FMO DATABASE

FMODB ID: 5J63Z

Calculation Name: 3F40-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F40

Chain ID: A

ChEMBL ID:

UniProt ID:

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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-956626.755729
FMO2-HF: Nuclear repulsion	909508.191264
FMO2-HF: Total energy	-47118.564465
FMO2-MP2: Total energy	-47251.90939

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.
-4.861	-0.182	0.127	-2.457	-2.349	0.003

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 : 0.050 / q_NPA : 0.009

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	3	THR	0	0.021	0.023	2.774	-4.174	0.032	0.121	-2.252	-2.074	0.004
4	A	4	GLN	0	-0.034	-0.021	3.601	-1.034	-0.561	0.006	-0.205	-0.275	-0.001
5	A	5	ILE	0	0.011	0.012	6.344	0.047	0.047	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.041	-0.047	7.959	-0.042	-0.042	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.034	-0.027	10.594	0.067	0.067	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.883	0.922	13.360	-0.275	-0.275	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.805	-0.871	11.315	0.574	0.574	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.019	0.018	9.651	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.020	0.007	13.354	-0.039	-0.039	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.015	-0.013	16.347	-0.038	-0.038	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.836	-0.898	11.859	0.956	0.956	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.014	0.000	16.116	-0.038	-0.038	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.009	0.001	18.179	-0.033	-0.033	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.019	0.011	18.585	-0.039	-0.039	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.021	0.006	18.362	-0.023	-0.023	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.006	-0.004	20.437	-0.028	-0.028	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.013	-0.024	23.619	-0.034	-0.034	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.088	-0.054	22.114	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.810	-0.901	24.678	0.167	0.167	0.000	0.000	0.000	0.000
22	A	22	ASN	0	0.010	0.019	19.203	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	23	PHE	0	0.081	0.021	20.385	0.036	0.036	0.000	0.000	0.000	0.000
24	A	24	PRO	0	0.022	0.007	19.144	0.018	0.018	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.028	-0.007	15.987	0.037	0.037	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.045	0.023	15.881	0.062	0.062	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.846	0.910	17.252	-0.209	-0.209	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.922	0.972	8.783	-0.911	-0.911	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.763	0.850	11.977	-0.685	-0.685	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.046	-0.010	14.212	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.003	-0.012	15.224	-0.027	-0.027	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.886	-0.933	16.420	0.139	0.139	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.057	-0.045	18.460	-0.027	-0.027	0.000	0.000	0.000	0.000
34	A	34	PHE	0	-0.022	-0.001	19.454	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.013	0.005	21.193	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	36	PHE	0	0.008	-0.009	24.496	0.011	0.011	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.005	0.002	26.976	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.081	0.038	29.910	0.009	0.009	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.050	-0.016	32.504	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	40	MET	0	-0.032	-0.004	35.296	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.014	0.003	35.155	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	42	HIS	0	0.008	-0.009	28.851	0.001	0.001	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.748	0.863	27.896	-0.122	-0.122	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.818	-0.906	26.835	0.131	0.131	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.022	0.018	23.279	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.032	-0.028	19.744	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.832	-0.906	21.766	0.188	0.188	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.894	0.929	23.795	-0.116	-0.116	0.000	0.000	0.000	0.000
49	A	49	TYR	0	0.019	0.008	23.505	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	50	MET	0	0.004	-0.003	21.011	0.000	0.000	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.014	-0.010	24.460	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.798	-0.870	27.502	0.110	0.110	0.000	0.000	0.000	0.000
53	A	53	MET	0	-0.018	0.007	24.517	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.900	-0.947	25.837	0.173	0.173	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.842	0.922	27.970	-0.126	-0.126	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.041	-0.019	30.850	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.843	0.930	29.336	-0.152	-0.152	0.000	0.000	0.000	0.000
58	A	58	PHE	0	0.005	0.013	29.227	0.000	0.000	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.770	0.886	27.700	-0.171	-0.171	0.000	0.000	0.000	0.000
60	A	60	TYR	0	0.026	0.005	26.171	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	61	VAL	0	0.018	0.015	27.655	0.009	0.009	0.000	0.000	0.000	0.000
62	A	62	VAL	0	-0.013	-0.009	23.618	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	63	HIS	0	-0.026	-0.021	26.840	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.883	0.930	26.899	-0.130	-0.130	0.000	0.000	0.000	0.000
65	A	65	MET	0	0.004	0.022	17.854	0.002	0.002	0.000	0.000	0.000	0.000
66	A	66	PHE	0	0.005	0.012	22.968	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.825	-0.903	16.658	0.321	0.321	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.882	-0.928	21.465	0.113	0.113	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.001	-0.001	19.889	0.008	0.008	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.074	-0.038	16.659	0.000	0.000	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.843	-0.893	18.851	0.206	0.206	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.034	0.020	17.712	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	73	CYS	0	-0.041	-0.024	20.981	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.033	-0.005	21.615	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.012	-0.003	25.426	-0.012	-0.012	0.000	0.000	0.000	0.000
76	A	76	TYR	0	-0.012	-0.033	25.720	0.004	0.004	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.789	-0.865	29.455	0.113	0.113	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.002	-0.013	29.769	0.013	0.013	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.070	-0.036	31.902	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	80	MET	0	-0.014	-0.015	33.011	0.007	0.007	0.000	0.000	0.000	0.000
81	A	81	ASN	0	-0.008	-0.018	34.842	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	82	GLY	0	0.053	0.038	37.064	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.775	0.872	38.916	-0.081	-0.081	0.000	0.000	0.000	0.000
84	A	84	THR	0	0.020	0.002	35.495	0.007	0.007	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.040	-0.009	35.248	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.059	0.043	34.335	0.008	0.008	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.041	-0.024	31.345	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	88	SER	0	0.016	0.005	29.758	0.004	0.004	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.007	-0.012	26.719	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.003	0.010	24.459	0.010	0.010	0.000	0.000	0.000	0.000
91	A	91	TYR	0	0.009	-0.004	19.873	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	HIS	1	0.831	0.896	20.219	-0.192	-0.192	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.012	-0.018	14.486	0.025	0.025	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.803	-0.897	14.879	0.179	0.179	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.871	0.929	11.373	-0.215	-0.215	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.007	0.020	9.203	0.129	0.129	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.891	-0.926	9.942	0.460	0.460	0.000	0.000	0.000	0.000
98	A	98	ILE	0	0.013	0.001	13.244	-0.049	-0.049	0.000	0.000	0.000	0.000
99	A	99	THR	0	-0.015	-0.022	16.705	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	100	SER	0	0.012	0.007	19.130	-0.029	-0.029	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.041	-0.008	21.909	0.016	0.016	0.000	0.000	0.000	0.000
102	A	102	HIS	0	0.010	0.011	24.313	-0.021	-0.021	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.028	-0.012	27.786	0.004	0.004	0.000	0.000	0.000	0.000
104	A	104	TYR	0	-0.011	-0.010	29.369	-0.013	-0.013	0.000	0.000	0.000	0.000
105	A	105	PHE	0	0.060	0.006	32.190	0.003	0.003	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.784	-0.864	35.907	0.073	0.073	0.000	0.000	0.000	0.000
107	A	107	PRO	0	0.025	0.002	38.109	0.002	0.002	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.874	0.911	39.545	-0.069	-0.069	0.000	0.000	0.000	0.000
109	A	109	PRO	0	0.046	0.019	41.318	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.038	-0.023	37.000	0.000	0.000	0.000	0.000	0.000	0.000
111	A	111	PHE	0	-0.060	-0.025	41.064	0.000	0.000	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.857	-0.892	44.661	0.068	0.068	0.000	0.000	0.000	0.000

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