FMO DATABASE

FMODB ID: 98MQ2

Calculation Name: 3MLF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MLF

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-22

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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-700557.306048
FMO2-HF: Nuclear repulsion	661432.157093
FMO2-HF: Total energy	-39125.148955
FMO2-MP2: Total energy	-39239.228957

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:-9:THR)

Summations of interaction energy for fragment #1(A:-9: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.
-0.635	4.16	2.387	-2.619	-4.563	0.001

Interaction energy analysis for fragmet #1(A:-9: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 : -0.012

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	-7	ASN	0	-0.059	-0.025	3.803	-0.451	1.582	-0.016	-0.859	-1.158	0.000
4	A	-6	LEU	0	-0.054	-0.012	2.664	-0.572	0.761	0.749	-0.739	-1.343	-0.001
5	A	-5	TYR	0	0.004	-0.004	2.003	0.389	1.548	1.652	-0.936	-1.875	0.002
6	A	-4	PHE	0	0.002	0.005	5.029	-0.537	-0.590	-0.001	-0.004	0.058	0.000
7	A	-3	GLN	0	0.011	0.008	7.451	0.032	0.032	0.000	0.000	0.000	0.000
8	A	-2	SER	0	-0.003	-0.011	8.911	0.320	0.320	0.000	0.000	0.000	0.000
9	A	-1	ASN	0	-0.039	-0.024	12.193	0.017	0.017	0.000	0.000	0.000	0.000
10	A	0	ALA	0	-0.024	-0.002	14.708	0.053	0.053	0.000	0.000	0.000	0.000
11	A	1	MET	0	0.045	0.039	15.039	-0.033	-0.033	0.000	0.000	0.000	0.000
12	A	2	LYS	1	0.800	0.892	13.808	0.326	0.326	0.000	0.000	0.000	0.000
13	A	3	THR	0	0.054	0.047	16.678	0.019	0.019	0.000	0.000	0.000	0.000
14	A	4	LEU	0	0.060	0.015	17.357	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	5	LYS	1	0.937	0.974	17.783	0.040	0.040	0.000	0.000	0.000	0.000
16	A	6	GLU	-1	-0.775	-0.884	16.857	-0.203	-0.203	0.000	0.000	0.000	0.000
17	A	7	LEU	0	0.039	0.040	11.928	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	8	ARG	1	0.737	0.820	13.886	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	9	THR	0	-0.074	-0.049	16.077	0.025	0.025	0.000	0.000	0.000	0.000
20	A	10	ASP	-1	-0.851	-0.906	12.987	-0.269	-0.269	0.000	0.000	0.000	0.000
21	A	11	TYR	0	-0.023	-0.014	8.057	-0.078	-0.078	0.000	0.000	0.000	0.000
22	A	12	GLY	0	-0.028	-0.001	13.504	0.059	0.059	0.000	0.000	0.000	0.000
23	A	13	LEU	0	0.015	0.033	14.548	0.024	0.024	0.000	0.000	0.000	0.000
24	A	14	THR	0	-0.028	-0.055	18.124	-0.033	-0.033	0.000	0.000	0.000	0.000
25	A	15	GLN	0	-0.074	-0.080	20.571	0.014	0.014	0.000	0.000	0.000	0.000
26	A	16	LYS	1	0.845	0.900	22.480	-0.111	-0.111	0.000	0.000	0.000	0.000
27	A	17	GLU	-1	-0.775	-0.839	19.194	0.148	0.148	0.000	0.000	0.000	0.000
28	A	18	LEU	0	0.045	0.030	15.740	0.019	0.019	0.000	0.000	0.000	0.000
29	A	19	GLY	0	0.006	0.003	18.891	0.013	0.013	0.000	0.000	0.000	0.000
30	A	20	ASP	-1	-0.828	-0.904	21.445	0.143	0.143	0.000	0.000	0.000	0.000
31	A	21	LEU	0	-0.035	-0.002	13.681	0.010	0.010	0.000	0.000	0.000	0.000
32	A	22	PHE	0	-0.016	-0.021	14.151	0.018	0.018	0.000	0.000	0.000	0.000
33	A	23	LYS	1	0.926	0.973	19.054	-0.227	-0.227	0.000	0.000	0.000	0.000
34	A	24	VAL	0	-0.025	-0.002	21.998	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	25	SER	0	0.054	0.035	24.534	0.002	0.002	0.000	0.000	0.000	0.000
36	A	26	SER	0	0.121	0.028	25.131	0.001	0.001	0.000	0.000	0.000	0.000
37	A	27	ARG	1	0.877	0.961	26.217	-0.031	-0.031	0.000	0.000	0.000	0.000
38	A	28	THR	0	0.009	-0.011	24.708	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	29	ILE	0	0.027	0.025	20.446	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	30	GLN	0	0.005	0.009	23.779	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	31	ASN	0	-0.005	-0.028	26.447	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	32	MET	0	0.023	0.035	23.099	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	33	GLU	-1	-0.756	-0.834	20.835	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	34	LYS	1	0.741	0.870	23.903	0.005	0.005	0.000	0.000	0.000	0.000
45	A	35	ASP	-1	-0.828	-0.904	27.428	-0.037	-0.037	0.000	0.000	0.000	0.000
46	A	36	SER	0	-0.033	-0.023	23.025	0.004	0.004	0.000	0.000	0.000	0.000
47	A	37	THR	0	-0.058	-0.044	25.132	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	38	ASN	0	-0.030	-0.022	27.484	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	39	ILE	0	-0.007	-0.005	20.560	0.012	0.012	0.000	0.000	0.000	0.000
50	A	40	LYS	1	0.934	0.970	24.357	-0.039	-0.039	0.000	0.000	0.000	0.000
51	A	41	ASP	-1	-0.806	-0.914	20.574	0.025	0.025	0.000	0.000	0.000	0.000
52	A	42	SER	0	-0.008	0.001	19.778	0.010	0.010	0.000	0.000	0.000	0.000
53	A	43	LEU	0	-0.057	-0.033	19.149	0.025	0.025	0.000	0.000	0.000	0.000
54	A	44	LEU	0	0.073	0.032	16.801	0.021	0.021	0.000	0.000	0.000	0.000
55	A	45	SER	0	0.072	0.025	15.588	0.000	0.000	0.000	0.000	0.000	0.000
56	A	46	LYS	1	0.806	0.907	14.024	-0.115	-0.115	0.000	0.000	0.000	0.000
57	A	47	TYR	0	-0.005	-0.007	13.187	0.075	0.075	0.000	0.000	0.000	0.000
58	A	48	MET	0	-0.013	0.003	11.717	0.007	0.007	0.000	0.000	0.000	0.000
59	A	49	SER	0	-0.021	-0.002	9.698	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	50	ALA	0	-0.052	-0.024	8.414	0.297	0.297	0.000	0.000	0.000	0.000
61	A	51	PHE	0	-0.028	-0.038	8.337	0.153	0.153	0.000	0.000	0.000	0.000
62	A	52	ASN	0	-0.031	0.010	3.864	0.214	0.537	0.003	-0.081	-0.245	0.000
63	A	53	VAL	0	-0.011	0.013	6.836	-0.437	-0.437	0.000	0.000	0.000	0.000
64	A	54	LYS	1	0.847	0.878	9.831	0.596	0.596	0.000	0.000	0.000	0.000
65	A	55	TYR	0	0.031	0.001	12.532	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	56	ASP	-1	-0.869	-0.934	16.105	-0.251	-0.251	0.000	0.000	0.000	0.000
67	A	57	ASP	-1	-0.830	-0.889	11.820	-0.554	-0.554	0.000	0.000	0.000	0.000
68	A	58	ILE	0	-0.053	-0.035	14.071	0.001	0.001	0.000	0.000	0.000	0.000
69	A	59	PHE	0	-0.015	-0.017	16.746	0.015	0.015	0.000	0.000	0.000	0.000
70	A	60	LEU	0	0.002	-0.017	19.836	0.018	0.018	0.000	0.000	0.000	0.000
71	A	61	GLY	0	0.077	0.038	22.692	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	62	ASN	0	-0.012	-0.011	26.303	0.006	0.006	0.000	0.000	0.000	0.000
73	A	63	GLU	-1	-0.789	-0.882	28.125	-0.030	-0.030	0.000	0.000	0.000	0.000
74	A	64	TYR	0	-0.020	-0.012	29.448	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	65	GLU	-1	-0.788	-0.889	27.575	-0.068	-0.068	0.000	0.000	0.000	0.000
76	A	66	ASN	0	0.014	-0.005	23.743	-0.020	-0.020	0.000	0.000	0.000	0.000
77	A	67	PHE	0	-0.044	-0.005	25.885	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	68	VAL	0	0.032	0.011	28.132	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	69	PHE	0	0.039	0.035	19.840	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	70	THR	0	-0.061	-0.048	22.175	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	71	ASN	0	-0.055	-0.031	24.401	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	72	ASP	-1	-0.789	-0.895	26.927	-0.105	-0.105	0.000	0.000	0.000	0.000
83	A	73	LYS	1	0.792	0.900	18.757	0.220	0.220	0.000	0.000	0.000	0.000
84	A	74	LYS	1	0.944	0.974	24.185	0.073	0.073	0.000	0.000	0.000	0.000
85	A	75	LYS	1	0.857	0.919	26.056	0.092	0.092	0.000	0.000	0.000	0.000
86	A	76	SER	0	-0.003	-0.012	24.946	0.002	0.002	0.000	0.000	0.000	0.000
87	A	77	ILE	0	-0.024	-0.001	21.118	0.002	0.002	0.000	0.000	0.000	0.000
88	A	78	ILE	0	-0.043	-0.028	25.266	0.006	0.006	0.000	0.000	0.000	0.000
89	A	79	LEU	0	0.003	0.008	28.844	0.006	0.006	0.000	0.000	0.000	0.000
90	A	80	ALA	0	0.046	0.011	26.144	0.003	0.003	0.000	0.000	0.000	0.000
91	A	81	PHE	0	-0.032	-0.010	27.062	0.003	0.003	0.000	0.000	0.000	0.000
92	A	82	LYS	1	0.967	0.965	28.710	0.082	0.082	0.000	0.000	0.000	0.000
93	A	83	GLU	-1	-0.945	-0.959	30.990	-0.100	-0.100	0.000	0.000	0.000	0.000
94	A	84	LYS	1	0.898	0.966	24.543	0.163	0.163	0.000	0.000	0.000	0.000
95	A	85	GLN	0	-0.084	-0.031	30.195	0.011	0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-9:THR)