FMO DATABASE

FMODB ID: 226VR

Calculation Name: 4IN3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IN3

Chain ID: A

ChEMBL ID:

UniProt ID: Q05029

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	80
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-418612.575694
FMO2-HF: Nuclear repulsion	387287.873044
FMO2-HF: Total energy	-31324.702649
FMO2-MP2: Total energy	-31416.484463

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:ASP)

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

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.
-15.874	-3.765	3.848	-7.192	-8.763	0.054

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.893 / q_NPA : -0.968

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	-1	GLU	-1	-0.867	-0.939	2.761	39.607	44.783	0.514	-2.541	-3.148	0.004
4	A	0	PHE	0	-0.017	-0.012	2.434	-21.647	-15.640	3.274	-4.212	-5.069	0.046
5	A	1	MET	0	-0.069	-0.036	3.728	-12.549	-11.705	0.061	-0.427	-0.478	0.004
6	A	2	SER	0	-0.037	-0.008	6.288	-4.880	-4.880	0.000	0.000	0.000	0.000
7	A	3	SER	0	-0.042	-0.002	5.766	-2.112	-2.112	0.000	0.000	0.000	0.000
8	A	4	VAL	0	-0.008	-0.007	7.691	-3.089	-3.089	0.000	0.000	0.000	0.000
9	A	5	ASP	-1	-0.868	-0.917	10.409	28.649	28.649	0.000	0.000	0.000	0.000
10	A	6	VAL	0	-0.001	-0.001	12.864	-1.545	-1.545	0.000	0.000	0.000	0.000
11	A	7	LEU	0	0.001	-0.006	16.414	0.311	0.311	0.000	0.000	0.000	0.000
12	A	8	LEU	0	-0.009	-0.004	18.377	-0.513	-0.513	0.000	0.000	0.000	0.000
13	A	9	THR	0	-0.025	-0.012	21.970	-0.051	-0.051	0.000	0.000	0.000	0.000
14	A	10	VAL	0	-0.005	-0.011	24.716	-0.138	-0.138	0.000	0.000	0.000	0.000
15	A	11	GLY	0	0.043	0.029	26.884	-0.387	-0.387	0.000	0.000	0.000	0.000
16	A	12	LYS	1	0.922	0.945	30.209	-8.844	-8.844	0.000	0.000	0.000	0.000
17	A	13	LEU	0	-0.014	-0.006	28.837	0.243	0.243	0.000	0.000	0.000	0.000
18	A	14	ASP	-1	-0.865	-0.927	31.526	8.864	8.864	0.000	0.000	0.000	0.000
19	A	15	ALA	0	-0.023	-0.021	31.871	0.232	0.232	0.000	0.000	0.000	0.000
20	A	16	SER	0	-0.059	-0.020	30.933	0.408	0.408	0.000	0.000	0.000	0.000
21	A	17	LEU	0	-0.002	-0.004	27.800	0.408	0.408	0.000	0.000	0.000	0.000
22	A	18	ALA	0	0.035	0.022	26.156	-0.365	-0.365	0.000	0.000	0.000	0.000
23	A	19	LEU	0	-0.006	0.004	27.283	0.163	0.163	0.000	0.000	0.000	0.000
24	A	20	LEU	0	-0.032	-0.015	21.941	-0.043	-0.043	0.000	0.000	0.000	0.000
25	A	21	THR	0	0.027	0.011	25.661	-0.201	-0.201	0.000	0.000	0.000	0.000
26	A	22	THR	0	-0.010	-0.035	21.466	0.127	0.127	0.000	0.000	0.000	0.000
27	A	23	GLN	0	-0.003	-0.019	23.504	-0.102	-0.102	0.000	0.000	0.000	0.000
28	A	24	ASP	-1	-0.872	-0.885	22.158	13.527	13.527	0.000	0.000	0.000	0.000
29	A	25	HIS	0	-0.051	-0.023	25.683	-0.336	-0.336	0.000	0.000	0.000	0.000
30	A	26	HIS	0	-0.012	-0.002	23.168	-0.386	-0.386	0.000	0.000	0.000	0.000
31	A	27	VAL	0	-0.028	-0.030	25.869	0.016	0.016	0.000	0.000	0.000	0.000
32	A	28	ILE	0	-0.027	-0.016	21.183	0.000	0.000	0.000	0.000	0.000	0.000
33	A	29	GLU	-1	-0.918	-0.953	25.304	10.208	10.208	0.000	0.000	0.000	0.000
34	A	30	PHE	0	-0.010	-0.020	19.045	0.526	0.526	0.000	0.000	0.000	0.000
35	A	31	PRO	0	0.060	0.022	22.683	-0.478	-0.478	0.000	0.000	0.000	0.000
36	A	32	THR	0	0.024	0.004	24.099	0.608	0.608	0.000	0.000	0.000	0.000
37	A	33	VAL	0	-0.027	-0.013	24.745	0.147	0.147	0.000	0.000	0.000	0.000
38	A	34	LEU	0	-0.033	-0.011	19.931	0.284	0.284	0.000	0.000	0.000	0.000
39	A	35	LEU	0	-0.039	-0.004	20.431	0.829	0.829	0.000	0.000	0.000	0.000
40	A	36	PRO	0	-0.011	-0.016	19.582	-0.283	-0.283	0.000	0.000	0.000	0.000
41	A	37	GLU	-1	-0.896	-0.943	22.351	12.502	12.502	0.000	0.000	0.000	0.000
42	A	38	ASN	0	-0.029	-0.020	25.614	-0.814	-0.814	0.000	0.000	0.000	0.000
43	A	39	VAL	0	-0.018	-0.005	23.191	-0.322	-0.322	0.000	0.000	0.000	0.000
44	A	40	LYS	1	0.932	0.992	26.290	-10.382	-10.382	0.000	0.000	0.000	0.000
45	A	41	ALA	0	0.066	0.020	29.576	0.059	0.059	0.000	0.000	0.000	0.000
46	A	42	GLY	0	-0.023	-0.006	30.112	-0.190	-0.190	0.000	0.000	0.000	0.000
47	A	43	SER	0	-0.073	-0.045	26.189	-0.122	-0.122	0.000	0.000	0.000	0.000
48	A	44	ILE	0	-0.003	0.000	22.004	0.060	0.060	0.000	0.000	0.000	0.000
49	A	45	ILE	0	-0.006	0.005	19.719	0.231	0.231	0.000	0.000	0.000	0.000
50	A	46	LYS	1	0.835	0.902	12.614	-24.594	-24.594	0.000	0.000	0.000	0.000
51	A	47	MET	0	-0.021	-0.006	14.431	0.392	0.392	0.000	0.000	0.000	0.000
52	A	48	GLN	0	0.028	0.015	9.535	-1.536	-1.536	0.000	0.000	0.000	0.000
53	A	49	VAL	0	0.003	0.007	10.180	1.074	1.074	0.000	0.000	0.000	0.000
54	A	50	SER	0	0.059	0.030	4.265	-0.423	-0.341	-0.001	-0.012	-0.068	0.000
55	A	51	GLN	0	-0.017	-0.010	6.552	-3.852	-3.852	0.000	0.000	0.000	0.000
56	A	52	ASN	0	0.057	0.008	6.722	3.506	3.506	0.000	0.000	0.000	0.000
57	A	53	LEU	0	0.067	0.040	6.480	-4.010	-4.010	0.000	0.000	0.000	0.000
58	A	54	GLU	-1	-0.975	-0.982	8.580	23.546	23.546	0.000	0.000	0.000	0.000
59	A	55	GLU	-1	-0.773	-0.925	10.075	17.762	17.762	0.000	0.000	0.000	0.000
60	A	56	GLU	-1	-0.775	-0.849	11.898	20.223	20.223	0.000	0.000	0.000	0.000
61	A	57	LYS	1	0.908	0.955	10.716	-24.844	-24.844	0.000	0.000	0.000	0.000
62	A	58	LYS	1	0.810	0.906	13.009	-22.451	-22.451	0.000	0.000	0.000	0.000
63	A	59	GLN	0	0.043	0.012	16.144	-1.960	-1.960	0.000	0.000	0.000	0.000
64	A	60	ARG	1	0.819	0.910	14.126	-19.308	-19.308	0.000	0.000	0.000	0.000
65	A	61	ASN	0	-0.030	-0.029	18.531	-1.088	-1.088	0.000	0.000	0.000	0.000
66	A	62	HIS	0	0.015	0.030	20.299	-0.652	-0.652	0.000	0.000	0.000	0.000
67	A	63	PHE	0	0.042	0.015	21.972	-0.719	-0.719	0.000	0.000	0.000	0.000
68	A	64	LYS	1	0.968	0.968	23.047	-13.053	-13.053	0.000	0.000	0.000	0.000
69	A	65	SER	0	-0.031	-0.003	24.770	-0.549	-0.549	0.000	0.000	0.000	0.000
70	A	66	ILE	0	0.030	0.014	26.304	-0.509	-0.509	0.000	0.000	0.000	0.000
71	A	67	GLN	0	-0.005	-0.006	27.874	-0.711	-0.711	0.000	0.000	0.000	0.000
72	A	68	ALA	0	-0.015	-0.002	29.215	-0.370	-0.370	0.000	0.000	0.000	0.000
73	A	69	LYS	1	0.804	0.889	30.639	-9.360	-9.360	0.000	0.000	0.000	0.000
74	A	70	ILE	0	-0.044	-0.032	31.607	-0.346	-0.346	0.000	0.000	0.000	0.000
75	A	71	LEU	0	-0.018	-0.010	33.834	-0.239	-0.239	0.000	0.000	0.000	0.000
76	A	72	GLU	-1	-0.831	-0.883	34.957	8.561	8.561	0.000	0.000	0.000	0.000
77	A	73	LYS	1	0.878	0.951	36.246	-8.575	-8.575	0.000	0.000	0.000	0.000
78	A	74	TYR	0	-0.012	-0.012	37.230	-0.148	-0.148	0.000	0.000	0.000	0.000
79	A	75	GLY	0	0.026	0.022	39.170	0.121	0.121	0.000	0.000	0.000	0.000
80	A	76	THR	0	-0.001	0.003	40.210	0.008	0.008	0.000	0.000	0.000	0.000

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