FMO DATABASE

FMODB ID: 4JYVN

Calculation Name: 3D7N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D7N

Chain ID: A

ChEMBL ID:

UniProt ID: A9CG77

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	157
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1487061.961326
FMO2-HF: Nuclear repulsion	1428024.959888
FMO2-HF: Total energy	-59037.001438
FMO2-MP2: Total energy	-59210.216763

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:6:SER)

Summations of interaction energy for fragment #1(A:6: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.
-11.06	-6.737	1.154	-2.125	-3.353	0.016

Interaction energy analysis for fragmet #1(A:6:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : -0.005

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	8	ASN	0	-0.041	-0.022	3.887	-1.936	-0.545	-0.010	-0.645	-0.736	0.001
4	A	9	THR	0	0.026	0.007	6.538	0.597	0.597	0.000	0.000	0.000	0.000
5	A	10	VAL	0	-0.013	-0.001	8.951	-0.236	-0.236	0.000	0.000	0.000	0.000
6	A	11	VAL	0	-0.015	0.002	12.486	0.117	0.117	0.000	0.000	0.000	0.000
7	A	12	VAL	0	0.001	0.001	15.243	-0.046	-0.046	0.000	0.000	0.000	0.000
8	A	13	TYR	0	-0.022	-0.038	18.686	0.035	0.035	0.000	0.000	0.000	0.000
9	A	14	HIS	0	0.042	0.055	21.593	-0.008	-0.008	0.000	0.000	0.000	0.000
10	A	15	SER	0	0.003	-0.002	25.098	0.001	0.001	0.000	0.000	0.000	0.000
11	A	16	GLY	0	0.020	0.030	26.975	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	17	TYR	0	-0.027	-0.030	29.876	0.003	0.003	0.000	0.000	0.000	0.000
13	A	18	GLY	0	0.040	0.029	27.614	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	19	HIS	0	-0.042	-0.038	26.233	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	20	THR	0	0.011	-0.016	24.173	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	21	HIS	0	-0.001	0.020	21.594	0.014	0.014	0.000	0.000	0.000	0.000
17	A	22	ARG	1	0.860	0.916	18.760	0.173	0.173	0.000	0.000	0.000	0.000
18	A	23	MET	0	0.005	0.006	20.586	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	24	ALA	0	0.014	0.004	18.261	0.008	0.008	0.000	0.000	0.000	0.000
20	A	25	GLU	-1	-0.829	-0.898	16.522	-0.236	-0.236	0.000	0.000	0.000	0.000
21	A	26	ALA	0	-0.002	0.009	15.706	-0.036	-0.036	0.000	0.000	0.000	0.000
22	A	27	VAL	0	-0.017	-0.012	13.939	0.012	0.012	0.000	0.000	0.000	0.000
23	A	28	ALA	0	0.002	-0.013	12.091	0.034	0.034	0.000	0.000	0.000	0.000
24	A	29	GLU	-1	-0.900	-0.951	10.938	-0.341	-0.341	0.000	0.000	0.000	0.000
25	A	30	GLY	0	-0.037	-0.018	11.289	-0.071	-0.071	0.000	0.000	0.000	0.000
26	A	31	ALA	0	-0.066	-0.036	8.879	0.076	0.076	0.000	0.000	0.000	0.000
27	A	32	GLU	-1	-0.897	-0.944	4.652	-2.320	-2.253	-0.001	-0.007	-0.059	0.000
28	A	33	ALA	0	-0.045	0.000	7.494	-0.259	-0.259	0.000	0.000	0.000	0.000
29	A	34	THR	0	0.005	0.002	9.705	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	35	LEU	0	-0.015	-0.017	12.211	0.102	0.102	0.000	0.000	0.000	0.000
31	A	36	HIS	0	0.004	0.006	15.562	0.013	0.013	0.000	0.000	0.000	0.000
32	A	37	ALA	0	0.008	0.013	18.627	0.035	0.035	0.000	0.000	0.000	0.000
33	A	38	ILE	0	-0.035	-0.015	22.223	0.001	0.001	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.737	-0.861	24.831	-0.076	-0.076	0.000	0.000	0.000	0.000
35	A	40	ALA	0	-0.007	-0.028	28.004	0.011	0.011	0.000	0.000	0.000	0.000
36	A	41	GLU	-1	-0.926	-0.956	31.174	-0.052	-0.052	0.000	0.000	0.000	0.000
37	A	42	GLY	0	0.013	0.010	29.051	0.009	0.009	0.000	0.000	0.000	0.000
38	A	43	ASN	0	-0.085	-0.043	28.238	0.018	0.018	0.000	0.000	0.000	0.000
39	A	44	LEU	0	0.018	0.002	20.281	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	45	SER	0	0.006	-0.010	22.235	0.011	0.011	0.000	0.000	0.000	0.000
41	A	46	GLU	-1	-0.896	-0.963	22.325	-0.116	-0.116	0.000	0.000	0.000	0.000
42	A	47	ASP	-1	-0.842	-0.900	18.839	-0.235	-0.235	0.000	0.000	0.000	0.000
43	A	48	GLY	0	0.021	0.015	17.713	-0.031	-0.031	0.000	0.000	0.000	0.000
44	A	49	TRP	0	-0.085	-0.053	17.989	0.018	0.018	0.000	0.000	0.000	0.000
45	A	50	ALA	0	0.006	0.005	17.430	0.023	0.023	0.000	0.000	0.000	0.000
46	A	51	ALA	0	0.002	0.006	13.956	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	52	LEU	0	-0.004	-0.013	13.665	0.008	0.008	0.000	0.000	0.000	0.000
48	A	53	ASP	-1	-0.831	-0.935	15.104	0.064	0.064	0.000	0.000	0.000	0.000
49	A	54	ALA	0	-0.043	-0.013	11.641	0.069	0.069	0.000	0.000	0.000	0.000
50	A	55	ALA	0	-0.027	0.018	10.467	-0.067	-0.067	0.000	0.000	0.000	0.000
51	A	56	ASP	-1	-0.743	-0.822	6.162	0.697	0.697	0.000	0.000	0.000	0.000
52	A	57	ALA	0	-0.025	-0.018	9.301	0.128	0.128	0.000	0.000	0.000	0.000
53	A	58	ILE	0	0.004	0.017	11.342	-0.152	-0.152	0.000	0.000	0.000	0.000
54	A	59	ILE	0	-0.033	-0.019	11.895	0.045	0.045	0.000	0.000	0.000	0.000
55	A	60	PHE	0	0.029	0.004	15.945	-0.055	-0.055	0.000	0.000	0.000	0.000
56	A	61	GLY	0	0.047	0.019	19.697	0.013	0.013	0.000	0.000	0.000	0.000
57	A	62	THR	0	-0.021	-0.030	21.663	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	63	PRO	0	0.011	0.026	25.477	0.007	0.007	0.000	0.000	0.000	0.000
59	A	64	THR	0	0.003	0.019	28.480	0.012	0.012	0.000	0.000	0.000	0.000
60	A	65	TYR	0	-0.026	-0.029	30.777	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	66	MET	0	-0.034	-0.018	34.254	0.003	0.003	0.000	0.000	0.000	0.000
62	A	67	GLY	0	0.079	0.055	36.099	0.002	0.002	0.000	0.000	0.000	0.000
63	A	68	GLY	0	-0.020	-0.004	32.306	0.008	0.008	0.000	0.000	0.000	0.000
64	A	69	PRO	0	0.020	0.017	28.333	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	70	SER	0	-0.011	-0.014	29.092	0.000	0.000	0.000	0.000	0.000	0.000
66	A	71	TRP	0	0.049	0.011	30.662	0.004	0.004	0.000	0.000	0.000	0.000
67	A	72	GLN	0	-0.013	-0.006	29.424	0.008	0.008	0.000	0.000	0.000	0.000
68	A	73	PHE	0	0.036	0.018	22.600	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	74	LYS	1	0.819	0.895	27.411	-0.028	-0.028	0.000	0.000	0.000	0.000
70	A	75	LYS	1	0.824	0.900	29.960	0.042	0.042	0.000	0.000	0.000	0.000
71	A	76	PHE	0	0.031	0.015	20.938	0.000	0.000	0.000	0.000	0.000	0.000
72	A	77	ALA	0	0.026	0.007	25.709	0.004	0.004	0.000	0.000	0.000	0.000
73	A	78	ASP	-1	-0.801	-0.859	26.761	0.039	0.039	0.000	0.000	0.000	0.000
74	A	79	ALA	0	-0.001	0.014	27.330	0.004	0.004	0.000	0.000	0.000	0.000
75	A	80	SER	0	-0.053	-0.044	23.278	0.007	0.007	0.000	0.000	0.000	0.000
76	A	81	SER	0	0.003	-0.026	25.028	0.014	0.014	0.000	0.000	0.000	0.000
77	A	82	LYS	1	0.985	1.001	25.047	0.037	0.037	0.000	0.000	0.000	0.000
78	A	83	PRO	0	0.004	0.004	21.345	0.006	0.006	0.000	0.000	0.000	0.000
79	A	84	TRP	0	-0.059	-0.007	22.807	0.010	0.010	0.000	0.000	0.000	0.000
80	A	85	PHE	0	0.001	-0.003	24.866	0.013	0.013	0.000	0.000	0.000	0.000
81	A	86	SER	0	-0.059	-0.041	24.399	0.002	0.002	0.000	0.000	0.000	0.000
82	A	87	ALA	0	0.022	0.003	22.835	0.006	0.006	0.000	0.000	0.000	0.000
83	A	88	LYS	1	0.891	0.967	19.121	-0.020	-0.020	0.000	0.000	0.000	0.000
84	A	89	TRP	0	-0.062	-0.066	17.185	0.004	0.004	0.000	0.000	0.000	0.000
85	A	90	GLN	0	-0.001	0.005	17.856	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	91	ASP	-1	-0.904	-0.944	15.777	0.424	0.424	0.000	0.000	0.000	0.000
87	A	92	LYS	1	0.756	0.889	12.967	-0.117	-0.117	0.000	0.000	0.000	0.000
88	A	93	VAL	0	0.008	0.007	10.649	-0.035	-0.035	0.000	0.000	0.000	0.000
89	A	94	PHE	0	-0.004	-0.010	13.283	-0.099	-0.099	0.000	0.000	0.000	0.000
90	A	95	GLY	0	0.044	0.016	15.930	0.054	0.054	0.000	0.000	0.000	0.000
91	A	96	GLY	0	-0.011	-0.018	17.141	-0.038	-0.038	0.000	0.000	0.000	0.000
92	A	97	PHE	0	-0.003	0.002	17.711	0.010	0.010	0.000	0.000	0.000	0.000
93	A	98	THR	0	-0.027	-0.018	21.519	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	99	ASN	0	0.043	-0.007	24.999	0.003	0.003	0.000	0.000	0.000	0.000
95	A	100	SER	0	0.014	-0.014	27.607	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	101	ALA	0	0.037	0.014	31.378	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	102	SER	0	-0.037	-0.024	33.934	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	103	LEU	0	0.040	0.026	33.837	0.003	0.003	0.000	0.000	0.000	0.000
99	A	104	ASN	0	0.037	-0.011	29.793	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	105	GLY	0	-0.012	0.006	32.072	0.007	0.007	0.000	0.000	0.000	0.000
101	A	106	ASP	-1	-0.822	-0.926	33.528	0.036	0.036	0.000	0.000	0.000	0.000
102	A	107	LYN	0	-0.020	0.017	28.681	0.002	0.002	0.000	0.000	0.000	0.000
103	A	108	LEU	0	-0.007	0.006	28.517	0.009	0.009	0.000	0.000	0.000	0.000
104	A	109	ASN	0	-0.003	-0.006	29.256	0.015	0.015	0.000	0.000	0.000	0.000
105	A	110	THR	0	-0.011	-0.026	26.885	0.005	0.005	0.000	0.000	0.000	0.000
106	A	111	LEU	0	-0.005	-0.003	23.141	0.005	0.005	0.000	0.000	0.000	0.000
107	A	112	GLN	0	-0.003	-0.006	25.318	0.008	0.008	0.000	0.000	0.000	0.000
108	A	113	TYR	0	0.029	0.015	27.568	0.005	0.005	0.000	0.000	0.000	0.000
109	A	114	LEU	0	-0.006	-0.002	22.141	0.004	0.004	0.000	0.000	0.000	0.000
110	A	115	VAL	0	-0.005	0.004	22.959	0.016	0.016	0.000	0.000	0.000	0.000
111	A	116	LEU	0	-0.028	-0.015	23.986	0.014	0.014	0.000	0.000	0.000	0.000
112	A	117	LEU	0	-0.024	0.006	23.440	0.004	0.004	0.000	0.000	0.000	0.000
113	A	118	ALA	0	0.013	-0.003	19.896	0.001	0.001	0.000	0.000	0.000	0.000
114	A	119	GLY	0	0.007	0.006	21.432	0.018	0.018	0.000	0.000	0.000	0.000
115	A	120	GLN	0	-0.048	-0.023	23.590	0.002	0.002	0.000	0.000	0.000	0.000
116	A	121	HIS	1	0.781	0.868	20.634	-0.118	-0.118	0.000	0.000	0.000	0.000
117	A	122	GLY	0	0.038	0.045	21.111	0.006	0.006	0.000	0.000	0.000	0.000
118	A	123	GLY	0	0.024	0.014	17.827	0.032	0.032	0.000	0.000	0.000	0.000
119	A	124	LEU	0	-0.044	-0.021	15.032	-0.032	-0.032	0.000	0.000	0.000	0.000
120	A	125	TRP	0	-0.022	-0.021	16.107	0.037	0.037	0.000	0.000	0.000	0.000
121	A	126	VAL	0	0.001	0.011	13.558	0.024	0.024	0.000	0.000	0.000	0.000
122	A	127	SER	0	0.010	0.019	16.998	-0.034	-0.034	0.000	0.000	0.000	0.000
123	A	128	LEU	0	0.020	0.012	18.083	0.040	0.040	0.000	0.000	0.000	0.000
124	A	129	GLY	0	-0.024	-0.008	18.657	0.013	0.013	0.000	0.000	0.000	0.000
125	A	149	TYR	0	0.045	0.005	24.313	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	150	ILE	0	0.011	0.008	23.000	0.026	0.026	0.000	0.000	0.000	0.000
127	A	151	ALA	0	0.044	0.023	20.607	0.028	0.028	0.000	0.000	0.000	0.000
128	A	152	PRO	0	-0.028	0.008	18.971	-0.013	-0.013	0.000	0.000	0.000	0.000
129	A	153	MET	0	-0.042	-0.013	22.153	-0.009	-0.009	0.000	0.000	0.000	0.000
130	A	154	ALA	0	0.014	0.012	24.806	0.001	0.001	0.000	0.000	0.000	0.000
131	A	155	GLN	0	-0.015	-0.011	26.780	0.004	0.004	0.000	0.000	0.000	0.000
132	A	156	SER	0	-0.016	-0.002	29.134	-0.009	-0.009	0.000	0.000	0.000	0.000
133	A	164	GLU	-1	-0.947	-0.974	28.110	-0.074	-0.074	0.000	0.000	0.000	0.000
134	A	165	MET	0	-0.019	-0.004	24.502	0.010	0.010	0.000	0.000	0.000	0.000
135	A	166	SER	0	-0.014	-0.029	26.777	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	167	VAL	0	0.083	0.013	23.390	0.000	0.000	0.000	0.000	0.000	0.000
137	A	168	GLY	0	0.025	0.027	23.128	0.001	0.001	0.000	0.000	0.000	0.000
138	A	169	ASP	-1	-0.820	-0.877	23.210	0.014	0.014	0.000	0.000	0.000	0.000
139	A	170	LEU	0	0.006	0.005	20.809	0.009	0.009	0.000	0.000	0.000	0.000
140	A	171	GLU	-1	-0.780	-0.853	18.434	-0.043	-0.043	0.000	0.000	0.000	0.000
141	A	172	THR	0	-0.069	-0.050	18.208	0.025	0.025	0.000	0.000	0.000	0.000
142	A	173	ALA	0	-0.012	-0.006	18.381	0.038	0.038	0.000	0.000	0.000	0.000
143	A	174	ARG	1	0.872	0.926	13.682	0.143	0.143	0.000	0.000	0.000	0.000
144	A	175	LEU	0	-0.016	-0.020	13.599	0.040	0.040	0.000	0.000	0.000	0.000
145	A	176	TYR	0	-0.067	-0.036	14.048	0.081	0.081	0.000	0.000	0.000	0.000
146	A	177	GLY	0	0.043	0.019	12.734	0.089	0.089	0.000	0.000	0.000	0.000
147	A	178	ALA	0	0.026	0.017	9.421	0.115	0.115	0.000	0.000	0.000	0.000
148	A	179	ARG	1	0.807	0.897	9.491	-0.154	-0.154	0.000	0.000	0.000	0.000
149	A	180	VAL	0	-0.001	-0.007	11.172	0.184	0.184	0.000	0.000	0.000	0.000
150	A	181	ALA	0	0.048	0.033	6.305	0.116	0.116	0.000	0.000	0.000	0.000
151	A	182	ASN	0	-0.018	-0.013	6.474	1.205	1.205	0.000	0.000	0.000	0.000
152	A	183	VAL	0	-0.009	-0.004	7.878	0.281	0.281	0.000	0.000	0.000	0.000
153	A	184	ALA	0	0.011	-0.002	7.100	0.052	0.052	0.000	0.000	0.000	0.000
154	A	185	ARG	1	0.766	0.884	2.571	-7.293	-5.060	1.165	-1.239	-2.160	0.014
155	A	186	GLN	0	-0.060	-0.027	4.900	-0.144	-0.069	-0.001	-0.002	-0.072	0.000
156	A	187	HIS	0	-0.058	-0.028	8.244	-0.276	-0.276	0.000	0.000	0.000	0.000
157	A	188	LYS	1	0.782	0.863	3.777	-1.962	-1.405	0.001	-0.232	-0.326	0.001

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:SER)