FMO DATABASE

FMODB ID: 82VRY

Calculation Name: 6PAX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 6PAX

Chain ID: A

ChEMBL ID:

UniProt ID: P26367

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	133
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-915492.649001
FMO2-HF: Nuclear repulsion	864582.741227
FMO2-HF: Total energy	-50909.907773
FMO2-MP2: Total energy	-51058.221434

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:1:SER)

Summations of interaction energy for fragment #1(A:1: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.
-11.119	-5.049	1.334	-3.153	-4.252	0.009

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.013

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	3	SER	0	0.016	-0.008	3.859	-0.628	2.119	-0.012	-1.535	-1.201	0.004
4	A	4	GLY	0	0.011	0.024	6.334	-0.097	-0.097	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.018	0.009	8.872	0.121	0.121	0.000	0.000	0.000	0.000
6	A	6	ASN	0	-0.027	-0.012	12.284	0.033	0.033	0.000	0.000	0.000	0.000
7	A	7	GLN	0	0.043	-0.004	14.113	0.006	0.006	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.044	-0.001	17.318	0.016	0.016	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.033	0.025	17.197	0.010	0.010	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.030	0.017	15.131	-0.043	-0.043	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.006	-0.006	10.648	-0.043	-0.043	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.078	-0.039	7.766	0.200	0.200	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.047	0.018	2.459	-1.237	-0.370	0.936	-0.654	-1.149	0.002
14	A	14	ASN	0	0.031	0.013	4.226	1.160	1.324	0.000	-0.048	-0.116	0.000
15	A	15	GLY	0	0.052	0.033	3.447	-0.005	0.721	0.032	-0.243	-0.515	-0.002
16	A	16	ARG	1	0.868	0.935	2.848	-6.775	-5.209	0.378	-0.673	-1.271	0.005
17	A	17	PRO	0	-0.029	-0.023	6.148	-0.739	-0.739	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.040	0.032	8.708	0.018	0.018	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.087	0.035	9.621	0.085	0.085	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.746	-0.859	11.892	0.462	0.462	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.049	0.043	15.223	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	22	THR	0	0.035	0.001	14.095	-0.046	-0.046	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.757	0.873	13.218	-0.540	-0.540	0.000	0.000	0.000	0.000
24	A	24	GLN	0	0.005	-0.009	17.799	0.017	0.017	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.865	0.916	19.558	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.021	-0.016	17.392	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.023	0.011	21.598	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.784	-0.861	23.828	0.028	0.028	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.004	-0.001	23.409	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.004	0.013	25.918	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	31	HIS	0	-0.041	-0.012	27.652	0.004	0.004	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.079	-0.047	29.526	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.049	0.031	30.921	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.062	-0.019	27.578	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.945	0.930	28.466	0.007	0.007	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.038	0.002	24.183	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	37	CYS	0	0.039	0.016	23.786	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.792	-0.856	25.258	-0.023	-0.023	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.016	0.013	21.357	-0.015	-0.015	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.098	-0.060	20.113	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.891	0.926	20.635	0.024	0.024	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.026	-0.013	22.620	-0.023	-0.023	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.026	-0.011	18.527	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.010	0.012	17.350	-0.031	-0.031	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.018	0.026	15.099	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.063	0.036	15.007	0.016	0.016	0.000	0.000	0.000	0.000
47	A	47	ASN	0	0.105	0.026	17.379	0.048	0.048	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.034	0.026	18.896	0.017	0.017	0.000	0.000	0.000	0.000
49	A	49	CYS	0	-0.094	-0.044	13.508	0.079	0.079	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.062	0.024	16.708	0.033	0.033	0.000	0.000	0.000	0.000
51	A	51	SER	0	0.008	0.012	19.600	0.016	0.016	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.950	0.979	14.790	-0.470	-0.470	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.042	-0.021	15.210	0.032	0.032	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.035	0.022	19.525	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.027	0.020	23.210	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.877	0.939	16.509	-0.518	-0.518	0.000	0.000	0.000	0.000
57	A	57	TYR	0	0.020	0.030	22.909	0.003	0.003	0.000	0.000	0.000	0.000
58	A	58	TYR	0	0.041	-0.005	24.287	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.008	0.019	25.955	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.104	-0.080	24.062	0.017	0.017	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.057	0.045	26.466	0.003	0.003	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.026	-0.012	21.335	0.003	0.003	0.000	0.000	0.000	0.000
63	A	63	ILE	0	0.075	0.032	18.880	0.024	0.024	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.830	0.904	14.532	-0.488	-0.488	0.000	0.000	0.000	0.000
65	A	65	PRO	0	-0.023	-0.016	12.398	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.959	0.974	14.872	-0.569	-0.569	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.045	0.017	13.747	0.129	0.129	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.012	-0.015	8.816	-0.032	-0.032	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.023	0.026	11.238	0.190	0.190	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.022	0.013	12.189	-0.156	-0.156	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.025	-0.013	15.011	-0.045	-0.045	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.988	0.994	18.382	-0.523	-0.523	0.000	0.000	0.000	0.000
73	A	73	PRO	0	0.023	0.001	22.039	0.015	0.015	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.913	0.940	20.900	-0.522	-0.522	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.050	0.042	26.524	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.010	0.012	28.132	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	77	THR	0	0.018	0.007	28.993	0.017	0.017	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.057	0.007	29.506	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.895	-0.912	32.174	0.179	0.179	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.037	0.018	33.045	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.045	-0.034	30.488	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.012	-0.011	33.877	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.829	0.910	37.013	-0.155	-0.155	0.000	0.000	0.000	0.000
84	A	84	ILE	0	-0.021	-0.015	33.956	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	85	ALA	0	-0.013	-0.013	37.025	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.020	-0.014	38.752	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	87	TYR	0	-0.030	-0.053	40.319	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.796	0.887	39.337	-0.140	-0.140	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.057	-0.016	42.347	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.764	-0.853	44.324	0.115	0.115	0.000	0.000	0.000	0.000
91	A	91	CYS	0	-0.008	-0.002	45.902	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	92	PRO	0	0.039	0.025	44.020	0.004	0.004	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.003	0.001	43.651	0.005	0.005	0.000	0.000	0.000	0.000
94	A	94	ILE	0	-0.036	0.011	42.166	0.001	0.001	0.000	0.000	0.000	0.000
95	A	95	PHE	0	0.026	-0.001	41.571	0.008	0.008	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.013	-0.026	36.509	0.004	0.004	0.000	0.000	0.000	0.000
97	A	97	TRP	0	-0.006	-0.008	38.513	0.010	0.010	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.764	-0.872	40.289	0.114	0.114	0.000	0.000	0.000	0.000
99	A	99	ILE	0	-0.021	-0.007	37.846	0.002	0.002	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.862	0.923	34.402	-0.182	-0.182	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.836	-0.929	39.083	0.138	0.138	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.778	0.897	42.422	-0.126	-0.126	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.035	-0.022	36.685	0.002	0.002	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.047	-0.019	38.750	0.003	0.003	0.000	0.000	0.000	0.000
105	A	105	SER	0	-0.041	-0.038	41.462	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.773	-0.857	43.338	0.130	0.130	0.000	0.000	0.000	0.000
107	A	107	GLY	0	-0.002	0.005	42.551	0.000	0.000	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.032	-0.007	37.393	0.006	0.006	0.000	0.000	0.000	0.000
109	A	109	CYS	0	-0.094	-0.048	35.745	0.017	0.017	0.000	0.000	0.000	0.000
110	A	110	THR	0	0.035	-0.006	36.644	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	111	ASN	0	0.014	-0.026	36.518	0.008	0.008	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.858	-0.890	33.677	0.196	0.196	0.000	0.000	0.000	0.000
113	A	113	ASN	0	-0.043	-0.022	31.605	0.011	0.011	0.000	0.000	0.000	0.000
114	A	114	ILE	0	0.042	0.043	32.392	0.012	0.012	0.000	0.000	0.000	0.000
115	A	115	PRO	0	0.002	-0.004	31.029	0.010	0.010	0.000	0.000	0.000	0.000
116	A	116	SER	0	0.037	0.027	28.771	-0.014	-0.014	0.000	0.000	0.000	0.000
117	A	117	VAL	0	0.134	0.048	31.822	0.006	0.006	0.000	0.000	0.000	0.000
118	A	118	SER	0	-0.014	0.004	28.352	0.000	0.000	0.000	0.000	0.000	0.000
119	A	119	SER	0	-0.025	-0.026	28.101	0.019	0.019	0.000	0.000	0.000	0.000
120	A	120	ILE	0	0.046	0.043	29.626	0.008	0.008	0.000	0.000	0.000	0.000
121	A	121	ASN	0	0.016	-0.012	32.487	-0.008	-0.008	0.000	0.000	0.000	0.000
122	A	122	ARG	1	0.872	0.943	24.940	-0.346	-0.346	0.000	0.000	0.000	0.000
123	A	123	VAL	0	0.015	0.010	29.566	0.007	0.007	0.000	0.000	0.000	0.000
124	A	124	LEU	0	0.033	0.025	31.112	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.956	0.979	27.727	-0.235	-0.235	0.000	0.000	0.000	0.000
126	A	126	ASN	0	-0.040	-0.015	25.931	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	127	LEU	0	0.058	0.030	29.971	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	128	ALA	0	-0.051	-0.024	33.523	-0.009	-0.009	0.000	0.000	0.000	0.000
129	A	129	SER	0	-0.014	-0.017	30.104	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.953	-0.979	30.455	0.247	0.247	0.000	0.000	0.000	0.000
131	A	131	LYS	1	0.943	0.968	32.077	-0.147	-0.147	0.000	0.000	0.000	0.000
132	A	132	GLN	0	-0.024	-0.004	33.986	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	133	GLN	0	-0.077	-0.022	28.561	-0.013	-0.013	0.000	0.000	0.000	0.000

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