FMO DATABASE

FMODB ID: 98892

Calculation Name: 1JD1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JD1

Chain ID: A

ChEMBL ID:

UniProt ID: P40037

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1021846.049589
FMO2-HF: Nuclear repulsion	973958.937055
FMO2-HF: Total energy	-47887.112534
FMO2-MP2: Total energy	-48025.718236

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:THR)

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

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.
-5.899	-4.194	10.591	-5.899	-6.397	-0.026

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.057 / q_NPA : -0.046

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	5	LEU	0	0.007	-0.002	3.019	-0.932	1.094	0.162	-0.640	-1.548	0.000
4	A	6	THR	0	-0.025	-0.017	4.828	0.417	0.449	-0.001	-0.005	-0.026	0.000
5	A	7	PRO	0	0.018	0.007	8.442	0.108	0.108	0.000	0.000	0.000	0.000
6	A	8	VAL	0	-0.015	-0.009	11.216	0.082	0.082	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.012	-0.009	14.158	-0.016	-0.016	0.000	0.000	0.000	0.000
8	A	10	CYS	0	-0.038	-0.022	17.686	0.045	0.045	0.000	0.000	0.000	0.000
9	A	11	GLU	-1	-0.913	-0.958	20.314	-0.106	-0.106	0.000	0.000	0.000	0.000
10	A	12	SER	0	-0.018	-0.007	23.758	0.008	0.008	0.000	0.000	0.000	0.000
11	A	13	ALA	0	-0.026	-0.018	22.310	0.011	0.011	0.000	0.000	0.000	0.000
12	A	14	PRO	0	0.010	0.019	24.428	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	15	ALA	0	0.001	0.006	23.800	-0.018	-0.018	0.000	0.000	0.000	0.000
14	A	16	ALA	0	-0.006	0.001	20.364	0.004	0.004	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.007	-0.001	22.402	0.007	0.007	0.000	0.000	0.000	0.000
16	A	18	ALA	0	-0.017	-0.017	21.979	0.003	0.003	0.000	0.000	0.000	0.000
17	A	19	SER	0	-0.023	-0.009	17.943	0.001	0.001	0.000	0.000	0.000	0.000
18	A	20	TYR	0	0.002	0.007	16.184	-0.049	-0.049	0.000	0.000	0.000	0.000
19	A	21	SER	0	0.007	0.011	13.429	0.008	0.008	0.000	0.000	0.000	0.000
20	A	22	HIS	0	0.026	0.015	15.544	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.032	0.008	13.440	0.034	0.034	0.000	0.000	0.000	0.000
22	A	24	MET	0	-0.011	0.012	7.576	-0.128	-0.128	0.000	0.000	0.000	0.000
23	A	25	LYS	1	0.850	0.921	8.056	0.013	0.013	0.000	0.000	0.000	0.000
24	A	26	VAL	0	0.031	0.013	2.348	-0.564	-1.037	1.926	-0.353	-1.100	-0.002
25	A	27	ASN	0	0.000	-0.006	1.882	-4.124	-4.074	8.505	-4.874	-3.681	-0.024
26	A	28	ASN	0	-0.015	-0.004	4.733	-0.218	-0.148	-0.001	-0.027	-0.042	0.000
27	A	29	LEU	0	0.001	0.015	6.787	-0.132	-0.132	0.000	0.000	0.000	0.000
28	A	30	ILE	0	0.009	0.010	7.907	-0.174	-0.174	0.000	0.000	0.000	0.000
29	A	31	PHE	0	-0.005	-0.010	7.999	0.046	0.046	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.011	-0.015	11.951	-0.050	-0.050	0.000	0.000	0.000	0.000
31	A	33	SER	0	-0.008	-0.017	15.396	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	34	GLY	0	-0.009	0.002	17.496	0.037	0.037	0.000	0.000	0.000	0.000
33	A	35	GLN	0	-0.028	-0.020	20.599	0.011	0.011	0.000	0.000	0.000	0.000
34	A	36	ILE	0	0.053	0.026	23.514	0.009	0.009	0.000	0.000	0.000	0.000
35	A	37	PRO	0	-0.014	-0.008	27.176	0.004	0.004	0.000	0.000	0.000	0.000
36	A	38	VAL	0	-0.014	-0.003	28.724	0.003	0.003	0.000	0.000	0.000	0.000
37	A	39	THR	0	0.003	-0.030	29.357	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	40	PRO	0	0.036	0.018	28.190	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.863	-0.903	29.206	-0.079	-0.079	0.000	0.000	0.000	0.000
40	A	42	ASN	0	-0.025	-0.025	27.901	0.001	0.001	0.000	0.000	0.000	0.000
41	A	43	LYS	1	0.883	0.954	31.236	0.083	0.083	0.000	0.000	0.000	0.000
42	A	44	LEU	0	0.023	0.012	32.329	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	45	VAL	0	-0.037	-0.013	33.123	0.006	0.006	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.877	-0.946	35.631	-0.065	-0.065	0.000	0.000	0.000	0.000
45	A	47	GLY	0	-0.052	-0.017	39.137	0.004	0.004	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.055	-0.061	39.639	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	49	ILE	0	0.040	0.015	35.184	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	50	ALA	0	0.014	0.000	35.061	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.799	-0.867	34.867	-0.036	-0.036	0.000	0.000	0.000	0.000
50	A	52	LYS	1	0.863	0.932	33.292	0.066	0.066	0.000	0.000	0.000	0.000
51	A	53	ALA	0	0.009	-0.007	30.833	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.778	-0.866	29.996	-0.016	-0.016	0.000	0.000	0.000	0.000
53	A	55	GLN	0	-0.030	-0.009	28.952	0.007	0.007	0.000	0.000	0.000	0.000
54	A	56	VAL	0	-0.015	-0.002	25.812	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	57	ILE	0	0.006	-0.009	25.550	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	58	GLN	0	0.020	0.013	25.432	0.006	0.006	0.000	0.000	0.000	0.000
57	A	59	ASN	0	-0.003	0.007	24.438	0.010	0.010	0.000	0.000	0.000	0.000
58	A	60	ILE	0	0.002	-0.002	20.138	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.842	0.917	20.932	0.023	0.023	0.000	0.000	0.000	0.000
60	A	62	ASN	0	0.007	0.007	22.045	0.027	0.027	0.000	0.000	0.000	0.000
61	A	63	VAL	0	0.034	0.015	17.069	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.035	-0.006	16.686	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.844	-0.895	17.712	0.106	0.106	0.000	0.000	0.000	0.000
64	A	66	ALA	0	0.004	0.003	18.547	0.018	0.018	0.000	0.000	0.000	0.000
65	A	67	SER	0	-0.061	-0.041	13.568	-0.036	-0.036	0.000	0.000	0.000	0.000
66	A	68	ASN	0	-0.067	-0.039	13.926	0.020	0.020	0.000	0.000	0.000	0.000
67	A	69	SER	0	0.018	-0.027	14.992	0.057	0.057	0.000	0.000	0.000	0.000
68	A	70	SER	0	-0.008	-0.041	16.953	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	71	LEU	0	0.057	0.021	19.477	0.003	0.003	0.000	0.000	0.000	0.000
70	A	72	ASP	-1	-0.884	-0.919	21.600	0.148	0.148	0.000	0.000	0.000	0.000
71	A	73	ARG	1	0.880	0.951	15.353	-0.334	-0.334	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.007	0.001	16.711	0.009	0.009	0.000	0.000	0.000	0.000
73	A	75	VAL	0	-0.021	-0.004	14.234	0.018	0.018	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.784	0.903	16.866	0.091	0.091	0.000	0.000	0.000	0.000
75	A	77	VAL	0	0.031	0.019	18.220	-0.018	-0.018	0.000	0.000	0.000	0.000
76	A	78	ASN	0	-0.040	-0.033	19.032	0.038	0.038	0.000	0.000	0.000	0.000
77	A	79	ILE	0	0.003	-0.009	22.251	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	80	PHE	0	0.022	0.012	21.560	0.004	0.004	0.000	0.000	0.000	0.000
79	A	81	LEU	0	-0.004	-0.015	27.257	0.002	0.002	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.030	0.023	30.994	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	83	ASP	-1	-0.758	-0.873	33.331	-0.062	-0.062	0.000	0.000	0.000	0.000
82	A	84	ILE	0	-0.007	-0.010	33.633	0.003	0.003	0.000	0.000	0.000	0.000
83	A	85	ASN	0	-0.094	-0.068	35.837	0.009	0.009	0.000	0.000	0.000	0.000
84	A	86	HIS	0	0.034	0.030	35.189	0.003	0.003	0.000	0.000	0.000	0.000
85	A	87	PHE	0	-0.010	-0.012	31.146	0.004	0.004	0.000	0.000	0.000	0.000
86	A	88	ALA	0	-0.015	-0.010	34.570	0.003	0.003	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.858	-0.940	36.617	-0.035	-0.035	0.000	0.000	0.000	0.000
88	A	90	PHE	0	0.035	0.015	27.558	0.004	0.004	0.000	0.000	0.000	0.000
89	A	91	ASN	0	-0.013	-0.017	31.632	0.003	0.003	0.000	0.000	0.000	0.000
90	A	92	SER	0	-0.023	0.007	33.031	0.008	0.008	0.000	0.000	0.000	0.000
91	A	93	VAL	0	0.025	0.021	31.629	0.006	0.006	0.000	0.000	0.000	0.000
92	A	94	TYR	0	0.016	-0.007	24.686	0.002	0.002	0.000	0.000	0.000	0.000
93	A	95	ALA	0	-0.011	-0.018	29.449	0.007	0.007	0.000	0.000	0.000	0.000
94	A	96	LYS	1	0.801	0.897	31.713	0.012	0.012	0.000	0.000	0.000	0.000
95	A	97	TYR	0	-0.067	-0.054	27.058	0.009	0.009	0.000	0.000	0.000	0.000
96	A	98	PHE	0	-0.053	-0.006	22.554	0.008	0.008	0.000	0.000	0.000	0.000
97	A	99	ASN	0	-0.006	0.003	27.579	0.000	0.000	0.000	0.000	0.000	0.000
98	A	100	THR	0	0.007	-0.020	28.697	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	101	HIS	0	-0.021	-0.008	20.578	0.011	0.011	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.920	0.960	25.495	-0.059	-0.059	0.000	0.000	0.000	0.000
101	A	103	PRO	0	-0.008	0.015	20.631	0.007	0.007	0.000	0.000	0.000	0.000
102	A	104	ALA	0	0.020	0.024	20.334	-0.010	-0.010	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.835	0.891	21.961	0.023	0.023	0.000	0.000	0.000	0.000
104	A	106	SER	0	-0.022	-0.011	23.393	0.001	0.001	0.000	0.000	0.000	0.000
105	A	107	CYS	0	0.012	0.005	25.074	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	108	VAL	0	-0.011	0.017	26.673	0.005	0.005	0.000	0.000	0.000	0.000
107	A	109	ALA	0	0.013	0.016	29.325	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	110	VAL	0	-0.020	-0.021	27.607	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	111	ALA	0	-0.006	-0.006	31.063	0.006	0.006	0.000	0.000	0.000	0.000
110	A	112	ALA	0	0.005	-0.003	31.606	0.007	0.007	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.015	0.016	27.253	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	114	PRO	0	0.039	0.011	25.883	0.008	0.008	0.000	0.000	0.000	0.000
113	A	115	LEU	0	-0.041	-0.039	29.195	0.007	0.007	0.000	0.000	0.000	0.000
114	A	116	GLY	0	-0.004	0.012	32.045	0.009	0.009	0.000	0.000	0.000	0.000
115	A	117	VAL	0	-0.031	0.004	29.372	0.010	0.010	0.000	0.000	0.000	0.000
116	A	118	ASP	-1	-0.775	-0.905	32.784	-0.081	-0.081	0.000	0.000	0.000	0.000
117	A	119	MET	0	-0.061	-0.035	29.168	0.004	0.004	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.871	-0.941	23.093	-0.211	-0.211	0.000	0.000	0.000	0.000
119	A	121	MET	0	-0.051	-0.019	22.702	0.011	0.011	0.000	0.000	0.000	0.000
120	A	122	GLU	-1	-0.797	-0.873	18.275	-0.260	-0.260	0.000	0.000	0.000	0.000
121	A	123	ALA	0	-0.020	-0.031	17.603	0.035	0.035	0.000	0.000	0.000	0.000
122	A	124	ILE	0	0.006	0.020	11.901	-0.041	-0.041	0.000	0.000	0.000	0.000
123	A	125	ALA	0	0.003	0.005	13.187	0.041	0.041	0.000	0.000	0.000	0.000
124	A	126	ALA	0	0.010	0.011	12.110	0.010	0.010	0.000	0.000	0.000	0.000
125	A	127	GLU	-1	-0.759	-0.842	10.660	0.254	0.254	0.000	0.000	0.000	0.000
126	A	128	ARG	1	0.758	0.866	12.966	-0.050	-0.050	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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