FMO DATABASE

FMODB ID: MNNYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1022993.752487
FMO2-HF: Nuclear repulsion	975106.528474
FMO2-HF: Total energy	-47887.224013
FMO2-MP2: Total energy	-48025.802522

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.
-12.093	-8.677	9.753	-5.531	-7.638	-0.015

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 : -0.047 / q_NPA : -0.028

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	A	5	LEU	0	0.030	0.004	2.922	-2.570	0.154	0.516	-1.229	-2.010	-0.003
4	A	6	THR	0	-0.063	-0.038	4.912	0.460	0.484	-0.001	-0.003	-0.020	0.000
5	A	7	PRO	0	0.036	0.018	8.669	0.113	0.113	0.000	0.000	0.000	0.000
6	A	8	VAL	0	-0.017	0.002	11.475	0.051	0.051	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.011	-0.011	14.391	-0.012	-0.012	0.000	0.000	0.000	0.000
8	A	10	CYS	0	-0.026	-0.012	18.009	0.032	0.032	0.000	0.000	0.000	0.000
9	A	11	GLU	-1	-0.913	-0.948	20.750	-0.060	-0.060	0.000	0.000	0.000	0.000
10	A	12	SER	0	-0.021	-0.011	23.706	0.005	0.005	0.000	0.000	0.000	0.000
11	A	13	ALA	0	0.003	-0.015	22.665	0.012	0.012	0.000	0.000	0.000	0.000
12	A	14	PRO	0	-0.020	0.011	24.822	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	15	ALA	0	0.008	0.003	24.049	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	16	ALA	0	0.005	0.006	20.769	0.007	0.007	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.004	0.000	22.827	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	18	ALA	0	-0.014	-0.014	22.228	0.000	0.000	0.000	0.000	0.000	0.000
17	A	19	SER	0	-0.018	-0.006	18.248	0.001	0.001	0.000	0.000	0.000	0.000
18	A	20	TYR	0	-0.017	-0.004	16.577	-0.040	-0.040	0.000	0.000	0.000	0.000
19	A	21	SER	0	0.020	0.014	14.012	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	22	HIS	0	0.038	0.022	16.142	-0.010	-0.010	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.025	0.009	13.451	0.036	0.036	0.000	0.000	0.000	0.000
22	A	24	MET	0	-0.024	0.003	7.971	-0.140	-0.140	0.000	0.000	0.000	0.000
23	A	25	LYS	1	0.822	0.903	7.810	0.001	0.001	0.000	0.000	0.000	0.000
24	A	26	VAL	0	0.022	-0.006	2.531	-0.842	-0.851	1.270	-0.299	-0.963	-0.002
25	A	27	ASN	0	0.018	0.003	2.120	-8.347	-7.749	7.969	-3.981	-4.586	-0.010
26	A	28	ASN	0	-0.018	-0.002	4.519	-0.379	-0.300	-0.001	-0.019	-0.059	0.000
27	A	29	LEU	0	-0.003	0.012	6.718	-0.169	-0.169	0.000	0.000	0.000	0.000
28	A	30	ILE	0	0.008	0.010	7.703	-0.166	-0.166	0.000	0.000	0.000	0.000
29	A	31	PHE	0	0.003	-0.001	8.092	0.048	0.048	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.009	-0.013	12.128	-0.058	-0.058	0.000	0.000	0.000	0.000
31	A	33	SER	0	0.013	-0.013	15.562	0.007	0.007	0.000	0.000	0.000	0.000
32	A	34	GLY	0	0.032	0.024	17.592	0.020	0.020	0.000	0.000	0.000	0.000
33	A	35	GLN	0	-0.070	-0.033	20.575	0.000	0.000	0.000	0.000	0.000	0.000
34	A	36	ILE	0	0.067	0.025	23.599	0.008	0.008	0.000	0.000	0.000	0.000
35	A	37	PRO	0	0.001	0.008	27.360	0.003	0.003	0.000	0.000	0.000	0.000
36	A	38	VAL	0	-0.025	-0.013	28.909	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	39	THR	0	0.009	-0.028	29.382	0.000	0.000	0.000	0.000	0.000	0.000
38	A	40	PRO	0	0.031	0.002	28.202	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.864	-0.894	29.213	-0.039	-0.039	0.000	0.000	0.000	0.000
40	A	42	ASN	0	-0.028	-0.013	27.526	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	43	LYS	1	0.874	0.945	31.111	0.043	0.043	0.000	0.000	0.000	0.000
42	A	44	LEU	0	0.019	0.011	32.709	0.002	0.002	0.000	0.000	0.000	0.000
43	A	45	VAL	0	-0.039	-0.015	33.309	0.003	0.003	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.832	-0.933	35.707	-0.024	-0.024	0.000	0.000	0.000	0.000
45	A	47	GLY	0	-0.041	-0.010	39.032	0.003	0.003	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.050	-0.049	39.569	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	49	ILE	0	0.015	0.001	35.015	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	50	ALA	0	0.012	-0.001	34.935	0.001	0.001	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.820	-0.884	34.774	0.003	0.003	0.000	0.000	0.000	0.000
50	A	52	LYS	1	0.791	0.897	33.577	0.021	0.021	0.000	0.000	0.000	0.000
51	A	53	ALA	0	0.023	0.003	30.792	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.799	-0.868	29.942	0.032	0.032	0.000	0.000	0.000	0.000
53	A	55	GLN	0	-0.010	0.006	28.574	0.005	0.005	0.000	0.000	0.000	0.000
54	A	56	VAL	0	-0.008	0.005	25.880	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	57	ILE	0	0.015	0.000	25.451	0.001	0.001	0.000	0.000	0.000	0.000
56	A	58	GLN	0	-0.001	-0.004	25.228	0.008	0.008	0.000	0.000	0.000	0.000
57	A	59	ASN	0	-0.003	0.002	24.291	0.005	0.005	0.000	0.000	0.000	0.000
58	A	60	ILE	0	-0.005	0.000	20.255	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.840	0.905	20.641	-0.025	-0.025	0.000	0.000	0.000	0.000
60	A	62	ASN	0	-0.007	0.003	21.875	0.021	0.021	0.000	0.000	0.000	0.000
61	A	63	VAL	0	0.042	0.012	17.004	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.044	-0.009	16.476	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.822	-0.871	17.234	0.136	0.136	0.000	0.000	0.000	0.000
64	A	66	ALA	0	0.012	0.005	18.428	0.013	0.013	0.000	0.000	0.000	0.000
65	A	67	SER	0	-0.040	-0.028	13.245	-0.036	-0.036	0.000	0.000	0.000	0.000
66	A	68	ASN	0	-0.058	-0.032	13.528	0.019	0.019	0.000	0.000	0.000	0.000
67	A	69	SER	0	0.003	-0.024	14.766	0.055	0.055	0.000	0.000	0.000	0.000
68	A	70	SER	0	-0.013	-0.045	16.665	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	71	LEU	0	0.048	0.014	19.432	0.014	0.014	0.000	0.000	0.000	0.000
70	A	72	ASP	-1	-0.859	-0.912	21.405	0.209	0.209	0.000	0.000	0.000	0.000
71	A	73	ARG	1	0.853	0.939	15.398	-0.374	-0.374	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.004	0.005	16.395	0.034	0.034	0.000	0.000	0.000	0.000
73	A	75	VAL	0	-0.031	-0.013	14.445	0.007	0.007	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.792	0.884	16.593	-0.080	-0.080	0.000	0.000	0.000	0.000
75	A	77	VAL	0	0.036	0.018	18.234	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	78	ASN	0	-0.074	-0.050	18.513	0.027	0.027	0.000	0.000	0.000	0.000
77	A	79	ILE	0	0.006	-0.004	21.978	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	80	PHE	0	0.021	0.007	21.581	0.001	0.001	0.000	0.000	0.000	0.000
79	A	81	LEU	0	-0.001	-0.002	27.348	0.001	0.001	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.045	0.019	31.115	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	83	ASP	-1	-0.794	-0.891	33.674	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	84	ILE	0	-0.007	-0.005	33.831	0.003	0.003	0.000	0.000	0.000	0.000
83	A	85	ASN	0	-0.080	-0.067	35.870	0.007	0.007	0.000	0.000	0.000	0.000
84	A	86	HIS	0	0.033	0.022	34.925	0.004	0.004	0.000	0.000	0.000	0.000
85	A	87	PHE	0	0.012	0.002	30.748	0.005	0.005	0.000	0.000	0.000	0.000
86	A	88	ALA	0	-0.013	-0.004	34.491	0.005	0.005	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.827	-0.935	36.745	0.006	0.006	0.000	0.000	0.000	0.000
88	A	90	PHE	0	0.042	0.021	27.483	0.004	0.004	0.000	0.000	0.000	0.000
89	A	91	ASN	0	0.001	-0.002	31.727	0.009	0.009	0.000	0.000	0.000	0.000
90	A	92	SER	0	-0.034	-0.001	33.162	0.008	0.008	0.000	0.000	0.000	0.000
91	A	93	VAL	0	0.027	0.023	31.366	0.005	0.005	0.000	0.000	0.000	0.000
92	A	94	TYR	0	0.015	-0.010	24.550	0.004	0.004	0.000	0.000	0.000	0.000
93	A	95	ALA	0	-0.007	-0.014	29.537	0.009	0.009	0.000	0.000	0.000	0.000
94	A	96	LYS	1	0.803	0.888	31.933	-0.028	-0.028	0.000	0.000	0.000	0.000
95	A	97	TYR	0	-0.071	-0.045	26.991	0.006	0.006	0.000	0.000	0.000	0.000
96	A	98	PHE	0	-0.041	-0.007	22.521	0.011	0.011	0.000	0.000	0.000	0.000
97	A	99	ASN	0	0.015	0.004	27.620	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	100	THR	0	-0.005	-0.026	28.674	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	101	HIS	0	-0.003	0.003	20.538	0.000	0.000	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.884	0.951	25.179	-0.104	-0.104	0.000	0.000	0.000	0.000
101	A	103	PRO	0	0.008	0.023	20.419	0.006	0.006	0.000	0.000	0.000	0.000
102	A	104	ALA	0	0.022	0.027	20.357	-0.020	-0.020	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.843	0.907	21.456	-0.049	-0.049	0.000	0.000	0.000	0.000
104	A	106	SER	0	-0.023	-0.007	23.024	0.002	0.002	0.000	0.000	0.000	0.000
105	A	107	CYS	0	0.004	0.001	24.730	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	108	VAL	0	-0.021	0.009	26.693	0.002	0.002	0.000	0.000	0.000	0.000
107	A	109	ALA	0	0.020	0.017	29.315	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	110	VAL	0	-0.020	-0.021	27.809	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	111	ALA	0	-0.001	-0.005	31.284	0.002	0.002	0.000	0.000	0.000	0.000
110	A	112	ALA	0	-0.005	-0.002	31.880	0.002	0.002	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.006	0.016	27.303	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	114	PRO	0	0.032	0.011	25.831	0.000	0.000	0.000	0.000	0.000	0.000
113	A	115	LEU	0	-0.041	-0.035	29.067	0.006	0.006	0.000	0.000	0.000	0.000
114	A	116	GLY	0	0.000	0.014	32.102	0.005	0.005	0.000	0.000	0.000	0.000
115	A	117	VAL	0	-0.046	-0.010	29.431	0.006	0.006	0.000	0.000	0.000	0.000
116	A	118	ASP	-1	-0.781	-0.902	32.578	-0.028	-0.028	0.000	0.000	0.000	0.000
117	A	119	MET	0	-0.060	-0.026	29.420	0.003	0.003	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.869	-0.945	23.270	-0.095	-0.095	0.000	0.000	0.000	0.000
119	A	121	MET	0	-0.048	-0.011	22.336	0.010	0.010	0.000	0.000	0.000	0.000
120	A	122	GLU	-1	-0.815	-0.879	18.187	-0.086	-0.086	0.000	0.000	0.000	0.000
121	A	123	ALA	0	-0.017	-0.024	17.585	0.023	0.023	0.000	0.000	0.000	0.000
122	A	124	ILE	0	-0.004	0.010	11.940	-0.023	-0.023	0.000	0.000	0.000	0.000
123	A	125	ALA	0	0.007	0.012	13.038	0.010	0.010	0.000	0.000	0.000	0.000
124	A	126	ALA	0	0.020	0.013	11.758	0.063	0.063	0.000	0.000	0.000	0.000
125	A	127	GLU	-1	-0.768	-0.849	10.494	0.249	0.249	0.000	0.000	0.000	0.000
126	A	128	ARG	1	0.746	0.847	12.785	-0.125	-0.125	0.000	0.000	0.000	0.000

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