FMO DATABASE

FMODB ID: QY8RY

Calculation Name: 1VC1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VC1

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X1F5

Base Structure: X-ray

Registration Date: 2023-06-21

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	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-885542.278552
FMO2-HF: Nuclear repulsion	842855.38487
FMO2-HF: Total energy	-42686.893682
FMO2-MP2: Total energy	-42812.98619

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:MET)

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

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.
-1.375	-4.33	21.344	-6.456	-11.932	-0.009

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / 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	A	3	ASN	0	0.021	0.003	3.778	-2.165	1.128	-0.051	-1.708	-1.534	0.007
4	A	4	LEU	0	0.093	0.063	6.287	0.103	0.103	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.925	0.973	8.878	0.439	0.439	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.016	-0.006	11.966	0.112	0.112	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.938	-0.962	14.480	-0.321	-0.321	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.010	-0.001	16.763	0.042	0.042	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.015	0.009	20.203	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.901	-0.938	24.009	-0.073	-0.073	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.026	-0.015	26.624	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.911	-0.940	30.090	-0.050	-0.050	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.877	-0.957	31.772	-0.019	-0.019	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.803	0.872	27.107	0.050	0.050	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.014	0.001	23.295	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.003	-0.004	22.548	0.018	0.018	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.009	0.009	16.434	-0.027	-0.027	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.921	0.971	18.782	0.218	0.218	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.014	0.009	12.939	-0.049	-0.049	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.042	-0.025	13.941	-0.064	-0.064	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.001	-0.007	10.627	-0.151	-0.151	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.838	-0.921	9.674	-0.144	-0.144	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.008	0.023	8.987	-0.018	-0.018	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.824	-0.931	6.429	0.511	0.511	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.043	-0.059	5.133	0.271	0.271	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.093	-0.032	1.846	4.114	-4.501	20.188	-3.633	-7.941	0.006
27	A	27	ASN	0	-0.014	-0.026	2.781	-2.003	0.321	1.208	-1.108	-2.423	-0.022
28	A	28	SER	0	-0.014	-0.005	5.065	-0.403	-0.360	-0.001	-0.007	-0.034	0.000
29	A	29	SER	0	-0.003	-0.015	6.015	-0.415	-0.415	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.843	-0.929	5.326	-0.783	-0.783	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.019	0.001	7.341	-0.115	-0.115	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.964	0.965	10.113	-0.694	-0.694	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.854	-0.925	10.195	0.307	0.307	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.008	-0.003	9.636	0.027	0.027	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.000	-0.003	13.348	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.887	0.965	14.956	-0.238	-0.238	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.009	-0.003	14.844	0.019	0.019	0.000	0.000	0.000	0.000
38	A	38	PHE	0	0.036	0.037	17.403	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.024	-0.021	19.297	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.119	-0.076	20.869	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.053	-0.017	21.737	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.014	-0.014	23.412	0.007	0.007	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.012	-0.015	25.305	0.013	0.013	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.872	0.961	26.680	0.069	0.069	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.958	0.965	27.816	-0.022	-0.022	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.871	0.957	27.390	0.009	0.009	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.000	-0.003	20.604	-0.014	-0.014	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.008	-0.005	23.328	0.021	0.021	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.008	0.007	16.725	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.822	-0.885	20.111	-0.117	-0.117	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.002	-0.033	16.712	-0.024	-0.024	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.030	0.006	19.069	-0.015	-0.015	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.102	-0.058	17.057	-0.019	-0.019	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.036	-0.002	14.157	-0.049	-0.049	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.027	-0.019	14.999	0.043	0.043	0.000	0.000	0.000	0.000
56	A	56	TYR	0	-0.034	-0.015	9.840	0.074	0.074	0.000	0.000	0.000	0.000
57	A	57	MET	0	0.020	0.008	12.288	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.757	-0.842	8.294	1.051	1.051	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.019	-0.021	11.919	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	60	ALA	0	-0.022	0.010	8.415	-0.035	-0.035	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.043	0.018	10.389	-0.025	-0.025	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.007	-0.009	11.519	-0.095	-0.095	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.013	0.010	14.001	-0.060	-0.060	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.010	-0.013	11.278	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.019	-0.001	13.764	-0.089	-0.089	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.011	0.004	16.619	-0.056	-0.056	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.045	-0.038	15.441	-0.045	-0.045	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.043	0.036	13.610	-0.033	-0.033	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.013	0.022	18.022	-0.049	-0.049	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.843	0.914	20.052	-0.367	-0.367	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.821	-0.925	18.500	0.310	0.310	0.000	0.000	0.000	0.000
72	A	72	ALA	0	-0.018	-0.006	21.479	-0.030	-0.030	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.933	0.968	22.847	-0.169	-0.169	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.036	0.008	23.287	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.054	-0.023	22.543	-0.019	-0.019	0.000	0.000	0.000	0.000
76	A	76	GLY	0	-0.022	-0.016	26.368	-0.017	-0.017	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.795	0.914	24.568	-0.047	-0.047	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.938	-0.968	26.934	0.055	0.055	0.000	0.000	0.000	0.000
79	A	79	PHE	0	-0.003	-0.009	18.342	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.044	-0.027	23.774	0.012	0.012	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.014	0.005	19.868	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.037	0.001	22.659	0.005	0.005	0.000	0.000	0.000	0.000
83	A	83	SER	0	0.035	0.016	22.684	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.022	0.004	21.308	-0.014	-0.014	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.964	1.004	19.043	0.169	0.169	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.862	-0.958	22.487	0.023	0.023	0.000	0.000	0.000	0.000
87	A	87	SER	0	-0.077	-0.040	18.663	0.015	0.015	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.042	0.008	16.452	0.037	0.037	0.000	0.000	0.000	0.000
89	A	89	SER	0	0.044	0.031	20.305	0.033	0.033	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.922	0.954	21.776	-0.094	-0.094	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.001	-0.003	16.950	0.013	0.013	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.016	0.018	19.361	0.028	0.028	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.974	0.999	22.240	-0.064	-0.064	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.058	-0.029	22.575	0.005	0.005	0.000	0.000	0.000	0.000
95	A	95	THR	0	-0.058	-0.035	19.477	0.012	0.012	0.000	0.000	0.000	0.000
96	A	96	HIS	0	-0.002	0.003	22.941	0.007	0.007	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.013	0.004	19.206	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.882	-0.947	23.553	0.122	0.122	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.934	0.972	26.101	-0.161	-0.161	0.000	0.000	0.000	0.000
100	A	100	ILE	0	-0.108	-0.046	23.447	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	101	PHE	0	-0.019	-0.023	19.308	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.966	1.007	25.175	-0.054	-0.054	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.009	-0.027	24.380	0.004	0.004	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.066	-0.036	26.728	0.001	0.001	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.888	-0.942	27.177	-0.022	-0.022	0.000	0.000	0.000	0.000
106	A	106	THR	0	0.029	0.024	28.029	-0.012	-0.012	0.000	0.000	0.000	0.000
107	A	107	VAL	0	0.040	0.013	24.808	0.012	0.012	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.903	-0.959	27.515	-0.070	-0.070	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.876	-0.943	31.095	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.041	0.011	28.171	0.014	0.014	0.000	0.000	0.000	0.000

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