FMO DATABASE

FMODB ID: 4J85N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-647747.316349
FMO2-HF: Nuclear repulsion	611958.563785
FMO2-HF: Total energy	-35788.752564
FMO2-MP2: Total energy	-35895.119524

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.
-4.404	-0.509	4.732	-2.9	-5.727	-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 : -0.010 / q_NPA : -0.017

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	0.027	-0.023	2.960	-4.635	-2.053	0.180	-1.305	-1.457	-0.006
4	A	5	PHE	0	0.030	0.020	5.677	0.136	0.136	0.000	0.000	0.000	0.000
5	A	6	ASP	-1	-0.818	-0.889	2.419	-2.587	-2.269	0.756	-0.315	-0.759	-0.003
6	A	7	ARG	1	0.879	0.947	2.360	3.131	4.045	3.796	-1.259	-3.451	-0.004
7	A	8	VAL	0	0.034	0.016	4.346	0.525	0.606	0.000	-0.021	-0.060	0.000
8	A	9	ALA	0	-0.010	-0.003	7.037	0.252	0.252	0.000	0.000	0.000	0.000
9	A	10	THR	0	-0.074	-0.050	5.122	0.231	0.231	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.014	-0.003	7.665	0.175	0.175	0.000	0.000	0.000	0.000
11	A	12	ILE	0	0.048	0.018	9.927	0.109	0.109	0.000	0.000	0.000	0.000
12	A	13	ALA	0	-0.043	-0.021	10.776	0.074	0.074	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.936	-0.957	10.886	-0.331	-0.331	0.000	0.000	0.000	0.000
14	A	15	THR	0	-0.067	-0.041	13.262	0.055	0.055	0.000	0.000	0.000	0.000
15	A	16	CYS	0	-0.056	-0.032	15.396	0.031	0.031	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.944	-0.951	16.542	-0.240	-0.240	0.000	0.000	0.000	0.000
17	A	18	ILE	0	-0.055	-0.017	15.493	0.018	0.018	0.000	0.000	0.000	0.000
18	A	19	PRO	0	-0.004	-0.006	14.589	-0.049	-0.049	0.000	0.000	0.000	0.000
19	A	20	ARG	1	0.952	0.971	6.758	1.187	1.187	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.965	-0.988	12.134	-0.467	-0.467	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.090	-0.056	13.753	0.033	0.033	0.000	0.000	0.000	0.000
22	A	23	ILE	0	0.006	0.027	11.287	0.004	0.004	0.000	0.000	0.000	0.000
23	A	24	THR	0	-0.012	-0.045	11.697	-0.089	-0.089	0.000	0.000	0.000	0.000
24	A	25	PRO	0	-0.046	-0.031	10.491	-0.020	-0.020	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.880	-0.940	12.493	-0.385	-0.385	0.000	0.000	0.000	0.000
26	A	27	SER	0	0.053	0.050	14.593	0.027	0.027	0.000	0.000	0.000	0.000
27	A	28	HIS	0	-0.075	-0.046	16.172	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	29	ALA	0	-0.032	-0.019	15.557	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.030	-0.022	17.132	0.014	0.014	0.000	0.000	0.000	0.000
30	A	31	ASP	-1	-0.907	-0.956	20.917	-0.204	-0.204	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.787	-0.902	18.875	-0.322	-0.322	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.073	-0.032	15.336	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	34	GLY	0	-0.042	-0.018	19.727	0.000	0.000	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.057	-0.014	16.749	0.006	0.006	0.000	0.000	0.000	0.000
35	A	36	ASP	-1	-0.855	-0.917	21.340	-0.182	-0.182	0.000	0.000	0.000	0.000
36	A	37	SER	0	-0.019	-0.041	23.037	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	38	LEU	0	-0.055	-0.035	23.886	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.727	-0.851	20.103	-0.260	-0.260	0.000	0.000	0.000	0.000
39	A	40	PHE	0	-0.011	-0.014	18.147	-0.026	-0.026	0.000	0.000	0.000	0.000
40	A	41	LEU	0	-0.087	-0.044	19.250	-0.019	-0.019	0.000	0.000	0.000	0.000
41	A	42	ASP	-1	-0.860	-0.923	18.919	-0.234	-0.234	0.000	0.000	0.000	0.000
42	A	43	ILE	0	-0.003	-0.002	14.039	-0.036	-0.036	0.000	0.000	0.000	0.000
43	A	44	ALA	0	-0.053	-0.030	15.234	-0.046	-0.046	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.017	-0.005	16.965	0.006	0.006	0.000	0.000	0.000	0.000
45	A	46	ALA	0	0.049	0.016	13.568	0.006	0.006	0.000	0.000	0.000	0.000
46	A	47	ILE	0	-0.006	-0.009	11.342	-0.043	-0.043	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.834	-0.908	12.918	-0.324	-0.324	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.884	0.934	14.910	0.212	0.212	0.000	0.000	0.000	0.000
49	A	50	ALA	0	-0.026	0.005	9.607	0.036	0.036	0.000	0.000	0.000	0.000
50	A	51	PHE	0	-0.043	-0.036	6.954	-0.063	-0.063	0.000	0.000	0.000	0.000
51	A	52	GLY	0	-0.008	0.021	11.158	0.059	0.059	0.000	0.000	0.000	0.000
52	A	53	ILE	0	-0.044	-0.033	13.384	0.041	0.041	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.915	0.957	16.285	0.205	0.205	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.023	0.014	15.023	0.012	0.012	0.000	0.000	0.000	0.000
55	A	56	PRO	0	-0.056	-0.013	19.033	0.027	0.027	0.000	0.000	0.000	0.000
56	A	57	LEU	0	0.057	0.009	20.401	0.011	0.011	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.940	-0.954	23.691	-0.114	-0.114	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.845	0.905	24.254	0.166	0.166	0.000	0.000	0.000	0.000
59	A	60	TRP	0	0.055	0.013	17.084	0.003	0.003	0.000	0.000	0.000	0.000
60	A	61	THR	0	0.015	0.003	24.889	0.005	0.005	0.000	0.000	0.000	0.000
61	A	62	GLN	0	-0.009	0.005	27.637	0.006	0.006	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.791	-0.881	25.155	-0.153	-0.153	0.000	0.000	0.000	0.000
63	A	64	VAL	0	-0.004	0.000	25.737	0.006	0.006	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.087	-0.047	28.572	0.012	0.012	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.894	-0.923	31.795	-0.089	-0.089	0.000	0.000	0.000	0.000
66	A	67	GLY	0	-0.013	-0.009	31.662	0.006	0.006	0.000	0.000	0.000	0.000
67	A	68	LYS	1	0.764	0.865	29.039	0.098	0.098	0.000	0.000	0.000	0.000
68	A	69	ALA	0	-0.019	0.002	24.736	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	70	THR	0	-0.020	-0.021	24.633	0.004	0.004	0.000	0.000	0.000	0.000
70	A	71	THR	0	0.058	0.003	23.776	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.787	-0.873	21.205	-0.217	-0.217	0.000	0.000	0.000	0.000
72	A	73	GLN	0	-0.046	-0.008	19.390	-0.023	-0.023	0.000	0.000	0.000	0.000
73	A	74	TYR	0	-0.036	-0.046	18.481	-0.023	-0.023	0.000	0.000	0.000	0.000
74	A	75	PHE	0	0.033	0.007	17.354	-0.038	-0.038	0.000	0.000	0.000	0.000
75	A	76	VAL	0	0.008	0.051	16.009	-0.024	-0.024	0.000	0.000	0.000	0.000
76	A	77	LEU	0	0.042	0.011	11.547	-0.039	-0.039	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.931	0.961	11.706	0.306	0.306	0.000	0.000	0.000	0.000
78	A	79	ASN	0	-0.081	-0.056	12.776	-0.014	-0.014	0.000	0.000	0.000	0.000
79	A	80	LEU	0	0.031	0.033	12.809	0.008	0.008	0.000	0.000	0.000	0.000
80	A	81	ALA	0	-0.007	-0.017	9.144	-0.029	-0.029	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.006	0.007	10.937	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	83	ARG	1	0.755	0.844	13.583	0.364	0.364	0.000	0.000	0.000	0.000
83	A	84	ILE	0	-0.005	-0.002	10.190	0.060	0.060	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.831	-0.895	9.655	-0.933	-0.933	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.857	-0.888	12.366	-0.167	-0.167	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.033	-0.023	15.445	0.058	0.058	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.011	0.007	10.601	0.053	0.053	0.000	0.000	0.000	0.000
88	A	89	ALA	0	-0.023	0.000	13.935	0.069	0.069	0.000	0.000	0.000	0.000
89	A	90	ALA	0	-0.035	-0.017	15.297	0.044	0.044	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.768	0.879	16.240	0.184	0.184	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.053	0.020	15.600	0.025	0.025	0.000	0.000	0.000	0.000
92	A	93	ALA	0	-0.052	-0.023	16.396	0.034	0.034	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.082	-0.030	19.578	0.015	0.015	0.000	0.000	0.000	0.000
94	A	95	GLU	-1	-0.926	-0.943	16.891	-0.070	-0.070	0.000	0.000	0.000	0.000

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