FMO DATABASE

FMODB ID: 6N6KZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1109420.593495
FMO2-HF: Nuclear repulsion	1059276.486344
FMO2-HF: Total energy	-50144.107151
FMO2-MP2: Total energy	-50290.000875

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.
-19.003	-20.74	21.856	-8.011	-12.108	-0.028

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 : -0.016 / q_NPA : 0.011

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	-0.785	-0.872	2.549	-4.908	-1.946	1.289	-1.898	-2.353	-0.007
4	A	4	LYS	1	0.819	0.894	2.510	-11.511	-20.955	16.646	-3.505	-3.697	0.013
5	A	5	PHE	0	-0.006	-0.018	6.456	-0.347	-0.347	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.008	0.016	10.273	0.231	0.231	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.014	-0.010	12.841	-0.115	-0.115	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.030	0.016	16.315	0.062	0.062	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.013	-0.005	19.097	-0.041	-0.041	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.024	-0.010	22.055	0.022	0.022	0.000	0.000	0.000	0.000
11	A	11	HIS	0	-0.021	-0.035	25.182	-0.018	-0.018	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.002	0.002	28.573	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.819	-0.905	28.731	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.028	0.003	24.442	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.071	0.008	23.114	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.807	0.890	22.835	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.019	0.007	24.581	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.042	-0.016	20.770	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.053	0.023	18.031	0.003	0.003	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.011	0.007	20.959	-0.017	-0.017	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.017	-0.012	23.711	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.048	0.005	18.192	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.857	-0.930	19.340	-0.219	-0.219	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.086	-0.035	20.813	-0.021	-0.021	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.074	-0.034	19.665	0.000	0.000	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.049	-0.025	14.687	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.018	0.025	17.376	-0.052	-0.052	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.782	0.877	18.524	0.316	0.316	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.017	-0.013	14.013	-0.054	-0.054	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.854	-0.916	14.342	-0.364	-0.364	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.066	-0.050	9.959	0.094	0.094	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.039	0.024	12.322	0.114	0.114	0.000	0.000	0.000	0.000
33	A	33	HIS	0	-0.001	0.008	14.983	-0.054	-0.054	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.041	-0.023	18.155	0.049	0.049	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.018	-0.008	21.152	-0.023	-0.023	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.015	0.007	23.680	0.020	0.020	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.040	-0.015	26.857	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.028	-0.044	29.530	0.006	0.006	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.012	-0.018	33.041	0.003	0.003	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.025	0.007	36.147	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.833	-0.878	31.609	0.011	0.011	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.005	-0.012	33.942	0.013	0.013	0.000	0.000	0.000	0.000
43	A	43	ILE	0	0.046	0.005	29.483	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.753	-0.836	29.201	0.084	0.084	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.032	-0.004	29.422	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.035	0.011	26.144	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.764	0.838	25.186	-0.109	-0.109	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.825	0.908	24.453	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.793	-0.887	24.872	-0.069	-0.069	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.000	-0.007	20.193	-0.016	-0.016	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.774	-0.884	20.144	0.022	0.022	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.774	0.880	20.140	0.066	0.066	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.005	0.001	17.648	-0.030	-0.030	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.018	0.003	15.339	-0.035	-0.035	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.874	0.948	15.651	0.020	0.020	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.837	-0.928	16.861	-0.215	-0.215	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.801	0.894	12.894	0.403	0.403	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.007	-0.003	11.528	-0.115	-0.115	0.000	0.000	0.000	0.000
59	A	59	GLN	0	-0.091	-0.055	13.300	-0.046	-0.046	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.858	-0.891	12.768	-0.690	-0.690	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.848	-0.917	8.830	-1.513	-1.513	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.822	0.919	7.862	0.735	0.735	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.885	-0.915	4.392	2.164	2.393	-0.001	-0.025	-0.204	0.000
64	A	64	ILE	0	-0.019	-0.009	7.370	0.165	0.165	0.000	0.000	0.000	0.000
65	A	65	ILE	0	0.024	0.017	7.810	0.130	0.130	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.017	-0.006	11.796	-0.158	-0.158	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.015	-0.007	14.621	0.076	0.076	0.000	0.000	0.000	0.000
68	A	68	VAL	0	0.000	0.001	17.241	-0.066	-0.066	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.741	-0.866	20.962	0.155	0.155	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.020	-0.014	23.953	0.006	0.006	0.000	0.000	0.000	0.000
71	A	71	PHE	0	0.009	0.009	23.388	0.011	0.011	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.012	-0.004	25.741	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.024	0.010	27.894	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	74	SER	0	0.000	-0.011	28.061	0.014	0.014	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.043	0.023	24.465	0.003	0.003	0.000	0.000	0.000	0.000
76	A	76	PHE	0	0.043	0.037	22.812	0.012	0.012	0.000	0.000	0.000	0.000
77	A	77	ASN	0	0.004	-0.008	23.849	0.027	0.027	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.006	0.016	22.371	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.044	0.036	19.607	0.005	0.005	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.014	0.008	19.794	0.028	0.028	0.000	0.000	0.000	0.000
81	A	81	SER	0	-0.060	-0.034	21.600	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	82	MET	0	0.005	0.007	18.138	-0.014	-0.014	0.000	0.000	0.000	0.000
83	A	83	MET	0	-0.007	0.003	16.616	0.001	0.001	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.764	0.864	18.023	-0.165	-0.165	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.834	-0.900	20.685	0.164	0.164	0.000	0.000	0.000	0.000
86	A	86	TYR	0	-0.057	-0.047	16.224	-0.048	-0.048	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.853	-0.906	13.083	0.728	0.728	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.015	0.024	12.398	0.112	0.112	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.827	0.908	9.382	-0.989	-0.989	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.019	-0.019	12.901	-0.086	-0.086	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.014	0.018	15.077	0.036	0.036	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.017	-0.016	17.234	-0.051	-0.051	0.000	0.000	0.000	0.000
93	A	93	GLY	0	-0.012	0.000	20.750	0.017	0.017	0.000	0.000	0.000	0.000
94	A	94	ILE	0	-0.048	-0.018	16.755	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	95	ASN	0	0.038	-0.006	19.765	-0.039	-0.039	0.000	0.000	0.000	0.000
96	A	96	MET	0	0.030	0.027	19.386	0.013	0.013	0.000	0.000	0.000	0.000
97	A	97	PRO	0	0.002	-0.002	18.570	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	98	MET	0	-0.022	0.029	15.953	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.020	0.010	14.536	0.051	0.051	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.023	0.003	14.404	-0.020	-0.020	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.857	-0.913	11.182	0.122	0.122	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.046	-0.004	9.657	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.006	-0.015	9.396	0.078	0.078	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.062	-0.046	10.182	-0.161	-0.161	0.000	0.000	0.000	0.000
105	A	105	SER	0	-0.012	-0.021	7.409	-0.124	-0.124	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.010	0.017	5.462	-0.077	-0.077	0.000	0.000	0.000	0.000
107	A	107	ASN	0	-0.038	-0.042	2.526	-0.278	1.007	0.572	-0.596	-1.260	-0.003
108	A	108	VAL	0	-0.065	-0.018	2.807	-3.369	-2.855	1.471	-0.530	-1.455	-0.010
109	A	109	TYR	0	0.025	0.023	3.341	-1.335	-0.586	0.085	-0.211	-0.623	-0.002
110	A	110	ASP	-1	-0.733	-0.852	3.258	5.558	7.708	1.797	-1.579	-2.368	-0.019
111	A	111	THR	0	-0.021	-0.058	4.271	-1.488	-1.670	-0.003	0.333	-0.148	0.000
112	A	112	THR	0	-0.079	-0.060	6.575	-1.055	-1.055	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.917	-0.971	6.937	1.184	1.184	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.045	-0.005	6.088	-0.500	-0.500	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.007	-0.014	8.529	-0.456	-0.456	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.857	-0.910	11.664	0.444	0.444	0.000	0.000	0.000	0.000
117	A	117	ASN	0	0.011	0.011	9.168	-0.212	-0.212	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.003	-0.002	11.693	-0.168	-0.168	0.000	0.000	0.000	0.000
119	A	119	SER	0	-0.041	-0.021	14.243	-0.142	-0.142	0.000	0.000	0.000	0.000
120	A	120	LYS	1	0.802	0.872	16.137	-0.377	-0.377	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.052	0.015	13.918	-0.056	-0.056	0.000	0.000	0.000	0.000
122	A	122	GLY	0	-0.004	-0.020	17.659	-0.050	-0.050	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.828	0.902	19.434	-0.441	-0.441	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.825	-0.890	20.620	0.230	0.230	0.000	0.000	0.000	0.000
125	A	125	GLY	0	-0.037	-0.008	21.711	-0.027	-0.027	0.000	0.000	0.000	0.000
126	A	126	ILE	0	-0.064	-0.020	23.096	-0.021	-0.021	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.919	0.951	26.290	-0.085	-0.085	0.000	0.000	0.000	0.000
128	A	128	VAL	0	0.031	0.021	29.249	-0.010	-0.010	0.000	0.000	0.000	0.000
129	A	129	ILE	0	-0.002	0.003	30.630	-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)