FMO DATABASE

FMODB ID: 52V8Z

Calculation Name: 3A7P-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A7P

Chain ID: B

ChEMBL ID:

UniProt ID: Q03818

Base Structure: X-ray

Registration Date: 2023-09-19

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	76
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-337134.437765
FMO2-HF: Nuclear repulsion	307315.553705
FMO2-HF: Total energy	-29818.88406
FMO2-MP2: Total energy	-29908.278949

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(B:58:VAL)

Summations of interaction energy for fragment #1(B:58:VAL)

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.
-3.255	-0.903	-0.006	-1.295	-1.05	0.003

Interaction energy analysis for fragmet #1(B:58:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.001

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	B	60	HIS	0	-0.012	-0.008	3.723	-1.846	0.441	-0.005	-1.288	-0.994	0.003
4	B	61	ASP	-1	-0.833	-0.915	6.736	-0.559	-0.559	0.000	0.000	0.000	0.000
5	B	62	ASP	-1	-0.861	-0.911	4.991	-1.904	-1.839	-0.001	-0.007	-0.056	0.000
6	B	63	ALA	0	0.014	-0.003	6.196	0.342	0.342	0.000	0.000	0.000	0.000
7	B	64	LEU	0	0.009	0.025	7.727	0.203	0.203	0.000	0.000	0.000	0.000
8	B	65	LEU	0	0.041	0.010	10.010	0.132	0.132	0.000	0.000	0.000	0.000
9	B	66	ASN	0	-0.004	0.000	9.295	0.095	0.095	0.000	0.000	0.000	0.000
10	B	67	THR	0	-0.029	-0.031	11.283	0.094	0.094	0.000	0.000	0.000	0.000
11	B	68	LEU	0	-0.009	-0.007	13.547	0.035	0.035	0.000	0.000	0.000	0.000
12	B	69	ALA	0	-0.004	-0.003	14.212	0.029	0.029	0.000	0.000	0.000	0.000
13	B	70	ILE	0	0.002	0.003	13.633	0.022	0.022	0.000	0.000	0.000	0.000
14	B	71	LEU	0	0.047	0.024	17.135	0.006	0.006	0.000	0.000	0.000	0.000
15	B	72	GLN	0	0.010	0.015	19.133	0.015	0.015	0.000	0.000	0.000	0.000
16	B	73	LYS	1	0.943	0.976	20.039	-0.011	-0.011	0.000	0.000	0.000	0.000
17	B	74	GLU	-1	-0.850	-0.923	21.051	0.044	0.044	0.000	0.000	0.000	0.000
18	B	75	LEU	0	-0.006	0.006	23.317	0.005	0.005	0.000	0.000	0.000	0.000
19	B	76	LYS	1	0.943	0.962	23.273	0.076	0.076	0.000	0.000	0.000	0.000
20	B	77	SER	0	-0.003	0.001	25.952	0.004	0.004	0.000	0.000	0.000	0.000
21	B	78	LYS	1	0.863	0.913	24.968	-0.021	-0.021	0.000	0.000	0.000	0.000
22	B	79	GLU	-1	-0.835	-0.907	29.341	-0.036	-0.036	0.000	0.000	0.000	0.000
23	B	80	GLN	0	-0.025	-0.007	30.381	0.005	0.005	0.000	0.000	0.000	0.000
24	B	81	GLU	-1	-0.849	-0.926	31.937	0.016	0.016	0.000	0.000	0.000	0.000
25	B	82	ILE	0	-0.016	-0.011	32.707	0.000	0.000	0.000	0.000	0.000	0.000
26	B	83	ARG	1	0.801	0.887	31.413	0.023	0.023	0.000	0.000	0.000	0.000
27	B	84	ARG	1	0.913	0.950	33.589	-0.006	-0.006	0.000	0.000	0.000	0.000
28	B	85	LEU	0	0.024	0.007	36.466	0.000	0.000	0.000	0.000	0.000	0.000
29	B	86	LYS	1	0.937	0.976	38.662	0.010	0.010	0.000	0.000	0.000	0.000
30	B	87	GLU	-1	-0.852	-0.914	41.492	-0.003	-0.003	0.000	0.000	0.000	0.000
31	B	88	VAL	0	-0.020	-0.015	41.065	0.001	0.001	0.000	0.000	0.000	0.000
32	B	89	ILE	0	0.003	-0.004	42.716	0.001	0.001	0.000	0.000	0.000	0.000
33	B	90	ALA	0	0.023	0.026	45.678	0.000	0.000	0.000	0.000	0.000	0.000
34	B	91	LEU	0	-0.010	-0.007	45.290	0.000	0.000	0.000	0.000	0.000	0.000
35	B	92	LYS	1	0.922	0.955	45.150	-0.014	-0.014	0.000	0.000	0.000	0.000
36	B	93	ASN	0	-0.034	-0.002	49.057	0.000	0.000	0.000	0.000	0.000	0.000
37	B	94	LYS	1	1.040	1.029	51.759	0.003	0.003	0.000	0.000	0.000	0.000
38	B	95	ASN	0	-0.021	-0.010	52.565	0.000	0.000	0.000	0.000	0.000	0.000
39	B	96	THR	0	-0.010	-0.016	52.804	0.001	0.001	0.000	0.000	0.000	0.000
40	B	97	GLU	-1	-0.883	-0.944	55.376	0.001	0.001	0.000	0.000	0.000	0.000
41	B	98	ARG	1	0.905	0.950	55.985	-0.006	-0.006	0.000	0.000	0.000	0.000
42	B	99	LEU	0	-0.005	-0.008	55.602	0.000	0.000	0.000	0.000	0.000	0.000
43	B	100	ASN	0	-0.035	-0.019	58.401	0.000	0.000	0.000	0.000	0.000	0.000
44	B	101	ALA	0	0.026	0.015	61.296	0.000	0.000	0.000	0.000	0.000	0.000
45	B	102	ALA	0	-0.010	-0.006	62.385	0.000	0.000	0.000	0.000	0.000	0.000
46	B	103	LEU	0	0.015	0.013	62.106	0.000	0.000	0.000	0.000	0.000	0.000
47	B	104	ILE	0	0.015	0.016	64.736	0.000	0.000	0.000	0.000	0.000	0.000
48	B	105	SER	0	0.029	0.014	67.247	0.000	0.000	0.000	0.000	0.000	0.000
49	B	106	GLY	0	0.030	0.017	67.882	0.000	0.000	0.000	0.000	0.000	0.000
50	B	107	THR	0	-0.050	-0.031	67.828	0.000	0.000	0.000	0.000	0.000	0.000
51	B	108	ILE	0	-0.007	-0.006	70.409	0.000	0.000	0.000	0.000	0.000	0.000
52	B	109	GLU	-1	-0.939	-0.964	72.598	0.006	0.006	0.000	0.000	0.000	0.000
53	B	110	ASN	0	-0.018	-0.029	71.020	0.000	0.000	0.000	0.000	0.000	0.000
54	B	111	ASN	0	-0.012	0.006	74.448	0.000	0.000	0.000	0.000	0.000	0.000
55	B	112	VAL	0	0.040	0.013	76.736	0.000	0.000	0.000	0.000	0.000	0.000
56	B	113	LEU	0	-0.018	-0.016	75.819	0.000	0.000	0.000	0.000	0.000	0.000
57	B	114	GLN	0	-0.006	-0.005	76.294	0.000	0.000	0.000	0.000	0.000	0.000
58	B	115	GLN	0	-0.030	-0.005	79.977	0.000	0.000	0.000	0.000	0.000	0.000
59	B	116	LYS	1	1.022	1.024	79.760	-0.005	-0.005	0.000	0.000	0.000	0.000
60	B	117	LEU	0	-0.004	0.004	80.442	0.000	0.000	0.000	0.000	0.000	0.000
61	B	118	SER	0	-0.074	-0.045	84.398	0.000	0.000	0.000	0.000	0.000	0.000
62	B	119	ASP	-1	-0.816	-0.900	86.346	0.005	0.005	0.000	0.000	0.000	0.000
63	B	120	LEU	0	0.061	0.035	86.932	0.000	0.000	0.000	0.000	0.000	0.000
64	B	121	LYS	1	0.939	0.971	87.958	-0.008	-0.008	0.000	0.000	0.000	0.000
65	B	122	LYS	1	0.800	0.885	87.612	-0.005	-0.005	0.000	0.000	0.000	0.000
66	B	123	GLU	-1	-0.866	-0.924	91.696	0.004	0.004	0.000	0.000	0.000	0.000
67	B	124	HIS	0	0.000	-0.002	92.609	0.000	0.000	0.000	0.000	0.000	0.000
68	B	125	SER	0	-0.080	-0.049	94.260	0.000	0.000	0.000	0.000	0.000	0.000
69	B	126	GLN	0	0.009	-0.005	96.074	0.000	0.000	0.000	0.000	0.000	0.000
70	B	127	LEU	0	-0.011	-0.002	96.656	0.000	0.000	0.000	0.000	0.000	0.000
71	B	128	VAL	0	0.022	0.002	97.169	0.000	0.000	0.000	0.000	0.000	0.000
72	B	129	ALA	0	0.018	0.010	99.928	0.000	0.000	0.000	0.000	0.000	0.000
73	B	130	ARG	1	0.906	0.954	102.132	-0.004	-0.004	0.000	0.000	0.000	0.000
74	B	131	TRP	0	0.027	0.010	100.969	0.000	0.000	0.000	0.000	0.000	0.000
75	B	132	LEU	0	-0.057	-0.006	104.103	0.000	0.000	0.000	0.000	0.000	0.000
76	B	133	LYS	1	0.872	0.943	105.753	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:58:VAL)