FMO DATABASE

FMODB ID: QVN8Y

Calculation Name: 3RD6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RD6

Chain ID: A

ChEMBL ID:

UniProt ID: Q98FZ2

Base Structure: X-ray

Registration Date: 2023-09-21

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	147
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1319757.368999
FMO2-HF: Nuclear repulsion	1263460.217086
FMO2-HF: Total energy	-56297.151913
FMO2-MP2: Total energy	-56463.864899

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:3:HIS)

Summations of interaction energy for fragment #1(A:3:HIS)

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.
-151.215	-141.746	10.731	-10.664	-9.537	-0.123

Interaction energy analysis for fragmet #1(A:3:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.910

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	5	VAL	0	0.005	0.007	3.820	-3.321	-0.815	-0.027	-1.363	-1.117	0.003
4	A	6	ILE	0	-0.007	0.022	6.382	2.674	2.674	0.000	0.000	0.000	0.000
5	A	7	HIS	0	0.012	0.001	9.592	1.090	1.090	0.000	0.000	0.000	0.000
6	A	8	SER	0	-0.052	-0.021	12.765	1.086	1.086	0.000	0.000	0.000	0.000
7	A	9	THR	0	0.006	-0.018	16.196	-0.179	-0.179	0.000	0.000	0.000	0.000
8	A	10	PHE	0	0.016	0.030	19.391	0.210	0.210	0.000	0.000	0.000	0.000
9	A	11	THR	0	0.028	-0.002	22.346	-0.146	-0.146	0.000	0.000	0.000	0.000
10	A	12	ILE	0	-0.026	-0.007	25.200	0.158	0.158	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.939	-0.960	28.503	-9.687	-9.687	0.000	0.000	0.000	0.000
12	A	14	ARG	1	0.905	0.943	32.151	9.014	9.014	0.000	0.000	0.000	0.000
13	A	15	THR	0	-0.029	-0.013	34.631	-0.095	-0.095	0.000	0.000	0.000	0.000
14	A	16	TYR	0	-0.034	-0.013	34.147	-0.039	-0.039	0.000	0.000	0.000	0.000
15	A	17	PRO	0	0.012	0.007	40.045	0.075	0.075	0.000	0.000	0.000	0.000
16	A	18	GLN	0	0.035	0.015	41.248	0.025	0.025	0.000	0.000	0.000	0.000
17	A	19	SER	0	0.087	0.042	42.366	-0.115	-0.115	0.000	0.000	0.000	0.000
18	A	20	PRO	0	0.032	-0.003	39.691	-0.129	-0.129	0.000	0.000	0.000	0.000
19	A	21	ASP	-1	-0.871	-0.935	39.545	-7.549	-7.549	0.000	0.000	0.000	0.000
20	A	22	ARG	1	0.810	0.918	39.461	7.713	7.713	0.000	0.000	0.000	0.000
21	A	23	VAL	0	0.035	-0.005	35.442	-0.129	-0.129	0.000	0.000	0.000	0.000
22	A	24	PHE	0	0.031	0.042	34.178	-0.311	-0.311	0.000	0.000	0.000	0.000
23	A	25	HIS	0	0.040	0.032	35.421	-0.283	-0.283	0.000	0.000	0.000	0.000
24	A	26	ALA	0	-0.038	-0.025	35.541	-0.110	-0.110	0.000	0.000	0.000	0.000
25	A	27	PHE	0	-0.028	-0.033	29.161	-0.351	-0.351	0.000	0.000	0.000	0.000
26	A	28	ALA	0	0.008	-0.001	31.790	-0.286	-0.286	0.000	0.000	0.000	0.000
27	A	29	ASP	-1	-0.837	-0.909	34.069	-8.256	-8.256	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.890	0.947	30.945	9.842	9.842	0.000	0.000	0.000	0.000
29	A	31	ALA	0	-0.001	-0.009	33.785	-0.165	-0.165	0.000	0.000	0.000	0.000
30	A	32	THR	0	-0.013	-0.004	35.771	0.002	0.002	0.000	0.000	0.000	0.000
31	A	33	VAL	0	0.008	0.009	29.823	-0.138	-0.138	0.000	0.000	0.000	0.000
32	A	34	ARG	1	0.789	0.901	31.265	9.563	9.563	0.000	0.000	0.000	0.000
33	A	35	ARG	1	0.908	0.988	32.505	8.276	8.276	0.000	0.000	0.000	0.000
34	A	36	TRP	0	-0.024	-0.002	29.832	-0.122	-0.122	0.000	0.000	0.000	0.000
35	A	37	ARG	1	0.841	0.907	25.344	11.391	11.391	0.000	0.000	0.000	0.000
36	A	38	VAL	0	-0.068	-0.027	26.717	-0.407	-0.407	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.830	-0.912	29.209	-9.798	-9.798	0.000	0.000	0.000	0.000
38	A	40	GLY	0	-0.151	-0.100	31.995	0.060	0.060	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.865	-0.948	33.278	-7.927	-7.927	0.000	0.000	0.000	0.000
40	A	42	GLY	0	-0.077	0.002	36.474	-0.103	-0.103	0.000	0.000	0.000	0.000
41	A	43	PHE	0	0.022	-0.034	33.427	0.199	0.199	0.000	0.000	0.000	0.000
42	A	44	THR	0	0.010	0.029	31.153	-0.119	-0.119	0.000	0.000	0.000	0.000
43	A	45	VAL	0	0.011	0.013	29.140	0.110	0.110	0.000	0.000	0.000	0.000
44	A	46	ALA	0	-0.033	-0.025	25.813	-0.112	-0.112	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.867	-0.919	24.713	-12.377	-12.377	0.000	0.000	0.000	0.000
46	A	48	PHE	0	0.026	0.000	26.098	-0.080	-0.080	0.000	0.000	0.000	0.000
47	A	49	SER	0	-0.047	-0.005	26.244	0.730	0.730	0.000	0.000	0.000	0.000
48	A	50	PHE	0	-0.029	-0.019	26.796	-0.352	-0.352	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.866	-0.918	28.448	-9.709	-9.709	0.000	0.000	0.000	0.000
50	A	52	PHE	0	0.014	0.006	29.452	-0.257	-0.257	0.000	0.000	0.000	0.000
51	A	53	ARG	1	0.903	0.942	29.728	10.681	10.681	0.000	0.000	0.000	0.000
52	A	54	VAL	0	0.044	0.034	28.499	-0.395	-0.395	0.000	0.000	0.000	0.000
53	A	55	GLY	0	-0.055	-0.029	26.617	0.258	0.258	0.000	0.000	0.000	0.000
54	A	56	GLY	0	-0.034	-0.009	26.640	-0.195	-0.195	0.000	0.000	0.000	0.000
55	A	57	GLY	0	0.049	0.009	24.415	-0.375	-0.375	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.887	-0.938	23.625	-11.952	-11.952	0.000	0.000	0.000	0.000
57	A	59	VAL	0	-0.014	-0.007	21.510	-0.660	-0.660	0.000	0.000	0.000	0.000
58	A	60	SER	0	0.002	0.013	21.817	0.901	0.901	0.000	0.000	0.000	0.000
59	A	61	ARG	1	0.780	0.859	21.057	12.309	12.309	0.000	0.000	0.000	0.000
60	A	62	PHE	0	0.049	0.025	21.651	0.653	0.653	0.000	0.000	0.000	0.000
61	A	63	SER	0	0.071	0.025	22.072	-0.664	-0.664	0.000	0.000	0.000	0.000
62	A	64	TYR	0	0.017	0.025	23.762	0.574	0.574	0.000	0.000	0.000	0.000
63	A	65	GLY	0	0.016	0.008	25.587	-0.215	-0.215	0.000	0.000	0.000	0.000
64	A	66	GLY	0	-0.008	-0.017	26.345	0.023	0.023	0.000	0.000	0.000	0.000
65	A	67	GLY	0	-0.056	-0.017	22.670	-0.319	-0.319	0.000	0.000	0.000	0.000
66	A	68	PRO	0	-0.001	-0.017	17.465	0.086	0.086	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.858	-0.920	19.281	-14.234	-14.234	0.000	0.000	0.000	0.000
68	A	70	VAL	0	-0.031	-0.023	17.601	-1.171	-1.171	0.000	0.000	0.000	0.000
69	A	71	ARG	1	0.879	0.926	16.744	16.836	16.836	0.000	0.000	0.000	0.000
70	A	72	LEU	0	-0.023	-0.006	16.619	-1.188	-1.188	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.868	-0.931	16.993	-15.690	-15.690	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.025	-0.002	18.121	-0.851	-0.851	0.000	0.000	0.000	0.000
73	A	75	GLN	0	-0.030	-0.010	20.718	0.413	0.413	0.000	0.000	0.000	0.000
74	A	76	PHE	0	0.010	0.001	22.800	-0.225	-0.225	0.000	0.000	0.000	0.000
75	A	77	GLN	0	-0.043	-0.044	22.139	-0.423	-0.423	0.000	0.000	0.000	0.000
76	A	78	ASP	-1	-0.846	-0.939	25.764	-9.866	-9.866	0.000	0.000	0.000	0.000
77	A	79	ILE	0	-0.002	0.013	28.989	-0.132	-0.132	0.000	0.000	0.000	0.000
78	A	80	VAL	0	-0.026	0.001	32.057	0.226	0.226	0.000	0.000	0.000	0.000
79	A	81	PRO	0	0.005	-0.010	35.042	-0.085	-0.085	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.820	-0.931	37.500	-7.799	-7.799	0.000	0.000	0.000	0.000
81	A	83	GLN	0	-0.083	-0.043	36.151	0.137	0.137	0.000	0.000	0.000	0.000
82	A	84	ARG	1	0.854	0.922	29.744	9.775	9.775	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.000	0.006	27.877	0.055	0.055	0.000	0.000	0.000	0.000
84	A	86	VAL	0	0.025	0.018	24.175	-0.281	-0.281	0.000	0.000	0.000	0.000
85	A	87	PHE	0	0.012	0.009	21.682	0.216	0.216	0.000	0.000	0.000	0.000
86	A	88	SER	0	0.011	0.040	18.110	-0.493	-0.493	0.000	0.000	0.000	0.000
87	A	89	TYR	0	-0.016	-0.036	17.131	0.208	0.208	0.000	0.000	0.000	0.000
88	A	90	ARG	1	0.954	0.987	12.759	18.194	18.194	0.000	0.000	0.000	0.000
89	A	91	MET	0	0.023	0.033	13.310	1.211	1.211	0.000	0.000	0.000	0.000
90	A	92	ALA	0	-0.014	-0.017	12.230	-2.362	-2.362	0.000	0.000	0.000	0.000
91	A	93	ILE	0	0.051	0.047	12.851	1.813	1.813	0.000	0.000	0.000	0.000
92	A	94	GLY	0	-0.007	0.005	13.448	-1.144	-1.144	0.000	0.000	0.000	0.000
93	A	95	PRO	0	-0.039	-0.030	10.771	0.083	0.083	0.000	0.000	0.000	0.000
94	A	96	GLN	0	-0.001	-0.002	7.578	-5.891	-5.891	0.000	0.000	0.000	0.000
95	A	97	PRO	0	-0.007	0.001	6.426	2.493	2.493	0.000	0.000	0.000	0.000
96	A	98	MET	0	0.072	0.028	7.468	-3.093	-3.093	0.000	0.000	0.000	0.000
97	A	99	SER	0	-0.001	-0.024	9.760	-0.268	-0.268	0.000	0.000	0.000	0.000
98	A	100	ALA	0	-0.047	-0.007	10.764	1.003	1.003	0.000	0.000	0.000	0.000
99	A	101	SER	0	-0.006	0.017	12.837	-0.941	-0.941	0.000	0.000	0.000	0.000
100	A	102	LEU	0	-0.023	-0.012	15.729	0.325	0.325	0.000	0.000	0.000	0.000
101	A	103	THR	0	0.015	0.001	19.077	-0.270	-0.270	0.000	0.000	0.000	0.000
102	A	104	THR	0	-0.021	-0.006	22.293	0.268	0.268	0.000	0.000	0.000	0.000
103	A	105	VAL	0	-0.024	-0.008	25.590	-0.037	-0.037	0.000	0.000	0.000	0.000
104	A	106	GLU	-1	-0.949	-0.970	28.802	-9.956	-9.956	0.000	0.000	0.000	0.000
105	A	107	LEU	0	-0.027	-0.022	31.840	0.029	0.029	0.000	0.000	0.000	0.000
106	A	108	THR	0	0.021	0.011	35.370	0.203	0.203	0.000	0.000	0.000	0.000
107	A	109	PRO	0	0.009	-0.006	37.993	0.021	0.021	0.000	0.000	0.000	0.000
108	A	110	SER	0	-0.019	-0.005	40.810	-0.083	-0.083	0.000	0.000	0.000	0.000
109	A	111	GLY	0	-0.037	-0.017	42.687	0.086	0.086	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.932	-0.967	46.418	-6.593	-6.593	0.000	0.000	0.000	0.000
111	A	113	GLY	0	0.005	0.024	43.435	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	114	THR	0	-0.098	-0.044	38.155	-0.068	-0.068	0.000	0.000	0.000	0.000
113	A	115	ARG	1	0.983	0.979	34.870	8.632	8.632	0.000	0.000	0.000	0.000
114	A	116	LEU	0	0.012	0.007	30.841	-0.078	-0.078	0.000	0.000	0.000	0.000
115	A	117	THR	0	-0.019	0.002	29.854	-0.159	-0.159	0.000	0.000	0.000	0.000
116	A	118	TYR	0	-0.004	-0.006	23.514	0.141	0.141	0.000	0.000	0.000	0.000
117	A	119	THR	0	0.027	0.000	22.878	-0.138	-0.138	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.830	-0.936	19.540	-15.219	-15.219	0.000	0.000	0.000	0.000
119	A	121	GLN	0	-0.038	-0.005	17.778	-0.164	-0.164	0.000	0.000	0.000	0.000
120	A	122	GLY	0	0.018	-0.019	14.861	-0.162	-0.162	0.000	0.000	0.000	0.000
121	A	123	ALA	0	0.000	0.003	9.684	-0.102	-0.102	0.000	0.000	0.000	0.000
122	A	124	PHE	0	-0.050	-0.034	9.982	-0.207	-0.207	0.000	0.000	0.000	0.000
123	A	125	PHE	0	-0.033	-0.010	5.088	-1.518	-1.518	0.000	0.000	0.000	0.000
124	A	126	ASP	-1	-0.737	-0.871	1.996	-114.787	-107.950	10.759	-9.280	-8.316	-0.126
125	A	127	GLY	0	-0.021	0.028	4.436	3.975	4.101	-0.001	-0.021	-0.104	0.000
126	A	128	VAL	0	-0.035	-0.042	7.023	4.004	4.004	0.000	0.000	0.000	0.000
127	A	129	ASP	-1	-0.832	-0.923	9.709	-21.225	-21.225	0.000	0.000	0.000	0.000
128	A	130	SER	0	-0.008	-0.014	12.334	1.556	1.556	0.000	0.000	0.000	0.000
129	A	131	ALA	0	0.001	0.010	14.892	1.142	1.142	0.000	0.000	0.000	0.000
130	A	132	LYS	1	0.925	0.960	16.271	17.637	17.637	0.000	0.000	0.000	0.000
131	A	133	GLY	0	0.070	0.031	18.503	0.658	0.658	0.000	0.000	0.000	0.000
132	A	134	ARG	1	0.872	0.921	14.062	19.446	19.446	0.000	0.000	0.000	0.000
133	A	135	GLU	-1	-0.886	-0.948	19.843	-12.105	-12.105	0.000	0.000	0.000	0.000
134	A	136	GLU	-1	-0.981	-0.988	22.503	-11.998	-11.998	0.000	0.000	0.000	0.000
135	A	137	GLY	0	0.033	0.016	23.233	0.533	0.533	0.000	0.000	0.000	0.000
136	A	138	THR	0	0.013	0.009	22.933	0.457	0.457	0.000	0.000	0.000	0.000
137	A	139	ARG	1	0.895	0.961	25.398	11.532	11.532	0.000	0.000	0.000	0.000
138	A	140	GLY	0	0.014	0.012	27.574	0.481	0.481	0.000	0.000	0.000	0.000
139	A	141	LEU	0	0.006	0.008	25.128	0.374	0.374	0.000	0.000	0.000	0.000
140	A	142	LEU	0	0.007	0.004	28.811	0.359	0.359	0.000	0.000	0.000	0.000
141	A	143	GLU	-1	-1.006	-0.991	31.189	-8.488	-8.488	0.000	0.000	0.000	0.000
142	A	144	ALA	0	0.051	0.011	32.048	0.304	0.304	0.000	0.000	0.000	0.000
143	A	145	LEU	0	-0.025	-0.015	32.825	0.285	0.285	0.000	0.000	0.000	0.000
144	A	146	ALA	0	-0.046	-0.029	34.544	0.288	0.288	0.000	0.000	0.000	0.000
145	A	147	ALA	0	-0.012	0.003	37.308	0.253	0.253	0.000	0.000	0.000	0.000
146	A	148	GLU	-1	-0.871	-0.935	36.454	-7.943	-7.943	0.000	0.000	0.000	0.000
147	A	149	LEU	0	-0.089	-0.026	37.567	0.297	0.297	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:HIS)