FMO DATABASE

FMODB ID: 9Q2L2

Calculation Name: 3D7N-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3D7N

Chain ID: A

ChEMBL ID:

UniProt ID: A9CG77

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	164
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1573477.96133
FMO2-HF: Nuclear repulsion	1512118.994365
FMO2-HF: Total energy	-61358.966965
FMO2-MP2: Total energy	-61538.923963

3D Structure Molmil

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.
-118.128	-114.619	1.307	-1.714	-3.103	0.007

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 : 1 / q_Mulliken : 0.838 / q_NPA : 0.900

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	-0.018	0.004	3.849	-1.583	-0.135	-0.014	-0.651	-0.783	-0.002
27	A	32	GLU	-1	-0.973	-0.986	4.800	-42.095	-42.041	-0.001	-0.002	-0.051	0.000
161	A	185	ARG	1	0.841	0.933	2.524	33.101	34.778	1.321	-1.002	-1.997	0.009
162	A	186	GLN	0	-0.056	-0.021	5.118	-0.932	-0.879	-0.001	0.000	-0.052	0.000
164	A	188	LYS	0	-0.037	-0.009	3.395	24.071	24.348	0.002	-0.059	-0.220	0.000
4	A	9	THR	0	0.022	0.007	6.755	2.815	2.815	0.000	0.000	0.000	0.000
5	A	10	VAL	0	0.003	0.012	9.487	0.518	0.518	0.000	0.000	0.000	0.000
6	A	11	VAL	0	-0.005	0.004	12.994	0.665	0.665	0.000	0.000	0.000	0.000
7	A	12	VAL	0	0.009	0.007	15.494	0.477	0.477	0.000	0.000	0.000	0.000
8	A	13	TYR	0	-0.026	-0.037	18.916	0.324	0.324	0.000	0.000	0.000	0.000
9	A	14	HIS	0	0.037	0.056	21.775	0.158	0.158	0.000	0.000	0.000	0.000
10	A	15	SER	0	-0.002	-0.016	25.148	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	16	GLY	0	0.023	0.020	26.977	0.259	0.259	0.000	0.000	0.000	0.000
12	A	17	TYR	0	0.003	-0.016	30.118	-0.117	-0.117	0.000	0.000	0.000	0.000
13	A	18	GLY	0	0.037	0.027	27.391	0.054	0.054	0.000	0.000	0.000	0.000
14	A	19	HIS	1	0.892	0.940	26.376	9.517	9.517	0.000	0.000	0.000	0.000
15	A	20	THR	0	0.003	0.002	24.388	-0.469	-0.469	0.000	0.000	0.000	0.000
16	A	21	HIS	0	-0.009	0.005	21.818	-0.523	-0.523	0.000	0.000	0.000	0.000
17	A	22	ARG	1	0.929	0.964	19.749	12.812	12.812	0.000	0.000	0.000	0.000
18	A	23	MET	0	0.004	0.009	20.671	-0.324	-0.324	0.000	0.000	0.000	0.000
19	A	24	ALA	0	0.004	-0.002	18.350	-0.727	-0.727	0.000	0.000	0.000	0.000
20	A	25	GLU	-1	-0.813	-0.901	16.631	-14.775	-14.775	0.000	0.000	0.000	0.000
21	A	26	ALA	0	0.021	0.025	15.837	-0.916	-0.916	0.000	0.000	0.000	0.000
22	A	27	VAL	0	-0.013	-0.010	14.194	-0.922	-0.922	0.000	0.000	0.000	0.000
23	A	28	ALA	0	-0.025	-0.024	12.316	-1.541	-1.541	0.000	0.000	0.000	0.000
24	A	29	GLU	-1	-0.947	-0.975	11.087	-18.541	-18.541	0.000	0.000	0.000	0.000
25	A	30	GLY	0	-0.017	-0.018	11.078	-0.912	-0.912	0.000	0.000	0.000	0.000
26	A	31	ALA	0	-0.091	-0.051	8.823	-1.404	-1.404	0.000	0.000	0.000	0.000
28	A	33	ALA	0	-0.063	-0.015	7.801	-2.238	-2.238	0.000	0.000	0.000	0.000
29	A	34	THR	0	-0.014	-0.011	10.106	2.037	2.037	0.000	0.000	0.000	0.000
30	A	35	LEU	0	-0.005	-0.006	12.576	0.362	0.362	0.000	0.000	0.000	0.000
31	A	36	HIS	0	0.003	0.000	15.115	1.231	1.231	0.000	0.000	0.000	0.000
32	A	37	ALA	0	0.012	0.012	18.741	0.216	0.216	0.000	0.000	0.000	0.000
33	A	38	ILE	0	-0.052	-0.025	22.356	0.227	0.227	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.751	-0.882	25.123	-10.451	-10.451	0.000	0.000	0.000	0.000
35	A	40	ALA	0	0.004	-0.022	28.330	0.070	0.070	0.000	0.000	0.000	0.000
36	A	41	GLU	-1	-0.933	-0.960	31.545	-8.873	-8.873	0.000	0.000	0.000	0.000
37	A	42	GLY	0	0.006	0.007	29.461	0.152	0.152	0.000	0.000	0.000	0.000
38	A	43	ASN	0	-0.079	-0.036	28.499	0.080	0.080	0.000	0.000	0.000	0.000
39	A	44	LEU	0	0.027	0.010	20.540	-0.191	-0.191	0.000	0.000	0.000	0.000
40	A	45	SER	0	0.008	-0.004	22.485	0.110	0.110	0.000	0.000	0.000	0.000
41	A	46	GLU	-1	-0.898	-0.963	22.667	-12.794	-12.794	0.000	0.000	0.000	0.000
42	A	47	ASP	-1	-0.847	-0.911	19.252	-15.205	-15.205	0.000	0.000	0.000	0.000
43	A	48	GLY	0	0.033	0.023	18.165	-1.140	-1.140	0.000	0.000	0.000	0.000
44	A	49	TRP	0	-0.097	-0.058	18.342	-0.986	-0.986	0.000	0.000	0.000	0.000
45	A	50	ALA	0	-0.006	-0.003	17.732	-0.542	-0.542	0.000	0.000	0.000	0.000
46	A	51	ALA	0	0.006	0.007	14.325	-1.350	-1.350	0.000	0.000	0.000	0.000
47	A	52	LEU	0	-0.013	-0.016	14.082	-1.447	-1.447	0.000	0.000	0.000	0.000
48	A	53	ASP	-1	-0.840	-0.931	15.327	-17.371	-17.371	0.000	0.000	0.000	0.000
49	A	54	ALA	0	-0.051	-0.021	11.998	-0.678	-0.678	0.000	0.000	0.000	0.000
50	A	55	ALA	0	-0.015	0.022	10.600	-3.366	-3.366	0.000	0.000	0.000	0.000
51	A	56	ASP	-1	-0.752	-0.857	6.131	-48.298	-48.298	0.000	0.000	0.000	0.000
52	A	57	ALA	0	-0.022	-0.016	9.522	2.268	2.268	0.000	0.000	0.000	0.000
53	A	58	ILE	0	0.000	0.013	11.411	-0.238	-0.238	0.000	0.000	0.000	0.000
54	A	59	ILE	0	-0.034	-0.018	12.130	1.007	1.007	0.000	0.000	0.000	0.000
55	A	60	PHE	0	0.015	-0.006	16.180	0.222	0.222	0.000	0.000	0.000	0.000
56	A	61	GLY	0	0.054	0.020	19.943	0.214	0.214	0.000	0.000	0.000	0.000
57	A	62	THR	0	-0.020	-0.032	21.763	0.362	0.362	0.000	0.000	0.000	0.000
58	A	63	PRO	0	0.005	0.029	25.600	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	64	THR	0	0.004	0.021	28.569	-0.084	-0.084	0.000	0.000	0.000	0.000
60	A	65	TYR	0	-0.012	-0.024	30.826	0.227	0.227	0.000	0.000	0.000	0.000
61	A	66	MET	0	-0.053	-0.026	34.262	0.016	0.016	0.000	0.000	0.000	0.000
62	A	67	GLY	0	0.091	0.061	36.060	0.099	0.099	0.000	0.000	0.000	0.000
63	A	68	GLY	0	-0.017	0.000	32.493	-0.074	-0.074	0.000	0.000	0.000	0.000
64	A	69	PRO	0	0.019	0.018	28.525	-0.047	-0.047	0.000	0.000	0.000	0.000
65	A	70	SER	0	-0.004	-0.011	29.227	0.275	0.275	0.000	0.000	0.000	0.000
66	A	71	TRP	0	0.041	0.008	30.837	-0.274	-0.274	0.000	0.000	0.000	0.000
67	A	72	GLN	0	-0.018	-0.007	29.621	-0.160	-0.160	0.000	0.000	0.000	0.000
68	A	73	PHE	0	0.040	0.020	22.767	-0.233	-0.233	0.000	0.000	0.000	0.000
69	A	74	LYS	1	0.814	0.893	27.610	9.702	9.702	0.000	0.000	0.000	0.000
70	A	75	LYS	1	0.832	0.910	30.158	9.964	9.964	0.000	0.000	0.000	0.000
71	A	76	PHE	0	0.033	0.018	21.227	-0.091	-0.091	0.000	0.000	0.000	0.000
72	A	77	ALA	0	0.016	-0.001	25.872	-0.291	-0.291	0.000	0.000	0.000	0.000
73	A	78	ASP	-1	-0.805	-0.859	26.919	-10.256	-10.256	0.000	0.000	0.000	0.000
74	A	79	ALA	0	0.002	0.015	27.642	0.083	0.083	0.000	0.000	0.000	0.000
75	A	80	SER	0	-0.051	-0.042	23.515	-0.354	-0.354	0.000	0.000	0.000	0.000
76	A	81	SER	0	0.005	-0.024	25.304	-0.312	-0.312	0.000	0.000	0.000	0.000
77	A	82	LYS	1	0.993	1.001	25.300	12.255	12.255	0.000	0.000	0.000	0.000
78	A	83	PRO	0	0.003	0.007	21.405	0.124	0.124	0.000	0.000	0.000	0.000
79	A	84	TRP	0	-0.062	-0.008	22.722	-0.147	-0.147	0.000	0.000	0.000	0.000
80	A	85	PHE	0	-0.001	-0.002	24.910	-0.027	-0.027	0.000	0.000	0.000	0.000
81	A	86	SER	0	-0.069	-0.048	24.144	-0.056	-0.056	0.000	0.000	0.000	0.000
82	A	87	ALA	0	0.023	0.006	22.396	-0.460	-0.460	0.000	0.000	0.000	0.000
83	A	88	LYS	1	0.895	0.961	18.845	15.045	15.045	0.000	0.000	0.000	0.000
84	A	89	TRP	0	-0.054	-0.064	17.112	-0.773	-0.773	0.000	0.000	0.000	0.000
85	A	90	GLN	0	0.051	0.046	17.849	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	91	ASP	-1	-0.963	-0.986	15.834	-18.008	-18.008	0.000	0.000	0.000	0.000
87	A	92	LYS	1	0.773	0.892	12.848	22.064	22.064	0.000	0.000	0.000	0.000
88	A	93	VAL	0	-0.031	-0.011	10.788	1.643	1.643	0.000	0.000	0.000	0.000
89	A	94	PHE	0	0.010	-0.002	13.331	-0.147	-0.147	0.000	0.000	0.000	0.000
90	A	95	GLY	0	0.050	0.018	16.068	0.038	0.038	0.000	0.000	0.000	0.000
91	A	96	GLY	0	-0.014	-0.021	17.308	0.141	0.141	0.000	0.000	0.000	0.000
92	A	97	PHE	0	0.004	0.008	17.741	0.033	0.033	0.000	0.000	0.000	0.000
93	A	98	THR	0	-0.041	-0.024	21.562	0.376	0.376	0.000	0.000	0.000	0.000
94	A	99	ASN	0	0.059	0.012	25.091	-0.301	-0.301	0.000	0.000	0.000	0.000
95	A	100	SER	0	-0.040	-0.058	27.577	0.199	0.199	0.000	0.000	0.000	0.000
96	A	101	ALA	0	0.079	0.040	31.418	-0.048	-0.048	0.000	0.000	0.000	0.000
97	A	102	SER	0	-0.055	-0.036	34.009	0.347	0.347	0.000	0.000	0.000	0.000
98	A	103	LEU	0	0.015	0.024	34.089	-0.188	-0.188	0.000	0.000	0.000	0.000
99	A	104	ASN	0	0.027	-0.011	30.132	0.097	0.097	0.000	0.000	0.000	0.000
100	A	105	GLY	0	-0.012	-0.004	32.065	-0.171	-0.171	0.000	0.000	0.000	0.000
101	A	106	ASP	-1	-0.839	-0.936	33.503	-8.681	-8.681	0.000	0.000	0.000	0.000
102	A	107	LYS	0	-0.009	0.034	28.566	-0.222	-0.222	0.000	0.000	0.000	0.000
103	A	108	LEU	0	0.000	0.013	28.579	-0.451	-0.451	0.000	0.000	0.000	0.000
104	A	109	ASN	0	-0.014	-0.014	29.370	-0.318	-0.318	0.000	0.000	0.000	0.000
105	A	110	THR	0	-0.013	-0.028	27.037	-0.109	-0.109	0.000	0.000	0.000	0.000
106	A	111	LEU	0	0.000	-0.001	23.317	-0.383	-0.383	0.000	0.000	0.000	0.000
107	A	112	GLN	0	-0.012	-0.009	25.423	-0.210	-0.210	0.000	0.000	0.000	0.000
108	A	113	TYR	0	0.014	0.009	27.689	-0.026	-0.026	0.000	0.000	0.000	0.000
109	A	114	LEU	0	-0.007	0.001	22.566	-0.242	-0.242	0.000	0.000	0.000	0.000
110	A	115	VAL	0	-0.005	0.006	23.097	-0.503	-0.503	0.000	0.000	0.000	0.000
111	A	116	LEU	0	-0.025	-0.013	24.119	-0.201	-0.201	0.000	0.000	0.000	0.000
112	A	117	LEU	0	-0.031	-0.001	23.496	-0.053	-0.053	0.000	0.000	0.000	0.000
113	A	118	ALA	0	0.023	0.000	19.985	-0.303	-0.303	0.000	0.000	0.000	0.000
114	A	119	GLY	0	0.001	0.004	21.588	-0.311	-0.311	0.000	0.000	0.000	0.000
115	A	120	GLN	0	-0.060	-0.029	23.856	0.131	0.131	0.000	0.000	0.000	0.000
116	A	121	HIS	1	0.797	0.876	20.681	14.333	14.333	0.000	0.000	0.000	0.000
117	A	122	GLY	0	0.041	0.047	21.047	-0.501	-0.501	0.000	0.000	0.000	0.000
118	A	123	GLY	0	0.037	0.024	17.901	-0.625	-0.625	0.000	0.000	0.000	0.000
119	A	124	LEU	0	-0.062	-0.034	15.060	0.920	0.920	0.000	0.000	0.000	0.000
120	A	125	TRP	0	-0.012	-0.012	16.382	-1.005	-1.005	0.000	0.000	0.000	0.000
121	A	126	VAL	0	-0.011	0.000	13.730	0.154	0.154	0.000	0.000	0.000	0.000
122	A	127	SER	0	-0.020	-0.006	17.169	0.159	0.159	0.000	0.000	0.000	0.000
123	A	128	LEU	0	-0.007	-0.004	18.163	-0.880	-0.880	0.000	0.000	0.000	0.000
124	A	129	GLY	-1	-0.931	-0.948	18.722	-14.239	-14.239	0.000	0.000	0.000	0.000
125	A	149	TYR	0	0.053	0.008	24.417	0.223	0.223	0.000	0.000	0.000	0.000
126	A	150	ILE	0	0.007	0.005	23.105	-0.483	-0.483	0.000	0.000	0.000	0.000
127	A	151	ALA	0	0.036	0.017	20.812	-0.643	-0.643	0.000	0.000	0.000	0.000
128	A	152	PRO	0	-0.022	0.011	18.952	0.637	0.637	0.000	0.000	0.000	0.000
129	A	153	MET	0	-0.018	-0.011	22.098	0.182	0.182	0.000	0.000	0.000	0.000
130	A	154	ALA	0	0.006	0.005	24.878	-0.019	-0.019	0.000	0.000	0.000	0.000
131	A	155	GLN	0	0.006	-0.008	26.933	0.059	0.059	0.000	0.000	0.000	0.000
132	A	156	SER	0	-0.070	-0.063	29.044	-0.419	-0.419	0.000	0.000	0.000	0.000
133	A	157	ASP	-1	-0.837	-0.895	31.374	-8.647	-8.647	0.000	0.000	0.000	0.000
134	A	158	ALA	0	-0.021	0.009	33.858	0.216	0.216	0.000	0.000	0.000	0.000
135	A	159	ASP	-1	-0.920	-0.968	33.450	-8.533	-8.533	0.000	0.000	0.000	0.000
136	A	160	ALA	0	0.013	0.013	33.409	-0.269	-0.269	0.000	0.000	0.000	0.000
137	A	161	ALA	0	-0.008	-0.011	30.029	-0.188	-0.188	0.000	0.000	0.000	0.000
138	A	162	PRO	0	-0.038	-0.026	29.209	-0.338	-0.338	0.000	0.000	0.000	0.000
139	A	163	GLU	-1	-0.955	-0.971	29.613	-8.748	-8.748	0.000	0.000	0.000	0.000
140	A	164	GLU	-1	-0.972	-0.995	27.727	-10.115	-10.115	0.000	0.000	0.000	0.000
141	A	165	MET	0	-0.036	0.007	22.597	0.220	0.220	0.000	0.000	0.000	0.000
142	A	166	SER	0	0.031	0.008	26.206	-0.290	-0.290	0.000	0.000	0.000	0.000
143	A	167	VAL	0	0.087	0.024	23.546	-0.400	-0.400	0.000	0.000	0.000	0.000
144	A	168	GLY	0	0.005	0.013	23.164	-0.466	-0.466	0.000	0.000	0.000	0.000
145	A	169	ASP	-1	-0.826	-0.912	23.201	-11.252	-11.252	0.000	0.000	0.000	0.000
146	A	170	LEU	0	-0.034	-0.014	20.783	-0.611	-0.611	0.000	0.000	0.000	0.000
147	A	171	GLU	-1	-0.764	-0.845	18.314	-15.966	-15.966	0.000	0.000	0.000	0.000
148	A	172	THR	0	-0.044	-0.041	18.159	-0.702	-0.702	0.000	0.000	0.000	0.000
149	A	173	ALA	0	-0.022	-0.009	18.414	-0.582	-0.582	0.000	0.000	0.000	0.000
150	A	174	ARG	1	0.855	0.915	13.309	16.295	16.295	0.000	0.000	0.000	0.000
151	A	175	LEU	0	-0.015	-0.016	13.579	-1.441	-1.441	0.000	0.000	0.000	0.000
152	A	176	TYR	0	-0.055	-0.029	13.949	-1.062	-1.062	0.000	0.000	0.000	0.000
153	A	177	GLY	0	0.039	0.017	12.675	-0.822	-0.822	0.000	0.000	0.000	0.000
154	A	178	ALA	0	0.023	0.018	9.354	-1.906	-1.906	0.000	0.000	0.000	0.000
155	A	179	ARG	1	0.822	0.905	9.453	14.512	14.512	0.000	0.000	0.000	0.000
156	A	180	VAL	0	0.009	-0.002	11.279	-0.989	-0.989	0.000	0.000	0.000	0.000
157	A	181	ALA	0	0.049	0.033	6.341	-1.307	-1.307	0.000	0.000	0.000	0.000
158	A	182	ASN	0	-0.027	-0.017	6.333	-6.239	-6.239	0.000	0.000	0.000	0.000
159	A	183	VAL	0	0.004	0.001	7.956	-1.340	-1.340	0.000	0.000	0.000	0.000
160	A	184	ALA	0	0.004	-0.006	7.206	-0.449	-0.449	0.000	0.000	0.000	0.000
163	A	187	HIS	1	0.825	0.914	8.480	24.750	24.750	0.000	0.000	0.000	0.000

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