Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: KG5L3

Calculation Name: 3WYD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WYD

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0A6

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 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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2317875.622301
FMO2-HF: Nuclear repulsion 2239558.787193
FMO2-HF: Total energy -78316.835108
FMO2-MP2: Total energy -78542.43756


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:304:PRO)


Summations of interaction energy for fragment #1(A:304:PRO)
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.
-0.1844.5341.94-2.429-4.23-0.004
Interaction energy analysis for fragmet #1(A:304:PRO)
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 : -0.011
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].
3A306ARG10.7690.8733.8460.0721.921-0.023-0.944-0.8820.001
4A307LEU00.009-0.0087.055-0.027-0.0270.0000.0000.0000.000
5A308TYR0-0.061-0.0569.8150.0120.0120.0000.0000.0000.000
6A309VAL00.018-0.00413.5760.0140.0140.0000.0000.0000.000
7A310PRO0-0.0240.00216.1100.0030.0030.0000.0000.0000.000
8A311THR0-0.052-0.04919.7920.0190.0190.0000.0000.0000.000
9A312THR00.005-0.00322.3550.0090.0090.0000.0000.0000.000
10A313TYR0-0.034-0.00918.5310.0060.0060.0000.0000.0000.000
11A314ASP-1-0.732-0.85321.8220.0450.0450.0000.0000.0000.000
12A315GLY00.0040.01321.7060.0090.0090.0000.0000.0000.000
13A316THR0-0.085-0.06822.4780.0040.0040.0000.0000.0000.000
14A317LYS10.8300.90625.049-0.028-0.0280.0000.0000.0000.000
15A318ALA0-0.027-0.01622.8870.0070.0070.0000.0000.0000.000
16A319PHE00.0190.00420.031-0.006-0.0060.0000.0000.0000.000
17A320PRO0-0.0240.00720.4480.0090.0090.0000.0000.0000.000
18A321LEU00.0180.00913.2880.0010.0010.0000.0000.0000.000
19A322VAL0-0.037-0.01416.182-0.002-0.0020.0000.0000.0000.000
20A323ILE00.0160.00910.947-0.039-0.0390.0000.0000.0000.000
21A324ALA00.0240.00512.2110.0400.0400.0000.0000.0000.000
22A325LEU00.0240.01810.499-0.165-0.1650.0000.0000.0000.000
23A326HIS00.0300.0348.357-0.059-0.0590.0000.0000.0000.000
24A327GLY00.0720.03512.3060.0100.0100.0000.0000.0000.000
25A328MET0-0.023-0.02213.024-0.059-0.0590.0000.0000.0000.000
26A329GLY0-0.014-0.00813.364-0.013-0.0130.0000.0000.0000.000
27A330GLY00.0000.00811.7490.0270.0270.0000.0000.0000.000
28A331ASP-1-0.860-0.9126.631-0.722-0.7220.0000.0000.0000.000
29A332GLU-1-0.704-0.8473.180-2.694-1.2850.107-0.676-0.840-0.006
30A333ASN0-0.010-0.0056.2340.2320.2320.0000.0000.0000.000
31A334SER0-0.017-0.0208.6760.1540.1540.0000.0000.0000.000
32A335TYR0-0.055-0.05511.3650.1090.1090.0000.0000.0000.000
33A336PHE0-0.015-0.0099.8680.0620.0620.0000.0000.0000.000
34A337ASP-1-0.736-0.85311.580-0.278-0.2780.0000.0000.0000.000
35A338SER0-0.093-0.05314.3490.0330.0330.0000.0000.0000.000
36A339TYR0-0.045-0.04513.936-0.003-0.0030.0000.0000.0000.000
37A340GLN00.0160.00018.2360.0110.0110.0000.0000.0000.000
38A341ARG10.9260.95718.1520.1460.1460.0000.0000.0000.000
39A342GLY00.1320.08616.6370.0150.0150.0000.0000.0000.000
40A343ALA0-0.037-0.02017.6050.0090.0090.0000.0000.0000.000
41A344PHE0-0.015-0.01616.5150.0090.0090.0000.0000.0000.000
42A345MET00.0230.01413.1190.0190.0190.0000.0000.0000.000
43A346ILE0-0.0080.01218.0030.0220.0220.0000.0000.0000.000
44A347GLU-1-0.772-0.87221.705-0.079-0.0790.0000.0000.0000.000
45A348ALA0-0.0070.00218.4660.0110.0110.0000.0000.0000.000
46A349GLU-1-0.749-0.82620.438-0.028-0.0280.0000.0000.0000.000
47A350ASN0-0.078-0.04822.1270.0160.0160.0000.0000.0000.000
48A351ARG10.6780.80724.0700.0920.0920.0000.0000.0000.000
49A352GLY0-0.0130.02122.6860.0050.0050.0000.0000.0000.000
50A353TYR0-0.078-0.08918.8200.0050.0050.0000.0000.0000.000
51A354ILE00.0110.00913.943-0.010-0.0100.0000.0000.0000.000
52A355VAL0-0.043-0.02113.024-0.013-0.0130.0000.0000.0000.000
53A356ALA00.0360.0219.1400.0150.0150.0000.0000.0000.000
54A357CYS0-0.053-0.0088.3280.1150.1150.0000.0000.0000.000
55A358PRO00.0610.0105.054-0.610-0.6100.0000.0000.0000.000
56A359LYS10.8230.9052.5110.4441.7561.857-0.796-2.3740.001
57A360GLY00.0810.0394.7570.0140.162-0.001-0.013-0.1340.000
58A361ARG10.7750.8876.2580.8650.8650.0000.0000.0000.000
59A362GLN00.0420.0177.9860.1760.1760.0000.0000.0000.000
60A363PRO0-0.004-0.00410.4720.0410.0410.0000.0000.0000.000
61A364ALA00.004-0.00613.2850.0220.0220.0000.0000.0000.000
62A365SER00.000-0.01912.6510.0170.0170.0000.0000.0000.000
63A366MET0-0.021-0.02715.1370.0220.0220.0000.0000.0000.000
64A367TYR00.0170.0079.252-0.024-0.0240.0000.0000.0000.000
65A368VAL00.0410.03112.8390.0390.0390.0000.0000.0000.000
66A369GLY00.002-0.00613.367-0.035-0.0350.0000.0000.0000.000
67A370PRO0-0.021-0.0139.9600.0340.0340.0000.0000.0000.000
68A371ALA00.0820.0418.5440.0140.0140.0000.0000.0000.000
69A372GLU-1-0.809-0.8729.331-0.169-0.1690.0000.0000.0000.000
70A373ARG10.8460.89910.6710.0640.0640.0000.0000.0000.000
71A374ASP-1-0.873-0.9225.210-0.358-0.3580.0000.0000.0000.000
72A375VAL0-0.040-0.0226.5890.1130.1130.0000.0000.0000.000
73A376MET0-0.046-0.0208.5970.0990.0990.0000.0000.0000.000
74A377ASP-1-0.815-0.9168.1360.7040.7040.0000.0000.0000.000
75A378VAL00.0040.0205.1660.1040.1040.0000.0000.0000.000
76A379ILE0-0.045-0.0288.079-0.036-0.0360.0000.0000.0000.000
77A380ALA0-0.044-0.02611.637-0.009-0.0090.0000.0000.0000.000
78A381GLU-1-0.804-0.8707.2241.7041.7040.0000.0000.0000.000
79A382VAL00.014-0.0039.681-0.071-0.0710.0000.0000.0000.000
80A383ARG10.8800.93112.056-0.150-0.1500.0000.0000.0000.000
81A384ARG10.7540.89210.223-0.838-0.8380.0000.0000.0000.000
82A385ASP-1-0.891-0.93911.9400.5030.5030.0000.0000.0000.000
83A386TYR0-0.037-0.02511.807-0.079-0.0790.0000.0000.0000.000
84A387LYS10.9090.96516.584-0.089-0.0890.0000.0000.0000.000
85A388ILE00.0100.01015.779-0.024-0.0240.0000.0000.0000.000
86A389ASP-1-0.787-0.89419.4010.0100.0100.0000.0000.0000.000
87A390PRO0-0.027-0.01621.455-0.009-0.0090.0000.0000.0000.000
88A391ASP-1-0.848-0.91722.5360.0010.0010.0000.0000.0000.000
89A392ARG10.8360.90422.7510.0340.0340.0000.0000.0000.000
90A393ILE00.0530.04816.610-0.004-0.0040.0000.0000.0000.000
91A394TYR0-0.014-0.01518.3210.0040.0040.0000.0000.0000.000
92A395MET0-0.0340.00214.727-0.033-0.0330.0000.0000.0000.000
93A396THR0-0.036-0.03116.0570.0280.0280.0000.0000.0000.000
94A397GLY00.0820.03415.433-0.065-0.0650.0000.0000.0000.000
95A398HIS00.0180.01416.0850.0190.0190.0000.0000.0000.000
96A399SER0-0.014-0.01316.700-0.054-0.0540.0000.0000.0000.000
97A400MET0-0.051-0.00411.0710.0400.0400.0000.0000.0000.000
98A401GLY00.0620.02414.377-0.007-0.0070.0000.0000.0000.000
99A402GLY0-0.0050.01915.0670.0220.0220.0000.0000.0000.000
100A403TYR0-0.015-0.02618.1850.0300.0300.0000.0000.0000.000
101A404GLY0-0.0040.01214.6140.0210.0210.0000.0000.0000.000
102A405THR0-0.030-0.02915.5650.0220.0220.0000.0000.0000.000
103A406TRP00.010-0.01317.2430.0290.0290.0000.0000.0000.000
104A407SER0-0.029-0.01616.5030.0190.0190.0000.0000.0000.000
105A408ILE00.0560.02012.2650.0250.0250.0000.0000.0000.000
106A409ALA0-0.002-0.00216.4700.0320.0320.0000.0000.0000.000
107A410MET0-0.070-0.03319.4540.0180.0180.0000.0000.0000.000
108A411ASN0-0.041-0.01817.9460.0220.0220.0000.0000.0000.000
109A412HIS0-0.036-0.01415.9610.0360.0360.0000.0000.0000.000
110A413PRO00.0440.02719.4520.0000.0000.0000.0000.0000.000
111A414ASP-1-0.884-0.94822.528-0.002-0.0020.0000.0000.0000.000
112A415VAL0-0.068-0.02816.6830.0130.0130.0000.0000.0000.000
113A416PHE00.022-0.00215.2880.0060.0060.0000.0000.0000.000
114A417ALA0-0.021-0.01720.6350.0080.0080.0000.0000.0000.000
115A418ALA00.007-0.00422.1980.0050.0050.0000.0000.0000.000
116A419LEU0-0.017-0.00819.463-0.011-0.0110.0000.0000.0000.000
117A420ALA00.0090.00020.4900.0140.0140.0000.0000.0000.000
118A421PRO00.0030.03820.115-0.027-0.0270.0000.0000.0000.000
119A422VAL00.024-0.00220.4440.0200.0200.0000.0000.0000.000
120A423ALA0-0.012-0.01521.005-0.025-0.0250.0000.0000.0000.000
121A424GLY00.014-0.00321.661-0.016-0.0160.0000.0000.0000.000
122A425GLY00.017-0.00422.1200.0190.0190.0000.0000.0000.000
123A426GLY00.017-0.01022.232-0.017-0.0170.0000.0000.0000.000
124A427ASN00.0330.01723.8170.0110.0110.0000.0000.0000.000
125A428PRO00.0760.02126.2360.0030.0030.0000.0000.0000.000
126A429LEU0-0.024-0.02029.1950.0050.0050.0000.0000.0000.000
127A430GLY00.0180.01026.2980.0060.0060.0000.0000.0000.000
128A431MET0-0.039-0.02026.475-0.003-0.0030.0000.0000.0000.000
129A432ALA00.0080.00828.1810.0020.0020.0000.0000.0000.000
130A433ASN0-0.057-0.02924.6530.0070.0070.0000.0000.0000.000
131A434ILE00.012-0.00523.0670.0020.0020.0000.0000.0000.000
132A435ALA00.0310.03226.345-0.003-0.0030.0000.0000.0000.000
133A436HIS0-0.059-0.02925.4720.0010.0010.0000.0000.0000.000
134A437ILE0-0.024-0.00522.8270.0020.0020.0000.0000.0000.000
135A438PRO0-0.0080.00926.458-0.008-0.0080.0000.0000.0000.000
136A439GLN0-0.010-0.01324.554-0.017-0.0170.0000.0000.0000.000
137A440LEU00.0020.00424.8320.0090.0090.0000.0000.0000.000
138A441VAL00.0240.02024.841-0.013-0.0130.0000.0000.0000.000
139A442VAL00.0130.00824.7260.0110.0110.0000.0000.0000.000
140A443HIS0-0.0160.00825.403-0.016-0.0160.0000.0000.0000.000
141A444GLY00.0340.03227.5590.0090.0090.0000.0000.0000.000
142A445ASP-1-0.844-0.93629.636-0.088-0.0880.0000.0000.0000.000
143A446ASN00.0040.01231.9360.0050.0050.0000.0000.0000.000
144A447ASP-1-0.720-0.84325.830-0.162-0.1620.0000.0000.0000.000
145A448LYS10.7810.86727.4970.1120.1120.0000.0000.0000.000
146A449THR0-0.042-0.00121.8210.0070.0070.0000.0000.0000.000
147A450VAL0-0.040-0.01922.354-0.003-0.0030.0000.0000.0000.000
148A451PRO00.0090.01225.6300.0030.0030.0000.0000.0000.000
149A452VAL00.0960.05728.796-0.004-0.0040.0000.0000.0000.000
150A453GLU-1-0.836-0.92630.282-0.091-0.0910.0000.0000.0000.000
151A454ARG10.8700.94126.2650.1170.1170.0000.0000.0000.000
152A455SER00.0690.01626.574-0.005-0.0050.0000.0000.0000.000
153A456ARG10.7600.84228.2530.0890.0890.0000.0000.0000.000
154A457VAL00.0360.00829.9770.0050.0050.0000.0000.0000.000
155A458MET0-0.0380.02224.4190.0080.0080.0000.0000.0000.000
156A459VAL00.0370.00729.2560.0050.0050.0000.0000.0000.000
157A460GLU-1-0.911-0.94331.210-0.055-0.0550.0000.0000.0000.000
158A461ALA0-0.009-0.01431.1120.0050.0050.0000.0000.0000.000
159A462ALA00.0280.01229.7440.0050.0050.0000.0000.0000.000
160A463LYS10.8870.95331.6130.0680.0680.0000.0000.0000.000
161A464LYS10.8440.92035.1590.0590.0590.0000.0000.0000.000
162A465HIS0-0.0050.00932.1710.0060.0060.0000.0000.0000.000
163A466GLY0-0.0090.00034.5630.0020.0020.0000.0000.0000.000
164A467THR0-0.050-0.02529.1540.0010.0010.0000.0000.0000.000
165A468GLU-1-0.857-0.90631.089-0.052-0.0520.0000.0000.0000.000
166A469ILE0-0.011-0.00928.536-0.006-0.0060.0000.0000.0000.000
167A470LYS10.8660.93930.1460.0900.0900.0000.0000.0000.000
168A471TYR0-0.072-0.07629.154-0.009-0.0090.0000.0000.0000.000
169A472ILE0-0.031-0.01028.3050.0070.0070.0000.0000.0000.000
170A473GLU-1-0.732-0.80829.714-0.095-0.0950.0000.0000.0000.000
171A474ILE0-0.064-0.04128.3830.0060.0060.0000.0000.0000.000
172A475PRO00.0430.01332.277-0.004-0.0040.0000.0000.0000.000
173A476GLY0-0.023-0.00334.4550.0000.0000.0000.0000.0000.000
174A477GLY0-0.026-0.01130.261-0.003-0.0030.0000.0000.0000.000
175A478ASP-1-0.788-0.87126.389-0.141-0.1410.0000.0000.0000.000
176A479HIS0-0.037-0.03121.355-0.026-0.0260.0000.0000.0000.000
177A480VAL0-0.011-0.00620.426-0.020-0.0200.0000.0000.0000.000
178A481SER0-0.031-0.03922.854-0.003-0.0030.0000.0000.0000.000
179A482VAL0-0.010-0.01624.1470.0030.0030.0000.0000.0000.000
180A483ALA00.0270.02620.1890.0040.0040.0000.0000.0000.000
181A484ALA00.0320.01221.2860.0060.0060.0000.0000.0000.000
182A485ARG10.9020.96222.4970.1110.1110.0000.0000.0000.000
183A486THR00.000-0.01124.6920.0080.0080.0000.0000.0000.000
184A487PHE00.0300.01118.065-0.004-0.0040.0000.0000.0000.000
185A488LYS10.8920.95323.0780.0780.0780.0000.0000.0000.000
186A489ASP-1-0.834-0.91626.258-0.090-0.0900.0000.0000.0000.000
187A490VAL0-0.007-0.01620.4900.0060.0060.0000.0000.0000.000
188A491PHE00.0420.02118.8890.0050.0050.0000.0000.0000.000
189A492ASP-1-0.775-0.86324.300-0.067-0.0670.0000.0000.0000.000
190A493TRP0-0.075-0.02025.0100.0130.0130.0000.0000.0000.000
191A494PHE00.0290.00819.7670.0050.0050.0000.0000.0000.000
192A495ASP-1-0.766-0.85324.859-0.056-0.0560.0000.0000.0000.000
193A496SER0-0.098-0.05827.5390.0070.0070.0000.0000.0000.000
194A497HIS10.7640.85826.9560.0660.0660.0000.0000.0000.000
195A498LYS10.8320.93726.3720.0000.0000.0000.0000.0000.000
196A499ARG10.8180.90022.611-0.006-0.0060.0000.0000.0000.000
197A500LYS10.8920.96426.6250.0340.0340.0000.0000.0000.000
198A501ARG10.8920.93723.542-0.009-0.0090.0000.0000.0000.000
199A502PRO00.0280.03229.7920.0050.0050.0000.0000.0000.000