FMO DATABASE

FMODB ID: 2J29R

Calculation Name: 3LFH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LFH

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RD55

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	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	129
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1107917.614778
FMO2-HF: Nuclear repulsion	1057773.731036
FMO2-HF: Total energy	-50143.883742
FMO2-MP2: Total energy	-50289.802624

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:1:MET)

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

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.
-18.076	-22.119	24.71	-7.376	-13.292	-0.027

Interaction energy analysis for fragmet #1(A:1:MET)

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 : 0.012

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	3	GLU	-1	-0.825	-0.907	2.549	-5.771	-2.633	1.159	-1.944	-2.353	-0.006
4	A	4	LYS	1	0.827	0.895	2.504	-10.263	-18.438	15.004	-3.304	-3.526	0.013
5	A	5	PHE	0	-0.013	-0.012	6.431	-0.263	-0.263	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.010	0.005	10.225	0.240	0.240	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.015	-0.004	12.609	-0.105	-0.105	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.004	0.001	16.020	0.075	0.075	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.003	0.000	18.788	-0.037	-0.037	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.004	0.001	21.794	0.021	0.021	0.000	0.000	0.000	0.000
11	A	11	HIS	0	-0.049	-0.049	24.899	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.008	-0.005	28.571	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.859	-0.930	28.117	-0.032	-0.032	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.017	0.004	24.133	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.069	0.016	22.915	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.834	0.906	22.745	0.019	0.019	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.028	0.014	24.524	-0.018	-0.018	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.040	-0.017	20.363	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.043	0.016	18.004	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.008	0.004	20.985	-0.022	-0.022	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.021	-0.006	23.728	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.035	-0.009	18.236	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.860	-0.922	19.232	-0.286	-0.286	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.087	-0.033	20.750	-0.020	-0.020	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.081	-0.031	19.928	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.036	-0.023	14.651	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.009	0.021	17.472	-0.057	-0.057	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.807	0.898	18.410	0.367	0.367	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.018	-0.022	13.956	-0.079	-0.079	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.879	-0.930	14.413	-0.429	-0.429	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.061	-0.041	10.082	0.122	0.122	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.046	0.027	12.459	0.094	0.094	0.000	0.000	0.000	0.000
33	A	33	HIS	0	-0.005	0.011	15.158	-0.043	-0.043	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.027	-0.008	18.122	0.049	0.049	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.017	-0.016	21.008	-0.019	-0.019	0.000	0.000	0.000	0.000
36	A	36	GLY	0	-0.008	0.004	23.484	0.020	0.020	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.026	-0.019	26.627	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.037	-0.038	29.219	0.004	0.004	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.023	-0.001	32.649	0.005	0.005	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.008	-0.006	36.071	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.803	-0.862	31.315	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.026	-0.023	33.976	0.014	0.014	0.000	0.000	0.000	0.000
43	A	43	ILE	0	0.049	0.005	29.349	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.761	-0.847	29.309	0.078	0.078	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.037	-0.010	29.675	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.038	0.012	26.023	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.798	0.861	25.259	-0.103	-0.103	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.842	0.920	24.577	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.788	-0.887	25.067	-0.075	-0.075	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.010	0.001	20.087	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.798	-0.899	20.291	0.024	0.024	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.767	0.872	20.441	0.066	0.066	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.009	0.009	17.187	-0.029	-0.029	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.014	0.002	15.306	-0.039	-0.039	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.904	0.963	15.723	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.865	-0.935	17.042	-0.222	-0.222	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.814	0.904	12.699	0.447	0.447	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.008	0.008	11.607	-0.120	-0.120	0.000	0.000	0.000	0.000
59	A	59	GLN	0	-0.084	-0.049	13.144	-0.061	-0.061	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.857	-0.890	12.917	-0.721	-0.721	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.876	-0.934	8.342	-1.536	-1.536	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.824	0.913	7.951	0.737	0.737	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.902	-0.916	4.216	2.771	3.043	-0.001	-0.035	-0.236	0.000
64	A	64	ILE	0	-0.027	-0.014	7.455	0.006	0.006	0.000	0.000	0.000	0.000
65	A	65	ILE	0	0.025	0.018	7.751	0.182	0.182	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.018	-0.015	11.684	-0.190	-0.190	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.004	0.001	14.641	0.068	0.068	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.011	-0.015	17.098	-0.062	-0.062	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.758	-0.877	20.796	0.124	0.124	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.038	-0.014	23.740	0.008	0.008	0.000	0.000	0.000	0.000
71	A	71	PHE	0	-0.003	0.006	23.339	0.006	0.006	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.036	0.016	25.602	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.034	0.008	28.141	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.010	-0.019	27.988	0.015	0.015	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.059	0.035	24.718	0.005	0.005	0.000	0.000	0.000	0.000
76	A	76	PHE	0	0.063	0.040	22.421	0.012	0.012	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.013	-0.015	23.583	0.032	0.032	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.007	-0.002	22.457	0.007	0.007	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.053	0.045	19.430	0.004	0.004	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.002	0.000	19.823	0.030	0.030	0.000	0.000	0.000	0.000
81	A	81	SER	0	-0.080	-0.044	21.549	0.002	0.002	0.000	0.000	0.000	0.000
82	A	82	MET	0	0.021	0.012	18.247	-0.016	-0.016	0.000	0.000	0.000	0.000
83	A	83	MET	0	-0.032	-0.001	16.441	0.011	0.011	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.816	0.899	18.088	-0.173	-0.173	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.899	-0.940	20.504	0.180	0.180	0.000	0.000	0.000	0.000
86	A	86	TYR	0	-0.048	-0.054	15.863	-0.035	-0.035	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.887	-0.925	13.070	0.807	0.807	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.008	0.024	12.142	0.130	0.130	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.861	0.929	9.558	-1.085	-1.085	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.018	-0.017	12.986	-0.099	-0.099	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.021	0.027	14.742	0.033	0.033	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.009	-0.015	16.911	-0.053	-0.053	0.000	0.000	0.000	0.000
93	A	93	GLY	0	-0.031	-0.014	20.254	0.017	0.017	0.000	0.000	0.000	0.000
94	A	94	ILE	0	-0.034	-0.005	16.619	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	95	ASN	0	0.050	-0.002	19.782	-0.034	-0.034	0.000	0.000	0.000	0.000
96	A	96	MET	0	0.020	0.016	19.452	0.005	0.005	0.000	0.000	0.000	0.000
97	A	97	PRO	0	-0.004	0.000	18.725	-0.017	-0.017	0.000	0.000	0.000	0.000
98	A	98	MET	0	-0.011	0.039	15.874	-0.020	-0.020	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.022	0.014	14.487	0.027	0.027	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.029	0.005	14.484	-0.035	-0.035	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.889	-0.928	11.089	-0.114	-0.114	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.036	-0.009	9.383	-0.037	-0.037	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.023	-0.029	9.469	-0.027	-0.027	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.075	-0.040	10.584	-0.176	-0.176	0.000	0.000	0.000	0.000
105	A	105	SER	0	-0.002	-0.006	7.501	-0.122	-0.122	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.018	0.016	5.500	-0.231	-0.231	0.000	0.000	0.000	0.000
107	A	107	ASN	0	-0.004	-0.018	2.854	0.260	0.894	0.111	-0.141	-0.604	0.000
108	A	108	VAL	0	-0.067	-0.014	2.554	-4.172	-3.697	2.553	-1.164	-1.864	-0.015
109	A	109	TYR	0	0.044	0.026	3.013	-2.205	-1.123	0.335	-0.382	-1.035	-0.005
110	A	110	ASP	-1	-0.732	-0.873	2.749	6.780	7.599	5.568	-3.000	-3.387	-0.013
111	A	111	THR	0	-0.027	-0.063	3.700	-0.346	-2.607	-0.018	2.597	-0.318	-0.001
112	A	112	THR	0	-0.077	-0.049	6.338	-1.204	-1.231	-0.001	-0.003	0.031	0.000
113	A	113	GLU	-1	-0.922	-0.966	7.091	0.711	0.711	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.042	-0.005	5.801	-0.541	-0.541	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.027	-0.028	8.200	-0.468	-0.468	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.912	-0.957	11.541	0.444	0.444	0.000	0.000	0.000	0.000
117	A	117	ASN	0	0.014	0.008	8.790	-0.178	-0.178	0.000	0.000	0.000	0.000
118	A	118	ILE	0	0.000	-0.007	11.337	-0.150	-0.150	0.000	0.000	0.000	0.000
119	A	119	SER	0	-0.039	-0.002	13.917	-0.127	-0.127	0.000	0.000	0.000	0.000
120	A	120	LYS	1	0.811	0.879	16.009	-0.310	-0.310	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.051	0.018	13.856	-0.048	-0.048	0.000	0.000	0.000	0.000
122	A	122	GLY	0	0.007	-0.016	17.607	-0.044	-0.044	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.878	0.935	19.515	-0.362	-0.362	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.826	-0.884	20.674	0.176	0.176	0.000	0.000	0.000	0.000
125	A	125	GLY	0	-0.031	-0.001	21.746	-0.025	-0.025	0.000	0.000	0.000	0.000
126	A	126	ILE	0	-0.075	-0.023	22.997	-0.021	-0.021	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.932	0.955	26.102	-0.052	-0.052	0.000	0.000	0.000	0.000
128	A	128	VAL	0	0.017	0.018	29.071	-0.009	-0.009	0.000	0.000	0.000	0.000
129	A	129	ILE	0	0.000	0.000	30.556	0.001	0.001	0.000	0.000	0.000	0.000

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