FMO DATABASE

FMODB ID: VQY91

Calculation Name: 3D7A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D7A

Chain ID: A

ChEMBL ID:

UniProt ID: O58738

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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1311649.301694
FMO2-HF: Nuclear repulsion	1255771.207862
FMO2-HF: Total energy	-55878.093833
FMO2-MP2: Total energy	-56040.434898

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:2:MET)

Summations of interaction energy for fragment #1(A:2: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.
-1.551	1.078	-0.011	-1.297	-1.322	0.005

Interaction energy analysis for fragmet #1(A:2:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.000

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	4	MET	0	0.033	0.036	3.877	-1.609	0.785	-0.013	-1.256	-1.126	0.005
4	A	5	PHE	0	-0.020	0.003	6.720	0.663	0.663	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.799	-0.873	7.820	-1.063	-1.063	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.861	-0.918	9.838	-0.353	-0.353	0.000	0.000	0.000	0.000
7	A	8	VAL	0	-0.036	-0.007	12.602	-0.058	-0.058	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.807	-0.876	15.031	-0.320	-0.320	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.022	-0.023	18.644	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.875	-0.941	21.565	-0.219	-0.219	0.000	0.000	0.000	0.000
11	A	12	ALA	0	-0.003	-0.017	25.257	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	13	TYR	0	0.046	0.035	28.515	0.005	0.005	0.000	0.000	0.000	0.000
13	A	14	VAL	0	-0.040	-0.019	31.512	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	15	TYR	0	0.076	0.032	34.154	0.004	0.004	0.000	0.000	0.000	0.000
15	A	16	PRO	0	0.020	-0.003	37.918	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	17	THR	0	-0.010	0.006	40.398	0.004	0.004	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.837	-0.891	35.058	-0.159	-0.159	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.803	-0.893	35.307	-0.128	-0.128	0.000	0.000	0.000	0.000
19	A	20	ILE	0	0.083	0.026	31.029	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.899	0.942	30.637	0.106	0.106	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.875	0.934	30.042	0.117	0.117	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.079	0.046	28.946	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.972	0.994	26.516	0.172	0.172	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.833	0.923	24.184	0.224	0.224	0.000	0.000	0.000	0.000
25	A	26	ALA	0	0.038	0.023	25.724	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	27	MET	0	-0.004	0.019	23.314	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.032	-0.022	20.643	-0.033	-0.033	0.000	0.000	0.000	0.000
28	A	29	ASN	0	-0.131	-0.062	21.477	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.031	-0.002	20.883	-0.011	-0.011	0.000	0.000	0.000	0.000
30	A	31	ILE	0	0.019	0.007	15.832	-0.065	-0.065	0.000	0.000	0.000	0.000
31	A	32	PRO	0	0.005	-0.006	15.862	0.049	0.049	0.000	0.000	0.000	0.000
32	A	33	GLY	0	-0.004	-0.011	16.444	-0.047	-0.047	0.000	0.000	0.000	0.000
33	A	34	LEU	0	-0.042	0.005	17.551	0.007	0.007	0.000	0.000	0.000	0.000
34	A	35	GLN	0	-0.030	-0.018	17.892	0.071	0.071	0.000	0.000	0.000	0.000
35	A	36	PHE	0	-0.004	-0.037	20.530	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.850	-0.901	23.464	-0.212	-0.212	0.000	0.000	0.000	0.000
37	A	38	ALA	0	-0.043	-0.042	26.037	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	39	PHE	0	-0.005	0.001	26.424	0.013	0.013	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.831	-0.917	31.875	-0.116	-0.116	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.844	0.921	33.106	0.142	0.142	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.009	0.027	37.605	0.004	0.004	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.944	-0.980	39.753	-0.112	-0.112	0.000	0.000	0.000	0.000
43	A	44	TYR	0	-0.074	-0.046	33.824	0.000	0.000	0.000	0.000	0.000	0.000
44	A	45	VAL	0	-0.020	-0.003	32.447	0.002	0.002	0.000	0.000	0.000	0.000
45	A	46	ILE	0	0.005	0.010	28.497	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.060	-0.032	27.031	0.005	0.005	0.000	0.000	0.000	0.000
47	A	48	VAL	0	0.068	0.024	22.536	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.031	-0.010	21.670	0.018	0.018	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.806	0.863	17.541	0.307	0.307	0.000	0.000	0.000	0.000
50	A	51	THR	0	-0.006	-0.013	13.824	0.010	0.010	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.903	0.918	10.595	0.554	0.554	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.826	-0.892	8.535	-1.022	-1.022	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.967	0.978	3.856	0.142	0.377	0.002	-0.041	-0.196	0.000
54	A	55	ARG	1	0.897	0.931	7.043	0.373	0.373	0.000	0.000	0.000	0.000
55	A	56	ALA	0	-0.015	0.011	9.612	0.148	0.148	0.000	0.000	0.000	0.000
56	A	57	LEU	0	0.068	0.024	11.177	0.131	0.131	0.000	0.000	0.000	0.000
57	A	58	GLN	0	-0.052	-0.029	11.576	-0.074	-0.074	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.882	0.938	13.104	0.449	0.449	0.000	0.000	0.000	0.000
59	A	60	LEU	0	0.053	0.026	16.257	0.061	0.061	0.000	0.000	0.000	0.000
60	A	61	TYR	0	-0.016	0.001	12.518	0.112	0.112	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.832	-0.893	15.695	-0.421	-0.421	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.039	-0.013	18.121	0.049	0.049	0.000	0.000	0.000	0.000
63	A	64	PHE	0	0.040	-0.004	18.127	0.042	0.042	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.796	0.898	15.379	0.663	0.663	0.000	0.000	0.000	0.000
65	A	66	GLY	0	-0.014	-0.009	21.292	0.034	0.034	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.059	-0.044	23.581	0.016	0.016	0.000	0.000	0.000	0.000
67	A	68	GLN	0	-0.011	-0.002	24.731	0.021	0.021	0.000	0.000	0.000	0.000
68	A	69	ILE	0	0.008	0.019	23.784	0.011	0.011	0.000	0.000	0.000	0.000
69	A	70	LEU	0	0.008	0.003	19.476	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.732	-0.833	22.737	-0.288	-0.288	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.005	0.004	25.104	0.001	0.001	0.000	0.000	0.000	0.000
72	A	73	ALA	0	-0.008	-0.005	21.292	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.679	0.785	18.904	0.415	0.415	0.000	0.000	0.000	0.000
74	A	75	MET	0	-0.021	-0.002	21.970	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	76	MET	0	0.040	0.013	24.259	0.006	0.006	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.056	-0.022	17.856	-0.021	-0.021	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.810	-0.919	20.274	-0.401	-0.401	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.959	-0.981	22.167	-0.223	-0.223	0.000	0.000	0.000	0.000
79	A	80	GLY	0	0.032	0.028	22.803	0.018	0.018	0.000	0.000	0.000	0.000
80	A	81	TYR	0	-0.132	-0.076	17.474	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	82	PHE	0	0.020	0.010	20.285	0.039	0.039	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.036	0.023	19.805	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.883	-0.932	14.168	-0.493	-0.493	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.902	-0.958	15.265	-0.501	-0.501	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.028	-0.009	15.157	0.019	0.019	0.000	0.000	0.000	0.000
86	A	87	ILE	0	-0.048	-0.020	18.506	-0.035	-0.035	0.000	0.000	0.000	0.000
87	A	88	ILE	0	0.011	0.008	20.273	0.018	0.018	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.892	0.944	23.295	0.249	0.249	0.000	0.000	0.000	0.000
89	A	90	VAL	0	0.015	-0.003	24.419	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	91	HIS	0	0.056	0.023	27.420	0.004	0.004	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.774	0.871	29.584	0.168	0.168	0.000	0.000	0.000	0.000
92	A	93	GLN	0	-0.025	-0.013	30.534	0.000	0.000	0.000	0.000	0.000	0.000
93	A	94	VAL	0	-0.013	-0.015	29.092	0.003	0.003	0.000	0.000	0.000	0.000
94	A	95	ALA	0	0.056	0.042	26.415	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	96	TYR	0	-0.019	-0.008	27.331	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	97	VAL	0	-0.046	-0.019	29.657	0.003	0.003	0.000	0.000	0.000	0.000
97	A	98	GLY	0	-0.035	-0.007	26.126	0.002	0.002	0.000	0.000	0.000	0.000
98	A	99	LYS	1	0.864	0.926	25.591	0.227	0.227	0.000	0.000	0.000	0.000
99	A	100	VAL	0	0.049	0.024	22.135	0.000	0.000	0.000	0.000	0.000	0.000
100	A	101	ASN	0	0.019	-0.005	25.497	0.013	0.013	0.000	0.000	0.000	0.000
101	A	102	PHE	0	0.061	0.032	22.872	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	103	ASN	0	-0.077	-0.043	28.661	0.009	0.009	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.780	-0.924	30.074	-0.233	-0.233	0.000	0.000	0.000	0.000
104	A	105	ASP	-1	-0.875	-0.898	33.019	-0.146	-0.146	0.000	0.000	0.000	0.000
105	A	106	SER	0	-0.021	-0.033	32.775	0.002	0.002	0.000	0.000	0.000	0.000
106	A	107	PRO	0	-0.047	-0.043	34.831	0.005	0.005	0.000	0.000	0.000	0.000
107	A	108	LEU	0	0.006	0.010	35.552	-0.008	-0.008	0.000	0.000	0.000	0.000
108	A	109	GLY	0	0.077	0.060	33.616	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	110	PRO	0	-0.007	0.015	29.157	0.000	0.000	0.000	0.000	0.000	0.000
110	A	111	ILE	0	-0.062	-0.032	24.570	0.001	0.001	0.000	0.000	0.000	0.000
111	A	112	THR	0	0.015	0.016	23.994	0.001	0.001	0.000	0.000	0.000	0.000
112	A	113	ILE	0	-0.034	-0.022	18.523	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	114	THR	0	0.075	0.037	18.236	0.009	0.009	0.000	0.000	0.000	0.000
114	A	115	ILE	0	-0.032	-0.014	13.275	-0.063	-0.063	0.000	0.000	0.000	0.000
115	A	116	ARG	1	0.878	0.930	12.289	0.588	0.588	0.000	0.000	0.000	0.000
116	A	117	THR	0	-0.049	-0.062	9.989	-0.132	-0.132	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.907	0.953	9.072	0.742	0.742	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.834	-0.900	6.784	-1.424	-1.424	0.000	0.000	0.000	0.000
119	A	120	PRO	0	0.056	0.036	10.955	-0.120	-0.120	0.000	0.000	0.000	0.000
120	A	121	GLN	0	0.040	0.011	13.787	-0.036	-0.036	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.815	0.891	7.112	1.075	1.075	0.000	0.000	0.000	0.000
122	A	123	LEU	0	0.019	0.013	10.325	-0.089	-0.089	0.000	0.000	0.000	0.000
123	A	124	MET	0	0.012	0.006	11.655	0.007	0.007	0.000	0.000	0.000	0.000
124	A	125	LYS	1	0.834	0.911	14.102	0.457	0.457	0.000	0.000	0.000	0.000
125	A	126	TRP	0	0.002	0.009	9.276	-0.020	-0.020	0.000	0.000	0.000	0.000
126	A	127	LEU	0	-0.003	-0.017	12.692	0.068	0.068	0.000	0.000	0.000	0.000
127	A	128	ALA	0	-0.020	-0.002	14.717	0.068	0.068	0.000	0.000	0.000	0.000
128	A	129	PRO	0	-0.004	0.028	16.282	0.036	0.036	0.000	0.000	0.000	0.000
129	A	130	ARG	1	0.846	0.879	18.560	0.296	0.296	0.000	0.000	0.000	0.000
130	A	131	THR	0	-0.052	-0.033	21.392	0.007	0.007	0.000	0.000	0.000	0.000
131	A	132	LYS	1	0.871	0.915	24.010	0.158	0.158	0.000	0.000	0.000	0.000
132	A	133	ASP	-1	-0.840	-0.904	27.257	-0.148	-0.148	0.000	0.000	0.000	0.000
133	A	134	GLY	0	0.014	0.015	24.074	0.006	0.006	0.000	0.000	0.000	0.000
134	A	135	VAL	0	-0.009	-0.001	22.801	-0.023	-0.023	0.000	0.000	0.000	0.000
135	A	136	PRO	0	0.004	-0.010	19.735	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	137	ILE	0	-0.029	-0.007	22.005	0.029	0.029	0.000	0.000	0.000	0.000
137	A	138	GLU	-1	-0.745	-0.816	19.081	-0.406	-0.406	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:MET)