FMO DATABASE

FMODB ID: V5L51

Calculation Name: 4O00-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4O00

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WZ42

Base Structure: X-ray

Registration Date: 2023-09-19

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-743227.667987
FMO2-HF: Nuclear repulsion	703590.541639
FMO2-HF: Total energy	-39637.126348
FMO2-MP2: Total energy	-39752.564307

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:3:SER)

Summations of interaction energy for fragment #1(A:3:SER)

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.
-18.741	-9.455	3.174	-5.826	-6.63	0.002

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / 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	5	ARG	1	0.878	0.930	3.808	0.683	3.586	-0.022	-1.607	-1.273	0.006
4	A	6	PRO	0	-0.024	0.013	6.585	-0.508	-0.508	0.000	0.000	0.000	0.000
5	A	7	SER	0	0.004	-0.007	8.106	-0.031	-0.031	0.000	0.000	0.000	0.000
6	A	8	PRO	0	0.023	-0.004	11.632	0.097	0.097	0.000	0.000	0.000	0.000
7	A	9	PRO	0	-0.062	-0.018	14.482	-0.007	-0.007	0.000	0.000	0.000	0.000
8	A	10	VAL	0	0.022	0.011	16.296	-0.032	-0.032	0.000	0.000	0.000	0.000
9	A	11	ASN	0	-0.022	-0.023	19.292	0.031	0.031	0.000	0.000	0.000	0.000
10	A	12	LEU	0	-0.010	0.011	22.038	0.026	0.026	0.000	0.000	0.000	0.000
11	A	13	THR	0	-0.045	-0.024	23.523	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	14	SER	0	-0.004	-0.019	26.825	0.010	0.010	0.000	0.000	0.000	0.000
13	A	15	SER	0	-0.005	-0.004	29.586	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	16	ASP	-1	-0.916	-0.958	32.377	0.042	0.042	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.054	-0.027	34.151	0.000	0.000	0.000	0.000	0.000	0.000
16	A	18	THR	0	0.015	0.011	35.630	0.001	0.001	0.000	0.000	0.000	0.000
17	A	19	GLN	0	0.001	-0.026	37.547	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	20	SER	0	0.002	0.009	37.322	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.062	-0.044	33.031	0.007	0.007	0.000	0.000	0.000	0.000
20	A	22	VAL	0	0.049	0.037	29.795	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	23	GLN	0	-0.030	-0.012	27.293	0.009	0.009	0.000	0.000	0.000	0.000
22	A	24	LEU	0	0.020	0.008	24.843	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	25	LYS	1	0.968	0.981	23.849	0.003	0.003	0.000	0.000	0.000	0.000
24	A	26	TRP	0	-0.009	0.016	17.446	-0.026	-0.026	0.000	0.000	0.000	0.000
25	A	27	GLU	-1	-0.884	-0.936	19.328	-0.043	-0.043	0.000	0.000	0.000	0.000
26	A	28	PRO	0	-0.010	-0.013	14.250	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	29	PRO	0	-0.019	-0.005	11.331	-0.032	-0.032	0.000	0.000	0.000	0.000
28	A	30	LEU	0	0.009	0.011	13.317	0.023	0.023	0.000	0.000	0.000	0.000
29	A	31	LYS	1	0.837	0.904	7.020	2.445	2.445	0.000	0.000	0.000	0.000
30	A	32	ASP	-1	-0.805	-0.913	7.011	-0.411	-0.411	0.000	0.000	0.000	0.000
31	A	33	GLY	0	-0.004	-0.002	4.687	0.197	0.301	-0.001	-0.023	-0.080	0.000
32	A	34	GLY	0	0.003	0.000	2.501	-6.840	-4.396	1.661	-2.076	-2.029	-0.021
33	A	35	SER	0	-0.058	-0.045	2.565	2.133	2.937	0.573	-0.477	-0.899	-0.001
34	A	36	PRO	0	0.012	0.015	4.158	-0.575	-0.561	0.001	-0.017	0.003	0.000
35	A	37	ILE	0	-0.005	-0.002	7.597	0.291	0.291	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.045	-0.025	9.087	0.032	0.032	0.000	0.000	0.000	0.000
37	A	39	GLY	0	0.002	-0.010	11.437	-0.086	-0.086	0.000	0.000	0.000	0.000
38	A	40	TYR	0	0.001	0.001	13.304	-0.036	-0.036	0.000	0.000	0.000	0.000
39	A	41	ILE	0	-0.034	-0.022	14.830	0.031	0.031	0.000	0.000	0.000	0.000
40	A	42	ILE	0	0.032	0.015	17.915	-0.047	-0.047	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.861	-0.921	20.396	-0.053	-0.053	0.000	0.000	0.000	0.000
42	A	44	ARG	1	0.974	0.978	23.496	-0.032	-0.032	0.000	0.000	0.000	0.000
43	A	45	CYS	0	-0.012	0.001	27.128	0.002	0.002	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.910	-0.943	29.504	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.876	-0.969	32.959	-0.062	-0.062	0.000	0.000	0.000	0.000
46	A	48	GLY	0	-0.031	0.001	33.971	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	49	LYS	1	0.828	0.917	33.096	0.030	0.030	0.000	0.000	0.000	0.000
48	A	50	ASP	-1	-0.863	-0.946	27.833	-0.142	-0.142	0.000	0.000	0.000	0.000
49	A	51	ASN	0	-0.047	-0.026	28.405	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	52	TRP	0	0.015	0.009	24.465	0.015	0.015	0.000	0.000	0.000	0.000
51	A	53	ILE	0	-0.020	-0.007	25.756	0.010	0.010	0.000	0.000	0.000	0.000
52	A	54	ARG	1	0.919	0.945	17.265	-0.230	-0.230	0.000	0.000	0.000	0.000
53	A	55	CYS	0	-0.066	-0.021	23.724	0.005	0.005	0.000	0.000	0.000	0.000
54	A	56	ASN	0	-0.003	0.007	19.165	-0.022	-0.022	0.000	0.000	0.000	0.000
55	A	57	MET	0	0.030	0.016	21.709	0.004	0.004	0.000	0.000	0.000	0.000
56	A	58	LYS	1	0.909	0.943	19.584	-0.324	-0.324	0.000	0.000	0.000	0.000
57	A	59	LEU	0	0.001	0.029	13.305	-0.057	-0.057	0.000	0.000	0.000	0.000
58	A	60	VAL	0	-0.011	0.005	17.519	0.020	0.020	0.000	0.000	0.000	0.000
59	A	61	PRO	0	0.009	0.015	16.224	0.002	0.002	0.000	0.000	0.000	0.000
60	A	62	GLU	-1	-0.891	-0.947	17.270	0.262	0.262	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.011	-0.010	17.165	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	64	THR	0	-0.026	-0.027	20.403	-0.034	-0.034	0.000	0.000	0.000	0.000
63	A	65	TYR	0	0.027	-0.004	22.968	0.025	0.025	0.000	0.000	0.000	0.000
64	A	66	LYS	1	0.961	1.006	24.946	-0.098	-0.098	0.000	0.000	0.000	0.000
65	A	67	VAL	0	0.023	0.017	26.651	0.010	0.010	0.000	0.000	0.000	0.000
66	A	68	THR	0	-0.031	-0.029	28.920	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	69	GLY	0	-0.012	-0.005	31.710	0.000	0.000	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.097	-0.028	31.595	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.904	-0.957	35.214	0.007	0.007	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.956	0.966	38.591	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	73	GLY	0	-0.002	0.016	40.878	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	74	ASN	0	-0.033	-0.001	37.184	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.922	0.965	36.255	0.041	0.041	0.000	0.000	0.000	0.000
74	A	76	TYR	0	0.021	0.014	31.142	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	77	LEU	0	0.017	0.023	28.468	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	78	TYR	0	0.015	-0.019	25.662	0.014	0.014	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.875	0.942	21.161	0.108	0.108	0.000	0.000	0.000	0.000
78	A	80	VAL	0	-0.002	0.007	17.609	0.034	0.034	0.000	0.000	0.000	0.000
79	A	81	SER	0	0.055	0.022	14.659	-0.063	-0.063	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.016	0.004	11.563	0.089	0.089	0.000	0.000	0.000	0.000
81	A	83	GLU	-1	-0.874	-0.932	9.971	0.563	0.563	0.000	0.000	0.000	0.000
82	A	84	ASN	0	0.010	0.002	4.274	0.672	0.734	-0.001	-0.017	-0.044	0.000
83	A	85	LYS	1	0.933	0.944	2.889	-12.734	-11.018	0.232	-0.825	-1.122	0.010
84	A	86	ALA	0	-0.049	-0.006	2.654	-1.515	-0.367	0.732	-0.760	-1.120	0.008
85	A	87	GLY	0	0.013	0.001	4.600	-1.682	-1.591	-0.001	-0.024	-0.066	0.000
86	A	88	VAL	0	0.002	0.002	8.222	0.101	0.101	0.000	0.000	0.000	0.000
87	A	89	SER	0	-0.001	0.011	10.987	-0.153	-0.153	0.000	0.000	0.000	0.000
88	A	90	ASP	-1	-0.874	-0.942	11.774	-0.620	-0.620	0.000	0.000	0.000	0.000
89	A	91	PRO	0	0.002	-0.010	15.177	0.024	0.024	0.000	0.000	0.000	0.000
90	A	92	SER	0	-0.017	-0.013	17.796	-0.030	-0.030	0.000	0.000	0.000	0.000
91	A	93	GLU	-1	-0.938	-0.965	19.273	-0.243	-0.243	0.000	0.000	0.000	0.000
92	A	94	ILE	0	-0.026	-0.016	22.664	0.026	0.026	0.000	0.000	0.000	0.000
93	A	95	LEU	0	-0.008	0.008	25.323	0.001	0.001	0.000	0.000	0.000	0.000
94	A	96	GLY	0	-0.009	-0.001	27.520	0.010	0.010	0.000	0.000	0.000	0.000
95	A	97	PRO	0	0.013	-0.011	31.171	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.046	-0.023	30.544	0.002	0.002	0.000	0.000	0.000	0.000
97	A	99	THR	0	0.005	-0.009	34.218	0.002	0.002	0.000	0.000	0.000	0.000
98	A	100	ALA	0	-0.028	0.002	36.495	0.003	0.003	0.000	0.000	0.000	0.000
99	A	101	ASP	-1	-0.900	-0.990	37.763	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	102	ASP	-1	-0.898	-0.925	39.807	0.014	0.014	0.000	0.000	0.000	0.000
101	A	103	ALA	0	-0.037	-0.016	40.424	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	104	PHE	0	-0.007	0.001	42.369	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)