FMO DATABASE

FMODB ID: KGMJ3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-647609.783278
FMO2-HF: Nuclear repulsion	611821.588081
FMO2-HF: Total energy	-35788.195197
FMO2-MP2: Total energy	-35894.572096

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.
-6.027	-3.298	9.058	-4.515	-7.273	-0.017

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 : -0.014 / q_NPA : -0.010

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

Sort

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	0.025	-0.030	2.633	-4.423	-1.047	0.685	-1.948	-2.113	-0.009
4	A	5	PHE	0	0.020	0.020	5.300	0.514	0.629	-0.001	-0.004	-0.110	0.000
5	A	6	ASP	-1	-0.850	-0.926	2.454	-2.470	-1.929	0.848	-0.438	-0.951	-0.003
6	A	7	ARG	1	0.918	0.954	1.955	0.760	-0.629	7.523	-2.098	-4.037	-0.005
7	A	8	VAL	0	0.036	0.019	4.158	0.583	0.669	0.003	-0.027	-0.062	0.000
8	A	9	ALA	0	-0.003	-0.001	6.997	0.292	0.292	0.000	0.000	0.000	0.000
9	A	10	THR	0	-0.071	-0.041	5.050	0.438	0.438	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.006	0.003	7.597	0.092	0.092	0.000	0.000	0.000	0.000
11	A	12	ILE	0	0.029	0.009	9.735	0.042	0.042	0.000	0.000	0.000	0.000
12	A	13	ALA	0	-0.042	-0.021	10.801	0.040	0.040	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.967	-0.984	10.622	0.377	0.377	0.000	0.000	0.000	0.000
14	A	15	THR	0	-0.025	-0.005	13.210	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	16	CYS	0	-0.044	-0.027	15.255	-0.026	-0.026	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.923	-0.937	16.502	0.217	0.217	0.000	0.000	0.000	0.000
17	A	18	ILE	0	-0.047	-0.019	15.396	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	19	PRO	0	-0.029	-0.007	14.615	0.041	0.041	0.000	0.000	0.000	0.000
19	A	20	ARG	1	1.010	1.000	6.373	0.233	0.233	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.960	-0.989	12.127	0.052	0.052	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.094	-0.061	13.732	-0.060	-0.060	0.000	0.000	0.000	0.000
22	A	23	ILE	0	0.018	0.035	11.362	-0.055	-0.055	0.000	0.000	0.000	0.000
23	A	24	THR	0	-0.020	-0.027	11.880	-0.053	-0.053	0.000	0.000	0.000	0.000
24	A	25	PRO	0	-0.040	-0.035	10.525	-0.033	-0.033	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.897	-0.971	12.506	-0.580	-0.580	0.000	0.000	0.000	0.000
26	A	27	SER	0	0.038	0.046	14.586	0.066	0.066	0.000	0.000	0.000	0.000
27	A	28	HIS	0	-0.055	-0.028	16.117	-0.062	-0.062	0.000	0.000	0.000	0.000
28	A	29	ALA	0	-0.032	-0.023	15.404	0.024	0.024	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.017	-0.020	17.010	0.032	0.032	0.000	0.000	0.000	0.000
30	A	31	ASP	-1	-0.915	-0.957	20.800	-0.176	-0.176	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.798	-0.920	19.021	-0.235	-0.235	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.074	-0.023	15.456	0.007	0.007	0.000	0.000	0.000	0.000
33	A	34	GLY	0	-0.044	-0.021	19.789	0.025	0.025	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.053	-0.010	16.813	0.014	0.014	0.000	0.000	0.000	0.000
35	A	36	ASP	-1	-0.875	-0.916	21.310	-0.057	-0.057	0.000	0.000	0.000	0.000
36	A	37	SER	0	-0.015	-0.049	22.932	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	38	LEU	0	-0.062	-0.036	23.725	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.713	-0.846	20.058	-0.022	-0.022	0.000	0.000	0.000	0.000
39	A	40	PHE	0	-0.020	-0.022	18.296	-0.016	-0.016	0.000	0.000	0.000	0.000
40	A	41	LEU	0	-0.097	-0.051	19.048	-0.024	-0.024	0.000	0.000	0.000	0.000
41	A	42	ASP	-1	-0.864	-0.924	18.670	0.007	0.007	0.000	0.000	0.000	0.000
42	A	43	ILE	0	-0.011	-0.008	13.828	0.000	0.000	0.000	0.000	0.000	0.000
43	A	44	ALA	0	-0.056	-0.034	14.995	-0.036	-0.036	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.020	-0.003	16.658	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	46	ALA	0	0.051	0.015	13.208	0.009	0.009	0.000	0.000	0.000	0.000
46	A	47	ILE	0	-0.013	-0.007	11.208	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.839	-0.916	12.778	-0.278	-0.278	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.888	0.934	14.907	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	50	ALA	0	-0.020	0.008	9.418	0.052	0.052	0.000	0.000	0.000	0.000
50	A	51	PHE	0	-0.044	-0.037	6.711	-0.032	-0.032	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.014	0.032	11.134	-0.036	-0.036	0.000	0.000	0.000	0.000
52	A	53	ILE	0	-0.067	-0.038	13.440	-0.029	-0.029	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.926	0.958	16.263	0.224	0.224	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.030	0.021	14.776	-0.036	-0.036	0.000	0.000	0.000	0.000
55	A	56	PRO	0	-0.076	-0.020	18.652	0.052	0.052	0.000	0.000	0.000	0.000
56	A	57	LEU	0	0.070	0.014	20.248	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.939	-0.956	23.348	-0.144	-0.144	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.941	0.962	23.569	0.321	0.321	0.000	0.000	0.000	0.000
59	A	60	TRP	0	0.060	0.018	16.815	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	61	THR	0	0.019	0.008	24.542	0.003	0.003	0.000	0.000	0.000	0.000
61	A	62	GLN	0	-0.020	-0.002	27.319	0.001	0.001	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.898	-0.953	24.990	-0.318	-0.318	0.000	0.000	0.000	0.000
63	A	64	VAL	0	-0.023	-0.009	25.528	0.002	0.002	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.104	-0.057	28.275	0.022	0.022	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.968	-0.976	31.496	-0.169	-0.169	0.000	0.000	0.000	0.000
66	A	67	GLY	0	-0.034	-0.018	31.374	0.001	0.001	0.000	0.000	0.000	0.000
67	A	68	LYS	1	0.879	0.934	28.617	0.218	0.218	0.000	0.000	0.000	0.000
68	A	69	ALA	0	-0.006	0.006	24.392	-0.025	-0.025	0.000	0.000	0.000	0.000
69	A	70	THR	0	0.022	0.019	24.194	0.017	0.017	0.000	0.000	0.000	0.000
70	A	71	THR	0	0.036	0.009	23.517	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.801	-0.916	21.034	-0.332	-0.332	0.000	0.000	0.000	0.000
72	A	73	GLN	0	-0.058	-0.014	19.186	-0.050	-0.050	0.000	0.000	0.000	0.000
73	A	74	TYR	0	-0.015	-0.018	18.196	-0.054	-0.054	0.000	0.000	0.000	0.000
74	A	75	PHE	0	0.033	0.005	17.097	-0.036	-0.036	0.000	0.000	0.000	0.000
75	A	76	VAL	0	0.012	0.056	15.996	0.002	0.002	0.000	0.000	0.000	0.000
76	A	77	LEU	0	0.047	0.015	11.478	-0.096	-0.096	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.933	0.961	11.556	0.962	0.962	0.000	0.000	0.000	0.000
78	A	79	ASN	0	-0.078	-0.055	12.630	-0.175	-0.175	0.000	0.000	0.000	0.000
79	A	80	LEU	0	0.027	0.033	12.493	-0.031	-0.031	0.000	0.000	0.000	0.000
80	A	81	ALA	0	-0.002	-0.016	8.901	-0.043	-0.043	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.007	0.007	10.626	-0.111	-0.111	0.000	0.000	0.000	0.000
82	A	83	ARG	1	0.774	0.867	13.248	0.721	0.721	0.000	0.000	0.000	0.000
83	A	84	ILE	0	0.001	0.002	9.884	0.079	0.079	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.835	-0.891	9.636	-2.232	-2.232	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.889	-0.926	12.230	-0.569	-0.569	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.038	-0.026	15.296	0.099	0.099	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.007	0.008	10.630	0.099	0.099	0.000	0.000	0.000	0.000
88	A	89	ALA	0	-0.021	0.000	13.878	0.092	0.092	0.000	0.000	0.000	0.000
89	A	90	ALA	0	-0.036	-0.017	15.199	0.083	0.083	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.872	0.935	16.146	0.281	0.281	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.051	0.014	15.566	0.057	0.057	0.000	0.000	0.000	0.000
92	A	93	ALA	0	-0.064	-0.028	16.374	0.053	0.053	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.089	-0.036	19.531	0.042	0.042	0.000	0.000	0.000	0.000
94	A	95	GLU	-1	-1.007	-0.990	16.425	-0.141	-0.141	0.000	0.000	0.000	0.000

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