FMO DATABASE

FMODB ID: R8Y18

Calculation Name: 3V4D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3V4D

Chain ID: A

ChEMBL ID:

UniProt ID: P0AFQ6

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	-1002083.763355
FMO2-HF: Nuclear repulsion	955149.940443
FMO2-HF: Total energy	-46933.822913
FMO2-MP2: Total energy	-47072.089093

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:2:PRO)

Summations of interaction energy for fragment #1(A:2:PRO)

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.
-1.335	-0.088	-0.007	-0.49	-0.75	0.003

Interaction energy analysis for fragmet #1(A:2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.020

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	4	SER	0	0.021	0.016	3.878	-0.558	0.689	-0.007	-0.490	-0.750	0.003
4	A	5	VAL	0	-0.032	-0.029	5.929	0.061	0.061	0.000	0.000	0.000	0.000
5	A	6	ILE	0	-0.011	0.009	8.964	0.039	0.039	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.015	-0.009	12.379	0.005	0.005	0.000	0.000	0.000	0.000
7	A	8	PRO	0	0.030	0.028	15.245	0.009	0.009	0.000	0.000	0.000	0.000
8	A	9	ALA	0	0.011	-0.002	18.109	0.001	0.001	0.000	0.000	0.000	0.000
9	A	10	GLY	0	0.001	-0.008	20.503	0.001	0.001	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.062	-0.035	18.580	0.000	0.000	0.000	0.000	0.000	0.000
11	A	12	SER	0	-0.002	0.009	20.001	0.002	0.002	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.002	0.007	21.736	0.000	0.000	0.000	0.000	0.000	0.000
13	A	14	PRO	0	-0.039	-0.021	24.180	0.001	0.001	0.000	0.000	0.000	0.000
14	A	15	LEU	0	0.018	0.026	18.359	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.025	0.010	19.231	0.001	0.001	0.000	0.000	0.000	0.000
16	A	17	PRO	0	-0.051	-0.021	17.488	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	18	PHE	0	-0.018	-0.014	15.115	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	19	VAL	0	0.020	0.017	11.721	0.005	0.005	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.029	0.016	15.172	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.096	0.043	14.018	0.009	0.009	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.119	-0.053	8.442	-0.031	-0.031	0.000	0.000	0.000	0.000
22	A	23	LEU	0	0.057	0.030	8.341	0.058	0.058	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.021	-0.020	5.680	-0.316	-0.316	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.911	-0.949	5.401	-0.583	-0.583	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.034	0.028	7.567	0.033	0.033	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.040	-0.010	10.132	0.018	0.018	0.000	0.000	0.000	0.000
27	A	28	VAL	0	0.005	-0.003	10.588	-0.060	-0.060	0.000	0.000	0.000	0.000
28	A	29	TYR	0	-0.010	-0.011	9.958	0.042	0.042	0.000	0.000	0.000	0.000
29	A	30	VAL	0	-0.020	-0.016	13.817	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	31	SER	0	0.000	-0.026	16.109	0.002	0.002	0.000	0.000	0.000	0.000
31	A	32	GLY	0	0.007	0.017	17.907	0.006	0.006	0.000	0.000	0.000	0.000
32	A	33	THR	0	-0.052	-0.021	21.217	0.001	0.001	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.017	-0.006	23.496	0.002	0.002	0.000	0.000	0.000	0.000
34	A	35	ALA	0	0.024	0.028	27.017	0.000	0.000	0.000	0.000	0.000	0.000
35	A	36	PHE	0	-0.031	-0.016	25.916	0.002	0.002	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.766	-0.887	28.568	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	38	GLN	0	0.005	0.005	24.828	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	39	HIS	0	-0.019	-0.020	27.118	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	40	ASN	0	-0.039	-0.010	24.978	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	41	ASN	0	-0.061	-0.034	28.508	0.000	0.000	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.003	0.006	31.713	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	43	LEU	0	0.010	0.008	31.481	0.002	0.002	0.000	0.000	0.000	0.000
43	A	44	PHE	0	-0.016	-0.035	33.371	0.000	0.000	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.046	0.043	37.189	0.000	0.000	0.000	0.000	0.000	0.000
45	A	46	ASP	-1	-0.887	-0.947	38.166	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.840	-0.923	39.100	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	48	PRO	0	0.004	0.002	36.015	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.786	0.886	35.156	0.010	0.010	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.012	-0.001	35.014	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	51	GLN	0	-0.023	-0.011	32.691	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	52	THR	0	0.004	-0.021	30.933	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.845	0.916	30.059	0.012	0.012	0.000	0.000	0.000	0.000
53	A	54	HIS	0	0.010	0.014	27.329	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	55	VAL	0	0.037	0.026	25.642	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	56	LEU	0	0.015	0.005	25.319	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.835	-0.882	25.650	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.060	-0.029	22.145	0.000	0.000	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.008	-0.015	20.839	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.838	0.880	20.712	0.013	0.013	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.943	0.974	21.032	0.015	0.015	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.045	-0.010	15.855	0.000	0.000	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.029	0.006	16.551	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.931	-0.957	17.486	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	65	THR	0	-0.095	-0.068	14.764	0.009	0.009	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.058	-0.026	13.263	0.004	0.004	0.000	0.000	0.000	0.000
66	A	67	GLY	0	-0.016	0.001	14.345	0.016	0.016	0.000	0.000	0.000	0.000
67	A	68	GLY	0	-0.011	0.005	17.081	0.006	0.006	0.000	0.000	0.000	0.000
68	A	69	THR	0	-0.068	-0.067	18.784	0.000	0.000	0.000	0.000	0.000	0.000
69	A	70	MET	0	0.011	0.000	21.397	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	71	ALA	0	-0.015	-0.009	23.907	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.798	-0.874	18.701	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	73	VAL	0	-0.041	-0.017	19.498	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	74	THR	0	0.002	0.002	18.251	0.003	0.003	0.000	0.000	0.000	0.000
74	A	75	PHE	0	-0.051	-0.031	20.606	0.003	0.003	0.000	0.000	0.000	0.000
75	A	76	ASN	0	0.007	0.014	21.394	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	77	SER	0	0.003	0.001	21.847	0.003	0.003	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.019	-0.007	24.225	0.000	0.000	0.000	0.000	0.000	0.000
78	A	79	PHE	0	0.032	0.003	23.662	0.001	0.001	0.000	0.000	0.000	0.000
79	A	80	ILE	0	0.005	0.000	29.137	0.001	0.001	0.000	0.000	0.000	0.000
80	A	81	THR	0	0.061	0.032	32.733	0.000	0.000	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.805	-0.892	35.518	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	83	TRP	0	0.020	0.010	34.545	0.000	0.000	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.807	0.887	39.121	0.013	0.013	0.000	0.000	0.000	0.000
84	A	85	ASN	0	0.049	0.024	37.294	0.001	0.001	0.000	0.000	0.000	0.000
85	A	86	TYR	0	0.034	0.019	33.760	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	87	ALA	0	-0.010	-0.008	36.842	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.031	0.010	38.594	0.000	0.000	0.000	0.000	0.000	0.000
88	A	89	ILE	0	0.036	0.020	32.413	0.000	0.000	0.000	0.000	0.000	0.000
89	A	90	ASN	0	-0.009	-0.008	33.927	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.835	-0.890	35.190	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.006	0.004	32.624	0.000	0.000	0.000	0.000	0.000	0.000
92	A	93	TYR	0	0.014	0.003	27.438	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.019	-0.014	31.176	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	95	GLU	-1	-0.842	-0.907	33.293	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	96	PHE	0	-0.014	-0.012	27.549	0.001	0.001	0.000	0.000	0.000	0.000
96	A	97	PHE	0	-0.001	0.009	24.567	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	98	PRO	0	0.048	0.035	29.564	0.000	0.000	0.000	0.000	0.000	0.000
98	A	99	GLY	0	-0.008	-0.005	30.846	0.001	0.001	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.900	-0.953	28.535	-0.015	-0.015	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.777	0.880	28.837	0.016	0.016	0.000	0.000	0.000	0.000
101	A	102	PRO	0	0.018	0.019	24.418	0.000	0.000	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.005	0.010	24.877	0.002	0.002	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.841	0.904	25.456	0.022	0.022	0.000	0.000	0.000	0.000
104	A	105	PHE	0	-0.013	0.004	23.850	0.002	0.002	0.000	0.000	0.000	0.000
105	A	106	CYS	0	-0.011	-0.009	28.232	0.000	0.000	0.000	0.000	0.000	0.000
106	A	107	ILE	0	-0.030	-0.003	28.121	0.002	0.002	0.000	0.000	0.000	0.000
107	A	108	GLN	0	-0.011	-0.013	31.743	0.000	0.000	0.000	0.000	0.000	0.000
108	A	109	CYS	0	-0.066	-0.039	30.172	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	110	GLY	0	0.022	0.019	32.482	0.001	0.001	0.000	0.000	0.000	0.000
110	A	111	LEU	0	0.010	0.000	28.514	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.001	0.000	26.756	0.002	0.002	0.000	0.000	0.000	0.000
112	A	113	LYS	1	0.878	0.930	29.447	0.019	0.019	0.000	0.000	0.000	0.000
113	A	114	PRO	0	0.004	-0.005	32.521	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.887	-0.939	35.312	-0.014	-0.014	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.007	0.008	31.356	0.000	0.000	0.000	0.000	0.000	0.000
116	A	117	LEU	0	-0.020	-0.011	33.410	0.000	0.000	0.000	0.000	0.000	0.000
117	A	118	VAL	0	-0.078	-0.051	29.586	0.000	0.000	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.871	-0.938	24.392	-0.037	-0.037	0.000	0.000	0.000	0.000
119	A	120	ILE	0	-0.051	-0.030	23.759	0.001	0.001	0.000	0.000	0.000	0.000
120	A	121	ALA	0	0.027	0.033	19.639	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	122	THR	0	-0.007	-0.025	19.292	0.005	0.005	0.000	0.000	0.000	0.000
122	A	123	ILE	0	-0.035	-0.012	15.389	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	124	ALA	0	0.030	0.012	16.220	0.013	0.013	0.000	0.000	0.000	0.000
124	A	125	HIS	0	-0.052	-0.022	14.889	-0.015	-0.015	0.000	0.000	0.000	0.000
125	A	126	ILE	0	0.023	0.024	12.524	0.008	0.008	0.000	0.000	0.000	0.000
126	A	127	ALA	0	-0.029	-0.010	13.356	0.008	0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:PRO)