FMO DATABASE

FMODB ID: 53LMZ

Calculation Name: 2XTC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2XTC

Chain ID: A

ChEMBL ID:

UniProt ID: O60907

Base Structure: X-ray

Registration Date: 2023-06-21

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	74
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-369501.154204
FMO2-HF: Nuclear repulsion	341701.031019
FMO2-HF: Total energy	-27800.123185
FMO2-MP2: Total energy	-27883.14266

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:SER)

Summations of interaction energy for fragment #1(A:2: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.
-0.572	0.451	-0.007	-0.276	-0.739	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.008

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	THR	0	0.021	-0.030	3.721	0.568	1.591	-0.007	-0.276	-0.739	0.003
4	A	5	SER	0	0.039	-0.010	6.699	0.643	0.643	0.000	0.000	0.000	0.000
5	A	6	ASP	-1	-0.852	-0.920	9.792	-1.094	-1.094	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.840	-0.892	5.575	-4.633	-4.633	0.000	0.000	0.000	0.000
7	A	8	VAL	0	-0.016	-0.004	9.020	0.400	0.400	0.000	0.000	0.000	0.000
8	A	9	ASN	0	0.043	0.014	10.481	0.301	0.301	0.000	0.000	0.000	0.000
9	A	10	PHE	0	0.033	0.012	12.769	0.194	0.194	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.024	-0.015	9.769	0.167	0.167	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.002	0.004	13.749	0.132	0.132	0.000	0.000	0.000	0.000
12	A	13	TYR	0	-0.012	-0.002	16.043	0.081	0.081	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.772	0.869	16.712	0.364	0.364	0.000	0.000	0.000	0.000
14	A	15	TYR	0	0.030	0.018	17.566	0.055	0.055	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.015	-0.005	19.300	0.043	0.043	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.032	-0.018	21.410	0.010	0.010	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.780	-0.875	19.973	-0.172	-0.172	0.000	0.000	0.000	0.000
18	A	19	SER	0	-0.056	-0.023	22.501	0.032	0.032	0.000	0.000	0.000	0.000
19	A	20	GLY	0	-0.014	0.000	25.124	0.013	0.013	0.000	0.000	0.000	0.000
20	A	21	PHE	0	-0.026	-0.011	23.700	0.009	0.009	0.000	0.000	0.000	0.000
21	A	22	SER	0	0.032	0.003	26.143	-0.022	-0.022	0.000	0.000	0.000	0.000
22	A	23	HIS	0	0.006	-0.003	28.316	-0.022	-0.022	0.000	0.000	0.000	0.000
23	A	24	SER	0	0.030	0.015	24.251	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.025	0.014	23.209	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	26	PHE	0	-0.036	-0.010	23.958	-0.034	-0.034	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.009	-0.011	25.544	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	28	PHE	0	0.034	0.019	16.435	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.014	0.014	21.142	-0.052	-0.052	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.045	-0.017	22.017	-0.034	-0.034	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.935	-0.969	21.662	-0.325	-0.325	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.112	-0.067	17.143	-0.045	-0.045	0.000	0.000	0.000	0.000
32	A	33	HIS	0	-0.001	-0.007	17.958	-0.078	-0.078	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.038	0.024	16.129	-0.056	-0.056	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.044	-0.014	18.499	-0.034	-0.034	0.000	0.000	0.000	0.000
35	A	36	GLN	0	-0.035	-0.013	19.223	0.034	0.034	0.000	0.000	0.000	0.000
36	A	37	SER	0	-0.018	0.004	14.327	-0.080	-0.080	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.041	-0.029	13.611	0.192	0.192	0.000	0.000	0.000	0.000
38	A	39	ILE	0	0.005	0.016	10.646	-0.034	-0.034	0.000	0.000	0.000	0.000
39	A	40	ASN	0	0.044	0.039	13.933	0.123	0.123	0.000	0.000	0.000	0.000
40	A	41	GLY	0	0.078	0.014	15.934	0.010	0.010	0.000	0.000	0.000	0.000
41	A	42	THR	0	-0.084	-0.058	17.541	0.043	0.043	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.021	-0.013	15.299	0.042	0.042	0.000	0.000	0.000	0.000
43	A	44	VAL	0	-0.023	0.012	13.080	0.001	0.001	0.000	0.000	0.000	0.000
44	A	45	PRO	0	0.021	0.019	14.167	0.035	0.035	0.000	0.000	0.000	0.000
45	A	46	PRO	0	0.016	-0.013	16.983	-0.026	-0.026	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.001	-0.003	18.592	0.029	0.029	0.000	0.000	0.000	0.000
47	A	48	ALA	0	0.013	0.024	13.198	0.052	0.052	0.000	0.000	0.000	0.000
48	A	49	LEU	0	0.028	0.011	12.459	0.048	0.048	0.000	0.000	0.000	0.000
49	A	50	ILE	0	0.032	0.001	13.879	0.076	0.076	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.043	-0.024	14.987	0.075	0.075	0.000	0.000	0.000	0.000
51	A	52	ILE	0	-0.026	-0.028	8.626	0.085	0.085	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.007	0.006	11.343	0.160	0.160	0.000	0.000	0.000	0.000
53	A	54	GLN	0	-0.007	0.004	13.178	0.098	0.098	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.994	0.989	12.414	-0.383	-0.383	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.016	0.027	11.301	0.117	0.117	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.012	-0.014	12.016	0.059	0.059	0.000	0.000	0.000	0.000
57	A	58	GLN	0	0.003	-0.003	15.600	0.038	0.038	0.000	0.000	0.000	0.000
58	A	59	TYR	0	-0.128	-0.063	11.289	0.037	0.037	0.000	0.000	0.000	0.000
59	A	60	VAL	0	0.039	0.014	13.180	0.014	0.014	0.000	0.000	0.000	0.000
60	A	61	GLU	-1	-0.923	-0.965	15.433	0.362	0.362	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.033	-0.009	16.969	-0.043	-0.043	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.883	-0.940	12.896	1.295	1.295	0.000	0.000	0.000	0.000
63	A	64	ILE	0	-0.061	-0.030	17.438	-0.040	-0.040	0.000	0.000	0.000	0.000
64	A	65	SER	0	0.021	-0.006	20.576	-0.024	-0.024	0.000	0.000	0.000	0.000
65	A	66	ILE	0	-0.082	-0.028	18.571	-0.033	-0.033	0.000	0.000	0.000	0.000
66	A	67	ASN	0	-0.097	-0.048	20.162	-0.045	-0.045	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.969	-0.970	23.916	0.303	0.303	0.000	0.000	0.000	0.000
68	A	69	ASP	-1	-0.943	-0.960	26.308	0.248	0.248	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.023	0.003	27.936	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.058	-0.071	29.115	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	72	VAL	0	-0.011	-0.022	31.824	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	73	PHE	0	-0.088	-0.052	33.890	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.840	-0.868	30.467	0.272	0.272	0.000	0.000	0.000	0.000
74	A	75	GLY	0	-0.052	-0.024	33.123	-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:SER)