	0.014	-0.001	16.414	0.001	0.001	0.000	0.000	0.000	0.000
13	B	12	SER	0	-0.082	-0.062	18.880	0.010	0.010	0.000	0.000	0.000	0.000
14	B	13	GLN	0	-0.043	-0.028	19.067	-0.001	-0.001	0.000	0.000	0.000	0.000
15	B	14	ALA	0	0.040	0.022	22.276	0.004	0.004	0.000	0.000	0.000	0.000
16	B	15	ASN	0	0.017	0.041	23.372	-0.004	-0.004	0.000	0.000	0.000	0.000
17	B	16	THR	0	0.056	0.018	26.454	0.008	0.008	0.000	0.000	0.000	0.000
18	B	17	GLY	0	-0.004	-0.017	29.280	-0.005	-0.005	0.000	0.000	0.000	0.000
19	B	18	GLY	0	0.033	0.020	32.364	-0.001	-0.001	0.000	0.000	0.000	0.000
20	B	19	VAL	0	-0.051	-0.027	26.448	-0.003	-0.003	0.000	0.000	0.000	0.000
21	B	20	GLN	0	-0.037	-0.019	29.161	0.010	0.010	0.000	0.000	0.000	0.000
22	B	21	SER	0	-0.047	-0.023	25.021	0.002	0.002	0.000	0.000	0.000	0.000
23	B	22	THR	0	0.008	-0.012	20.357	-0.007	-0.007	0.000	0.000	0.000	0.000
24	B	23	LEU	0	-0.040	-0.027	20.209	0.005	0.005	0.000	0.000	0.000	0.000
25	B	24	LEU	0	0.023	0.019	12.815	-0.006	-0.006	0.000	0.000	0.000	0.000
26	B	25	LEU	0	0.005	0.004	17.478	0.013	0.013	0.000	0.000	0.000	0.000
27	B	26	ASN	0	0.068	0.029	16.670	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	27	ASN	0	0.032	-0.006	17.928	0.056	0.056	0.000	0.000	0.000	0.000
29	B	28	GLU	-1	-0.794	-0.878	20.701	-0.193	-0.193	0.000	0.000	0.000	0.000
30	B	29	GLY	0	0.004	0.015	21.591	0.024	0.024	0.000	0.000	0.000	0.000
31	B	30	SER	0	-0.071	-0.037	18.875	0.012	0.012	0.000	0.000	0.000	0.000
32	B	31	LEU	0	-0.031	-0.014	18.837	-0.031	-0.031	0.000	0.000	0.000	0.000
33	B	32	LEU	0	-0.047	-0.017	12.506	-0.004	-0.004	0.000	0.000	0.000	0.000
34	B	33	ALA	0	-0.036	-0.022	15.170	0.019	0.019	0.000	0.000	0.000	0.000
35	B	34	TYR	0	-0.023	-0.014	17.150	-0.009	-0.009	0.000	0.000	0.000	0.000
36	B	35	SER	0	0.003	0.001	20.219	0.020	0.020	0.000	0.000	0.000	0.000
37	B	36	GLY	0	0.030	0.021	22.222	-0.007	-0.007	0.000	0.000	0.000	0.000
38	B	37	TYR	0	-0.031	-0.030	25.959	-0.005	-0.005	0.000	0.000	0.000	0.000
39	B	38	GLY	0	0.046	0.026	28.736	0.001	0.001	0.000	0.000	0.000	0.000
40	B	39	ASP	-1	-0.909	-0.945	31.842	-0.039	-0.039	0.000	0.000	0.000	0.000
41	B	40	THR	0	-0.041	-0.010	30.549	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	41	ASP	-1	-0.775	-0.860	27.706	-0.080	-0.080	0.000	0.000	0.000	0.000
43	B	42	ALA	0	0.067	0.033	23.741	-0.007	-0.007	0.000	0.000	0.000	0.000
44	B	43	ARG	1	0.863	0.891	24.118	0.061	0.061	0.000	0.000	0.000	0.000
45	B	44	VAL	0	0.014	0.015	25.530	-0.009	-0.009	0.000	0.000	0.000	0.000
46	B	45	THR	0	-0.009	-0.015	26.075	-0.002	-0.002	0.000	0.000	0.000	0.000
47	B	46	ALA	0	-0.012	-0.005	22.526	-0.006	-0.006	0.000	0.000	0.000	0.000
48	B	47	ALA	0	0.035	0.019	24.383	-0.010	-0.010	0.000	0.000	0.000	0.000
49	B	48	ILE	0	0.002	0.009	26.818	-0.001	-0.001	0.000	0.000	0.000	0.000
50	B	49	ALA	0	-0.004	-0.005	24.646	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	50	SER	0	0.004	-0.008	23.671	0.000	0.000	0.000	0.000	0.000	0.000
52	B	51	ASN	0	-0.035	-0.025	25.234	0.002	0.002	0.000	0.000	0.000	0.000
53	B	52	ILE	0	0.005	-0.004	28.928	0.003	0.003	0.000	0.000	0.000	0.000
54	B	53	TRP	0	-0.004	-0.008	23.413	0.005	0.005	0.000	0.000	0.000	0.000
55	B	54	ALA	0	0.026	0.001	26.498	0.000	0.000	0.000	0.000	0.000	0.000
56	B	55	ALA	0	-0.020	0.001	27.724	0.003	0.003	0.000	0.000	0.000	0.000
57	B	56	TYR	0	-0.011	-0.015	30.092	0.006	0.006	0.000	0.000	0.000	0.000
58	B	57	ASP	-1	-0.832	-0.887	25.242	-0.211	-0.211	0.000	0.000	0.000	0.000
59	B	58	ARG	1	0.838	0.900	25.263	0.184	0.184	0.000	0.000	0.000	0.000
60	B	59	ASN	0	-0.055	-0.026	30.133	0.005	0.005	0.000	0.000	0.000	0.000
61	B	60	GLY	0	0.012	0.025	31.799	0.007	0.007	0.000	0.000	0.000	0.000
62	B	61	ASN	0	-0.013	-0.002	29.491	-0.006	-0.006	0.000	0.000	0.000	0.000
63	B	62	GLN	0	-0.023	-0.014	31.330	0.013	0.013	0.000	0.000	0.000	0.000
64	B	63	ALA	0	-0.008	-0.006	32.711	-0.006	-0.006	0.000	0.000	0.000	0.000
65	B	64	PHE	0	-0.048	-0.035	32.686	0.005	0.005	0.000	0.000	0.000	0.000
66	B	65	ASN	0	-0.011	-0.005	32.261	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	66	GLU	-1	-0.814	-0.891	25.513	-0.215	-0.215	0.000	0.000	0.000	0.000
68	B	67	ASP	-1	-0.917	-0.922	27.755	-0.144	-0.144	0.000	0.000	0.000	0.000
69	B	68	ASN	0	-0.058	-0.044	24.323	0.016	0.016	0.000	0.000	0.000	0.000
70	B	69	LEU	0	-0.001	0.008	26.283	0.007	0.007	0.000	0.000	0.000	0.000
71	B	70	LYS	1	0.827	0.891	24.234	0.141	0.141	0.000	0.000	0.000	0.000
72	B	71	PHE	0	-0.026	-0.038	23.598	-0.008	-0.008	0.000	0.000	0.000	0.000
73	B	72	ILE	0	0.025	0.036	26.307	0.008	0.008	0.000	0.000	0.000	0.000
74	B	73	LEU	0	-0.045	-0.023	27.962	-0.003	-0.003	0.000	0.000	0.000	0.000
75	B	74	MET	0	0.003	0.007	30.726	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	75	ASP	-1	-0.759	-0.861	33.277	-0.062	-0.062	0.000	0.000	0.000	0.000
77	B	76	CYS	0	-0.039	-0.021	36.377	-0.001	-0.001	0.000	0.000	0.000	0.000
78	B	77	MET	0	0.008	-0.007	38.228	0.002	0.002	0.000	0.000	0.000	0.000
79	B	78	GLU	-1	-0.931	-0.945	39.202	-0.038	-0.038	0.000	0.000	0.000	0.000
80	B	79	GLY	0	-0.025	-0.023	35.149	0.001	0.001	0.000	0.000	0.000	0.000
81	B	80	ARG	1	0.729	0.852	32.827	0.060	0.060	0.000	0.000	0.000	0.000
82	B	81	VAL	0	0.006	-0.009	27.962	-0.001	-0.001	0.000	0.000	0.000	0.000
83	B	82	ALA	0	-0.011	-0.009	26.121	0.002	0.002	0.000	0.000	0.000	0.000
84	B	83	ILE	0	0.011	-0.003	23.448	-0.004	-0.004	0.000	0.000	0.000	0.000
85	B	84	THR	0	-0.019	-0.015	20.468	0.003	0.003	0.000	0.000	0.000	0.000
86	B	85	ARG	1	0.821	0.889	18.519	0.253	0.253	0.000	0.000	0.000	0.000
87	B	86	VAL	0	-0.027	-0.006	13.435	0.022	0.022	0.000	0.000	0.000	0.000
88	B	87	ALA	0	0.028	0.018	11.424	-0.046	-0.046	0.000	0.000	0.000	0.000
89	B	88	ASN	0	-0.080	-0.038	11.610	0.035	0.035	0.000	0.000	0.000	0.000
90	B	89	LEU	0	-0.081	-0.043	11.928	0.040	0.040	0.000	0.000	0.000	0.000
91	B	90	LEU	0	0.019	0.007	15.772	0.028	0.028	0.000	0.000	0.000	0.000
92	B	91	LEU	0	-0.017	0.008	17.551	-0.001	-0.001	0.000	0.000	0.000	0.000
93	B	92	CYS	0	-0.053	-0.032	19.311	0.019	0.019	0.000	0.000	0.000	0.000
94	B	93	MET	0	-0.014	0.006	22.456	0.006	0.006	0.000	0.000	0.000	0.000
95	B	94	TYR	0	0.029	0.015	24.969	0.004	0.004	0.000	0.000	0.000	0.000
96	B	95	ALA	0	0.002	-0.001	28.599	0.005	0.005	0.000	0.000	0.000	0.000
97	B	96	LYS	1	0.922	0.952	31.375	0.040	0.040	0.000	0.000	0.000	0.000
98	B	97	GLU	-1	-0.756	-0.863	34.919	-0.047	-0.047	0.000	0.000	0.000	0.000
99	B	98	THR	0	-0.014	-0.013	36.941	0.000	0.000	0.000	0.000	0.000	0.000
100	B	99	VAL	0	-0.063	-0.007	31.250	0.002	0.002	0.000	0.000	0.000	0.000
101	B	100	GLY	0	0.033	0.019	34.739	-0.003	-0.003	0.000	0.000	0.000	0.000
102	B	101	PHE	0	0.047	-0.005	31.813	-0.002	-0.002	0.000	0.000	0.000	0.000
103	B	102	GLY	0	-0.018	0.000	30.894	-0.006	-0.006	0.000	0.000	0.000	0.000
104	B	103	MET	0	0.026	0.017	29.634	-0.006	-0.006	0.000	0.000	0.000	0.000
105	B	104	LEU	0	0.033	0.019	27.952	-0.004	-0.004	0.000	0.000	0.000	0.000
106	B	105	LYS	1	0.940	0.968	26.418	0.101	0.101	0.000	0.000	0.000	0.000
107	B	106	ALA	0	-0.018	0.000	25.330	-0.011	-0.011	0.000	0.000	0.000	0.000
108	B	107	LYS	1	0.842	0.907	24.020	0.054	0.054	0.000	0.000	0.000	0.000
109	B	108	ALA	0	0.031	0.018	21.961	-0.009	-0.009	0.000	0.000	0.000	0.000
110	B	109	GLN	0	0.045	0.010	20.584	-0.006	-0.006	0.000	0.000	0.000	0.000
111	B	110	ALA	0	-0.017	0.001	20.121	-0.014	-0.014	0.000	0.000	0.000	0.000
112	B	111	LEU	0	-0.003	-0.006	17.493	-0.008	-0.008	0.000	0.000	0.000	0.000
113	B	112	VAL	0	0.010	0.002	16.018	-0.028	-0.028	0.000	0.000	0.000	0.000
114	B	113	GLN	0	-0.024	-0.014	15.359	-0.053	-0.053	0.000	0.000	0.000	0.000
115	B	114	TYR	0	-0.053	-0.020	12.731	-0.005	-0.005	0.000	0.000	0.000	0.000
116	B	115	LEU	0	-0.009	-0.019	11.624	-0.017	-0.017	0.000	0.000	0.000	0.000
117	B	116	GLU	-1	-0.792	-0.893	10.717	-0.565	-0.565	0.000	0.000	0.000	0.000
118	B	117	GLU	-1	-0.871	-0.909	8.450	-0.589	-0.589	0.000	0.000	0.000	0.000
119	B	118	PRO	0	0.036	0.013	6.316	-0.205	-0.205	0.000	0.000	0.000	0.000
120	B	119	LEU	0	-0.040	-0.031	5.738	-0.372	-0.372	0.000	0.000	0.000	0.000
121	B	120	THR	0	0.000	-0.012	7.346	-0.219	-0.219	0.000	0.000	0.000	0.000
122	B	121	GLN	0	-0.134	-0.076	3.055	-0.574	-0.182	0.049	-0.079	-0.363	0.000
123	B	122	VAL	0	-0.090	-0.040	2.510	-3.015	-1.441	0.872	-0.943	-1.504	-0.008
124	B	123	ALA	0	0.003	0.013	4.369	0.210	0.250	0.000	-0.012	-0.027	0.000
125	B	124	ALA	0	0.008	0.015	7.696	0.209	0.209	0.000	0.000	0.000	0.000
126	B	125	SER	0	0.024	0.019	9.569	0.192	0.192	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:0:ALA)