FMO DATABASE

FMODB ID: 4918N

Calculation Name: 3E29-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E29

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-09-20

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1134037.109436
FMO2-HF: Nuclear repulsion	1082298.02958
FMO2-HF: Total energy	-51739.079856
FMO2-MP2: Total energy	-51888.524451

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.
-1.09	-9.243	22.024	-5.588	-8.283	-0.031

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 : -0.022 / q_NPA : -0.026

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	SER	0	0.064	0.023	3.873	-0.124	1.787	-0.021	-0.981	-0.910	0.000
4	A	4	THR	0	0.048	0.016	6.968	0.234	0.234	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.013	0.007	4.351	0.179	0.276	-0.001	-0.018	-0.078	0.000
6	A	6	LEU	0	0.022	0.001	4.510	0.089	0.237	-0.001	-0.011	-0.135	0.000
7	A	7	GLU	-1	-0.936	-0.968	6.646	-0.192	-0.192	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.046	-0.007	9.581	0.112	0.112	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.051	0.013	8.432	0.074	0.074	0.000	0.000	0.000	0.000
10	A	10	SER	0	0.018	0.012	10.241	0.070	0.070	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.887	0.953	11.913	0.248	0.248	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.061	-0.041	12.473	0.021	0.021	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.047	0.036	12.684	0.010	0.010	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.038	0.007	15.378	0.022	0.022	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.918	0.971	17.982	0.080	0.080	0.000	0.000	0.000	0.000
16	A	16	SER	0	0.007	0.022	19.731	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	17	PRO	0	0.008	-0.010	21.584	0.011	0.011	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.042	0.027	23.178	0.007	0.007	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.044	0.012	17.667	0.019	0.019	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.894	0.931	20.144	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	21	TRP	0	-0.027	0.001	21.499	0.011	0.011	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.008	0.009	20.695	0.005	0.005	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.017	0.016	20.291	0.018	0.018	0.000	0.000	0.000	0.000
24	A	24	MET	0	-0.057	-0.024	14.896	0.020	0.020	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.053	-0.017	13.417	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.013	-0.008	7.265	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.047	-0.020	8.848	0.034	0.034	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.859	-0.926	3.902	2.122	2.363	0.000	-0.036	-0.206	0.000
29	A	29	ALA	0	0.060	0.017	3.032	-2.078	-0.792	0.020	-0.717	-0.588	0.000
30	A	30	GLY	0	0.009	0.011	1.854	-3.612	-11.614	20.983	-8.550	-4.431	-0.028
31	A	31	GLU	-1	-0.952	-0.970	2.201	3.475	-0.930	1.039	4.850	-1.484	-0.003
32	A	32	GLN	0	-0.004	0.007	3.650	-1.227	-0.712	0.006	-0.124	-0.397	0.000
33	A	33	GLY	0	0.019	0.011	5.254	-0.070	-0.070	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.062	-0.023	5.125	-0.304	-0.248	-0.001	-0.001	-0.054	0.000
35	A	35	VAL	0	0.025	0.021	6.765	0.036	0.036	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.018	0.001	8.807	0.034	0.034	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.032	0.016	11.717	0.039	0.039	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.041	-0.017	14.593	-0.037	-0.037	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.925	0.963	18.079	-0.246	-0.246	0.000	0.000	0.000	0.000
40	A	40	TRP	0	-0.003	0.005	21.115	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.850	0.905	24.236	-0.100	-0.100	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.831	-0.935	27.558	0.099	0.099	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.896	-0.945	29.869	0.084	0.084	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.062	-0.028	23.959	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.042	-0.004	28.620	0.004	0.004	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.062	-0.019	31.393	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.005	-0.006	33.105	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.057	0.007	34.847	0.006	0.006	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.956	-0.969	37.022	0.072	0.072	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.042	-0.030	33.091	0.002	0.002	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.948	0.980	32.296	-0.091	-0.091	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.038	0.022	29.957	0.007	0.007	0.000	0.000	0.000	0.000
53	A	53	THR	0	0.018	0.003	24.696	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	54	HIS	0	0.036	0.030	27.877	0.005	0.005	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.068	0.028	26.777	0.008	0.008	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.012	-0.013	26.013	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	ILE	0	0.000	0.002	22.716	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.023	0.003	21.883	0.009	0.009	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.020	0.008	21.258	0.009	0.009	0.000	0.000	0.000	0.000
60	A	60	THR	0	0.001	-0.008	20.470	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.026	-0.015	16.658	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	62	VAL	0	-0.022	-0.002	16.771	0.014	0.014	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.852	-0.916	17.399	0.063	0.063	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.037	0.019	15.885	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.004	-0.008	12.818	-0.013	-0.013	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.030	-0.003	12.523	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.832	-0.910	14.374	-0.025	-0.025	0.000	0.000	0.000	0.000
68	A	68	TYR	0	0.048	-0.005	11.139	-0.031	-0.031	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.001	0.008	9.583	-0.057	-0.057	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.028	-0.020	10.649	-0.039	-0.039	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.017	-0.002	12.484	-0.040	-0.040	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.077	-0.032	5.837	-0.073	-0.073	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.896	0.953	8.501	0.001	0.001	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.030	-0.004	11.586	-0.021	-0.021	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.009	0.010	13.591	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	76	HIS	0	-0.124	-0.076	14.523	0.001	0.001	0.000	0.000	0.000	0.000
77	A	77	PRO	0	0.021	-0.005	15.990	0.006	0.006	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.061	-0.014	16.808	-0.011	-0.011	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.023	0.003	19.374	0.012	0.012	0.000	0.000	0.000	0.000
80	A	80	THR	0	0.038	-0.019	21.415	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	81	MET	0	-0.122	-0.048	22.970	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.832	-0.922	24.866	0.049	0.049	0.000	0.000	0.000	0.000
83	A	83	MET	0	-0.011	-0.012	22.253	0.001	0.001	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.068	-0.019	23.839	-0.012	-0.012	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.013	-0.014	22.862	0.010	0.010	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.891	-0.931	23.816	0.115	0.115	0.000	0.000	0.000	0.000
87	A	87	TYR	0	-0.038	-0.040	24.244	0.011	0.011	0.000	0.000	0.000	0.000
88	A	88	HIS	0	-0.029	0.003	22.664	0.002	0.002	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.915	0.946	23.415	-0.206	-0.206	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.006	0.006	26.397	0.000	0.000	0.000	0.000	0.000	0.000
91	A	91	ALA	0	0.045	0.032	24.143	0.009	0.009	0.000	0.000	0.000	0.000
92	A	92	THR	0	0.030	0.012	25.814	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	93	PRO	0	-0.047	-0.018	26.070	0.010	0.010	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.025	0.016	24.054	0.003	0.003	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.871	-0.925	18.986	0.231	0.231	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.027	-0.016	18.708	0.004	0.004	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.881	0.936	8.843	-0.858	-0.858	0.000	0.000	0.000	0.000
98	A	98	ALA	0	-0.016	-0.001	13.595	-0.029	-0.029	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.868	-0.938	10.334	0.606	0.606	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.017	0.007	10.226	-0.046	-0.046	0.000	0.000	0.000	0.000
101	A	101	GLN	0	-0.052	-0.037	8.989	-0.033	-0.033	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.006	0.002	11.486	-0.024	-0.024	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.011	0.005	13.360	0.018	0.018	0.000	0.000	0.000	0.000
104	A	104	HIS	0	-0.006	-0.019	16.149	-0.016	-0.016	0.000	0.000	0.000	0.000
105	A	105	PHE	0	0.040	0.016	15.290	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	106	GLY	0	0.015	-0.009	17.416	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.946	0.967	19.789	0.077	0.077	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.875	0.961	22.054	0.010	0.010	0.000	0.000	0.000	0.000
109	A	109	PHE	0	0.060	0.027	22.383	0.002	0.002	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.024	0.020	17.148	-0.007	-0.007	0.000	0.000	0.000	0.000
111	A	111	THR	0	-0.007	0.008	18.621	0.004	0.004	0.000	0.000	0.000	0.000
112	A	112	ALA	0	0.007	0.020	14.763	0.002	0.002	0.000	0.000	0.000	0.000
113	A	113	HIS	0	0.027	0.007	15.228	-0.014	-0.014	0.000	0.000	0.000	0.000
114	A	114	ALA	0	0.011	0.001	14.439	0.015	0.015	0.000	0.000	0.000	0.000
115	A	115	ARG	1	0.903	0.957	14.200	-0.390	-0.390	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.008	0.007	15.120	0.028	0.028	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.035	-0.033	13.977	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.765	-0.889	17.683	0.257	0.257	0.000	0.000	0.000	0.000
119	A	119	MET	0	-0.043	-0.034	17.921	0.040	0.040	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.939	-0.952	19.175	0.274	0.274	0.000	0.000	0.000	0.000
121	A	121	GLY	0	-0.060	-0.018	17.317	0.014	0.014	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.056	-0.021	18.200	0.005	0.005	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.037	-0.020	18.186	0.005	0.005	0.000	0.000	0.000	0.000
124	A	124	VAL	0	0.002	0.000	20.336	-0.022	-0.022	0.000	0.000	0.000	0.000
125	A	125	ALA	0	0.018	0.003	20.898	-0.022	-0.022	0.000	0.000	0.000	0.000
126	A	126	SER	0	-0.016	-0.014	19.289	0.026	0.026	0.000	0.000	0.000	0.000
127	A	127	GLY	0	0.063	0.033	19.301	-0.018	-0.018	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.823	0.939	19.002	-0.064	-0.064	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.038	0.013	19.552	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.024	0.004	20.189	0.000	0.000	0.000	0.000	0.000	0.000
131	A	131	TYR	0	0.046	0.018	17.708	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.049	-0.033	21.236	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	133	ILE	0	-0.016	-0.006	18.530	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	134	ARG	1	0.962	0.979	21.786	0.031	0.031	0.000	0.000	0.000	0.000

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