FMO DATABASE

FMODB ID: 6YV9Z

Calculation Name: 3A7L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A7L

Chain ID: A

ChEMBL ID:

UniProt ID: P0A6T9

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	128
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1036683.526043
FMO2-HF: Nuclear repulsion	988725.332989
FMO2-HF: Total energy	-47958.193053
FMO2-MP2: Total energy	-48099.109951

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:SER)

Summations of interaction energy for fragment #1(A:1:SER)

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.
-7.32	-1.803	4.479	-3.717	-6.278	0.011

Interaction energy analysis for fragmet #1(A:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.028

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	3	VAL	0	0.064	0.057	3.809	-0.292	2.306	-0.004	-1.304	-1.290	0.006
4	A	4	PRO	0	-0.015	0.007	6.172	-0.214	-0.214	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.045	0.010	9.362	0.121	0.121	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-1.014	-1.010	12.205	-0.113	-0.113	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.065	-0.006	9.940	0.028	0.028	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.920	0.966	13.229	-0.008	-0.008	0.000	0.000	0.000	0.000
9	A	9	TYR	0	0.055	0.003	7.874	0.109	0.109	0.000	0.000	0.000	0.000
10	A	10	SER	0	0.023	0.011	11.865	-0.067	-0.067	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.945	0.948	11.299	-0.017	-0.017	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.879	-0.922	12.122	0.250	0.250	0.000	0.000	0.000	0.000
13	A	13	HIS	0	0.020	0.067	7.702	0.344	0.344	0.000	0.000	0.000	0.000
14	A	14	GLH	0	-0.032	-0.057	9.566	0.079	0.079	0.000	0.000	0.000	0.000
15	A	15	TRP	0	-0.034	-0.017	9.253	-0.053	-0.053	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.005	-0.012	11.952	-0.041	-0.041	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.872	0.929	14.950	-0.075	-0.075	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.925	0.977	16.794	0.005	0.005	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.793	-0.860	19.824	0.022	0.022	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.031	-0.028	22.647	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.897	-0.937	25.953	0.021	0.021	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.072	-0.041	25.663	0.000	0.000	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.062	-0.033	24.368	0.006	0.006	0.000	0.000	0.000	0.000
24	A	24	TYR	0	0.023	0.004	18.996	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.042	-0.038	16.616	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.030	0.015	15.488	0.002	0.002	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.062	0.028	12.907	-0.032	-0.032	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.027	0.031	9.393	0.015	0.015	0.000	0.000	0.000	0.000
29	A	29	THR	0	-0.024	-0.033	5.432	-0.081	-0.081	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.919	-0.975	2.301	-0.590	-0.275	1.586	-0.655	-1.246	-0.003
31	A	31	HIS	0	-0.072	-0.037	2.365	-3.408	-2.058	2.293	-1.230	-2.413	0.007
32	A	32	ALA	0	0.039	0.021	3.898	-1.370	-1.028	0.040	-0.129	-0.252	0.001
33	A	33	GLN	0	0.003	0.010	5.576	-0.259	-0.259	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.953	-0.962	4.847	0.568	0.568	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.056	-0.029	6.805	-0.138	-0.138	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.014	-0.002	8.779	-0.100	-0.100	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.062	-0.015	10.539	-0.069	-0.069	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.958	-0.980	12.154	0.209	0.209	0.000	0.000	0.000	0.000
39	A	39	MET	0	0.031	0.013	12.281	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.059	-0.045	15.913	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.030	-0.012	18.984	-0.019	-0.019	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.003	-0.007	16.947	0.024	0.024	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.934	-0.948	19.667	0.101	0.101	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.026	-0.020	20.457	0.012	0.012	0.000	0.000	0.000	0.000
45	A	45	PRO	0	0.027	0.021	21.914	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.930	-0.977	24.961	0.065	0.065	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.036	-0.026	27.184	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.044	-0.017	28.896	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.030	-0.005	28.044	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.073	-0.044	28.893	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.002	0.005	24.336	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.028	-0.025	26.804	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.022	-0.015	22.477	0.010	0.010	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.050	-0.033	20.972	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.850	-0.916	22.030	0.085	0.085	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.925	-0.956	21.446	0.131	0.131	0.000	0.000	0.000	0.000
57	A	57	CYS	0	-0.092	-0.053	21.336	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.018	0.008	18.934	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.006	0.022	19.078	0.010	0.010	0.000	0.000	0.000	0.000
60	A	60	ALA	0	-0.010	0.001	14.905	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.912	-0.967	16.881	0.164	0.164	0.000	0.000	0.000	0.000
62	A	62	SER	0	0.009	-0.016	14.845	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.042	-0.022	16.853	-0.018	-0.018	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.822	0.910	12.039	-0.361	-0.361	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.037	-0.015	15.313	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.033	0.020	17.454	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.045	-0.022	15.071	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.885	-0.926	17.085	0.164	0.164	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.057	-0.022	15.121	0.039	0.039	0.000	0.000	0.000	0.000
70	A	70	TYR	0	0.071	0.028	16.578	-0.026	-0.026	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.020	0.048	18.075	0.021	0.021	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.044	-0.017	16.722	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.031	-0.021	18.793	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.025	-0.059	22.207	0.009	0.009	0.000	0.000	0.000	0.000
75	A	75	GLY	0	-0.017	-0.022	25.757	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.972	-0.970	27.382	0.047	0.047	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.035	0.020	23.410	0.001	0.001	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.018	-0.018	25.609	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	79	ALA	0	-0.054	-0.038	24.084	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.054	0.026	22.347	0.008	0.008	0.000	0.000	0.000	0.000
81	A	81	ASN	0	-0.027	-0.017	17.756	-0.025	-0.025	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.877	-0.951	21.443	0.085	0.085	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.050	-0.024	20.975	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.033	-0.014	16.711	0.003	0.003	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.021	-0.007	20.256	0.009	0.009	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.979	-0.983	23.462	0.079	0.079	0.000	0.000	0.000	0.000
87	A	87	SER	0	-0.084	-0.040	19.777	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	88	PRO	0	0.037	0.033	17.908	0.008	0.008	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.840	-0.931	15.218	0.161	0.161	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.041	-0.026	14.014	0.011	0.011	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.035	-0.018	11.136	0.009	0.009	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.011	-0.027	9.843	0.016	0.016	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.028	-0.008	9.296	0.006	0.006	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.928	-0.968	10.613	0.016	0.016	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.074	0.065	6.684	-0.032	-0.032	0.000	0.000	0.000	0.000
96	A	96	TYR	0	-0.058	-0.055	4.578	0.110	0.155	-0.001	-0.005	-0.039	0.000
97	A	97	ALA	0	-0.078	-0.051	10.659	-0.045	-0.045	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.021	-0.018	13.895	0.013	0.013	0.000	0.000	0.000	0.000
99	A	99	GLY	0	0.030	0.017	13.225	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	100	TRP	0	-0.111	-0.040	14.103	0.030	0.030	0.000	0.000	0.000	0.000
101	A	101	ILE	0	0.068	0.037	13.906	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	102	PHE	0	0.017	-0.001	17.400	-0.024	-0.024	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.850	0.923	19.209	-0.061	-0.061	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.039	0.028	21.178	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.928	0.962	23.691	-0.036	-0.036	0.000	0.000	0.000	0.000
106	A	106	ALA	0	0.024	0.014	24.429	0.001	0.001	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.019	-0.024	26.279	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.871	-0.916	27.656	0.019	0.019	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.934	-0.978	26.474	0.018	0.018	0.000	0.000	0.000	0.000
110	A	110	SER	0	-0.084	-0.060	25.778	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.727	-0.822	23.479	0.054	0.054	0.000	0.000	0.000	0.000
112	A	112	LEU	0	-0.047	-0.031	21.242	0.008	0.008	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-1.007	-0.994	20.513	-0.009	-0.009	0.000	0.000	0.000	0.000
114	A	114	SER	0	-0.077	-0.029	20.303	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.077	-0.029	16.358	0.017	0.017	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.043	-0.011	11.682	-0.033	-0.033	0.000	0.000	0.000	0.000
117	A	117	ASP	-1	-0.909	-0.973	13.751	-0.151	-0.151	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.061	0.013	9.965	0.036	0.036	0.000	0.000	0.000	0.000
119	A	119	THR	0	0.026	0.031	9.479	-0.091	-0.091	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.038	-0.020	10.802	-0.052	-0.052	0.000	0.000	0.000	0.000
121	A	121	TYR	0	-0.009	-0.049	4.656	0.097	0.194	-0.001	-0.009	-0.087	0.000
122	A	122	GLU	-1	-0.888	-0.957	5.784	-1.233	-1.233	0.000	0.000	0.000	0.000
123	A	123	ALA	0	-0.016	-0.007	7.132	-0.153	-0.153	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.034	-0.021	8.989	0.024	0.024	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.004	-0.001	2.433	-0.554	0.216	0.566	-0.385	-0.951	0.000
126	A	126	GLU	-1	-1.042	-1.018	6.388	-1.037	-1.037	0.000	0.000	0.000	0.000
127	A	127	ASP	-1	-1.017	-1.001	8.455	0.007	0.007	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.998	-0.977	7.311	0.260	0.260	0.000	0.000	0.000	0.000

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