FMO DATABASE

FMODB ID: 2NNMR

Calculation Name: 4WVR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4WVR

Chain ID: A

ChEMBL ID:

UniProt ID: Q0E9H6

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-651455.933754
FMO2-HF: Nuclear repulsion	614805.514766
FMO2-HF: Total energy	-36650.418989
FMO2-MP2: Total energy	-36757.017716

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:5:SER)

Summations of interaction energy for fragment #1(A:5: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.
-7.97	-6.13	5.215	-3.306	-3.75	-0.034

Interaction energy analysis for fragmet #1(A:5:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / 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

Sort

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	7	PRO	0	0.039	0.032	3.810	0.786	2.309	-0.018	-0.653	-0.852	0.002
4	A	8	PRO	0	-0.024	-0.020	6.361	0.236	0.236	0.000	0.000	0.000	0.000
5	A	9	SER	0	-0.001	0.009	9.601	0.221	0.221	0.000	0.000	0.000	0.000
6	A	10	ILE	0	-0.023	-0.018	12.509	0.017	0.017	0.000	0.000	0.000	0.000
7	A	11	ALA	0	0.006	0.016	15.891	0.029	0.029	0.000	0.000	0.000	0.000
8	A	12	PRO	0	-0.006	-0.003	19.002	0.015	0.015	0.000	0.000	0.000	0.000
9	A	13	PHE	0	0.020	-0.003	20.982	0.004	0.004	0.000	0.000	0.000	0.000
10	A	14	SER	0	-0.013	-0.031	24.766	0.009	0.009	0.000	0.000	0.000	0.000
11	A	15	PHE	0	0.017	0.009	28.395	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	16	GLY	0	0.004	0.007	31.357	0.012	0.012	0.000	0.000	0.000	0.000
13	A	17	ASP	-1	-0.972	-0.976	33.438	-0.216	-0.216	0.000	0.000	0.000	0.000
14	A	18	ASP	-1	-0.929	-0.956	35.525	-0.150	-0.150	0.000	0.000	0.000	0.000
15	A	19	PRO	0	-0.099	-0.064	37.612	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	20	VAL	0	0.023	0.015	36.121	0.003	0.003	0.000	0.000	0.000	0.000
17	A	21	ASN	0	-0.061	-0.046	39.477	0.012	0.012	0.000	0.000	0.000	0.000
18	A	22	THR	0	-0.005	-0.023	41.272	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	23	GLY	0	-0.024	-0.017	41.548	0.005	0.005	0.000	0.000	0.000	0.000
20	A	24	GLU	-1	-0.872	-0.921	39.205	-0.147	-0.147	0.000	0.000	0.000	0.000
21	A	25	ASN	0	0.015	0.021	35.354	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	26	ALA	0	0.054	0.035	33.539	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	27	GLY	0	0.012	-0.010	30.013	0.003	0.003	0.000	0.000	0.000	0.000
24	A	28	VAL	0	-0.027	0.013	25.459	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	29	GLN	0	0.003	-0.001	22.730	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	30	CYS	0	-0.062	0.004	18.594	-0.045	-0.045	0.000	0.000	0.000	0.000
27	A	31	MET	0	0.016	0.002	17.995	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	32	VAL	0	0.011	0.000	11.414	-0.042	-0.042	0.000	0.000	0.000	0.000
29	A	33	GLN	0	-0.020	-0.014	13.668	0.036	0.036	0.000	0.000	0.000	0.000
30	A	34	LYS	1	0.937	0.964	9.088	1.401	1.401	0.000	0.000	0.000	0.000
31	A	35	GLY	0	0.069	0.029	6.555	0.185	0.185	0.000	0.000	0.000	0.000
32	A	36	ASP	-1	-0.861	-0.919	2.074	-13.233	-13.246	4.590	-2.311	-2.266	-0.035
33	A	37	VAL	0	0.015	0.021	5.581	0.405	0.405	0.000	0.000	0.000	0.000
34	A	38	PRO	0	-0.026	-0.026	7.668	0.088	0.088	0.000	0.000	0.000	0.000
35	A	39	ILE	0	0.015	-0.005	8.953	-0.105	-0.105	0.000	0.000	0.000	0.000
36	A	40	THR	0	-0.028	-0.014	11.232	0.130	0.130	0.000	0.000	0.000	0.000
37	A	41	ILE	0	-0.022	-0.020	14.353	-0.086	-0.086	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.838	0.913	16.564	0.392	0.392	0.000	0.000	0.000	0.000
39	A	43	TRP	0	0.089	0.020	19.884	-0.049	-0.049	0.000	0.000	0.000	0.000
40	A	44	THR	0	-0.066	-0.028	22.425	0.029	0.029	0.000	0.000	0.000	0.000
41	A	45	LEU	0	0.083	0.043	24.958	-0.020	-0.020	0.000	0.000	0.000	0.000
42	A	46	ASN	0	-0.007	-0.010	28.435	0.009	0.009	0.000	0.000	0.000	0.000
43	A	47	SER	0	-0.033	-0.026	25.639	0.007	0.007	0.000	0.000	0.000	0.000
44	A	48	ARG	1	0.888	0.951	26.118	0.143	0.143	0.000	0.000	0.000	0.000
45	A	49	PRO	0	-0.043	-0.043	24.266	-0.016	-0.016	0.000	0.000	0.000	0.000
46	A	50	ILE	0	0.030	0.044	25.440	0.011	0.011	0.000	0.000	0.000	0.000
47	A	51	ILE	0	-0.059	-0.024	25.619	-0.020	-0.020	0.000	0.000	0.000	0.000
48	A	52	ASN	0	0.011	-0.011	27.255	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.004	0.000	28.783	0.014	0.014	0.000	0.000	0.000	0.000
50	A	54	GLU	-1	-0.878	-0.938	29.934	-0.129	-0.129	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.834	-0.909	32.707	-0.129	-0.129	0.000	0.000	0.000	0.000
52	A	56	GLY	0	0.013	0.020	35.273	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	57	ILE	0	-0.052	-0.015	29.380	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	58	THR	0	-0.005	0.004	29.177	0.004	0.004	0.000	0.000	0.000	0.000
55	A	59	ILE	0	-0.013	-0.020	24.019	-0.022	-0.022	0.000	0.000	0.000	0.000
56	A	60	LEU	0	0.025	0.012	24.707	0.015	0.015	0.000	0.000	0.000	0.000
57	A	61	LYS	1	0.834	0.922	14.996	0.498	0.498	0.000	0.000	0.000	0.000
58	A	62	LEU	0	0.032	0.026	21.227	0.019	0.019	0.000	0.000	0.000	0.000
59	A	63	SER	0	0.039	0.016	17.979	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	64	PRO	0	0.011	-0.014	13.502	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	65	LYS	1	0.822	0.911	9.318	1.637	1.637	0.000	0.000	0.000	0.000
62	A	66	THR	0	-0.003	0.008	14.788	-0.033	-0.033	0.000	0.000	0.000	0.000
63	A	67	SER	0	-0.040	0.000	18.322	0.049	0.049	0.000	0.000	0.000	0.000
64	A	68	VAL	0	0.015	-0.002	20.680	-0.022	-0.022	0.000	0.000	0.000	0.000
65	A	69	LEU	0	0.017	0.023	24.350	0.017	0.017	0.000	0.000	0.000	0.000
66	A	70	ASN	0	-0.069	-0.063	26.800	0.005	0.005	0.000	0.000	0.000	0.000
67	A	71	ILE	0	0.023	0.017	30.531	0.006	0.006	0.000	0.000	0.000	0.000
68	A	72	ALA	0	0.024	0.012	33.639	0.003	0.003	0.000	0.000	0.000	0.000
69	A	73	ALA	0	0.008	-0.003	36.433	0.004	0.004	0.000	0.000	0.000	0.000
70	A	74	VAL	0	-0.033	-0.006	35.961	0.002	0.002	0.000	0.000	0.000	0.000
71	A	75	GLU	-1	-0.864	-0.933	38.463	-0.100	-0.100	0.000	0.000	0.000	0.000
72	A	76	GLN	0	0.018	-0.015	38.899	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	77	ASP	-1	-0.880	-0.934	38.294	-0.108	-0.108	0.000	0.000	0.000	0.000
74	A	78	HIS	0	-0.036	-0.013	34.580	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	79	ARG	1	0.828	0.914	34.043	0.105	0.105	0.000	0.000	0.000	0.000
76	A	80	GLY	0	0.011	0.010	32.605	0.005	0.005	0.000	0.000	0.000	0.000
77	A	81	VAL	0	-0.039	-0.021	26.361	-0.015	-0.015	0.000	0.000	0.000	0.000
78	A	82	PHE	0	0.076	0.047	26.475	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	83	LYS	1	0.876	0.946	20.233	0.307	0.307	0.000	0.000	0.000	0.000
80	A	85	ILE	0	-0.017	-0.025	15.446	-0.048	-0.048	0.000	0.000	0.000	0.000
81	A	86	ALA	0	0.011	0.009	12.956	0.031	0.031	0.000	0.000	0.000	0.000
82	A	87	GLU	-1	-0.803	-0.901	10.809	-0.546	-0.546	0.000	0.000	0.000	0.000
83	A	88	ASN	0	-0.014	-0.037	5.222	0.309	0.309	0.000	0.000	0.000	0.000
84	A	89	LYS	1	0.960	0.971	5.542	-0.767	-0.767	0.000	0.000	0.000	0.000
85	A	90	ALA	0	-0.035	0.012	2.575	0.477	0.703	0.643	-0.316	-0.554	-0.001
86	A	91	GLY	0	0.061	0.023	4.185	0.422	0.526	0.000	-0.026	-0.078	0.000
87	A	92	SER	0	-0.040	-0.018	7.572	-0.026	-0.026	0.000	0.000	0.000	0.000
88	A	93	SER	0	0.010	0.010	10.927	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	94	PHE	0	0.021	-0.011	13.331	0.077	0.077	0.000	0.000	0.000	0.000
90	A	95	THR	0	0.009	0.016	17.074	0.003	0.003	0.000	0.000	0.000	0.000
91	A	96	THR	0	0.000	-0.017	20.011	0.020	0.020	0.000	0.000	0.000	0.000
92	A	97	SER	0	0.001	0.012	23.706	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	98	GLU	-1	-0.867	-0.931	27.259	-0.179	-0.179	0.000	0.000	0.000	0.000
94	A	99	LEU	0	0.007	0.029	30.541	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	100	LYS	1	0.895	0.935	33.229	0.190	0.190	0.000	0.000	0.000	0.000
96	A	101	VAL	0	0.017	0.028	36.746	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	102	ASN	0	-0.009	0.004	39.812	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:5:SER)