FMO DATABASE

FMODB ID: 5J84Z

Calculation Name: 3LMO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LMO

Chain ID: A

ChEMBL ID:

UniProt ID: Q6N882

Base Structure: X-ray

Registration Date: 2023-09-23

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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-649653.734436
FMO2-HF: Nuclear repulsion	613864.793123
FMO2-HF: Total energy	-35788.941313
FMO2-MP2: Total energy	-35895.276871

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:2:THR)

Summations of interaction energy for fragment #1(A:2: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.
-2.443	1.887	3.487	-2.696	-5.119	-0.013

Interaction energy analysis for fragmet #1(A:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.006

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	4	THR	0	0.013	-0.024	2.854	-4.867	-2.200	0.300	-1.446	-1.520	-0.008
4	A	5	PHE	0	0.037	0.021	5.611	0.209	0.209	0.000	0.000	0.000	0.000
5	A	6	ASP	-1	-0.810	-0.873	2.385	-0.715	-0.519	1.039	-0.346	-0.889	-0.002
6	A	7	ARG	1	0.858	0.943	2.382	4.122	5.522	2.148	-0.889	-2.659	-0.003
7	A	8	VAL	0	0.039	0.023	4.481	0.409	0.476	0.000	-0.015	-0.051	0.000
8	A	9	ALA	0	0.005	-0.001	7.081	0.189	0.189	0.000	0.000	0.000	0.000
9	A	10	THR	0	-0.073	-0.055	4.913	0.336	0.336	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.025	-0.012	7.441	0.083	0.083	0.000	0.000	0.000	0.000
11	A	12	ILE	0	0.018	0.000	9.911	0.070	0.070	0.000	0.000	0.000	0.000
12	A	13	ALA	0	-0.024	-0.005	10.446	0.046	0.046	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.938	-0.962	10.631	-0.173	-0.173	0.000	0.000	0.000	0.000
14	A	15	THR	0	-0.063	-0.054	13.038	0.001	0.001	0.000	0.000	0.000	0.000
15	A	16	CYS	0	-0.057	-0.032	15.260	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.942	-0.951	16.426	0.002	0.002	0.000	0.000	0.000	0.000
17	A	18	ILE	0	-0.042	-0.004	15.048	0.017	0.017	0.000	0.000	0.000	0.000
18	A	19	PRO	0	0.003	-0.002	14.274	0.010	0.010	0.000	0.000	0.000	0.000
19	A	20	ARG	1	0.919	0.947	6.570	0.038	0.038	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.947	-0.978	11.689	0.126	0.126	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.095	-0.061	13.486	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	23	ILE	0	0.004	0.032	11.084	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	24	THR	0	-0.015	-0.040	11.721	0.020	0.020	0.000	0.000	0.000	0.000
24	A	25	PRO	0	-0.033	-0.036	10.265	-0.047	-0.047	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.808	-0.895	12.309	-0.080	-0.080	0.000	0.000	0.000	0.000
26	A	27	SER	0	0.076	0.059	14.332	0.013	0.013	0.000	0.000	0.000	0.000
27	A	28	HIS	0	-0.097	-0.057	15.822	-0.031	-0.031	0.000	0.000	0.000	0.000
28	A	29	ALA	0	-0.015	-0.013	15.326	0.001	0.001	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.012	-0.013	16.883	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	31	ASP	-1	-0.917	-0.962	20.718	-0.097	-0.097	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.797	-0.891	18.391	-0.080	-0.080	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.075	-0.051	14.800	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	34	GLY	0	-0.039	-0.013	19.190	0.008	0.008	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.070	-0.019	16.334	0.000	0.000	0.000	0.000	0.000	0.000
35	A	36	ASP	-1	-0.806	-0.905	20.828	-0.088	-0.088	0.000	0.000	0.000	0.000
36	A	37	SER	0	-0.053	-0.043	22.600	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	38	LEU	0	-0.078	-0.042	23.818	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.716	-0.844	19.526	-0.121	-0.121	0.000	0.000	0.000	0.000
39	A	40	PHE	0	-0.006	-0.004	18.118	-0.029	-0.029	0.000	0.000	0.000	0.000
40	A	41	LEU	0	-0.068	-0.030	18.876	-0.030	-0.030	0.000	0.000	0.000	0.000
41	A	42	ASP	-1	-0.873	-0.931	18.855	-0.178	-0.178	0.000	0.000	0.000	0.000
42	A	43	ILE	0	0.017	0.001	13.765	-0.041	-0.041	0.000	0.000	0.000	0.000
43	A	44	ALA	0	-0.051	-0.026	14.781	-0.065	-0.065	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.015	-0.010	16.428	-0.038	-0.038	0.000	0.000	0.000	0.000
45	A	46	ALA	0	0.058	0.018	13.422	-0.020	-0.020	0.000	0.000	0.000	0.000
46	A	47	ILE	0	-0.010	-0.009	10.997	-0.083	-0.083	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.826	-0.919	12.864	-0.412	-0.412	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.793	0.900	15.009	0.278	0.278	0.000	0.000	0.000	0.000
49	A	50	ALA	0	-0.014	0.006	9.363	-0.021	-0.021	0.000	0.000	0.000	0.000
50	A	51	PHE	0	-0.037	-0.025	6.787	-0.242	-0.242	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.002	0.024	11.116	0.023	0.023	0.000	0.000	0.000	0.000
52	A	53	ILE	0	-0.034	-0.026	13.583	0.054	0.054	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.900	0.947	16.505	0.274	0.274	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.065	0.038	14.803	0.005	0.005	0.000	0.000	0.000	0.000
55	A	56	PRO	0	-0.049	-0.012	18.784	0.035	0.035	0.000	0.000	0.000	0.000
56	A	57	LEU	0	0.037	0.002	19.689	0.018	0.018	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.927	-0.939	23.150	-0.132	-0.132	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.855	0.918	23.938	0.207	0.207	0.000	0.000	0.000	0.000
59	A	60	TRP	0	0.035	0.002	16.728	0.006	0.006	0.000	0.000	0.000	0.000
60	A	61	THR	0	0.017	-0.002	24.521	0.013	0.013	0.000	0.000	0.000	0.000
61	A	62	GLN	0	-0.036	-0.005	27.182	0.005	0.005	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.799	-0.881	24.926	-0.175	-0.175	0.000	0.000	0.000	0.000
63	A	64	VAL	0	0.008	0.007	25.755	0.007	0.007	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.079	-0.044	28.538	0.016	0.016	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.879	-0.933	31.471	-0.099	-0.099	0.000	0.000	0.000	0.000
66	A	67	GLY	0	-0.019	-0.006	31.722	0.004	0.004	0.000	0.000	0.000	0.000
67	A	68	LYS	1	0.769	0.873	28.912	0.114	0.114	0.000	0.000	0.000	0.000
68	A	69	ALA	0	-0.024	0.000	24.858	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	70	THR	0	-0.031	-0.034	24.668	0.006	0.006	0.000	0.000	0.000	0.000
70	A	71	THR	0	0.055	0.002	23.668	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.772	-0.861	21.016	-0.136	-0.136	0.000	0.000	0.000	0.000
72	A	73	GLN	0	-0.023	0.003	19.218	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	74	TYR	0	-0.030	-0.055	18.371	-0.031	-0.031	0.000	0.000	0.000	0.000
74	A	75	PHE	0	0.022	0.017	17.537	-0.031	-0.031	0.000	0.000	0.000	0.000
75	A	76	VAL	0	-0.009	0.031	15.697	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	77	LEU	0	0.035	0.011	11.221	-0.054	-0.054	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.824	0.894	11.596	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	79	ASN	0	-0.090	-0.046	12.817	-0.028	-0.028	0.000	0.000	0.000	0.000
79	A	80	LEU	0	0.020	0.015	12.667	-0.030	-0.030	0.000	0.000	0.000	0.000
80	A	81	ALA	0	0.014	0.001	9.017	-0.068	-0.068	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.030	0.020	10.633	-0.058	-0.058	0.000	0.000	0.000	0.000
82	A	83	ARG	1	0.753	0.834	13.300	0.313	0.313	0.000	0.000	0.000	0.000
83	A	84	ILE	0	0.000	0.006	10.034	0.032	0.032	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.829	-0.893	9.749	-1.211	-1.211	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.848	-0.885	12.417	-0.262	-0.262	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.039	-0.019	15.433	0.043	0.043	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.011	0.002	10.813	0.036	0.036	0.000	0.000	0.000	0.000
88	A	89	ALA	0	-0.033	-0.008	14.020	0.035	0.035	0.000	0.000	0.000	0.000
89	A	90	ALA	0	-0.030	-0.017	15.791	0.042	0.042	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.747	0.869	16.334	0.481	0.481	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.061	0.022	16.152	0.025	0.025	0.000	0.000	0.000	0.000
92	A	93	ALA	0	-0.066	-0.027	17.036	0.038	0.038	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.069	-0.021	20.092	0.032	0.032	0.000	0.000	0.000	0.000
94	A	95	GLU	-1	-0.924	-0.948	17.475	-0.384	-0.384	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)