FMO DATABASE

FMODB ID: KGVL3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1485157.757512
FMO2-HF: Nuclear repulsion	1426121.287898
FMO2-HF: Total energy	-59036.469614
FMO2-MP2: Total energy	-59209.606076

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.
-14.001	-9.51	1.061	-2.226	-3.326	0.019

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 : -0.003 / q_NPA : -0.024

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	0.008	0.025	3.811	-2.387	-0.984	-0.017	-0.669	-0.718	0.001
4	A	9	THR	0	0.039	0.014	6.969	0.603	0.603	0.000	0.000	0.000	0.000
5	A	10	VAL	0	0.001	0.005	9.883	-0.223	-0.223	0.000	0.000	0.000	0.000
6	A	11	VAL	0	0.000	0.002	13.397	0.110	0.110	0.000	0.000	0.000	0.000
7	A	12	VAL	0	0.013	0.010	16.060	-0.056	-0.056	0.000	0.000	0.000	0.000
8	A	13	TYR	0	-0.041	-0.050	19.460	0.034	0.034	0.000	0.000	0.000	0.000
9	A	14	HIS	0	0.080	0.070	22.395	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	15	SER	0	-0.016	0.008	25.993	0.003	0.003	0.000	0.000	0.000	0.000
11	A	16	GLY	0	0.018	0.022	27.698	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	17	TYR	0	-0.023	-0.036	31.395	0.007	0.007	0.000	0.000	0.000	0.000
13	A	18	GLY	0	0.048	0.025	27.980	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	19	HIS	0	-0.020	-0.011	27.187	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	20	THR	0	-0.010	-0.038	25.020	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	21	HIS	0	0.001	0.009	22.671	0.020	0.020	0.000	0.000	0.000	0.000
17	A	22	ARG	1	0.922	0.957	20.211	0.131	0.131	0.000	0.000	0.000	0.000
18	A	23	MET	0	0.004	0.007	21.293	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	24	ALA	0	0.019	0.011	18.956	0.012	0.012	0.000	0.000	0.000	0.000
20	A	25	GLU	-1	-0.821	-0.890	17.263	-0.187	-0.187	0.000	0.000	0.000	0.000
21	A	26	ALA	0	0.009	0.018	16.484	-0.034	-0.034	0.000	0.000	0.000	0.000
22	A	27	VAL	0	-0.019	-0.010	14.623	0.008	0.008	0.000	0.000	0.000	0.000
23	A	28	ALA	0	-0.018	-0.029	13.083	0.032	0.032	0.000	0.000	0.000	0.000
24	A	29	GLU	-1	-0.921	-0.958	11.715	-0.318	-0.318	0.000	0.000	0.000	0.000
25	A	30	GLY	0	-0.012	-0.010	11.326	-0.077	-0.077	0.000	0.000	0.000	0.000
26	A	31	ALA	0	-0.106	-0.059	9.018	0.092	0.092	0.000	0.000	0.000	0.000
27	A	32	GLU	-1	-0.975	-0.983	5.689	-2.009	-2.009	0.000	0.000	0.000	0.000
28	A	33	ALA	0	-0.067	-0.017	8.272	-0.182	-0.182	0.000	0.000	0.000	0.000
29	A	34	THR	0	0.001	0.002	10.718	-0.038	-0.038	0.000	0.000	0.000	0.000
30	A	35	LEU	0	-0.012	-0.012	13.300	0.106	0.106	0.000	0.000	0.000	0.000
31	A	36	HIS	0	-0.012	-0.006	16.382	0.001	0.001	0.000	0.000	0.000	0.000
32	A	37	ALA	0	0.006	0.011	19.559	0.034	0.034	0.000	0.000	0.000	0.000
33	A	38	ILE	0	-0.038	-0.016	23.163	0.000	0.000	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.746	-0.880	25.859	-0.039	-0.039	0.000	0.000	0.000	0.000
35	A	40	ALA	0	-0.015	-0.028	28.884	0.013	0.013	0.000	0.000	0.000	0.000
36	A	41	GLU	-1	-0.927	-0.960	32.065	-0.022	-0.022	0.000	0.000	0.000	0.000
37	A	42	GLY	0	0.012	0.007	29.902	0.008	0.008	0.000	0.000	0.000	0.000
38	A	43	ASN	0	-0.078	-0.038	28.994	0.021	0.021	0.000	0.000	0.000	0.000
39	A	44	LEU	0	0.006	0.012	21.070	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	45	SER	0	0.011	-0.021	23.069	0.009	0.009	0.000	0.000	0.000	0.000
41	A	46	GLU	-1	-0.904	-0.966	23.183	-0.054	-0.054	0.000	0.000	0.000	0.000
42	A	47	ASP	-1	-0.841	-0.900	19.790	-0.163	-0.163	0.000	0.000	0.000	0.000
43	A	48	GLY	0	0.015	0.010	18.622	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	49	TRP	0	-0.058	-0.038	18.635	0.034	0.034	0.000	0.000	0.000	0.000
45	A	50	ALA	0	-0.006	0.000	17.841	0.038	0.038	0.000	0.000	0.000	0.000
46	A	51	ALA	0	0.004	0.007	14.608	0.020	0.020	0.000	0.000	0.000	0.000
47	A	52	LEU	0	-0.017	-0.015	14.159	0.043	0.043	0.000	0.000	0.000	0.000
48	A	53	ASP	-1	-0.834	-0.934	15.194	0.235	0.235	0.000	0.000	0.000	0.000
49	A	54	ALA	0	-0.055	-0.017	11.847	0.082	0.082	0.000	0.000	0.000	0.000
50	A	55	ALA	0	-0.027	0.005	10.514	0.022	0.022	0.000	0.000	0.000	0.000
51	A	56	ASP	-1	-0.745	-0.872	6.133	2.186	2.186	0.000	0.000	0.000	0.000
52	A	57	ALA	0	-0.023	-0.020	9.314	0.110	0.110	0.000	0.000	0.000	0.000
53	A	58	ILE	0	-0.005	0.014	11.306	-0.165	-0.165	0.000	0.000	0.000	0.000
54	A	59	ILE	0	-0.025	-0.013	12.733	0.042	0.042	0.000	0.000	0.000	0.000
55	A	60	PHE	0	0.008	-0.001	16.538	-0.057	-0.057	0.000	0.000	0.000	0.000
56	A	61	GLY	0	0.048	0.013	20.240	0.010	0.010	0.000	0.000	0.000	0.000
57	A	62	THR	0	-0.028	-0.025	22.219	-0.017	-0.017	0.000	0.000	0.000	0.000
58	A	63	PRO	0	0.016	0.033	26.008	0.008	0.008	0.000	0.000	0.000	0.000
59	A	64	THR	0	-0.003	0.021	29.082	0.012	0.012	0.000	0.000	0.000	0.000
60	A	65	TYR	0	-0.037	-0.037	31.546	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	66	MET	0	-0.003	-0.011	34.807	0.003	0.003	0.000	0.000	0.000	0.000
62	A	67	GLY	0	0.071	0.045	36.049	0.002	0.002	0.000	0.000	0.000	0.000
63	A	68	GLY	0	0.005	0.017	32.802	0.009	0.009	0.000	0.000	0.000	0.000
64	A	69	PRO	0	0.010	0.020	28.758	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	70	SER	0	-0.019	-0.014	29.963	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	71	TRP	0	0.061	0.011	31.336	0.007	0.007	0.000	0.000	0.000	0.000
67	A	72	GLN	0	-0.028	-0.007	30.187	0.010	0.010	0.000	0.000	0.000	0.000
68	A	73	PHE	0	0.038	0.015	23.218	0.002	0.002	0.000	0.000	0.000	0.000
69	A	74	LYS	1	0.831	0.902	27.825	-0.079	-0.079	0.000	0.000	0.000	0.000
70	A	75	LYS	1	0.826	0.907	30.107	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	76	PHE	0	0.044	0.024	21.334	0.001	0.001	0.000	0.000	0.000	0.000
72	A	77	ALA	0	0.025	0.004	25.901	0.010	0.010	0.000	0.000	0.000	0.000
73	A	78	ASP	-1	-0.811	-0.873	26.960	0.097	0.097	0.000	0.000	0.000	0.000
74	A	79	ALA	0	-0.007	0.016	27.762	0.005	0.005	0.000	0.000	0.000	0.000
75	A	80	SER	0	-0.030	-0.032	23.519	0.011	0.011	0.000	0.000	0.000	0.000
76	A	81	SER	0	-0.013	-0.036	25.393	0.019	0.019	0.000	0.000	0.000	0.000
77	A	82	LYS	1	0.985	0.993	25.348	-0.043	-0.043	0.000	0.000	0.000	0.000
78	A	83	PRO	0	-0.015	-0.006	21.736	0.006	0.006	0.000	0.000	0.000	0.000
79	A	84	TRP	0	-0.059	-0.013	23.301	0.012	0.012	0.000	0.000	0.000	0.000
80	A	85	PHE	0	0.004	0.014	25.014	0.011	0.011	0.000	0.000	0.000	0.000
81	A	86	SER	0	-0.061	-0.039	24.082	0.002	0.002	0.000	0.000	0.000	0.000
82	A	87	ALA	0	0.019	0.009	22.543	0.015	0.015	0.000	0.000	0.000	0.000
83	A	88	LYS	1	0.906	0.965	19.234	-0.147	-0.147	0.000	0.000	0.000	0.000
84	A	89	TRP	0	-0.070	-0.072	17.171	0.027	0.027	0.000	0.000	0.000	0.000
85	A	90	GLN	0	-0.037	-0.007	17.498	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	91	ASP	-1	-0.901	-0.953	15.621	0.615	0.615	0.000	0.000	0.000	0.000
87	A	92	LYS	1	0.785	0.915	12.967	-0.381	-0.381	0.000	0.000	0.000	0.000
88	A	93	VAL	0	-0.007	0.001	10.846	-0.079	-0.079	0.000	0.000	0.000	0.000
89	A	94	PHE	0	0.030	0.010	13.259	-0.072	-0.072	0.000	0.000	0.000	0.000
90	A	95	GLY	0	0.036	0.010	15.968	0.046	0.046	0.000	0.000	0.000	0.000
91	A	96	GLY	0	-0.028	-0.025	17.449	-0.038	-0.038	0.000	0.000	0.000	0.000
92	A	97	PHE	0	-0.010	0.000	18.343	0.004	0.004	0.000	0.000	0.000	0.000
93	A	98	THR	0	-0.023	-0.028	22.187	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	99	ASN	0	0.037	-0.007	25.683	0.002	0.002	0.000	0.000	0.000	0.000
95	A	100	SER	0	-0.028	-0.035	28.064	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	101	ALA	0	0.060	0.021	31.797	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	102	SER	0	-0.048	-0.036	34.513	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	103	LEU	0	0.067	0.061	34.637	0.003	0.003	0.000	0.000	0.000	0.000
99	A	104	ASN	0	-0.013	-0.022	30.451	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	105	GLY	0	-0.018	-0.020	33.007	0.007	0.007	0.000	0.000	0.000	0.000
101	A	106	ASP	-1	-0.818	-0.924	34.036	0.070	0.070	0.000	0.000	0.000	0.000
102	A	107	LYN	0	-0.053	0.020	29.356	0.005	0.005	0.000	0.000	0.000	0.000
103	A	108	LEU	0	0.005	0.006	29.006	0.011	0.011	0.000	0.000	0.000	0.000
104	A	109	ASN	0	-0.005	-0.016	29.875	0.019	0.019	0.000	0.000	0.000	0.000
105	A	110	THR	0	-0.016	-0.027	27.303	0.007	0.007	0.000	0.000	0.000	0.000
106	A	111	LEU	0	-0.006	-0.003	23.882	0.011	0.011	0.000	0.000	0.000	0.000
107	A	112	GLN	0	0.005	-0.010	25.597	0.013	0.013	0.000	0.000	0.000	0.000
108	A	113	TYR	0	0.033	0.016	27.613	0.008	0.008	0.000	0.000	0.000	0.000
109	A	114	LEU	0	-0.006	-0.002	22.706	0.009	0.009	0.000	0.000	0.000	0.000
110	A	115	VAL	0	-0.009	0.005	22.897	0.024	0.024	0.000	0.000	0.000	0.000
111	A	116	LEU	0	-0.023	-0.011	23.889	0.019	0.019	0.000	0.000	0.000	0.000
112	A	117	LEU	0	-0.034	0.008	23.283	0.007	0.007	0.000	0.000	0.000	0.000
113	A	118	ALA	0	0.024	-0.006	19.827	0.006	0.006	0.000	0.000	0.000	0.000
114	A	119	GLY	0	0.022	0.016	21.281	0.026	0.026	0.000	0.000	0.000	0.000
115	A	120	GLN	0	-0.047	-0.014	23.537	0.004	0.004	0.000	0.000	0.000	0.000
116	A	121	HIS	1	0.791	0.880	20.484	-0.242	-0.242	0.000	0.000	0.000	0.000
117	A	122	GLY	0	0.028	0.032	20.712	0.021	0.021	0.000	0.000	0.000	0.000
118	A	123	GLY	0	0.022	0.017	17.560	0.046	0.046	0.000	0.000	0.000	0.000
119	A	124	LEU	0	-0.042	-0.012	14.556	-0.039	-0.039	0.000	0.000	0.000	0.000
120	A	125	TRP	0	-0.010	-0.009	16.422	0.024	0.024	0.000	0.000	0.000	0.000
121	A	126	VAL	0	0.014	0.014	13.566	0.018	0.018	0.000	0.000	0.000	0.000
122	A	127	SER	0	0.008	0.024	17.012	-0.039	-0.039	0.000	0.000	0.000	0.000
123	A	128	LEU	0	-0.011	-0.006	18.412	0.047	0.047	0.000	0.000	0.000	0.000
124	A	129	GLY	0	-0.018	-0.005	18.284	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	149	TYR	0	0.043	0.001	24.700	-0.008	-0.008	0.000	0.000	0.000	0.000
126	A	150	ILE	0	0.029	0.014	23.331	0.028	0.028	0.000	0.000	0.000	0.000
127	A	151	ALA	0	0.025	0.006	21.007	0.038	0.038	0.000	0.000	0.000	0.000
128	A	152	PRO	0	-0.024	0.011	19.581	-0.021	-0.021	0.000	0.000	0.000	0.000
129	A	153	MET	0	-0.010	-0.006	22.741	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	154	ALA	0	0.018	0.020	25.620	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	155	GLN	0	0.053	0.022	27.618	0.004	0.004	0.000	0.000	0.000	0.000
132	A	156	SER	0	-0.031	-0.010	29.905	-0.010	-0.010	0.000	0.000	0.000	0.000
133	A	164	GLU	-1	-0.948	-0.977	28.668	-0.062	-0.062	0.000	0.000	0.000	0.000
134	A	165	MET	0	-0.018	-0.020	25.399	0.011	0.011	0.000	0.000	0.000	0.000
135	A	166	SER	0	-0.050	-0.040	27.798	-0.011	-0.011	0.000	0.000	0.000	0.000
136	A	167	VAL	0	0.098	0.024	23.798	0.002	0.002	0.000	0.000	0.000	0.000
137	A	168	GLY	0	0.030	0.027	23.734	0.003	0.003	0.000	0.000	0.000	0.000
138	A	169	ASP	-1	-0.844	-0.897	23.845	0.044	0.044	0.000	0.000	0.000	0.000
139	A	170	LEU	0	-0.001	-0.002	21.496	0.012	0.012	0.000	0.000	0.000	0.000
140	A	171	GLU	-1	-0.776	-0.855	18.877	-0.023	-0.023	0.000	0.000	0.000	0.000
141	A	172	THR	0	-0.060	-0.037	18.724	0.025	0.025	0.000	0.000	0.000	0.000
142	A	173	ALA	0	-0.031	-0.014	18.778	0.042	0.042	0.000	0.000	0.000	0.000
143	A	174	ARG	1	0.874	0.916	13.901	0.119	0.119	0.000	0.000	0.000	0.000
144	A	175	LEU	0	-0.024	-0.015	14.081	0.042	0.042	0.000	0.000	0.000	0.000
145	A	176	TYR	0	-0.055	-0.040	14.271	0.088	0.088	0.000	0.000	0.000	0.000
146	A	177	GLY	0	0.037	0.024	13.121	0.101	0.101	0.000	0.000	0.000	0.000
147	A	178	ALA	0	0.040	0.025	9.766	0.122	0.122	0.000	0.000	0.000	0.000
148	A	179	ARG	1	0.803	0.893	9.904	-0.229	-0.229	0.000	0.000	0.000	0.000
149	A	180	VAL	0	-0.002	-0.007	11.364	0.175	0.175	0.000	0.000	0.000	0.000
150	A	181	ALA	0	0.037	0.035	6.426	0.224	0.224	0.000	0.000	0.000	0.000
151	A	182	ASN	0	-0.012	-0.016	6.921	1.138	1.138	0.000	0.000	0.000	0.000
152	A	183	VAL	0	-0.004	-0.001	8.073	0.299	0.299	0.000	0.000	0.000	0.000
153	A	184	ALA	0	0.011	0.002	7.208	0.088	0.088	0.000	0.000	0.000	0.000
154	A	185	ARG	1	0.857	0.933	2.572	-7.315	-5.419	1.033	-1.037	-1.892	0.013
155	A	186	GLN	0	-0.087	-0.032	4.931	0.009	0.079	-0.001	-0.001	-0.067	0.000
156	A	187	HIS	0	-0.028	-0.016	7.872	-0.398	-0.398	0.000	0.000	0.000	0.000
157	A	188	LYS	1	0.835	0.937	3.217	-6.619	-5.497	0.046	-0.519	-0.649	0.005

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