FMO DATABASE

FMODB ID: QVLGY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1485919.447241
FMO2-HF: Nuclear repulsion	1426884.167918
FMO2-HF: Total energy	-59035.279323
FMO2-MP2: Total energy	-59208.46081

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.
-23.893	-19.104	4.719	-3.929	-5.579	0.046

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 : 0.017 / q_NPA : -0.015

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	0.046	0.046	3.811	-2.495	-0.970	-0.016	-0.734	-0.775	0.000
4	A	9	THR	0	0.030	0.012	6.969	0.574	0.574	0.000	0.000	0.000	0.000
5	A	10	VAL	0	0.008	0.012	9.892	-0.225	-0.225	0.000	0.000	0.000	0.000
6	A	11	VAL	0	0.000	0.000	13.397	0.106	0.106	0.000	0.000	0.000	0.000
7	A	12	VAL	0	0.005	0.011	16.184	-0.059	-0.059	0.000	0.000	0.000	0.000
8	A	13	TYR	0	-0.026	-0.031	19.548	0.033	0.033	0.000	0.000	0.000	0.000
9	A	14	HIS	0	0.073	0.060	22.519	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	15	SER	0	0.003	-0.016	26.190	0.001	0.001	0.000	0.000	0.000	0.000
11	A	16	GLY	0	0.017	0.028	27.909	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	17	TYR	0	-0.023	-0.037	31.599	0.007	0.007	0.000	0.000	0.000	0.000
13	A	18	GLY	0	0.043	0.020	28.173	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	19	HIS	0	0.008	-0.002	27.372	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	20	THR	0	-0.025	-0.020	25.113	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	21	HIS	0	0.008	0.006	22.370	0.024	0.024	0.000	0.000	0.000	0.000
17	A	22	ARG	1	0.975	1.006	20.583	0.110	0.110	0.000	0.000	0.000	0.000
18	A	23	MET	0	0.003	0.005	21.465	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	24	ALA	0	0.025	0.010	19.152	0.013	0.013	0.000	0.000	0.000	0.000
20	A	25	GLU	-1	-0.872	-0.942	17.456	-0.163	-0.163	0.000	0.000	0.000	0.000
21	A	26	ALA	0	0.003	0.015	16.650	-0.032	-0.032	0.000	0.000	0.000	0.000
22	A	27	VAL	0	-0.025	-0.012	14.763	0.012	0.012	0.000	0.000	0.000	0.000
23	A	28	ALA	0	-0.016	-0.028	13.294	0.041	0.041	0.000	0.000	0.000	0.000
24	A	29	GLU	-1	-0.936	-0.955	11.891	-0.312	-0.312	0.000	0.000	0.000	0.000
25	A	30	GLY	0	-0.023	-0.020	11.457	-0.072	-0.072	0.000	0.000	0.000	0.000
26	A	31	ALA	0	-0.099	-0.059	9.171	0.098	0.098	0.000	0.000	0.000	0.000
27	A	32	GLU	-1	-0.983	-0.980	5.763	-2.006	-2.006	0.000	0.000	0.000	0.000
28	A	33	ALA	0	-0.066	-0.018	8.462	-0.165	-0.165	0.000	0.000	0.000	0.000
29	A	34	THR	0	-0.005	-0.002	10.924	-0.051	-0.051	0.000	0.000	0.000	0.000
30	A	35	LEU	0	-0.003	-0.011	13.344	0.108	0.108	0.000	0.000	0.000	0.000
31	A	36	HIS	0	-0.014	-0.007	16.088	0.002	0.002	0.000	0.000	0.000	0.000
32	A	37	ALA	0	0.006	0.012	19.606	0.034	0.034	0.000	0.000	0.000	0.000
33	A	38	ILE	0	-0.044	-0.015	23.210	0.000	0.000	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.785	-0.906	25.908	-0.027	-0.027	0.000	0.000	0.000	0.000
35	A	40	ALA	0	-0.012	-0.028	28.932	0.013	0.013	0.000	0.000	0.000	0.000
36	A	41	GLU	-1	-0.944	-0.976	32.125	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	42	GLY	0	-0.033	-0.034	29.910	0.008	0.008	0.000	0.000	0.000	0.000
38	A	43	ASN	0	-0.057	-0.018	28.982	0.023	0.023	0.000	0.000	0.000	0.000
39	A	44	LEU	0	0.018	0.015	21.061	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	45	SER	0	0.054	0.029	22.808	0.011	0.011	0.000	0.000	0.000	0.000
41	A	46	GLU	-1	-0.894	-0.963	23.216	-0.037	-0.037	0.000	0.000	0.000	0.000
42	A	47	ASP	-1	-0.915	-0.960	19.879	-0.142	-0.142	0.000	0.000	0.000	0.000
43	A	48	GLY	0	0.024	0.013	18.653	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	49	TRP	0	-0.056	-0.042	18.669	0.040	0.040	0.000	0.000	0.000	0.000
45	A	50	ALA	0	0.007	0.007	17.824	0.041	0.041	0.000	0.000	0.000	0.000
46	A	51	ALA	0	0.000	0.005	14.641	0.027	0.027	0.000	0.000	0.000	0.000
47	A	52	LEU	0	-0.041	-0.023	14.197	0.052	0.052	0.000	0.000	0.000	0.000
48	A	53	ASP	-1	-0.858	-0.933	15.194	0.271	0.271	0.000	0.000	0.000	0.000
49	A	54	ALA	0	-0.059	-0.025	11.781	0.084	0.084	0.000	0.000	0.000	0.000
50	A	55	ALA	0	-0.032	-0.001	10.493	0.043	0.043	0.000	0.000	0.000	0.000
51	A	56	ASP	-1	-0.803	-0.917	6.278	2.304	2.304	0.000	0.000	0.000	0.000
52	A	57	ALA	0	-0.031	-0.024	9.311	0.090	0.090	0.000	0.000	0.000	0.000
53	A	58	ILE	0	-0.003	0.014	11.295	-0.165	-0.165	0.000	0.000	0.000	0.000
54	A	59	ILE	0	-0.042	-0.019	12.888	0.037	0.037	0.000	0.000	0.000	0.000
55	A	60	PHE	0	0.011	-0.001	16.641	-0.058	-0.058	0.000	0.000	0.000	0.000
56	A	61	GLY	0	0.043	0.014	20.354	0.009	0.009	0.000	0.000	0.000	0.000
57	A	62	THR	0	-0.010	-0.027	22.342	-0.019	-0.019	0.000	0.000	0.000	0.000
58	A	63	PRO	0	-0.007	0.045	26.131	0.008	0.008	0.000	0.000	0.000	0.000
59	A	64	THR	0	0.008	0.021	29.212	0.013	0.013	0.000	0.000	0.000	0.000
60	A	65	TYR	0	-0.034	-0.039	31.664	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	66	MET	0	-0.011	-0.013	34.928	0.003	0.003	0.000	0.000	0.000	0.000
62	A	67	GLY	0	0.068	0.041	36.170	0.002	0.002	0.000	0.000	0.000	0.000
63	A	68	GLY	0	0.020	0.024	32.904	0.009	0.009	0.000	0.000	0.000	0.000
64	A	69	PRO	0	0.007	0.020	28.850	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	70	SER	0	-0.012	-0.009	29.879	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	71	TRP	0	0.048	0.009	31.436	0.009	0.009	0.000	0.000	0.000	0.000
67	A	72	GLN	0	-0.028	-0.009	30.298	0.012	0.012	0.000	0.000	0.000	0.000
68	A	73	PHE	0	0.046	0.023	23.280	0.004	0.004	0.000	0.000	0.000	0.000
69	A	74	LYS	1	0.855	0.910	27.825	-0.097	-0.097	0.000	0.000	0.000	0.000
70	A	75	LYS	1	0.908	0.976	30.107	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	76	PHE	0	0.055	0.028	21.441	0.002	0.002	0.000	0.000	0.000	0.000
72	A	77	ALA	0	0.004	-0.005	25.894	0.012	0.012	0.000	0.000	0.000	0.000
73	A	78	ASP	-1	-0.844	-0.887	26.957	0.115	0.115	0.000	0.000	0.000	0.000
74	A	79	ALA	0	-0.006	0.005	27.706	0.005	0.005	0.000	0.000	0.000	0.000
75	A	80	SER	0	-0.041	-0.049	23.511	0.012	0.012	0.000	0.000	0.000	0.000
76	A	81	SER	0	0.008	-0.015	25.393	0.021	0.021	0.000	0.000	0.000	0.000
77	A	82	LYS	1	0.994	0.996	25.463	-0.070	-0.070	0.000	0.000	0.000	0.000
78	A	83	PRO	0	-0.013	-0.001	21.807	0.006	0.006	0.000	0.000	0.000	0.000
79	A	84	TRP	0	-0.069	-0.019	23.302	0.015	0.015	0.000	0.000	0.000	0.000
80	A	85	PHE	0	0.007	0.015	25.013	0.011	0.011	0.000	0.000	0.000	0.000
81	A	86	SER	0	-0.079	-0.043	24.169	0.003	0.003	0.000	0.000	0.000	0.000
82	A	87	ALA	0	0.026	0.012	22.505	0.016	0.016	0.000	0.000	0.000	0.000
83	A	88	LYS	1	0.932	0.973	19.271	-0.179	-0.179	0.000	0.000	0.000	0.000
84	A	89	TRP	0	-0.074	-0.072	17.169	0.035	0.035	0.000	0.000	0.000	0.000
85	A	90	GLN	0	0.025	0.020	17.497	0.012	0.012	0.000	0.000	0.000	0.000
86	A	91	ASP	-1	-0.941	-0.976	15.397	0.687	0.687	0.000	0.000	0.000	0.000
87	A	92	LYS	1	0.782	0.917	12.964	-0.483	-0.483	0.000	0.000	0.000	0.000
88	A	93	VAL	0	-0.001	0.006	10.757	-0.088	-0.088	0.000	0.000	0.000	0.000
89	A	94	PHE	0	0.019	0.004	13.251	-0.072	-0.072	0.000	0.000	0.000	0.000
90	A	95	GLY	0	0.046	0.011	15.956	0.045	0.045	0.000	0.000	0.000	0.000
91	A	96	GLY	0	-0.026	-0.024	17.433	-0.038	-0.038	0.000	0.000	0.000	0.000
92	A	97	PHE	0	-0.016	-0.007	18.491	0.004	0.004	0.000	0.000	0.000	0.000
93	A	98	THR	0	-0.022	-0.034	22.300	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	99	ASN	0	0.049	-0.002	25.794	0.004	0.004	0.000	0.000	0.000	0.000
95	A	100	SER	0	-0.026	-0.006	28.258	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	101	ALA	0	0.030	0.007	31.992	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	102	SER	0	-0.003	-0.010	34.677	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	103	LEU	0	-0.053	0.202	34.817	0.004	0.004	0.000	0.000	0.000	0.000
99	A	104	ASN	0	-0.011	-0.011	31.122	0.000	0.000	0.000	0.000	0.000	0.000
100	A	105	GLY	0	0.063	-0.170	33.106	0.007	0.007	0.000	0.000	0.000	0.000
101	A	106	ASP	-1	-0.847	-0.957	34.144	0.082	0.082	0.000	0.000	0.000	0.000
102	A	107	LYN	0	-0.044	-0.001	29.137	0.007	0.007	0.000	0.000	0.000	0.000
103	A	108	LEU	0	0.021	0.012	28.885	0.012	0.012	0.000	0.000	0.000	0.000
104	A	109	ASN	0	-0.007	-0.017	29.901	0.020	0.020	0.000	0.000	0.000	0.000
105	A	110	THR	0	-0.020	-0.021	27.380	0.007	0.007	0.000	0.000	0.000	0.000
106	A	111	LEU	0	0.000	-0.001	24.105	0.012	0.012	0.000	0.000	0.000	0.000
107	A	112	GLN	0	-0.007	-0.014	25.582	0.014	0.014	0.000	0.000	0.000	0.000
108	A	113	TYR	0	0.017	0.013	27.440	0.011	0.011	0.000	0.000	0.000	0.000
109	A	114	LEU	0	-0.005	-0.005	23.028	0.009	0.009	0.000	0.000	0.000	0.000
110	A	115	VAL	0	-0.002	0.010	22.886	0.026	0.026	0.000	0.000	0.000	0.000
111	A	116	LEU	0	-0.027	-0.013	23.880	0.020	0.020	0.000	0.000	0.000	0.000
112	A	117	LEU	0	-0.031	0.011	23.177	0.007	0.007	0.000	0.000	0.000	0.000
113	A	118	ALA	0	0.025	-0.003	19.775	0.006	0.006	0.000	0.000	0.000	0.000
114	A	119	GLY	0	0.025	0.013	21.276	0.028	0.028	0.000	0.000	0.000	0.000
115	A	120	GLN	0	-0.050	-0.019	23.531	0.007	0.007	0.000	0.000	0.000	0.000
116	A	121	HIS	1	0.792	0.881	20.469	-0.278	-0.278	0.000	0.000	0.000	0.000
117	A	122	GLY	0	0.037	0.043	20.711	0.024	0.024	0.000	0.000	0.000	0.000
118	A	123	GLY	0	0.020	0.017	17.559	0.049	0.049	0.000	0.000	0.000	0.000
119	A	124	LEU	0	-0.037	-0.009	14.320	-0.047	-0.047	0.000	0.000	0.000	0.000
120	A	125	TRP	0	-0.021	-0.014	16.413	0.029	0.029	0.000	0.000	0.000	0.000
121	A	126	VAL	0	0.018	0.017	13.552	0.015	0.015	0.000	0.000	0.000	0.000
122	A	127	SER	0	0.001	0.023	16.999	-0.040	-0.040	0.000	0.000	0.000	0.000
123	A	128	LEU	0	-0.006	0.001	18.498	0.048	0.048	0.000	0.000	0.000	0.000
124	A	129	GLY	0	-0.024	-0.007	18.346	-0.012	-0.012	0.000	0.000	0.000	0.000
125	A	149	TYR	0	0.047	0.004	24.785	-0.009	-0.009	0.000	0.000	0.000	0.000
126	A	150	ILE	0	0.020	0.010	23.419	0.028	0.028	0.000	0.000	0.000	0.000
127	A	151	ALA	0	0.030	0.007	21.103	0.040	0.040	0.000	0.000	0.000	0.000
128	A	152	PRO	0	-0.024	0.009	19.751	-0.024	-0.024	0.000	0.000	0.000	0.000
129	A	153	MET	0	-0.010	0.000	22.835	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	154	ALA	0	0.006	0.011	25.853	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	155	GLN	0	0.059	0.033	27.792	0.006	0.006	0.000	0.000	0.000	0.000
132	A	156	SER	0	-0.033	-0.010	30.075	-0.011	-0.011	0.000	0.000	0.000	0.000
133	A	164	GLU	-1	-0.960	-0.989	28.843	-0.056	-0.056	0.000	0.000	0.000	0.000
134	A	165	MET	0	-0.024	-0.018	25.508	0.013	0.013	0.000	0.000	0.000	0.000
135	A	166	SER	0	-0.007	0.015	27.907	-0.012	-0.012	0.000	0.000	0.000	0.000
136	A	167	VAL	0	0.111	0.032	23.892	0.004	0.004	0.000	0.000	0.000	0.000
137	A	168	GLY	0	0.018	0.021	23.851	0.004	0.004	0.000	0.000	0.000	0.000
138	A	169	ASP	-1	-0.856	-0.935	23.969	0.063	0.063	0.000	0.000	0.000	0.000
139	A	170	LEU	0	-0.024	-0.012	21.592	0.015	0.015	0.000	0.000	0.000	0.000
140	A	171	GLU	-1	-0.783	-0.875	19.103	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	172	THR	0	-0.044	-0.036	18.844	0.027	0.027	0.000	0.000	0.000	0.000
142	A	173	ALA	0	-0.032	-0.017	18.920	0.045	0.045	0.000	0.000	0.000	0.000
143	A	174	ARG	1	0.900	0.942	13.696	0.085	0.085	0.000	0.000	0.000	0.000
144	A	175	LEU	0	-0.036	-0.023	14.218	0.047	0.047	0.000	0.000	0.000	0.000
145	A	176	TYR	0	-0.057	-0.046	14.398	0.096	0.096	0.000	0.000	0.000	0.000
146	A	177	GLY	0	0.036	0.022	13.297	0.105	0.105	0.000	0.000	0.000	0.000
147	A	178	ALA	0	0.042	0.026	9.910	0.133	0.133	0.000	0.000	0.000	0.000
148	A	179	ARG	1	0.811	0.891	9.968	-0.245	-0.245	0.000	0.000	0.000	0.000
149	A	180	VAL	0	0.006	-0.002	11.314	0.177	0.177	0.000	0.000	0.000	0.000
150	A	181	ALA	0	0.035	0.026	6.499	0.233	0.233	0.000	0.000	0.000	0.000
151	A	182	ASN	0	-0.046	-0.031	6.915	1.139	1.139	0.000	0.000	0.000	0.000
152	A	183	VAL	0	-0.009	-0.005	8.062	0.301	0.301	0.000	0.000	0.000	0.000
153	A	184	ALA	0	0.015	0.001	7.220	0.100	0.100	0.000	0.000	0.000	0.000
154	A	185	ARG	1	0.885	0.948	2.310	-10.053	-8.590	3.188	-1.723	-2.928	0.021
155	A	186	GLN	0	-0.088	-0.027	4.926	0.041	0.108	-0.001	-0.001	-0.065	0.000
156	A	187	HIS	0	-0.029	-0.016	7.916	-0.398	-0.398	0.000	0.000	0.000	0.000
157	A	188	LYS	1	0.906	0.986	2.457	-13.932	-12.198	1.548	-1.471	-1.811	0.025

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