FMO DATABASE

FMODB ID: LNN49

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1021680.023134
FMO2-HF: Nuclear repulsion	973793.268882
FMO2-HF: Total energy	-47886.754252
FMO2-MP2: Total energy	-48025.402246

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.
-8.728	-4.04	6.045	-4.771	-5.962	-0.022

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 : -0.021 / q_NPA : -0.009

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	0.017	-0.004	2.706	-0.758	2.034	0.503	-1.177	-2.118	0.004
4	A	6	THR	0	-0.022	-0.013	4.750	0.087	0.117	-0.001	-0.005	-0.024	0.000
5	A	7	PRO	0	0.005	-0.002	8.422	0.268	0.268	0.000	0.000	0.000	0.000
6	A	8	VAL	0	-0.007	-0.002	11.188	-0.025	-0.025	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.014	-0.011	14.216	0.048	0.048	0.000	0.000	0.000	0.000
8	A	10	CYS	0	-0.045	-0.015	17.703	0.011	0.011	0.000	0.000	0.000	0.000
9	A	11	GLU	-1	-0.908	-0.958	20.358	-0.223	-0.223	0.000	0.000	0.000	0.000
10	A	12	SER	0	-0.039	-0.018	23.810	0.017	0.017	0.000	0.000	0.000	0.000
11	A	13	ALA	0	-0.007	-0.008	22.379	0.024	0.024	0.000	0.000	0.000	0.000
12	A	14	PRO	0	0.005	0.017	24.437	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	15	ALA	0	0.011	0.015	23.867	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	16	ALA	0	-0.018	-0.006	20.358	0.017	0.017	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.006	-0.003	22.407	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	18	ALA	0	-0.016	-0.017	21.838	0.008	0.008	0.000	0.000	0.000	0.000
17	A	19	SER	0	-0.019	-0.007	17.911	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	20	TYR	0	0.012	0.014	16.125	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	21	SER	0	0.012	0.014	13.451	-0.050	-0.050	0.000	0.000	0.000	0.000
20	A	22	HIS	0	0.017	0.015	15.543	0.024	0.024	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.042	0.013	13.139	0.072	0.072	0.000	0.000	0.000	0.000
22	A	24	MET	0	-0.008	0.015	7.625	-0.245	-0.245	0.000	0.000	0.000	0.000
23	A	25	LYS	1	0.846	0.928	7.862	0.711	0.711	0.000	0.000	0.000	0.000
24	A	26	VAL	0	0.042	0.022	2.244	-0.637	-1.079	1.886	-0.350	-1.094	-0.001
25	A	27	ASN	0	0.026	0.000	2.165	-6.729	-4.471	3.658	-3.220	-2.696	-0.025
26	A	28	ASN	0	-0.019	-0.008	4.807	-0.348	-0.298	-0.001	-0.019	-0.030	0.000
27	A	29	LEU	0	-0.002	0.013	6.975	-0.122	-0.122	0.000	0.000	0.000	0.000
28	A	30	ILE	0	0.006	0.007	7.940	-0.198	-0.198	0.000	0.000	0.000	0.000
29	A	31	PHE	0	-0.005	-0.010	7.925	0.109	0.109	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.020	-0.021	11.926	-0.116	-0.116	0.000	0.000	0.000	0.000
31	A	33	SER	0	-0.018	-0.024	15.309	0.046	0.046	0.000	0.000	0.000	0.000
32	A	34	GLY	0	-0.006	0.004	17.531	0.012	0.012	0.000	0.000	0.000	0.000
33	A	35	GLN	0	-0.022	-0.018	20.487	-0.026	-0.026	0.000	0.000	0.000	0.000
34	A	36	ILE	0	0.051	0.026	23.453	0.018	0.018	0.000	0.000	0.000	0.000
35	A	37	PRO	0	-0.020	-0.012	27.156	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	38	VAL	0	-0.017	0.001	28.802	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	39	THR	0	0.004	-0.027	29.338	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	40	PRO	0	0.036	0.014	28.246	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.871	-0.908	29.252	-0.085	-0.085	0.000	0.000	0.000	0.000
40	A	42	ASN	0	-0.015	-0.027	28.343	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	43	LYS	1	0.876	0.948	31.299	0.077	0.077	0.000	0.000	0.000	0.000
42	A	44	LEU	0	0.032	0.011	32.081	0.000	0.000	0.000	0.000	0.000	0.000
43	A	45	VAL	0	-0.028	-0.006	33.075	0.000	0.000	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.903	-0.952	35.594	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	47	GLY	0	-0.031	-0.008	39.087	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.052	-0.026	39.516	0.004	0.004	0.000	0.000	0.000	0.000
47	A	49	ILE	0	0.041	0.020	35.106	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	50	ALA	0	0.012	-0.006	35.043	0.002	0.002	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.804	-0.906	34.843	0.006	0.006	0.000	0.000	0.000	0.000
50	A	52	LYS	1	0.877	0.934	33.123	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	53	ALA	0	0.014	-0.009	30.813	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.797	-0.869	29.971	0.027	0.027	0.000	0.000	0.000	0.000
53	A	55	GLN	0	-0.022	0.003	28.969	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	56	VAL	0	-0.008	0.000	25.673	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	57	ILE	0	0.008	-0.008	25.478	0.000	0.000	0.000	0.000	0.000	0.000
56	A	58	GLN	0	-0.010	-0.001	25.387	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	59	ASN	0	0.002	0.010	24.238	-0.017	-0.017	0.000	0.000	0.000	0.000
58	A	60	ILE	0	-0.004	-0.005	20.272	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.861	0.937	20.856	0.040	0.040	0.000	0.000	0.000	0.000
60	A	62	ASN	0	0.039	0.013	21.953	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	63	VAL	0	0.008	-0.004	16.924	-0.029	-0.029	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.027	0.000	16.695	-0.025	-0.025	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.858	-0.901	17.622	-0.083	-0.083	0.000	0.000	0.000	0.000
64	A	66	ALA	0	0.018	0.002	18.317	-0.024	-0.024	0.000	0.000	0.000	0.000
65	A	67	SER	0	-0.061	-0.041	13.398	-0.078	-0.078	0.000	0.000	0.000	0.000
66	A	68	ASN	0	-0.054	-0.037	13.810	0.026	0.026	0.000	0.000	0.000	0.000
67	A	69	SER	0	0.013	-0.019	15.014	0.053	0.053	0.000	0.000	0.000	0.000
68	A	70	SER	0	-0.045	-0.084	16.956	-0.028	-0.028	0.000	0.000	0.000	0.000
69	A	71	LEU	0	0.075	0.024	19.563	0.028	0.028	0.000	0.000	0.000	0.000
70	A	72	ASP	-1	-0.870	-0.887	21.742	0.155	0.155	0.000	0.000	0.000	0.000
71	A	73	ARG	1	0.895	0.959	15.684	-0.263	-0.263	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.005	-0.001	16.900	0.048	0.048	0.000	0.000	0.000	0.000
73	A	75	VAL	0	-0.025	-0.005	14.494	0.009	0.009	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.865	0.942	17.062	-0.341	-0.341	0.000	0.000	0.000	0.000
75	A	77	VAL	0	0.018	0.020	18.381	-0.017	-0.017	0.000	0.000	0.000	0.000
76	A	78	ASN	0	-0.029	-0.023	19.965	0.042	0.042	0.000	0.000	0.000	0.000
77	A	79	ILE	0	0.008	-0.003	22.351	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	80	PHE	0	0.025	0.011	21.807	0.014	0.014	0.000	0.000	0.000	0.000
79	A	81	LEU	0	-0.007	-0.020	27.267	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.029	0.025	30.998	0.004	0.004	0.000	0.000	0.000	0.000
81	A	83	ASP	-1	-0.802	-0.902	33.313	0.046	0.046	0.000	0.000	0.000	0.000
82	A	84	ILE	0	-0.014	-0.014	33.776	0.004	0.004	0.000	0.000	0.000	0.000
83	A	85	ASN	0	-0.040	-0.030	35.875	0.008	0.008	0.000	0.000	0.000	0.000
84	A	86	HIS	0	0.052	0.037	35.313	0.000	0.000	0.000	0.000	0.000	0.000
85	A	87	PHE	0	-0.028	-0.019	31.442	0.003	0.003	0.000	0.000	0.000	0.000
86	A	88	ALA	0	-0.009	-0.008	34.684	0.003	0.003	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.866	-0.944	36.732	0.039	0.039	0.000	0.000	0.000	0.000
88	A	90	PHE	0	0.038	0.015	27.556	0.000	0.000	0.000	0.000	0.000	0.000
89	A	91	ASN	0	-0.007	-0.025	31.855	0.008	0.008	0.000	0.000	0.000	0.000
90	A	92	SER	0	-0.030	0.001	33.164	0.004	0.004	0.000	0.000	0.000	0.000
91	A	93	VAL	0	0.024	0.023	31.608	0.001	0.001	0.000	0.000	0.000	0.000
92	A	94	TYR	0	0.009	-0.010	24.156	0.006	0.006	0.000	0.000	0.000	0.000
93	A	95	ALA	0	-0.008	-0.019	29.570	0.006	0.006	0.000	0.000	0.000	0.000
94	A	96	LYS	1	0.811	0.917	31.862	-0.033	-0.033	0.000	0.000	0.000	0.000
95	A	97	TYR	0	-0.075	-0.081	27.154	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	98	PHE	0	-0.051	-0.003	22.773	0.008	0.008	0.000	0.000	0.000	0.000
97	A	99	ASN	0	-0.004	0.007	27.744	0.009	0.009	0.000	0.000	0.000	0.000
98	A	100	THR	0	0.013	-0.022	28.801	0.007	0.007	0.000	0.000	0.000	0.000
99	A	101	HIS	0	-0.024	-0.006	20.699	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.915	0.954	25.779	-0.159	-0.159	0.000	0.000	0.000	0.000
101	A	103	PRO	0	-0.002	0.017	20.958	0.019	0.019	0.000	0.000	0.000	0.000
102	A	104	ALA	0	0.028	0.029	20.634	-0.016	-0.016	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.854	0.915	22.202	-0.152	-0.152	0.000	0.000	0.000	0.000
104	A	106	SER	0	-0.041	-0.020	23.405	0.017	0.017	0.000	0.000	0.000	0.000
105	A	107	CYS	0	-0.008	-0.009	25.179	-0.012	-0.012	0.000	0.000	0.000	0.000
106	A	108	VAL	0	-0.014	0.019	26.981	0.004	0.004	0.000	0.000	0.000	0.000
107	A	109	ALA	0	0.017	0.018	29.385	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	110	VAL	0	-0.022	-0.024	27.608	0.006	0.006	0.000	0.000	0.000	0.000
109	A	111	ALA	0	-0.008	-0.008	31.067	-0.005	-0.005	0.000	0.000	0.000	0.000
110	A	112	ALA	0	0.007	-0.004	31.569	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.015	0.017	27.284	0.006	0.006	0.000	0.000	0.000	0.000
112	A	114	PRO	0	0.038	0.010	25.913	-0.007	-0.007	0.000	0.000	0.000	0.000
113	A	115	LEU	0	-0.038	-0.037	29.223	0.001	0.001	0.000	0.000	0.000	0.000
114	A	116	GLY	0	-0.006	0.013	32.120	0.000	0.000	0.000	0.000	0.000	0.000
115	A	117	VAL	0	-0.032	0.002	29.451	0.003	0.003	0.000	0.000	0.000	0.000
116	A	118	ASP	-1	-0.776	-0.901	32.819	0.022	0.022	0.000	0.000	0.000	0.000
117	A	119	MET	0	-0.083	-0.045	29.058	0.008	0.008	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.873	-0.937	22.926	0.014	0.014	0.000	0.000	0.000	0.000
119	A	121	MET	0	-0.048	-0.021	22.650	0.018	0.018	0.000	0.000	0.000	0.000
120	A	122	GLU	-1	-0.852	-0.909	18.241	0.159	0.159	0.000	0.000	0.000	0.000
121	A	123	ALA	0	-0.025	-0.038	17.606	0.019	0.019	0.000	0.000	0.000	0.000
122	A	124	ILE	0	0.016	0.028	12.159	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	125	ALA	0	0.000	0.001	13.293	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	126	ALA	0	0.004	0.009	12.310	0.076	0.076	0.000	0.000	0.000	0.000
125	A	127	GLU	-1	-0.793	-0.879	10.525	-0.370	-0.370	0.000	0.000	0.000	0.000
126	A	128	ARG	1	0.752	0.883	13.045	0.148	0.148	0.000	0.000	0.000	0.000

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