FMO DATABASE

FMODB ID: R95J8

Calculation Name: 3VDY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VDY

Chain ID: A

ChEMBL ID:

UniProt ID: C0SPB6

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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-723479.03349
FMO2-HF: Nuclear repulsion	681911.331023
FMO2-HF: Total energy	-41567.702467
FMO2-MP2: Total energy	-41686.652198

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:0:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
1.793	3.624	-0.023	-0.929	-0.879	0

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.940 / q_NPA : 0.960

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].
3	A	2	PHE	0	0.030	0.005	3.847	-0.182	1.649	-0.023	-0.929	-0.879
4	A	3	ASN	0	-0.026	-0.011	6.511	2.757	2.757	0.000	0.000	0.000
5	A	4	GLN	0	-0.009	0.000	10.232	1.378	1.378	0.000	0.000	0.000
6	A	5	VAL	0	0.021	0.020	13.052	0.219	0.219	0.000	0.000	0.000
7	A	6	MET	0	-0.019	-0.014	16.653	0.214	0.214	0.000	0.000	0.000
8	A	7	LEU	0	-0.004	-0.002	19.685	0.165	0.165	0.000	0.000	0.000
9	A	8	VAL	0	0.030	0.011	23.213	0.125	0.125	0.000	0.000	0.000
10	A	9	GLY	0	0.015	0.013	26.782	0.074	0.074	0.000	0.000	0.000
11	A	10	ARG	1	0.874	0.924	29.420	8.790	8.790	0.000	0.000	0.000
12	A	11	LEU	0	0.001	0.030	30.478	-0.199	-0.199	0.000	0.000	0.000
13	A	12	THR	0	0.000	-0.010	32.841	0.432	0.432	0.000	0.000	0.000
14	A	13	LYS	1	0.887	0.931	34.712	8.606	8.606	0.000	0.000	0.000
15	A	14	ASP	-1	-0.845	-0.929	35.001	-8.395	-8.395	0.000	0.000	0.000
16	A	15	PRO	0	-0.007	0.002	31.809	-0.148	-0.148	0.000	0.000	0.000
17	A	16	ASP	-1	-0.830	-0.869	31.642	-9.402	-9.402	0.000	0.000	0.000
18	A	17	LEU	0	-0.017	-0.007	31.137	-0.366	-0.366	0.000	0.000	0.000
19	A	18	ARG	1	0.812	0.874	30.527	9.864	9.864	0.000	0.000	0.000
20	A	19	TYR	0	0.000	-0.039	30.469	-0.184	-0.184	0.000	0.000	0.000
21	A	20	THR	0	0.008	0.004	25.870	0.214	0.214	0.000	0.000	0.000
22	A	21	SER	0	0.028	0.015	29.341	0.051	0.051	0.000	0.000	0.000
23	A	22	ALA	0	-0.013	-0.008	27.426	0.153	0.153	0.000	0.000	0.000
24	A	23	GLY	0	0.018	0.007	29.411	0.129	0.129	0.000	0.000	0.000
25	A	24	ALA	0	-0.094	-0.039	25.978	0.008	0.008	0.000	0.000	0.000
26	A	25	ALA	0	0.050	0.041	28.067	0.039	0.039	0.000	0.000	0.000
27	A	26	VAL	0	-0.056	-0.039	24.831	-0.533	-0.533	0.000	0.000	0.000
28	A	27	ALA	0	0.022	0.014	26.754	0.442	0.442	0.000	0.000	0.000
29	A	28	HIS	0	0.001	0.016	25.076	-0.702	-0.702	0.000	0.000	0.000
30	A	29	VAL	0	0.051	0.020	27.750	0.500	0.500	0.000	0.000	0.000
31	A	30	THR	0	0.011	0.015	28.003	-0.317	-0.317	0.000	0.000	0.000
32	A	31	LEU	0	0.024	0.004	25.803	0.381	0.381	0.000	0.000	0.000
33	A	32	ALA	0	0.011	0.005	28.949	-0.199	-0.199	0.000	0.000	0.000
34	A	33	VAL	0	-0.019	-0.021	25.907	0.121	0.121	0.000	0.000	0.000
35	A	34	ASN	0	-0.015	-0.010	29.195	-0.056	-0.056	0.000	0.000	0.000
36	A	35	ARG	1	0.803	0.872	29.127	10.121	10.121	0.000	0.000	0.000
37	A	36	SER	0	-0.012	-0.009	29.423	0.133	0.133	0.000	0.000	0.000
38	A	37	PHE	0	-0.019	-0.004	28.657	0.286	0.286	0.000	0.000	0.000
39	A	38	LYS	1	0.903	0.950	33.493	7.814	7.814	0.000	0.000	0.000
40	A	39	ASN	0	0.013	-0.007	35.916	0.058	0.058	0.000	0.000	0.000
41	A	40	ALA	0	0.006	-0.007	37.530	0.103	0.103	0.000	0.000	0.000
42	A	41	SER	0	-0.017	-0.005	40.471	0.220	0.220	0.000	0.000	0.000
43	A	42	GLY	0	-0.016	0.006	40.823	0.154	0.154	0.000	0.000	0.000
44	A	43	GLU	-1	-0.887	-0.950	40.099	-7.465	-7.465	0.000	0.000	0.000
45	A	44	ILE	0	-0.050	-0.029	34.625	-0.169	-0.169	0.000	0.000	0.000
46	A	45	GLU	-1	-0.843	-0.891	33.951	-9.012	-9.012	0.000	0.000	0.000
47	A	46	ALA	0	-0.010	-0.020	31.740	-0.170	-0.170	0.000	0.000	0.000
48	A	47	ASP	-1	-0.828	-0.869	27.131	-11.177	-11.177	0.000	0.000	0.000
49	A	48	TYR	0	0.002	-0.014	29.063	0.076	0.076	0.000	0.000	0.000
50	A	49	VAL	0	0.020	0.019	22.950	-0.294	-0.294	0.000	0.000	0.000
51	A	50	ASN	0	0.011	0.005	25.292	0.656	0.656	0.000	0.000	0.000
52	A	51	CYS	0	-0.032	-0.018	23.362	-0.788	-0.788	0.000	0.000	0.000
53	A	52	THR	0	0.023	0.019	21.903	0.351	0.351	0.000	0.000	0.000
54	A	53	LEU	0	-0.028	-0.008	22.450	-0.618	-0.618	0.000	0.000	0.000
55	A	54	TRP	0	0.072	0.019	21.050	0.454	0.454	0.000	0.000	0.000
56	A	55	ARG	1	0.968	0.974	23.959	12.044	12.044	0.000	0.000	0.000
57	A	56	LYS	1	1.043	1.006	26.373	10.377	10.377	0.000	0.000	0.000
58	A	57	THR	0	-0.006	0.031	24.195	0.491	0.491	0.000	0.000	0.000
59	A	58	ALA	0	0.037	0.024	27.019	0.221	0.221	0.000	0.000	0.000
60	A	59	GLU	-1	-0.844	-0.906	28.460	-9.584	-9.584	0.000	0.000	0.000
61	A	60	ASN	0	-0.030	-0.036	30.452	0.518	0.518	0.000	0.000	0.000
62	A	61	THR	0	0.023	-0.009	28.483	0.098	0.098	0.000	0.000	0.000
63	A	62	ALA	0	-0.075	-0.032	31.675	0.199	0.199	0.000	0.000	0.000
64	A	63	LEU	0	-0.034	-0.004	33.946	0.231	0.231	0.000	0.000	0.000
65	A	64	TYR	0	-0.058	-0.032	33.807	0.301	0.301	0.000	0.000	0.000
66	A	65	CYS	0	-0.051	-0.008	33.369	-0.021	-0.021	0.000	0.000	0.000
67	A	66	GLN	0	0.043	0.017	35.429	0.058	0.058	0.000	0.000	0.000
68	A	67	LYS	1	0.948	0.971	36.472	7.633	7.633	0.000	0.000	0.000
69	A	68	GLY	0	-0.048	-0.021	36.481	0.217	0.217	0.000	0.000	0.000
70	A	69	SER	0	0.004	-0.014	34.300	0.013	0.013	0.000	0.000	0.000
71	A	70	LEU	0	-0.075	-0.028	31.591	-0.252	-0.252	0.000	0.000	0.000
72	A	71	VAL	0	0.017	-0.002	27.602	0.018	0.018	0.000	0.000	0.000
73	A	72	GLY	0	0.006	0.004	26.267	-0.115	-0.115	0.000	0.000	0.000
74	A	73	VAL	0	0.002	-0.003	21.594	0.018	0.018	0.000	0.000	0.000
75	A	74	SER	0	-0.013	-0.001	18.191	-0.304	-0.304	0.000	0.000	0.000
76	A	75	GLY	0	0.070	0.042	16.984	0.456	0.456	0.000	0.000	0.000
77	A	76	ARG	1	0.935	0.987	12.344	20.562	20.562	0.000	0.000	0.000
78	A	77	ILE	0	0.035	0.022	14.728	1.097	1.097	0.000	0.000	0.000
79	A	78	GLN	0	-0.087	-0.049	14.506	-2.598	-2.598	0.000	0.000	0.000
80	A	79	THR	0	0.005	-0.005	15.460	0.850	0.850	0.000	0.000	0.000
81	A	80	ARG	1	0.869	0.930	16.982	13.305	13.305	0.000	0.000	0.000
82	A	81	SER	0	0.029	0.016	19.599	-0.008	-0.008	0.000	0.000	0.000
83	A	82	TYR	0	-0.074	-0.035	21.922	-0.291	-0.291	0.000	0.000	0.000
84	A	83	GLU	-1	-0.797	-0.913	25.132	-10.707	-10.707	0.000	0.000	0.000
85	A	84	ASN	0	-0.126	-0.067	28.464	0.044	0.044	0.000	0.000	0.000
86	A	85	GLU	-1	-0.888	-0.932	31.293	-8.380	-8.380	0.000	0.000	0.000
87	A	86	GLU	-1	-0.924	-0.955	31.865	-9.276	-9.276	0.000	0.000	0.000
88	A	87	GLY	0	-0.058	-0.024	31.385	0.256	0.256	0.000	0.000	0.000
89	A	88	VAL	0	-0.057	-0.036	30.756	0.158	0.158	0.000	0.000	0.000
90	A	89	ASN	0	0.004	0.014	25.004	0.185	0.185	0.000	0.000	0.000
91	A	90	VAL	0	-0.038	-0.008	26.441	-0.092	-0.092	0.000	0.000	0.000
92	A	91	TYR	0	-0.011	-0.016	20.736	-0.358	-0.358	0.000	0.000	0.000
93	A	92	VAL	0	-0.008	-0.002	22.109	0.363	0.363	0.000	0.000	0.000
94	A	93	THR	0	-0.016	-0.025	19.649	-0.876	-0.876	0.000	0.000	0.000
95	A	94	GLU	-1	-0.838	-0.899	19.814	-13.413	-13.413	0.000	0.000	0.000
96	A	95	VAL	0	0.020	0.003	18.826	-1.113	-1.113	0.000	0.000	0.000
97	A	96	LEU	0	-0.052	-0.028	16.486	0.734	0.734	0.000	0.000	0.000
98	A	97	ALA	0	-0.024	-0.019	18.452	-0.690	-0.690	0.000	0.000	0.000
99	A	98	ASP	-1	-0.894	-0.944	16.400	-18.189	-18.189	0.000	0.000	0.000
100	A	99	THR	0	-0.071	-0.045	19.954	0.839	0.839	0.000	0.000	0.000
101	A	100	VAL	0	0.041	-0.006	22.640	-0.131	-0.131	0.000	0.000	0.000
102	A	101	ARG	1	0.906	0.967	25.582	10.709	10.709	0.000	0.000	0.000
103	A	102	PHE	0	0.037	0.001	27.894	0.005	0.005	0.000	0.000	0.000
104	A	103	MET	0	-0.063	-0.039	29.283	-0.027	-0.027	0.000	0.000	0.000
105	A	104	ASP	-1	-0.788	-0.843	32.781	-8.494	-8.494	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)