FMO DATABASE

FMODB ID: 94JM2

Calculation Name: 1P3F-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P3F

Chain ID: B

ChEMBL ID:

UniProt ID: P06897

Base Structure: X-ray

Registration Date: 2023-09-20

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. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-462816.87034
FMO2-HF: Nuclear repulsion	431608.631107
FMO2-HF: Total energy	-31208.239233
FMO2-MP2: Total energy	-31300.128894

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:23:ARG)

Summations of interaction energy for fragment #1(B:23:ARG)

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.
149.088	152.254	5.995	-2.825	-6.333	-0.014

Interaction energy analysis for fragmet #1(B:23:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.969 / q_NPA : 0.983

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	B	25	ASN	0	0.040	-0.007	2.609	-13.420	-10.732	1.997	-1.858	-2.826	-0.012
4	B	26	ILE	0	0.022	0.034	4.347	-1.974	-1.811	-0.001	-0.003	-0.159	0.000
5	B	27	GLN	0	-0.043	-0.036	3.115	-1.031	-0.495	0.034	-0.080	-0.490	0.000
6	B	28	GLY	0	-0.044	-0.031	2.078	-11.644	-11.628	3.839	-2.041	-1.813	0.000
7	B	29	ILE	0	-0.036	0.006	3.056	1.566	0.712	0.030	1.349	-0.525	-0.002
8	B	30	THR	0	0.026	0.010	2.992	4.369	4.986	0.096	-0.192	-0.520	0.000
9	B	31	LYS	1	1.051	1.028	5.559	27.735	27.735	0.000	0.000	0.000	0.000
10	B	32	PRO	0	0.022	-0.002	6.928	3.068	3.068	0.000	0.000	0.000	0.000
11	B	33	ALA	0	-0.012	0.017	8.073	2.690	2.690	0.000	0.000	0.000	0.000
12	B	34	ILE	0	0.068	0.031	9.549	2.514	2.514	0.000	0.000	0.000	0.000
13	B	35	ARG	1	0.875	0.945	11.533	20.762	20.762	0.000	0.000	0.000	0.000
14	B	36	ARG	1	0.967	0.951	8.913	26.556	26.556	0.000	0.000	0.000	0.000
15	B	37	LEU	0	-0.009	0.008	12.797	1.302	1.302	0.000	0.000	0.000	0.000
16	B	38	ALA	0	0.078	0.028	15.596	1.234	1.234	0.000	0.000	0.000	0.000
17	B	39	ARG	1	0.797	0.901	17.229	16.100	16.100	0.000	0.000	0.000	0.000
18	B	40	ARG	1	0.963	0.992	18.313	16.062	16.062	0.000	0.000	0.000	0.000
19	B	41	GLY	0	-0.026	-0.009	19.906	0.607	0.607	0.000	0.000	0.000	0.000
20	B	42	GLY	0	0.024	0.021	21.880	0.435	0.435	0.000	0.000	0.000	0.000
21	B	43	VAL	0	0.013	0.017	20.327	0.374	0.374	0.000	0.000	0.000	0.000
22	B	44	LYS	1	0.999	0.995	21.148	10.558	10.558	0.000	0.000	0.000	0.000
23	B	45	CYS	0	-0.017	-0.021	21.576	-0.375	-0.375	0.000	0.000	0.000	0.000
24	B	46	ILE	0	0.007	-0.005	16.446	-0.025	-0.025	0.000	0.000	0.000	0.000
25	B	47	SER	0	0.073	0.039	18.209	-0.812	-0.812	0.000	0.000	0.000	0.000
26	B	48	GLY	0	0.006	-0.010	15.984	-0.793	-0.793	0.000	0.000	0.000	0.000
27	B	49	LEU	0	0.059	0.021	15.337	-1.329	-1.329	0.000	0.000	0.000	0.000
28	B	50	ILE	0	0.007	0.022	15.549	-0.260	-0.260	0.000	0.000	0.000	0.000
29	B	51	TYR	0	0.018	0.011	11.018	-0.578	-0.578	0.000	0.000	0.000	0.000
30	B	52	GLU	-1	-0.779	-0.858	9.971	-28.925	-28.925	0.000	0.000	0.000	0.000
31	B	53	GLU	-1	-0.866	-0.937	12.925	-16.230	-16.230	0.000	0.000	0.000	0.000
32	B	54	THR	0	-0.085	-0.064	13.390	0.531	0.531	0.000	0.000	0.000	0.000
33	B	55	ARG	1	0.789	0.878	6.427	36.507	36.507	0.000	0.000	0.000	0.000
34	B	56	GLY	0	0.067	0.042	12.418	0.081	0.081	0.000	0.000	0.000	0.000
35	B	57	VAL	0	0.048	0.036	14.689	0.799	0.799	0.000	0.000	0.000	0.000
36	B	58	LEU	0	-0.051	-0.042	11.088	0.359	0.359	0.000	0.000	0.000	0.000
37	B	59	LYS	1	0.811	0.891	12.178	19.376	19.376	0.000	0.000	0.000	0.000
38	B	60	VAL	0	0.050	0.023	14.257	0.676	0.676	0.000	0.000	0.000	0.000
39	B	61	PHE	0	-0.073	-0.023	17.288	0.881	0.881	0.000	0.000	0.000	0.000
40	B	62	LEU	0	0.027	-0.004	12.959	0.599	0.599	0.000	0.000	0.000	0.000
41	B	63	GLU	-1	-0.823	-0.903	15.775	-17.262	-17.262	0.000	0.000	0.000	0.000
42	B	64	ASN	0	0.012	0.005	18.079	0.955	0.955	0.000	0.000	0.000	0.000
43	B	65	VAL	0	-0.002	0.011	20.058	0.535	0.535	0.000	0.000	0.000	0.000
44	B	66	ILE	0	0.028	0.006	15.807	0.546	0.546	0.000	0.000	0.000	0.000
45	B	67	ARG	1	0.953	1.002	20.263	13.731	13.731	0.000	0.000	0.000	0.000
46	B	68	ASP	-1	-0.801	-0.864	22.278	-11.016	-11.016	0.000	0.000	0.000	0.000
47	B	69	ALA	0	-0.025	-0.024	22.294	0.362	0.362	0.000	0.000	0.000	0.000
48	B	70	VAL	0	0.002	-0.019	20.384	0.260	0.260	0.000	0.000	0.000	0.000
49	B	71	THR	0	0.024	0.010	23.720	0.396	0.396	0.000	0.000	0.000	0.000
50	B	72	TYR	0	-0.051	-0.024	26.890	0.449	0.449	0.000	0.000	0.000	0.000
51	B	73	THR	0	-0.047	-0.051	24.754	0.129	0.129	0.000	0.000	0.000	0.000
52	B	74	GLU	-1	-0.896	-0.936	26.134	-11.033	-11.033	0.000	0.000	0.000	0.000
53	B	75	HIS	0	-0.016	0.026	28.670	0.304	0.304	0.000	0.000	0.000	0.000
54	B	76	ALA	0	-0.062	-0.047	30.811	0.354	0.354	0.000	0.000	0.000	0.000
55	B	77	LYS	1	0.876	0.932	31.075	8.581	8.581	0.000	0.000	0.000	0.000
56	B	78	ARG	1	0.823	0.893	27.232	10.864	10.864	0.000	0.000	0.000	0.000
57	B	79	LYS	1	0.998	0.980	24.490	11.477	11.477	0.000	0.000	0.000	0.000
58	B	80	THR	0	-0.019	-0.010	22.854	-0.502	-0.502	0.000	0.000	0.000	0.000
59	B	81	VAL	0	0.029	0.029	20.610	0.426	0.426	0.000	0.000	0.000	0.000
60	B	82	THR	0	-0.037	-0.040	22.906	-0.082	-0.082	0.000	0.000	0.000	0.000
61	B	83	ALA	0	0.036	0.013	23.513	-0.084	-0.084	0.000	0.000	0.000	0.000
62	B	84	MET	0	0.045	0.020	24.553	-0.141	-0.141	0.000	0.000	0.000	0.000
63	B	85	ASP	-1	-0.727	-0.785	25.047	-11.285	-11.285	0.000	0.000	0.000	0.000
64	B	86	VAL	0	0.014	-0.009	20.890	-0.112	-0.112	0.000	0.000	0.000	0.000
65	B	87	VAL	0	-0.031	0.007	23.880	0.087	0.087	0.000	0.000	0.000	0.000
66	B	88	TYR	0	-0.014	-0.024	26.569	0.333	0.333	0.000	0.000	0.000	0.000
67	B	89	ALA	0	0.016	0.017	24.451	0.223	0.223	0.000	0.000	0.000	0.000
68	B	90	LEU	0	0.005	-0.011	21.795	0.089	0.089	0.000	0.000	0.000	0.000
69	B	91	LYS	1	0.947	0.978	25.797	9.808	9.808	0.000	0.000	0.000	0.000
70	B	92	ARG	1	0.890	0.947	28.868	10.602	10.602	0.000	0.000	0.000	0.000
71	B	93	GLN	0	-0.076	-0.045	24.448	-0.066	-0.066	0.000	0.000	0.000	0.000
72	B	94	GLY	0	0.021	0.023	27.709	0.021	0.021	0.000	0.000	0.000	0.000
73	B	95	ARG	1	0.839	0.913	23.653	12.350	12.350	0.000	0.000	0.000	0.000
74	B	96	THR	0	-0.005	-0.018	26.196	-0.355	-0.355	0.000	0.000	0.000	0.000
75	B	97	LEU	0	0.001	0.007	22.777	-0.106	-0.106	0.000	0.000	0.000	0.000
76	B	98	TYR	0	0.007	-0.002	26.810	0.263	0.263	0.000	0.000	0.000	0.000
77	B	99	GLY	0	0.031	0.006	26.866	-0.326	-0.326	0.000	0.000	0.000	0.000
78	B	100	PHE	0	-0.034	-0.012	21.850	-0.277	-0.277	0.000	0.000	0.000	0.000
79	B	101	GLY	0	0.044	0.050	27.018	-0.007	-0.007	0.000	0.000	0.000	0.000
80	B	102	GLY	0	0.002	-0.025	26.967	0.252	0.252	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:23:ARG)