FMO DATABASE

FMODB ID: K9RY3

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	OptHSide
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	-885631.220173
FMO2-HF: Nuclear repulsion	842943.538675
FMO2-HF: Total energy	-42687.681498
FMO2-MP2: Total energy	-42813.714619

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.
-5.069	0.451	8.589	-4.713	-9.396	-0.012

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 : 0.004 / q_NPA : 0.014

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	0.015	0.007	3.778	-2.146	0.982	-0.046	-1.660	-1.422	0.007
4	A	4	LEU	0	0.091	0.056	6.350	0.204	0.204	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.891	0.960	8.809	0.231	0.231	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.011	-0.005	11.884	0.109	0.109	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.914	-0.952	14.411	-0.258	-0.258	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.016	0.013	16.713	0.035	0.035	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.001	-0.001	20.138	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.820	-0.867	23.945	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.061	-0.036	26.567	-0.017	-0.017	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.856	-0.922	30.043	-0.017	-0.017	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.840	-0.912	31.737	0.014	0.014	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.846	0.921	27.169	0.015	0.015	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.004	-0.001	23.324	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	16	ILE	0	0.004	-0.001	22.526	0.019	0.019	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.000	0.003	16.425	-0.025	-0.025	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.920	0.957	18.728	0.151	0.151	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.002	0.005	12.939	-0.037	-0.037	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.018	-0.014	13.958	-0.036	-0.036	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.015	0.000	10.688	-0.116	-0.116	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.846	-0.922	9.728	0.027	0.027	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.024	0.027	9.033	0.060	0.060	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.815	-0.917	6.358	1.228	1.228	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.000	-0.007	5.052	0.365	0.365	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.092	-0.036	2.185	-1.772	-0.516	6.797	-2.720	-5.332	0.002
27	A	27	ASN	0	-0.019	-0.026	2.834	-0.487	0.607	1.839	-0.320	-2.614	-0.021
28	A	28	SER	0	0.002	-0.019	5.078	-0.583	-0.541	-0.001	-0.013	-0.028	0.000
29	A	29	SER	0	-0.036	-0.025	5.925	-0.561	-0.561	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.839	-0.913	5.561	-0.723	-0.723	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.007	0.006	7.330	-0.152	-0.152	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.883	0.927	10.104	-0.624	-0.624	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.809	-0.891	10.221	0.265	0.265	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.011	-0.009	9.460	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.010	0.002	13.316	-0.026	-0.026	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.835	0.923	14.897	-0.253	-0.253	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.027	-0.027	14.680	-0.023	-0.023	0.000	0.000	0.000	0.000
38	A	38	PHE	0	0.047	0.033	17.375	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.017	-0.012	18.931	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.081	-0.044	20.855	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.042	-0.018	21.426	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.022	-0.028	23.378	0.003	0.003	0.000	0.000	0.000	0.000
43	A	43	SER	0	0.001	-0.007	25.269	0.012	0.012	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.821	0.919	26.672	0.031	0.031	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.920	0.933	27.793	-0.049	-0.049	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.820	0.924	27.385	-0.018	-0.018	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.012	-0.010	20.681	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.002	-0.003	23.305	0.019	0.019	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.008	0.009	16.473	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.810	-0.880	20.088	-0.039	-0.039	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.007	-0.030	16.762	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.034	0.006	19.118	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.106	-0.061	17.239	-0.021	-0.021	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.047	-0.009	13.825	-0.032	-0.032	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.008	-0.007	15.025	0.015	0.015	0.000	0.000	0.000	0.000
56	A	56	TYR	0	-0.039	-0.022	10.115	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	57	MET	0	0.023	0.009	12.576	0.019	0.019	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.784	-0.876	8.421	1.173	1.173	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.003	-0.019	12.071	0.026	0.026	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.028	0.028	8.389	-0.050	-0.050	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.034	0.024	10.341	-0.016	-0.016	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.002	-0.011	11.705	-0.105	-0.105	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.015	0.012	14.018	-0.066	-0.066	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.028	-0.033	11.094	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.009	-0.002	13.441	-0.096	-0.096	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.003	0.006	16.307	-0.063	-0.063	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.035	-0.028	15.155	-0.053	-0.053	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.014	0.019	13.576	-0.039	-0.039	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.006	0.022	18.001	-0.052	-0.052	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.856	0.914	20.184	-0.357	-0.357	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.768	-0.884	18.427	0.322	0.322	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.004	0.013	21.491	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.957	0.982	22.861	-0.190	-0.190	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.040	0.000	23.397	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.077	-0.044	22.818	-0.026	-0.026	0.000	0.000	0.000	0.000
76	A	76	GLY	0	-0.004	-0.002	26.379	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.770	0.899	24.696	-0.070	-0.070	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.855	-0.917	26.942	0.082	0.082	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.007	-0.008	18.200	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.052	-0.033	23.762	0.008	0.008	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.008	0.010	19.734	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.040	0.002	22.641	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	83	SER	0	0.033	0.014	22.737	0.001	0.001	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.023	0.004	21.361	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.937	0.985	18.577	0.067	0.067	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.781	-0.917	22.525	0.073	0.073	0.000	0.000	0.000	0.000
87	A	87	SER	0	-0.107	-0.049	18.657	0.009	0.009	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.013	-0.004	16.465	0.032	0.032	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.014	0.004	20.334	0.027	0.027	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.956	0.966	21.725	-0.126	-0.126	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.007	-0.003	17.121	0.007	0.007	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.024	0.026	19.700	0.021	0.021	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.913	0.960	22.457	-0.106	-0.106	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.053	-0.026	22.940	0.001	0.001	0.000	0.000	0.000	0.000
95	A	95	THR	0	-0.047	-0.042	19.531	0.007	0.007	0.000	0.000	0.000	0.000
96	A	96	HIS	0	-0.021	-0.007	23.000	0.004	0.004	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.026	0.011	19.266	0.000	0.000	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.840	-0.917	23.668	0.136	0.136	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.918	0.968	26.294	-0.168	-0.168	0.000	0.000	0.000	0.000
100	A	100	ILE	0	-0.096	-0.048	23.599	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	101	PHE	0	-0.014	-0.014	19.118	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.893	0.958	25.090	-0.084	-0.084	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.021	-0.032	24.629	0.008	0.008	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.046	-0.019	26.744	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.897	-0.947	27.226	0.023	0.023	0.000	0.000	0.000	0.000
106	A	106	THR	0	-0.002	-0.022	28.080	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	107	VAL	0	0.027	0.005	24.688	0.010	0.010	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.924	-0.982	27.482	-0.025	-0.025	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.818	-0.889	31.058	0.023	0.023	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.093	-0.027	28.187	0.011	0.011	0.000	0.000	0.000	0.000

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