FMO DATABASE

FMODB ID: ZVN2N

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	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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1000214.469291
FMO2-HF: Nuclear repulsion	953280.792853
FMO2-HF: Total energy	-46933.676438
FMO2-MP2: Total energy	-47071.890627

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.
-1.938	-0.219	-0.007	-0.849	-0.864	0.004

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 : 0.016 / q_NPA : -0.004

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	0.013	0.018	3.759	-1.574	0.145	-0.007	-0.849	-0.864	0.004
4	A	5	VAL	0	-0.035	-0.030	6.287	0.065	0.065	0.000	0.000	0.000	0.000
5	A	6	ILE	0	-0.006	0.009	9.068	0.029	0.029	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.009	-0.013	12.514	0.003	0.003	0.000	0.000	0.000	0.000
7	A	8	PRO	0	0.020	0.024	15.282	0.006	0.006	0.000	0.000	0.000	0.000
8	A	9	ALA	0	0.027	0.007	18.480	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	10	GLY	0	0.003	-0.007	20.830	0.002	0.002	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.068	-0.048	18.450	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	12	SER	0	-0.004	0.008	19.724	0.001	0.001	0.000	0.000	0.000	0.000
12	A	13	ALA	0	-0.008	0.003	21.692	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	14	PRO	0	-0.027	-0.014	23.636	0.000	0.000	0.000	0.000	0.000	0.000
14	A	15	LEU	0	0.014	0.024	18.425	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.022	0.005	18.732	0.003	0.003	0.000	0.000	0.000	0.000
16	A	17	PRO	0	-0.050	-0.016	16.875	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	18	PHE	0	-0.022	-0.013	14.850	0.000	0.000	0.000	0.000	0.000	0.000
18	A	19	VAL	0	0.020	0.010	11.157	0.000	0.000	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.030	0.013	14.442	0.002	0.002	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.091	0.043	13.883	0.012	0.012	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.117	-0.046	8.467	-0.030	-0.030	0.000	0.000	0.000	0.000
22	A	23	LEU	0	0.068	0.037	8.295	0.043	0.043	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.020	-0.026	5.607	-0.191	-0.191	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.908	-0.942	5.621	-0.277	-0.277	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.022	0.010	7.638	-0.031	-0.031	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.023	0.007	10.051	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.003	-0.008	10.541	-0.027	-0.027	0.000	0.000	0.000	0.000
28	A	29	TYR	0	-0.003	-0.005	9.834	0.018	0.018	0.000	0.000	0.000	0.000
29	A	30	VAL	0	-0.025	-0.020	13.768	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.018	-0.040	16.088	0.002	0.002	0.000	0.000	0.000	0.000
31	A	32	GLY	0	-0.009	0.010	17.878	0.004	0.004	0.000	0.000	0.000	0.000
32	A	33	THR	0	-0.042	-0.012	21.234	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.022	-0.011	23.449	0.002	0.002	0.000	0.000	0.000	0.000
34	A	35	ALA	0	0.018	0.017	26.709	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	36	PHE	0	-0.047	-0.014	25.380	0.001	0.001	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.762	-0.893	28.210	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	38	GLN	0	0.019	0.008	24.683	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	39	HIS	0	-0.029	-0.025	27.182	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	40	ASN	0	-0.040	-0.012	24.303	0.000	0.000	0.000	0.000	0.000	0.000
40	A	41	ASN	0	-0.065	-0.030	28.318	0.001	0.001	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.010	0.004	31.236	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	43	LEU	0	0.001	0.003	31.088	0.001	0.001	0.000	0.000	0.000	0.000
43	A	44	PHE	0	-0.028	-0.038	33.120	0.000	0.000	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.060	0.038	37.120	0.000	0.000	0.000	0.000	0.000	0.000
45	A	46	ASP	-1	-0.892	-0.936	38.149	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.880	-0.951	38.724	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	48	PRO	0	0.014	0.002	36.085	0.000	0.000	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.803	0.899	35.171	0.003	0.003	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.016	0.007	35.080	0.000	0.000	0.000	0.000	0.000	0.000
50	A	51	GLN	0	-0.019	-0.014	32.491	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.004	-0.018	30.892	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.866	0.919	30.077	0.003	0.003	0.000	0.000	0.000	0.000
53	A	54	HIS	0	0.006	0.007	27.529	0.000	0.000	0.000	0.000	0.000	0.000
54	A	55	VAL	0	0.029	0.014	25.570	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	56	LEU	0	0.006	0.002	25.357	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.836	-0.888	25.507	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.050	-0.021	21.964	0.000	0.000	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.007	-0.007	20.679	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.877	0.911	20.569	0.002	0.002	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.957	0.996	21.215	0.013	0.013	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.058	-0.021	15.905	0.000	0.000	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.015	-0.006	16.771	0.000	0.000	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.948	-0.961	17.511	0.009	0.009	0.000	0.000	0.000	0.000
64	A	65	THR	0	-0.100	-0.062	15.442	0.004	0.004	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.065	-0.035	13.297	0.004	0.004	0.000	0.000	0.000	0.000
66	A	67	GLY	0	-0.013	0.002	14.465	0.021	0.021	0.000	0.000	0.000	0.000
67	A	68	GLY	0	-0.007	0.008	17.144	0.004	0.004	0.000	0.000	0.000	0.000
68	A	69	THR	0	-0.040	-0.048	18.691	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	70	MET	0	-0.004	-0.016	21.430	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	71	ALA	0	-0.026	-0.012	23.717	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.784	-0.875	18.767	0.017	0.017	0.000	0.000	0.000	0.000
72	A	73	VAL	0	-0.053	-0.021	19.704	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	74	THR	0	-0.005	-0.001	18.735	0.000	0.000	0.000	0.000	0.000	0.000
74	A	75	PHE	0	-0.030	-0.025	20.523	0.001	0.001	0.000	0.000	0.000	0.000
75	A	76	ASN	0	-0.015	0.007	21.175	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	77	SER	0	-0.016	-0.003	21.855	0.001	0.001	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.008	-0.005	24.174	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	79	PHE	0	0.018	0.001	23.530	0.001	0.001	0.000	0.000	0.000	0.000
79	A	80	ILE	0	0.031	0.006	29.034	0.000	0.000	0.000	0.000	0.000	0.000
80	A	81	THR	0	0.077	0.043	32.610	0.000	0.000	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.788	-0.884	35.348	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	83	TRP	0	-0.001	0.003	34.407	0.000	0.000	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.810	0.892	39.280	0.004	0.004	0.000	0.000	0.000	0.000
84	A	85	ASN	0	0.040	0.015	37.563	0.001	0.001	0.000	0.000	0.000	0.000
85	A	86	TYR	0	0.035	0.014	33.812	0.000	0.000	0.000	0.000	0.000	0.000
86	A	87	ALA	0	-0.007	-0.006	36.901	0.000	0.000	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.039	0.014	38.621	0.000	0.000	0.000	0.000	0.000	0.000
88	A	89	ILE	0	0.038	0.023	32.399	0.000	0.000	0.000	0.000	0.000	0.000
89	A	90	ASN	0	-0.003	-0.009	33.931	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.831	-0.878	34.974	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.003	-0.003	32.656	0.000	0.000	0.000	0.000	0.000	0.000
92	A	93	TYR	0	0.026	0.007	27.168	0.000	0.000	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.013	-0.014	31.067	0.000	0.000	0.000	0.000	0.000	0.000
94	A	95	GLU	-1	-0.858	-0.909	33.086	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	96	PHE	0	-0.028	-0.017	27.670	0.001	0.001	0.000	0.000	0.000	0.000
96	A	97	PHE	0	-0.023	-0.004	24.485	0.000	0.000	0.000	0.000	0.000	0.000
97	A	98	PRO	0	0.043	0.028	29.605	0.000	0.000	0.000	0.000	0.000	0.000
98	A	99	GLY	0	-0.010	-0.004	30.566	0.000	0.000	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.903	-0.953	28.580	0.001	0.001	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.772	0.883	28.385	0.001	0.001	0.000	0.000	0.000	0.000
101	A	102	PRO	0	0.020	0.017	24.257	0.000	0.000	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.014	0.014	24.793	0.000	0.000	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.846	0.898	25.368	0.006	0.006	0.000	0.000	0.000	0.000
104	A	105	PHE	0	-0.007	0.006	23.661	0.001	0.001	0.000	0.000	0.000	0.000
105	A	106	CYS	0	-0.002	-0.003	27.942	0.000	0.000	0.000	0.000	0.000	0.000
106	A	107	ILE	0	-0.016	0.007	27.923	0.001	0.001	0.000	0.000	0.000	0.000
107	A	108	GLN	0	-0.028	-0.024	31.443	0.000	0.000	0.000	0.000	0.000	0.000
108	A	109	CYS	0	-0.051	-0.030	29.772	0.000	0.000	0.000	0.000	0.000	0.000
109	A	110	GLY	0	0.023	0.021	32.030	0.000	0.000	0.000	0.000	0.000	0.000
110	A	111	LEU	0	0.009	0.000	28.355	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	112	VAL	0	-0.012	-0.006	26.724	0.001	0.001	0.000	0.000	0.000	0.000
112	A	113	LYS	1	0.909	0.950	29.403	0.011	0.011	0.000	0.000	0.000	0.000
113	A	114	PRO	0	0.007	-0.007	32.241	0.000	0.000	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.875	-0.936	35.331	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.037	0.000	31.173	0.000	0.000	0.000	0.000	0.000	0.000
116	A	117	LEU	0	-0.036	-0.021	33.202	0.000	0.000	0.000	0.000	0.000	0.000
117	A	118	VAL	0	-0.067	-0.045	29.467	0.000	0.000	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.881	-0.946	24.049	-0.018	-0.018	0.000	0.000	0.000	0.000
119	A	120	ILE	0	-0.044	-0.028	23.642	0.001	0.001	0.000	0.000	0.000	0.000
120	A	121	ALA	0	0.050	0.046	19.503	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	122	THR	0	-0.008	-0.023	19.055	0.003	0.003	0.000	0.000	0.000	0.000
122	A	123	ILE	0	-0.021	0.002	15.203	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	124	ALA	0	0.038	0.011	15.977	0.005	0.005	0.000	0.000	0.000	0.000
124	A	125	HIS	0	-0.063	-0.021	14.989	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	126	ILE	0	0.047	0.032	12.651	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	127	ALA	0	-0.031	-0.014	13.188	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:2:PRO)