FMO DATABASE

FMODB ID: YVR42

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1309983.517177
FMO2-HF: Nuclear repulsion	1254105.88334
FMO2-HF: Total energy	-55877.633837
FMO2-MP2: Total energy	-56039.996745

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.
-4.117	-1.495	-0.011	-1.269	-1.342	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 : 0.004 / q_NPA : -0.010

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	0.037	0.032	3.820	-2.154	0.152	-0.016	-1.195	-1.094	0.005
4	A	5	PHE	0	-0.022	-0.001	6.759	0.721	0.721	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.850	-0.906	7.833	-1.227	-1.227	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.890	-0.968	9.935	-0.417	-0.417	0.000	0.000	0.000	0.000
7	A	8	VAL	0	-0.035	-0.010	12.895	-0.043	-0.043	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.807	-0.879	15.361	-0.310	-0.310	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.019	-0.018	19.035	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.885	-0.946	21.736	-0.222	-0.222	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.010	-0.008	25.361	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	13	TYR	0	0.028	0.028	28.674	0.004	0.004	0.000	0.000	0.000	0.000
13	A	14	VAL	0	-0.025	-0.016	31.530	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	15	TYR	0	0.052	0.005	34.073	0.004	0.004	0.000	0.000	0.000	0.000
15	A	16	PRO	0	0.058	0.029	37.789	0.001	0.001	0.000	0.000	0.000	0.000
16	A	17	THR	0	-0.010	-0.003	40.638	0.003	0.003	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.879	-0.910	34.948	-0.150	-0.150	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.804	-0.896	35.376	-0.107	-0.107	0.000	0.000	0.000	0.000
19	A	20	ILE	0	0.064	0.015	31.133	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.956	0.967	30.879	0.087	0.087	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.883	0.937	30.335	0.101	0.101	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.060	0.034	28.969	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.969	0.988	26.667	0.144	0.144	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.845	0.930	24.580	0.178	0.178	0.000	0.000	0.000	0.000
25	A	26	ALA	0	0.037	0.013	25.951	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	27	MET	0	-0.008	0.014	23.370	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.040	-0.017	20.783	-0.029	-0.029	0.000	0.000	0.000	0.000
28	A	29	ASN	0	-0.115	-0.051	21.243	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.027	0.006	20.891	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	31	ILE	0	0.017	0.002	15.912	-0.058	-0.058	0.000	0.000	0.000	0.000
31	A	32	PRO	0	0.002	-0.004	16.184	0.043	0.043	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.002	-0.004	16.424	-0.041	-0.041	0.000	0.000	0.000	0.000
33	A	34	LEU	0	-0.052	-0.005	17.422	0.000	0.000	0.000	0.000	0.000	0.000
34	A	35	GLN	0	-0.046	-0.025	18.118	0.065	0.065	0.000	0.000	0.000	0.000
35	A	36	PHE	0	-0.002	-0.038	20.737	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.914	-0.938	24.016	-0.193	-0.193	0.000	0.000	0.000	0.000
37	A	38	ALA	0	-0.040	-0.034	26.449	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	39	PHE	0	-0.013	0.000	26.810	0.012	0.012	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.849	-0.926	32.162	-0.110	-0.110	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.900	0.950	33.169	0.141	0.141	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.014	0.020	37.464	0.003	0.003	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.963	-0.982	39.738	-0.111	-0.111	0.000	0.000	0.000	0.000
43	A	44	TYR	0	-0.059	-0.040	34.043	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	45	VAL	0	-0.014	0.006	32.375	0.002	0.002	0.000	0.000	0.000	0.000
45	A	46	ILE	0	-0.005	0.004	28.620	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.064	-0.037	27.263	0.007	0.007	0.000	0.000	0.000	0.000
47	A	48	VAL	0	0.062	0.020	22.722	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.030	-0.014	21.739	0.018	0.018	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.854	0.906	17.842	0.308	0.308	0.000	0.000	0.000	0.000
50	A	51	THR	0	0.022	-0.005	13.843	0.024	0.024	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.967	0.993	10.911	0.433	0.433	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.883	-0.925	9.325	-0.665	-0.665	0.000	0.000	0.000	0.000
53	A	54	LYS	1	1.012	0.991	3.500	-1.495	-1.179	0.005	-0.074	-0.248	0.000
54	A	55	ARG	1	0.910	0.942	7.137	-0.175	-0.175	0.000	0.000	0.000	0.000
55	A	56	ALA	0	0.005	0.012	9.651	0.118	0.118	0.000	0.000	0.000	0.000
56	A	57	LEU	0	0.031	0.018	10.937	0.108	0.108	0.000	0.000	0.000	0.000
57	A	58	GLN	0	-0.067	-0.034	11.522	-0.088	-0.088	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.906	0.947	12.977	0.379	0.379	0.000	0.000	0.000	0.000
59	A	60	LEU	0	0.068	0.024	15.948	0.043	0.043	0.000	0.000	0.000	0.000
60	A	61	TYR	0	0.007	0.008	11.958	0.120	0.120	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.849	-0.902	15.365	-0.331	-0.331	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.052	-0.025	17.753	0.050	0.050	0.000	0.000	0.000	0.000
63	A	64	PHE	0	0.048	0.009	18.025	0.037	0.037	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.796	0.908	14.768	0.656	0.656	0.000	0.000	0.000	0.000
65	A	66	GLY	0	0.004	0.003	20.785	0.032	0.032	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.062	-0.043	23.238	0.018	0.018	0.000	0.000	0.000	0.000
67	A	68	GLN	0	-0.025	0.001	24.197	0.019	0.019	0.000	0.000	0.000	0.000
68	A	69	ILE	0	0.015	0.011	23.353	0.013	0.013	0.000	0.000	0.000	0.000
69	A	70	LEU	0	0.010	0.000	18.977	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.774	-0.859	22.346	-0.299	-0.299	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.003	-0.001	24.952	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	73	ALA	0	-0.007	-0.007	20.678	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.680	0.798	18.831	0.455	0.455	0.000	0.000	0.000	0.000
74	A	75	MET	0	-0.015	-0.004	21.708	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	76	MET	0	0.020	0.010	23.773	0.008	0.008	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.052	-0.032	17.352	-0.017	-0.017	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.823	-0.927	20.757	-0.456	-0.456	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.949	-0.966	22.613	-0.246	-0.246	0.000	0.000	0.000	0.000
79	A	80	GLY	0	-0.010	0.007	23.072	0.019	0.019	0.000	0.000	0.000	0.000
80	A	81	TYR	0	-0.093	-0.043	17.661	-0.030	-0.030	0.000	0.000	0.000	0.000
81	A	82	PHE	0	0.022	0.011	20.695	0.039	0.039	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.000	0.004	20.162	-0.015	-0.015	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.893	-0.952	14.491	-0.607	-0.607	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.913	-0.966	15.717	-0.527	-0.527	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.032	-0.011	15.330	0.011	0.011	0.000	0.000	0.000	0.000
86	A	87	ILE	0	-0.056	-0.015	18.936	-0.026	-0.026	0.000	0.000	0.000	0.000
87	A	88	ILE	0	0.023	0.013	20.125	0.018	0.018	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.888	0.947	23.285	0.253	0.253	0.000	0.000	0.000	0.000
89	A	90	VAL	0	0.012	-0.002	23.890	0.002	0.002	0.000	0.000	0.000	0.000
90	A	91	HIS	0	0.068	0.021	26.967	0.008	0.008	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.792	0.881	29.035	0.160	0.160	0.000	0.000	0.000	0.000
92	A	93	GLN	0	-0.019	-0.022	30.344	0.002	0.002	0.000	0.000	0.000	0.000
93	A	94	VAL	0	-0.021	-0.019	28.818	0.005	0.005	0.000	0.000	0.000	0.000
94	A	95	ALA	0	0.058	0.045	26.192	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	96	TYR	0	-0.033	-0.009	27.287	0.001	0.001	0.000	0.000	0.000	0.000
96	A	97	VAL	0	-0.040	-0.017	29.833	0.008	0.008	0.000	0.000	0.000	0.000
97	A	98	GLY	0	-0.047	-0.016	25.886	0.004	0.004	0.000	0.000	0.000	0.000
98	A	99	LYS	1	0.873	0.938	25.083	0.200	0.200	0.000	0.000	0.000	0.000
99	A	100	VAL	0	0.036	0.006	21.881	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	101	ASN	0	0.023	0.003	25.322	0.009	0.009	0.000	0.000	0.000	0.000
101	A	102	PHE	0	0.070	0.028	22.315	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	103	ASN	0	-0.047	-0.013	28.226	0.008	0.008	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.858	-0.954	30.281	-0.229	-0.229	0.000	0.000	0.000	0.000
104	A	105	ASP	-1	-0.855	-0.925	32.937	-0.143	-0.143	0.000	0.000	0.000	0.000
105	A	106	SER	0	-0.034	-0.019	32.524	0.004	0.004	0.000	0.000	0.000	0.000
106	A	107	PRO	0	-0.036	-0.036	34.634	0.004	0.004	0.000	0.000	0.000	0.000
107	A	108	LEU	0	0.015	0.008	35.538	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	109	GLY	0	0.047	0.054	33.475	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	110	PRO	0	0.014	0.030	29.168	0.002	0.002	0.000	0.000	0.000	0.000
110	A	111	ILE	0	-0.051	-0.031	24.545	0.004	0.004	0.000	0.000	0.000	0.000
111	A	112	THR	0	-0.003	0.010	24.094	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	113	ILE	0	-0.037	-0.020	18.602	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	114	THR	0	0.083	0.035	18.660	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	115	ILE	0	-0.054	-0.027	13.368	-0.054	-0.054	0.000	0.000	0.000	0.000
115	A	116	ARG	1	0.927	0.964	12.590	0.654	0.654	0.000	0.000	0.000	0.000
116	A	117	THR	0	-0.045	-0.064	10.279	-0.159	-0.159	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.927	0.969	9.027	0.965	0.965	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.866	-0.920	7.159	-1.932	-1.932	0.000	0.000	0.000	0.000
119	A	120	PRO	0	0.071	0.043	11.021	-0.173	-0.173	0.000	0.000	0.000	0.000
120	A	121	GLN	0	0.040	0.015	13.914	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.848	0.901	7.370	1.534	1.534	0.000	0.000	0.000	0.000
122	A	123	LEU	0	0.010	0.022	10.588	-0.064	-0.064	0.000	0.000	0.000	0.000
123	A	124	MET	0	0.027	0.015	11.940	0.037	0.037	0.000	0.000	0.000	0.000
124	A	125	LYS	1	0.846	0.933	14.025	0.561	0.561	0.000	0.000	0.000	0.000
125	A	126	TRP	0	-0.012	0.006	8.841	-0.018	-0.018	0.000	0.000	0.000	0.000
126	A	127	LEU	0	-0.010	-0.014	12.497	0.081	0.081	0.000	0.000	0.000	0.000
127	A	128	ALA	0	-0.026	-0.012	14.170	0.090	0.090	0.000	0.000	0.000	0.000
128	A	129	PRO	0	0.007	0.030	15.901	0.039	0.039	0.000	0.000	0.000	0.000
129	A	130	ARG	1	0.850	0.897	18.241	0.334	0.334	0.000	0.000	0.000	0.000
130	A	131	THR	0	-0.042	-0.030	20.889	0.009	0.009	0.000	0.000	0.000	0.000
131	A	132	LYS	1	0.892	0.927	23.547	0.161	0.161	0.000	0.000	0.000	0.000
132	A	133	ASP	-1	-0.826	-0.895	26.913	-0.148	-0.148	0.000	0.000	0.000	0.000
133	A	134	GLY	0	0.006	0.005	23.421	0.008	0.008	0.000	0.000	0.000	0.000
134	A	135	VAL	0	-0.025	-0.012	22.425	-0.019	-0.019	0.000	0.000	0.000	0.000
135	A	136	PRO	0	-0.007	-0.007	19.562	-0.006	-0.006	0.000	0.000	0.000	0.000
136	A	137	ILE	0	-0.020	-0.006	21.703	0.028	0.028	0.000	0.000	0.000	0.000
137	A	138	GLU	-1	-0.737	-0.835	18.753	-0.461	-0.461	0.000	0.000	0.000	0.000

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