FMO DATABASE

FMODB ID: R8Q88

Calculation Name: 1ALY-A-Xray372

Preferred Name: CD40 ligand

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1ALY

Chain ID: A

ChEMBL ID: CHEMBL3580491

UniProt ID: P29965

Base Structure: X-ray

Registration Date: 2023-09-22

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	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	145
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1270115.204146
FMO2-HF: Nuclear repulsion	1214772.477964
FMO2-HF: Total energy	-55342.726181
FMO2-MP2: Total energy	-55504.681918

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:116:GLY)

Summations of interaction energy for fragment #1(A:116:GLY)

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.
-1.598	-8.35	13.901	-1.263	-5.884	-0.011

Interaction energy analysis for fragmet #1(A:116:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.020

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	118	GLN	0	0.035	0.007	2.323	3.583	0.842	2.929	2.396	-2.583	-0.023
4	A	119	ASN	0	-0.071	-0.051	1.997	-3.726	-7.858	10.970	-3.621	-3.216	0.012
5	A	120	PRO	0	0.016	0.016	3.600	-0.523	-0.402	0.002	-0.038	-0.085	0.000
6	A	121	GLN	0	0.036	0.024	6.736	-0.245	-0.245	0.000	0.000	0.000	0.000
7	A	122	ILE	0	-0.068	-0.005	9.593	0.291	0.291	0.000	0.000	0.000	0.000
8	A	123	ALA	0	-0.002	-0.016	11.548	-0.217	-0.217	0.000	0.000	0.000	0.000
9	A	124	ALA	0	0.012	0.013	12.145	0.212	0.212	0.000	0.000	0.000	0.000
10	A	125	HIS	0	0.014	0.031	14.412	-0.114	-0.114	0.000	0.000	0.000	0.000
11	A	126	VAL	0	-0.002	0.006	15.357	0.071	0.071	0.000	0.000	0.000	0.000
12	A	127	ILE	0	0.029	0.016	17.414	-0.060	-0.060	0.000	0.000	0.000	0.000
13	A	128	SER	0	0.013	0.005	20.601	0.012	0.012	0.000	0.000	0.000	0.000
14	A	129	GLU	-1	-0.911	-0.964	24.175	0.307	0.307	0.000	0.000	0.000	0.000
15	A	130	ALA	0	0.032	0.021	26.336	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	131	SER	0	-0.009	-0.011	29.875	0.014	0.014	0.000	0.000	0.000	0.000
17	A	132	SER	0	0.004	0.010	31.496	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	133	LYS	1	0.920	0.955	33.837	-0.164	-0.164	0.000	0.000	0.000	0.000
19	A	134	THR	0	0.075	0.029	35.184	0.005	0.005	0.000	0.000	0.000	0.000
20	A	135	THR	0	-0.029	-0.001	32.232	0.001	0.001	0.000	0.000	0.000	0.000
21	A	136	SER	0	0.003	0.002	34.000	0.005	0.005	0.000	0.000	0.000	0.000
22	A	137	VAL	0	-0.017	-0.025	30.082	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	138	LEU	0	-0.022	-0.016	27.730	0.002	0.002	0.000	0.000	0.000	0.000
24	A	139	GLN	0	0.026	0.014	26.555	0.034	0.034	0.000	0.000	0.000	0.000
25	A	140	TRP	0	0.046	0.011	21.522	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	141	ALA	0	0.030	0.001	20.299	0.007	0.007	0.000	0.000	0.000	0.000
27	A	142	GLU	-1	-0.840	-0.942	13.792	0.994	0.994	0.000	0.000	0.000	0.000
28	A	143	LYS	1	0.875	0.939	16.270	-0.281	-0.281	0.000	0.000	0.000	0.000
29	A	144	GLY	0	0.025	0.008	17.272	-0.017	-0.017	0.000	0.000	0.000	0.000
30	A	145	TYR	0	-0.010	-0.005	14.500	0.058	0.058	0.000	0.000	0.000	0.000
31	A	146	TYR	0	-0.011	0.001	11.746	-0.045	-0.045	0.000	0.000	0.000	0.000
32	A	147	THR	0	-0.045	-0.035	9.500	0.022	0.022	0.000	0.000	0.000	0.000
33	A	148	MET	0	-0.002	0.009	10.006	-0.260	-0.260	0.000	0.000	0.000	0.000
34	A	149	SER	0	-0.035	-0.024	7.677	0.265	0.265	0.000	0.000	0.000	0.000
35	A	150	ASN	0	0.036	0.005	6.717	0.706	0.706	0.000	0.000	0.000	0.000
36	A	151	ASN	0	0.102	0.046	8.891	-0.232	-0.232	0.000	0.000	0.000	0.000
37	A	152	LEU	0	-0.040	-0.016	11.856	-0.296	-0.296	0.000	0.000	0.000	0.000
38	A	153	VAL	0	-0.045	-0.021	12.595	-0.216	-0.216	0.000	0.000	0.000	0.000
39	A	154	THR	0	0.036	-0.029	14.136	0.151	0.151	0.000	0.000	0.000	0.000
40	A	155	LEU	0	-0.018	0.014	16.469	-0.093	-0.093	0.000	0.000	0.000	0.000
41	A	156	GLU	-1	-0.834	-0.867	18.943	0.569	0.569	0.000	0.000	0.000	0.000
42	A	157	ASN	0	0.017	-0.015	21.970	-0.034	-0.034	0.000	0.000	0.000	0.000
43	A	158	GLY	0	-0.044	0.008	25.014	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	159	LYS	1	0.755	0.893	23.115	-0.358	-0.358	0.000	0.000	0.000	0.000
45	A	160	GLN	0	0.032	0.017	23.489	-0.037	-0.037	0.000	0.000	0.000	0.000
46	A	161	LEU	0	0.018	0.022	17.693	0.047	0.047	0.000	0.000	0.000	0.000
47	A	162	THR	0	-0.019	-0.033	19.332	-0.070	-0.070	0.000	0.000	0.000	0.000
48	A	163	VAL	0	0.017	0.022	17.312	0.079	0.079	0.000	0.000	0.000	0.000
49	A	164	LYS	1	0.829	0.899	15.762	-0.910	-0.910	0.000	0.000	0.000	0.000
50	A	165	ARG	1	0.957	0.977	15.864	-0.461	-0.461	0.000	0.000	0.000	0.000
51	A	166	GLN	0	-0.018	-0.006	19.099	0.010	0.010	0.000	0.000	0.000	0.000
52	A	167	GLY	0	-0.026	-0.018	20.739	0.009	0.009	0.000	0.000	0.000	0.000
53	A	168	LEU	0	0.007	-0.007	22.624	0.012	0.012	0.000	0.000	0.000	0.000
54	A	169	TYR	0	0.005	-0.022	16.671	0.045	0.045	0.000	0.000	0.000	0.000
55	A	170	TYR	0	0.026	0.022	20.077	-0.032	-0.032	0.000	0.000	0.000	0.000
56	A	171	ILE	0	-0.027	-0.014	20.203	0.046	0.046	0.000	0.000	0.000	0.000
57	A	172	TYR	0	-0.040	-0.042	17.858	-0.035	-0.035	0.000	0.000	0.000	0.000
58	A	173	ALA	0	0.019	0.000	23.030	0.032	0.032	0.000	0.000	0.000	0.000
59	A	174	GLN	0	-0.065	-0.021	24.902	-0.029	-0.029	0.000	0.000	0.000	0.000
60	A	175	VAL	0	0.056	0.017	26.258	0.017	0.017	0.000	0.000	0.000	0.000
61	A	176	THR	0	-0.007	0.010	29.002	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	177	PHE	0	0.053	0.022	31.387	0.008	0.008	0.000	0.000	0.000	0.000
63	A	178	CYS	0	-0.058	-0.013	34.453	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	179	SER	0	0.013	-0.012	37.514	0.002	0.002	0.000	0.000	0.000	0.000
65	A	180	ASN	0	-0.015	-0.015	40.625	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	181	ARG	1	0.826	0.905	42.408	-0.054	-0.054	0.000	0.000	0.000	0.000
67	A	182	GLU	-1	-0.737	-0.857	46.217	0.053	0.053	0.000	0.000	0.000	0.000
68	A	183	ALA	0	-0.053	-0.009	45.362	0.000	0.000	0.000	0.000	0.000	0.000
69	A	184	SER	0	-0.016	-0.023	42.154	0.001	0.001	0.000	0.000	0.000	0.000
70	A	185	SER	0	-0.020	-0.017	45.082	0.002	0.002	0.000	0.000	0.000	0.000
71	A	186	GLN	0	-0.060	-0.031	42.035	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	187	ALA	0	-0.005	-0.005	45.993	0.001	0.001	0.000	0.000	0.000	0.000
73	A	188	PRO	0	-0.063	-0.032	41.760	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	189	PHE	0	0.034	0.034	33.811	0.005	0.005	0.000	0.000	0.000	0.000
75	A	190	ILE	0	-0.042	-0.038	36.666	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	191	ALA	0	0.041	0.035	31.703	0.006	0.006	0.000	0.000	0.000	0.000
77	A	192	SER	0	-0.048	-0.036	32.877	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	193	LEU	0	0.034	0.030	25.851	0.009	0.009	0.000	0.000	0.000	0.000
79	A	194	CYS	0	-0.030	-0.021	29.027	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	195	LEU	0	0.014	0.002	26.287	0.023	0.023	0.000	0.000	0.000	0.000
81	A	196	LYS	1	0.932	0.989	26.015	-0.342	-0.342	0.000	0.000	0.000	0.000
82	A	197	SER	0	-0.026	-0.022	27.988	0.011	0.011	0.000	0.000	0.000	0.000
83	A	198	PRO	0	-0.002	-0.008	27.097	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	199	GLY	0	0.019	0.017	30.003	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	200	ARG	1	0.892	0.938	31.132	-0.211	-0.211	0.000	0.000	0.000	0.000
86	A	201	PHE	0	0.025	0.010	33.910	0.010	0.010	0.000	0.000	0.000	0.000
87	A	202	GLU	-1	-0.887	-0.941	32.194	0.206	0.206	0.000	0.000	0.000	0.000
88	A	203	ARG	1	0.915	0.961	30.430	-0.197	-0.197	0.000	0.000	0.000	0.000
89	A	204	ILE	0	0.029	0.020	32.145	0.012	0.012	0.000	0.000	0.000	0.000
90	A	205	LEU	0	-0.072	-0.027	27.433	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	206	LEU	0	0.017	0.004	28.410	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	207	ARG	1	0.895	0.936	31.985	-0.112	-0.112	0.000	0.000	0.000	0.000
93	A	208	ALA	0	0.018	0.025	33.888	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	209	ALA	0	0.005	-0.009	35.572	0.005	0.005	0.000	0.000	0.000	0.000
95	A	210	ASN	0	-0.021	0.004	36.405	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	211	THR	0	0.019	0.000	39.492	0.002	0.002	0.000	0.000	0.000	0.000
97	A	212	HIS	0	0.074	0.069	39.892	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	213	SER	0	-0.051	-0.039	43.503	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	214	SER	0	0.010	-0.004	46.924	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	215	ALA	0	0.038	0.021	49.970	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	216	LYS	1	0.901	0.955	46.613	-0.037	-0.037	0.000	0.000	0.000	0.000
102	A	217	PRO	0	0.073	0.030	45.726	0.003	0.003	0.000	0.000	0.000	0.000
103	A	219	GLY	0	0.013	0.018	40.454	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	220	GLN	0	-0.014	0.003	31.839	0.007	0.007	0.000	0.000	0.000	0.000
105	A	221	GLN	0	-0.022	0.007	36.193	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	222	SER	0	0.026	-0.014	31.186	0.007	0.007	0.000	0.000	0.000	0.000
107	A	223	ILE	0	-0.008	0.009	30.805	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	224	HIS	0	0.048	0.026	23.928	0.004	0.004	0.000	0.000	0.000	0.000
109	A	225	LEU	0	-0.033	-0.012	27.649	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	226	GLY	0	0.027	-0.003	26.087	0.015	0.015	0.000	0.000	0.000	0.000
111	A	227	GLY	0	-0.015	0.003	25.723	-0.021	-0.021	0.000	0.000	0.000	0.000
112	A	228	VAL	0	-0.003	-0.003	23.979	0.021	0.021	0.000	0.000	0.000	0.000
113	A	229	PHE	0	0.029	0.011	24.801	-0.016	-0.016	0.000	0.000	0.000	0.000
114	A	230	GLU	-1	-0.813	-0.908	24.419	0.272	0.272	0.000	0.000	0.000	0.000
115	A	231	LEU	0	-0.034	-0.010	21.203	0.000	0.000	0.000	0.000	0.000	0.000
116	A	232	GLN	0	0.048	0.025	22.959	0.012	0.012	0.000	0.000	0.000	0.000
117	A	233	PRO	0	-0.009	0.009	22.073	0.025	0.025	0.000	0.000	0.000	0.000
118	A	234	GLY	0	0.031	0.016	21.911	-0.026	-0.026	0.000	0.000	0.000	0.000
119	A	235	ALA	0	-0.045	-0.001	21.611	-0.010	-0.010	0.000	0.000	0.000	0.000
120	A	236	SER	0	-0.020	-0.044	23.451	-0.031	-0.031	0.000	0.000	0.000	0.000
121	A	237	VAL	0	0.012	0.009	22.460	-0.033	-0.033	0.000	0.000	0.000	0.000
122	A	238	PHE	0	0.015	0.002	24.174	0.034	0.034	0.000	0.000	0.000	0.000
123	A	239	VAL	0	0.023	0.015	26.062	-0.016	-0.016	0.000	0.000	0.000	0.000
124	A	240	ASN	0	0.038	0.043	28.734	0.006	0.006	0.000	0.000	0.000	0.000
125	A	241	VAL	0	-0.006	-0.010	31.919	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	242	THR	0	0.026	-0.001	34.658	0.003	0.003	0.000	0.000	0.000	0.000
127	A	243	ASP	-1	-0.774	-0.845	37.192	0.093	0.093	0.000	0.000	0.000	0.000
128	A	244	PRO	0	0.028	-0.007	34.120	0.001	0.001	0.000	0.000	0.000	0.000
129	A	245	SER	0	-0.028	-0.014	34.211	0.008	0.008	0.000	0.000	0.000	0.000
130	A	246	GLN	0	0.032	0.020	36.590	0.002	0.002	0.000	0.000	0.000	0.000
131	A	247	VAL	0	-0.061	-0.022	30.664	-0.004	-0.004	0.000	0.000	0.000	0.000
132	A	248	SER	0	-0.013	-0.030	31.077	0.002	0.002	0.000	0.000	0.000	0.000
133	A	249	HIS	0	0.015	0.014	27.714	0.017	0.017	0.000	0.000	0.000	0.000
134	A	250	GLY	0	-0.058	-0.009	25.494	0.009	0.009	0.000	0.000	0.000	0.000
135	A	251	THR	0	0.043	-0.006	22.787	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	252	GLY	0	0.010	0.008	22.414	-0.014	-0.014	0.000	0.000	0.000	0.000
137	A	253	PHE	0	-0.048	-0.030	23.464	0.011	0.011	0.000	0.000	0.000	0.000
138	A	254	THR	0	0.029	0.010	25.437	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	255	SER	0	-0.038	-0.028	20.613	0.017	0.017	0.000	0.000	0.000	0.000
140	A	256	PHE	0	-0.003	-0.006	20.875	-0.025	-0.025	0.000	0.000	0.000	0.000
141	A	257	GLY	0	0.055	0.020	18.570	0.048	0.048	0.000	0.000	0.000	0.000
142	A	258	LEU	0	-0.041	-0.019	16.339	-0.051	-0.051	0.000	0.000	0.000	0.000
143	A	259	LEU	0	0.023	0.015	15.145	0.077	0.077	0.000	0.000	0.000	0.000
144	A	260	LYS	1	0.909	0.972	15.366	-0.404	-0.404	0.000	0.000	0.000	0.000
145	A	261	LEU	0	-0.005	0.006	16.608	-0.010	-0.010	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:116:GLY)