FMO DATABASE

FMODB ID: K9473

Calculation Name: 1VJH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VJH

Chain ID: A

ChEMBL ID:

UniProt ID: P0C0B0

Base Structure: X-ray

Registration Date: 2023-09-20

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-980118.208114
FMO2-HF: Nuclear repulsion	933158.373065
FMO2-HF: Total energy	-46959.835049
FMO2-MP2: Total energy	-47098.137305

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:1:SER)

Summations of interaction energy for fragment #1(A:1: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.
-12.256	-16.54	19.474	-6.666	-8.523	0.04

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.011

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	3	LEU	0	-0.015	0.008	1.876	-4.737	-8.022	11.015	-3.692	-4.038	0.019
4	A	4	LYS	1	0.918	0.969	1.868	-3.720	-5.148	8.451	-2.836	-4.187	0.021
5	A	5	GLY	0	0.043	0.024	3.650	-0.001	0.104	0.008	-0.022	-0.091	0.001
6	A	6	ALA	0	-0.025	-0.017	7.118	-0.086	-0.086	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.005	0.012	10.745	0.027	0.027	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.031	-0.016	14.121	0.006	0.006	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.023	0.025	17.263	0.017	0.017	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.975	0.979	20.985	0.137	0.137	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.066	-0.030	23.993	0.012	0.012	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.796	-0.873	27.488	-0.109	-0.109	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.078	-0.033	30.250	0.004	0.004	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.917	0.928	32.963	0.059	0.059	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.051	-0.010	34.755	0.002	0.002	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.030	0.023	35.409	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.041	0.009	32.257	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.876	-0.941	32.880	-0.108	-0.108	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.933	0.968	34.443	0.070	0.070	0.000	0.000	0.000	0.000
20	A	20	PHE	0	0.016	-0.007	28.351	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.023	0.005	26.242	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.002	-0.001	30.152	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.006	0.007	32.484	0.001	0.001	0.000	0.000	0.000	0.000
24	A	24	PHE	0	0.024	0.011	23.245	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.008	-0.016	27.572	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.906	-0.942	28.885	-0.097	-0.097	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.858	-0.907	29.371	-0.090	-0.090	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.094	-0.054	24.737	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.037	-0.010	26.957	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.861	0.944	29.302	0.079	0.079	0.000	0.000	0.000	0.000
31	A	31	PRO	0	0.008	0.006	25.282	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.023	0.005	22.420	0.007	0.007	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.831	-0.915	20.849	-0.075	-0.075	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.937	0.970	25.094	0.039	0.039	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.033	-0.026	24.320	0.001	0.001	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.004	0.001	22.545	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.869	0.948	19.641	0.198	0.198	0.000	0.000	0.000	0.000
38	A	38	THR	0	0.034	0.004	20.991	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.900	-0.950	19.339	-0.220	-0.220	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.033	0.012	20.640	-0.024	-0.024	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.854	-0.922	16.346	-0.429	-0.429	0.000	0.000	0.000	0.000
42	A	42	ALA	0	-0.011	-0.008	20.561	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.010	-0.007	22.361	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.842	-0.915	25.489	-0.154	-0.154	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.049	0.008	28.097	0.001	0.001	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.016	0.017	31.121	0.008	0.008	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.858	0.905	27.034	0.163	0.163	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.910	0.992	28.447	0.116	0.116	0.000	0.000	0.000	0.000
49	A	49	THR	0	-0.017	-0.012	23.329	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	50	MET	0	0.016	0.004	22.879	0.012	0.012	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.037	-0.020	16.646	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.022	0.011	18.976	0.012	0.012	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.014	-0.008	14.555	-0.054	-0.054	0.000	0.000	0.000	0.000
54	A	54	MET	0	-0.039	-0.008	16.413	0.043	0.043	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.095	-0.050	16.374	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.102	0.042	18.175	0.013	0.013	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.009	-0.006	18.774	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.868	-0.913	19.684	0.000	0.000	0.000	0.000	0.000	0.000
59	A	59	ILE	0	0.036	0.026	15.269	0.012	0.012	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.043	0.012	14.329	0.021	0.021	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.795	0.894	14.773	0.017	0.017	0.000	0.000	0.000	0.000
62	A	62	TYR	0	-0.024	-0.001	13.455	0.042	0.042	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.016	-0.017	9.451	0.063	0.063	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.905	0.969	6.323	0.550	0.550	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.008	-0.002	8.958	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	66	LEU	0	0.006	0.008	10.095	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.884	0.931	12.150	0.597	0.597	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.014	0.006	14.353	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.012	0.001	16.450	0.008	0.008	0.000	0.000	0.000	0.000
70	A	70	ILE	0	-0.028	-0.004	18.869	0.008	0.008	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.002	-0.002	22.388	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	72	VAL	0	-0.011	0.002	24.463	0.007	0.007	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.034	-0.026	27.690	0.002	0.002	0.000	0.000	0.000	0.000
74	A	74	PRO	0	0.029	0.008	30.351	0.003	0.003	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.059	-0.018	33.031	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.036	0.003	34.709	0.000	0.000	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.079	-0.032	38.186	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	78	GLY	0	-0.034	-0.011	40.603	0.003	0.003	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.825	-0.915	38.304	-0.066	-0.066	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.007	0.017	36.306	0.000	0.000	0.000	0.000	0.000	0.000
81	A	81	SER	0	-0.084	-0.078	31.675	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	82	HIS	1	0.817	0.890	28.070	0.113	0.113	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.027	0.013	24.878	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	84	VAL	0	-0.025	-0.013	20.301	0.003	0.003	0.000	0.000	0.000	0.000
85	A	85	TRP	0	0.020	0.013	19.581	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	86	THR	0	0.014	0.000	14.479	0.002	0.002	0.000	0.000	0.000	0.000
87	A	87	PHE	0	0.066	0.032	13.429	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	88	HIS	0	-0.019	-0.010	10.596	0.035	0.035	0.000	0.000	0.000	0.000
89	A	89	PHE	0	0.012	0.004	7.399	0.000	0.000	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.920	-0.976	3.941	-3.954	-3.630	0.000	-0.116	-0.207	-0.001
91	A	91	LYS	1	0.841	0.909	5.833	-0.397	-0.397	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.040	-0.020	6.977	-0.037	-0.037	0.000	0.000	0.000	0.000
93	A	93	HIS	0	0.007	-0.011	8.349	0.121	0.121	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.960	0.949	7.258	-0.836	-0.836	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.904	-0.934	8.223	0.397	0.397	0.000	0.000	0.000	0.000
96	A	96	ILE	0	-0.099	-0.022	10.229	-0.097	-0.097	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.849	-0.920	11.066	0.198	0.198	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.883	-0.940	10.308	0.044	0.044	0.000	0.000	0.000	0.000
99	A	99	PRO	0	-0.009	0.006	11.853	0.000	0.000	0.000	0.000	0.000	0.000
100	A	100	HIS	0	0.022	-0.016	14.938	-0.033	-0.033	0.000	0.000	0.000	0.000
101	A	101	SER	0	0.034	0.015	17.875	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	102	ILE	0	0.037	0.017	16.219	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.029	-0.008	16.976	-0.009	-0.009	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.859	-0.932	19.694	-0.069	-0.069	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.904	-0.962	22.730	-0.052	-0.052	0.000	0.000	0.000	0.000
106	A	106	SER	0	-0.026	-0.013	21.059	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	107	VAL	0	-0.004	0.006	23.247	0.000	0.000	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.857	0.938	25.501	0.058	0.058	0.000	0.000	0.000	0.000
109	A	109	TYR	0	-0.114	-0.089	25.925	0.002	0.002	0.000	0.000	0.000	0.000
110	A	110	PHE	0	0.035	0.001	22.936	0.004	0.004	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.940	0.968	28.431	0.083	0.083	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.940	0.972	30.230	0.066	0.066	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.027	0.033	29.725	0.004	0.004	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.764	-0.885	32.538	-0.077	-0.077	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.851	-0.916	34.308	-0.055	-0.055	0.000	0.000	0.000	0.000
116	A	116	ALA	0	-0.017	0.002	35.787	0.004	0.004	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.057	-0.046	34.131	0.002	0.002	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.064	-0.031	38.196	0.001	0.001	0.000	0.000	0.000	0.000
119	A	119	ASN	0	-0.055	-0.028	40.044	0.004	0.004	0.000	0.000	0.000	0.000
120	A	120	PHE	0	-0.039	0.009	41.206	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:1:SER)