FMO DATABASE

FMODB ID: VR4Q1

Calculation Name: 1JRH-I-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JRH

Chain ID: I

ChEMBL ID:

UniProt ID: P01869

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	OptH
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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-682596.69804
FMO2-HF: Nuclear repulsion	644351.106831
FMO2-HF: Total energy	-38245.591208
FMO2-MP2: Total energy	-38356.214789

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(I:11:SER)

Summations of interaction energy for fragment #1(I:11: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.
-8.344	-6.719	-0.016	-0.669	-0.94	0

Interaction energy analysis for fragmet #1(I:11:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.037

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].
3	I	13	PRO	0	0.024	0.021	3.857	-1.649	-0.157	-0.015	-0.658	-0.818
4	I	14	THR	0	0.027	0.020	6.385	0.688	0.688	0.000	0.000	0.000
5	I	15	PRO	0	-0.019	-0.007	8.381	0.004	0.004	0.000	0.000	0.000
6	I	16	THR	0	-0.027	-0.014	12.128	-0.057	-0.057	0.000	0.000	0.000
7	I	17	ASN	0	0.006	-0.009	14.732	0.086	0.086	0.000	0.000	0.000
8	I	18	VAL	0	0.008	0.006	16.472	0.037	0.037	0.000	0.000	0.000
9	I	19	THR	0	0.027	0.030	19.180	0.004	0.004	0.000	0.000	0.000
10	I	20	ILE	0	-0.002	-0.007	22.971	0.014	0.014	0.000	0.000	0.000
11	I	21	GLU	-1	-0.920	-0.974	25.514	-0.180	-0.180	0.000	0.000	0.000
12	I	22	SER	0	-0.011	-0.015	28.843	0.013	0.013	0.000	0.000	0.000
13	I	23	TYR	0	0.006	0.041	32.184	0.002	0.002	0.000	0.000	0.000
14	I	24	ASN	0	-0.029	-0.029	35.512	0.005	0.005	0.000	0.000	0.000
15	I	25	MET	0	0.011	-0.007	35.608	-0.008	-0.008	0.000	0.000	0.000
16	I	26	ASN	0	0.019	0.021	32.746	0.013	0.013	0.000	0.000	0.000
17	I	27	PRO	0	0.024	0.023	28.852	-0.007	-0.007	0.000	0.000	0.000
18	I	28	ILE	0	-0.033	-0.010	25.960	0.014	0.014	0.000	0.000	0.000
19	I	29	VAL	0	-0.023	0.001	20.786	-0.016	-0.016	0.000	0.000	0.000
20	I	30	TYR	0	0.040	0.013	22.237	0.025	0.025	0.000	0.000	0.000
21	I	31	TRP	0	-0.055	-0.018	15.958	-0.011	-0.011	0.000	0.000	0.000
22	I	32	GLU	-1	-0.872	-0.939	17.414	-0.344	-0.344	0.000	0.000	0.000
23	I	33	TYR	0	-0.056	-0.060	8.813	-0.043	-0.043	0.000	0.000	0.000
24	I	34	GLN	0	0.006	0.027	9.844	-0.179	-0.179	0.000	0.000	0.000
25	I	35	ILE	0	0.013	0.010	14.072	0.068	0.068	0.000	0.000	0.000
26	I	36	MET	0	-0.013	-0.029	8.541	-0.110	-0.110	0.000	0.000	0.000
27	I	37	PRO	0	-0.019	-0.003	11.411	0.043	0.043	0.000	0.000	0.000
28	I	38	GLN	0	-0.025	-0.012	11.587	0.032	0.032	0.000	0.000	0.000
29	I	39	VAL	0	0.034	0.006	14.101	-0.090	-0.090	0.000	0.000	0.000
30	I	40	PRO	0	-0.028	-0.013	12.201	0.081	0.081	0.000	0.000	0.000
31	I	41	VAL	0	-0.033	0.010	13.110	-0.034	-0.034	0.000	0.000	0.000
32	I	42	PHE	0	0.008	-0.011	13.094	0.009	0.009	0.000	0.000	0.000
33	I	43	THR	0	-0.004	0.001	14.700	0.087	0.087	0.000	0.000	0.000
34	I	44	VAL	0	-0.020	-0.012	16.254	-0.063	-0.063	0.000	0.000	0.000
35	I	45	GLU	-1	-0.713	-0.846	17.021	0.009	0.009	0.000	0.000	0.000
36	I	46	VAL	0	0.050	0.018	20.283	-0.044	-0.044	0.000	0.000	0.000
37	I	47	LYS	1	0.883	0.952	22.670	0.128	0.128	0.000	0.000	0.000
38	I	48	ASN	0	0.043	0.013	25.057	-0.013	-0.013	0.000	0.000	0.000
39	I	49	TYR	0	-0.080	-0.055	27.692	0.006	0.006	0.000	0.000	0.000
40	I	50	GLY	0	0.068	0.043	29.724	-0.005	-0.005	0.000	0.000	0.000
41	I	51	VAL	0	-0.029	0.004	33.006	0.005	0.005	0.000	0.000	0.000
42	I	52	LYS	1	0.930	0.957	32.891	0.037	0.037	0.000	0.000	0.000
43	I	53	ASN	0	-0.022	-0.033	29.113	-0.007	-0.007	0.000	0.000	0.000
44	I	54	SER	0	0.010	0.026	26.816	0.004	0.004	0.000	0.000	0.000
45	I	55	GLU	-1	-0.935	-0.965	24.307	0.022	0.022	0.000	0.000	0.000
46	I	56	TRP	0	-0.100	-0.049	20.219	-0.020	-0.020	0.000	0.000	0.000
47	I	57	ILE	0	0.026	0.020	22.478	0.024	0.024	0.000	0.000	0.000
48	I	58	ASP	-1	-0.925	-0.971	20.036	0.058	0.058	0.000	0.000	0.000
49	I	59	ALA	0	-0.019	-0.003	22.058	0.000	0.000	0.000	0.000	0.000
50	I	60	CYS	0	-0.069	-0.035	21.257	0.034	0.034	0.000	0.000	0.000
51	I	61	ILE	0	0.051	0.016	18.639	-0.011	-0.011	0.000	0.000	0.000
52	I	62	ASN	0	-0.072	-0.050	16.731	0.034	0.034	0.000	0.000	0.000
53	I	63	ILE	0	0.021	0.039	17.939	0.019	0.019	0.000	0.000	0.000
54	I	64	SER	0	0.003	-0.018	17.851	-0.011	-0.011	0.000	0.000	0.000
55	I	65	HIS	0	-0.012	0.002	18.774	-0.017	-0.017	0.000	0.000	0.000
56	I	66	HIS	0	-0.022	-0.018	16.874	-0.026	-0.026	0.000	0.000	0.000
57	I	67	TYR	0	0.064	0.018	20.515	-0.018	-0.018	0.000	0.000	0.000
58	I	69	ASN	0	-0.012	-0.002	24.127	-0.009	-0.009	0.000	0.000	0.000
59	I	70	ILE	0	0.035	-0.009	24.809	0.009	0.009	0.000	0.000	0.000
60	I	71	SER	0	0.045	0.003	27.925	-0.003	-0.003	0.000	0.000	0.000
61	I	72	ASP	-1	-0.968	-0.976	30.256	-0.019	-0.019	0.000	0.000	0.000
62	I	73	HIS	0	0.011	0.009	27.299	0.003	0.003	0.000	0.000	0.000
63	I	74	VAL	0	-0.045	-0.002	30.105	-0.009	-0.009	0.000	0.000	0.000
64	I	75	GLY	0	0.010	-0.022	32.217	0.010	0.010	0.000	0.000	0.000
65	I	76	ASP	-1	-0.956	-0.977	34.469	-0.060	-0.060	0.000	0.000	0.000
66	I	77	PRO	0	-0.002	-0.019	35.455	-0.005	-0.005	0.000	0.000	0.000
67	I	78	SER	0	-0.006	0.012	36.240	-0.007	-0.007	0.000	0.000	0.000
68	I	79	ASN	0	-0.077	-0.023	31.774	-0.006	-0.006	0.000	0.000	0.000
69	I	80	SER	0	0.036	0.034	29.185	0.003	0.003	0.000	0.000	0.000
70	I	81	LEU	0	-0.034	-0.031	26.850	0.008	0.008	0.000	0.000	0.000
71	I	82	TRP	0	-0.026	0.007	22.506	-0.028	-0.028	0.000	0.000	0.000
72	I	83	VAL	0	0.033	0.005	19.564	0.024	0.024	0.000	0.000	0.000
73	I	84	ARG	1	0.804	0.911	15.290	0.091	0.091	0.000	0.000	0.000
74	I	85	VAL	0	0.025	0.023	14.424	0.056	0.056	0.000	0.000	0.000
75	I	86	LYS	1	0.878	0.972	10.737	-0.324	-0.324	0.000	0.000	0.000
76	I	87	ALA	0	0.032	0.001	9.543	0.083	0.083	0.000	0.000	0.000
77	I	88	ARG	1	0.937	0.968	8.903	-0.616	-0.616	0.000	0.000	0.000
78	I	89	VAL	0	0.033	0.015	8.377	-0.131	-0.131	0.000	0.000	0.000
79	I	90	GLY	0	0.010	0.024	8.799	0.478	0.478	0.000	0.000	0.000
80	I	91	GLN	0	-0.037	-0.034	10.031	-0.312	-0.312	0.000	0.000	0.000
81	I	92	LYS	1	0.951	0.985	4.280	-6.981	-6.848	-0.001	-0.011	-0.122
82	I	93	GLU	-1	-0.844	-0.938	6.259	0.105	0.105	0.000	0.000	0.000
83	I	94	SER	0	-0.030	-0.003	5.395	0.271	0.271	0.000	0.000	0.000
84	I	95	ALA	0	-0.018	-0.004	6.394	0.364	0.364	0.000	0.000	0.000
85	I	96	TYR	0	-0.041	-0.053	8.059	-0.029	-0.029	0.000	0.000	0.000
86	I	97	ALA	0	0.000	0.021	11.641	-0.110	-0.110	0.000	0.000	0.000
87	I	98	LYS	1	0.909	0.923	13.340	0.633	0.633	0.000	0.000	0.000
88	I	99	SER	0	0.002	0.004	16.400	-0.036	-0.036	0.000	0.000	0.000
89	I	100	GLU	-1	-0.977	-0.982	19.646	-0.292	-0.292	0.000	0.000	0.000
90	I	101	GLU	-1	-0.879	-0.957	22.820	-0.158	-0.158	0.000	0.000	0.000
91	I	102	PHE	0	0.024	0.018	26.152	-0.004	-0.004	0.000	0.000	0.000
92	I	103	ALA	0	0.032	0.016	28.566	0.010	0.010	0.000	0.000	0.000
93	I	104	VAL	0	-0.012	-0.006	32.240	0.010	0.010	0.000	0.000	0.000
94	I	105	SER	0	-0.011	0.001	34.193	-0.005	-0.005	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(I:11:SER)