FMO DATABASE

FMODB ID: YY232

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	OptAll
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	-370491.591998
FMO2-HF: Nuclear repulsion	342691.286358
FMO2-HF: Total energy	-27800.30564
FMO2-MP2: Total energy	-27883.289593

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.
-2.86	-1.012	-0.01	-0.984	-0.854	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 : 0.021 / q_NPA : 0.005

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	-0.010	-0.040	3.627	-1.680	0.168	-0.010	-0.984	-0.854	0.003
4	A	5	SER	0	0.027	-0.015	6.085	0.735	0.735	0.000	0.000	0.000	0.000
5	A	6	ASP	-1	-0.829	-0.913	9.162	-1.225	-1.225	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.827	-0.885	6.038	-4.990	-4.990	0.000	0.000	0.000	0.000
7	A	8	VAL	0	0.000	0.002	8.845	0.438	0.438	0.000	0.000	0.000	0.000
8	A	9	ASN	0	0.038	0.015	10.605	0.336	0.336	0.000	0.000	0.000	0.000
9	A	10	PHE	0	0.036	0.015	13.444	0.220	0.220	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.019	-0.016	10.254	0.182	0.182	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.007	0.004	14.044	0.155	0.155	0.000	0.000	0.000	0.000
12	A	13	TYR	0	-0.006	0.001	16.336	0.097	0.097	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.779	0.878	17.410	0.516	0.516	0.000	0.000	0.000	0.000
14	A	15	TYR	0	0.032	0.022	17.819	0.066	0.066	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.018	-0.005	19.578	0.059	0.059	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.034	-0.023	22.164	0.014	0.014	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.792	-0.886	20.648	-0.299	-0.299	0.000	0.000	0.000	0.000
18	A	19	SER	0	-0.048	-0.021	22.661	0.037	0.037	0.000	0.000	0.000	0.000
19	A	20	GLY	0	-0.006	0.004	25.258	0.019	0.019	0.000	0.000	0.000	0.000
20	A	21	PHE	0	-0.015	0.005	23.864	0.012	0.012	0.000	0.000	0.000	0.000
21	A	22	SER	0	0.016	-0.008	26.461	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	23	HIS	0	0.011	0.000	27.786	-0.027	-0.027	0.000	0.000	0.000	0.000
23	A	24	SER	0	0.028	0.023	24.036	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.023	0.009	22.974	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	26	PHE	0	-0.038	-0.019	23.552	-0.036	-0.036	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.020	-0.020	25.032	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	28	PHE	0	0.056	0.029	15.579	-0.018	-0.018	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.011	0.021	20.267	-0.063	-0.063	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.048	-0.015	21.477	-0.036	-0.036	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.942	-0.975	20.771	-0.371	-0.371	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.097	-0.068	16.379	-0.050	-0.050	0.000	0.000	0.000	0.000
32	A	33	HIS	0	-0.004	-0.009	17.227	-0.086	-0.086	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.033	0.028	16.502	-0.048	-0.048	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.045	-0.025	19.166	-0.032	-0.032	0.000	0.000	0.000	0.000
35	A	36	GLN	0	-0.047	-0.024	19.372	0.044	0.044	0.000	0.000	0.000	0.000
36	A	37	SER	0	-0.019	0.008	14.890	-0.076	-0.076	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.038	-0.021	13.555	0.204	0.204	0.000	0.000	0.000	0.000
38	A	39	ILE	0	-0.007	0.003	11.090	-0.078	-0.078	0.000	0.000	0.000	0.000
39	A	40	ASN	0	0.047	0.042	14.663	0.140	0.140	0.000	0.000	0.000	0.000
40	A	41	GLY	0	0.061	0.012	16.610	0.002	0.002	0.000	0.000	0.000	0.000
41	A	42	THR	0	-0.085	-0.066	17.879	0.040	0.040	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.023	-0.011	15.590	0.051	0.051	0.000	0.000	0.000	0.000
43	A	44	VAL	0	-0.009	0.019	13.411	-0.031	-0.031	0.000	0.000	0.000	0.000
44	A	45	PRO	0	0.020	0.013	14.555	0.055	0.055	0.000	0.000	0.000	0.000
45	A	46	PRO	0	0.024	-0.012	17.442	-0.031	-0.031	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.003	-0.001	18.896	0.020	0.020	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.001	0.017	13.510	0.042	0.042	0.000	0.000	0.000	0.000
48	A	49	LEU	0	0.046	0.017	12.465	0.032	0.032	0.000	0.000	0.000	0.000
49	A	50	ILE	0	0.020	0.008	13.862	0.078	0.078	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.031	-0.025	15.209	0.085	0.085	0.000	0.000	0.000	0.000
51	A	52	ILE	0	-0.029	-0.016	8.906	0.083	0.083	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.013	0.011	11.886	0.153	0.153	0.000	0.000	0.000	0.000
53	A	54	GLN	0	-0.002	0.006	13.299	0.116	0.116	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.967	0.974	12.845	-0.147	-0.147	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.003	0.014	11.396	0.115	0.115	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.025	-0.016	12.115	0.081	0.081	0.000	0.000	0.000	0.000
57	A	58	GLN	0	0.025	0.003	15.727	0.051	0.051	0.000	0.000	0.000	0.000
58	A	59	TYR	0	-0.133	-0.071	11.563	0.051	0.051	0.000	0.000	0.000	0.000
59	A	60	VAL	0	0.040	0.017	13.197	0.023	0.023	0.000	0.000	0.000	0.000
60	A	61	GLU	-1	-0.918	-0.966	15.498	0.307	0.307	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.023	0.009	16.861	-0.039	-0.039	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.879	-0.928	13.576	1.263	1.263	0.000	0.000	0.000	0.000
63	A	64	ILE	0	-0.048	-0.020	17.758	-0.032	-0.032	0.000	0.000	0.000	0.000
64	A	65	SER	0	0.032	-0.003	20.770	-0.023	-0.023	0.000	0.000	0.000	0.000
65	A	66	ILE	0	-0.103	-0.048	18.926	-0.028	-0.028	0.000	0.000	0.000	0.000
66	A	67	ASN	0	-0.092	-0.056	20.322	-0.024	-0.024	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.979	-0.976	24.287	0.289	0.289	0.000	0.000	0.000	0.000
68	A	69	ASP	-1	-0.943	-0.968	26.671	0.243	0.243	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.031	0.006	28.502	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.054	-0.074	29.736	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	72	VAL	0	-0.029	-0.027	32.352	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	73	PHE	0	-0.089	-0.051	34.346	-0.017	-0.017	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.818	-0.854	31.013	0.289	0.289	0.000	0.000	0.000	0.000
74	A	75	GLY	0	-0.065	-0.031	33.307	-0.010	-0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)