FMO DATABASE

FMODB ID: 22QVR

Calculation Name: 2XG8-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2XG8

Chain ID: F

ChEMBL ID:

UniProt ID: P0A3F4

Base Structure: X-ray

Registration Date: 2023-06-20

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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-497315.149665
FMO2-HF: Nuclear repulsion	464651.461791
FMO2-HF: Total energy	-32663.687874
FMO2-MP2: Total energy	-32760.011322

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(F:3:SER)

Summations of interaction energy for fragment #1(F: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.
-3.687	-1.281	-0.01	-1.112	-1.283	0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.002

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	F	5	ASN	0	0.029	0.017	3.626	-2.181	0.182	-0.009	-1.098	-1.256	0.004
4	F	6	TYR	0	-0.076	-0.077	6.086	0.513	0.513	0.000	0.000	0.000	0.000
5	F	7	LEU	0	0.004	0.004	9.820	0.201	0.201	0.000	0.000	0.000	0.000
6	F	8	ASN	0	0.015	0.000	12.769	0.054	0.054	0.000	0.000	0.000	0.000
7	F	9	HIS	0	0.020	0.021	16.505	0.061	0.061	0.000	0.000	0.000	0.000
8	F	10	PRO	0	-0.002	-0.015	18.628	0.016	0.016	0.000	0.000	0.000	0.000
9	F	11	THR	0	-0.032	-0.007	22.156	0.033	0.033	0.000	0.000	0.000	0.000
10	F	12	PHE	0	-0.023	-0.031	19.770	0.021	0.021	0.000	0.000	0.000	0.000
11	F	13	GLY	0	0.042	0.037	19.491	-0.037	-0.037	0.000	0.000	0.000	0.000
12	F	14	LEU	0	0.003	0.016	13.344	-0.041	-0.041	0.000	0.000	0.000	0.000
13	F	15	LEU	0	-0.043	-0.027	12.713	0.075	0.075	0.000	0.000	0.000	0.000
14	F	16	TYR	0	0.011	-0.003	9.158	-0.028	-0.028	0.000	0.000	0.000	0.000
15	F	17	GLN	0	-0.013	-0.012	4.379	-1.113	-1.070	-0.001	-0.014	-0.027	0.000
16	F	18	ILE	0	-0.066	-0.025	6.822	-0.321	-0.321	0.000	0.000	0.000	0.000
17	F	19	CYS	0	-0.036	-0.021	6.462	0.174	0.174	0.000	0.000	0.000	0.000
18	F	20	SER	0	0.066	0.025	6.914	-0.211	-0.211	0.000	0.000	0.000	0.000
19	F	21	PHE	0	-0.038	-0.031	8.506	0.250	0.250	0.000	0.000	0.000	0.000
20	F	22	GLY	0	0.060	0.050	11.591	0.057	0.057	0.000	0.000	0.000	0.000
21	F	23	ASP	-1	-0.994	-1.016	11.100	0.038	0.038	0.000	0.000	0.000	0.000
22	F	24	SER	0	0.009	0.011	12.605	-0.023	-0.023	0.000	0.000	0.000	0.000
23	F	25	LYS	1	0.911	0.970	13.371	0.257	0.257	0.000	0.000	0.000	0.000
24	F	26	GLU	-1	-0.873	-0.928	7.033	-1.750	-1.750	0.000	0.000	0.000	0.000
25	F	27	LEU	0	-0.038	-0.008	10.001	0.083	0.083	0.000	0.000	0.000	0.000
26	F	28	PHE	0	0.035	0.004	8.521	-0.343	-0.343	0.000	0.000	0.000	0.000
27	F	29	ALA	0	-0.009	-0.005	11.667	0.288	0.288	0.000	0.000	0.000	0.000
28	F	30	THR	0	0.004	0.000	13.717	-0.113	-0.113	0.000	0.000	0.000	0.000
29	F	31	LEU	0	0.030	0.023	12.760	0.024	0.024	0.000	0.000	0.000	0.000
30	F	32	TYR	0	0.047	0.022	16.068	0.058	0.058	0.000	0.000	0.000	0.000
31	F	33	ALA	0	0.030	0.031	19.502	0.073	0.073	0.000	0.000	0.000	0.000
32	F	34	GLN	0	0.001	0.009	19.246	-0.126	-0.126	0.000	0.000	0.000	0.000
33	F	35	ARG	1	0.856	0.893	15.778	0.848	0.848	0.000	0.000	0.000	0.000
34	F	36	LEU	0	-0.072	-0.009	18.855	0.059	0.059	0.000	0.000	0.000	0.000
35	F	37	PHE	0	0.016	-0.005	14.796	-0.080	-0.080	0.000	0.000	0.000	0.000
36	F	38	PHE	0	0.009	-0.008	15.228	0.098	0.098	0.000	0.000	0.000	0.000
37	F	39	LEU	0	-0.017	-0.005	14.331	-0.117	-0.117	0.000	0.000	0.000	0.000
38	F	40	VAL	0	-0.006	-0.003	12.644	0.088	0.088	0.000	0.000	0.000	0.000
39	F	41	ALA	0	0.031	0.008	13.912	0.018	0.018	0.000	0.000	0.000	0.000
40	F	42	PHE	0	0.014	-0.008	11.236	-0.005	-0.005	0.000	0.000	0.000	0.000
41	F	43	ASP	-1	-0.771	-0.866	17.359	-0.298	-0.298	0.000	0.000	0.000	0.000
42	F	44	ALA	0	-0.118	-0.018	20.276	0.032	0.032	0.000	0.000	0.000	0.000
43	F	45	ARG	1	0.976	0.978	20.710	0.230	0.230	0.000	0.000	0.000	0.000
44	F	46	GLY	0	0.037	-0.002	21.623	0.022	0.022	0.000	0.000	0.000	0.000
45	F	47	THR	0	-0.001	-0.002	16.487	0.000	0.000	0.000	0.000	0.000	0.000
46	F	48	ARG	1	0.846	0.919	18.388	0.309	0.309	0.000	0.000	0.000	0.000
47	F	49	PHE	0	0.027	0.000	15.531	-0.071	-0.071	0.000	0.000	0.000	0.000
48	F	50	GLU	-1	-0.849	-0.921	18.431	-0.292	-0.292	0.000	0.000	0.000	0.000
49	F	51	PRO	0	-0.004	0.015	18.942	-0.044	-0.044	0.000	0.000	0.000	0.000
50	F	52	ILE	0	0.021	0.014	16.779	0.050	0.050	0.000	0.000	0.000	0.000
51	F	53	GLY	0	0.042	0.018	20.212	-0.031	-0.031	0.000	0.000	0.000	0.000
52	F	54	ARG	1	1.009	0.986	19.654	0.374	0.374	0.000	0.000	0.000	0.000
53	F	55	ASN	0	-0.001	0.001	19.999	-0.012	-0.012	0.000	0.000	0.000	0.000
54	F	56	GLU	-1	-0.830	-0.899	19.993	-0.214	-0.214	0.000	0.000	0.000	0.000
55	F	57	ALA	0	0.027	0.009	16.124	0.010	0.010	0.000	0.000	0.000	0.000
56	F	58	ARG	1	0.874	0.922	16.464	0.225	0.225	0.000	0.000	0.000	0.000
57	F	59	MET	0	0.015	0.011	17.936	0.030	0.030	0.000	0.000	0.000	0.000
58	F	60	LEU	0	-0.001	-0.001	15.732	0.036	0.036	0.000	0.000	0.000	0.000
59	F	61	VAL	0	0.004	-0.008	12.346	0.041	0.041	0.000	0.000	0.000	0.000
60	F	62	ASP	-1	-0.818	-0.876	14.364	0.029	0.029	0.000	0.000	0.000	0.000
61	F	63	ASN	0	0.006	-0.006	17.049	0.093	0.093	0.000	0.000	0.000	0.000
62	F	64	ARG	1	0.879	0.942	10.086	-0.234	-0.234	0.000	0.000	0.000	0.000
63	F	65	LEU	0	0.012	-0.011	12.515	0.142	0.142	0.000	0.000	0.000	0.000
64	F	66	ARG	1	0.794	0.869	14.391	0.070	0.070	0.000	0.000	0.000	0.000
65	F	67	GLN	0	0.040	0.029	14.778	0.054	0.054	0.000	0.000	0.000	0.000
66	F	68	LEU	0	-0.026	0.015	9.331	0.037	0.037	0.000	0.000	0.000	0.000
67	F	69	ARG	1	0.897	0.938	13.236	-0.102	-0.102	0.000	0.000	0.000	0.000
68	F	70	ARG	1	0.937	0.991	15.004	-0.644	-0.644	0.000	0.000	0.000	0.000
69	F	79	GLN	0	0.042	0.016	22.088	0.021	0.021	0.000	0.000	0.000	0.000
70	F	80	LEU	0	0.059	0.019	21.172	-0.032	-0.032	0.000	0.000	0.000	0.000
71	F	81	GLN	0	0.044	0.017	22.156	-0.052	-0.052	0.000	0.000	0.000	0.000
72	F	82	GLN	0	0.003	0.004	24.074	-0.015	-0.015	0.000	0.000	0.000	0.000
73	F	83	VAL	0	0.049	0.019	26.665	-0.021	-0.021	0.000	0.000	0.000	0.000
74	F	84	PHE	0	-0.002	0.008	26.042	-0.020	-0.020	0.000	0.000	0.000	0.000
75	F	85	LYS	1	0.936	0.958	26.014	-0.275	-0.275	0.000	0.000	0.000	0.000
76	F	86	GLN	0	-0.019	-0.001	29.744	-0.001	-0.001	0.000	0.000	0.000	0.000
77	F	87	THR	0	-0.061	-0.041	31.071	-0.012	-0.012	0.000	0.000	0.000	0.000
78	F	88	PHE	0	-0.031	-0.018	29.078	-0.011	-0.011	0.000	0.000	0.000	0.000
79	F	89	LEU	0	-0.021	0.019	29.641	-0.009	-0.009	0.000	0.000	0.000	0.000

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