FMO DATABASE

FMODB ID: 7G12K

Calculation Name: 3P04-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P04

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NNN6

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	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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-459255.226486
FMO2-HF: Nuclear repulsion	429557.220728
FMO2-HF: Total energy	-29698.005758
FMO2-MP2: Total energy	-29783.961579

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:64:SER)

Summations of interaction energy for fragment #1(A:64: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.
-11.734	-11.409	8.636	-4.422	-4.537	0.018

Interaction energy analysis for fragmet #1(A:64:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.022

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

Sort

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	66	GLN	0	0.000	-0.006	3.288	-2.317	-0.175	0.042	-1.025	-1.159	-0.001
4	A	67	SER	0	-0.060	-0.032	5.830	0.222	0.222	0.000	0.000	0.000	0.000
5	A	68	THR	0	-0.018	-0.015	9.628	-0.075	-0.075	0.000	0.000	0.000	0.000
6	A	69	ILE	0	-0.051	-0.017	12.357	0.037	0.037	0.000	0.000	0.000	0.000
7	A	70	VAL	0	0.053	0.029	12.082	0.071	0.071	0.000	0.000	0.000	0.000
8	A	71	PRO	0	-0.019	-0.012	14.747	0.050	0.050	0.000	0.000	0.000	0.000
9	A	72	VAL	0	-0.025	-0.015	17.566	0.010	0.010	0.000	0.000	0.000	0.000
10	A	73	GLH	0	-0.064	-0.065	20.334	0.008	0.008	0.000	0.000	0.000	0.000
11	A	74	LEU	0	-0.032	-0.013	21.738	0.005	0.005	0.000	0.000	0.000	0.000
12	A	75	HIS	0	-0.053	-0.044	25.581	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	76	SER	0	-0.013	-0.008	27.797	0.010	0.010	0.000	0.000	0.000	0.000
14	A	77	PHE	0	0.013	-0.019	25.822	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	78	GLU	-1	-0.916	-0.954	25.394	0.000	0.000	0.000	0.000	0.000	0.000
16	A	79	ASP	-1	-0.788	-0.886	23.510	-0.064	-0.064	0.000	0.000	0.000	0.000
17	A	80	ALA	0	0.018	0.008	21.124	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	81	GLN	0	-0.033	-0.017	19.309	0.014	0.014	0.000	0.000	0.000	0.000
19	A	82	VAL	0	-0.013	-0.005	17.558	0.006	0.006	0.000	0.000	0.000	0.000
20	A	83	ILE	0	0.000	0.000	15.954	-0.029	-0.029	0.000	0.000	0.000	0.000
21	A	84	GLY	0	0.015	-0.004	14.539	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	85	GLY	0	-0.035	-0.009	13.918	0.049	0.049	0.000	0.000	0.000	0.000
23	A	86	ALA	0	0.063	0.028	11.263	0.033	0.033	0.000	0.000	0.000	0.000
24	A	87	PHE	0	0.000	-0.005	9.666	-0.065	-0.065	0.000	0.000	0.000	0.000
25	A	88	ARG	1	0.776	0.854	9.567	-0.100	-0.100	0.000	0.000	0.000	0.000
26	A	89	ASP	-1	-0.860	-0.894	8.390	0.410	0.410	0.000	0.000	0.000	0.000
27	A	90	GLY	0	0.029	0.023	4.892	-0.022	-0.022	0.000	0.000	0.000	0.000
28	A	91	ASP	-1	-0.856	-0.917	5.799	-1.906	-1.906	0.000	0.000	0.000	0.000
29	A	92	ALA	0	-0.018	-0.011	8.213	0.291	0.291	0.000	0.000	0.000	0.000
30	A	93	VAL	0	-0.025	-0.009	10.795	-0.025	-0.025	0.000	0.000	0.000	0.000
31	A	94	VAL	0	-0.031	-0.023	14.241	0.039	0.039	0.000	0.000	0.000	0.000
32	A	95	PHE	0	0.041	0.006	17.819	0.006	0.006	0.000	0.000	0.000	0.000
33	A	96	ASP	-1	-0.725	-0.810	20.897	-0.109	-0.109	0.000	0.000	0.000	0.000
34	A	97	MET	0	-0.049	-0.014	24.715	0.013	0.013	0.000	0.000	0.000	0.000
35	A	98	SER	0	-0.038	-0.053	27.526	0.012	0.012	0.000	0.000	0.000	0.000
36	A	99	LEU	0	-0.059	-0.013	29.363	0.006	0.006	0.000	0.000	0.000	0.000
37	A	100	LEU	0	-0.012	0.021	26.707	0.006	0.006	0.000	0.000	0.000	0.000
38	A	101	SER	0	-0.037	-0.048	31.355	0.002	0.002	0.000	0.000	0.000	0.000
39	A	102	ARG	1	0.963	0.956	32.166	0.023	0.023	0.000	0.000	0.000	0.000
40	A	103	GLU	-1	-0.881	-0.937	32.494	0.000	0.000	0.000	0.000	0.000	0.000
41	A	104	GLU	-1	-0.767	-0.858	29.490	-0.027	-0.027	0.000	0.000	0.000	0.000
42	A	105	ALA	0	0.052	0.019	27.870	0.001	0.001	0.000	0.000	0.000	0.000
43	A	106	ARG	1	0.777	0.860	26.933	0.002	0.002	0.000	0.000	0.000	0.000
44	A	107	ARG	1	0.885	0.935	27.438	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	108	ILE	0	0.003	0.014	22.653	0.010	0.010	0.000	0.000	0.000	0.000
46	A	109	VAL	0	-0.012	-0.005	22.693	0.004	0.004	0.000	0.000	0.000	0.000
47	A	110	ASP	-1	-0.814	-0.882	22.928	0.022	0.022	0.000	0.000	0.000	0.000
48	A	111	PHE	0	-0.026	-0.009	19.118	0.020	0.020	0.000	0.000	0.000	0.000
49	A	112	ALA	0	0.026	0.014	18.634	0.019	0.019	0.000	0.000	0.000	0.000
50	A	113	ALA	0	0.008	-0.001	18.290	0.012	0.012	0.000	0.000	0.000	0.000
51	A	114	GLY	0	-0.011	-0.005	19.636	0.021	0.021	0.000	0.000	0.000	0.000
52	A	115	LEU	0	-0.025	-0.010	15.184	0.036	0.036	0.000	0.000	0.000	0.000
53	A	116	CYS	0	-0.064	-0.033	15.042	0.036	0.036	0.000	0.000	0.000	0.000
54	A	117	PHE	0	-0.030	-0.020	15.568	0.047	0.047	0.000	0.000	0.000	0.000
55	A	118	ALA	0	-0.036	-0.014	16.115	0.028	0.028	0.000	0.000	0.000	0.000
56	A	119	LEU	0	-0.041	-0.014	10.676	0.063	0.063	0.000	0.000	0.000	0.000
57	A	120	HIS	0	-0.019	0.003	11.508	0.010	0.010	0.000	0.000	0.000	0.000
58	A	121	GLY	0	0.030	0.038	12.328	-0.035	-0.035	0.000	0.000	0.000	0.000
59	A	122	LYS	1	0.827	0.895	13.106	0.102	0.102	0.000	0.000	0.000	0.000
60	A	123	MET	0	0.026	0.016	15.441	-0.051	-0.051	0.000	0.000	0.000	0.000
61	A	124	GLN	0	-0.040	-0.015	17.136	0.017	0.017	0.000	0.000	0.000	0.000
62	A	125	LYS	1	0.916	0.978	19.817	0.084	0.084	0.000	0.000	0.000	0.000
63	A	126	ILE	0	-0.048	-0.020	19.792	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	127	ASP	-1	-0.749	-0.852	23.953	-0.118	-0.118	0.000	0.000	0.000	0.000
65	A	128	SER	0	-0.115	-0.081	27.278	0.008	0.008	0.000	0.000	0.000	0.000
66	A	129	VAL	0	-0.022	-0.021	28.007	0.010	0.010	0.000	0.000	0.000	0.000
67	A	130	THR	0	0.018	0.015	22.392	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	131	PHE	0	-0.036	-0.039	21.320	0.011	0.011	0.000	0.000	0.000	0.000
69	A	132	ALA	0	0.011	0.004	16.614	-0.024	-0.024	0.000	0.000	0.000	0.000
70	A	133	VAL	0	-0.027	-0.008	14.078	0.042	0.042	0.000	0.000	0.000	0.000
71	A	134	VAL	0	-0.004	-0.003	10.310	-0.091	-0.091	0.000	0.000	0.000	0.000
72	A	135	PRO	0	0.055	0.033	7.258	0.091	0.091	0.000	0.000	0.000	0.000
73	A	136	GLU	-1	-0.892	-0.944	8.770	0.537	0.537	0.000	0.000	0.000	0.000
74	A	137	LEU	0	-0.037	-0.019	6.096	0.221	0.221	0.000	0.000	0.000	0.000
75	A	138	SER	0	0.012	-0.007	1.910	-7.834	-9.763	8.595	-3.382	-3.283	0.019
76	A	139	ASN	0	-0.069	-0.034	4.530	-1.961	-1.849	-0.001	-0.015	-0.095	0.000
77	A	140	ILE	0	0.015	0.021	4.952	0.386	0.386	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:64:SER)