Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 2J7VR

Calculation Name: 4MXN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4MXN

Chain ID: A

ChEMBL ID:

UniProt ID: A7AB45

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptHSide
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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2596881.061376
FMO2-HF: Nuclear repulsion 2511196.787142
FMO2-HF: Total energy -85684.274235
FMO2-MP2: Total energy -85929.503066


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:23:LYS)


Summations of interaction energy for fragment #1(A:23:LYS)
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.
-89.778-84.42322.591-11.773-16.17-0.128
Interaction energy analysis for fragmet #1(A:23:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.920 / q_NPA : 0.962
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   
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].
3A25TYR00.014-0.0041.840-67.044-63.50222.454-11.180-14.815-0.126
4A26GLN00.0500.0293.58814.22814.4390.023-0.003-0.231-0.001
5A27VAL00.0650.0246.479-1.135-1.1350.0000.0000.0000.000
6A28ALA00.0200.0099.1980.9250.9250.0000.0000.0000.000
7A29MET0-0.069-0.0345.1351.9251.9250.0000.0000.0000.000
8A30PHE00.0070.0055.0950.0780.0780.0000.0000.0000.000
9A31GLY0-0.028-0.0099.9582.3512.3510.0000.0000.0000.000
10A32ILE0-0.069-0.01310.5681.8331.8330.0000.0000.0000.000
11A33LYS10.9220.95213.72817.11517.1150.0000.0000.0000.000
12A34SER0-0.0040.00816.1070.4040.4040.0000.0000.0000.000
13A35ASP-1-0.777-0.87217.842-14.574-14.5740.0000.0000.0000.000
14A36GLY0-0.030-0.01521.0010.7440.7440.0000.0000.0000.000
15A37VAL0-0.045-0.02822.9320.5610.5610.0000.0000.0000.000
16A38THR0-0.054-0.05219.3650.4650.4650.0000.0000.0000.000
17A39LEU0-0.033-0.00320.943-0.536-0.5360.0000.0000.0000.000
18A40ASN0-0.007-0.01116.322-0.873-0.8730.0000.0000.0000.000
19A41THR00.0620.04016.721-1.210-1.2100.0000.0000.0000.000
20A42ARG10.9870.99317.08714.33214.3320.0000.0000.0000.000
21A43SER00.0130.01013.807-0.286-0.2860.0000.0000.0000.000
22A44ILE00.0170.00312.504-2.356-2.3560.0000.0000.0000.000
23A45GLN0-0.019-0.00312.335-1.005-1.0050.0000.0000.0000.000
24A46ARG10.9560.98011.89020.18220.1820.0000.0000.0000.000
25A47ALA00.0070.0038.293-1.553-1.5530.0000.0000.0000.000
26A48VAL0-0.007-0.0048.467-3.288-3.2880.0000.0000.0000.000
27A49ASP-1-0.816-0.91110.480-21.425-21.4250.0000.0000.0000.000
28A50TYR0-0.071-0.0405.048-2.051-2.0510.0000.0000.0000.000
29A51ILE0-0.014-0.0154.776-1.962-1.828-0.001-0.012-0.1190.000
30A52SER0-0.032-0.0317.0240.3460.3460.0000.0000.0000.000
31A53GLU-1-0.940-0.9599.574-21.617-21.6170.0000.0000.0000.000
32A54GLN0-0.090-0.0365.5181.5061.5060.0000.0000.0000.000
33A55GLY0-0.0100.0026.831-0.694-0.6940.0000.0000.0000.000
34A56GLY0-0.028-0.0125.8102.2142.2140.0000.0000.0000.000
35A57GLY0-0.045-0.0242.983-8.387-7.4360.111-0.462-0.599-0.001
36A58ARG10.8160.8633.52740.84241.3590.004-0.116-0.4060.000
37A59LEU00.0080.0125.765-8.740-8.7400.0000.0000.0000.000
38A60ILE0-0.035-0.0236.5124.2094.2090.0000.0000.0000.000
39A61PHE00.0480.0139.044-0.607-0.6070.0000.0000.0000.000
40A62TYR00.006-0.00310.2400.5050.5050.0000.0000.0000.000
41A63VAL00.0280.01413.2891.2741.2740.0000.0000.0000.000
42A64GLY00.0270.03416.695-0.618-0.6180.0000.0000.0000.000
43A65ARG10.8940.93919.38612.72612.7260.0000.0000.0000.000
44A66TYR0-0.016-0.03414.269-0.944-0.9440.0000.0000.0000.000
45A67LEU0-0.0180.01418.9740.1800.1800.0000.0000.0000.000
46A68THR0-0.022-0.03719.027-1.116-1.1160.0000.0000.0000.000
47A69GLY00.0660.04421.0140.7380.7380.0000.0000.0000.000
48A70SER0-0.054-0.04821.087-0.429-0.4290.0000.0000.0000.000
49A71ILE0-0.077-0.03515.442-0.493-0.4930.0000.0000.0000.000
50A72GLU-1-0.823-0.88817.908-15.181-15.1810.0000.0000.0000.000
51A73LEU0-0.025-0.02312.048-1.378-1.3780.0000.0000.0000.000
52A74LYS10.8420.92712.47219.59619.5960.0000.0000.0000.000
53A75SER00.0560.00212.010-0.673-0.6730.0000.0000.0000.000
54A76ASN0-0.0070.0278.019-0.244-0.2440.0000.0000.0000.000
55A77VAL00.0010.0237.118-3.582-3.5820.0000.0000.0000.000
56A78THR0-0.006-0.0027.8833.1003.1000.0000.0000.0000.000
57A79ILE0-0.013-0.0039.012-3.687-3.6870.0000.0000.0000.000
58A80ARG10.7540.8589.31124.05524.0550.0000.0000.0000.000
59A81ILE00.0190.00812.145-1.246-1.2460.0000.0000.0000.000
60A82GLU-1-0.804-0.87912.183-22.022-22.0220.0000.0000.0000.000
61A83GLU-1-0.778-0.88815.633-13.736-13.7360.0000.0000.0000.000
62A84GLY00.0000.00418.495-0.367-0.3670.0000.0000.0000.000
63A85ALA0-0.069-0.02316.3910.1550.1550.0000.0000.0000.000
64A86VAL0-0.016-0.02018.4310.6030.6030.0000.0000.0000.000
65A87LEU0-0.0050.01116.888-0.376-0.3760.0000.0000.0000.000
66A88VAL0-0.040-0.03319.9090.7640.7640.0000.0000.0000.000
67A89ALA00.0450.03223.075-0.345-0.3450.0000.0000.0000.000
68A90VAL00.012-0.00125.0100.4090.4090.0000.0000.0000.000
69A91PRO0-0.049-0.03626.5840.1300.1300.0000.0000.0000.000
70A92SER0-0.045-0.05328.7260.5370.5370.0000.0000.0000.000
71A93VAL00.0390.01629.290-0.358-0.3580.0000.0000.0000.000
72A94TYR0-0.019-0.03430.320-0.154-0.1540.0000.0000.0000.000
73A95ASP-1-0.891-0.91025.437-12.343-12.3430.0000.0000.0000.000
74A96PHE0-0.052-0.03424.622-0.787-0.7870.0000.0000.0000.000
75A97LYS10.8710.95425.01711.43311.4330.0000.0000.0000.000
76A98GLY00.0160.00926.8480.2820.2820.0000.0000.0000.000
77A99VAL00.0210.00330.591-0.170-0.1700.0000.0000.0000.000
78A100GLY0-0.020-0.00532.044-0.116-0.1160.0000.0000.0000.000
79A101GLY00.0320.01628.671-0.324-0.3240.0000.0000.0000.000
80A102CYS0-0.043-0.01722.1310.9100.9100.0000.0000.0000.000
81A103ASN00.0320.02525.982-0.662-0.6620.0000.0000.0000.000
82A104ALA0-0.003-0.00423.4400.3420.3420.0000.0000.0000.000
83A105ILE00.0030.02620.573-0.258-0.2580.0000.0000.0000.000
84A106ILE0-0.0090.00016.646-0.878-0.8780.0000.0000.0000.000
85A107TYR0-0.034-0.04719.7950.7260.7260.0000.0000.0000.000
86A108ALA00.0090.00717.634-1.013-1.0130.0000.0000.0000.000
87A109ASP-1-0.762-0.87219.382-11.668-11.6680.0000.0000.0000.000
88A110LYS10.8130.89420.60511.38611.3860.0000.0000.0000.000
89A111GLN0-0.030-0.01115.494-1.409-1.4090.0000.0000.0000.000
90A112LYS10.9640.96312.11318.83418.8340.0000.0000.0000.000
91A113ASN0-0.046-0.0389.115-1.021-1.0210.0000.0000.0000.000
92A114ILE0-0.0150.01211.056-1.739-1.7390.0000.0000.0000.000
93A115GLY00.0570.01612.0501.1141.1140.0000.0000.0000.000
94A116ILE0-0.027-0.00912.716-1.382-1.3820.0000.0000.0000.000
95A117GLY00.0360.01413.4380.9740.9740.0000.0000.0000.000
96A118GLY0-0.0030.00414.239-0.883-0.8830.0000.0000.0000.000
97A119LYS10.8130.88515.31915.26415.2640.0000.0000.0000.000
98A120GLY0-0.0040.02018.0570.7920.7920.0000.0000.0000.000
99A121ILE0-0.030-0.02419.6570.5400.5400.0000.0000.0000.000
100A122ILE00.0240.02019.032-0.718-0.7180.0000.0000.0000.000
101A123ASP-1-0.879-0.94922.470-11.377-11.3770.0000.0000.0000.000
102A124GLY00.0590.00125.620-0.252-0.2520.0000.0000.0000.000
103A125ARG10.9040.96427.78511.08111.0810.0000.0000.0000.000
104A126SER0-0.019-0.02530.3090.3170.3170.0000.0000.0000.000
105A127ILE00.0230.01032.8550.1370.1370.0000.0000.0000.000
106A128ALA0-0.023-0.01832.5640.1400.1400.0000.0000.0000.000
107A129VAL00.0090.00629.2800.1030.1030.0000.0000.0000.000
108A130ARG10.9120.94732.4608.9178.9170.0000.0000.0000.000
109A131ALA00.0520.04235.6540.1760.1760.0000.0000.0000.000
110A132SER00.0110.01733.7450.1170.1170.0000.0000.0000.000
111A133VAL0-0.016-0.01833.9570.1160.1160.0000.0000.0000.000
112A134GLU-1-0.907-0.97136.379-7.997-7.9970.0000.0000.0000.000
113A135GLU-1-0.873-0.91638.846-7.991-7.9910.0000.0000.0000.000
114A136GLN00.0040.01636.2670.2420.2420.0000.0000.0000.000
115A137LEU00.0040.00739.4700.1180.1180.0000.0000.0000.000
116A138GLN0-0.055-0.02341.6590.1760.1760.0000.0000.0000.000
117A139LYS10.7530.86841.4387.9547.9540.0000.0000.0000.000
118A140GLY00.0400.03443.8440.1010.1010.0000.0000.0000.000
119A141HIS0-0.106-0.05939.3620.1630.1630.0000.0000.0000.000
120A142ILE0-0.053-0.01936.247-0.214-0.2140.0000.0000.0000.000
121A143GLU-1-0.874-0.93239.686-7.075-7.0750.0000.0000.0000.000
122A144GLY0-0.0050.01340.355-0.220-0.2200.0000.0000.0000.000
123A145ASN0-0.070-0.03940.4180.3050.3050.0000.0000.0000.000
124A146VAL00.0460.00236.822-0.214-0.2140.0000.0000.0000.000
125A147SER0-0.041-0.02336.088-0.220-0.2200.0000.0000.0000.000
126A148ASP-1-0.812-0.90034.888-8.522-8.5220.0000.0000.0000.000
127A149TYR0-0.026-0.04333.182-0.359-0.3590.0000.0000.0000.000
128A150ALA0-0.031-0.00331.731-0.369-0.3690.0000.0000.0000.000
129A151PRO0-0.0260.02027.0110.0640.0640.0000.0000.0000.000
130A152ALA00.010-0.00626.7400.1700.1700.0000.0000.0000.000
131A153LEU0-0.035-0.01524.047-0.332-0.3320.0000.0000.0000.000
132A154ILE0-0.003-0.01219.825-0.746-0.7460.0000.0000.0000.000
133A156MET0-0.0090.00017.428-0.481-0.4810.0000.0000.0000.000
134A157GLU-1-0.843-0.95322.139-10.308-10.3080.0000.0000.0000.000
135A158GLY00.0270.01223.031-0.376-0.3760.0000.0000.0000.000
136A159CYS0-0.087-0.03118.673-0.495-0.4950.0000.0000.0000.000
137A160GLU-1-0.908-0.95918.640-11.940-11.9400.0000.0000.0000.000
138A161ASP-1-0.906-0.93715.531-15.393-15.3930.0000.0000.0000.000
139A162VAL0-0.038-0.01815.360-1.052-1.0520.0000.0000.0000.000
140A163LYS10.8520.92012.58018.88618.8860.0000.0000.0000.000
141A164ILE0-0.009-0.00414.824-1.138-1.1380.0000.0000.0000.000
142A165GLU-1-0.807-0.91313.175-17.839-17.8390.0000.0000.0000.000
143A166GLN0-0.021-0.00815.373-1.812-1.8120.0000.0000.0000.000
144A167VAL00.0090.01217.2250.3630.3630.0000.0000.0000.000
145A168THR0-0.0040.00519.8720.8960.8960.0000.0000.0000.000
146A169LEU0-0.032-0.01921.430-0.407-0.4070.0000.0000.0000.000
147A170GLN00.032-0.01024.8800.6410.6410.0000.0000.0000.000
148A171ASP-1-0.770-0.86027.878-10.200-10.2000.0000.0000.0000.000
149A172ALA00.0270.02628.888-0.119-0.1190.0000.0000.0000.000
150A173ALA00.0380.01829.8590.4410.4410.0000.0000.0000.000
151A174ASN0-0.061-0.03930.9740.6200.6200.0000.0000.0000.000
152A175VAL00.0240.03329.4840.1230.1230.0000.0000.0000.000
153A176ALA0-0.004-0.01326.870-0.307-0.3070.0000.0000.0000.000
154A177GLU-1-0.851-0.90823.777-12.756-12.7560.0000.0000.0000.000
155A178ILE00.019-0.00125.2790.5090.5090.0000.0000.0000.000
156A179TYR0-0.046-0.04921.237-0.665-0.6650.0000.0000.0000.000
157A180LYS10.8880.91625.60810.32610.3260.0000.0000.0000.000
158A181ASP-1-0.844-0.90225.955-10.310-10.3100.0000.0000.0000.000
159A182CYS0-0.052-0.01722.475-0.452-0.4520.0000.0000.0000.000
160A183HIS00.0140.00222.4630.6230.6230.0000.0000.0000.000
161A184ASN0-0.108-0.06318.799-0.234-0.2340.0000.0000.0000.000
162A185VAL00.0240.01919.489-0.664-0.6640.0000.0000.0000.000
163A186THR0-0.026-0.01618.0020.4130.4130.0000.0000.0000.000
164A187VAL00.0290.01219.190-0.634-0.6340.0000.0000.0000.000
165A188ASP-1-0.805-0.90519.309-11.991-11.9910.0000.0000.0000.000
166A189LYS10.7790.85720.14411.72411.7240.0000.0000.0000.000
167A190VAL00.0150.02220.626-0.321-0.3210.0000.0000.0000.000
168A191VAL00.0080.01022.9510.6290.6290.0000.0000.0000.000
169A192VAL00.0080.00825.539-0.328-0.3280.0000.0000.0000.000
170A193ASN0-0.041-0.03027.9910.6500.6500.0000.0000.0000.000
171A194ALA00.0490.00530.395-0.215-0.2150.0000.0000.0000.000
172A195GLY0-0.029-0.01333.133-0.115-0.1150.0000.0000.0000.000
173A196ALA0-0.028-0.02733.9450.2760.2760.0000.0000.0000.000
174A197SER0-0.049-0.02333.6400.3070.3070.0000.0000.0000.000
175A198ASP-1-0.879-0.93735.823-8.186-8.1860.0000.0000.0000.000
176A199ARG10.8120.91734.1049.3079.3070.0000.0000.0000.000
177A200LYS10.7980.89033.7778.2588.2580.0000.0000.0000.000
178A201ALA00.013-0.00129.823-0.202-0.2020.0000.0000.0000.000
179A202ILE0-0.003-0.01227.290-0.360-0.3600.0000.0000.0000.000
180A203SER00.005-0.00829.2560.3800.3800.0000.0000.0000.000
181A204ILE0-0.010-0.00228.126-0.376-0.3760.0000.0000.0000.000
182A205SER0-0.042-0.03129.7260.4440.4440.0000.0000.0000.000
183A206GLY00.0730.03329.738-0.313-0.3130.0000.0000.0000.000
184A207CYS0-0.0530.00926.719-0.303-0.3030.0000.0000.0000.000
185A208ASP-1-0.780-0.87726.700-9.376-9.3760.0000.0000.0000.000
186A209GLY00.0270.01425.368-0.349-0.3490.0000.0000.0000.000
187A210VAL0-0.0050.00024.191-0.414-0.4140.0000.0000.0000.000
188A211LYS10.9170.96323.00311.32011.3200.0000.0000.0000.000
189A212MET00.0260.01723.195-0.332-0.3320.0000.0000.0000.000
190A213THR00.022-0.00623.2790.7180.7180.0000.0000.0000.000
191A214ASP-1-0.840-0.90424.233-11.376-11.3760.0000.0000.0000.000
192A215CYS0-0.048-0.00424.798-0.435-0.4350.0000.0000.0000.000
193A216TYR00.0370.01226.7540.4320.4320.0000.0000.0000.000
194A217PHE00.0430.00728.144-0.271-0.2710.0000.0000.0000.000
195A218ASN00.0430.01831.4270.3150.3150.0000.0000.0000.000
196A219MET0-0.0220.01033.5070.1350.1350.0000.0000.0000.000
197A220ALA00.022-0.00436.0860.0270.0270.0000.0000.0000.000
198A221GLY00.0050.00739.3190.0880.0880.0000.0000.0000.000
199A222ASN00.015-0.00136.569-0.329-0.3290.0000.0000.0000.000
200A223PRO00.0870.03532.4500.0310.0310.0000.0000.0000.000
201A224LEU00.0040.01930.989-0.230-0.2300.0000.0000.0000.000
202A225GLU-1-0.892-0.91333.208-8.495-8.4950.0000.0000.0000.000
203A226SER00.0240.00233.210-0.275-0.2750.0000.0000.0000.000
204A227ALA00.0100.00834.4990.2180.2180.0000.0000.0000.000
205A228GLY0-0.013-0.00435.8730.2070.2070.0000.0000.0000.000
206A229THR00.003-0.00434.5590.0490.0490.0000.0000.0000.000
207A230SER0-0.0020.01430.452-0.228-0.2280.0000.0000.0000.000
208A231ARG10.8140.88829.7499.4629.4620.0000.0000.0000.000
209A232ASN0-0.047-0.03328.793-0.088-0.0880.0000.0000.0000.000
210A233LEU00.0220.02528.304-0.327-0.3270.0000.0000.0000.000
211A234ILE0-0.036-0.02727.7130.2830.2830.0000.0000.0000.000
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